10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

☒   QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2019

OR

☐   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from            to

Commission file number: 001-34620

IRONWOOD PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

Delaware	04-3404176
(State or other jurisdiction of	(I.R.S. Employer
incorporation or organization)	Identification Number)

100 Summer Street, Suite 2300
Boston, Massachusetts	02110
(Address of Principal Executive Offices)	(Zip Code)

(617) 621-7722

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Class A common stock, $0.001 par value	IRWD	Nasdaq Global Select Market

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒  No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ⌧  No ◻

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large Accelerated Filer ☒	Accelerated Filer ☐
Non-accelerated Filer ☐	Smaller Reporting Company ☐
	Emerging Growth Company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). ☐ Yes ☒ No

As of October 25, 2019, there were 156,818,126 shares of Class A common stock outstanding.

NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q, including the sections titled “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and “Risk Factors”, contains forward-looking statements. All statements contained in this Quarterly Report on Form 10-Q other than statements of historical fact are forward-looking statements. Forward-looking statements include statements regarding our future financial position, business strategy, budgets, projected costs, plans and objectives of management for future operations. The words “may,” “continue,” “estimate,” “intend,” “plan,” “will,” “believe,” “project,” “expect,” “seek,” “anticipate” and similar expressions may identify forward-looking statements, but the absence of these words does not necessarily mean that a statement is not forward-looking. These forward-looking statements include, among other things, statements about:

● the demand and market potential for our products in the countries where they are approved for marketing, as well as the revenues therefrom;

● the timing, investment and associated activities involved in commercializing LINZESS^® by us and Allergan plc in the U.S.;

● the timing and execution of the launches and commercialization of CONSTELLA^® in Europe and LINZESS in Japan and China, as well as our expectations regarding revenue generated from our partners;

● the timing, investment and associated activities involved in developing, obtaining regulatory approval for, launching, and commercializing our products and product candidates by us and our partners worldwide;

● our ability and the ability of our partners to secure and maintain adequate reimbursement for our products;

● our ability and the ability of our partners and third parties to manufacture and distribute sufficient amounts of linaclotide active pharmaceutical ingredient, drug product and finished goods, as applicable, on a commercial scale;

● our expectations regarding U.S. and foreign regulatory requirements for our products and our product candidates, including our post-approval development and regulatory requirements;

● the ability of our product candidates to meet existing or future regulatory standards;

● the safety profile and related adverse events of our products and our product candidates;

● the therapeutic benefits and effectiveness of our products and our product candidates and the potential indications and market opportunities therefor;

● our and our partners’ ability to obtain and maintain intellectual property protection for our products and our product candidates and the strength thereof, as well as Abbreviated New Drug Applications filed by generic drug manufacturers and potential U.S. Food and Drug Administration approval thereof, and associated patent infringement suits that we have filed or may file, or other action that we may take against such companies, and the timing and resolution thereof;

● our and our partners’ ability to perform our respective obligations under our collaboration, license and other agreements, and our ability to achieve milestone and other payments under such agreements;

● our plans with respect to the development, manufacture or sale of our product candidates and the associated timing thereof, including the design and results of pre-clinical and clinical studies;

● the in-licensing or acquisition of externally discovered businesses, products or technologies, as well as partnering arrangements, including expectations relating to the completion of, or the realization of the expected benefits from, such transactions;

2

● our expectations as to future financial performance, revenues, expense levels, payments, cash flows, profitability, tax obligations, capital raising and liquidity sources, real estate needs and concentration of voting control, as well as the timing and drivers thereof, and internal control over financial reporting;

● our expectations as to the costs associated with transitioning to a new headquarters location;

● our ability to repay our outstanding indebtedness when due, or redeem or repurchase all or a portion of such debt, as well as the potential benefits of the note hedge transactions and capped call transactions described herein;

● inventory levels and write downs, or asset impairments, and the drivers thereof, and inventory purchase commitments;

● our ability to compete with other companies that are or may be developing or selling products that are competitive with our products and product candidates;

● the status of government regulation in the life sciences industry, particularly with respect to healthcare reform;

● trends and challenges in our potential markets;

● our ability to attract and motivate key personnel;

● any benefits or costs of the separation of the Company’s operations into two independent, publicly traded companies, including the tax treatment; and

● other factors discussed elsewhere in this Quarterly Report on Form 10-Q.

Any or all of our forward-looking statements in this Quarterly Report on Form 10-Q may turn out to be inaccurate. These forward-looking statements may be affected by inaccurate assumptions or by known or unknown risks and uncertainties, including the risks, uncertainties and assumptions identified under the heading “Risk Factors” in this Quarterly Report on Form 10-Q. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed in this Quarterly Report on Form 10-Q may not occur as contemplated, and actual results could differ materially from those anticipated or implied by the forward-looking statements.

You should not unduly rely on these forward-looking statements, which speak only as of the date of this Quarterly Report on Form 10-Q. Unless required by law, we undertake no obligation to publicly update or revise any forward-looking statements to reflect new information or future events or otherwise. You should, however, review the factors and risks we describe in the reports we will file from time to time with the U.S. Securities and Exchange Commission, or the SEC, after the date of this Quarterly Report on Form 10-Q.

NOTE REGARDING TRADEMARKS

LINZESS^® and CONSTELLA^® are trademarks of Ironwood Pharmaceuticals, Inc. ZURAMPIC^® and DUZALLO^® are trademarks of AstraZeneca AB. Any other trademarks referred to in this Quarterly Report on Form 10-Q are the property of their respective owners. All rights reserved.

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IRONWOOD PHARMACEUTICALS, INC.

QUARTERLY REPORT ON FORM 10-Q

FOR THE QUARTER ENDED SEPTEMBER 30, 2019

TABLE OF CONTENTS

		Page
	PART I — FINANCIAL INFORMATION
Item 1.	Financial Statements (unaudited)
	Condensed Consolidated Balance Sheets as of September 30, 2019 and December 31, 2018	5
	Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2019 and 2018	6
	Condensed Consolidated Statements of Comprehensive Income (Loss) for the Three and Nine Months Ended September 30, 2019 and 2018	7
	Condensed Consolidated Statements of Stockholders’ Deficit for the Three and Nine Months Ended September 30, 2019 and 2018	8
	Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2019 and 2018	11
	Notes to Condensed Consolidated Financial Statements	12
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	48
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	66
Item 4.	Controls and Procedures	68
	PART II — OTHER INFORMATION
Item 1.	Legal Proceedings	68
Item 1A.	Risk Factors	69
Item 6.	Exhibits	96
	Signatures	99

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PART I — FINANCIAL INFORMATION

Item 1. Financial Statements

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(In thousands, except share and per share amounts)

(unaudited)

	September 30,		December 31,
	2019		2018
ASSETS
Current assets:
Cash and cash equivalents	$	139,231	$	173,172
Accounts receivable, net		2,017		20,991
Related party accounts receivable, net		94,553		59,959
Inventory, net		2,298		—
Prepaid expenses and other current assets		11,863		10,216
Restricted cash		7,676		1,250
Current assets of discontinued operations		—		847
Total current assets		257,638		266,435
Restricted cash, net of current portion		971		6,426
Accounts receivable, net of current portion		32,398		—
Property and equipment, net		11,381		7,652
Operating lease right-of-use assets		19,793		—
Convertible note hedges		11,357		41,020
Goodwill		785		785
Other assets		20		89
Non-current assets of discontinued operations		—		9,643
Total assets	$	334,343	$	332,050
LIABILITIES AND STOCKHOLDERS' DEFICIT
Current liabilities:
Accounts payable	$	4,505	$	14,891
Related party accounts payable, net		1,593		—
Accrued research and development costs		4,956		2,963
Accrued expenses and other current liabilities		30,529		38,001
Capital lease obligations		—		73
Current portion of deferred rent		—		252
Current portion of 2026 Notes		—		47,554
Current portion of operating lease liabilities		9,934		—
Current portion of contingent consideration		—		51
Deferred revenue		1,278		—
Current liabilities of discontinued operations		—		15,739
Total current liabilities		52,795		119,524
Capital lease obligations, net of current portion		—		158
Deferred rent, net of current portion		—		6,308
Note hedge warrants		8,768		33,763
Convertible senior notes		402,675		265,601
Operating lease liabilities, net of current portion		22,660		—
2026 Notes, net of current portion		—		100,537
Other liabilities		492		2,530
Commitments and contingencies
Stockholders’ deficit:
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding		—		—
Class A common stock, $0.001 par value, 500,000,000 shares authorized and 156,808,126 issued and outstanding at September 30, 2019 and 500,000,000 shares authorized and 154,414,691 shares issued and outstanding at December 31, 2018		157		154
Additional paid-in capital		1,466,886		1,394,603
Accumulated deficit		(1,620,090)		(1,591,128)
Total stockholders’ deficit		(153,047)		(196,371)
Total liabilities and stockholders’ deficit	$	334,343	$	332,050

The accompanying notes are an integral part of these condensed consolidated financial statements.

5

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations

(In thousands, except per share amounts)

(unaudited)

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Revenues:
Collaborative arrangements revenue	$	130,524	$	54,194	$	273,998	$	188,487
Product revenue, net		—		1,235		—		2,966
Sale of active pharmaceutical ingredient		643		10,257		28,114		24,494
Total revenues		131,167		65,686		302,112		215,947
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets		506		4,616		12,862		11,288
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments		(3,530)		(1,589)		(3,530)		247
Research and development		27,551		29,158		88,507		72,821
Selling, general and administrative		40,919		50,536		133,260		169,252
Amortization of acquired intangible assets		—		1,159		—		8,111
Gain on fair value remeasurement of contingent consideration		—		(33,519)		—		(31,045)
Gain on lease modification		—		—		(3,169)		—
Restructuring expenses		(166)		10,102		3,652		14,010
Impairment of intangible assets		—		151,794		—		151,794
Total cost and expenses		65,280		212,257		231,582		396,478
Income (loss) from operations		65,887		(146,571)		70,530		(180,531)
Other (expense) income:
Interest expense		(10,457)		(9,482)		(29,479)		(28,138)
Interest and investment income		893		741		2,297		2,154
(Loss) gain on derivatives		(4,766)		3,489		(1,494)		3,996
Loss on extinguishment of debt		(30,977)		—		(30,977)		—
Other income		68		—		208		—
Other expense, net		(45,239)		(5,252)		(59,445)		(21,988)
Net income (loss) from continuing operations		20,648		(151,823)		11,085		(202,519)
Net loss from discontinued operations		—		(22,528)		(37,438)		(64,356)
Net income (loss)	$	20,648	$	(174,351)	$	(26,353)	$	(266,875)
Net income (loss) per share from continuing operations—basic and diluted	$	0.13	$	(0.99)	$	0.07	$	(1.33)
Net loss per share from discontinued operations—basic and diluted	$	—	$	(0.15)	$	(0.24)	$	(0.42)
Net income (loss) per share—basic and diluted	$	0.13	$	(1.14)	$	(0.17)	$	(1.75)
Weighted average number of common shares—basic and diluted:		156,436		153,227		155,752		152,143

The accompanying notes are an integral part of these condensed consolidated financial statements.

6

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Comprehensive Income (Loss)

(In thousands)

(unaudited)

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Net income (loss)	$	20,648	$	(174,351)	$	(26,353)	$	(266,875)
Other comprehensive income:
Unrealized gains on available-for-sale securities		—		35		—		70
Total other comprehensive income		—		35		—		70
Comprehensive income (loss)	$	20,648	$	(174,316)	$	(26,353)	$	(266,805)

The accompanying notes are an integral part of these condensed consolidated financial statements.

7

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

(In thousands, except share amounts)

(unaudited)

	Class A			Additional				Total
	common stock			paid-in		Accumulated		Stockholders’
	Shares	Amount		capital		deficit		deficit
Balance at December 31, 2018	154,414,691	$	154	$	1,394,603	$	(1,591,128)	$	(196,371)
Issuance of common stock related to share-based awards and employee stock purchase plan	1,210,858		2		3,486		—		3,488
Share-based compensation expense related to share-based awards and employee stock purchase plan	—		—		14,988		—		14,988
Net loss	—		—		—		(59,284)		(59,284)
Balance at March 31, 2019	155,625,549	$	156	$	1,413,077	$	(1,650,412)	$	(237,179)
Issuance of common stock related to share-based awards and employee stock purchase plan, net of cancellations	621,588		—		1,801		—		1,801
Share-based compensation expense related to share-based awards and employee stock purchase plan	195,195		—		6,337		—		6,337
Dividend of sGC business	—		—		—		(2,609)		(2,609)
Net income	—		—		—		12,283		12,283
Balance at June 30, 2019	156,442,332	$	156	$	1,421,215	$	(1,640,738)	$	(219,367)
Issuance of common stock related to share-based awards and employee stock purchase plan	364,102		1		1,859		—		1,860
Share-based compensation expense related to share-based awards and employee stock purchase plan	1,692		—		5,520		—		5,520
Equity component of convertible senior notes	—		—		92,502		—		92,502
Equity component of issuance costs for convertible senior notes	—		—		(2,092)		—		(2,092)
Equity component of the partial repurchase of the 2022 Convertible Notes	—		—		(26,959)		—		(26,959)
Purchase of capped calls	—		—		(25,159)		—		(25,159)
Net income	—		—		—		20,648		20,648
Balance at September 30, 2019	156,808,126	$	157	$	1,466,886	$	(1,620,090)	$	(153,047)

8

											Accumulated
	Class A			Class B			Additional				other		Total
	common stock			common stock			paid-in		Accumulated		comprehensive		Stockholders’
	Shares	Amount		Shares	Amount		capital		deficit		income (loss)		deficit
Balance at December 31, 2017	136,465,526	$	137	13,983,762	$	14	$	1,318,536	$	(1,308,760)	$	(79)	$	9,848
Issuance of common stock related to share-based awards and employee stock purchase plan	882,448		1	272,146		—		6,193		—		—		6,194
Issuance of common stock awards	162		—	—		—		—		—		—		—
Conversion of Class B common stock to Class A common stock	258,551		—	(258,551)		—		—		—		—		—
Share-based compensation expense related to share-based awards and employee stock purchase plan	—		—	—		—		9,062		—		—		9,062
Unrealized losses on available-for-sale securities	—		—	—		—		—		—		(12)		(12)
Net loss	—		—	—		—		—		(43,144)		—		(43,144)
Balance at March 31, 2018	137,606,687	$	138	13,997,357	$	14	$	1,333,791	$	(1,351,904)	$	(91)	$	(18,052)
Issuance of common stock related to share-based awards and employee stock purchase plan	989,830		1	129,501		—		12,865		—		—		12,866
Issuance of common stock awards	130,045		—	—		—		—		—		—		—
Conversion of Class B common stock to Class A common stock	134,367		—	(134,367)		—		—		—		—		—
Share-based compensation expense related to share-based awards and employee stock purchase plan	—		—	—		—		10,568		—		—		10,568

9

Unrealized gains on available-for-sale securities	—		—	—		—		—		—		47		47
Net loss	—		—	—		—		—		(49,380)		—		(49,380)
Balance at June 30, 2018	138,860,929	$	139	13,992,491	$	14	$	1,357,224	$	(1,401,284)	$	(44)	$	(43,951)
Issuance of common stock upon exercise of stock options, employee stock purchase plan and restricted stock units	621,420		1	307,051		—		8,319		—		—		8,320
Issuance of common stock awards	272		—	—		—		—		—		—		—
Conversion of Class B common stock into Class A common stock	322,687		—	(322,687)		—		—		—		—		—
Share-based compensation expense related to share-based awards to employees and employee stock purchase plan	—		—	—		—		12,652		—		—		12,652
Unrealized gain on short-term investments	—		—	—		—		—		—		35		35
Net loss	—		—	—		—		—		(174,351)		—		(174,351)
Balance at September 30, 2018	139,805,308	$	140	13,976,855	$	14	$	1,378,195	$	(1,575,635)	$	(9)	$	(197,295)

The accompanying notes are an integral part of these condensed consolidated financial statements.

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Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flows

(In thousands)

(unaudited)

	Nine Months Ended
	September 30,
	2019		2018
Cash flows from operating activities:
Net loss	$	(26,353)	$	(266,875)
Adjustments to reconcile net loss to net cash used in operating activities:		—
Depreciation and amortization		4,713		3,165
Amortization of acquired intangible assets		—		8,111
Impairment of intangible assets		—		151,794
Loss (gain) on disposal of property and equipment		109		(1,591)
Gain on lease modification		(3,169)		—
Share-based compensation expense		25,792		30,165
Change in fair value of note hedge warrants		740		30,590
Change in fair value of convertible note hedges		754		(34,586)
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments		(3,530)		247
Write-down of excess non-cancellable ZURAMPIC and DUZALLO sample purchase commitments		—		390
Accretion of discount/premium on investment securities		—		(157)
Non-cash interest expense		15,532		13,044
Non-cash change in fair value of contingent consideration		—		(31,045)
Loss on extinguishment of debt		30,977		—
Changes in assets and liabilities:
Accounts receivable and related party accounts receivable, net		(46,712)		16,782
Prepaid expenses and other current assets		(421)		(13,513)
Inventory, net		(1,086)		(713)
Other assets		—		119
Accounts payable, related party accounts payable and accrued expenses		(37,275)		(6,988)
Accrued research and development costs		1,021		(1,241)
Operating lease right-of-use assets		12,091		—
Operating lease liabilities		(2,680)		—
Deferred revenue		1,278		13,521
Deferred rent		—		716
Net cash used in continuing operating activities		(28,219)		(88,065)
Net cash provided by discontinued operating activities		11,364		7,910
Net cashed used in operating activities		(16,855)		(80,155)
Cash flows from investing activities:
Purchases of available-for-sale securities		—		(3,241)
Sales and maturities of available-for-sale securities		—		79,312
Purchases of property and equipment		(4,521)		(97)
Proceeds from sale of property and equipment		261		627
Net cash (used in) provided by continuing investing activities		(4,260)		76,601
Net cash used in discontinued investing activities		(4,223)		(5,223)
Net cash (used in) provided by investing activities		(8,483)		71,378
Cash flows from financing activities:
Proceeds from issuance of convertible senior notes		400,000		—
Purchase of capped calls		(25,159)		—
Proceeds from partial termination of convertible note hedges and warrants		3,174		—
Costs associated with issuance of convertible senior notes		(9,048)		—
Proceeds from exercise of stock options and employee stock purchase plan		7,148		27,152
Payments on capital lease obligations		—		(1,822)
Payments for partial repurchase of 2022 Convertible Notes		(227,338)		—
Payments on 2026 Notes		(156,409)		—
Payments on contingent purchase price consideration		—		(107)
Net cash (used in) provided by continuing financing activities		(7,632)		25,223
Net cash (used in) provided by discontinued financing activities		—		—
Net cash (used in) provided by financing activities		(7,632)		25,223
Net (decrease) increase in cash, cash equivalents and restricted cash		(32,970)		16,446
Cash, cash equivalents and restricted cash, beginning of period		180,848		132,792
Cash, cash equivalents and restricted cash, end of period	$	147,878	$	149,238
Reconciliation of cash, cash equivalents, and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$	139,231	$	141,562
Restricted cash		8,647		7,676
Total cash, cash equivalents, and restricted cash	$	147,878	$	149,238

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The accompanying notes are an integral part of these condensed consolidated financial statements.

Ironwood Pharmaceuticals, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

1. Nature of Business

Overview

Ironwood Pharmaceuticals, Inc. (“Ironwood” or the “Company”) is a gastrointestinal (“GI”) focused healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. The Company is advancing innovative product opportunities in areas of large unmet need, capitalizing on its proven development and commercial capabilities and its deep expertise in GI diseases. On April 1, 2019, the Company completed its tax-free spin-off of its soluble guanylate cyclase (“sGC”) business into a separate publicly traded company, Cyclerion Therapeutics, Inc. (“Cyclerion”).

The Company’s commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation (“IBS-C”), or chronic idiopathic constipation (“CIC”), in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms.

Linaclotide is available under the trademarked name LINZESS^® (linaclotide) to adult men and women suffering from IBS-C or CIC in the United States (the “U.S.”) and Mexico and to adult men and women suffering from IBS-C in Japan. Linaclotide is available under the trademarked name CONSTELLA^® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries.

The Company has strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. The Company and its partner, Allergan plc (together with its affiliates, “Allergan”), began commercializing LINZESS in the U.S. in December 2012. Under the Company’s collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party and the resulting amount is shared equally between the Company and Allergan. Allergan also has an exclusive license from the Company to develop and commercialize linaclotide in all countries other than China, including Hong Kong and Macau, Japan and the countries and territories of North America (the “Allergan License Territory”). On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS.

Astellas Pharma Inc. (“Astellas”), the Company’s partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adults with chronic constipation in Japan. On August 1, 2019, the Company amended and restated its license agreement with Astellas. Beginning in 2020, the Company will no longer be responsible for the supply of linaclotide active pharmaceutical ingredient (“API”) to Astellas (Note 4).

In October 2012, the Company and AstraZeneca AB (together with its affiliates, “AstraZeneca”), entered into a collaboration agreement to co-develop and co-commercialize linaclotide in China, including Hong Kong and Macau (the “AstraZeneca License Territory”). In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. On September 16, 2019, the Company amended its existing collaboration agreement with AstraZeneca. As of September 16, 2019, AstraZeneca has the exclusive right to develop, manufacture, and commercialize products containing linaclotide in the AstraZeneca License Territory (Note 4).

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The Company and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations, and formulations to assess its potential to treat various conditions. In June 2019, the Company announced positive topline data from its Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C.

The Company and Allergan are advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain-relieving agent for patients suffering from abdominal pain associated with certain GI diseases. There are an estimated 16 million Americans who suffer from symptoms of IBS with diarrhea (“IBS-D”), according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, the Company and Allergan initiated a Phase II clinical trial evaluating MD-7246 in adult patients with IBS-D.

The Company is advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of persistent gastroesophageal reflux disease (“GERD”). There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al. in Gut; a Lieberman HCP Survey, 2019; a Lieberman GI patient landscape survey, 2010; a survey conducted by American Gastroenterological Association; and 2019 U.S. census data. In June 2018, the Company initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

The Company periodically enters into co-promotion agreements to maximize its salesforce productivity, such as its co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D. In August 2019, the Company entered into a disease education and promotional agreement with Alnylam Pharmaceuticals, Inc. (“Alnylam”) for Alnylam’s givosiran, an investigational RNAi therapeutic for the treatment of patients with acute hepatic porphyria (“AHP”). Under the agreement, the Company will perform disease awareness activities related to AHP and, if givosiran is approved by the U.S. Food and Drug Administration (“FDA”), future sales detailing activities of a product containing givosiran (Note 4).

On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into Cyclerion (the “Separation”). The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of all outstanding shares of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019 (Note 2).

On June 11, 2019, the Company entered into a non-cancelable operating lease (the “Summer Street Lease”) for approximately 39,000 square feet of office space on the 23^rd floor of 100 Summer Street, Boston, Massachusetts (the “Summer Street Property”). The Summer Street Property became the Company’s new headquarters in October 2019, replacing its prior headquarters at 301 Binney Street (Note 8).

In August 2019, the Company issued $200.0 million in aggregate principal amount of 0.75% Convertible Senior Notes due 2024 (the “2024 Convertible Notes”) and $200.0 million in aggregate principal amount of 1.50% Convertible Senior Notes due 2026 (the “2026 Convertible Notes”). The Company received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million.

The proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used in August 2019 to pay the cost of associated capped call transactions (the “Capped Calls”) and to repurchase $215.0 million aggregate principal amount of the existing 2.25% Convertible Senior Notes due 2022 (the “2022 Convertible Notes”). The proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes were also used to redeem all of the outstanding principal balance of the 8.375% Notes due 2026 (the “2026 Notes”) on September 16, 2019 (Note 9). The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. During the three months ended September 30, 2019, the Company recognized a loss on extinguishment of debt of approximately $31.0 million related to the redemption of the 2026 Notes and the partial repurchase of the 2022 Convertible Notes.

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Basis of Presentation

The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”).

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of September 30, 2019, and the results of its operations for the three and nine months ended September 30, 2019 and 2018, its statements of stockholders’ deficit for the three and nine months ended September 30, 2019 and 2018, and its cash flows for the nine months ended September 30, 2019 and 2018. The results of operations for the three and nine months ended September 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period.

The Company has presented its sGC business as discontinued operations in its condensed consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly (Note 2). For periods following the Separation, the Company continues to report financial results under one business segment.

Principles of Consolidation

The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of September 30, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent, publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation.

Use of Estimates

The preparation of condensed consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance and repurchase of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Reclassifications of Prior Period Financial Statements

Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation.

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Summary of Significant Accounting Policies

The Company’s significant accounting policies are described in Note 2, Summary of Significant Accounting Policies, in the 2018 Annual Report on Form 10-K. During the nine months ended September 30, 2019, the Company adopted the following additional significant accounting policies:

Discontinued Operations

During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations (“ASC 205-20”). Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements.

Leases

Effective January 1, 2019, the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and nine months ended September 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases (“ASC 840”). Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary.

The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s condensed consolidated financial statements.

As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include:

● Accounting policy election to use the short-term lease exception by asset class;

● Election of the practical expedient package during transition, which includes:

o An entity need not reassess whether any expired or existing contracts are or contain leases.

o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

o An entity need not reassess initial direct costs for any existing leases.

Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

The Company’s lease portfolio for the three and nine months ended September 30, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s condensed consolidated balance sheets. As of September 30, 2019, the Company did not have any finance leases.

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Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company.

Derivative Assets and Liabilities

In June 2015, in connection with the issuance of the 2022 Convertible Notes, the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 12). In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, the Company terminated its Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging (“ASC 815”).

These derivatives are recorded as assets or liabilities at fair value each reporting period and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of the Company’s Class A common stock on the date of valuation, time to maturity of the derivative instruments, the strike prices of the derivative instruments, the risk-free interest rate, and the volatility of the Company’s Class A common stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. Subject to customary anti-dilution and certain other adjustments, the Capped Calls cover the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met.

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (the “FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as set forth below, the Company did not adopt any new accounting pronouncements during the three and nine months ended September 30, 2019 that had a material effect on its condensed consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which supersedes the lease accounting requirements in ASC 840 and most industry-specific guidance with ASC 842. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, lease arrangements exceeding a 12-month term must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation are recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization and interest expense for financing leases. The balance sheet amounts recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. ASU 2016-02 is effective for fiscal

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years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. Subsequent to the issuance of ASU 2016-02, the FASB issued ASU No. 2018-10, Leases (Topic 842), Codification Improvements (“ASU 2018-10”), ASU No. 2018-11, Leases (Topic 842), Targeted Improvements (“ASU 2018-11”), and ASU No. 2019-01 Leases (Topic 842), Codification Improvements (“ASU 2019-01”) to provide additional guidance for the adoption of Topic 842. ASU 2018-10 clarifies certain provisions and corrects unintended applications of the guidance, such as the rate implicit in a lease, impairment of the net investment in a lease, lessee reassessment of lease classifications, lessor reassessment of lease term and purchase options, variable payments that depend on an index or rate and certain transition adjustments. The amendments in ASU 2018-11 allow for an additional transition method, whereby at the adoption date the entity recognizes a cumulative-effect adjustment to the opening balance of retained earnings in the period of adoption, while the comparative period disclosures continue recognition under ASC 840. Additionally, ASU 2018-11 includes a practical expedient for separating contract components for lessors. The Company adopted ASC 842 using the optional transition method outlined in ASU 2018-11 as of January 1, 2019. The adoption of ASC 842 resulted in the recognition of operating lease right-of-use assets of approximately $88.3 million and corresponding lease liabilities of approximately $94.9 million. The adoption of these ASUs did not have a material impact on the Company’s results of operations; however, the adoption resulted in significant changes to the Company’s financial statement disclosures.

In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”). ASU 2016-13 will change how companies account for credit losses for most financial assets and certain other instruments. For trade receivables, loans and held-to-maturity debt securities, companies will be required to recognize an allowance for credit losses rather than reducing the carrying value of the asset. Subsequent to the issuance of ASU 2016-13, the FASB issued ASU No. 2019-04, Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments (“ASU 2019-04”) and ASU No. 2019-05, Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief (“ASU 2019-05”) to provide additional guidance on the adoption of ASU 2016-13. ASU 2019-04 added Topic 326, Financial Instruments—Credit Losses, and made several amendments to the codification and also modified the accounting for available-for-sale debt securities. ASU 2019-05 provides targeted transition relief by providing an option to irrevocably elect the fair value option for certain financial assets previously measured at amortized cost basis. ASU 2016-13, ASU 2019-04 and ASU 2019-05 are effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have on the Company’s financial position and results of operations.

In January 2017, the FASB issued ASU No. 2017-04, Intangibles—Goodwill and Other (Topic 350) (“ASU 2017-04”) to simplify the accounting for goodwill impairment by removing Step 2 of the goodwill impairment test. ASU 2017-04 is effective for fiscal years beginning after December 15, 2019. Early adoption is permitted. The Company is evaluating the potential impact that the adoption of ASU 2017-04 may have on the Company’s financial position and results of operations.

In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) (“Topic 718”): Improvements to Nonemployee Share-Based Payment Accounting (“ASU 2018-07”). ASU 2018-07 expands the scope of Topic 718 to include share-based payment transactions for acquiring goods and services from non-employees, and as a result, the accounting for share-based payments to non-employees will be substantially aligned. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within that fiscal year. Early adoption is permitted but not earlier than an entity’s adoption date of Topic 606. The Company adopted this standard during the three months ended March 31, 2019. The adoption of ASU 2018-07 did not have a material impact on the Company’s financial position and results of operations.

In July 2018, the FASB issued ASU 2018-09, Codification Improvements (“ASU 2018-09”). The amendments in ASU 2018-09 affect a wide variety of Topics in the FASB codification and apply to all reporting entities within the scope of the affected accounting guidance. The Company has evaluated ASU 2018-09 in its entirety and determined that the amendments related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, are the only provisions that currently apply to the Company. The amendments in ASU 2018-09 related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, clarify that an entity should recognize excess tax benefits related to stock compensation transactions in the period in which the amount of the deduction is determined. The amendments in ASU 2018-09 related to Topic 718-740 are effective for fiscal years beginning after December 15, 2018, with early adoption permitted. The Company adopted this standard during the three months ended March 31, 2019. The adoption of this standard did not have a material impact on the Company’s financial position and results of operations.

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In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirement for Fair Value Measurement (“ASU 2018-13”) which amends the disclosure requirements for fair value measurements. The amendments in ASU 2018-13 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-13 may have on the Company’s financial position and results of operations.

In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement that is a Service Contract (a consensus of the FASB Emerging Issues Task Force) (“ASU 2018-15)” which provides additional guidance on the accounting for costs of implementation activities performed in a cloud computing arrangement that is a service contract. The amendments in ASU 2018-15 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-15 may have on the Company’s financial position and results of operations.

In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities (“ASU 2018-17”). The update is intended to improve general purpose financial reporting by considering indirect interests held through related parties in common control arrangements on a proportional basis for determining whether fees paid to decision makers and service providers are variable interests. The amendments in ASU 2018-17 will be effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-17 may have on the Company’s financial position and results of operations.

In July 2019, the FASB issued ASU No. 2019-07, Disclosure Update and Simplification and Investment Company Reporting Modernization (“ASU 2019-07”). The update is intended to simplify disclosure requirements to reflect the amendments of various Securities and Exchange Commission (“SEC”) disclosure requirements that the SEC determined were redundant, duplicative, overlapping, outdated or superseded and is effective upon issuance. The adoption of ASU 2019-07 did not have a material impact on the Company’s financial position, results of operations, or financial statement disclosures.

No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption.

2. Cyclerion Separation

On April 1, 2019, Ironwood completed the Separation of Cyclerion. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019. Prior to the Separation on April 1, 2019, as described in Note 1, Nature of Business, Cyclerion was a wholly owned subsidiary of the Company. On March 30, 2019, the Company entered into certain agreements with Cyclerion relating to the Separation, including a separation agreement, a tax matters agreement, and an employee matters agreement.

Agreements with Cyclerion

The separation agreement with Cyclerion, dated as of March 30, 2019, sets forth, among other things, the Company’s agreements with Cyclerion regarding the principal actions to be taken in connection with the Separation, including the distribution, which was effective as of April 1, 2019. The separation agreement identifies assets transferred, liabilities assumed by and contracts assigned to each of Cyclerion and Ironwood as part of the Separation, and it provides for when and how these transfers, assumptions and assignments occur. The purpose of the separation agreement is to provide Cyclerion and Ironwood with assets to operate their respective businesses and retain or assume liabilities related to those assets.

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The transfer of assets and liabilities to Cyclerion was effected through a contribution in accordance with the separation agreement as summarized below (in thousands):

		As of April 1, 2019
Assets:
Prepaid expenses and other current assets	$	1,169
Property and equipment, net		10,241
Other assets		21
	$	11,431
Liabilities:
Accrued research and development costs	$	5,673
Accrued expenses and other current liabilities		3,149
	$	8,822
Net Assets Transferred to Cyclerion	$	2,609

In addition, the Company received approximately $1.3 million during the three months ended September 30, 2019 associated with tenant improvement reimbursement provisions related to the Cyclerion lease in accordance with the separation agreement.

The tax matters agreement, dated as of March 30, 2019, governs each party’s rights, responsibilities and obligations with respect to taxes, including taxes, if any, incurred as a result of any failure of the Separation to qualify as tax-free. In general, if the parties incur tax liabilities in the event that the Separation is not tax-free, each party is expected to be responsible for any taxes imposed on Ironwood or Cyclerion that arise from the failure of the Separation to qualify as a transaction that is generally tax-free for U.S. federal income tax purposes, under Sections 355 and 368(a)(1)(D) and certain other relevant provisions of the Internal Revenue Code of 1986, as amended, to the extent that the failure to so qualify is attributable to an acquisition of stock or assets of, or certain actions, omissions or failures to act of, such party. If both Ironwood and Cyclerion are responsible for such failure, liability will be shared according to relative fault. U.S. tax otherwise resulting from the failure of the Separation to qualify as a transaction that is tax-free generally will be the responsibility of Ironwood. Each party otherwise agreed to indemnify the other party from and against any liability for taxes allocated to such party under the tax matters agreement and any taxes resulting from breach of any such party’s covenants under the tax matters agreement, the separation agreement, or any ancillary agreement entered into in connection with the Separation. Cyclerion agreed to certain covenants that contain restrictions intended to preserve the tax-free status of the distribution and certain related transactions.

The employee matters agreement, dated as of March 30, 2019, allocates assets, liabilities and responsibilities relating to the employment, compensation, and employee benefits of Ironwood and Cyclerion employees, and other related matters in connection with the Separation, including the treatment of outstanding Ironwood incentive equity awards. Pursuant to the employee matters agreement, the outstanding Ironwood equity awards held by Cyclerion and Ironwood employees were adjusted in connection with the Separation, with the intent to maintain, immediately following the Separation, the economic value of the awards. No incremental stock-based compensation expense was recognized during the three or nine months ended September 30, 2019 (Note 10).

Additionally, the Company entered into two transition services agreements and a development agreement with Cyclerion.

Pursuant to the transition service agreements, the Company is obligated to provide and is entitled to receive certain transition services related to corporate functions, such as finance, procurement, facilities and development. Services provided by the Company to Cyclerion will continue for an initial term of one to two years from the date of the Separation (as applicable), unless earlier terminated or extended according to the terms of the transition services agreement. Services provided by Cyclerion to the Company will continue for an initial term of one year from the date of the Separation, unless earlier terminated or extended according to the terms of such transition services agreement. Services received and performed are paid at a mutually agreed upon rate. Amounts for services provided to Cyclerion are recorded as other income and amounts for services provided by Cyclerion are recorded as selling, general and administrative expense and research and development expense, as applicable. During the three and nine months ended September 30, 2019, the Company recorded an insignificant amount and approximately $0.2 million as other income for services provided to Cyclerion, respectively. During each of the three and nine months ended September 30, 2019, the

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Company recorded an insignificant amount in both selling, general and administrative expense and research and development expense for services provided by Cyclerion.

Pursuant to the development agreement, Cyclerion is obligated to provide the Company with certain research and development services with respect to certain of Ironwood’s products and product candidates, including MD-7246 and IW-3718. Such research and development activities are governed by a joint steering committee comprised of representatives from both Cyclerion and Ironwood. Services received are paid at a mutually agreed upon rate. The Company recorded approximately $1.4 million and approximately $3.0 million in research and development expenses under the development agreement during the three and nine months ended September 30, 2019, respectively.

Discontinued Operations

Upon Separation, the Company determined its sGC business qualified for discontinued operations accounting treatment in accordance with ASC 205-20. The following is a summary of expenses of Cyclerion for the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Costs and expenses:
Research and development		—		17,636		21,792		49,410
Selling, general and administrative		—		4,712		15,646		13,860
Restructuring expenses		—		180		—		1,086
Net loss from discontinued operations		—		22,528		37,438		64,356

There were no assets and liabilities related to discontinued operations as of September 30, 2019, as all balances were transferred to Cyclerion upon Separation. The following is a summary of assets and liabilities of discontinued operations as of December 31, 2018 (in thousands):

Assets:
Prepaid expenses and other current assets	$	847
Property and equipment, net		9,618
Other assets		25
	$	10,490
Liabilities:
Accounts payable	$	3,232
Accrued research and development costs		5,256
Accrued expenses and other current liabilities		7,251
	$	15,739

3. Net Income (Loss) Per Share

Basic and diluted net income (loss) per common share is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period.

In June 2015, in connection with the issuance of approximately $335.7 million in aggregate principal amount of 2022 Convertible Notes (Note 9), the Company entered into the Convertible Note Hedges. The Convertible Note Hedges are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2022 Convertible Notes and/or offset any cash payments the Company is required to make in excess of the principal amount of converted 2022 Convertible Notes in the event that the market price per share of the Company’s Class A common stock, as measured under the terms of the Convertible Note Hedges, is greater than the conversion price of the 2022 Convertible Notes. The Convertible Note Hedges are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive. A proportionate amount of these Convertible Note Hedges were terminated in connection with the partial repurchase of the 2022 Convertible Notes in August 2019.

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Concurrently with entering into the Convertible Note Hedges, the Company also entered into the Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 9). The Note Hedge Warrants could have a dilutive effect on the Company’s Class A common stock to the extent that the market price per share of the Class A common stock exceeds the applicable strike price of such warrants. The Note Hedge Warrants are not considered for purposes of calculating the number of diluted weighted averages shares outstanding, as their effect would be anti-dilutive. A proportionate amount of these Note Hedge Warrants were terminated in connection with the partial repurchase of the 2022 Convertible Notes in August 2019.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls. The Capped Calls are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2024 Convertible Notes or the 2026 Convertible Notes and/or offset any cash payments that the Company is required to make in excess of the principal amount of converted 2024 Convertible Notes or 2026 Convertible Notes in the event that the market price per share of the Company’s Class A common stock, as measured under the terms of the Capped Calls, is greater than the conversion price of the 2024 Convertible Notes or the 2026 Convertible Notes. The Capped Calls are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive.

The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands):

	As of September 30,
	2019	2018
Options to purchase Class A common stock	17,889	20,860
Shares subject to repurchase	182	97
Restricted stock units	2,838	3,238
Shares subject to issuance under Employee Stock Purchase Plan	67	59
Note Hedge Warrants	8,318	20,250
2022 Convertible Notes	8,318	20,250
2024 Convertible Notes	14,934	—
2026 Convertible Notes	14,934	—
Total	67,480	64,754

During the three and nine months ended September 30, 2019, the Company recorded net income of approximately $20.6 million and net loss of approximately $26.4 million, respectively. The inclusion of applicable securities in the calculation of diluted earnings per share was anti-dilutive for the three months ended September 30, 2019. As a result, diluted earnings per share is equivalent to basic earnings per share for the three and nine months ended September 30, 2019.

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4. Collaboration, License, Co-Promotion and Other Commercial Agreements

For the three and nine months ended September 30, 2019, the Company had linaclotide collaboration agreements with Allergan for North America and AstraZeneca for China, including Hong Kong and Macau, as well as linaclotide license agreements with Astellas for Japan and with Allergan for the Allergan License Territory. The Company also had agreements with Allergan to co-promote VIBERZI in the U.S. and Alnylam to perform disease awareness activities for AHP and, if givosiran is approved by the FDA, future sales detailing activities of a product containing givosiran. The following table provides amounts included in the Company’s condensed consolidated statements of operations as collaborative arrangements revenue and sale of active pharmaceutical ingredient (“API”) attributable to transactions from these arrangements (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
Collaborative Arrangements Revenue	2019		2018		2019		2018
Linaclotide Collaboration Agreements:
Allergan (North America)	$	85,107	$	52,724	$	225,390	$	184,133
Allergan (Europe and other)		526		255		1,208		831
AstraZeneca (China, including Hong Kong and Macau)		32,401		—		32,401		—
Astellas (Japan)		10,059		—		10,059		—
Co-Promotion and Other Agreements:
Allergan (VIBERZI)		1,363		750		2,602		2,250
Alnylam (givosiran)		722		—		722		—
Other		346		465		1,616		1,273
Total collaborative arrangements revenue	$	130,524	$	54,194	$	273,998	$	188,487
Sale of API (1)
Linaclotide License Agreements:
Astellas (Japan)	$	—	$	9,501	$	27,468	$	23,738
AstraZeneca (China, including Hong Kong and Macau)		643		—		646		—
Other (1)		—		756		—		756
Total sale of API	$	643	$	10,257	$	28,114	$	24,494

(1) During the three months ended September 30, 2018, the Company recorded approximately $0.8 million in revenue related to the sale of API to Allergan.

Accounts receivable, net and related party accounts receivable, net included approximately $129.0 million related to collaborative arrangements revenue and sale of API as of September 30, 2019, net of approximately $3.8 million related to related party accounts payable.

As of September 30, 2019, there were no impairment indicators for the accounts receivable recorded.

Linaclotide Agreements

Collaboration Agreement for North America with Allergan

In September 2007, the Company entered into a collaboration agreement with Allergan to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in North America. Under the terms of this collaboration agreement, the Company received a non-refundable, upfront licensing fee and shares equally with Allergan all development costs as well as net profits or losses from the development and sale of linaclotide in the U.S. The Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Allergan is solely responsible for the further development, regulatory approval and commercialization of linaclotide in those countries and funding any costs. The collaboration agreement for North America also includes contingent milestone payments, as well as a contingent equity investment, based on the achievement of specific development and commercial milestones. At September 30, 2019, $205.0 million in license fees and all six development milestone payments had been received by the Company, as well as a $25.0 million equity investment in the Company’s capital stock (Note 11). The Company can also achieve up to $100.0 million in a sales-related milestone if certain conditions are met, which will be recognized as

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collaborative arrangements revenue when it is probable that a significant reversal of revenue would not occur and the associated constraints have been lifted.

As a result of the research and development cost-sharing provisions of the linaclotide collaboration for North America, the Company offset approximately $0.9 million and approximately $6.5 million in incremental research and development costs during the three and nine months ended September 30, 2019, respectively, and offset approximately $2.5 million and approximately $5.8 million in incremental research and development costs during the three and nine months ended September 30, 2018, respectively, to reflect the obligations of each party under the collaboration to bear half of the development costs incurred.

The Company and Allergan began commercializing LINZESS in the U.S. in December 2012. The Company receives 50% of the net profits and bears 50% of the net losses from the commercial sale of LINZESS in the U.S. Net profits or net losses consist of net sales of LINZESS to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. LINZESS net sales are calculated and recorded by Allergan and may include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions. If either party provided fewer calls on physicians in a particular year than it was contractually required to provide, such party’s share of the net profits would be adjusted as set forth in the collaboration agreement for North America. The Company has completed its obligations under the terms of the commercial agreement with Allergan, pursuant to which it promoted CANASA, and these adjustments to the share of the net profits have been eliminated, in full, in 2018 and all subsequent years.

The Company evaluated this collaboration arrangement under ASC 606, Revenue from Contracts with Customers (“ASC 606”) and concluded that all development-period performance obligations had been satisfied as of September 2012. However, the Company has determined that there are three remaining commercial-period performance obligations, which include the sales detailing of LINZESS, participation in the joint commercialization committee, and approved additional trials. The consideration remaining includes cost reimbursements in the U.S., as well as commercial sales-based milestones and net profit and loss sharing payments based on net sales in the U.S. Additionally, the Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Royalties, commercial sales-based milestones, and net profit and loss sharing payments will be recorded as collaborative arrangements revenue or expense in the period earned, in accordance with the sales-based royalty exception, as these payments relate predominately to the license granted to Allergan. The Company records royalty revenue in the period earned based on royalty reports from its partner, if available, or based on the projected sales and historical trends. The cost reimbursements received from Allergan during the commercialization period will be recognized as billed in accordance with the right-to-invoice exemption, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period.

Under the Company’s collaboration agreement with Allergan for North America, LINZESS net sales are calculated and recorded by Allergan and include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions, as noted above. These amounts include the use of estimates and judgments, which could be adjusted based on actual results in the future. The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis less commercial expenses and presents the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. This treatment is in accordance with the Company’s revenue recognition policy, given that the Company is not the primary obligor and does not have the inventory risks in the collaboration agreement with Allergan for North America. The Company relies on Allergan to provide accurate and complete information related to net sales of LINZESS in accordance with U.S. generally accepted accounting principles in order to calculate its settlement payments to and from Allergan and record collaboration expense or collaborative arrangements revenue, as applicable. 

From time to time, in accordance with the terms of the collaboration with Allergan for North America, the Company engages an independent certified public accounting firm to review the accuracy of the financial reporting from Allergan to the Company. In connection with such a review during the three months ended September 30, 2018, Allergan reported to the Company an approximately $59.3 million negative adjustment to LINZESS net sales. Such adjustment related to the cumulative difference between certain previously estimated LINZESS gross-to-net sales reserves and allowances made by Allergan during the years ended December 31, 2015, 2016 and 2017, and subsequent actual payments made. This adjustment was primarily associated with estimated governmental and contractual rebates, as reported by Allergan. Accordingly, upon receiving this information from Allergan, the Company recorded a change in

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accounting estimate to reduce collaborative arrangements revenue by approximately $29.7 million during the three months ended September 30, 2018 related to the Company’s share of this adjustment.

The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the three and nine months ended September 30, 2019 and 2018 as follows (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.	$	84,565	$	52,261	$	223,831	$	182,675
Royalty revenue		542		463		1,559		1,458
Total collaborative arrangements revenue	$	85,107	$	52,724	$	225,390	$	184,133

The collaborative arrangements revenue recognized in the three and nine months ended September 30, 2019 and 2018 primarily represents the Company’s share of the net profits and net losses on the sale of LINZESS in the U.S.

The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.(1)(2)	$	84,565	$	52,261	$	223,831	$	182,675
Selling, general and administrative costs incurred by the Company(1)		(9,129)		(10,915)		(29,764)		(33,556)
The Company’s share of net profit	$	75,436	$	41,346	$	194,067	$	149,119

(1) Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and nine months ended September 30, 2019 and 2018.

In May 2014, CONSTELLA became commercially available in Canada and in June 2014, LINZESS became commercially available in Mexico. The Company records royalties on sales of CONSTELLA in Canada and LINZESS in Mexico in the period earned. The Company recognized approximately $0.5 million and approximately $1.6 million of combined royalty revenues from Canada and Mexico during the three and nine months ended September 30, 2019, respectively. The Company recognized approximately $0.5 million and approximately $1.5 million of combined royalty revenues from Canada and Mexico during the three and nine months ended September 30, 2018, respectively.

License Agreement with Allergan (All countries other than the countries and territories of North America, China, including Hong Kong and Macau, and Japan)

In April 2009, the Company entered into a license agreement with Almirall, S.A. (“Almirall”) to develop and commercialize linaclotide in Europe (including the Commonwealth of Independent States and Turkey) for the treatment of IBS-C, CIC and other GI conditions (the “European License Agreement”). In accordance with the European License Agreement, the Company granted Almirall a right to access its U.S. Phase III clinical trial data for the purposes of supporting European regulatory approval. Additionally, the Company was required to participate on a joint development committee during linaclotide’s development period and is required to participate in a joint commercialization committee while linaclotide is commercially available. In October 2015, Almirall transferred its exclusive license to develop and commercialize linaclotide in Europe to Allergan.

Additionally, in October 2015, the Company and Allergan separately entered into an amendment to the European License Agreement relating to the development and commercialization of linaclotide in Europe. Pursuant to the terms of the amendment, (i) certain sales-based milestones payable to the Company under the European License Agreement were modified to increase the total milestone payments such that, when aggregated with certain commercial launch milestones, they could total up to $42.5 million, (ii) the royalties payable to the Company during the term of the European License Agreement were modified such that the royalties based on sales volume in Europe begin in the mid-single digit percent and escalate to the upper-teens percent by calendar year 2019, and (iii) Allergan assumed

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responsibility for the manufacturing of linaclotide API for Europe from the Company, as well as the associated costs. The Company concluded that the 2015 amendment to the European License Agreement was not a modification to the linaclotide collaboration agreement with Allergan for North America.

In January 2017, concurrently with entering into the commercial agreement as described below in Commercial Agreement with Allergan, the Company and Allergan entered into an amendment to the European License Agreement (the “2017 Amendment”). The European License Agreement, as amended (the “Allergan License Agreement”), extended the license to develop and commercialize linaclotide in all countries other than China, including Hong Kong and Macau, Japan, and the countries and territories of North America. On a country-by-country and product-by-product basis in such additional territory, Allergan is obligated to pay the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient in the upper-single digits for five years following the first commercial sale of a linaclotide product in a country, and in the low-double digits thereafter. The royalty rate for products in the expanded territory will decrease, on a country-by-country basis, to the lower-single digits, or cease entirely, following the occurrence of certain events. Allergan also is obligated to assume certain purchase commitments for quantities of linaclotide API under the Company’s agreements with third-party API suppliers. The amendment to the European License Agreement did not modify any of the milestones or royalty terms related to Europe.

Prior to the adoption of ASC 606, the Company concluded that the 2017 Amendment was a material modification to the European License Agreement; however, this modification did not have a material impact on the Company's condensed consolidated financial statements as there was no deferred revenue associated with the European License Agreement. The Company also concluded that the 2017 Amendment was not a material modification to the linaclotide collaboration agreement with Allergan for North America.

In evaluating the terms of the 2009 European License Agreement under ASC 606, the Company determined that there are no remaining performance obligations as of September 2012. However, the Company continues to be eligible to receive consideration in the form of commercial launch milestones, sales-based milestones, and royalties.

The commercial launch milestones, sales-based milestones and royalties under the European License Agreement have historically been recognized as revenue as earned. Under ASC 606, the Company applied the sales-based royalty exception to royalties and sales-based milestones, as these payments relate predominantly to the license granted to Allergan (formerly Almirall). Accordingly, the royalties and sales-based milestones are recorded as revenue in the period earned. The Company records royalties on sales of CONSTELLA in Europe in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends. The commercial launch milestones are recognized as revenue when it is probable that a significant reversal of revenue would not occur and the associated constraint has been lifted.

Additionally, the Company evaluated the terms of the 2017 Amendment under ASC 606 and determined that it would be treated as a separate contract given that it adds a distinct good or service at an amount that reflects standalone selling price. The Company determined that all performance obligations in the 2017 Amendment were satisfied in January 2017 when the license for the additional territory was transferred. The Company continues to receive royalties under this agreement, which are recorded in the period earned pursuant to the sales-based royalty exception, as they related predominantly to the license granted to Allergan.

The Company recognized approximately $0.5 million and approximately $1.2 million of royalty revenue from the European License Agreement during the three and nine months ended September 30, 2019, respectively, and recognized approximately $0.2 million and approximately $0.8 million during the three and nine months ended September 30, 2018, respectively.

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License Agreement for Japan with Astellas

In November 2009, the Company entered into a license agreement with Astellas, as amended, to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in Japan (the “2009 License Agreement with Astellas”). Astellas is responsible for all activities relating to development, regulatory approval and commercialization in Japan as well as funding the associated costs and the Company is required to participate on a joint development committee over linaclotide’s development period. During the year ended December 31, 2017, the Company and Astellas entered into a commercial API supply agreement (the “Astellas Commercial Supply Agreement”). Pursuant to the Astellas Commercial Supply Agreement, the Company sells linaclotide API supply to Astellas at a contractually defined rate and recognizes related revenue as sale of API. Under the 2009 License Agreement with Astellas, the Company received royalties which escalated based on sales volume, beginning in the low-twenties percent, less the transfer price paid for the API included in the product sold and other contractual deductions.

Under the 2009 License Agreement with Astellas, the Company received an up-front licensing fee of $30.0 million and three development milestone payments that totaled up to $45.0 million, which were recognized as revenue prior to the adoption of ASC 606 on January 1, 2018.

The Company had evaluated the terms of the 2009 License Agreement with Astellas under ASC 606 and determined that there were no remaining performance obligations as of the adoption of ASC 606.

Additionally, under the terms of the Astellas Commercial Supply Agreement, the Company determined it had an ongoing performance obligation to supply API. Upon adoption of ASC 606, product revenue is recognized when the customer obtains control of the Company’s product, which occurs at a point in time, typically upon shipment of the product to the customer. This results in earlier revenue recognition than the Company’s historical accounting.

On August 1, 2019, the Company and Astellas amended and restated the 2009 License Agreement with Astellas (the “Amended Astellas License Agreement”). This amendment is considered a modification to the 2009 License Agreement with Astellas and is accounted for as a new and separate contract. Under the terms of this Amended Astellas License Agreement, the Company will no longer be responsible for the supply of linaclotide API to Astellas, and Astellas will be responsible for its own supply of linaclotide API for sale in Japan, beginning in 2020. Astellas has committed to purchase certain quantities of linaclotide API from the Company in 2019.

In connection with the execution of the Amended Astellas License Agreement, Astellas paid the Company a non-refundable upfront payment of $10.0 million in August 2019. Further, beginning in 2020, Astellas will, in lieu of the royalty payment terms set forth in the 2009 License Agreement with Astellas, pay royalties to the Company at rates beginning in the mid-single digit percent and escalating to low-double-digit percent, based on aggregate annual net sales in Japan of products containing linaclotide API. These royalty payments will be subject to reduction following the expiration of certain licensed patents and the occurrence of generic competition in Japan. The Company will continue to supply linaclotide API for Japan during 2019 at a contractually defined rate. Additionally, Astellas will reimburse the Company for the Company’s performance of adverse event reporting services at a fixed monthly rate until such services are terminated.

The Company identified the following performance obligations under the Amended Astellas License Agreement:

● delivery of the expanded license of intellectual property, including the applicable manufacturing know-how,

● obligation to supply linaclotide API for 2019, and

● adverse event reporting services.

The Company allocated the $10.0 million upfront payment to the delivery of the expanded license of intellectual property and recognized it as collaborative arrangements revenue at contract inception. The Company allocated the approximately $20.4 million in remaining purchase orders for API to the obligation to supply linaclotide API to Astellas for 2019. Consideration for the supply of linaclotide API will be recognized over the performance period using an output method as linaclotide API is shipped to Astellas. Consideration allocated to the adverse event reporting services will be recognized as such services are provided over the performance period using an output method based on the amount to which the Company has a right to invoice.

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Royalties on sales of LINZESS in Japan relate predominantly to the license granted to Astellas. Accordingly, the Company applies the sales-based royalty exception and records royalties on sales of LINZESS in Japan in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends.

The Company recognized $10.0 million in collaborative arrangements revenue during the three and nine months ended September 30, 2019 related to the upfront fee associated with the execution of the Amended Astellas License Agreement. The Company recognized no revenue and approximately $27.5 million from the sale of API to Astellas under the Amended License Agreement, the 2009 License Agreement with Astellas and the Astellas Commercial Supply Agreement during the three and nine months ended September 30, 2019, respectively, and recognized approximately $9.5 million and approximately $23.7 million during the three and nine months ended September 30, 2018, respectively. The royalties on sales of LINZESS in Japan did not exceed the transfer price of API sold and other contractual deductions during each of the periods presented. The Company recognized an insignificant amount of collaborative arrangements revenue related to adverse event reporting services in each of the three and nine months ended September 30, 2019.

Collaboration Agreement for China (including Hong Kong and Macau) with AstraZeneca

In October 2012, the Company entered into a collaboration agreement with AstraZeneca to co-develop and co-commercialize linaclotide in the AstraZeneca License Territory (the “AstraZeneca Collaboration Agreement”). The collaboration provided AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the AstraZeneca License Territory. The parties shared responsibility for continued development and commercialization of linaclotide under a joint development plan and a joint commercialization plan, respectively, with AstraZeneca having primary responsibility for the local operational execution. In September 2019, the Company and AstraZeneca entered into an amendment and restatement of the AstraZeneca Collaboration Agreement (the “Amended AstraZeneca Agreement”), under which AstraZeneca obtained the exclusive right to develop, manufacture and commercialize products containing linaclotide in the AstraZeneca License Territory (the “AstraZeneca License”).

Prior to the execution of the Amended AstraZeneca Agreement, the Company identified the following performance obligations under the AstraZeneca Collaboration Agreement:
​

● research, development and regulatory services pursuant to the development plan (“R&D Services”),

● Joint Development Committee (“JDC”) services,

● obligation to supply clinical trial material, and

● Joint Commercialization Committee (“JCC”) services.

Under the AstraZeneca Collaboration Agreement, the Company shared development costs with AstraZeneca, with AstraZeneca incurring 55% of the net losses from the development and commercialization of linaclotide in the AstraZeneca License Territory. Payments from AstraZeneca with respect to both research and development and selling, general and administrative costs incurred by the Company prior to the commercialization of linaclotide in the AstraZeneca License Territory were recorded as a reduction in expense, in accordance with the Company’s policy. Development costs incurred by the Company that pertained to the joint development plan and subsequent amendments to the joint development plan, as approved by the JDC, were recorded as research and development expense as incurred. Payments to AstraZeneca were recorded as incremental research and development expense.

During the three and nine months ended September 30, 2019, the Company incurred no costs and offset an insignificant amount of costs related to R&D Services and JDC Services, respectively, under the AstraZeneca Collaboration Agreement. During the three and nine months ended September 30, 2018, the Company offset an insignificant amount of costs and approximately $0.8 million, respectively, related to R&D Services and JDC Services. During the three and nine months ended September 30, 2019, the Company recognized an insignificant amount of revenue related to sale of linaclotide drug product and API under the AstraZeneca Collaboration Agreement. The Company recorded no revenue related to sale of linaclotide drug product and API during each of the three and nine months ended September 30, 2018. Additionally, the Company incurred approximately $0.7 million and approximately $1.2 million in costs related to pre-launch commercial services and supply chain services during the three and nine months ended September 30, 2019, respectively.

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Under the Amended AstraZeneca Agreement, the Company will receive non-contingent payments totaling $35.0 million in three installments through 2024. In addition, AstraZeneca may be required to make milestone payments totaling up to $90.0 million contingent on the achievement of certain sales targets and will be required to pay tiered royalties to the Company at rates beginning in the mid-single-digit percent and increasing up to twenty percent based on the aggregate annual net sales of products containing linaclotide in the AstraZeneca License Territory. In connection with the Amended AstraZeneca Agreement, the Company and AstraZeneca entered into a transition services agreement (“AstraZeneca TSA”) and an amended commercial supply agreement (“AstraZeneca CSA”). Under the terms of the AstraZeneca TSA, the Company will provide certain regulatory and administrative services for a term of approximately two years from the date of execution, unless earlier terminated or extended according to the terms of the transition services agreement. Services performed are paid at a mutually agreed upon rate. Amounts for AstraZeneca TSA services are recorded as collaborative arrangements revenue. Under the terms of the AstraZeneca CSA, the Company will supply linaclotide API, drug product and finished goods for the Licensed Territory through no later than March 31, 2020 at predetermined rates.

The Company evaluated the Amended AstraZeneca Agreement in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the Amended AstraZeneca Agreement were identified:

● delivery of the AstraZeneca License,

● AstraZeneca TSA services, and

● supply of linaclotide API, drug product and finished goods under the AstraZeneca CSA.

The Company determined that the non-contingent payments should be allocated to the delivery of the AstraZeneca License. The non-contingent payments totaling $35.0 million will be paid in installments through 2024. The Company determined that the performance obligation related to the transfer of the AstraZeneca License was satisfied as of the execution date of the Amended AstraZeneca Agreement. As a portion of the payments relating to the transfer of the AstraZeneca License are due significantly after the performance obligation was satisfied, the Company adjusted its transaction price for the significant financing component of approximately $2.6 million. Accordingly, the Company recognized approximately $32.4 million relating to the delivery of the AstraZeneca license as collaborative arrangements revenue during the three months ended September 30, 2019 and will recognize the approximately $2.6 million relating to the significant financing component as interest income through 2024. Consideration allocated to the AstraZeneca TSA services will be recognized as collaborative arrangements revenue as such services are provided over the performance period using an output method based on the amount to which the Company has a right to invoice. Consideration for the supply of linaclotide API, drug product and finished goods under the AstraZeneca CSA will be recognized over the performance period using an output method as linaclotide API, drug product and finished goods are shipped to AstraZeneca.

During each of the three and nine months ended September 30, 2019, the Company recognized approximately $32.4 million in collaborative arrangements revenue related to the Amended AstraZeneca License, of which approximately $32.4 million related to the delivery of the AstraZeneca License and an insignificant amount related to the AstraZeneca TSA services. During each of the three and nine months ended September 30, 2019, the Company recognized approximately $0.6 million of sale of API on its condensed consolidated statement of operations, relating to the supply of linaclotide drug product and finished goods under the AstraZeneca CSA.

Co-Promotion and Other Agreements

Co-Promotion Agreements with Allergan

In January 2017, concurrently with entering into the amendment to the European License Agreement, the Company and Allergan entered into an agreement under which the adjustments to the Company’s or Allergan’s share of the net profits under the share adjustment provision of the collaboration agreement for linaclotide in North America relating to the contractually required calls on physicians in each year were eliminated, in full, in 2018 and all subsequent years (the “Commercial Agreement”). Pursuant to the Commercial Agreement, Allergan appointed the Company, on a non-exclusive basis, to promote CANASA, approved for the treatment of ulcerative proctitis in the U.S. for approximately two years through February 2019. Under the terms of the Commercial Agreement, the Company was obligated to perform third position sales details and offer samples of such products to gastroenterology prescribers who were on the then-current call panel for LINZESS to which the Company was providing first or second position details.

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On a product-by-product basis, Allergan paid the Company a royalty in the mid-teens on incremental sales of CANASA above a mutually agreed upon sales baseline. The Company discontinued its promotion of CANASA on December 31, 2018.

Upon adoption of ASC 606, the Company evaluated the commercial agreement and the amendment to the European License Agreement under the contract combination and contract modification guidance in ASC 606. The Company determined that the agreements should be accounted for as separate contracts because each agreement adds distinct goods or services at an amount that reflects standalone selling price. The Company concluded that the CANASA sales detailing deliverable under ASC 605 was also considered a performance obligation in accordance with ASC 606. Accordingly, the Company recorded royalties on sales of CANASA and any estimated detailing shortfall penalty over the period of performance for the sales details; collaborative arrangements revenue was recognized when it was probable that a significant reversal of revenue would not occur and the associated constraint has been lifted. The Company estimated sales detailing royalties based on royalty reports from its partner, if available, or the projected sales and historical trends. At the inception of the arrangement, the consideration associated with the agreement comprised of royalties and a sales detailing shortfall penalty are fully constrained. During each of the three and nine months ended September 30, 2018, the Company did not recognize royalty revenue related to the Commercial Agreement with Allergan for sales of CANASA.

In December 2017, the Company and Allergan entered into an amendment to the commercial agreement with Allergan (the “VIBERZI Amendment”), as described below, to include the VIBERZI promotional activities through December 31, 2018. Under the terms of the VIBERZI Amendment, the Company’s clinical sales specialists detailed VIBERZI in the second position to the same health care practitioners to whom they detailed LINZESS in the first position and provided certain medical education services. The Company had the potential to achieve a milestone payment of up to $7.5 million based on the net sales of VIBERZI during 2018 and was compensated approximately $3.0 million over the term of the agreement for its medical education initiatives. The Company evaluated the VIBERZI Amendment in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the VIBERZI Amendment were identified:

● sales detailing of VIBERZI in either first or second position, and

● medical education services.

The sales-based milestone payment was recognized as collaborative arrangements revenue when it was probable that a significant reversal of revenue would not occur and the associated constraint had been lifted. During the three months ended December 31, 2018, the Company determined the sales-based milestone payment was no longer constrained and recognized approximately $1.3 million in collaborative arrangements revenue. The consideration related to medical education events of approximately $3.0 million was recognized over the period of performance that medical education services are provided. During the three and nine months ended September 30, 2018, the Company recognized approximately $0.8 million and approximately $2.3 million of collaborative arrangements revenue, respectively, related to VIBERZI medical education services. In December 2018 and in March 2019, the Company extended the VIBERZI Amendment through April 2019.

In April 2019, the Company entered into a new agreement with Allergan to perform sales detailing activities for VIBERZI, effective April 1, 2019 through December 31, 2019 (the “VIBERZI Promotion Agreement”). Under the terms of the VIBERZI Promotion Agreement, the Company’s clinical sales specialists will continue detailing VIBERZI in the second position to the same health care practitioners to whom they detail LINZESS in the first position. The Company has the potential to achieve a milestone payment of up to approximately $4.2 million based on the number of VIBERZI prescription extended units filled over the term of the agreement. The Company will be compensated based on the number of VIBERZI sales details performed, up to a maximum amount of approximately $4.1 million over the term of the agreement. In accordance with ASC 606, the VIBERZI Promotion Agreement will be accounted for as a separate contract as it contains distinct services at an amount that reflects standalone selling price, incremental to past agreements. The Company identified the performance of VIBERZI second position sales details as the sole performance obligation under the agreement.

The milestone payment will be recognized as collaborative arrangements revenue when it is probable that a significant reversal of revenue will not occur and the associated constraint has been lifted. As of September 30, 2019, the Company determined the milestone payment was fully constrained. The compensation related to the VIBERZI sales

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details is recognized over the term of the agreement using an output method based on estimated amounts for which the Company has the right to invoice based on the number of sales details performed during the associated period. During each of the three and nine months ended September 30, 2019, the Company recognized approximately $1.4 million and approximately $2.6 million of collaborative arrangements revenue related to VIBERZI sales details, respectively.

Disease Education and Promotional Agreement with Alnylam

On August 9, 2019, the Company and Alnylam entered into a disease education and promotional agreement for Alnylam’s investigational RNAi therapeutic givosiran for the potential treatment of AHP (the “Alnylam Agreement”). As of September 30, 2019, givosiran was not yet approved by the FDA. Under the terms of the agreement, the Company’s sales force will perform disease awareness activities and, if givosiran is approved by the FDA, future sales detailing activities of a product containing givosiran to gastroenterologists and health care practitioners to whom they detail LINZESS in the first position.

The Company is entitled to receive service fees, payable by Alnylam quarterly, totaling up to $9.5 million over the term of the agreement, which is approximately three years. The Company also is eligible to receive a royalty based on a percentage of net sales of an FDA-approved product containing givosiran that are directly attributable to the Company’s promotional efforts. The Company identified the following performance obligation under the Alnylam Agreement:

● performance of disease education activities for AHP and performance of sales details for an FDA-approved product containing givosiran (together “Givosiran Education and Promotion Activities”).

The Company allocated the service fees to the performance of Givosiran Education and Promotion Activities and recognizes collaborative arrangements revenue over the term of the agreement as the services are performed using an output method based on the amount to which the Company has a right to invoice. Royalties will be recognized as collaborative arrangements revenue using an output method for Givosiran Education and Promotion Activities based on the amount to which the Company has a right to invoice when the associated constraints have been lifted. At contract inception, the royalty revenue is fully constrained because givosiran has not yet been approved by the FDA.

During each of the three and nine months ended September 30, 2019, the Company recognized approximately $0.7 million in collaborative arrangements revenue related to the service fees. As of September 30, 2019, the Company had a deferred revenue balance of approximately $1.3 million related to the Givosiran Education and Promotion Activities performed in accordance with the Alnylam Agreement. The Company did not recognize any royalty revenue related to the Alnylam Agreement as revenue remains fully constrained.

Other Collaboration and License Agreements

The Company has other collaboration and license agreements that are not individually significant to its business. Pursuant to the terms of one agreement, the Company was required to pay $7.5 million for development milestones, all of which had been paid as of September 30, 2019. The Company may also be required to pay up to $18.0 million for regulatory milestones, none of which had been paid as of September 30, 2019. Pursuant to the terms of another license agreement, the Company recognized no revenue and approximately $0.5 million in collaborative arrangements revenue during the three and nine months ended September 30, 2019, respectively, related to a nonrefundable upfront payment. The Company is eligible to receive up to $63.5 million in development and sales-based milestones, as well as a royalty as a percentage of net sales of a product, under the terms of this agreement. The Company recorded no research and development expenses associated with the Company’s other collaboration and license agreements during each of the three and nine months ended September 30, 2019. The Company recorded approximately $5.0 million in research and development expenses associated with the Company’s other collaboration and license agreements during each of the three and nine months ended September 30, 2018.

5. Fair Value of Financial Instruments

The tables below present information about the Company’s assets that are measured at fair value on a recurring basis as of September 30, 2019 and December 31, 2018 and indicate the fair value hierarchy of the valuation techniques

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the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize observable inputs such as quoted prices in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are either directly or indirectly observable, such as quoted prices for similar instruments in active markets, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.

The Company’s investment portfolio may include fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company apply other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare valuations. In addition, model processes are used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data. The Company validates the prices provided by its third-party pricing services by obtaining market values from other pricing sources and analyzing pricing data in certain instances. The Company also invests in certain reverse repurchase agreements which are collateralized by deposits in the form of Government Securities and Obligations for an amount not less than 102% of their principal amount. The Company does not record an asset or liability for the collateral as the Company is not permitted to sell or re-pledge the collateral. The collateral has at least the prevailing credit rating of U.S. Government Treasuries and Agencies. The Company utilizes a third-party custodian to manage the exchange of funds and ensure the collateral received is maintained at 102% of the reverse repurchase agreements principal amount on a daily basis.

The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands):

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	September 30, 2019		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	101,207	$	101,207	$	—	$	—
Repurchase agreements		37,800		37,800		—		—
Convertible Note Hedges		11,357		—		—		11,357
Total assets measured at fair value	$	150,364	$	139,007	$	—	$	11,357
Liabilities:
Note Hedge Warrants	$	8,768	$	—	$	—	$	8,768
Total liabilities measured at fair value	$	8,768	$	—	$	—	$	8,768

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	December 31, 2018		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	142,218	$	142,218	$	—	$	—
Repurchase agreements		30,875		30,875		—		—
Convertible Note Hedges		41,020		—		—		41,020
Total assets measured at fair value	$	214,113	$	173,093	$	—	$	41,020
Liabilities:
Note Hedge Warrants	$	33,763	$	—	$	—	$	33,763
Contingent Consideration		51		—		—		51
Total liabilities measured at fair value	$	33,814	$	—	$	—	$	33,814

There were no transfers between fair value measurement levels during each of the three and nine months ended September 30, 2019 or 2018.

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Cash equivalents, accounts receivable, related party accounts receivable, prepaid expenses and other current assets, accounts payable, related party accounts payable, accrued expenses and other current liabilities, the current portion of capital lease obligations, deferred rent, deferred revenue and operating lease obligations at September 30, 2019 and December 31, 2018 are carried at amounts that approximate fair value due to their short-term maturities.

Convertible Note Hedges and Note Hedge Warrants

The Company’s Convertible Note Hedges and the Note Hedge Warrants are recorded as derivative assets and liabilities, and are classified as Level 3 under the fair value hierarchy. These derivatives are not actively traded and are valued using the Black-Scholes option-pricing model which requires the use of subjective assumptions. Significant inputs used to determine the fair value as of September 30, 2019 included the price per share of the Company’s Class A common stock, time to maturity of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, expected volatility of the Company’s Class A common stock, and expected dividend yield. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants.

In April 2019, the Company announced an adjustment to the conversion rate applicable to the 2022 Convertible Notes, effective April 15, 2019 (Note 9).

In August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes, which triggered a partial termination of the outstanding Convertible Note Hedges and Note Hedge Warrants. During the three and nine months ended September 30, 2019, the Company recorded a loss of approximately $4.8 million and approximately $1.5 million on derivatives, respectively, as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and the change in fair value of the remaining Convertible Note Hedges and Note Hedge Warrants during the quarter (Note 9).

The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of September 30, 2019 and December 31, 2018:

	Nine Months Ended						Year Ended
	September 30,						December 31,
	2019						2018
	Convertible			Note Hedge			Convertible			Note Hedge
	Note Hedges			Warrants			Note Hedges			Warrants
Risk-free interest rate (1)		1.6	%		1.6	%		2.5	%		2.5	%
Time to maturity		2.7			3.3			3.5			4.1
Stock price (2)	$	8.59		$	8.59		$	10.36		$	10.36
Strike price (3)	$	14.51		$	18.82		$	16.58		$	21.50
Common stock volatility (4)		47.8	%		46.5	%		43.8	%		43.6	%
Dividend yield		—	%		—	%		—	%		—	%

(1) Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants.

(2) The closing price of the Company’s Class A common stock on the last trading day of the quarter ended September 30, 2019 and December 31, 2018, respectively.

(3) As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 9).

(4) Expected volatility based on historical volatility of the Company’s Class A common stock.

(5) The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero.

The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting period and changes in fair value are recorded in other expense, net within the Company’s condensed consolidated statements of operations. Gains and losses for these derivative financial instruments are presented separately in the Company’s condensed consolidated statements of cash flows.

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The following table reflects the change in the Company’s Level 3 Convertible Note Hedges and Note Hedge Warrants from December 31, 2018 through September 30, 2019 (in thousands):

	Convertible		Note Hedge
	Note Hedges		Warrants
Balance at December 31, 2018	$	41,020	$	(33,763)
Cash settlement (received) paid upon early termination of derivatives		(28,909)		25,735
Change in fair value, recorded as a component of gain (loss) on derivatives		(754)		(740)
Balance at September 30, 2019	$	11,357	$	(8,768)

Convertible Senior Notes

In June 2015, the Company issued approximately $335.7 million aggregate principal amount of its 2022 Convertible Notes. In August 2019, the Company repurchased $215.0 million aggregate principal amount of its 2022 Convertible Notes. Additionally, in August 2019, the Company issued $200.0 million aggregate principal amount of its 2024 Convertible Notes and $200.0 million aggregate principal amount of its 2026 Convertible Notes. The Company separately accounted for the liability and equity components of each of the 2022 Convertible Notes, 2024 Convertible Notes, and 2026 Convertible Notes, and together the Convertible Senior Notes, by allocating the proceeds between the liability component and equity component (Note 9). The fair value of the respective Convertible Senior Notes, which differs from their carrying value, is influenced by interest rates, the price of the Company’s Class A common stock and the volatility thereof, and the prices for the respective Convertible Senior Notes observed in market trading, which are Level 2 inputs.

The estimated fair value of the 2022 Convertible Notes was approximately $120.0 million and approximately $315.0 million as of September 30, 2019 and December 31, 2018, respectively. The estimated fair value of the 2024 Convertible Notes was approximately $185.9 million as of September 30, 2019. The estimated fair value of the 2026 Convertible Notes was approximately $183.6 million as of September 30, 2019.

Capped Calls

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. The Capped Calls cover 29,867,480 shares of Class A common stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes, and have a cap price of approximately $17.05 per share (Note 9). These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met (Note 1).

8.375% Notes Due 2026

In September 2016, the Company closed a direct private placement pursuant to which the Company issued $150.0 million in aggregate principal amount of the 2026 Notes in January 2017. The outstanding principal balance of the 2026 Notes was redeemed in September 2019 (Note 9). The estimated fair value of the 2026 Notes was approximately $148.2 million as of December 31, 2018. This valuation was calculated using a discounted cash flow estimate of expected interest and principal payments and was determined using Level 3 inputs, including significant estimates related to expected LINZESS sales and a discount rate equivalent to market participant interest rates.

Nonrecurring fair value measurements – Intangible Assets

On August 2, 2018, the Company delivered to AstraZeneca notice of termination of the lesinurad license agreement for the development, manufacture, and commercialization of products in the U.S. containing lesinurad as an active ingredient (the “Lesinurad License”). During the three months ended September 30, 2018, the Company recorded an approximately $151.8 million impairment charge related to its acquired intangible assets. The impairment assessment

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performed utilized the revised projected revenue and net cash flows assumed through the termination of the lesinurad license agreement, resulting in an impairment of the full carrying value of the intangible assets.

6. Inventory

Inventory consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Raw Materials	$	1,134	$	—
Work in Progress		707		—
Finished Goods		457
	$	2,298	$	—

The Company’s inventory represents linaclotide API, drug product, and finished goods. The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified.

No impairment of inventory was recorded during the three and nine months ended September 30, 2019. The Company wrote down approximately $0.6 million and approximately $2.5 million related to lesinurad inventory and commercial supply purchase commitments during the three and nine months ended September 30, 2018, respectively, as a result of revised demand forecasts and the termination of the Lesinurad License. The adjustment was recorded as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments.

7. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

p
	September 30, 2019		December 31, 2018
Salaries	$	1,703	$	3,054
Accrued vacation		2,647		3,493
Accrued incentive compensation		8,647		13,867
Other employee benefits		1,340		1,883
Professional fees		5,177		1,735
Accrued interest		1,392		873
Restructuring accruals		432		2,885
Other		9,191		10,211
	$	30,529	$	38,001

As of September 30, 2019, other accrued expenses of approximately $9.2 million included approximately $4.0 million related to activities associated with the Company’s move to the Summer Street Property, approximately $1.2 million related to unbilled inventory, and approximately $0.7 million related to contracted services for strategy-related GI research.

During the three months ended September 30, 2019, the Company relieved approximately $4.0 million of previously accrued non-cancelable purchase commitments recorded as accrued expenses related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments, as well as certain excess non-cancelable linaclotide purchase commitments. In addition, during the three months ended September 30, 2019, the Company also relieved approximately $2.5 million of previously accrued non-cancelable purchase commitments recorded as other liabilities related to the assignment of certain linaclotide excess non-cancelable purchase commitments to AstraZeneca in connection with the Amended AstraZeneca Collaboration Agreement. Accordingly, the Company recorded a settlement of approximately $3.5 million as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments related to certain of the aforementioned reversals.

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During the three months ended September 30, 2018, the Company assigned to Allergan certain linaclotide excess non-cancelable purchase commitments that the Company had previously accrued for. Accordingly, the Company relieved the previous accrual of approximately $2.5 million, which was recorded as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments.

As of December 31, 2018, other accrued expenses of approximately $10.2 million included approximately $2.5 million related to linaclotide excess purchase commitments, and approximately $1.4 million related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments.

8. Leases

Effective January 1, 2019, the Company adopted ASC 842 using the optional transition method. The Company’s lease portfolio for the nine months ended September 30, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment.

Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the three and nine months ended September 30, 2019 are as follows (in thousands):

	Three Months Ended		Nine Months Ended
	September 30,		September 30,
	2019		2019
Operating lease cost during period, net(1)	$	6,244		13,924
Variable lease payments		654		1,308
Short-term lease cost		375		1,143
Total lease cost	$	7,273		16,375

(1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the nine months ended September 30, 2019. Sublease income relates to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019.

Supplemental cash flow information related to leases for the periods reported is as follows:

	Nine Months Ended
	September 30,
	2019
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands)	$	88,299
Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands)		(40,427)
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands)		(34,440)
Right-of-use assets obtained in exchange for new operating lease liabilities(1) (in thousands)		18,452
Cash paid for amounts included in the measurement of lease liabilities (in thousands)		8,869
Weighted-average remaining lease term of operating leases (in years)		8.0
Weighted-average discount rate of operating leases		5.4	%

(1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease.

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Future minimum lease payments under non-cancelable operating leases under ASC 842 as of September 30, 2019 are as follows (in thousands):

	Operating
	Lease
	Payments
2019(1)	$	9,729
2020		1,146
2021		3,128
2022		3,129
2023		3,065
2024 and thereafter		21,170
Total future minimum lease payments		41,367
Less: present value adjustment		8,773
Operating lease liabilities at September 30, 2019		32,594
Less: current portion of operating lease liabilities		9,934
Operating lease liabilities, net of current portion	$	22,660

(1) Amounts are for the three months ending December 31, 2019.

At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands):

	Operating
	Lease
	Payments
2019	$	18,736
2020		18,312
2021		18,863
2022		19,365
2023		19,818
2024 and thereafter		22,118
Total future minimum lease payments	$	117,212

Summer Street Lease (current headquarters)

On June 11, 2019, the Company entered into the Summer Street Lease, a non-cancelable operating lease with MA-100 Summer Street Owner, L.L.C. (the “Summer Street Landlord”) for the Summer Street Property. The Summer Street Property began serving as the Company’s headquarters beginning in October 2019, replacing its prior headquarters at 301 Binney Street in Cambridge, Massachusetts. The Summer Street Lease terminates on June 11, 2030 and includes an option to extend the term of the lease for an additional five years at a market base rental rate, a 2% annual rent escalation, free rent periods, and a tenant improvement allowance. The rent expense for the Summer Street Property, inclusive of the escalating rent payments and lease incentives, is recognized on a straight-line basis over the lease term. Additionally, the Summer Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $1.0 million, which is collateralized by a money market account recorded as restricted cash on the Company’s condensed consolidated balance sheets as of September 30, 2019.

At lease inception, the Company recorded a right-of-use asset and a lease liability associated with the Summer Street Lease using an incremental borrowing rate of approximately 5.8%. At September 30, 2019, the balance of the right-of-use asset for the Summer Street Lease was approximately $18.0 million. At September 30, 2019, the balance of the lease liability for the Summer Street Lease was approximately $22.5 million.

The Company recorded an asset retirement obligation in connection with the estimated future costs related to the removal of certain leasehold improvements at the Summer Street Property upon termination of the lease. The balance of the Company’s asset retirement obligation for the Summer Street Lease was approximately $0.5 million as of September 30, 2019.

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Lease cost related to the Summer Street Lease recorded during the three and nine months ended September 30, 2019 was approximately $0.6 million and $0.8 million, respectively.

Binney Street Lease (prior headquarters)

The Company rented office space at 301 Binney Street, Cambridge, Massachusetts (“Binney Street Property”) under a non-cancelable operating lease, entered into in January 2007, as amended (“Binney Street Lease”) through October 2019. The Binney Street Property previously served as the Company’s headquarters but was replaced by the Summer Street Property in October 2019, as discussed above.

Prior to the modifications discussed below, the term of the Binney Street Lease was through January 31, 2025 for approximately 223,000 square feet of laboratory and office space. The Binney Street Lease included an option to extend the term of the lease for an additional five years at a market base rental rate, a 3% annual rent escalation, free rent periods, a tenant improvement allowance, and an option to extend the term of the lease for an additional five years at a market base rental rate. The rent expense for the Binney Street Lease, inclusive of the escalating rent payments, lease incentives and free rent periods, was to be recognized on a straight-line basis over the lease term through January 2025. Additionally, the Binney Street Lease required a letter of credit to secure the Company’s obligations under the lease agreement of approximately $6.4 million, which is recorded as restricted cash.

As of January 1, 2019, in conjunction with the adoption of ASC 842, the Company recorded a right-of-use asset of approximately $87.7 million and a lease liability of approximately $94.3 million associated with the Binney Street Lease.

On April 1, 2019, the Company modified its lease with BMR-Rogers Street LLC (“Binney Street Landlord”), to reduce its leased premises to approximately 108,000 rentable square feet of office space on the first and third floors. The surrendered portion of approximately 114,000 rentable square feet on the first and second floor of the building is now occupied by Cyclerion under a direct lease between Cyclerion and the Binney Street Landlord. As a result of the modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 5.1% in accordance with ASC 842, and recognized a gain of approximately $3.2 million, recorded as operating expenses on its condensed consolidated statement of operations. The Company elected to determine the proportionate reduction in the right-of-use asset based on the reduction to the lease liability and will apply that methodology consistently to all comparable modifications that decrease the scope of the lease.

On June 11, 2019, the Company entered into a lease termination agreement (the “Lease Termination”) with the Binney Street Landlord to terminate the Company’s existing lease for approximately 108,000 square feet of office space. The Lease Termination was effective during the fourth quarter of 2019 in exchange for an approximately $9.0 million payment to the Binney Street Landlord. The Company determined that the Lease Termination would be accounted for as a lease modification that reduces the term of the existing lease. As a result of this modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 4.0%.

At September 30, 2019, the balances of the right-of-use asset and lease liability for the Binney Street Lease were approximately $1.8 million and approximately $9.7 million, respectively.

Lease cost related to the Binney Street Lease recorded during the three months ended September 30, 2019 was approximately $6.2 million. Lease cost related to the Binney Street Lease recorded during the nine months ended September 30, 2019 was approximately $14.3 million, net of sublease income of approximately $0.3 million. Under ASC 840, rent expense related to the Binney Street Lease recorded during the three and nine months ended September 30, 2018 was approximately $2.5 million and $7.6 million, respectively.

Data center colocation lease

The Company rents space for its data center at a colocation in Boston, Massachusetts under a non-cancelable operating lease (the “Data Center Lease”). The Data Center Lease contains various provisions, including a 4% annual rent escalation. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term through August 2022. The Company recorded a right-of-use asset of approximately $0.6 million, and a lease liability of approximately $0.6 million associated with the Data Center Lease upon adoption of ASC 842. During the

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three months ended March 31, 2019, the Company migrated its data management process to a cloud-based services system, rendering its current data center technology and assets obsolete. As a result, the Company considered the right-of-use asset associated with the Data Center Lease to be impaired. The Company recorded a charge of approximately $0.5 million to selling, general, and administrative expenses on its condensed consolidated statement of operations as a result of the impairment during the three months ended March 31, 2019.

At September 30, 2019, the lease liability associated with the Data Center Lease was approximately $0.5 million, and the right-of-use asset remained fully impaired. The incremental borrowing rate for the outstanding Data Center Lease obligation upon adoption of ASC 842 was approximately 6.0%.

Under ASC 842, the lease costs related to the Data Center Lease were insignificant for each of the three and nine months ended September 30, 2019. Under ASC 840, rent expenses related to the Data Center Lease were insignificant for each of the three and nine months ended September 30, 2018.

Vehicle fleet leases

During April 2018, the Company entered into a master services agreement containing 12-month leases (the “2018 Vehicle Leases”) for certain vehicles within its fleet for its field-based sales force and medical science liaisons. These leases are classified as short-term in accordance with the practical expedient in ASC 842. The 2018 Vehicle Leases expire at varying times beginning in June 2019, with a monthly renewal provision. In accordance with the terms of the 2018 Vehicle Leases, the Company maintains a letter of credit securing its obligation under the lease agreements of $1.3 million, which is collateralized by a money market account recorded as restricted cash.

Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million and approximately $1.1 million for the three and nine months ended September 30, 2019, respectively. Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million for each of the three and nine months ended September 30, 2018.

Prior to the adoption of ASC 842, during 2018, the Company had certain ongoing vehicle leases for its field-based sales force and medical science liaisons (the “2015 Vehicle Leases”). These leases were classified as capital leases under ASC 840. The 2015 Vehicle Leases expired at varying times through December 2018. In connection with entering into the 2018 Vehicle Leases, all of the 2015 Vehicle Leases were terminated through December 31, 2018. At December 31, 2018, the Company had no remaining capital lease obligations related to the 2015 Vehicle Leases.

Other leases

Prior to the adoption of ASC 842, the Company entered into leases for certain computer and office equipment that expired in 2018. These leases were classified as capital leases under ASC 840. At December 31, 2018, the Company had approximately $0.2 million in capital lease obligations. At December 31, 2018, the weighted average interest rate on the outstanding capital lease obligations was approximately 3.4%.

9. Notes Payable

8.375% Notes due 2026

On September 23, 2016, the Company closed a direct private placement, pursuant to which the Company issued $150.0 million in aggregate principal amount of 8.375% notes due 2026 on January 5, 2017. The Company capitalized approximately $0.5 million of debt issuance costs, which were netted against the carrying value of the 2026 Notes. Proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used, in part, to redeem the outstanding principal balance of the 2026 Notes in September 2019. The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. The redemption of the 2026 Notes resulted in a loss on extinguishment of debt of approximately $7.6 million related to the prepayment premium and write-off of the remaining 2026 Notes, the unamortized debt issuance costs, and the unamortized debt discount.

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The 2026 Notes had an annual interest rate of 8.375%, with interest payable March 15, June 15, September 15 and December 15 of each year (each an “8.375% Payment Date”), which began June 15, 2017. Principal of the 2026 Notes was payable on the 8.375% Payment Dates beginning March 15, 2019 through the redemption of the 2026 Notes. From March 15, 2019, the Company made quarterly payments on the 2026 Notes equal to the greater of (i) 7.5% of net sales of linaclotide in the U.S. for the preceding quarter (the “8.375% Synthetic Royalty Amount”) and (ii) accrued and unpaid interest on the 2026 Notes (the “8.375% Required Interest Amount”). Principal on the 2026 Notes was due to be repaid in an amount equal to the 8.375% Synthetic Royalty Amount minus the 8.375% Required Interest Amount, when this is a positive number, until the principal had been paid in full.

Convertible Senior Notes

2.25% Convertible Senior Notes due 2022

In June 2015, the Company issued approximately $335.7 million aggregate principal amount of the 2022 Convertible Notes. The Company received net proceeds of approximately $324.0 million from the sale of the 2022 Convertible Notes, after deducting fees and expenses of approximately $11.7 million. The Company used approximately $21.1 million of the net proceeds from the sale of the 2022 Convertible Notes to pay the net cost of the Convertible Note Hedges (after such cost was partially offset by the proceeds to the Company from the sale of the Note Hedge Warrants), as described below.

The 2022 Convertible Notes are governed by an indenture (the “2022 Indenture”) between the Company and U.S. Bank National Association, as the trustee. The 2022 Convertible Notes are senior unsecured obligations and bear cash interest at the annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. The 2022 Convertible Notes will mature on June 15, 2022, unless earlier converted or repurchased. The Company may settle conversions of the 2022 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A common stock of the Company or a combination of cash and shares of Class A common stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the 2022 Indenture). The initial conversion rate for the 2022 Convertible Notes was 60.3209 shares of Class A common stock (subject to adjustment as provided for in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes, which was equal to an initial conversion price of approximately $16.58 per share and 20,249,665 shares.

In connection with the Separation in April 2019, the conversion rate under the 2022 Indenture was adjusted to equal 68.9172 shares of Ironwood Class A common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equal to an adjusted conversion price of approximately $14.51 per share and 23,135,435 shares.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes in August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes.

Holders of the 2022 Convertible Notes may convert their 2022 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2021 in multiples of $1,000 principal amount, only under the following circumstances:

● during any calendar quarter commencing after the calendar quarter ending on September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s Class A common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the 2022 Convertible Notes on each applicable trading day;

● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s Class A common stock and the conversion rate for the 2022 Convertible Notes on each such trading day; or

● upon the occurrence of specified corporate events described in the 2022 Indenture.

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On or after December 15, 2021, until the close of business on the second scheduled trading day immediately preceding June 15, 2022, holders may convert their 2022 Convertible Notes, in multiples of $1,000 principal amount, at the option of the holder regardless of the foregoing circumstances.

If a make-whole fundamental change, as described in the 2022 Indenture, occurs and a holder elects to convert its 2022 Convertible Notes in connection with such make-whole fundamental change, such holder may be entitled to an increase in the conversion rate as described in the 2022 Indenture. The Company may not redeem the 2022 Convertible Notes prior to the maturity date and no “sinking fund” is provided for by the 2022 Convertible Notes, which means that the Company is not required to periodically redeem or retire the 2022 Convertible Notes. Upon the occurrence of certain fundamental changes involving the Company, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest.

The 2022 Indenture does not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The 2022 Indenture provides for customary events of default. In the case of an event of default with respect to the 2022 Convertible Notes arising from specified events of bankruptcy or insolvency, all outstanding 2022 Convertible Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the 2022 Convertible Notes under the 2022 Indenture occurs or is continuing, the trustee or holders of at least 25% in aggregate principal amount of the then outstanding 2022 Convertible Notes may declare the principal amount of the 2022 Convertible Notes to be immediately due and payable. Notwithstanding the foregoing, the 2022 Indenture provides that, upon the Company’s election, and for up to 180 days, the sole remedy for an event of default relating to certain failures by the Company to comply with certain reporting covenants in the 2022 Indenture consists exclusively of the right to receive additional interest on the 2022 Convertible Notes.

In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2022 Convertible Notes by allocating the proceeds between the liability component and the embedded conversion option, or equity component, due to the Company’s ability to settle the 2022 Convertible Notes in cash, its Class A common stock, or a combination of cash and Class A common stock at the option of the Company. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The equity component of the 2022 Convertible Notes was recognized as a debt discount and represents the difference between the gross proceeds from the issuance of the 2022 Convertible Notes and the fair value of the liability of the 2022 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over seven years, or the expected life of the 2022 Convertible Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes in August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes were repurchased at a premium totaling approximately $227.3 million. Accordingly, the Company recognized a loss on extinguishment of debt of approximately $23.4 million related to the prepayment premium and proportional write-off of the 2022 Convertible Notes unamortized debt issuance costs and unamortized debt discount. Additionally, the repurchase resulted in a reduction to additional paid-in capital by approximately $27.0 million related to the equity component of the 2022 Convertible Notes.

0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026

In August 2019, the Company issued $200.0 million aggregate principal amount of the 2024 Convertible Notes and $200.0 million aggregate principal amount of the 2026 Convertible Notes. The Company received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million. The Company used approximately $25.2 million of the net proceeds from the sale of the 2024 Convertible Notes and 2026 Convertible Notes to pay the net cost of the Capped Calls, as described below. For purposes of this section, “Notes” refer to the 2024 Convertible Notes and the 2026 Convertible Notes, collectively.

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The 2024 Convertible Notes and 2026 Convertible Notes were issued by the Company on August 12, 2019, pursuant to separate Indentures, each dated as of such date (each an “Indenture” and together the “Indentures”), between the Company and U.S. Bank National Association, as trustee (the “Trustee”). The 2024 Convertible Notes will bear cash interest at the annual rate of 0.75% and the 2026 Convertible Notes will bear cash interest at the annual rate of 1.50%, each payable on June 15 and December 15 of each year, beginning on December 15, 2019. The 2024 Convertible Notes will mature on June 15, 2024 and the 2026 Convertible Notes will mature on June 15, 2026, unless earlier converted or repurchased. The Company will settle conversions of the 2024 Convertible Notes and 2026 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A common stock of the Company or a combination of cash and shares of Class A common stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the applicable Indenture). The initial conversion rate for each of the 2024 Convertible Notes and the 2026 Convertible Notes is 74.6687 shares of Class A common stock (subject to adjustment as provided for in the applicable Indenture) per $1,000 principal amount of the 2024 Convertible Notes and 2026 Convertible Notes, which is equal to an initial conversion price of approximately $13.39 per share, representing a conversion premium of approximately 37.5% above the last reported sale price of Class A common stock of $9.74 per share on August 7, 2019.

Holders of the 2024 Convertible Notes and 2026 Convertible Notes may convert their Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, in multiples of $1,000 principal amount, only under the following circumstances:

● during any calendar quarter commencing after the calendar quarter ending on December 31, 2019 (and only during such calendar quarter), if the last reported sale price of Class A common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the Notes on each applicable trading day;

● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in each Indenture) per $1,000 principal amount of Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of Class A common stock and the conversion rate for the Notes on each such trading day; or

● upon the occurrence of specified corporate events described in each Indenture.

On or after December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, until the close of business on the second scheduled trading day immediately preceding the applicable maturity date, the holders of the Notes may convert their Notes, in multiples of $1,000 principal amount, regardless of the foregoing conditions.

If the Company experiences a fundamental change, as described in the Indentures, prior to the maturity date of the respective Notes, holders of such Notes will, subject to specified conditions, have the right, at their option, to require the Company to repurchase for cash all or a portion of their Notes at a repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date. In addition, following certain corporate events that occur prior to the applicable maturity date of the Notes, the Company will increase the conversion rate for a holder who elects to convert its Notes in connection with such corporate event.

The Indentures do not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The Indentures provide for customary events of default. In the case of an event of default with respect to a series of Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes of such series will become due and payable immediately without further action or notice. If any other event of default with respect to a series of Notes under the relevant Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes of such series may declare the principal amount of such Notes to be immediately due and payable.

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In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2024 Convertible Notes and the 2026 Convertible Notes by allocating the proceeds between the liability components and the embedded conversion options, or equity components, due to the Company’s ability to settle the 2024 Convertible Notes and the 2026 Convertible Notes in cash, its Class A common stock, or a combination of cash and Class A common stock at the option of the Company. The carrying amount of the respective liability components were calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The respective equity components of the 2024 Convertible Notes and the 2026 Convertible Notes were recognized as a debt discount and represent the difference between the gross proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes and the fair value of the liability of the 2024 Convertible Notes and 2026 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over approximately five and seven years, or the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes, respectively. The respective equity components are not remeasured as long as they continue to meet the conditions for equity classification.

The Company’s outstanding balances for the Convertible Senior Notes as of September 30, 2019 and December 31, 2018 consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Liability component:
Principal:
2022 Convertible Notes	$	120,699	$	335,699
2024 Convertible Notes		200,000		—
2026 Convertible Notes		200,000		—
Less: unamortized debt discount		(109,685)		(65,094)
Less: unamortized debt issuance costs		(8,339)		(5,004)
Net carrying amount	$	402,675	$	265,601
Equity Component:
2022 Convertible Notes	$	19,807	$	114,199
2024 Convertible Notes		41,152		—
2026 Convertible Notes		51,350		—
Total Equity component	$	112,309	$	114,199

In connection with the issuance of the 2022 Convertible Notes, the Company incurred approximately $11.7 million of debt issuance costs, which primarily consisted of initial purchasers’ discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $4.0 million were recorded as a reduction to additional paid-in capital upon issuance. The portion of these costs allocated to the liability components totaling approximately $7.7 million were recorded as a reduction in the carrying value of the debt on the balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2022 Convertible Notes. In connection with the partial repurchase of the 2022 Convertible Notes, the Company recorded a loss on extinguishment of debt of approximately $23.4 million, of which approximately $2.8 million related to the initial debt issuance costs.

The Company determined the expected life of the 2022 Convertible Notes was equal to their seven-year term. The effective interest rate on the liability components of the 2022 Convertible Notes for the period from the date of issuance through June 30, 2019 was 9.34%. From the date of the partial repurchase of the 2022 Convertible Notes in

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August 2019 through September 30, 2019, the effective interest rate on the liability component of the 2022 Convertible Notes was 9.37%.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company incurred approximately $9.0 million of debt issuance costs, which primarily consisted of initial purchaser’s discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $2.1 million were recorded as a reduction to additional paid-in capital. The portion of these costs allocated to the liability components totaling approximately $6.9 million were recorded as a reduction in the carrying value of the debt on the balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes.

The Company determined the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes was equal to their approximately five and seven-year terms, respectively. The effective interest rates on the liability components of the 2024 Convertible Notes and the 2026 Convertible Notes for the period from the date of issuance through September 30, 2019 was 6.1% and 6.5%, respectively.

The following table sets forth total interest expense recognized related to the 2022 Convertible Notes, 2024 Convertible Notes, and 2026 Convertible Notes during the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Contractual interest expense	$	1,780	$	1,889	$	5,557	$	5,665
Amortization of debt issuance costs		301		249		856		712
Amortization of debt discount		4,460		3,900		12,699		11,450
Total interest expense	$	6,541	$	6,038	$	19,112	$	17,827

Future minimum payments under the Convertible Senior Notes as of September 30, 2019 are as follows (in thousands):

2019(1)	$	2,895
2020		7,216
2021		7,216
2022		126,556
2023		4,500
2024		203,750
Thereafter		204,500
Total future minimum payments under the convertible senior notes		556,633
Less: amounts representing interest		(35,934)
Less: unamortized debt discount		(109,685)
Less: unamortized debt issuance costs		(8,339)
Convertible senior notes balance	$	402,675

(1) Amounts are for the three months ending December 31, 2019.

Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Convertible Notes

To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2022 Convertible Notes, the Company entered into the Convertible Note Hedges covering 20,249,665 shares of the Company’s Class A common stock in connection with the issuance of the 2022 Convertible Notes. The Convertible Note Hedges had an initial exercise price of $16.58 per share, subject to adjustment upon the occurrence of certain corporate events or transactions, and were exercisable if the 2022 Convertible Notes were converted. In connection with the adjustment to the conversion rate of the 2022 Indenture, the exercise price of the Convertible Note Hedges and the Note Hedge Warrants were adjusted to $14.51 per share and $18.82 per share, respectively (Note 5). If upon conversion of the 2022 Convertible Notes, the price of the Company’s Class A common stock is above the exercise price of the

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Convertible Note Hedges, the counterparties are obligated to deliver shares of the Company’s Class A common stock and/or cash with an aggregate value approximately equal to the difference between the price of the Company’s Class A common stock at the conversion date and the exercise price, multiplied by the number of shares of the Company’s Class A common stock related to the Convertible Note Hedge being exercised.

Concurrently with entering into the Convertible Note Hedges, the Company also sold Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments. The strike price of the Note Hedge Warrants was initially $21.50 per share, subject to adjustment, and such warrants are exercisable over the 150 trading day period beginning on September 15, 2022. In connection with the Separation in April 2019, the exercise price was adjusted to $18.82 per share and the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. The Note Hedge Warrants could have a dilutive effect on the Class A common stock to the extent that the market price per share of the Company’s Class A common stock exceeds the applicable strike price of such warrants.

The Convertible Note Hedges and the Note Hedge Warrants are separate transactions entered into by the Company and are not part of the terms of the 2022 Convertible Notes. Holders of the 2022 Convertible Notes and the Note Hedge Warrants do not have any rights with respect to the Convertible Note Hedges. The Company paid approximately $91.9 million for the Convertible Note Hedges and recorded this amount as a long-term asset on its condensed consolidated balance sheet. The Company received approximately $70.8 million for the Note Hedge Warrants and recorded this amount as a long-term liability, resulting in a net cost to the Company of approximately $21.1 million.

In August 2019, concurrently with the repurchase of $215.0 million aggregate principal amount of the 2022 Convertible Notes, the Company terminated the respective portion of the Convertible Note Hedges and Note Hedge Warrants. The Company received approximately $3.2 million related to net termination payments from the counterparties of the Convertible Note Hedges and Note Hedge Warrants. During the three months ended September 30, 2019, the Company recorded approximately $4.8 million in loss on derivatives as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and change in fair value over the period.

The Convertible Note Hedges and Note Hedge Warrants are accounted for as derivative assets and liabilities, respectively, in accordance with ASC Topic 815, Derivatives and Hedging (Note 5).

Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes

To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into separate Capped Calls in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes. The Company paid the counterparties approximately $25.2 million to enter into the Capped Calls.

The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have a cap price of approximately $17.05 per share, representing an approximately 75% premium over the last reported sale price of the Class A common stock as of August 7, 2019, which cap price is subject to certain adjustments under the terms of the Capped Calls. The Capped Calls cover 29,867,480 shares of Class A common stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes.

The Capped Calls are expected generally to reduce the potential dilution to the Class A common stock upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes in the event that the market price per share of Class A common stock, as measured under the terms of the Capped Calls, is greater than the strike price of the Capped Calls as adjusted pursuant to the anti-dilution adjustments. If, however, the market price per share of Class A common stock, as measured under the terms of the Capped Calls, exceeds the cap price of the Capped Calls, there would nevertheless be dilution upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes to the extent that such market price exceeds the cap price of the Capped Calls.

The Capped Calls are separate transactions entered into by and between the Company and the Capped Calls counterparties and are not part of the terms of the 2024 Convertible Notes or the 2026 Convertible Notes. Holders of the

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2024 Convertible Notes and the 2026 Convertible Notes do not have any rights with respect to the Capped Calls. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. The Company recorded a reduction to additional paid-in capital of approximately $25.0 million related to the premium payments for the Capped Calls. Additionally, the Company recorded an approximately $0.2 million reduction to equity related to transaction costs incurred in connection with the Capped Calls.

10. Employee Stock Benefit Plans

The Company has several share-based compensation plans under which stock options, restricted stock awards, restricted stock units (“RSUs”), and other share-based awards are available for grant to employees, officers, directors and consultants of the Company.

In May 2019, the Company’s stockholders approved the 2019 Equity Incentive Plan (the “2019 Equity Plan”) under which stock options, restricted stock awards, RSUs, and other stock-based awards may be granted to employees, officers, directors, or consultants of the Company. Under the 2019 Equity Plan, 10,000,000 shares of Class A common stock were initially reserved for issuance. As of September 30, 2019, 11,276,185 shares were available for future grant under the 2019 Equity Plan.

The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Research and development	$	1,208	$	2,974	$	5,306	$	8,446
Selling, general and administrative		4,312		7,643		19,832		19,708
Restructuring expenses		—		1,551		654		2,068
	$	5,520	$	12,168	$	25,792	$	30,222

During the three months ended March 31, 2018, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position, resulting in a modification to certain share-based payment awards. As a result of the modification, the Company recorded stock-based compensation expense of approximately $0.2 million to restructuring expenses during the three months ended March 31, 2018.

During the three months ended June 30, 2018, the Company initiated a reduction in headquarter-based workforce by approximately 40 employees associated with the Separation. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded approximately $1.0 million and $1.3 million of restructuring expenses during the three and nine months ended September 30, 2018, respectively.

During the three months ended September 30, 2018, the Company reduced its workforce by approximately 100 employees, primarily consisting of field-based sales representatives as a result of the termination of the Lesinurad License. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded share-based compensation expense of approximately $0.6 million to restructuring expenses during the three months ended September 30, 2018.

In February 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded no share-based compensation expense and approximately $0.7 million to restructuring expenses during the three and nine months ended September 30, 2019, respectively.

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In April 2019, in connection with the Separation, all outstanding share-based payment awards were modified in accordance with the equity conversion-related provisions of the employee matters agreement. No share-based compensation expense was recognized in connection with these modifications. Additionally, modifications with respect to the Company’s Employee Stock Purchase Plan (“ESPP”) were made due to the change in share price as a result of the Separation. As a result of the modification to the ESPP, the Company recorded approximately $0.3 million of share-based compensation expense during the nine months ended September 30, 2019.

In connection with certain other modifications of share-based payment awards during the three and nine months ended September 30, 2019, the Company recognized approximately $0.2 million and approximately $2.8 million in share-based compensation expense, respectively.

11. Related Party Transactions

In September 2009, Allergan became a related party when the Company sold to Allergan 2,083,333 shares of the Company’s convertible preferred stock. Under the collaboration agreement, the Company and Allergan equally support the development and commercialization of linaclotide (Note 4). Amounts due to and due from Allergan are reflected as related party accounts payable and related party accounts receivable, respectively. These balances are reported net of any balances due to or from the related party. As of September 30, 2019 and December 31, 2018, the Company had approximately $94.4 million and approximately $60.0 million, respectively, in related party accounts receivable, net of related party accounts payable, associated with Allergan.

The Company has and currently obtains health insurance services for its employees from an insurance provider whose President and Chief Executive Officer became a member of the Company’s Board of Directors in April 2016. The Company paid approximately $1.7 million and approximately $5.8 million in insurance premiums to this insurance provider during the three and nine months ended September 30, 2019, respectively, and paid approximately $2.9 million and approximately $9.2 million during the three and nine months ended September 30, 2018, respectively. At September 30, 2019 and December 31, 2018, the Company had no accounts payable due to this related party.

The Company has and currently obtains commercial market and prescription data from a vendor whose Senior Vice President of Strategy, Marketing and Communications became a member of the Company’s Board of Directors in April 2019. The Company paid approximately $0.8 million and approximately $2.0 million in fees to this company during the three and nine months ended September 30, 2019, respectively, and approximately $0.8 million and approximately $2.6 million during the three and nine months ended September 30, 2018, respectively. As of September 30, 2019 and December 31, 2018, the Company had an insignificant amount of accounts payable due to this related party.

In connection with the Separation, the Company executed certain contracts with Cyclerion whose President became a member of the Company’s Board of Directors in April 2019 (Note 2). As of September 30, 2019, the Company had $1.3 million of accounts payable, net of accounts receivable, due to Cyclerion.

12. Workforce Reduction

On January 30, 2018, the Company commenced an initiative to evaluate the optimal mix of investments for the lesinurad franchise. As part of this effort, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position. During the three months ended March 31, 2018, the Company substantially completed the implementation of this reduction in field-based workforce and, in accordance with ASC Topic 420, Exit or Disposal Activities (“ASC 420”), recorded approximately $2.4 million of costs in its condensed consolidated statement of operations.

On June 27, 2018, the Company determined the initial organizational designs of the two new businesses, including employees’ roles and responsibilities, in connection with the Separation. As part of this process, the Company initiated a reduction in its headquarter-based workforce by approximately 40 employees. During the three and nine months ended September 30, 2019, the Company recorded an insignificant amount of costs in connection with this workforce reduction. During the three and nine months ended September 30, 2018, the Company recorded approximately $2.5 million and $4.0 million, respectively, of costs in connection with the reduction in workforce in

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accordance with ASC 420. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

On August 16, 2018, the Company initiated a reduction in its workforce by approximately 100 employees, primarily consisting of field-based sales representatives in connection with the termination of the Lesinurad License. During the three and nine months ended September 30, 2019, the Company did not record any restructuring costs related to this workforce reduction. During each of the three and nine months ended September 30, 2018, the Company recorded approximately $7.6 million of costs in connection with the reduction in workforce. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

On February 7, 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. During the three and nine months ended September 30, 2019, the Company reversed approximately $0.2 million and recorded approximately $3.7 million, respectively, of costs that are reflected in the condensed consolidated statement of operations as restructuring expenses.

The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the three and nine months ended September 30, 2019 (in thousands):

	Amounts								Amounts
	Accrued at								Accrued at
	December 31, 2018		Charges		Amount Paid		Adjustments		September 30, 2019
Employee severance, benefits and related costs
June 2018 Reduction		696		16		(689)		(23)		—
August 2018 Reduction		1,756		—		(1,708)		(48)		—
February 2019 Reduction		—		3,182		(2,765)		(89)		328
Total	$	2,452	$	3,198	$	(5,162)	$	(160)	$	328
Contract related costs
August 2018 Reduction	$	433	$	—		(287)		(42)	$	104
Total	$	433	$	—	$	(287)	$	(42)	$	104

During the three and nine months ended September 30, 2019, the Company reversed approximately $0.2 million and recorded approximately $3.7 million in restructuring expenses, respectively, and recorded approximately $10.1 million and approximately $14.0 million in restructuring expenses during the three and nine months ended September 30, 2018, respectively.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Forward-Looking Information

The following discussion of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and the notes to those financial statements appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K. This discussion contains forward-looking statements that involve significant risks and uncertainties. As a result of many factors, such as those set forth under “Risk Factors” in Item 1A of this Quarterly Report on Form 10-Q, our actual results may differ materially from those anticipated in these forward-looking statements.

Overview

We are a gastrointestinal, or GI, focused healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. We are advancing innovative product opportunities in areas of large unmet need, capitalizing on our proven development and commercial capabilities and our deep expertise in GI diseases. On April 1, 2019, we completed our tax-free spin-off of our soluble guanylate cyclase, or sGC, business into a separate publicly traded company, Cyclerion Therapeutics, Inc., or Cyclerion.

Our commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation, or IBS-C, or chronic idiopathic constipation, or CIC, in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms.

Linaclotide is available under the trademarked name LINZESS^® (linaclotide) to adult men and women suffering from IBS-C or CIC in the United States, or the U.S., and Mexico, and to adult men and women suffering from IBS-C in Japan. Linaclotide is available under the trademarked name CONSTELLA^® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries.

We have strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. We and our partner Allergan plc (together with its affiliates), or Allergan, began commercializing LINZESS in the U.S. in December 2012. Under our collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between us and Allergan. Allergan has an exclusive license from us to develop and commercialize linaclotide in the Allergan License Territory, which is comprised of all countries other than China, including Hong Kong and Macau, Japan and the countries and territories of North America. On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays us royalties as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS.

Astellas Pharma Inc., or Astellas, our partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adult patients with chronic constipation in Japan. On August 1, 2019, we amended and restated our license agreement with Astellas, or the Amended Astellas License Agreement. Beginning in 2020, we will no longer be responsible for the supply of linaclotide active pharmaceutical ingredient, or API, to Astellas.

In October 2012, we and AstraZeneca AB, together with its affiliates, or AstraZeneca, entered into a collaboration agreement to co-develop and co-commercialize linaclotide in China, including Hong Kong and Macau, or the AstraZeneca License Territory, or the AstraZeneca Collaboration Agreement. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. On September 16, 2019, we and AstraZeneca entered into an amendment and restatement of the AstraZeneca Collaboration

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Agreement, or the Amended AstraZeneca Agreement, under which AstraZeneca obtained the exclusive right to develop, manufacture, and commercialize products containing linaclotide in the AstraZeneca License Territory, or the AstraZeneca License.

We and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, we announced positive topline data from our Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C.

We and Allergan are advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain-relieving agent for patients suffering from abdominal pain associated with certain GI diseases. There are an estimated 16 million Americans who suffer from symptoms of IBS with diarrhea, or IBS-D, according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, we and Allergan initiated a Phase II clinical trial evaluating MD-7246 in adult patients with IBS-D.

We are also advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of persistent gastroesophageal reflux disease, or persistent GERD. There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al. in Gut; a Lieberman HCP Survey, 2019; a Lieberman GI patient landscape survey, 2010; a survey conducted by American Gastroenterological Association; and 2019 U.S. census data. In June 2018, we initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

As part of our strategy, we have established development and commercial capabilities with the intent of playing an active role in the development and commercialization of our products in the U.S., while establishing a strong global brand by out-licensing commercialization rights in other territories. Additionally, we have periodically entered into co-promotion agreements to maximize our salesforce productivity, such as our co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D. In August 2019, we entered into a disease education and promotional agreement with Alnylam Pharmaceuticals, Inc., or Alnylam, for Alnylam’s givosiran, an investigational RNAi therapeutic for the potential treatment of patients with acute hepatic porphyria (“AHP). Under the agreement, we will perform disease awareness activities related to AHP and, if givosiran is approved by the U.S. FDA, future sales detailing activities of a product containing givosiran. These agreements are more fully described in Note 4, Collaborations, License, Co-Promotion and Other Commercial Agreements, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

We were incorporated in Delaware on January 5, 1998 as Microbia, Inc. On April 7, 2008, we changed our name to Ironwood Pharmaceuticals, Inc. We operate in one reportable business segment—human therapeutics.

To date, we have dedicated a majority of our activities to the research, development and commercialization of linaclotide and the commercialization of lesinurad, as well as to the research and development of our other product candidates. We have incurred significant operating losses since our inception in 1998. As of September 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We are unable to predict the extent of any future losses or guarantee that our company will be able to achieve or maintain positive cash flows.

On April 1, 2019, we completed the separation of our sGC business, and certain other assets and liabilities, into a separate, independent publicly traded company, or the Separation. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion, through a dividend of Cyclerion’s common stock to our stockholders of record as of the close of business on March 19, 2019. The Separation is more fully described in Note 2, Cyclerion Separation, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

On June 11, 2019, we entered into a non-cancelable operating lease, or the Summer Street Lease, for approximately 39,000 square feet of office space on the 23^rd floor of 100 Summer Street, Boston, Massachusetts, or the Summer Street Property. The Summer Street Property began serving as our new headquarters in October 2019, replacing our prior headquarters at 301 Binney Street in Cambridge, Massachusetts. This agreement is more fully described in

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Note 8, Leases, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

In August 2019, we issued $200.0 million in aggregate principal amount of 0.75% Convertible Senior Notes due 2024, or the 2024 Convertible Notes, and $200.0 million in aggregate principal amount of 1.50% Convertible Senior Notes due 2026, or the 2026 Convertible Notes. We received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million.

The proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used in August 2019 to pay the cost of associated capped call transactions, or the Capped Calls, and to repurchase $215.0 million aggregate principal amount of the existing 2.25% Convertible Senior Notes due 2022. The proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes were also used to redeem the outstanding principal balance of the 8.375% Notes due 2026, or the 2026 Notes, on September 16, 2019. We retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. During the three months ended September 30, 2019, we recognized a loss on extinguishment of debt of approximately $31.0 million related to the redemption of the 2026 Notes and the partial repurchase of the 2022 Convertible Notes. In connection with the partial repurchase of the 2022 Convertible Notes, we also terminated the respective portion of our existing convertible note hedges transactions, or the Convertible Note Hedges, and the respective portion of our existing warrants, or the Note Hedge Warrants. These transactions are more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Financial Overview

Revenues. Our revenues are generated primarily through our collaborative arrangements and license agreements related to research and development and commercialization of linaclotide, as well as co-promotion arrangements in the U.S. Effective January 1, 2018, we adopted Accounting Standards Codification, or ASC, Topic 606, Revenue from Contracts with Customers, or ASC 606, using the modified retrospective transition method. The adoption of ASC 606 represents a change in accounting principle that aims to more closely align revenue recognition with the delivery of our services and will provide financial statement readers with enhanced disclosures. In accordance with ASC 606, we recognize revenue when the customer obtains control of a promised good or service, in an amount that reflects the consideration which we expect to receive in exchange for the good or service. The reported results for the three and nine months ended as of September 30, 2019 and 2018 reflect the application of ASC 606 guidance. Upon adoption of ASC 606, we concluded that no cumulative-effect adjustment to the accumulative deficit as of January 1, 2018 was necessary. The adoption of ASC 606 had no impact on our condensed consolidated statement of operations, condensed consolidated balance sheets, or condensed consolidated statement of cash flows.

The terms of the collaborative research and development, license and co-promotion agreements contain multiple performance obligations which may include (i) licenses, (ii) research and development activities, (iii) the manufacture of finished drug product, API, or development materials for a partner which are reimbursed at a contractually determined rate, and (iv) co-promotion activities by our clinical sales specialists. Payments to us may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API or development materials, (iv) payments based upon the achievement of certain milestones, (v) payments for sales detailing, promotional support services and medical education initiatives and (vi) royalties on product sales.

We record our share of the net profits and losses from the sales of LINZESS in the U.S. on a net basis and present the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. Net profits or losses consist of net sales to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. Although we expect net sales to increase over time, the settlement payments between Allergan and us, resulting in collaborative arrangements revenue or collaboration expense, are subject to fluctuation based on the ratio of selling, general and administrative expenses incurred by each party. In addition, our collaborative arrangements revenue may fluctuate as a result of the timing and amount of license fees and clinical and commercial milestones received and recognized under our current and future strategic partnerships as well as timing and amount of royalties from the sales of linaclotide in the European, Canadian or Mexican markets or any other markets where linaclotide receives approval.

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Through December 31, 2018, product revenue consisted of sales of ZURAMPIC and DUZALLO, or the Lesinurad Products, in the U.S. Product revenue was recognized when a particular national wholesaler or a selected regional wholesaler, or a Distributor, obtained control of our product, which occurred at a point in time, typically upon shipment of the Lesinurad Products to the Distributor.

Cost of Revenues. Cost of revenues primarily includes cost of collaborative arrangements revenue related to the sales of linaclotide API and drug product. Cost related to the sales of linaclotide API and drug product are recognized upon shipment of linaclotide API and drug product to certain of our partners outside of the U.S. Our cost of collaborative arrangements revenue for linaclotide consists of the internal and external costs of producing such API and drug product for certain of our partners outside of the U.S.

Research and Development Expense. Research and development expense consists of expenses incurred in connection with the research into and development of product candidates. These expenses consist primarily of compensation, benefits and other employee-related expenses, research and development related facility costs, third-party contract costs relating to nonclinical study and clinical trial activities, development of manufacturing processes, regulatory registration of third-party manufacturing facilities, as well as licensing fees for our product candidates. We charge all research and development expenses to operations as incurred. Under our linaclotide collaboration agreements with Allergan for the U.S. and, prior to the execution of the Amended AstraZeneca Agreement, AstraZeneca for China, including Hong Kong and Macau, we were reimbursed for certain research and development activities and we netted these reimbursements against our research and development expenses as incurred. Amounts owed to Allergan on an ongoing basis, or AstraZeneca prior to the execution of the Amended AstraZeneca Agreement, for such linaclotide territories are recorded as incremental research and development expense.

The core of our research and development strategy is to leverage our development capabilities, as well as our pharmacologic expertise, to bring multiple medicines to patients. We are advancing innovative product opportunities in areas of large unmet need, including IBS-C and CIC, abdominal pain associated with lower GI disorders, and persistent GERD.

Linaclotide. Our commercial product, linaclotide, is available to adult men and women suffering from IBS-C or CIC in certain countries around the world. LINZESS® (linaclotide) is the first FDA-approved guanylate cyclase type-C, or GC-C, agonist and is commercially available in the U.S. for the treatment of IBS-C or CIC. Linaclotide also is approved and commercially available in Japan and in a number of E.U. and other countries. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China.

We and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, we announced positive topline data from our Phase IIIb trial demonstrating the efficacy and safety of linaclotide 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort in adult patients with IBS-C. In addition, we and Allergan have established a plan with the FDA for clinical pediatric programs with linaclotide, as described below.

MD-7246. We and Allergan are exploring MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain-relieving agent for patients suffering from abdominal pain associated with certain GI diseases. In May 2019, we and Allergan initiated patient dosing in a Phase II clinical trial evaluating MD-7246 in adult patients who have IBS-D.

IW-3718. We are advancing our persistent GERD program through the development of IW-3718, a gastric retentive formulation of a bile acid sequestrant. IW-3718 is a novel formulation of bile acid sequestrant designed to release in the stomach over an extended period of time, bind to bile that refluxes into the stomach, and potentially provide symptomatic relief in patients with persistent GERD. In June 2018, we announced the initiation of two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

Early research and development. After the Separation, our early research and development efforts are focused on supporting our development stage GI programs, including exploring strategic options for further development of certain of our internal programs, as well as evaluating potential external development stage GI programs.

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The following table sets forth our research and development expenses related to our product pipeline for the three and nine months ended September 30, 2019 and 2018. These expenses relate primarily to internal compensation, benefits and other employee-related expenses and external costs associated with nonclinical studies and clinical trial costs for our product candidates. We allocate costs related to facilities, depreciation, share-based compensation, research and development support services, laboratory supplies and certain other costs directly to programs.

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
	(in thousands)				(in thousands)
Linaclotide(1)	$	11,218	$	8,245	$	29,365	$	23,723
Lesinurad(2)		96		1,064		467		4,503
IW-3718		16,114		15,437		51,578		27,477
Early research and development		123		4,412		7,097		17,118
Total research and development expenses	$	27,551	$	29,158	$	88,507	$	72,821

(1) Includes linaclotide immediate release in all indications, populations and formulations, and costs associated with MD-7246 (delayed release formulation).

(2) Includes lesinurad in all indications, populations and formulations.

Since 2004, the date we began tracking costs by program, we have incurred approximately $492.0 million of research and development expenses related to linaclotide. The expenses for linaclotide include both our portion of the research and development costs incurred by Allergan for the U.S. and AstraZeneca for China, including Hong Kong and Macau, prior to the execution of the Amended AstraZeneca Agreement, and invoiced to us under the cost-sharing provisions of our collaboration agreements, as well as the unreimbursed portion of research and development costs incurred by us under such cost-sharing provisions.

The lengthy process of securing regulatory approvals for new drugs requires the expenditure of substantial resources. Any failure by us to obtain, or any delay in obtaining, regulatory approvals would materially adversely affect our product development efforts and our business overall.

In connection with the FDA approval of LINZESS, we are required to conduct certain nonclinical and clinical studies, including those aimed at understanding: (a) whether orally administered linaclotide can be detected in breast milk, (b) the potential for antibodies to be developed to linaclotide, and if so, (c) whether antibodies specific for linaclotide could have any therapeutic or safety implications. In addition, we and Allergan established a nonclinical and clinical post-marketing plan with the FDA to understand the efficacy and safety of LINZESS in pediatric patients, and clinical pediatric programs in IBS-C and functional constipation are currently ongoing. We and Allergan are also exploring development opportunities to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. We cannot currently estimate with any degree of certainty the amount of time or money that we will be required to expend in the future on linaclotide for other geographic markets within IBS-C and CIC, or in additional indications, populations or formulations.

Given the inherent uncertainties that come with the development of pharmaceutical products, we cannot estimate with any degree of certainty how our programs will evolve, and therefore the amount of time or money that would be required to obtain regulatory approval to market them.

As a result of these uncertainties surrounding the timing and outcome of any approvals, we are currently unable to estimate precisely when, if ever, linaclotide’s utility will be expanded within its currently approved indications; if or when linaclotide will be developed outside of its current markets, indications, populations or formulations; or when, if ever, any of our other product candidates will generate revenues and cash flows.

We invest carefully in our pipeline, and the commitment of funding for each subsequent stage of our development programs is dependent upon the receipt of clear, supportive data. In addition, we intend to access externally discovered drug candidates that fit within our core strategy. In evaluating these potential assets, we apply the same investment criteria as those used for investments in internally discovered assets.

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The successful development of our product candidates is highly uncertain and subject to a number of risks including, but not limited to:

● The duration of clinical trials may vary substantially according to the type, complexity and novelty of the product candidate.

● The FDA and comparable agencies in foreign countries impose substantial and varying requirements on the introduction of therapeutic pharmaceutical products, typically requiring lengthy and detailed laboratory and clinical testing procedures, sampling activities and other costly and time-consuming procedures.

● Data obtained from nonclinical and clinical activities at any step in the testing process may be adverse and lead to discontinuation or redirection of development activity. Data obtained from these activities also are susceptible to varying interpretations, which could delay, limit or prevent regulatory approval.

● The duration and cost of early research and development, including nonclinical studies and clinical trials may vary significantly over the life of a product candidate and are difficult to predict.

● The costs, timing and outcome of regulatory review of a product candidate may not be favorable, and, even if approved, a product may face post-approval development and regulatory requirements.

● There may be substantial costs, delays and difficulties in successfully integrating externally developed product candidates into our business operations.

● The emergence of competing technologies and products and other adverse market developments may negatively impact us.

As a result of the factors discussed above, including the factors discussed under “Risk Factors” in Item 1A of this Quarterly Report on Form 10-Q, we are unable to determine the duration and costs to complete current or future nonclinical and clinical stages of our product candidates or when, or to what extent, we will generate revenues from the commercialization and sale of our product candidates. Development timelines, probability of success and development costs vary widely. We anticipate that we will make determinations as to which additional programs to pursue and how much funding to direct to each program on an ongoing basis in response to the data of each product candidate, the competitive landscape and ongoing assessments of such product candidate’s commercial potential.

We expect to invest in our development programs for the foreseeable future. We will continue to invest in linaclotide, including the investigation of ways to enhance the clinical profile within its currently approved indications, and the exploration of its potential utility in other indications, populations and formulations. We will also continue to invest in our other GI-focused product candidates as we advance them through clinical trials, in addition to funding full-time equivalents for research and development activities under our external collaboration and license agreements.

Selling, General and Administrative Expense. Selling, general and administrative expense consists primarily of compensation, benefits and other employee-related expenses for personnel in our administrative, finance, legal, information technology, business development, commercial, sales, marketing, communications and human resource functions. Other costs include the legal costs of pursuing patent protection of our intellectual property, general and administrative related facility costs, insurance costs and professional fees for accounting and legal services. As we continue to invest in the commercialization of LINZESS, we expect our selling, general and administrative expenses will be substantial for the foreseeable future. We record all selling, general and administrative expenses as incurred.

Prior to the execution of the Amended AstraZeneca Agreement, we were reimbursed for certain selling, general and administrative expenses and we netted these reimbursements against our selling, general and administrative expenses as incurred. Under the Amended AstraZeneca Agreement, AstraZeneca is responsible for all costs and expenses incurred under the AstraZeneca License. We include Allergan’s selling, general and administrative cost-sharing payments in the calculation of the net profits and net losses from the sale of LINZESS in the U.S. and present the net payment to or from Allergan as collaboration expense or collaborative arrangements revenue, respectively.

Restructuring Expenses. We record costs and liabilities associated with exit and disposal activities in accordance with ASC Topic 420, Exit or Disposal Cost Obligations, or ASC 420. Such costs are based on estimates of

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fair value in the period the liabilities are incurred in accordance with ASC 420. We evaluate and adjust these costs as appropriate for changes in circumstances as additional information becomes available.

Other (Expense) Income. Interest expense consists primarily of cash and non-cash interest costs related to the convertible senior notes and the 2026 Notes. Non-cash interest expense consists of amortization of the debt discount and associated debt issuance costs associated with the convertible senior notes and the 2026 Notes. We amortize these costs using the effective interest rate method over the life of the respective note agreements as interest expense in our condensed consolidated statements of operations.

In June 2015, in connection with the issuance of the 2022 Convertible Notes, we entered into convertible note hedge transactions, or the Convertible Note Hedges. Concurrently with entering into the Convertible Note Hedges, we also entered into certain warrant transactions in which we sold note hedge warrants, or the Note Hedge Warrants, to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of our Class A common stock, subject to customary anti-dilution adjustments. In April 2019, in connection with the Separation, the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. Gain (loss) on derivatives consists of the change in fair value of the Convertible Note Hedges and Note Hedge Warrants, which are recorded as derivative assets and liabilities. The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting period and changes in fair value are recorded in our condensed consolidated statements of operations. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

In September 2016, we closed a direct private placement, pursuant to which we issued $150.0 million in aggregate principal amount of the 2026 Notes on January 5, 2017. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

In August 2019, we issued $200.0 million in aggregate principal amount of the 2024 Convertible Notes and $200.0 million in aggregate principal amount of the 2026 Convertible Notes. We received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million. The proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible notes were used to redeem all of the outstanding principal balance of the 2026 Convertible Notes, repurchase $215.0 million aggregate principal amount of the 2022 Convertible Notes and pay the cost of the Capped Calls. We recognized a loss on extinguishment of debt of approximately $31.0 million related to the redemption of the 2026 Notes and the partial repurchase of the 2022 Notes. In connection with the partial repurchase of the 2022 Notes, we also terminated the respective portion of our existing Convertible Note Hedges and Note Hedge Warrants. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, we entered into the Capped Calls. The Capped Calls cover 29,867,480 shares of Class A common stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes, and have a cap price of approximately $17.05 per share. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. These transactions are more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Interest income consists of interest earned on our cash, cash equivalents and marketable securities as well as significant financing components identified under ASC 606.

Discontinued Operations. We have recast all historical expenses directly associated with our sGC business as discontinued operations in accordance with ASC Subtopic 250-20, Discontinued Operations. For additional information refer to Note 2, Cyclerion Separation, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

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Critical Accounting Policies and Estimates

Our discussion and analysis of our financial condition and results of operations is based upon our condensed consolidated financial statements prepared in accordance with U.S. generally accepted accounting principles. The preparation of these financial statements requires us to make certain estimates and assumptions that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates and assumptions in our condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. We base our estimates on our historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from our estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Except as outlined below, during the three and nine months ended September 30, 2019, there were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission, or SEC, on February 25, 2019, or the 2018 Annual Report on Form 10-K.

Discontinued Operations

During the three months ended June 30, 2019, we determined that the Separation of our sGC business on April 1, 2019 met the criteria for classification as a discontinued operation in accordance with ASC Topic 205-20, Discontinued Operations. Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Leases

Effective January 1, 2019, we adopted ASC Topic 842, Leases, or ASC 842, using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use, or ROU, assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and nine months ended September 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases, or ASC 840. Because there were no material changes to the values of existing capital leases as a result of the adoption of ASC 842, we concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary. The recognition of right-of-use assets and lease liabilities related to our operating leases under ASC 842 has had a material impact on our condensed consolidated financial statements.

As part of the ASC 842 adoption, we elected certain practical expedients outlined in the guidance. These practical expedients include:

● A policy election to use the short-term lease exception by asset class;

● Election of the practical expedient package during transition, which includes:

o An entity need not reassess whether any expired or existing contracts are or contain leases.

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o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

o An entity need not reassess initial direct costs for any existing leases.

Subsequent to our adoption of ASC 842, we elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

Our lease portfolio for the three and nine months ended September 30, 2019 includes: leases for our prior and current headquarters locations, a data center colocation lease, vehicle leases for our salesforce representatives, and leases for computer and office equipment. We determine if an arrangement is a lease at the inception of the contract. The asset component of our operating leases is recorded as the operating lease right-of-use asset, and the liability component is recorded as the current portion of operating lease liabilities and operating lease liabilities, net of current portion in our condensed consolidated balance sheet. As of September 30, 2019, we did not have any finance leases.

Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in our lease portfolio as of the adoption date were valued as of January 1, 2019. We use an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. We recognize variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by us.

Derivative Assets and Liabilities

In June 2015, in connection with the issuance of the 2022 Convertible Notes, we entered into the Convertible Note Hedges. Concurrently with entering into the Convertible Note Hedges, we also entered into certain warrant transactions in which we sold Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire shares of our Class A common stock, subject to customary anti-dilution adjustments. In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, we terminated our Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging.

These derivatives are recorded as assets or liabilities at fair value each reporting period and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of our Class A common stock on the date of valuation, time to maturity of the derivative instruments, the strike prices of the derivative instruments, the risk-free interest rate, and the volatility of our Class A common stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, we entered into the Capped Calls. The Capped Calls cover the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes (subject to anti-dilution and certain other adjustments). These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met.

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Results of Operations

The following discussion summarizes the key factors our management believes are necessary for an understanding of our condensed consolidated financial statements.

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
	(in thousands)				(in thousands)
Revenues:
Collaborative arrangements revenue	$	130,524	$	54,194	$	273,998	$	188,487
Product revenue, net		—		1,235		—		2,966
Sale of active pharmaceutical ingredient		643		10,257		28,114		24,494
Total revenues		131,167		65,686		302,112		215,947
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets		506		4,616		12,862		11,288
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments		(3,530)		(1,589)		(3,530)		247
Research and development		27,551		29,158		88,507		72,821
Selling, general and administrative		40,919		50,536		133,260		169,252
Amortization of acquired intangible assets		—		1,159		—		8,111
Gain on fair value remeasurement of contingent consideration		—		(33,519)		—		(31,045)
Gain on lease modification		—		—		(3,169)		—
Restructuring expenses		(166)		10,102		3,652		14,010
Impairment of intangible assets		—		151,794		—		151,794
Total cost and expenses		65,280		212,257		231,582		396,478
Income (loss) from operations		65,887		(146,571)		70,530		(180,531)
Other (expense) income:
Interest expense		(10,457)		(9,482)		(29,479)		(28,138)
Interest and investment income		893		741		2,297		2,154
(Loss) gain on derivatives		(4,766)		3,489		(1,494)		3,996
Loss on extinguishment of debt		(30,977)		—		(30,977)		—
Other income		68		—		208		—
Other expense, net		(45,239)		(5,252)		(59,445)		(21,988)
Net income (loss) from continuing operations		20,648		(151,823)		11,085		(202,519)
Net loss from discontinued operations		—		(22,528)		(37,438)		(64,356)
Net income (loss)	$	20,648	$	(174,351)	$	(26,353)	$	(266,875)

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Three and nine months ended September 30, 2019 compared to three and nine months ended September 30, 2018

Revenues

	Three Months Ended								Nine Months Ended
	September 30,				Change				September 30,				Change
	2019		2018		$		%		2019		2018		$		%
	(dollars in thousands)								(dollars in thousands)
Revenues:
Collaborative arrangements revenue	$	130,524	$	54,194	$	76,330	141	%	$	273,998	$	188,487	$	85,511	45	%
Product revenue, net		—		1,235		(1,235)	(100)	%		—		2,966		(2,966)	(100)	%
Sale of active pharmaceutical ingredient		643		10,257		(9,614)	(94)	%		28,114		24,494		3,620	15	%
Total revenues	$	131,167		65,686		65,481	100	%		302,112		215,947		86,165	40	%

Collaborative Arrangements Revenue. The increase in revenue from collaborative arrangements of approximately $76.3 million for the three months ended September 30, 2019 compared to the three months ended September 30, 2018 was primarily related to an approximately $32.4 million increase in revenue recognized related to non-contingent payments outlined in the Amended AstraZeneca Agreement; an approximately $29.7 million negative adjustment during the three months ended September 30, 2018 related to a change in estimate of gross-to-net sales reserves and allowances, primarily associated with governmental and contractual rebates; approximately $10.0 million from an up-front payment received in connection with the Amended Astellas License agreement; an approximately $2.6 million increase in our share of the net profits from the sale of LINZESS in the U.S. driven by increased prescription demand an approximately $1.3 million increase in co-promotion revenue.

The increase in revenue from collaborative arrangements of approximately $85.5 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 was primarily related to an approximately $32.4 million increase in revenue recognized related to non-contingent payments outlined in the Amended AstraZeneca Agreement; an approximately $29.7 million negative adjustment during the three months ended September 30, 2018 related to a change in estimate of gross-to-net sales reserves and allowances, primarily associated with governmental and contractual rebates; an approximately $11.5 million increase in our share of the net profits from the sale of LINZESS in the U.S. driven by increased prescription demand; an approximately $10.0 million from an up-front payment received in connection with the Amended Astellas Agreement; and an approximately $1.6 million increase in co-promotion and royalty revenue.

Product Revenue, net. The decrease in net product revenue of approximately $1.2 million and approximately $3.0 million for the three and nine months ended September 30, 2019 compared to the three and nine months ended September 30, 2018, respectively, was due to our termination of the license agreement with AstraZeneca for the development, manufacture, and commercialization of products in the U.S. containing lesinurad as an active ingredient, or the Lesinurad License, in January 2019. As a result of this termination, we are no longer commercializing the Lesinurad Products.

Sale of Active Pharmaceutical Ingredient. The decrease in sale of API of approximately $9.6 million for the three months ended September 30, 2019, compared to the three months ended September 30, 2018, was primarily due to decreased shipments of linaclotide API to Astellas in Japan during the three months ended September 30, 2019 pursuant to the Amended Astellas License Agreement. The increase in sale of API of $3.6 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018, was primarily due to increased shipments of linaclotide API to Astellas in Japan during the nine months ended September 30, 2019.

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Cost and Expenses

	Three Months Ended								Nine Months Ended
	September 30,				Change				September 30,				Change
	2019		2018		$		%		2019		2018		$		%
	(dollars in thousands)								(dollars in thousands)
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets	$	506	$	4,616	$	(4,110)	(89)	%	$	12,862	$	11,288	$	1,574	14	%
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments		(3,530)		(1,589)		(1,941)	122	%		(3,530)		247		(3,777)	(1,529)	%
Research and development		27,551		29,158		(1,607)	(6)	%		88,507		72,821		15,686	22	%
Selling, general and administrative		40,919		50,536		(9,617)	(19)	%		133,260		169,252		(35,992)	(21)	%
Amortization of acquired intangible assets		—		1,159		(1,159)	(100)	%		—		8,111		(8,111)	(100)	%
Gain on fair value remeasurement of contingent consideration		—		(33,519)		33,519	(100)	%		—		(31,045)		31,045	(100)	%
Gain on lease modification		—		—		—	—	%		(3,169)		—		(3,169)	100	%
Restructuring expenses		(166)		10,102		(10,268)	(102)	%		3,652		14,010		(10,358)	(74)	%
Impairment of intangible assets		—		151,794		(151,794)	100	%		—		151,794		(151,794)	100	%
Total cost and expenses	$	65,280	$	212,257	$	(146,977)	(69)	%	$	231,582	$	396,478	$	(164,896)	(42)	%

Cost of Revenue, excluding amortization of acquired intangible assets. The decrease of approximately $4.1 million for the three months ended September 30, 2019 compared to the three months ended September 30, 2018 primarily related to a decrease in linaclotide API sales to Astellas in Japan pursuant to the Amended Astellas License Agreement, partially offset by approximately $0.5 million in costs associated with the shipment of finished goods to AstraZeneca during the three months ended September 30, 2019. The increase of approximately $1.6 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 primarily related to an increase in shipments of API to Astellas and the shipment of finished goods to AstraZeneca during the nine months ended September 30, 2019.

Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments. The decrease in write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments of approximately $1.9 million and approximately $3.8 million for the three and nine months ended September 30, 2019 compared to the three and nine months ended September 30, 2018, respectively, was primarily due to the settlement of certain commercial supply purchase commitments that occurred during the three months ended September 30, 2019. In connection with the Amended AstraZeneca Collaboration certain of our previously written-down linaclotide excess purchase commitments were assumed by AstraZeneca and therefore resulted in a settlement. During the nine months ended September 30, 2018, we recorded write-downs of lesinurad inventory and purchase commitments.

Research and Development Expense. The decrease in research and development expense of approximately $1.6 million for the three months ended September 30, 2019 compared to the three months ended September 30, 2018 was primarily related to a decrease of approximately $4.1 million in compensation, benefits, and other employee-related expenses; a decrease of approximately $1.5 million in research costs related to our early research and development efforts; and a decrease of approximately $1.3 million in operating expenses, including facilities. These decreases were partially offset by an increase of approximately $4.4 million related to linaclotide development; and an increase of approximately $1.2 million in professional services fees.

The increase in research and development expense of approximately $15.7 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 was primarily related to an increase of approximately $22.9 million in external development costs related to IW-3718; an increase of approximately $8.1 million related to linaclotide development; and an increase of approximately $0.7 million in professional services fees. These increases were partially offset by a decrease of approximately $11.0 million in compensation, benefits and other employee-related expenses; a decrease of approximately $3.0 million in operating expenses, including facilities; a decrease of approximately $1.1 million related to lesinurad development due to the termination of the Lesinurad License; and a decrease of approximately $0.9 million in research costs related to our early research and development efforts.

Selling, General and Administrative Expense. Selling, general and administrative expenses decreased for the three months ended September 30, 2019 compared to the three months ended September 30, 2018 primarily as a result of the Separation which was completed on April 1, 2019 and the termination of the Lesinurad License in January 2019. The

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approximately $9.6 million decrease in selling, general and administrative expense included an approximately $10.1 million decrease in non-Separation costs and an approximately $0.5 million increase in costs associated with the Separation. The approximately $10.1 million decrease in non-Separation costs includes an approximately $8.3 million decrease in compensation, benefits, and employee-related expenses as a result of a decrease in headcount related to the Lesinurad License termination; an approximately $3.3 million decrease in sales and marketing programs; an approximately $1.1 million decrease in operating expenses, including facilities; and an approximately $0.8 million decrease in legal expenses. These decreases were partially offset by an approximately $3.4 million increase in professional services fees. The approximately $0.5 million increase in costs associated with the Separation includes an approximately $5.5 million increase in other operating costs, including facilities, primarily due to asset disposals related to the change in headquarters location. This increase was offset by an approximately $3.7 million decrease in professional services fees, an approximately $0.9 million decrease in compensation, benefits and other employee-related expenses, and an approximately $0.4 million decrease in legal expenses.

Selling, general and administrative expenses decreased for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 primarily as a result of the Separation which was completed on April 1, 2019 and the termination of the Lesinurad License in January 2019. The decrease of approximately $36.0 million was primarily due to decreases in non-Separation costs of approximately $55.9 million offset by an approximately $19.9 million increase in costs associated with the Separation. The approximately $55.9 million decrease in non-Separation costs primarily includes an approximately $23.4 million decrease in other compensation, benefits and employee-related expenses as a result of a decrease in headcount; an approximately $17.5 million decrease in sales and marketing programs; an approximately $8.2 million decrease in other operating costs, including facilities; and an approximately $7.1 million decrease in professional services fees. The approximately $19.9 million increase in costs associated with the Separation includes an approximately $11.0 million increase in operating expenses, including facilities, primarily due to asset disposals related to the change in headquarters location; an approximately $5.1 million increase in compensation, benefits and other employee-related expenses; and an approximately $3.8 million increase in Separation-related legal expenses, consulting and investment banking costs.

Amortization of Acquired Intangible Assets. The decrease in amortization of acquired intangible assets expense of approximately $1.2 million and $8.1 million for the three and nine months ended September 30, 2019 compared to the three and nine months ended September 30, 2018, respectively, was due to the impairment of the Lesinurad Products intangible assets as a result of revised cash flow assumptions and the termination of the Lesinurad License.

Gain on Fair Value Remeasurement of Contingent Consideration. The increase in the gain on fair value of the contingent consideration obligation of approximately $33.5 million for the three months ended September 30, 2019 compared to the three months ended September 30, 2018 and approximately $31.0 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018, was due to the termination of the Lesinurad License.

Gain on Lease Modification. The increase in the gain on lease modification of approximately $3.2 million for the three and nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 was due to the modification of the Binney Street Lease in connection with the Separation.

Restructuring Expenses. The decrease in restructuring expenses of approximately $10.3 million for the three months ended September 30, 2019 compared to the three months ended September 30, 2018, and $10.4 million for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 was primarily due to costs associated with the workforce reductions that occurred in January 2018, June 2018, and August 2018, which exceeded the costs incurred in the February 2019 workforce reduction.

Impairment of Intangible Assets. The decrease in the impairment of intangible assets of approximately $151.8 million for each of the three and nine months ended September 30, 2019 compared to each of the three and nine months ended September 30, 2018 was due to the full asset impairment of the intangible assets related to the Lesinurad Products as a result of revised net cash flow assumptions and the exit of the Lesinurad License.

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Other (Expense) Income, Net

	Three Months Ended								Nine Months Ended
	September 30,				Change				September 30,				Change
	2019		2018		$		%		2019		2018		$		%
	(dollars in thousands)								(dollars in thousands)
Other (expense) income:
Interest expense	$	(10,457)	$	(9,482)	$	(975)	10	%	$	(29,479)	$	(28,138)	$	(1,341)	5	%
Interest and investment income		893		741		152	21	%		2,297		2,154		143	7	%
(Loss) gain on derivatives		(4,766)		3,489		(8,255)	(237)	%		(1,494)		3,996		(5,490)	(137)	%
Loss on extinguishment of debt		(30,977)		—		(30,977)	(100)	%		(30,977)		—		(30,977)	(100)	%
Other income		68		—		68	100	%		208		—		208	100	%
Total other expense, net	$	(45,239)	$	(5,252)	$	(39,987)	761	%	$	(59,445)	$	(21,988)	$	(37,457)	170	%

Interest Expense. Interest expense increased by approximately $1.0 million during the three months ended September 30, 2019 compared to the three months ended September 30, 2018, mainly due to an increase of approximately $2.5 million in interest expense associated with the 2024 Convertible Notes and the 2026 Convertible Notes, partially offset by a decrease of approximately $0.9 million in interest expense associated with the 2026 Notes and a decrease of approximately $0.7 million in interest expense associated with the 2022 Convertible Notes. Interest expense increased by approximately $1.3 million during the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018, mainly due to an increase of approximately $2.5 million in interest expense associated with the 2024 Convertible Notes and the 2026 Convertible Notes, partially offset by a decrease of $1.3 million in interest expense associated with the 2026 Notes.

Interest and Investment Income. Interest and investment income increased by approximately $0.2 million and an insignificant amount during the three and nine months ended September 30, 2019 compared to the three and nine months ended September 30, 2018, mainly due to higher cash and cash equivalent balances as a result of proceeds from the 2024 Convertible Note and 2026 Convertible Note issuances.

Loss (gain) on Derivatives. For the three months ended September 30, 2019, we recorded a loss on derivatives of approximately $4.8 million resulting from an approximately $49.4 million decrease in the fair value of the Convertible Note Hedges and an approximately $41.4 million decrease in the fair value of the Note Hedge Warrants, partially offset by an approximately $3.2 million cash settlement received upon the partial termination of the Convertible Note Hedges and the Note Hedge Warrants associated with the partial repurchase of the 2022 Convertible Notes. For the three months ended September 30, 2018, we recorded a gain on derivatives of approximately $3.5 million resulting from an approximately $16.7 million increase in the fair value of the Convertible Note Hedges and an approximately $20.2 million increase in the fair value of the Note Hedge Warrants.

For the nine months ended September 30, 2019, we recorded a loss on derivatives of approximately $1.5 million resulting from an approximately $29.7 million decrease in the fair value of the Convertible Note Hedges and an approximately $25.0 million decrease in the fair value of the Note Hedge Warrants, offset by an approximately $3.2 million cash settlement received upon the partial termination of the Convertible Note Hedges and the Note Hedge Warrants associated with the partial repurchase of the 2022 Convertible Notes. For the nine months ended September 30, 2018, we recorded a gain on derivatives of approximately $4.0 million resulting from an approximately $34.6 million increase in the fair value of the Convertible Note Hedges and an approximately $30.6 million increase in the fair value of the Note Hedge Warrants.

Loss on Extinguishment of Debt. The loss on extinguishment of debt was approximately $31.0 million during each of the three and nine months ended September 30, 2019 due to the write-off of unamortized debt issuance costs and debt discount related to the partial repurchase of the 2022 Convertible Notes in August 2019 and write-off of the remaining unamortized debt issuance costs and debt discount on the 2026 Notes as part of the redemption of all of the outstanding principal amount of the 2026 Notes in September 2019.

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Other Income. Other income increased by an insignificant amount and approximately $0.2 million during the three and nine months ended September 30, 2019 compared to the three and nine months ended September 30, 2018, respectively, due to income related to a transition service agreement with Cyclerion.

Net Loss from Discontinued Operations

Net loss from discontinued operations was approximately $22.5 million for the three months ended September 30, 2018. There was no net loss from discontinued operations for the three months ended September 30, 2019 as the Separation was completed on April 1, 2019. Net loss from discontinued operations for the nine months ended September 30, 2019 compared to the nine months ended September 30, 2018 decreased by approximately $26.9 million primarily related to a decrease in research and development expense related to our sGC business. For additional information on discontinued operations, see Note 2, Cyclerion Separation, to our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q.

Liquidity and Capital Resources

At September 30, 2019, we had approximately $139.2 million of unrestricted cash and cash equivalents. Our cash equivalents include amounts held in money market funds and repurchase agreements. We invest cash in excess of immediate requirements in accordance with our investment policy, which limits the amounts we may invest in any one type of investment and requires all investments held by us to be at least A- rated, with a remaining final maturity when purchased of less than twenty-four months, so as to achieve liquidity and capital preservation objectives.

During the nine months ended September 30, 2019, our balances of cash and cash equivalents decreased by approximately $33.0 million. This decrease is primarily due to approximately $16.9 million of cash used to operate our business, of which approximately $28.2 million related to cash used in continuing operations and approximately $11.4 million related to cash provided by discontinued operations. The decrease in cash used to operate our business includes payments related to, among other things, research and development, and selling, general and administrative expenses, including payroll and compensation expense, and activities supporting the Separation that occurred on April 1, 2019. In addition, we made payments of approximately $227.3 million to repurchase $215.0 million aggregate principal amount of the 2022 Convertible Notes, principal, interest, and prepayment premium payments totaling $156.4 million to fully redeem the approximately $116.5 million outstanding principal balance of the 2026 Notes. We also purchased Capped Calls for approximately $25.2 million. Additionally, we invested approximately $4.5 million in capital expenditures. These cash outflows were partially offset by approximately $391.0 million in net proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses, approximately $7.1 million in proceeds from the exercise of stock options, and approximately $3.2 million in proceeds from the partial termination of the Convertible Notes Hedges and Note Hedge Warrants.

We may from time to time seek to retire, redeem or repurchase all or part of our outstanding debt through cash purchases and/or exchanges, in open market purchases, privately negotiated transactions, by tender offer or otherwise. Such repurchases, redemptions or exchanges, if any, will depend on prevailing market conditions, liquidity requirements, contractual restrictions and other factors, and the amounts involved may be material.

Sources of Liquidity

We have incurred losses since our inception in 1998 and, as of September 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We have financed our operations to date primarily through both the private sale of our preferred stock and the public sale of our Class A common stock, including approximately $203.2 million of net proceeds from our initial public offering, or IPO, in February 2010, and approximately $413.4 million of net proceeds from our follow-on public offerings; payments received under our strategic collaborative arrangements, including upfront and milestone payments, royalties and our share of net profits, as well as reimbursement of certain expenses; and debt financings, including approximately $324.0 million of net proceeds from the private placement of our 2022 Convertible Notes in June 2015, of which $215.0 million of principal was repurchased, approximately $11.2 million of net proceeds from the private placement of our 2026 Notes in January 2017 of which, no principal remains outstanding, and approximately $391.0 million of net proceeds from the private placement of our 2024 Convertible Notes and 2026 Convertible Notes in August 2019.

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Funding Requirements

We began commercializing LINZESS in the U.S. with our collaboration partner, Allergan, in the fourth quarter of 2012, and we currently derive a significant portion of our revenue from this collaboration. In addition, we are deploying significant resources to advance product opportunities in IBS-C and CIC, abdominal pain associated with IBS and persistent GERD, as well as to fulfill FDA requirements for linaclotide. We have also historically derived revenue from the sale of linaclotide API to Astellas for Japan; beginning on January 1, 2020, however, we will no longer be responsible for the supply of linaclotide API to Astellas. Our goal is to become cash flow positive, driven by increased revenue generated through sales of LINZESS and other commercial activities and financial discipline.

Under our collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between us and Allergan. Additionally, we receive royalties from Allergan based on sales of linaclotide in its licensed territories outside of the U.S. We believe revenues from our LINZESS partnership for the U.S. with Allergan will continue to constitute a significant portion of our total revenue for the foreseeable future and we cannot be certain that such revenues, as well as the revenues from our other commercial activities, will enable us to achieve or maintain positive cash flows, or to do so in the timeframes we expect. We also anticipate that we will continue to incur substantial expenses for the next several years as we further develop and commercialize linaclotide in the U.S. and other markets, develop and commercialize other products, and invest in our pipeline and potentially other external opportunities. We believe that our cash on hand as of September 30, 2019 will be sufficient to meet our projected operating needs at least through the next twelve months from the issuance of these financial statements.

Our forecast of the period of time through which our financial resources will be adequate to support our operations, including the underlying estimates regarding the costs to develop our product candidates and obtain regulatory approvals and the costs to commercialize linaclotide in the U.S. and other markets, and develop and commercialize other products, our expectations regarding revenue from Astellas for Japan and AstraZeneca for China, including Hong Kong and Macau, as well as our goal to become cash flow positive, are forward-looking statements that involve risks and uncertainties. Our actual results could vary materially and negatively from these and other forward-looking statements as a result of a number of factors, including the factors discussed in the “Risk Factors” section of this Quarterly Report on Form 10-Q. We have based our estimates on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect.

Due to the numerous risks and uncertainties associated with the development and commercialization of our product candidates, we are unable to estimate precisely the amounts of capital outlays and operating expenditures necessary to develop, obtain regulatory approval for, and commercialize linaclotide and our other product candidates, in each case, for all of the markets, indications, populations and formulations for which we believe each is suited. Our funding requirements will depend on many factors, including, but not limited to, the following:

● the revenue generated by sales of LINZESS, CONSTELLA and any other sources;

● the rate of progress and cost of our commercialization activities, including the expense we incur in marketing and selling LINZESS in the U.S. and any other products;

● the success of our third-party manufacturing activities;

● the time and costs involved in developing, and obtaining regulatory approvals for, our product candidates, as well as the timing and cost of any post-approval development and regulatory requirements;

● the success of our research and development efforts;

● the emergence of competing or complementary products;

● the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights;
​

● the terms and timing of any additional collaborative, licensing or other arrangements that we may establish, including royalties or other payments due or payable under such agreements; and

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● the acquisition of businesses, products and technologies and the impact of other strategic transactions, as well as the cost and timing of integrating any such assets into our business operations.

Financing Strategy

We may, from time to time, consider additional funding through a combination of new collaborative arrangements, strategic alliances, and additional equity and debt financings or from other sources. We will continue to manage our capital structure and to consider all financing opportunities, whenever they may occur, that could strengthen our long-term liquidity profile. Any such capital transactions may or may not be similar to transactions in which we have engaged in the past. There can be no assurance that any such financing opportunities will also be available on acceptable terms, if at all.

Contractual Commitments and Obligations

Notes Payable

In June 2015, we issued approximately $335.7 million in aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes are governed by an indenture between us and U.S. Bank National Association, as the trustee, or the 2022 Indenture. The 2022 Convertible Notes are senior unsecured obligations and bear interest at a rate of 2.25% per year, payable on June 15 and December 15 of each year, which began on December 15, 2015. The 2022 Convertible Notes will mature on June 15, 2022, unless earlier converted or repurchased. In August 2019, we repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes, and we partially terminated the proportionate portion of the Convertible Note Hedges and Note Hedge Warrants we entered into in connection with the issuance of the 2022 Convertible Notes. In connection with the partial termination, we have marked the remaining Convertible Note Hedges and Note Hedge Warrants to fair value at the reporting date using the Black-Scholes option-pricing model, with changes in fair value recorded as (loss) gain on derivatives in our condensed consolidated statement of operations. During the three and nine months ended September 30, 2019, the Company recorded a loss of approximately $4.8 million and approximately $1.5 million on derivatives, respectively, as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and the change in fair value of the remaining Convertible Note Hedges and Note Hedge Warrants during the three months ended September 30, 2019.

In August 2019, we issued $200.0 million in aggregate principal amount of the 2024 Convertible Notes and $200.0 million in aggregate principal amount of the 2026 Convertible Notes. The 2024 Convertible Notes and 2026 Convertible Notes are governed by separate indentures, each dated as of August 12, 2019, each an Indenture and collectively the Indentures, between us and U.S. Bank National Association, as trustee. The 2024 Convertible Notes and the 2026 Convertible Notes are senior unsecured obligations. The 2024 Convertible Notes will bear cash interest at the annual rate of 0.75% and the 2026 Convertible Notes will bear cash interest at the annual rate of 1.50%, each payable on June 15 and December 15 of each year, beginning on December 15, 2019. The 2024 Convertible Notes will mature on June 15, 2024 and the 2026 Convertible Notes will mature on June 15, 2026, unless earlier converted or repurchased. To minimize the impact of potential dilution to our Class A common stockholders upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes, we entered into separate Capped Calls in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes. We paid the counterparties approximately $25.2 million to enter into the Capped Calls.

The following table summarizes our obligations under our Convertible Senior Notes as of September 30, 2019:

	Payments Due by Period
			Less Than						More Than
	Total		1 Year		1 - 3 Years		3 - 5 Years		5 Years
	(in thousands)
2022 Convertible Notes (including interest)		128,845		2,715		126,130		—		—
2024 Convertible Notes (including interest)		207,263		1,263		3,000		203,000		—
2026 Convertible Notes (including interest)		220,525		2,525		6,000		6,000		206,000

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The Convertible Senior Notes, Convertible Note Hedges, Note Hedge Warrants, and the Capped Calls are more fully described in Note 9, Notes Payable, in the accompanying notes to our financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

In September 2016, we closed a direct private placement, pursuant to which we subsequently issued $150.0 million in aggregate principal amount of 2026 Notes on January 5, 2017. In September 2019, we redeemed all of the outstanding principal of approximately $116.5 million of the 2026 Notes and recognized a loss on extinguishment of debt of approximately $7.6 million due to the prepayment premium and write-off of the remaining unamortized debt issuance costs and debt discount. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

The disclosure of our contractual obligations and commitments was reported in our 2018 Annual Report on Form 10-K. Except for commitments related to our prior and current headquarters leases and debt transactions, there have not been any material changes from the contractual commitments and obligations previously disclosed in our 2018 Annual Report on Form 10-K. Refer to Note 8, Leases and Note 9, Notes Payable to these condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q for details on revised commitments.

Off-Balance Sheet Arrangements

We do not have any relationships with unconsolidated entities or financial partnerships, such as entities often referred to as structured finance or special purpose entities, that would have been established for the purpose of facilitating off-balance sheet arrangements (as that term is defined in Item 303(a)(4)(ii) of Regulation S-K) or other contractually narrow or limited purposes. As such, we are not exposed to any financing, liquidity, market or credit risk that could arise if we had engaged in those types of relationships. We enter into guarantees in the ordinary course of business related to the guarantee of our own performance and the performance of our subsidiaries.

New Accounting Pronouncements

For a discussion of recent accounting pronouncements, please refer to Note 2, Summary of Significant Accounting Policies, in our 2018 Annual Report on Form 10-K and Note 1, Nature of Business, appearing elsewhere in this Quarterly Report on Form 10-Q. We did not otherwise adopt any new accounting pronouncements during the three and nine months ended September 30, 2019 that had a material effect on our condensed consolidated financial statements included in this report.

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Item 3. Quantitative and Qualitative Disclosures about Market Risk

Interest Rate Risk

We are exposed to market risk related to changes in interest rates. We invest our cash in a variety of financial instruments, principally securities issued by the U.S. government and its agencies, collateralized reverse repurchase agreements, and money market instruments. The goals of our investment policy are preservation of capital, fulfillment of liquidity needs and fiduciary control of cash and investments. We also seek to maximize income from our investments without assuming significant risk.

Our primary exposure to market risk is interest income sensitivity, which is affected by changes in the general level of interest rates, particularly because our investments are in short-term marketable securities. Due to the primarily short-term duration of our investment portfolio and the low risk profile of our investments, an immediate 1% change in interest rates would not have a material effect on the fair market value of our portfolio. Accordingly, we would not expect our operating results or cash flows to be affected to any significant degree by the effect of a sudden change in market interest rates on our investment portfolio.

We do not believe our cash and cash equivalents have significant risk of default or illiquidity. While we believe our cash and cash equivalents do not contain excessive risk, we cannot provide absolute assurance that in the future our investments will not be subject to adverse changes in market value. In addition, we maintain significant amounts of cash and cash equivalents at one or more financial institutions that are in excess of federally insured limits. Given the potential instability of financial institutions, we cannot provide assurance that we will not experience losses on these deposits.

Our Convertible Senior Notes bear interest at a fixed rate and therefore have minimal exposure to changes in interest rates; however, because these interest rates are fixed, we may be paying a higher interest rate, relative to market, in the future if our credit rating improves or other circumstances change.

Equity Price Risk

2022 Convertible Notes

Our 2022 Convertible Notes include conversion and settlement provisions that are based on the price of our Class A common stock at conversion or at maturity of the 2022 Convertible Notes. The amount of cash we may be required to pay is determined by the price of our Class A common stock. The fair value of our 2022 Convertible Notes is dependent on the price and volatility of our Class A common stock and will generally increase or decrease as the market price of our Class A common stock changes.

The 2022 Convertible Notes are convertible into Class A common stock at an adjusted conversion rate of 68.9172 shares of Class A common stock (subject to adjustment as provided for in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes, which is equal to a conversion price of approximately $14.51 per share. The 2022 Convertible Notes will mature on June 15, 2022 unless earlier converted or repurchased. We will settle conversions of the 2022 Convertible Notes through payment or delivery, as the case may be, of cash, shares of our Class A common stock or a combination of cash and shares of Class A common stock, at our option (subject to, and in accordance with, the settlement provisions of the 2022 Indenture). The 2022 Convertible Notes bear cash interest at an annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. As of September 30, 2019, the fair value of the 2022 Convertible Notes was estimated by us to be approximately $120.0 million, which decreased during the three months ended September 30, 2019 due to the repurchase of $215.0 million aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes are more fully described in Note 5, Fair Value of Financial Instruments, and Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Convertible Notes

To minimize the impact of potential dilution to our common stock upon conversion of the 2022 Convertible Notes, we entered into Convertible Note Hedges to acquire, subject to customary adjustments, 23,135,435 shares of our Class A common stock at a strike price of $14.51 per share, as adjusted. Concurrently with entering into the Convertible

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Note Hedges, we entered into warrant transactions whereby we sold Note Hedge Warrants to acquire, subject to customary adjustments, 23,135,435 shares of our Class A common stock at a strike price of $18.82 per share, as adjusted. In August 2019, in connection with the repurchase of a portion of the 2022 Convertible Notes, we partially terminated the respective portion of the Convertible Note Hedges and Note Hedge Warrants. In connection with the partial termination, we have marked the remaining Convertible Note Hedges and Note Hedge Warrants to fair value at the reporting date using the Black-Scholes option-pricing model, with changes in fair value recorded as (loss) gain on derivatives in our condensed consolidated statement of operations. The Convertible Note Hedges and Note Hedge Warrants are more fully described in Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

2024 Convertible Notes and 2026 Convertible Notes

Our 2024 Convertible Notes and 2026 Convertible Notes include conversion and settlement provisions that are based on the price of our Class A common stock at conversion or at maturity of the 2024 Convertible Notes and 2026 Convertible Notes. The amount of cash we may be required to pay is determined by the price of our Class A common stock. The fair value of our 2024 Convertible Notes and 2026 Convertible Notes is dependent on the price and volatility of our Class A common stock and will generally increase or decrease as the market price of our Class A common stock changes.

The initial conversion rate for each of the 2024 Convertible Notes and 2026 Convertible Notes is 74.6687 shares of Class A common stock (subject to adjustment as provided for in the applicable Indenture) per $1,000 principal amount of the 2024 Convertible Notes and 2026 Convertible Notes, which is equal to an initial conversion price of approximately $13.39 per share. The 2024 Convertible Notes will mature on June 15, 2024 and the 2026 Convertible Notes will mature on June 15, 2026, unless earlier converted or repurchased. We will settle conversions of the 2024 Convertible Notes and 2026 Convertible Notes through payment or delivery, as the case may be, of cash, shares of our Class A common stock or a combination of cash and shares of Class A common stock, at our option (subject to, and in accordance with, the settlement provisions of the applicable Indenture). The 2024 Convertible Notes will bear cash interest at the annual rate of 0.75% and the 2026 Convertible Notes will bear cash interest at the annual rate of 1.50%, each payable on June 15 and December 15 of each year, beginning on December 15, 2019. As of September 30, 2019, the fair value of the 2024 Convertible Notes and 2026 Convertible Notes was estimated by us to be approximately $185.9 million and approximately $183.6 million, respectively. The 2024 Convertible Notes and 2026 Convertible Notes are more fully described in Note 5, Fair Value of Financial Instruments, and Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, we entered into the Capped Calls with certain financial institutions. Subject to customary anti-dilution and certain other adjustments, the Capped Calls cover the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit on our condensed consolidated balance sheet and are not subsequently remeasured as long as the conditions for equity classification continue to be met. The Capped Calls are more fully described in Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Foreign Currency Risk

We have no significant operations outside the U.S. and we do not expect to be impacted significantly by foreign currency fluctuations.

Effects of Inflation

We do not believe that inflation and changing prices over the three and nine months ended September 30, 2019 and 2018 had a significant impact on our results of operations.

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Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures

As required by Rule 13a-15(b) of the Securities Exchange Act of 1934, or the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation as of the end of the period covered by this Quarterly Report on Form 10-Q of the effectiveness of the design and operation of our disclosure controls and procedures. Based on that evaluation, our principal executive officer and principal financial officer concluded that our disclosure controls and procedures are effective at the reasonable assurance level in ensuring that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports we file under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and principal financial officer, as appropriate to allow timely decisions regarding required disclosure.

Changes in Internal Control

As required by Rule 13a-15(d) of the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation of the internal control over financial reporting to determine whether any changes occurred during the period covered by this Quarterly Report on Form 10-Q that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Based on that evaluation, our principal executive officer and principal financial officer concluded no changes during the period covered by this Quarterly Report on Form 10-Q materially affected, or were reasonably likely to materially affect, our internal control over financial reporting.

PART II OTHER INFORMATION

Item 1. Legal Proceedings

Actions in which we are the Plaintiff

LINZESS

We and Allergan have received Paragraph IV certification notice letters, or Notice Letters, regarding Abbreviated New Drug Applications, or ANDAs, submitted to the FDA by generic drug manufacturers requesting approval to engage in commercial manufacture, use, sale and offer for sale of (i) 145 mcg and 290 mcg linaclotide capsules, or the Potential Generic Products, and/or (ii) 72 mcg linaclotide capsules, or the Potential 72mcg Generic Products, each proposed generic versions of our FDA-approved drug LINZESS.

In October 2016, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Teva Pharmaceuticals USA, Inc., or Teva. Teva’s Notice Letter contends that United States patents for LINZESS (U.S. Patent Nos. 7,371,727, 7,704,947, 7,745,409, 8,080,526, and 8,110,553 (expiring 2024); 7,304,036 (expiring 2026); and 8,748,573, 8,802,628, and 8,933,030 (expiring 2031), or the Challenged Patents) listed in the FDA’s list of Approved Drug Products with Therapeutic Equivalence Evaluations, commonly referred to as the Orange Book, are invalid, unenforceable and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential Generic Products. In September 2017, we received a second Notice Letter relating to the ANDA submitted to the FDA by Teva contending that U.S. Patent No. 9,708,371 (expiring 2033) listed in the Orange Book is invalid and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential Generic Products. In December 2017, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Teva, contending that U.S. Patent Nos. 7,371,727, 7,704,947, 7,745,409, 8,080,526, and 8,110,553; 7,304,036; 8,933,030; and 9,708,371, or the 72mcg Challenged Patents, are invalid, unenforceable and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential 72 mcg Generic Product.

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In November 2016, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Sandoz Inc., or Sandoz, contending that all of the Challenged Patents are invalid, unenforceable and/or would not be infringed by Sandoz’s manufacture, use, sale or offer for sale of the Potential Generic Products. In January 2018, we received a second Notice Letter relating to the ANDA submitted to the FDA by Sandoz contending that U.S. Patent No. 9,708,371 is invalid and/or would not be infringed by Sandoz’s manufacture, use, sale or offer for sale of the Potential Generic Products.

In response to the ANDAs for which we received Notice Letters in 2016, we and Allergan filed a lawsuit against the generic drug manufacturers in Delaware District Court in November 2016. We asserted that the Challenged Patents are valid and infringed by Teva and Sandoz. In accordance with the Hatch-Waxman Act, the timely filing of the lawsuits against the ANDA filers with respect to the Challenged Patents triggered an automatic stay of the FDA’s approval of the ANDAs until as early as February 29, 2020 (unless there is a final court decision adverse to us and Allergan sooner). In October 2017 and January 2018, we and Allergan filed lawsuits against Teva and Sandoz, respectively, each in Delaware District Court, related to each of their respective second Notice Letters. We asserted that U.S. Patent No. 9,708,371 is valid and infringed by each of Teva and Sandoz. The lawsuits filed in October 2017 and January 2018 against Teva and Sandoz, respectively, have been consolidated with the lawsuit filed in November 2016.

In January 2017, each of Teva and Sandoz filed an answer and counterclaims seeking declaratory judgment of invalidity and non-infringement of the Challenged Patents. In November 2017 and February 2018, each of Teva and Sandoz, respectively, filed an answer and counterclaims seeking declaratory judgment of invalidity and non-infringement of U.S. Patent No. 9,708,371. In February 2018, we and Allergan filed a lawsuit against Teva in Delaware District Court asserting that the 72mcg Challenged Patents are valid and infringed. This lawsuit was consolidated with the lawsuit filed in November 2016.

In May 2018 and August 2018, we, Allergan, Teva and Sandoz stipulated to dismiss without prejudice all claims, counterclaims and defenses with respect to U.S. Patent Nos. 9,708,371 and 8,933,030, respectively. In May 2019, we, Allergan, Teva and Sandoz stipulated to dismiss without prejudice all claims, counterclaims and defenses with respect to U.S. Patent Nos. 7,745,409 and 8,110,553.

The trial for the action involving Teva and Sandoz was originally scheduled to begin in June 2019. However, the trial was postponed as a result of the unavailability of one of the expert witnesses for Teva and Sandoz to testify in person at the trial due to a serious health issue. In July 2019, we, Allergan, Teva and Sandoz filed a proposed stipulation with the Delaware District Court and, in August 2019, the court entered an order approving the stipulation. The stipulation and order provide for the trial to be rescheduled to begin on January 7, 2020. In an effort to preserve the status quo, the stipulation and order prohibit Teva and Sandoz from commercially selling or importing into the U.S. any proposed generic version of LINZESS until the earlier of (i) the date the court issues its trial decision in the lawsuit, and (ii) September 20, 2020.

We and Allergan previously entered into settlement agreements with Sun Pharma Global FZE, Aurobindo Pharma Ltd. and an affiliate of Aurobindo, and Mylan Pharmaceuticals Inc.

Item 1A. Risk Factors

In addition to the other information in this Quarterly Report on Form 10-Q, any of the factors described below could significantly and negatively affect our business, financial condition, results of operations or prospects. The trading price of our common stock may decline due to these risks.

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Risks Related to Our Business and Industry

We are highly dependent on the commercial success of LINZESS in the U.S. for the foreseeable future; we cannot guarantee that we will generate sufficient revenues from LINZESS to cover our expenses.

We and our partner, Allergan plc (together with its affiliates), or Allergan, began selling LINZESS in the U.S. during December 2012. Revenues from our LINZESS collaboration constitute a significant portion of our total revenue, and we believe they will continue to do so for the foreseeable future. The commercial success of LINZESS depends on a number of factors, including:

● the effectiveness of LINZESS as a treatment for adult patients with IBS-C or CIC;

● the size of the treatable patient population;

● the effectiveness of the sales, managed markets and marketing efforts by us and Allergan;

● the adoption of LINZESS by physicians, which depends on whether physicians view it as safe and effective treatment for adult patients with IBS-C and CIC;

● our success in educating and activating adult IBS-C and CIC patients to enable them to more effectively communicate their symptoms and treatment history to their physicians;

● our ability to both secure and maintain adequate reimbursement for, and optimize patient access to, LINZESS and our ability to demonstrate that LINZESS is safer, more efficacious and/or more cost-effective than alternative therapies;

● the effectiveness of our partners’ distribution networks;

● the occurrence of any side effects, adverse reactions or misuse, or any unfavorable publicity in these or other areas, associated with linaclotide; and

● the development or commercialization of competing products or therapies for the treatment of IBS-C or CIC, or their associated symptoms.

Our revenues from the commercialization of LINZESS are subject to these and other factors, and therefore may be unpredictable from quarter-to-quarter. Revenues from LINZESS or other sources in any quarter may be insufficient to cover our expenses or sustain net income.

Our products may cause undesirable side effects or have other properties that could limit their commercial potential.

The most commonly reported adverse reaction since linaclotide became commercially available, as well as in the clinical trials for linaclotide in IBS-C and CIC, has been diarrhea. In the linaclotide Phase III IBS-C and CIC trials, severe diarrhea was reported in 2% or less of the linaclotide-treated patients and its incidence was similar between the IBS-C and CIC populations. Linaclotide has been prescribed to millions of patients since its launch in the U.S. and other territories beginning in December 2012, and, as a result, it has been used in wider populations and in less rigorously controlled environments than in the clinical studies supporting its approval.

Further, if and as we and our partners conduct clinical trials, including in new or existing territories, indications, populations or formulations, as well as explore potential combination products, the number of patients treated with our products within and outside of such products’ currently approved indications and patient populations has grown and continues to do so.

As patient experience increases and expands, we and others may identify previously unknown side effects, known side effects may be found to be more frequent or severe than in the past, and we and others may detect

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unexpected safety signals for our products or any products perceived to be similar to our products.  The foregoing, or the perception of the foregoing, may have the following effects, among others:

● sales of our products may be impaired;

● regulatory approvals for our products may be delayed, denied, restricted or withdrawn;

● we or our partners may decide to, or be required to, change the products’ label or send product warning letters or field alerts to physicians, pharmacists and hospitals;

● reformulation of the products, additional nonclinical or clinical studies, changes in labeling or changes to or re-approvals of manufacturing facilities may be required;

● we or our partners may be precluded from pursuing approval of linaclotide in new territories or from studying additional development opportunities to enhance our products’ clinical profiles, including within new or existing indications, populations and formulations, as well as in potential combination products;

● our or our products’ reputation in the marketplace may suffer; and

● government investigations or lawsuits, including class action suits, may be brought against us or our partners.

Any of the above occurrences would harm or prevent sales of our products, increase expenses and impair our and our partners’ ability to successfully commercialize our products. 

In addition, the U.S. Food and Drug Administration, or FDA, -approved label for LINZESS contains a boxed warning about its use in pediatric patients. LINZESS is contraindicated in pediatric patients up to six years of age based on nonclinical data from studies in neonatal mice approximately equivalent to human pediatric patients less than two years of age. There is also a warning advising physicians to avoid the use of LINZESS in pediatric patients six to less than 18 years of age. This warning is based on data in young juvenile mice and the lack of clinical safety and efficacy data in pediatric patients of any age group. We and Allergan have established a nonclinical and clinical post-marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatric patients, which is discussed below. These and other restrictions could limit the commercial potential of LINZESS.

We rely entirely on contract manufacturers, our partners and other third parties to manufacture and distribute linaclotide. If they are unable to comply with applicable regulatory requirements, unable to source sufficient raw materials, experience manufacturing or distribution difficulties, or are otherwise unable to manufacture and distribute sufficient quantities to meet demand, our development and commercialization efforts may be materially harmed.

We have no internal manufacturing or distribution capabilities. Instead, we rely on a combination of contract manufacturers and our partners to manufacture active pharmaceutical ingredient, or API, and final drug product. We rely on our partners to store and distribute linaclotide to third party purchasers. We and certain of our partners have commercial supply agreements with independent third parties to manufacture the linaclotide API used to support all of our partnered territories. Each of Allergan and Astellas is responsible for linaclotide drug product and finished goods manufacturing (including bottling and packaging) for its respective territories and distributing the finished goods to wholesalers. Under the terms of the amendment and restatement of our license with Astellas in August 2019, following a transition period, Astellas will also be responsible for its own supply of linaclotide API for sale in Japan. Under the terms of the amendment and restatement of our collaboration agreement with AstraZeneca in September 2019, AstraZeneca will continue to be accountable for finished goods manufacturing for Hong Kong and Macau and, following a transition period, will assume full responsibility for linaclotide API, drug product and finished goods for China and for drug product manufacturing for Hong Kong and Macau. During this transition period, we will continue to be responsible for linaclotide API and drug product in China, Hong Kong and Macau and finished goods in China. Should we or any of our partners experience setbacks or challenges in our manufacturing efforts, our development and commercialization efforts may be materially harmed.

Each of our API and drug product manufacturers must comply with current good manufacturing practices, or GMP, and other stringent regulatory requirements enforced by the FDA and foreign regulatory authorities in other

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jurisdictions. These requirements include, among other things, quality control, quality assurance and the maintenance of records and documentation, which occur in addition to our own quality assurance releases. Manufacturers of our products may be unable to comply with these GMP requirements and with other regulatory requirements. We have little control over our manufacturers’ or partners’ compliance with these regulations and standards.

Our manufacturers may experience problems with their respective manufacturing and distribution operations and processes, including for example, quality issues, such as product specification and stability failures, procedural deviations, improper equipment installation or operation, utility failures, contamination and natural disasters. In addition, the raw materials necessary to make API for our products are acquired from a limited number of sources. Any delay or disruption in the availability of these raw materials or a change in raw material suppliers could result in production disruptions, delays or higher costs with consequent adverse effects on us.

The manufacture of pharmaceutical products requires significant expertise and capital investment, including the development of advanced manufacturing techniques and process controls. Manufacturers of pharmaceutical products often encounter difficulties in commercial production. These problems include difficulties with production costs and yields, quality control, including stability of the product and quality assurance testing, and shortages of qualified personnel, as well as compliance with federal, state and foreign regulations and the challenges associated with complex supply chain management. Even if our manufacturers or partners do not experience problems and commercial manufacturing is achieved, their maximum or available manufacturing capacities may be insufficient to meet commercial demand. Finding alternative manufacturers or adding additional manufacturers requires a significant amount of time and involves significant expense. New manufacturers would need to develop and implement the necessary production techniques and processes, which along with their facilities, would need to be inspected and approved by the regulatory authorities in each applicable territory.

If our API or drug product manufacturers fail to adhere to applicable GMP or other regulatory requirements, experience delays or disruptions in the availability of raw materials or experience manufacturing or distribution problems, we will suffer significant consequences, including product seizures or recalls, loss of product approval, fines and sanctions, reputational damage, shipment delays, inventory shortages, inventory write-offs and other product-related charges and increased manufacturing costs. If we experience any of these results, or if our manufacturers’ maximum or available capacities are insufficient to meet demand, we may not be able to successfully commercialize our products.

The transition of lesinurad to AstraZeneca could require additional financial and managerial resources, and we may not be successful.

In June 2016, we entered into a license agreement for exclusive rights to commercialize products containing lesinurad in the U.S., and we terminated such license effective January 2019. We have encountered and may continue to encounter costs and delays related to transitioning lesinurad to AstraZeneca. We have never undertaken the process of transitioning a marketed product to a third party, and we may encounter challenges and costs that we do not currently anticipate. Our reputation with patients or physicians may be harmed as a result of transitioning lesinurad, and unforeseen complications with the FDA or other regulatory agencies could arise. If we are unable to complete the orderly transition of lesinurad to AstraZeneca, this could potentially lead to costly administrative procedures or litigation, distract management from other business activities, and could have an adverse impact on our financial condition. For additional information relating to our costs and expenses of exiting lesinurad, see Note 12, Workforce Reduction, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

If any of our linaclotide partners undergoes a change of control or in management, this may adversely affect our collaborative relationship or the success of the commercialization of linaclotide in the U.S. or in the other countries where it is approved, or the ability to achieve regulatory approval, launch and commercialize linaclotide in other territories.

We work jointly and collaboratively with each of our partners on many aspects of the development, manufacturing and commercialization of linaclotide. In doing so, we have established relationships with several key members of the management teams of our linaclotide partners in functional areas such as development, quality, regulatory, drug safety and pharmacovigilance, operations, marketing, sales, field operations and medical science.

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Further, the success of our collaborations is highly dependent on the resources, efforts and skills of our partners and their key employees. As we and our partners develop and commercialize linaclotide in the U.S. and the other countries where it is approved, and develop, launch and commercialize linaclotide in other parts of the world, the drug’s success becomes more dependent on us maintaining highly collaborative and well aligned partnerships. For example, in June 2019, Allergan and AbbVie, Inc., or AbbVie, entered into a definitive agreement providing for the combination of the two companies. If the transaction is completed, or if any of our linaclotide partners otherwise undergo a change of control or in management, we would need to reestablish many relationships and confirm continued alignment on our development and commercialization strategy for linaclotide. Further, in connection with any change of control or in management, there is inherent uncertainty and disruption in operations, which could result in distraction, inefficiencies, and misalignment of priorities. As a result, in the event of a change of control or in management at one of our linaclotide partners, we cannot be sure that we will be able to successfully execute on our development and commercialization strategy for linaclotide in an effective and efficient manner and without disruption or reduced performance. Finally, any change of control or in management may result in a reprioritization of linaclotide within a partner’s portfolio, or such partner may fail to maintain the financial or other resources necessary to continue supporting its portion of the development, manufacturing or commercialization of linaclotide.

If any of our linaclotide partners undergoes a change of control and the acquirer either (i) is unable to perform such partner’s obligations under its collaboration or license agreement with us or (ii) does not comply with the divestiture or certain other provisions of the applicable agreement, we have the right to terminate the collaboration or license agreement and reacquire that partner’s rights with respect to linaclotide. If we elect to exercise these rights in such circumstances, we will need to either establish the capability to develop, manufacture and commercialize linaclotide in that partnered territory on our own or we will need to establish a relationship with a new partner. We have assembled a team of specialists in manufacturing, quality, sales, marketing, payer, pricing and field operations, and specialized medical scientists, who represent the functional areas necessary for a successful commercial launch of a high potential, gastrointestinal, or GI, therapy and who support the commercialization of LINZESS in the U.S. If Allergan was subject to a change of control that allowed us to further commercialize LINZESS in the U.S. on our own, and we chose to do so, we would need to enhance each of these functional aspects to replace the capabilities that Allergan was previously providing to the collaboration. Any such transition might result in a period of reduced efficiency or performance by our operations and commercialization teams, which could adversely affect our ability to commercialize LINZESS.

Although many members of our global operations, commercial and medical affairs teams have strategic oversight of, and a certain level of involvement in, their functional areas globally, we do not have corresponding operational capabilities in these areas outside of the U.S. If Allergan, Astellas or AstraZeneca was subject to a change of control that allowed us to continue linaclotide’s development or commercialization anywhere outside of the U.S. on our own, and we chose to do so rather than establishing a relationship with a new partner, we would need to build operational capabilities in the relevant territory. In any of these situations, the timeline and likelihood of achieving regulatory approval and, ultimately, the commercialization of linaclotide could be negatively impacted.

We must work effectively and collaboratively with Allergan to market and sell LINZESS in the U.S. in order for it to achieve its maximum commercial potential.

We are working closely with Allergan to execute our joint commercialization plan for LINZESS. The commercialization plan includes an agreed upon marketing campaign that targets the physicians who see patients who could benefit from LINZESS treatment. Our marketing campaign also targets the adult men and women who suffer from IBS-C or CIC. Our commercialization plan also includes an integrated call plan for our sales forces to optimize the education of specific gastroenterologists and primary care physicians on whom our and Allergan’s sales representatives call, and the frequency with which the representatives meet with them.

In order to optimize the commercial potential of LINZESS, we and Allergan must execute upon this commercialization plan effectively and efficiently. In addition, we and Allergan must continually assess and modify our commercialization plan in a coordinated and integrated fashion in order to adapt to the promotional response. Further, we and Allergan must continue to focus and refine our marketing campaign to ensure a clear and understandable physician-patient dialogue around IBS-C, CIC and the potential for LINZESS as an appropriate therapy. In addition, we and Allergan must provide our sales forces with the highest quality support, guidance and oversight in order for them to continue to effectively promote LINZESS to gastroenterologists and primary care physicians. Should the merger of Allergan and AbbVie be consummated, we and AbbVie must work together to ensure an orderly transition of this work

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plan and to continue these commercialization efforts. If we and Allergan (or AbbVie, should the merger be consummated) fail to perform these commercial functions in the highest quality manner and in accordance with our joint commercialization plan and related agreements, LINZESS will not achieve its maximum commercial potential and we may suffer financial harm. Our efforts to further target and engage adult patients with IBS-C or CIC may not effectively increase appropriate patient awareness or patient/physician dialogue, and may not increase the revenues that we generate from LINZESS.

We are subject to uncertainty relating to pricing and reimbursement policies in the U.S. which, if not favorable for our products, could hinder or prevent our products’ commercial success.

Our and our partner’s ability to commercialize our products successfully depend in part on the coverage and reimbursement levels set by governmental authorities, private health insurers and other third-party payers. In determining whether to approve reimbursement for our products and at what level, we expect that third-party payers will consider factors that include the efficacy, cost effectiveness and safety of our products, as well as the availability of other treatments including generic prescription drugs and over-the-counter alternatives. Further, in order to obtain and maintain acceptable reimbursement levels and access for patients at copay levels that are reasonable and customary, we may face increasing pressure to offer discounts or rebates from list prices or discounts to a greater number of third-party payers or other unfavorable pricing modifications. Obtaining and maintaining favorable reimbursement can be a time consuming and expensive process, and there is no guarantee that we or Allergan will be able to negotiate or continue to negotiate pricing terms with third-party payers at levels that are profitable to us, or at all. Certain third-party payers also require prior authorization for, or even refuse to provide, reimbursement for our products, and others may do so in the future. Our business would be materially adversely affected if we and our partners are not able to receive approval for reimbursement of our products from third-party payers on a broad, timely or satisfactory basis; if reimbursement is subject to overly broad or restrictive prior authorization requirements; or if reimbursement is not maintained at satisfactory levels or becomes subject to prior authorization. In addition, our business could be adversely affected if government healthcare programs, private health insurers, including managed care organizations, or other reimbursing bodies or payers limit or reduce the indications for or conditions under which our products may be reimbursed.

We expect to experience pricing pressures in connection with the sale of our current and future products due to the healthcare reforms discussed below, as well as the trend toward initiatives aimed at reducing healthcare costs, the increasing influence of managed care, the scrutiny of pharmaceutical pricing, the ongoing debates on reducing government spending and additional legislative proposals. There have been a number of recent federal and state efforts to address drug costs, which generally have focused on increasing transparency around drug costs or limiting drug prices or price increases. Healthcare reform efforts or any future legislation or regulatory actions aimed at controlling and reducing healthcare costs, including through measures designed to limit reimbursement, restrict access or impose unfavorable pricing modifications on pharmaceutical products, could impact our and our partners’ ability to obtain or maintain reimbursement for our products at satisfactory levels, or at all, which could materially harm our business and financial results.

We and our linaclotide partners are subject to uncertainty relating to pricing and reimbursement policies outside the U.S., as well as risks relating to the improper importation of linaclotide and sale of counterfeit versions of linaclotide. If such policies are not favorable, or if linaclotide is improperly imported or is counterfeited, our business and financial results could be adversely affected.

In some foreign countries, particularly Canada, the countries of Europe, Japan and China, the pricing and payment of prescription pharmaceuticals is subject to governmental control. In these countries, pricing negotiations with governmental authorities can take six to 12 months or longer after the receipt of regulatory approval and product launch. Reimbursement sources are different in each country, and each country may include a combination of distinct potential payers, including private insurance and governmental payers. Some countries may restrict the range of medicinal products for which their national health insurance systems provide reimbursement and control the prices of medicinal products for human use. To obtain favorable reimbursement for the indications sought or pricing approval in some countries, we and our partners may be required to conduct a clinical trial that compares the cost and clinical effectiveness of linaclotide to other available therapies. In addition, in countries in which linaclotide is the only approved therapy for a particular indication, such as CONSTELLA as the only prescription product approved for the symptomatic treatment of moderate to severe IBS-C in adults in Europe and LINZESS as the only prescription treatment approved for the treatment of adults with IBS-C in Japan, there may be disagreement as to what the most comparable product is, or if there even is one. Further, several countries have implemented government measures to either freeze or reduce pricing of

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pharmaceutical products. Many third-party payers and governmental authorities also consider the price for which the same product is being sold in other countries to determine their own pricing and reimbursement strategy, so if linaclotide is priced low or gets limited reimbursement in a particular country, this could result in similarly low pricing and reimbursement in other countries. If reimbursement for linaclotide is unavailable in any country in which reimbursement is sought, limited in scope or amount, or if pricing is set at or reduced to unsatisfactory levels, our and our partners’ ability to successfully commercialize linaclotide in such country would be impacted negatively. Furthermore, if these measures prevent us or any of our partners from selling linaclotide on a profitable basis in a particular country, they could prevent the commercial launch or continued sale of linaclotide in that country.

CONSTELLA was first launched in certain European countries for the symptomatic treatment of moderate to severe IBS-C in adults in the second quarter of 2013 and our partner Allergan is currently commercializing CONSTELLA in a number of European countries, including the United Kingdom, Italy and Spain. LINZESS was first launched in Japan for the treatment of IBS-C in adults in the first quarter of 2017, and for the treatment of chronic constipation in adults in the third quarter of 2018, and our partner Astellas is currently commercializing LINZESS in Japan. In the first quarter of 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. The pricing and reimbursement strategy is a key component of our partners’ commercialization plans for CONSTELLA in Europe and LINZESS in Japan and China. Our revenues may suffer if our partners are unable to successfully and timely conclude reimbursement, price approval or funding processes and market CONSTELLA in key member states of the E.U. or LINZESS in Japan or China, or if coverage and reimbursement for either CONSTELLA or LINZESS is limited or reduced. If our partners are not able to obtain coverage, pricing or reimbursement on acceptable terms or at all, or if such terms change in any countries in its territory, our partners may not be able to, or may decide not to, sell either CONSTELLA or LINZESS in such countries.

We and our partners also face the risk that linaclotide is imported or reimported into markets with relatively higher prices from markets with relatively lower prices, which would result in a decrease of sales and any payments we receive from the affected market. Additionally, third parties may illegally produce, distribute and/or sell counterfeit or otherwise unfit or adulterated versions of linaclotide. In either case, we and our partners may not be able to detect or, if detected, prevent or prohibit the sale of such products, which could result in dangerous health consequences for patients, loss of confidence in us, our partners and our products, and adverse regulatory or legal consequences. Any of the foregoing or other consequences could adversely impact our reputation, financial results and business.

Because we work with partners to develop, manufacture and commercialize our products, we are dependent upon third parties, and our and our partners’ relationships with those third parties, in our and our partners’ efforts to obtain regulatory approval for, and to commercialize, our products, as well as to comply with regulatory and other obligations with respect to such products.

Allergan played a significant role in the conduct of the clinical trials for linaclotide and in the subsequent collection and analysis of data, and Allergan holds the new drug application, or NDA, for LINZESS. In addition, we are commercializing LINZESS in the U.S. with Allergan. Allergan is also responsible for the development, regulatory approval and commercialization of linaclotide in countries worldwide other than Japan and China (including Hong Kong and Macau). Allergan is commercializing LINZESS in Mexico and CONSTELLA in Canada, as well as commercializing CONSTELLA in certain countries in Europe. Astellas and AstraZeneca are responsible for development and commercialization of LINZESS in Japan and China (including Hong Kong and Macau), respectively. Each of Astellas, AstraZeneca and Allergan is responsible for commercializing linaclotide in its respective territory and for reporting adverse event information from its territory to us. Each of Allergan and Astellas is responsible for linaclotide drug product and finished goods manufacturing (including bottling and packaging) for its respective territories and distributing the finished goods to wholesalers. Under the terms of the amendment and restatement of our license with Astellas in August 2019, following a transition period, Astellas will also be responsible for its own supply of linaclotide API for sale in Japan. Under the terms of the amendment and restatement of our collaboration agreement with AstraZeneca in September 2019, AstraZeneca will continue to be accountable for finished goods manufacturing for Hong Kong and Macau and, following a transition period, will assume full responsibility for linaclotide API, drug product and finished goods for China and for linaclotide API and drug product manufacturing for Hong Kong and Macau. During this transition period, we will continue to be responsible for linaclotide API and drug product in China, Hong Kong and Macau and finished goods in China. The integration of our efforts with our partners’ efforts is subject to the uncertainty of the markets for pharmaceutical products in each partner’s respective territories, and accordingly, these relationships must evolve to meet any new challenges that arise in those regions. These integrated functions may not be carried out effectively and efficiently if we fail to communicate and coordinate with our linaclotide partners, and vice

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versa. Our linaclotide partnering strategy imposes obligations, risks and operational requirements on us as the central node in our global network of partners. If we do not effectively communicate with each partner and ensure that the entire network is making integrated and cohesive decisions focused on the global brand for linaclotide, linaclotide will not achieve its maximum commercial potential. Further, we have limited ability to control the amount or timing of resources that our partners devote to linaclotide. If any of our partners fails to devote sufficient time and resources to linaclotide, or if its performance is substandard, it will delay the potential submission or approval of regulatory applications for linaclotide, as well as the manufacturing and commercialization of linaclotide in the particular territory. A material breach by any of our partners of our collaboration or license agreement with such partner, or a significant disagreement between us and a partner, could also delay the regulatory approval and commercialization of linaclotide, potentially lead to costly litigation, and could have a material adverse impact on our financial condition. Moreover, although we have non-compete restrictions in place with each of our linaclotide partners, they may have competitive products or relationships with other commercial entities, some of which may compete with us. If any of our partners competes with us or assists our competitors, it could harm our competitive position.

In addition, adverse event reporting requires significant coordination with our partners and third parties. We are the holder of the global safety database for linaclotide responsible for coordinating the safety surveillance and adverse event reporting efforts worldwide with respect to linaclotide, and an AstraZeneca partner is the holder of the global safety database for lesinurad responsible for coordinating the safety surveillance and adverse event reporting efforts worldwide with respect to lesinurad. If we or AstraZeneca’s partner fails to perform such activities and maintain each safety database or if such parties do not report adverse events related to such products, or fail to do so in a timely manner, we may not receive the information that we are required to report to the FDA regarding such products. Furthermore, we or such parties may fail to adequately monitor, identify or investigate adverse events, or to report adverse events to the FDA or foreign regulatory authority accurately and within the prescribed timeframe. If we or such parties are unsuccessful in any of the foregoing due to poor process, execution, systems, oversight, communication, adjudication or otherwise, then we may suffer any number of consequences, including the imposition of additional restrictions on the use of such products, removal of such products from the market, criminal prosecution, the imposition of civil monetary penalties, seizure of such products, or delay in approval of future products.

Even though LINZESS is approved by the FDA, it faces post-approval development and regulatory requirements, which present additional challenges.

In August 2012, the FDA approved LINZESS as a once-daily treatment for adult men and women suffering from IBS-C or CIC. LINZESS is subject to ongoing FDA requirements, including those governing the testing, manufacturing, labeling, packaging, storage, advertising, promotion, sale, distribution, recordkeeping and submission of safety and other post-market information.

LINZESS is contraindicated in pediatric patients up to six years of age based on nonclinical data from studies in neonatal mice approximately equivalent to human pediatric patients less than two years of age. There is also a boxed warning advising physicians to avoid the use of LINZESS in pediatric patients six to less than 18 years of age. This warning is based on data in young juvenile mice and the lack of clinical safety and efficacy data in pediatric patients of any age group. We and Allergan have established a nonclinical and clinical post-marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatric patients, and clinical pediatric programs in IBS-C and functional constipation currently are ongoing. Our ability to expand the indication or label information for LINZESS to pediatrics will depend on, among other things, our successful completion of pediatric clinical programs. In addition, we and Allergan have also committed to certain nonclinical and clinical studies aimed at understanding: (a) whether orally administered linaclotide can be detected in breast milk, (b) the potential for antibodies to be developed to linaclotide, and if so, (c) whether antibodies specific for linaclotide could have any therapeutic or safety implications. We expect to complete these studies over the next two to four years.

In addition, as the holder of the approved NDA for each of ZURAMPIC and DUZALLO, we are obligated to monitor and report adverse events and any failure of such products to meet the specifications in the applicable NDA, to submit new or supplemental applications and to obtain FDA approval for certain changes to such products, including changes to product labeling and manufacturing processes. The FDA has required a post-marketing clinical study to further evaluate the renal and cardiovascular safety of lesinurad, and has required that enrollment include patients with moderate renal impairment. In connection with the termination of the lesinurad license, the post-marketing clinical study has been terminated.

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These post-approval requirements impose burdens and costs on us. Failure to effectively, appropriately and timely conduct and complete the required studies relating to our products, monitor and report adverse events and meet our other post-approval commitments would lead to negative regulatory action at the FDA, which could include withdrawal of regulatory approval of our products for their currently approved indications and patient populations.

Manufacturers of drug products and their facilities are subject to continual review and periodic inspections by the FDA and other regulatory authorities for compliance with GMP and other applicable regulations. If we or a regulatory agency discovers previously unknown problems with a product, such as adverse events of unanticipated severity or frequency, or problems with a facility where the product is manufactured, a regulatory agency may impose restrictions on that product or the manufacturer, including withdrawal of the product from the market or suspension of manufacturing. If we, our partners or the manufacturing facilities for our products fail to comply with applicable regulatory requirements, a regulatory agency may take the following actions, among others:

●issue warning letters or untitled letters;

●impose civil or criminal penalties;

●suspend or withdraw regulatory approval;

●suspend any ongoing clinical trials;

●refuse to approve pending applications or supplements to applications submitted by us or our partners;

●impose restrictions on operations, including costly new manufacturing requirements; or

●seize or detain products or require us to initiate a product recall.

Even though linaclotide is approved for marketing in the U.S. and in a number of other countries, we or our partners may never receive approval to commercialize linaclotide in additional parts of the world.

In order to market any products outside of the countries where linaclotide is currently approved, we or our partners must comply with numerous and varying regulatory requirements of other jurisdictions regarding, among other things, safety and efficacy. Approval procedures vary among jurisdictions and can involve product testing and administrative review periods different from, and greater than, those in the U.S. and the other countries where linaclotide is approved. Potential risks include that the regulatory authorities:

● may not deem linaclotide safe and effective;

● may not find the data from nonclinical studies and clinical trials sufficient to support approval;

● may not approve of manufacturing processes and facilities;

● may not approve linaclotide for any or all indications or patient populations for which approval is sought;

● may require significant warnings or restrictions on use to the product label for linaclotide; or

● may change their approval policies or adopt new regulations.

If any of the foregoing were to occur, our receipt of regulatory approval in the applicable jurisdiction could be delayed or we may never receive approval at all. Further, regulatory approval in one jurisdiction does not ensure regulatory approval in another, but a failure or delay in obtaining regulatory approval in one jurisdiction may have a negative effect on the regulatory processes in others. If linaclotide is not approved for all indications or patient populations or with the label requested, this would limit the uses of linaclotide and have an adverse effect on its commercial potential or require costly post-marketing studies.

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We face potential product liability exposure, and, if claims brought against us are successful, we could incur substantial liabilities.

The use of our product candidates in clinical trials and the sale of our approved products, including the sale of linaclotide and lesinurad, expose us to product liability claims. If we do not successfully defend ourselves against product liability claims, we could incur substantial liabilities. In addition, regardless of merit or eventual outcome, product liability claims may result in:

● decreased demand for approved products;

● impairment of our business reputation;

● withdrawal of clinical trial participants;

● initiation of investigations by regulators;

● litigation costs;

● distraction of management’s attention from our primary business;

● substantial monetary awards to patients or other claimants;

● loss of revenues; and

● the inability to commercialize our product candidates.

We currently have product liability insurance coverage for the commercial sale of our products and for the clinical trials of our product candidates which is subject to industry-standard terms, conditions and exclusions. Our insurance coverage may not be sufficient to reimburse us for expenses or losses associated with claims. Moreover, insurance coverage is becoming increasingly expensive, and, in the future, we may not be able to maintain insurance coverage at a reasonable cost or in sufficient amounts to protect us against losses. On occasion, large judgments have been awarded in lawsuits based on drugs that had unanticipated side effects. A successful product liability claim or series of claims could cause our stock price to decline and, if judgments exceed our insurance coverage, could decrease our cash and adversely affect our business.

We face competition and new products may emerge that provide different or better alternatives for treatment of the conditions that our products are approved to treat.

The pharmaceutical industry and the markets in which we operate are intensely competitive. We compete in the marketing and sale of our products, the development of new products and the acquisition of rights to new products with commercial potential. Certain of our competitors have substantially greater financial, technical and human resources than us. Mergers and acquisitions in the pharmaceutical industry may result in even more resources being concentrated in our competitors and enable them to compete more effectively. For example, in March 2019, Bausch Health Companies Inc., or Bausch Health, acquired TRULANCE (plecanatide), which, as referenced below, is a competitor to LINZESS, from Synergy Pharmaceuticals, Inc. Competition may also increase further as a result of advances made in the commercial applicability of technologies and greater availability of capital for investment in these fields. Additionally, new developments, including the development of other drug technologies and methods of preventing the incidence of disease, occur in the pharmaceutical and medical technology industries at a rapid pace. These developments may render our products obsolete or noncompetitive.

Our products compete with certain prescription therapies and over-the-counter products for the treatment of the indications for which they are approved, or their associated symptoms, and in many cases with products that have attained significant levels of market acceptance. The availability of prescription competitors and over-the-counter products for such conditions could limit the demand, and the price we are able to charge, for our products unless we are

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able to achieve market acceptance among the medical community and patients and differentiate our products on the basis of their cost and/or actual or perceived benefits. For example, Takeda’s AMITIZA (lubiprostone) is approved by the FDA for sale in the U.S. for the treatment of IBS-C, CIC and opioid-induced constipation, Bausch Health’s TRULANCE (plecanatide) is approved by the FDA for sale in the U.S. for the treatment of adults with IBS-C and CIC, Takeda’s MOTEGRITY (prucalopride) is approved by the FDA for sale in the U.S. for the treatment of CIC in adults, and Alfasigma USA Inc.’s ZELNORM (tegaserod) is approved for sale in the U.S. for treatment of IBS-C in women under the age of 65. Additionally, we believe other companies are developing products which could compete with our products, should they be approved by the FDA or foreign regulatory authorities. Currently, there are other compounds in late stage development and other potential competitors are in earlier stages of development for the treatment of the indications for which our products are approved. If our current or potential competitors are successful in completing drug development for their drug candidates and obtain approval from the FDA or foreign regulatory authorities, they could limit the demand for our products.

We will incur significant liability if it is determined that we are promoting any “off-label” uses of our products.

Physicians are permitted to prescribe drug products and medical devices for uses that are not described in the product’s labeling and that differ from those approved by the FDA or other applicable regulatory agencies. Such “off-label” uses are common across medical specialties. Although the FDA and other regulatory agencies do not regulate a physician’s choice of treatments, the FDA and other regulatory agencies do restrict manufacturer communications on off-label use. Companies are not permitted to promote drugs or medical devices for off-label uses or to promote unapproved drugs or medical devices. Accordingly, we do not permit promotion of any product that we develop, license, commercialize, promote, co-promote or otherwise partner prior to approval or for any indication, population or use not described in or consistent with such product’s label. The FDA and other regulatory and enforcement authorities actively enforce laws and regulations prohibiting promotion of off-label uses and the promotion of products for which marketing approval has not been obtained. A company that is found to have promoted off-label uses will be subject to significant liability, including civil and administrative remedies as well as criminal sanctions. Even if it is later determined that we were not in violation of these laws, we may be faced with negative publicity, incur significant expenses defending our actions and have to divert significant management resources from other matters.

Notwithstanding the regulatory restrictions on off-label promotion, the FDA and other regulatory authorities allow companies to engage in truthful, non-misleading, and non-promotional scientific exchange concerning their products. We intend to engage in medical education activities and communicate with healthcare providers in compliance with all applicable laws, regulatory guidance and industry best practices. Although we believe we have put in place a robust compliance program, which is designed to ensure that all such activities are performed in a legal and compliant manner, we cannot be certain that our program will address all areas of potential exposure and the risks in this area cannot be entirely eliminated.

If we fail to comply with healthcare and other regulations, we could face substantial penalties and our business, operations and financial condition could be adversely affected.

The products that we promote are marketed in the U.S. and/or covered by federal healthcare programs, and, as a result, certain federal and state healthcare laws and regulations pertaining to product promotion and fraud and abuse are applicable to, and may affect, our business. These laws and regulations include:

● federal healthcare program anti-kickback laws, which prohibit, among other things, persons from offering, soliciting, receiving or providing remuneration, directly or indirectly, to induce either the referral of an individual, for an item or service or the purchasing or ordering of a good or service, for which payment may be made under federal healthcare programs such as Medicare and Medicaid;

● federal false claims laws which prohibit, among other things, individuals or entities from knowingly presenting, or causing to be presented, information or claims for payment from Medicare, Medicaid, or other third-party payers that are false or fraudulent, and which may apply to us for reasons including providing coding and billing advice to customers;

● the federal Health Insurance Portability and Accountability Act of 1996, which prohibits executing a scheme to defraud any healthcare benefit program or making false statements relating to healthcare matters

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and which also imposes certain requirements relating to the privacy, security and transmission of individually identifiable health information;

● the Federal Food, Drug, and Cosmetic Act, which among other things, strictly regulates drug product and medical device marketing, prohibits manufacturers from marketing such products prior to approval or for off-label use and regulates the distribution of samples;

● federal laws, including the Medicaid Drug Rebate Program, that require pharmaceutical manufacturers to report certain calculated product prices to the government or provide certain discounts or rebates to government authorities or private entities, often as a condition of reimbursement under government healthcare programs;

● the so-called “federal sunshine” law, which requires pharmaceutical and medical device companies to monitor and report certain financial interactions with physicians and teaching hospitals (and additional categories of health care practitioners beginning with reports submitted in 2022) to the federal government for re-disclosure to the public; and

● state law equivalents of the above federal laws, such as anti-kickback and false claims laws which may apply to items or services reimbursed by any third-party payer, including commercial insurers, state transparency laws, state laws limiting interactions between pharmaceutical manufacturers and members of the healthcare industry, and state laws governing the privacy and security of health information in certain circumstances, many of which differ from each other in significant ways and often are not preempted by federal laws, thus complicating compliance efforts.

Our global activities are subject to the U.S. Foreign Corrupt Practices Act which prohibits corporations and individuals from paying, offering to pay, or authorizing the payment of anything of value to any foreign government official, government staff member, political party, or political candidate in an attempt to obtain or retain business or to otherwise influence a person working in an official capacity. We are also subject to similar anti-bribery laws in the other countries in which we do business.

In addition, we may be subject to privacy and security laws in the various jurisdictions in which we operate, obtain or store personally identifiable information. The legislative and regulatory landscape for privacy and data protection continues to evolve, and there has been an increasing focus on privacy and data protection issues with the potential to affect our business. For example, the processing of personal data in the European Economic Area, or the EEA, is subject to the General Data Protection Regulation, or the GDPR, which took effect in May 2018. The GDPR increases obligations with respect to clinical trials conducted in the EEA, such as in relation to the provision of fair processing notices, exercising data subject rights and reporting certain data breaches to regulators and affected individuals, as well as how we document our relationships with third parties that process GDPR-covered personal data on our behalf. The GDPR also increases the scrutiny applied to transfers of personal data from the EEA (including from clinical trial sites in the EEA) to countries that are considered by the European Commission to lack an adequate level of data protection, such as the United States.  In addition, we expect that we will be impacted by the California Consumer Privacy Act, or CCPA, that is scheduled to become effective on January 1, 2020. The CCPA gives California consumers (defined to include all California residents) certain rights, including the right to ask companies to disclose the types of personal information collected, specific pieces of information collected by a company, the categories of sources from which such information was collected, the business purpose for collecting or selling the consumer’s personal information, and the categories of third parties with whom a company shares personal information. The CCPA also imposes several obligations on companies to provide notice to California consumers regarding a company’s data processing activities. Additionally, the CCPA gives California consumers the right to ask companies to delete a consumer’s personal information and it places limitations on a company’s ability to sell personal information, including providing consumers a right to opt out of sales of their personal information. The compliance obligations imposed by the GDPR have required us to revise our operations, and we expect that the CCPA will require us to make additional revisions to our operations. In addition, the GDPR and the CCPA impose substantial fines and other regulatory penalties for breaches of data protection requirements, and they confer a private right of action on data subjects (in the case of the GDPR) and consumers (in the case of the CCPA) and their representatives for breaches of certain data protection requirements.

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If our operations are found to be in violation of any of the laws described above or any other laws, rules or regulations that apply to us, we will be subject to penalties, including civil and criminal penalties, damages, fines and the curtailment or restructuring of our operations. Any penalties, damages, fines, curtailment or restructuring of our operations could adversely affect our ability to operate our business and our financial results. Although compliance programs can mitigate the risk of investigation and prosecution for violations of these laws, rules or regulations, we cannot be certain that our program will address all areas of potential exposure and the risks in this area cannot be entirely eliminated, particularly because the requirements and government interpretations of the requirements in this space are constantly evolving. Any action against us for violation of these laws, rules or regulations, even if we successfully defend against it, could cause us to incur significant legal expenses and divert our management’s attention from the operation of our business, as well as damage our business or reputation. Moreover, achieving and sustaining compliance with applicable federal and state privacy, security, fraud and reporting laws may prove costly.

Healthcare reform and other governmental and private payer initiatives may have an adverse effect upon, and could prevent, our products’ or product candidates’ commercial success.

The U.S. government and individual states have been aggressively pursuing healthcare reform designed to impact delivery of, and/or payment for, healthcare, which include initiatives intended to reduce the cost of healthcare. For example, in March 2010, the U.S. Congress enacted the Patient Protection and Affordable Care Act, as modified by the Health Care and Education Reconciliation Act, or the ACA, which, among other things, expanded healthcare coverage through Medicaid expansion and the implementation of the individual health insurance mandate; included changes to the coverage and reimbursement of drug products under government healthcare programs; imposed an annual fee on manufacturers of branded drugs; and expanded government enforcement authority. We face uncertainties because there have been, and may be additional, federal legislative and administrative efforts to repeal, substantially modify or invalidate some or all of the provisions of the ACA. Such efforts may lead to fewer Americans having more comprehensive health insurance compliant with the ACA, even in the absence of a legislative repeal. For example, tax reform legislation was enacted at the end of 2017 that includes provisions to eliminate the tax penalty for individuals who do not maintain sufficient health insurance coverage beginning in 2019. The ACA has also been subject to judicial challenge. In December 2018, a federal district court judge, in a challenge brought by a number of state attorneys general, found the ACA unconstitutional in its entirety. Pending appeals, which could take some time, the ACA is still operational in all respects. Adoption of new healthcare reform legislation at the federal or state level could affect demand for, or pricing of, our products or product candidates if approved for sale. However, we cannot predict the ultimate content, timing or effect of any healthcare reform legislation or action, or its impact on us, and healthcare reform could increase compliance costs and may adversely affect our future business and financial results.

In addition, other legislative changes have been adopted that could have an adverse effect upon, and could prevent, our products’ or product candidates’ commercial success. More broadly, the Budget Control Act of 2011, as amended, or the Budget Control Act, includes provisions intended to reduce the federal deficit, including reductions in Medicare payments to providers through 2029. Any significant spending reductions affecting Medicare, Medicaid or other publicly funded or subsidized health programs, or any significant taxes or fees imposed as part of any broader deficit reduction effort or legislative replacement to the Budget Control Act, or otherwise, could have an adverse impact on our anticipated product revenues.

In addition to governmental efforts in the U.S., foreign jurisdictions as well as private health insurers and managed care plans are likely to continue challenging manufacturers’ ability to obtain reimbursement, as well as the level of reimbursement, for pharmaceuticals and other healthcare-related products and services. These cost-control initiatives could significantly decrease the available coverage and the price we might establish for our products, which would have an adverse effect on our financial results.

The Food and Drug Administration Amendments Act of 2007 also provides the FDA enhanced post-marketing authority, including the authority to require post-marketing studies and clinical trials, labeling changes based on new safety information, and compliance with risk evaluation and mitigation strategies approved by the FDA. We and Allergan have established a nonclinical and clinical post-marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatrics. The FDA’s exercise of this authority has resulted (and is expected to continue to result) in increased development-related costs following the commercial launch of our products, and could result in potential restrictions on the sale and/or distribution of our products, even in such products’ approved indications and patient populations.

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If we are unable to successfully partner with other companies to develop and commercialize our products and/or product candidates, our ability to grow would be impaired and our business would be adversely affected.

As part of our business strategy, we may partner with pharmaceutical, biotechnology or other companies to develop and commercialize our products or product candidates. Although we have entered into such arrangements with respect to the development and commercialization of linaclotide worldwide, there can be no assurance that we will be able to do so in the future with respect to other products or product candidates or that we will be able to gain the interest of potential partners; establish and maintain development, manufacturing, marketing, sales or distribution relationships on acceptable terms; that such relationships, if established, will be successful or on favorable terms; or that we will gain market acceptance for such products or product candidates. The process of proposing, negotiating and implementing a partnership arrangement is lengthy and complex. If we enter into any partnering arrangements with third parties, any revenues we receive will depend upon the efforts of such third parties. If we are unable to establish successful partnering arrangements, we may not gain access to the financial resources and industry experience necessary to develop, commercialize or successfully market our products or product candidates, may be forced to curtail, delay or stop a development program or one or more of our other development programs, delay commercialization, reduce the scope of our planned sales or marketing activities or undertake development or commercialization activities at our own expense, and therefore may be unable to generate revenue from our products or product candidates or do so to their full potential.

In pursuing our growth strategy, we will incur a variety of costs and may devote resources to potential opportunities that are never completed or for which we never receive the benefit. Our failure to successfully acquire, develop and market additional product candidates or approved products would impair our ability to grow and/or adversely affect our business.

As part of our growth strategy, we intend to explore further linaclotide development opportunities. We and Allergan are exploring development opportunities to enhance the clinical profile of LINZESS by studying linaclotide in new or existing indications, populations and formulations to assess its potential to treat various conditions. These development efforts may fail or may not increase the revenues that we generate from LINZESS. Furthermore, they may result in adverse events, or perceived adverse events, in certain patient populations that are then attributed to the currently approved patient population, which may result in adverse regulatory action at the FDA or in other countries or harm linaclotide’s reputation in the marketplace, each of which could materially harm our revenues from linaclotide.

We are also pursuing various other programs in our pipeline. We may spend several years and make significant investments in developing any current or future internal product candidate, and failure may occur at any point. Our product candidates are in various stages of development and must satisfy rigorous standards of safety and efficacy before they can be approved for sale by the FDA. To satisfy these standards, we must allocate resources among our various development programs and we must engage in costly and lengthy research and development efforts, which are subject to unanticipated delays and other significant uncertainties. Despite our efforts, our product candidates may not offer therapeutic or other improvement over existing competitive drugs, be proven safe and effective in clinical trials, or meet applicable regulatory standards. It is possible that none of the product candidates we are developing will be approved for commercial sale, which would impair our ability to grow.

We have ongoing or planned nonclinical and clinical trials for linaclotide and our product candidates, including MD-7246, a delayed release form of linaclotide that is being developed as an oral, intestinal, non-opioid pain relieving agent for patients suffering from abdominal pain associated with certain GI diseases, the potential treatment of IBS-D, and IW-3718, a gastric retentive formulation of a bile acid sequestrant for the potential treatment of persistent gastroesophageal reflux disease, and the strength of our company’s pipeline will depend in large part on the outcomes of these studies. Many companies in the pharmaceutical industry have suffered significant setbacks in clinical trials even after achieving promising results in earlier nonclinical or clinical trials. The findings from our completed nonclinical studies may not be replicated in later clinical trials, and our clinical trials may not be predictive of the results we may obtain in later-stage clinical trials or of the likelihood of regulatory approval. Results from our clinical trials and findings from our nonclinical studies could lead to abrupt changes in our development activities, including the possible limitation or cessation of development activities associated with a particular product candidate or program. Furthermore, our analysis of data obtained from nonclinical and clinical activities is subject to confirmation and interpretation by the FDA and other applicable regulatory authorities, which could delay, limit or prevent regulatory approval. Satisfaction of FDA or other applicable regulatory requirements is costly, time-consuming, uncertain and subject to unanticipated delays.

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In addition, because our internal research capabilities are limited, we may be dependent upon pharmaceutical and biotechnology companies, academic scientists and other researchers to sell or license products or technology to us. The success of this strategy depends partly upon our ability to identify, select and acquire promising pharmaceutical product candidates and products. The process of proposing, negotiating and implementing a license or acquisition of a product candidate or approved product is lengthy and complex. Other companies, including some with substantially greater financial, marketing and sales resources, may compete with us for the license or acquisition of product candidates and approved products. We have limited resources to identify and execute the acquisition or in-licensing of third-party products, businesses and technologies and integrate them into our current infrastructure. Moreover, we may devote resources to potential acquisitions or in-licensing opportunities that are never completed, or we may fail to realize the anticipated benefits of such efforts. We may not be able to acquire the rights to additional products or product candidates on terms that we find acceptable, or at all.

In addition, such acquisitions may entail numerous operational and financial risks, including:

● exposure to unknown liabilities;

● disruption of our business and diversion of our management’s time and attention to develop acquired products, product candidates or technologies;

● incurrence of substantial debt, dilutive issuances of securities or depletion of cash to pay for acquisitions;

● higher than expected acquisition and integration costs;

● difficulty in combining the operations and personnel of any acquired businesses with our operations and personnel;

● increased amortization expenses;

● impairment of relationships with key suppliers or customers of any acquired businesses due to changes in management and ownership; and

● inability to motivate key employees of any acquired businesses.

Furthermore, we may have little or no insight or control over the development and commercialization of any product that we in-license outside the licensed territory. If other licensees do not effectively develop or commercialize any such product outside the licensed territory, our reputation or the reputation of any such product may be impacted. Also, any product candidate that we acquire may require additional development efforts prior to commercial sale, including extensive clinical testing and approval by the FDA and applicable foreign regulatory authorities. All product candidates are prone to risks of failure typical of pharmaceutical product development, including the possibility that a product candidate will not be shown to be sufficiently safe and effective for approval by regulatory authorities.

We may incur operational difficulties or be exposed to claims and liabilities as a result of the separation of Cyclerion.

On April 1, 2019, we distributed all of the outstanding shares of Cyclerion Therapeutics, Inc., or Cyclerion, common stock to Ironwood stockholders in connection with the separation of our soluble guanylate cyclase business, or the Separation. In connection with the distribution, we entered into a separation agreement and various other agreements (including a tax matters agreement, an employee matters agreement, transition services agreements, an intellectual property license agreement and a development agreement). These agreements govern the separation and distribution and the relationship between the us and Cyclerion going forward, including with respect to potential tax-related losses associated with the separation and distribution. They also provide for the performance of services by each company for the benefit of the other for a period of time.

The separation agreement provides for indemnification obligations designed to make Cyclerion financially responsible for many liabilities that may exist relating to its business activities, whether incurred prior to or after the distribution, including any pending or future litigation, but we cannot guarantee that Cyclerion will be able to satisfy its indemnification obligations. It is also possible that a court would disregard the allocation agreed to between us and Cyclerion and require us to assume responsibility for obligations allocated to Cyclerion. Third parties could also seek to hold us responsible for any of these liabilities or obligations, and the indemnity rights we have under the separation

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agreement may not be sufficient to fully cover all of these liabilities and obligations. Even if we are successful in obtaining indemnification, we may have to bear costs temporarily. In addition, our indemnity obligations to Cyclerion, including those related to assets or liabilities allocated to us, may be significant. These risks could negatively affect our business, financial condition or results of operations.

The separation of Cyclerion continues to involve a number of additional risks, including, among other things, the potential that management’s and our employees’ attention will be significantly diverted by the provision of transitional services or that we may incur other operational challenges or difficulties as a result of the Separation. Certain of the agreements described above provide for the performance of services by each company for the benefit of the other for a period of time. If Cyclerion is unable to satisfy its obligations under these agreements, we could incur losses and may not have sufficient resources available for such services. These arrangements could also lead to disputes over rights to certain shared property and over the allocation of costs and revenues for products and operations. Our inability to effectively manage the transition activities and related events could adversely affect our business, financial condition or results of operations.

If the distribution of the shares of Cyclerion common stock in connection with the Separation is not generally tax-free for U.S. federal income tax purposes, we and our stockholders could be subject to significant tax liabilities.

The distribution, together with certain related transactions, is intended to qualify for tax-free treatment to us and our stockholders for U.S. federal income tax purposes. We received a favorable private letter ruling from the Internal Revenue Service, or IRS, under the pilot program established in Revenue Procedure 2017-52 relating to the U.S. federal income tax treatment of the distribution. Consistent with the guidelines set forth in Revenue Procedure 2017-52, the IRS private letter ruling does not cover all of the issues that are relevant to determining whether the distribution is generally tax free for U.S. federal income tax purposes. Accordingly, completion of the distribution was conditioned upon, among other things, our receipt of an opinion from an outside tax advisor that the distribution will qualify as a transaction that is generally tax-free to both us and our stockholders for U.S. federal income tax purposes under Sections 355 and 368(a)(1)(D) of the Internal Revenue Code. The private letter ruling and opinion were based on and relied on, among other things, certain facts and assumptions, as well as certain representations, statements and undertakings from us and Cyclerion (including those relating to the past and future conduct of us and Cyclerion). If any of these facts, assumptions, representations, statements or undertakings is, or becomes, inaccurate or incomplete, or if we or Cyclerion breach any of our respective covenants relating to the distribution, the IRS private letter ruling and any tax opinion may be invalid. Moreover, the opinion is not binding on the IRS or any courts. Accordingly, notwithstanding receipt of the IRS private letter ruling and the opinion, the IRS could determine that the distribution and certain related transactions should be treated as taxable transactions for U.S. federal income tax purposes.

If the distribution, together with certain related transactions, fails to qualify as a transaction that is generally tax-free under Sections 355 and 368(a)(1)(D) of the Internal Revenue Code, in general, for U.S. federal income tax purposes, we would recognize taxable gain with respect to Cyclerion’s distributed common stock and our stockholders who received shares of Cyclerion common stock in the distribution would be subject to tax as if they had received a taxable distribution equal to the fair market value of such shares.

We may not achieve some or all of the anticipated benefits of the Separation, which may adversely affect our business.

We may not be able to achieve the full strategic, financial or other benefits expected to result from the Separation, or such benefits may be delayed or not occur at all. If we fail to achieve some or all of the expected benefits of the Separation, or if such benefits are delayed, our business, financial condition, results of operations and the value of our stock could be adversely impacted. The combined value of the common stock of the two publicly traded companies may not be equal to or greater than what the value of our common stock would have been had the Separation not occurred. In addition, we are smaller and less diversified, with a narrower business focus, than we were before the Separation and therefore may be more vulnerable to changing market conditions. The Separation also presents a number of significant risks to our internal processes, including the failure to maintain an adequate control environment due to changes to our infrastructure technology systems and financial reporting processes.

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Completion of the Separation resulted in substantial changes in our board of directors and management.

Completion of the Separation resulted in substantial changes in our board of directors and management. In particular, our former chief executive officer and director, Peter M. Hecht, resigned from each of those positions. In addition, William Huyett, our former chief operating officer, and Mark Currie, our former senior vice president, chief scientific officer and president of research and development, resigned from those positions to join management positions with Cyclerion. Furthermore, Marsha Fanucci, Terrance McGuire, Amy Schulman and Douglas Williams resigned as members of our board of directors upon the completion of the Separation. These senior officer and board level changes could be disruptive to our operations, present significant management challenges and could harm our business. 

Delays in the completion of clinical testing of any of our product candidates could result in increased costs and delay or limit our ability to generate revenues.

Delays in the completion of clinical testing could significantly affect our product development costs. We do not know whether planned clinical trials will be completed on schedule, if at all. The commencement and completion of clinical trials can be delayed for a number of reasons, including delays related to:

● obtaining regulatory approval to commence a clinical trial;

● reaching agreement on acceptable terms with prospective clinical research organizations, or CROs, and trial sites, the terms of which can be subject to extensive negotiation and may vary significantly among different CROs and trial sites;

● manufacturing sufficient quantities of a product candidate for use in clinical trials;

● obtaining institutional review board approval to conduct a clinical trial at a prospective site;

● recruiting and enrolling patients to participate in clinical trials for a variety of reasons, including competition from other clinical trial programs for the treatment of similar conditions; and

● maintaining patients who have initiated a clinical trial but may be prone to withdraw due to side effects from the therapy, lack of efficacy or personal issues, or who are lost to further follow-up.

Clinical trials may also be delayed or discontinued as a result of ambiguous or negative interim results. In addition, a clinical trial may be suspended or terminated by us, an institutional review board overseeing the clinical trial at a clinical trial site (with respect to that site), the FDA, or other regulatory authorities due to a number of factors, including:

● failure to conduct the clinical trial in accordance with regulatory requirements or the study protocols;

● inspection of the clinical trial operations or trial sites by the FDA or other regulatory authorities resulting in the imposition of a clinical hold;

● unforeseen safety issues; or

● lack of adequate enrollment or funding to continue the clinical trial.

Additionally, changes in regulatory requirements and guidance may occur, and we may need to amend clinical trial protocols to reflect these changes. Each protocol amendment would require institutional review board review and approval, which may adversely impact the costs, timing or successful completion of the associated clinical trials. If we or our partners terminate or experience delays in the completion of any clinical trials, the commercial prospects for our product candidates may be harmed, and our ability to generate product revenues will be delayed. In addition, many of the factors that cause, or lead to, a delay in the commencement or completion of clinical trials may also ultimately lead to the denial of regulatory approval.

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We may not be able to manage our business effectively if we lose any of our current management team or if we are unable to attract and motivate key personnel.

We may not be able to attract or motivate qualified management and scientific, clinical, operations and commercial personnel in the future due to the intense competition for qualified personnel among biotechnology, pharmaceutical and other businesses, particularly in the greater-Boston area. If we are not able to attract and motivate necessary personnel to accomplish our business objectives, we will experience constraints that will significantly impede the achievement of our objectives.

We are highly dependent on the drug research, development, regulatory, commercial, financial and other expertise of our management, particularly Mark Mallon, our chief executive officer; Gina Consylman, our senior vice president, chief financial officer, and treasurer; Halley E. Gilbert, our senior vice president, corporate development and chief administrative officer; and Thomas A. McCourt, our president. Transitions in our senior management team and other key employees, including as a result of the Separation, may result in operational disruptions, and our business may be harmed as a result. In addition to the competition for personnel, the Boston area in particular is characterized by a high cost of living. As such, we could have difficulty attracting experienced personnel to our company and may be required to expend significant financial resources in our employee recruitment efforts, which may or may not be successful.

We also have scientific and clinical advisors who assist us in formulating our product development, clinical strategies and our global supply chain plans, as well as sales and marketing advisors who have assisted us in our commercialization strategy and brand plan for our products. These advisors are not our employees and may have commitments to, or consulting or advisory contracts with, other entities that may limit their availability to us, or may have arrangements with other companies to assist in the development and commercialization of products that may compete with ours.

Security breaches and other disruptions to our information technology structure could compromise our information, disrupt our business and expose us to liability, which would cause our business and reputation to suffer.

In the ordinary course of our business, we collect, process and store sensitive data, including intellectual property, our proprietary business information and that of our suppliers and business partners, as well as personally identifiable information of our patients, clinical trial participants and employees. We also rely to a large extent on information technology systems to operate our business, including to deliver our products. We have outsourced elements of our confidential information processing and information technology structure, and as a result, we are managing independent vendor relationships with third parties who may or could have access to our confidential information. Similarly, our business partners and other third-party providers possess certain of our sensitive data. The secure maintenance of this information is critical to our operations and business strategy. Despite our security measures, our large and complex information technology and infrastructure (and those of our partners, vendors and third-party providers) may be vulnerable to attacks by hackers or breached due to employee error, malfeasance or other disruptions. We, our partners, vendors and other third-party providers could be susceptible to third party attacks on our, and their, information security systems, which attacks are of ever-increasing levels of sophistication and are made by groups and individuals with a wide range of motives and expertise, including organized criminal groups, hacktivists, nation states and others. While we have invested in information technology and security and the protection of confidential information, there can be no assurance that our efforts will prevent service interruptions or security breaches. Any such interruptions or breach would substantially impair our ability to operate our business and would compromise our, and their, networks and the information stored there could be accessed, publicly disclosed, lost or stolen. Any such access, disclosure or other loss of information could result in legal claims or proceedings, liability under laws that protect the privacy of personal information, disrupt our operations, and damage our reputation, any of which could adversely affect our business. While we maintain cyber liability insurance, this insurance may not be sufficient to cover the losses that may result from an interruption or breach of our (or our partners’, vendors’ and third-party providers’) systems.

Our business could be negatively affected as a result of a proxy contest or certain other stockholder actions.

Responding to certain stockholder actions can be costly, disruptive and time-consuming, and could also impact our ability to attract, retain and motivate our employees. For example, a proxy contest for our annual meeting of stockholders relating to stockholder proposals or director nominees would require significant time and could divert the attention of our management, other employees and our board of directors. In addition, a proxy contest would require us to incur significant costs, including legal fees and proxy solicitation expenses.

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We moved our headquarters and may face disruption and additional costs.

In October 2019, we relocated our corporate headquarters to 100 Summer Street, Boston, Massachusetts. In connection with this relocation, we could experience unexpected costs or business disruption and diversion of management attention, which could disrupt our business operations and result in additional costs to us.

We must comply with environmental laws and regulations, which can be expensive.

We are subject to federal, state, city and local laws and regulations governing the use, manufacture, storage, handling and disposal of hazardous materials. Although we believe that the safety procedures we have used for handling and disposing of these materials comply with the standards prescribed by these laws and regulations, the risk of accidental contamination or injury from these materials cannot not be eliminated. Any such event could have an adverse effect on our business. We do not currently maintain hazardous materials insurance coverage.

Risks Related to Intellectual Property

Limitations on the patent rights relating to our products and our product candidates may limit our ability to prevent third parties from competing against us.

Our success depends on our ability to obtain and maintain patent protection for our products and product candidates, preserve our trade secrets, prevent third parties from infringing upon our proprietary rights and operate without infringing upon the proprietary rights of others.

The strength of patents in the pharmaceutical industry involves complex legal and scientific questions and can be uncertain. Patent applications in the U.S. and most other countries are confidential for a period of time until they are published, and publication of discoveries in scientific or patent literature typically lags actual discoveries by several months or more. As a result, we cannot be certain that we were the first to conceive inventions covered by our patents and pending patent applications or that we were the first to file patent applications for such inventions. In addition, we cannot be certain that our patent applications will be granted, that any issued patents will adequately protect our intellectual property, or that such patents will not be challenged, narrowed, invalidated or circumvented.

We have several issued patents and pending applications in the U.S. related to LINZESS (linaclotide), including a LINZESS composition of matter and methods of use patent (U.S. Patent 7,304,036) expiring in 2026. Additional U.S. patents and pending applications related to LINZESS include multiple patents relating to our commercial, room temperature stable formulation of linaclotide and methods of using this formulation, the latest of which expire in the early 2030s, as well as other patents and pending patent applications covering processes for making LINZESS, formulations and dosing regimens thereof, and molecules related to LINZESS. Although none of these issued patents currently is subject to a patent reexamination or review, we cannot guarantee that they will not be subject to reexamination or review by the U.S. Patent and Trademark Office, or the USPTO, in the future. We believe in the strength of our LINZESS patent portfolio and that we have sufficient freedom to operate; however, if any of our present or future patents is invalidated, this could have an adverse effect on our business and financial results. In March 2013, an opposition to one of our granted patents covering linaclotide was filed in Europe. In April 2015, the patent was upheld in its entirety by the European Patent Office, affirming the strength of our intellectual property and our belief that the opposition was without merit. The associated appeal was withdrawn by the opponent in January 2019.

Furthermore, the America Invents Act, which was signed into law in 2011, has made several major changes in the U.S. patent statutes. These changes permit third parties to challenge our patents more easily and create uncertainty with respect to the interpretation and practice of U.S. patent law. Moreover, the U.S. Supreme Court has ruled on several patent cases in recent years, narrowing the scope of patent protection available and weakening the rights of patent owners in certain circumstances. Depending on the impact of these decisions and other actions by the U.S. Congress, the federal courts, the USPTO, and their foreign counterparts, the laws and regulations governing patents may change, or their interpretation or implementation may change, in unpredictable ways that could impact, potentially adversely, our ability to obtain new patents or to enforce and defend patents that we have already obtained or that we might obtain in the future. For example, such changes may increase the costs and complexity associated with obtaining, enforcing or defending our patents, including in abbreviated new drug application, or ANDA, litigation.

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We also rely upon unpatented trade secrets, unpatented know-how and continuing technological innovation to develop and maintain our competitive position, which we seek to protect, in part, by confidentiality agreements with our employees and our partners and consultants. We also have agreements with our employees and selected consultants that obligate them to assign their inventions to us. It is possible, however, that technology relevant to our business will be independently developed by a person that is not a party to such an agreement. Furthermore, if the employees and consultants that are parties to these agreements breach or violate the terms of these agreements, we may not have adequate remedies, and we could lose our trade secrets through such breaches or violations. Additionally, our trade secrets could otherwise become known or be independently discovered by our competitors.

In addition, the laws of certain foreign countries do not protect proprietary rights to the same extent or in the same manner as the U.S., and, therefore, we may encounter problems in protecting and defending our intellectual property in certain foreign jurisdictions.

If we are sued for infringing intellectual property rights of third parties, it will be costly and time consuming, and an unfavorable outcome in such litigation could have a material adverse effect on our business.

Our commercial success depends on our ability, and the ability of our partners, to develop, manufacture, market and sell our products and use our proprietary technologies without infringing the proprietary rights of third parties. Numerous U.S. and foreign issued patents and pending patent applications, which are owned by third parties, exist in the fields in which we and our partners are developing products. As the biotechnology and pharmaceutical industry expands and more patents are issued, the risk increases that our potential products may give rise to claims of infringement of the patent rights of others. There may be issued patents of third parties of which we are currently unaware that may be infringed by LINZESS or our product candidates. Because patent applications can take many years to issue, there may be currently pending applications which may later result in issued patents that LINZESS or our product candidates may infringe.

We may be exposed to, or threatened with, litigation by third parties alleging that LINZESS or our product candidates infringe their intellectual property rights. If LINZESS or one of our product candidates is found to infringe the intellectual property rights of a third party, we or our partners could be enjoined by a court and required to pay damages and could be unable to develop or commercialize LINZESS or the applicable product candidate unless we obtain a license to the intellectual property rights. A license may not be available to us on acceptable terms, if at all. In addition, during litigation, the counter-party could obtain a preliminary injunction or other equitable relief which could prohibit us from making, using or selling our products, pending a trial on the merits, which may not occur for several years.

There is a substantial amount of litigation involving patent and other intellectual property rights in the biotechnology and pharmaceutical industries generally. If a third party claims that we or our partners infringe its intellectual property rights, we may face a number of issues, including, but not limited to:

● infringement and other intellectual property claims which, regardless of merit, may be expensive and time-consuming to litigate and may divert our management’s attention from our core business;

● substantial damages for infringement, which we may have to pay if a court decides that the product at issue infringes on or violates the third party’s rights, and, if the court finds that the infringement was willful, we could be ordered to pay treble damages and the patent owner’s attorneys’ fees;

● a court prohibiting us from selling our product unless the third party licenses its rights to us, which it is not required to do;

● if a license is available from a third party, we may have to pay substantial royalties, fees or grant cross-licenses to our intellectual property rights; and

● redesigning our products so they do not infringe, which may not be possible or may require substantial monetary expenditures and time.

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We have received notices of Paragraph IV certifications related to LINZESS in conjunction with ANDAs filed by generic drug manufacturers, and we may receive additional notices from others in the future. We have, and may continue to, become involved in legal proceedings to protect or enforce intellectual property rights relating to our products and our product candidates, which could be expensive and time consuming, and unfavorable outcomes in such proceedings could have a material adverse effect on our business.

Competitors may infringe the patents relating to our products and our product candidates or may assert that such patents are invalid. To counter ongoing or potential infringement or unauthorized use, we may be required to file infringement claims, which can be expensive and time-consuming. Litigation with generic manufacturers has become increasingly common in the biotechnology and pharmaceutical industries. In addition, in an infringement or invalidity proceeding, a court or patent administrative body may determine that a patent of ours is not valid or is unenforceable, or may refuse to stop the other party from using the technology at issue on the grounds that our patents do not cover the technology in question. Generic drug manufacturers were first able to file ANDAs for generic versions of LINZESS in August 2016, but we may not become aware of these filings for several months after any such submission due to procedures specified under applicable FDA regulations. When filing an ANDA for one of our products, a generic drug manufacturer may choose to challenge one or more of the patents that cover such product. As such, we have brought, and may bring in the future, legal proceedings against generic drug manufacturers.

We and Allergan have received Paragraph IV certification notice letters, or Notice Letters, regarding ANDAs submitted to the FDA by generic drug manufacturers requesting approval to engage in commercial manufacture, use, sale and offer for sale of linaclotide capsules (72 mcg, 145 mcg and 290 mcg), proposed generic versions of our FDA-approved drug LINZESS. For additional information relating to such ANDAs, see Item 1, Legal Proceedings, elsewhere in this Quarterly Report on Form 10-Q. Frequently, innovators receive multiple ANDA filings. Consequently, we expect to receive additional notice letters regarding ANDAs submitted to the FDA, and may receive amendments to the Notice Letters.

After evaluation, we have in the past filed, and may, in the future, file patent infringement lawsuits or take other action against companies making ANDA filings. If a patent infringement suit has been filed within 45 days of receipt of a notice letter, the FDA is not permitted to approve any ANDA that is the subject of such lawsuit for 30 months from the date of the NDA holder’s and patent owner’s receipt of the ANDA filer’s notice letter, or until a court decides that the relevant patents are invalid, unenforceable and/or not infringed. In the case of suits filed before expiration of the new chemical entity, or NCE, exclusivity period for a particular drug, the 30-month stay would be calculated from the end of the applicable NCE exclusivity period. In addition to shortening the 30-month stay based on a decision that the relevant patents are invalid, unenforceable and/or not infringed, a court can also shorten or lengthen the 30-month stay under certain limited circumstances. The NCE exclusivity period for LINZESS expired on August 30, 2017, and the defendants in the current patent infringement lawsuits filed by us are prohibited from commercially selling or importing into the U.S. any proposed generic version of LINZESS until the earlier of (i) the date the court issues its trial decision in the lawsuit, and (ii) September 20, 2020.We have filed patent infringement lawsuits against the companies, including Teva and Sandoz, making such ANDA filings, and we have entered into settlement agreements with three other such companies. For additional information relating to such lawsuits and settlements, see Item 1, Legal Proceedings, elsewhere in this Quarterly Report on Form 10-Q. Additionally, the validity of the patents relating to our products and our product candidates may be challenged by third parties pursuant to administrative procedures introduced by the America Invents Act, specifically inter partes review, or IPR, and/or post grant review, or PGR, before the USPTO. Generic drug manufacturers may challenge our patents through IPRs or PGRs instead of or in addition to ANDA legal proceedings.

Patent litigation (including any lawsuits that we file against generic drug manufacturers in connection with the receipt of a notice letter), IPRs and PGRs involve complex legal and factual questions and we may need to devote significant resources to such legal proceedings. We can provide no assurance concerning the duration or the outcome of any such patent-related lawsuits or administrative proceedings, including any settlements or other resolutions thereof which could, in addition to other risks, result in a shortening of exclusivity periods. An adverse result in any litigation or defense proceedings could put one or more of the patents relating to our products and our product candidates at risk of being invalidated or interpreted narrowly, or could otherwise result in a loss of patent protection for the product or product candidate at issue, and could put our patent applications at risk of not issuing, which would materially harm our business. Upon any loss of patent protection for one of our products, or upon an “at-risk” launch (despite pending patent infringement litigation, before any court decision or while an appeal of a lower court decision is pending) by a

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manufacturer of a generic version of one of our patented products, our revenues for that product could be significantly reduced in a short period of time, which would materially and adversely affect our business.

Interference or derivation proceedings brought by the USPTO may be necessary to determine the priority of inventions with respect to the patents relating to our products and our product candidates and patent applications or those of our partners. An unfavorable outcome could require us to cease using the technology or to attempt to license rights to it from the prevailing party. Our business could be harmed if a prevailing party does not offer us a license on terms that are acceptable to us. Litigation or interference proceedings may fail and, even if successful, may result in substantial costs and distraction of our management and other employees. In addition, we may not be able to prevent, alone or with our partners, misappropriation of our proprietary rights, particularly in countries where the laws may not protect those rights as fully as in the U.S.

Furthermore, because of the substantial amount of discovery required in connection with intellectual property litigation, as well as the potential for public announcements of the results of hearings, motions or other interim proceeding or developments, there is a risk that some of our confidential information could be compromised by disclosure during this type of litigation.

Risks Related to Our Finances and Capital Requirements

We have incurred significant losses since our inception, and we may incur losses in future periods.

In recent years, we have focused primarily on developing, manufacturing and commercializing our products, as well as developing our other product candidates. We have financed our business to date primarily through the issuance of equity, our collaboration and license arrangements, and debt issuances, including our June 2015 issuance of our 2.25% Convertible Senior Notes due June 15, 2022, or the 2022 Convertible Notes, our January 2017 issuance of our 8.375% Notes due 2026, and our August 2019 issuance of our 0.75% Convertible Senior Notes due 2024, or the 2024 Convertible Notes, and our 1.50% Convertible Senior Notes due 2026, or the 2026 Convertible Notes, and together with the 2022 Convertible Notes and the 2024 Convertible Notes, the Outstanding Convertible Notes. We have incurred losses in each year since our inception in 1998. We currently derive a significant portion of our revenue from our LINZESS collaboration with Allergan for the U.S. We believe that the revenues from the LINZESS collaboration will continue to constitute a significant portion of our total revenue for the foreseeable future. Although we had net income of approximately $20.6 million in the three months ended September 30, 2019, we incurred net losses of approximately $26.4 million and approximately $266.9 million in the nine months ended September 30, 2019 and 2018, respectively. As of September 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We cannot be certain that sales of our products, and the revenue from our other commercial activities will not fall short of our projections or be delayed. Further, we expect to continue to incur substantial expenses in connection with our efforts to commercialize linaclotide and research and develop our product candidates. Because of the numerous risks and uncertainties associated with developing and commercializing pharmaceutical products, as well as those related to our expectations for our products and our other activities, we are unable to predict the extent of any future losses. Failure to achieve sustainable net income and positive cash flow would have an adverse effect on stockholders’ equity and working capital.

We may need additional funding and may be unable to raise capital when needed, which could cause us to delay, reduce or eliminate our product development programs or commercialization efforts.

We have previously raised funds to finance our operations through capital raising activities, including the sale of shares of our common stock in public offerings and convertible and other debt issuances. However, marketing and selling primary care drugs, purchasing commercial quantities of pharmaceutical products, developing product candidates, conducting clinical trials and accessing externally developed products are expensive and uncertain. Circumstances, our strategic imperatives, or opportunities to create or acquire new programs, as well as maturities, redemptions or repurchases of our outstanding debt securities, could require us to, or we may choose to, seek to raise additional funds. The amount and timing of our future funding requirements will depend on many factors, including, but not limited to:

● the level of underlying demand for our products by prescribers and patients in the countries in which they are approved;

● the costs associated with commercializing our products in the U.S.;

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● the costs of establishing, maintaining and/or expanding sales, marketing, distribution, and market access capabilities for our products;

● the regulatory approval of linaclotide outside of the U.S. and the other countries where it is approved and the timing of commercial launches in those countries, and the regulatory approval of linaclotide within new indications, populations and formulations, as well as the associated development and commercial milestones and royalties;

● the rate of progress, the cost of our clinical trials and the other costs associated with our linaclotide product development programs, including our post-approval nonclinical and clinical studies of linaclotide in pediatrics and our investment to enhance the clinical profile of LINZESS within IBS-C and CIC, as well as to study linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions;

● the costs and timing of in-licensing additional products or product candidates or acquiring other complementary companies or assets;

● the achievement and timing of milestone payments and royalties due or payable under our collaboration and license agreements;

● the status, terms and timing of any collaboration, licensing, co-commercialization or other arrangements;

● the timing of any regulatory approvals of our product candidates;

● whether the holders of our Outstanding Convertible Notes hold the notes to maturity without conversion into our common stock and whether we are required to repurchase any of our Outstanding Convertible Notes prior to maturity upon a fundamental change, as defined in each of the indentures governing the Outstanding Convertible Notes;

● whether we seek to redeem or repurchase all or part of our outstanding debt through cash purchases and/or exchanges, in open market purchases, privately negotiated transactions, by tender offer or otherwise; and

● any difficulties implementing the Separation.

Additional funding may not be available on acceptable terms or at all. If adequate funds are not available, we may be required to delay or reduce the scope of our commercialization efforts, delay, reduce or eliminate one or more of our development programs or delay or abandon potential strategic opportunities.

Our ability to pay principal of and interest on our outstanding debt securities will depend in part on the receipt of payments from Allergan under our collaboration agreement for North America.

In June 2015, we issued approximately $335.7 million aggregate principal amount of our 2022 Convertible Notes bearing an annual interest rate of 2.25%. In August 2019, we issued $200.0 million aggregate principal amount of our 2024 Convertible Notes bearing an annual interest rate of 0.75% and $200.0 million aggregate principal amount of our 2026 Convertible Notes bearing an annual interest rate of 1.50%, and we used a portion of the proceeds from this offering to repurchase $215.0 million aggregate principal amount of the 2022 Convertible Notes. Semi-annual payments on our 2022 Convertible Notes commenced on December 15, 2015 and semi-annual payments on each of our 2024 Convertible Notes and 2026 Convertible Notes are scheduled to begin on December 15, 2019. We expect that for the next few years, at a minimum, the net quarterly payments from Allergan will be a significant source of cash flow from operations. If the cash flows derived from the net quarterly payments that we receive from Allergan under the collaboration agreement for North America are insufficient on any particular payment date to fund the interest payment on our outstanding indebtedness, at a minimum, we will be obligated to pay the amounts of such shortfall out of our general funds. The determination of whether Allergan will be obligated to make a net quarterly payment to us in respect of a particular quarterly period is a function of the revenue generated by LINZESS in the U.S. as well as the development, manufacturing and commercialization expenses incurred by each of us and Allergan under the collaboration agreement for North America. Accordingly, since we cannot guarantee that our company will sustain net income or attain or sustain positive cash flow, we cannot provide assurances that (i) we will have the available funds to fund the interest payment on our outstanding indebtedness, at a minimum, in the event that there is a deficiency in the

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net quarterly payment received from Allergan, (ii) there will be a net quarterly payment from Allergan at all or (iii) we will not also be required to make a true-up payment to Allergan under the collaboration agreement for North America, in each case, in respect of a particular quarterly period.

Our indebtedness could adversely affect our financial condition or restrict our future operations.

As of September 30, 2019, we had total indebtedness of approximately $520.7 million and available cash and cash equivalents of approximately $139.2 million. We chose to issue our Outstanding Convertible Notes based on the additional strategic optionality that they create for us, and the limited restrictions that these debt securities place on our ability to run our business compared to other potential available financing transactions. However, our indebtedness, combined with our other financial obligations and contractual commitments, could have other important consequences on our business, including:

● limiting our ability to obtain additional financing to fund future working capital, capital expenditures or other general corporate purposes, including product development, commercialization efforts, research and development activities, strategic arrangements, acquisitions and refinancing of our outstanding debt;

● requiring a substantial portion of our cash flow to be dedicated to debt service payments instead of other purposes, thereby reducing the amount of cash flow available for working capital, capital expenditures, corporate transactions and other general corporate purposes;

● increasing our vulnerability to adverse changes in general economic, industry and competitive conditions;

● limiting our flexibility in planning for and reacting to changes in the industry in which we compete;

● placing us at a disadvantage compared to other, less leveraged competitors or competitors with comparable debt at more favorable interest rates; and

● increasing our cost of borrowing.

If we do not generate sufficient cash flow from operations or if future borrowings are not available to us in an amount sufficient to pay our indebtedness, including payments of principal when due on our outstanding indebtedness or, in the case of our Outstanding Convertible Notes, in connection with a transaction involving us that constitutes a fundamental change under the indentures governing the Outstanding Convertible Notes, or to fund our liquidity needs, we may be forced to refinance all or a portion of our indebtedness on or before the maturity dates thereof, sell assets, reduce or delay currently planned activities or curtail operations, seek to raise additional capital or take other actions. We may not be able to execute any of these actions on commercially reasonable terms or at all. This, together with any of the factors described above, could materially and adversely affect our business, financial condition and results of operations.

In addition, while none of the indentures governing our Outstanding Convertible Notes include covenants restricting the operation of our business except in certain limited circumstances, in the event of a default under any of the Outstanding Convertible Notes, the applicable noteholders or the trustee under the indentures governing the Outstanding Convertible Notes may accelerate our payment obligations under the applicable Outstanding Convertible Notes, which could have a material adverse effect on our business, financial condition and results of operations. We are also required to offer to repurchase the Outstanding Convertible Notes upon the occurrence of a fundamental change, which could include, among other things, any acquisition of our company (other than an acquisition in which at least 90% of the consideration is common stock listed on The Nasdaq Global or Global Select Market or The New York Stock Exchange), subject to the terms of each of the indenture governing the Outstanding Convertible Notes. The repurchase price must be paid in cash, and this obligation may have the effect of discouraging, delaying or preventing an acquisition of our company that would otherwise be beneficial to our security holders.

Each of the indentures governing our Outstanding Convertible Notes also includes cross-default features providing that certain failures to pay for outstanding indebtedness, would result in a default under the indentures governing our Outstanding Convertible Notes. In the event of such default, the trustee or noteholders could elect to declare all amounts outstanding to be immediately due and payable under the applicable indenture, which could have a material adverse effect on our business, financial condition and results of operations.

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Convertible note hedge and warrant transactions entered into in connection with our 2022 Convertible Notes and capped call transactions entered into in connection with our 2024 Convertible Notes and our 2026 Convertible Notes may affect the value of our common stock.

In connection with the issuance of our 2022 Convertible Notes, we entered into Convertible Note Hedge transactions, or the Convertible Note Hedges, and separate Note Hedge Warrant transactions, or the Note Hedge Warrants, with certain financial institutions, which were partially terminated in connection with the repurchase of $215.0 million aggregate principal amount of the 2022 Convertible Notes in August 2019. Additionally, in connection with the issuance of our 2024 Convertible Notes and our 2026 Convertible Notes, we entered into capped call transactions, or the Capped Calls, with certain financial institutions. These transactions are expected generally to reduce the potential dilution upon any conversion of our 2022 Convertible Notes, our 2024 Convertible Notes or our 2026 Convertible Notes, as applicable, or offset any cash payments we are required to make in excess of the principal amount of converted 2022 Convertible Notes, as the case may be.

In connection with these transactions, the financial institutions purchased our common stock in secondary market transactions and entered into various over-the-counter derivative transactions with respect to our common stock. These entities or their affiliates are likely to modify their hedge positions from time to time prior to conversion or maturity of the 2022 Convertible Notes, the 2024 Convertible Notes and the 2026 Convertible Notes, as applicable, by purchasing and selling shares of our common stock or other instruments they may wish to use in connection with such hedging. Any of these activities could adversely affect the value of our common stock and, as a result, the number of shares and the value of the common stock noteholders will receive upon conversion of the 2022 Convertible Notes, the 2024 Convertible Notes or the 2026 Convertible Notes, as applicable. In addition, under certain circumstances the counterparties have the right to terminate the Convertible Note Hedges and Capped Calls and settle the Note Hedge Warrants at fair value (as defined in the applicable confirmations), which may result in us not receiving all or any portion of the anticipated benefit of the Convertible Note Hedges and Capped Calls. If the price of our common stock increases such that the hedge transactions settle in our favor, we could also be exposed to credit risk related to the counterparties to the Convertible Note Hedges and Capped Calls, which would limit or eliminate the benefit of such transactions to us.

Our quarterly and annual operating results may fluctuate significantly.

We expect our operating results to be subject to frequent fluctuations. Our net loss and other operating results will be affected by numerous factors, including:

● the level of underlying demand for our products in the countries in which they are approved;

● wholesalers’ buying patterns with respect to our products;

● the costs associated with commercializing our products in the U.S.;

● the achievement and timing of milestone payments and royalties due or payable under our collaboration and license agreements;

● our execution of any collaboration, partnership, licensing or other strategic arrangements, and the timing of payments we may make or receive under these arrangements;

● any excess or obsolete inventory or impairments of assets or goodwill, and associated write-downs;

● any variations in the level of expenses related to our development programs;

● addition or termination of clinical trials;

● regulatory developments affecting our products and product candidates; and

● any material lawsuit in which we may become involved.

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If our operating results fall below the expectations of investors or securities analysts for any of the foregoing reasons or otherwise, the price of our common stock could decline substantially. Furthermore, any quarterly or annual fluctuations in our operating results may, in turn, cause the price of our stock to fluctuate substantially.

Our ability to use net operating loss and tax credit carryforwards and certain built-in losses to reduce future tax payments is limited by provisions of the Internal Revenue Code, and it is possible that our net operating loss and tax credit carryforwards may expire before we generate sufficient taxable income to use such carryforwards, or that certain transactions or a combination of certain transactions may result in material additional limitations on our ability to use our net operating loss and tax credit carryforwards.

We have incurred significant net losses since our inception. To the extent that we do not generate federal and state taxable income in the future, unused net operating loss and tax credit carryforwards will carry forward to offset future taxable income, if any, until the date, if any, on which such unused carryforwards expire. Sections 382 and 383 of the Internal Revenue Code of 1986, as amended, contain rules that limit the ability of a company that undergoes an ownership change, which is generally any change in ownership of more than 50% of its stock over a three-year period, to utilize its net operating loss and tax credit carryforwards and certain built-in losses recognized in years after the ownership change. These rules generally operate by focusing on ownership changes involving stockholders owning directly or indirectly 5% or more of the stock of a company and any change in ownership arising from a new issuance of stock by the company. Generally, if an ownership change occurs, the yearly taxable income limitation on the use of net operating loss and tax credit carryforwards and certain built-in losses is equal to the product of the applicable long term tax exempt rate and the value of the company’s stock immediately before the ownership change.

If we do not generate sufficient taxable income prior to the expiration, if any, of the applicable carryforwards or if the carryforwards are subject to the limitations described above, we may be unable to offset our taxable income with losses, or our tax liability with credits, before such losses and credits expire and therefore would incur larger federal or state income tax liability. We have completed several financings since our inception which may have resulted in a change in control as defined by Section 382, or could result in a change in control in the future.

Risks Related to Securities Markets and Investment in Our Stock

Anti-takeover provisions under our charter documents and Delaware law could delay or prevent a change of control which could negatively impact the market price of our common stock.

Provisions in our certificate of incorporation and bylaws may have the effect of delaying or preventing a change of control. These provisions include the following:

● Our board of directors is currently divided into three classes serving staggered terms, such that not all members of the board are elected at one time. This staggered board structure prevents stockholders from replacing the entire board at a single stockholders’ meeting. At our 2019 annual meeting of stockholders, our stockholders approved an amendment to our certificate of incorporation to declassify our board of directors to allow our stockholders to vote on the election of the entire board of directors on an annual basis, rather than on a staggered basis. This declassification will be phased in such that, once completed in 2022, stockholders will have the opportunity to replace the entire board at a single stockholders’ meeting. As required by Delaware law, the amendment to our certificate of incorporation also reflects that, once the board of directors is declassified, stockholders may remove directors with or without cause.

● Our board of directors has the right to elect directors to fill a vacancy created by the expansion of the board of directors or the resignation, death or removal of a director, which prevents stockholders from being able to fill vacancies on our board of directors.

● Our board of directors may issue, without stockholder approval, shares of preferred stock. The ability to authorize preferred stock makes it possible for our board of directors to issue preferred stock with voting or other rights or preferences that could impede the success of any attempt to acquire us.

● Stockholders must provide advance notice to nominate individuals for election to the board of directors or to propose matters that can be acted upon at a stockholders’ meeting. Furthermore, as described above, until our board of directors is declassified, stockholders may only remove a member of our board of

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directors for cause. These provisions may discourage or deter a potential acquirer from conducting a solicitation of proxies to elect such acquirer’s own slate of directors or otherwise attempting to obtain control of our company.

● Our stockholders may not act by written consent. As a result, a holder, or holders, controlling a majority of our capital stock are not able to take certain actions outside of a stockholders’ meeting.

● Special meetings of stockholders may be called only by the chairman of our board of directors, our chief executive officer or a majority of our board of directors. As a result, a holder, or holders, controlling a majority of our capital stock are not able to call a special meeting.

● A super-majority (80%) of the outstanding shares of common stock are required to amend our bylaws, which make it more difficult to change the provisions described above.

In addition, we are governed by the provisions of Section 203 of the Delaware General Corporation Law, which may prohibit certain business combinations with stockholders owning 15% or more of our outstanding voting stock. These and other provisions in our certificate of incorporation and our bylaws and in the Delaware General Corporation Law could make it more difficult for stockholders or potential acquirers to obtain control of our board of directors or initiate actions that are opposed by the then-current board of directors.

If we identify a material weakness in our internal control over financial reporting, it could have an adverse effect on our business and financial results and our ability to meet our reporting obligations could be negatively affected, each of which could negatively affect the trading price of our common stock.

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis. Accordingly, a material weakness increases the risk that the financial information we report contains material errors.

We regularly review and update our internal controls, disclosure controls and procedures, and corporate governance policies. In addition, we are required under the Sarbanes-Oxley Act of 2002 to report annually on our internal control over financial reporting. Our system of internal controls, however well-designed and operated, is based in part on certain assumptions and includes elements that rely on information from third parties, including our partners. Our system can provide only reasonable, not absolute, assurances that the objectives of the system are met. If we, or our independent registered public accounting firm, determine that our internal controls over financial reporting are not effective, or we discover areas that need improvement in the future, these shortcomings could have an adverse effect on our business and financial results, and the price of our common stock could be negatively affected.

Further, we are dependent on our partners for information related to our results of operations. Our net profit or net loss generated from the sales of LINZESS in the U.S. is partially determined based on amounts provided by Allergan and involves the use of estimates and judgments, which could be modified in the future. We are highly dependent on our linaclotide partners for timely and accurate information regarding any revenues realized from sales of linaclotide in their respective territories, and in the case of Allergan for the U.S. and AstraZeneca for China, Hong Kong and Macau, the costs incurred in developing and commercializing it in order to accurately report our results of operations. Our results of operations are also dependent on the timeliness and accuracy of information from any other licensing, collaboration or other partners we may have, as well as our and our partners’ use of estimates and judgments. If we do not receive timely and accurate information or if estimated activity levels associated with the relevant collaboration or partnership at a given point in time are incorrect, whether the result of a material weakness or not, we could be required to record adjustments in future periods. Such adjustments, if significant, could have an adverse effect on our financial results, which could lead to a decline in our common stock price.

If we cannot conclude that we have effective internal control over our financial reporting, or if our independent registered public accounting firm is unable to provide an unqualified opinion regarding the effectiveness of our internal control over financial reporting, investors could lose confidence in the reliability of our financial statements, which could lead to a decline in our stock price. Failure to comply with reporting requirements could also subject us to sanctions and/or investigations by the SEC, The Nasdaq Stock Market or other regulatory authorities.

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We expect that the price of our common stock will fluctuate substantially.

The market price of our common stock may be highly volatile due to many factors, including:

● the commercial performance of our products in the countries in which they are approved, as well as the costs associated with such activities;

● any third-party coverage and reimbursement policies for our products;

● market conditions in the pharmaceutical and biotechnology sectors;

● developments, litigation or public concern about the safety of our products or our potential products;

● announcements of the introduction of new products by us or our competitors;

● announcements concerning product development results, including clinical trial results, or intellectual property rights of us or others;

● actual and anticipated fluctuations in our quarterly and annual operating results;

● deviations in our operating results from any guidance we may provide or the estimates of securities analysts;

● sales of additional shares of our common stock or sales of securities convertible into common stock or the perception that these sales might occur;

● additions or departures of key personnel;

● developments concerning current or future collaboration, partnership, licensing or other strategic arrangements, or the Separation; and

● discussion of us or our stock price in the financial or scientific press or in online investor communities.

The realization of any of the risks described in these “Risk Factors” could have a dramatic and material adverse impact on the market price of our common stock. In addition, class action litigation has often been instituted against companies whose securities have experienced periods of volatility. Any such litigation brought against us could result in substantial costs and a diversion of management attention, which could hurt our business, operating results and financial condition.

Item 6. Exhibits

See the Exhibit Index on the following page of this Quarterly Report on Form 10-Q.

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EXHIBIT INDEX

Exhibit No:	Description
3.1	Eleventh Amended and Restated Certificate of Incorporation. Incorporated by reference to Exhibit 3.1 of Ironwood Pharmaceuticals, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2009, filed with the SEC on March 30, 2010.
3.2	Certificate of Retirement. Incorporated by reference to Exhibit 3.2 of Ironwood Pharmaceuticals, Inc.’s Amendment No. 1 to Form 8-A, filed on January 3, 2019.
3.3	Certificate of Amendment of Eleventh Amended and Restated Certificate of Incorporation. Incorporated by reference to Exhibit 3.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on May 31, 2019.
3.4	Fifth Amended and Restated Bylaws. Incorporated by reference to Exhibit 3.2 of Ironwood Pharmaceuticals, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2009, filed with the SEC on March 30, 2010.
4.1	Indenture, dated as of August 12, 2019, by and between Ironwood Pharmaceuticals, Inc. and U.S. Bank National Association (including the form of the 0.75% Convertible Senior Note due 2024). Incorporated by reference to Exhibit 4.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
4.2	Indenture, dated as of August 12, 2019, by and between Ironwood Pharmaceuticals, Inc. and U.S. Bank National Association (including the form of the 1.50% Convertible Senior Note due 2026). Incorporated by reference to Exhibit 4.2 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
4.3	Form of 0.75% Convertible Senior Note due 2024. Incorporated by reference to Exhibit 4.3 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
4.4	Form of 1.50% Convertible Senior Note due 2026. Incorporated by reference to Exhibit 4.4 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.1+	Amended and Restated License Agreement, dated as of August 1, 2019, by and between Ironwood Pharmaceuticals, Inc. and Astellas Pharma Inc. Incorporated by reference to Exhibit 10.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 1, 2019.
10.2+	Amended and Restated License and Collaboration Agreement, dated as of September 16, 2019, by and between AstraZeneca AB and Ironwood Pharmaceuticals, Inc. Incorporated by reference to Exhibit 10.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on September 18, 2019.
10.3	Base Call Option Transaction Confirmation for the 2024 Notes, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and JPMorgan Chase Bank, National Association. Incorporated by reference to Exhibit 10.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.4	Base Call Option Transaction Confirmation for the 2026 Notes, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and JPMorgan Chase Bank, National Association. Incorporated by reference to Exhibit 10.2 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.

97

10.5	Base Call Option Transaction Confirmation for the 2024 Notes, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and Credit Suisse Capital LLC. Incorporated by reference to Exhibit 10.3 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.6	Base Call Option Transaction Confirmation, for the 2026 Notes, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and Credit Suisse Capital LLC. Incorporated by reference to Exhibit 10.4 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.7	Additional Call Option Transaction Confirmation for the 2024 Notes, dated as of August 12, 2019, between Ironwood Pharmaceuticals, Inc. and JPMorgan Chase Bank, National Association. Incorporated by reference to Exhibit 10.5 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.8	Additional Call Option Transaction Confirmation for the 2026 Notes, dated as of August 12, 2019, between Ironwood Pharmaceuticals, Inc. and JPMorgan Chase Bank, National Association. Incorporated by reference to Exhibit 10.6 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.9	Additional Call Option Transaction Confirmation for the 2024 Notes, dated as of August 12, 2019, between Ironwood Pharmaceuticals, Inc. and Credit Suisse Capital LLC. Incorporated by reference to Exhibit 10.7 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.10	Additional Call Option Transaction Confirmation for the 2026 Notes, dated as of August 12, 2019, between Ironwood Pharmaceuticals, Inc. and Credit Suisse Capital LLC. Incorporated by reference to Exhibit 10.8 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.11	Call Spread Unwind Agreement, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and JPMorgan Chase Bank, National Association. Incorporated by reference to Exhibit 10.9 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
10.12	Call Spread Unwind Agreement, dated as of August 7, 2019, between Ironwood Pharmaceuticals, Inc. and Credit Suisse Capital LLC. Incorporated by reference to Exhibit 10.10 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on August 13, 2019.
31.1*	Certification of Chief Executive Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.
31.2*	Certification of Chief Financial Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.
32.1‡	Certification of Chief Executive Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
32.2‡	Certification of Chief Financial Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
101.INS*	XBRL Instance Document – The Instance Document does not appear in the Interactive Data Files because its XBRL tags are embedded within the Inline XBRL document.
101.SCH*	XBRL Taxonomy Extension Schema Document.
101.CAL*	XBRL Taxonomy Extension Calculation Linkbase Document.

98

101.LAB*	XBRL Taxonomy Extension Label Linkbase Database
101.PRE*	XBRL Taxonomy Extension Presentation Linkbase Document
101.DEF* 104	XBRL Taxonomy Extension Definition Linkbase Document The cover page from this Quarterly Report on Form 10-Q, formatted in Inline XBRL.

*     Filed herewith.

‡     Furnished herewith.

+ Pursuant to 17 C.F.R §§230.406 and 230.83, the confidential portions of this exhibit have been omitted and are marked accordingly.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

	Ironwood Pharmaceuticals, Inc.
Date: October 31, 2019	By:	/s/ MARK MALLON
		Mark Mallon
		Chief Executive Officer and Director
		(Principal Executive Officer)
Date: October 31, 2019	By:	/s/ KELLY MACDONALD
		Kelly MacDonald
		Vice President, Finance and Chief Accounting Officer
		(Principal Accounting Officer)

99

EX-31.1

EXHIBIT 31.1

CERTIFICATION PURSUANT

TO RULES 13a-14(a) OR 15d-14(a) UNDER

THE SECURITIES EXCHANGE ACT OF 1934

I, Mark Mallon, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Ironwood Pharmaceuticals, Inc. (the “registrant”);

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: October 31, 2019

/s/ MARK MALLON

Mark Mallon

Chief Executive Officer

EX-31.2

EXHIBIT 31.2

CERTIFICATION PURSUANT

TO RULES 13a-14(a) OR 15d-14(a) UNDER

THE SECURITIES EXCHANGE ACT OF 1934

I, Gina Consylman, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Ironwood Pharmaceuticals, Inc. (the “registrant”);

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: October 31, 2019

/s/ GINA CONSYLMAN

Gina Consylman

Chief Financial Officer

EX-32.1

EXHIBIT 32.1

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Quarterly Report of Ironwood Pharmaceuticals, Inc. (the “Company”) on Form 10-Q for the period ended September  30, 2019 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Mark Mallon, Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to my knowledge that:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

/s/ MARK MALLON

Mark Mallon

Chief Executive Officer

October 31, 2019

A signed original of this written statement required by Section 906 has been provided to the Company and will be retained by the Company and furnished to the Securities and Exchange Commission or its staff upon request.

EX-32.2

EXHIBIT 32.2

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Quarterly Report of Ironwood Pharmaceuticals, Inc. (the “Company”) on Form 10-Q for the period ended September 30, 2019 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Gina Consylman, Chief Financial Officer of the Company, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to my knowledge that:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

ovem

/s/ GINA CONSYLMAN

Gina Consylman

Chief Financial Officer

October 31, 2019

A signed original of this written statement required by Section 906 has been provided to the Company and will be retained by the Company and furnished to the Securities and Exchange Commission or its staff upon request.

XML

Cyclerion Separation - Summary of Expenses of Cyclerion (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Net Loss from Discontinued Operations
Net loss from discontinued operations	$ 22,528	$ 37,438	$ 64,356
sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff
Net Loss from Discontinued Operations
Net loss from discontinued operations	22,528	37,438	64,356
sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | Research and development
Net Loss from Discontinued Operations
Net loss from discontinued operations	17,636	21,792	49,410
sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | Selling, general and administrative
Net Loss from Discontinued Operations
Net loss from discontinued operations	4,712	$ 15,646	13,860
sGC Business | Discontinued Operations, Disposed of by Means Other than Sale, Spinoff | Restructuring expenses
Net Loss from Discontinued Operations
Net loss from discontinued operations	$ 180		$ 1,086

XML

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2019	Dec. 31, 2018
Preferred stock
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	75,000,000	75,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	156,808,126	154,414,691
Common stock, shares outstanding	156,808,126	154,414,691

XML

Net Income (Loss) Per Share - Computation of EPS (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended						9 Months Ended
	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Sep. 30, 2019	Sep. 30, 2018
Numerator:
Net income (loss)	$ 20,648	$ 12,283	$ (59,284)	$ (174,351)	$ (49,380)	$ (43,144)	$ (26,353)	$ (266,875)
Denominator:
Weighted average number of common shares used in net loss per share-basic and diluted	156,436			153,227			155,752	152,143
Net income (loss) per share-basic and diluted (in dollars per share)	$ 0.13			$ (1.14)			$ (0.17)	$ (1.75)

XML

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Cash flows from operating activities:
Net loss	$ (26,353)	$ (266,875)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,713	3,165
Amortization of acquired intangible assets		8,111
Impairment of intangible assets		151,794
Loss (gain) on disposal of property and equipment	109	(1,591)
Gain on lease modification	(3,169)
Share-based compensation expense	25,792	30,165
Change in fair value of note hedge warrants	740	30,590
Change in fair value of convertible note hedges	754	(34,586)
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments	(3,530)	247
Write-down of excess non-cancellable ZURAMPIC and DUZALLO sample purchase commitments		390
Accretion of discount/premium on investment securities		(157)
Non-cash interest expense	15,532	13,044
Non-cash change in fair value of contingent consideration		(31,045)
Loss on extinguishment of debt	30,977
Changes in assets and liabilities:
Accounts receivable and related party accounts receivable, net	(46,712)	16,782
Prepaid expenses and other current assets	(421)	(13,513)
Inventory, net	(1,086)	(713)
Other assets		119
Accounts payable, related party accounts payable and accrued expenses	(37,275)	(6,988)
Accrued research and development costs	1,021	(1,241)
Operating lease right-of-use assets	12,091
Operating lease liabilities	(2,680)
Deferred revenue	1,278	13,521
Deferred rent		716
Net cash used in continuing operating activities	(28,219)	(88,065)
Net cash provided by discontinued operating activities	11,364	7,910
Net cashed used in operating activities	(16,855)	(80,155)
Cash flows from investing activities:
Purchases of available-for-sale securities		(3,241)
Sales and maturities of available-for-sale securities		79,312
Purchases of property and equipment	(4,521)	(97)
Proceeds from sale of property and equipment	261	627
Net cash (used in) provided by continuing investing activities	(4,260)	76,601
Net cash used in discontinued investing activities	(4,223)	(5,223)
Net cash (used in) provided by investing activities	(8,483)	71,378
Cash flows from financing activities:
Proceeds from issuance of convertible senior notes	400,000
Purchase of capped calls	(25,159)
Proceeds from partial termination of convertible note hedges and warrants	3,174
Costs associated with issuance of convertible senior notes	(9,048)
Proceeds from exercise of stock options and employee stock purchase plan	7,148	27,152
Payments on capital lease obligations		(1,822)
Payments for partial repurchase of 2022 Convertible Notes	(227,338)
Payments on 2026 Notes	(156,409)
Payments on contingent purchase price consideration		(107)
Net cash (used in) provided by continuing financing activities	(7,632)	25,223
Net cash (used in) provided by financing activities	(7,632)	25,223
Net (decrease) increase in cash, cash equivalents and restricted cash	(32,970)	16,446
Cash, cash equivalents and restricted cash, beginning of period	180,848	132,792
Cash, cash equivalents and restricted cash, end of period	$ 147,878	$ 149,238

XML

Inventory - Tabular Disclosure (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Inventory
Raw Materials	$ 1,134
Work in Progress	707
Finished Goods	457
Total	$ 2,298

XML

Workforce Reduction - Tabular Disclosure (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Workforce Reduction
Charges	$ (166)	$ 10,102	$ 3,652	$ 14,010
Employee severance, benefits and related costs
Workforce Reduction
Balance at beginning of period			2,452
Charges			3,198
Amounts paid			(5,162)
Adjustments			(160)
Balance at end of period	328		328
Employee severance, benefits and related costs | Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Balance at beginning of period			696
Charges			16
Amounts paid			(689)
Adjustments			(23)
Balance at end of period	0		0
Employee severance, benefits and related costs | Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Balance at beginning of period			1,756
Amounts paid			(1,708)
Adjustments			(48)
Balance at end of period	0		0
Employee severance, benefits and related costs | Reduction in Workforce, February 7, 2019
Workforce Reduction
Balance at beginning of period			0
Charges			3,182
Amounts paid			(2,765)
Adjustments			(89)
Balance at end of period	328		328
Contract related costs
Workforce Reduction
Balance at beginning of period			433
Amounts paid			(287)
Adjustments			(42)
Balance at end of period	104		104
Contract related costs | Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Balance at beginning of period			433
Amounts paid			(287)
Adjustments			(42)
Balance at end of period	$ 104		$ 104

XML

Employee Stock Benefit Plans - Workforce Reduction (Details) $ in Thousands					3 Months Ended			9 Months Ended
	Feb. 07, 2019 employee	Aug. 16, 2018 employee	Jun. 27, 2018 employee	Jan. 30, 2018 employee	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Mar. 31, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)
Employee Stock Benefit Plans
Share-based compensation expense					$ 5,520	$ 12,168		$ 25,792	$ 30,222
Spin-off | Share-based Payment Awards, Excluding Employee Stock Purchase Plan [Member]
Employee Stock Benefit Plans
Share-based compensation expense					0			0
Spin-off | Shares subject to issuance under Employee Stock Purchase Plan
Employee Stock Benefit Plans
Share-based compensation expense								300
Research and development
Employee Stock Benefit Plans
Share-based compensation expense					1,208	2,974		5,306	8,446
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense					4,312	7,643		19,832	19,708
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense						1,551		654	2,068
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee				60
Reduction in Field-based Workforce, January 30, 2018 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense							$ 200
Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Number of employees expected to be eliminated | employee			40
Reduction in Headquarter-based Workforce, June 27, 2018 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense						1,000			$ 1,300
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Number of employees eliminated | employee		100
Number of employees expected to be eliminated | employee		100
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018 | Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense						$ 600
Reduction in Workforce, February 7, 2019
Workforce Reduction
Number of employees expected to be eliminated | employee	35
Reduction in Workforce, February 7, 2019 | Restructuring expenses | Employee severance, benefits and related costs
Employee Stock Benefit Plans
Share-based compensation expense					$ 0			$ 700

XML

Fair Value of Financial Instruments - Change in Level 3 - Note Hedge Warrants (Details) - Warrants $ in Thousands	9 Months Ended
	Sep. 30, 2019 USD ($)
Change in Level 3 Liabilities
Balance at beginning of period	$ (33,763)
Cash settlement (received) paid upon early termination of derivatives	25,735
Change in fair value, recorded as a component of gain (loss) on derivatives	(740)
Balance at end of period	$ (8,768)

XML

Fair Value of Financial Instruments - Transfers Between Fair Value Measurement Levels (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Fair value transfers
Fair value transfer between measurement levels	$ 0	$ 0	$ 0	$ 0

XML

Notes Payable - Convertible Note Hedge and Warrant Transactions (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
	Jun. 30, 2015	Sep. 30, 2019	Sep. 30, 2019	Apr. 15, 2019	Dec. 31, 2018
Notes Payable
Long-term asset		$ 11,357	$ 11,357		$ 41,020
Long-term liability		8,768	$ 8,768		$ 33,763
Net derivative issuance cost	$ 21,100
(Loss) gain on derivatives		$ 4,800
Convertible Note Hedge
Notes Payable
Shares issuable upon conversion of debt (in shares)			20,249,665
Conversion price (in dollars per share)		$ 16.58	$ 16.58	$ 14.51
Long-term asset	91,900
Note Hedge Warrant Derivatives
Notes Payable
Shares into which warrants may be converted (in shares)		20,249,665	20,249,665
Trading day period			150 days
Long-term liability	$ 70,800
Note Hedge Warrants
Notes Payable
Warrants strike price (in dollars per share)		$ 21.50	$ 21.50	$ 18.82

XML

Accrued Expenses and Other Current Liabilities (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of accrued expenses and other current liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

p
	September 30, 2019		December 31, 2018
Salaries	$	1,703	$	3,054
Accrued vacation		2,647		3,493
Accrued incentive compensation		8,647		13,867
Other employee benefits		1,340		1,883
Professional fees		5,177		1,735
Accrued interest		1,392		873
Restructuring accruals		432		2,885
Other		9,191		10,211
	$	30,529	$	38,001

XML

Net Income (Loss) Per Share (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of potentially dilutive securities that have been excluded from computation of diluted weighted average shares outstanding

The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands):

	As of September 30,
	2019	2018
Options to purchase Class A common stock	17,889	20,860
Shares subject to repurchase	182	97
Restricted stock units	2,838	3,238
Shares subject to issuance under Employee Stock Purchase Plan	67	59
Note Hedge Warrants	8,318	20,250
2022 Convertible Notes	8,318	20,250
2024 Convertible Notes	14,934	—
2026 Convertible Notes	14,934	—
Total	67,480	64,754

XML

Related Party Transactions

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Related Party Transactions

11. Related Party Transactions

In September 2009, Allergan became a related party when the Company sold to Allergan 2,083,333 shares of the Company’s convertible preferred stock. Under the collaboration agreement, the Company and Allergan equally support the development and commercialization of linaclotide (Note 4). Amounts due to and due from Allergan are reflected as related party accounts payable and related party accounts receivable, respectively. These balances are reported net of any balances due to or from the related party. As of September 30, 2019 and December 31, 2018, the Company had approximately $94.4 million and approximately $60.0 million, respectively, in related party accounts receivable, net of related party accounts payable, associated with Allergan.

The Company has and currently obtains health insurance services for its employees from an insurance provider whose President and Chief Executive Officer became a member of the Company’s Board of Directors in April 2016. The Company paid approximately $1.7 million and approximately $5.8 million in insurance premiums to this insurance provider during the three and nine months ended September 30, 2019, respectively, and paid approximately $2.9 million and approximately $9.2 million during the three and nine months ended September 30, 2018, respectively. At September 30, 2019 and December 31, 2018, the Company had no accounts payable due to this related party.

The Company has and currently obtains commercial market and prescription data from a vendor whose Senior Vice President of Strategy, Marketing and Communications became a member of the Company’s Board of Directors in April 2019. The Company paid approximately $0.8 million and approximately $2.0 million in fees to this company during the three and nine months ended September 30, 2019, respectively, and approximately $0.8 million and approximately $2.6 million during the three and nine months ended September 30, 2018, respectively. As of September 30, 2019 and December 31, 2018, the Company had an insignificant amount of accounts payable due to this related party.

In connection with the Separation, the Company executed certain contracts with Cyclerion whose President became a member of the Company’s Board of Directors in April 2019 (Note 2). As of September 30, 2019, the Company had $1.3 million of accounts payable, net of accounts receivable, due to Cyclerion.

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Accrued Expenses and Other Current Liabilities

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Accrued Expenses and Other Current Liabilities

7. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

p
	September 30, 2019		December 31, 2018
Salaries	$	1,703	$	3,054
Accrued vacation		2,647		3,493
Accrued incentive compensation		8,647		13,867
Other employee benefits		1,340		1,883
Professional fees		5,177		1,735
Accrued interest		1,392		873
Restructuring accruals		432		2,885
Other		9,191		10,211
	$	30,529	$	38,001

As of September 30, 2019, other accrued expenses of approximately $9.2 million included approximately $4.0 million related to activities associated with the Company’s move to the Summer Street Property, approximately $1.2 million related to unbilled inventory, and approximately $0.7 million related to contracted services for strategy-related GI research.

During the three months ended September 30, 2019, the Company relieved approximately $4.0 million of previously accrued non-cancelable purchase commitments recorded as accrued expenses related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments, as well as certain excess non-cancelable linaclotide purchase commitments. In addition, during the three months ended September 30, 2019, the Company also relieved approximately $2.5 million of previously accrued non-cancelable purchase commitments recorded as other liabilities related to the assignment of certain linaclotide excess non-cancelable purchase commitments to AstraZeneca in connection with the Amended AstraZeneca Collaboration Agreement. Accordingly, the Company recorded a settlement of approximately $3.5 million as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments related to certain of the aforementioned reversals.

During the three months ended September 30, 2018, the Company assigned to Allergan certain linaclotide excess non-cancelable purchase commitments that the Company had previously accrued for. Accordingly, the Company relieved the previous accrual of approximately $2.5 million, which was recorded as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments.

As of December 31, 2018, other accrued expenses of approximately $10.2 million included approximately $2.5 million related to linaclotide excess purchase commitments, and approximately $1.4 million related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments.

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Net Income (Loss) Per Share

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Net Income (Loss) Per Share

3. Net Income (Loss) Per Share

Basic and diluted net income (loss) per common share is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period.

In June 2015, in connection with the issuance of approximately $335.7 million in aggregate principal amount of 2022 Convertible Notes (Note 9), the Company entered into the Convertible Note Hedges. The Convertible Note Hedges are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2022 Convertible Notes and/or offset any cash payments the Company is required to make in excess of the principal amount of converted 2022 Convertible Notes in the event that the market price per share of the Company’s Class A common stock, as measured under the terms of the Convertible Note Hedges, is greater than the conversion price of the 2022 Convertible Notes. The Convertible Note Hedges are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive. A proportionate amount of these Convertible Note Hedges were terminated in connection with the partial repurchase of the 2022 Convertible Notes in August 2019.

Concurrently with entering into the Convertible Note Hedges, the Company also entered into the Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 9). The Note Hedge Warrants could have a dilutive effect on the Company’s Class A common stock to the extent that the market price per share of the Class A common stock exceeds the applicable strike price of such warrants. The Note Hedge Warrants are not considered for purposes of calculating the number of diluted weighted averages shares outstanding, as their effect would be anti-dilutive. A proportionate amount of these Note Hedge Warrants were terminated in connection with the partial repurchase of the 2022 Convertible Notes in August 2019.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls. The Capped Calls are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2024 Convertible Notes or the 2026 Convertible Notes and/or offset any cash payments that the Company is required to make in excess of the principal amount of converted 2024 Convertible Notes or 2026 Convertible Notes in the event that the market price per share of the Company’s Class A common stock, as measured under the terms of the Capped Calls, is greater than the conversion price of the 2024 Convertible Notes or the 2026 Convertible Notes. The Capped Calls are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive.

The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands):

	As of September 30,
	2019	2018
Options to purchase Class A common stock	17,889	20,860
Shares subject to repurchase	182	97
Restricted stock units	2,838	3,238
Shares subject to issuance under Employee Stock Purchase Plan	67	59
Note Hedge Warrants	8,318	20,250
2022 Convertible Notes	8,318	20,250
2024 Convertible Notes	14,934	—
2026 Convertible Notes	14,934	—
Total	67,480	64,754

During the three and nine months ended September 30, 2019, the Company recorded net income of approximately $20.6 million and net loss of approximately $26.4 million, respectively. The inclusion of applicable securities in the calculation of diluted earnings per share was anti-dilutive for the three months ended September 30, 2019. As a result, diluted earnings per share is equivalent to basic earnings per share for the three and nine months ended September 30, 2019.

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Nature of Business - Linaclotide (Details) person in Millions	9 Months Ended
	Sep. 30, 2019 person
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Number of adults suffering with irritable bowel syndrome with constipation ("IBS-C")	13
Number of adults suffering with chronic idiopathic constipation ("CIC")	35
Number of adults suffering with irritable bowel syndrome with diarrhea ("IBS-D")	16
Number of adults suffering with gastroesophageal reflux disease ("GERD")	10

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Nature of Business - Leases - Cumulative Adjustment (Details) $ in Millions	Jan. 01, 2019 USD ($)
Accounting Standards Update 2016-02
New Accounting Pronouncements
Cumulative effect of adoption of accounting standard	$ 0.0

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Collaboration, License, Co-Promotion and Other Commercial Agreements - Co-Promotion Agreements (Details) - USD ($) $ in Thousands		3 Months Ended			9 Months Ended			12 Months Ended
	Aug. 09, 2019	Sep. 30, 2019	Dec. 31, 2018	Sep. 30, 2018	Dec. 31, 2019	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Collaboration, License and Co-Promotion Agreements
Revenue		$ 131,167		$ 65,686		$ 302,112	$ 215,947
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue		130,524		54,194		273,998	188,487
Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue						2,600
Collaborative arrangement, promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue		1,400				1,400
Allergan | Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue		1,363	$ 1,300	$ 750		2,602	$ 2,250
Milestone payment to be received by company upon milestone achievement								$ 7,500
Collaborative arrangement compensated amount								$ 3,000
Allergan | Collaborative arrangement, promotion agreements
Collaboration, License and Co-Promotion Agreements
Milestone payment to be received by company upon milestone achievement					$ 4,200
Collaborative arrangement compensated amount					$ 4,100
Alnylam | Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Revenue		722				722
Alnylam | Collaborative arrangement, promotion agreements
Collaboration, License and Co-Promotion Agreements
Deferred revenue		$ 1,300				1,300
Revenue						700
Total annual service fees due	$ 9,500
Term of agreement	3 years
Sales milestones | Allergan | Collaborative arrangement, co-promotion agreements
Collaboration, License and Co-Promotion Agreements
Milestone payment to be received by company upon milestone achievement						$ 3,000

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Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Royalty Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Revenue	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Revenues:
Revenue	130,524	54,194	273,998	188,487
Collaborative arrangements revenue | North America | Allergan
Revenues:
Revenue	85,107	52,724	225,390	184,133
Royalty | North America | Allergan
Revenues:
Revenue	542	463	1,559	1,458
Royalty | Canada and Mexico | Allergan
Revenues:
Revenue	$ 500	$ 500	$ 1,600	$ 1,500

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Leases - Operating Leases - Data center colocation lease (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Sep. 30, 2019	Jan. 01, 2019
Operating leases
Operating lease right-of-use assets		$ 19,793	$ 88,300
Lease liability		$ 32,594	94,900
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)		5.40%
Data Center Lease, Boston, Massachusetts
Operating leases
Annual rent escalation (as a percent)		4.00%
Operating lease right-of-use assets		$ 0	600
Lease liability		$ 500	$ 600
Asset impairment charge
Weighted-average discount rate of operating leases (as a percent)		6.00%
Data Center Lease, Boston, Massachusetts | Selling, general and administrative
Asset impairment charge
Asset impairment charge	$ 500

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Inventory - General Information (Details) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Inventory
Write-down of inventory	$ 0.0	$ 2.5	$ 0.0
Lesinurad
Inventory
Write-down of inventory		$ 0.6
Commercial and Sample Supply Commitments
Inventory
Write-down of inventory				$ 2.5

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Leases - Operating Leases - Supplemental Cash Flow Information (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2019 USD ($)
Operating leases
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842	$ 88,299
Adjustment to right-of-use assets as a result of the lease modification at the Separation date	(40,427)
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease	(34,440)
Right-of-use assets obtained in exchange for new operating lease liabilities	18,452
Cash paid for amounts included in the measurement of lease liabilities	$ 8,869
Weighted-average remaining lease term of operating leases (in years)	8 years
Weighted-average discount rate of operating leases (as a percent)	5.40%

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Notes Payable - 2.25% Convertible Senior Notes due 2022 - General Information (Details)		1 Months Ended		9 Months Ended
	Apr. 15, 2019 USD ($) $ / shares shares	Aug. 31, 2019 USD ($)	Jun. 30, 2015 USD ($) D $ / shares shares	Sep. 30, 2019 USD ($) $ / shares shares	Sep. 16, 2019	Dec. 31, 2018 USD ($)
Notes Payable
Payments for convertible note hedges		$ 25,200,000	$ 21,100,000
Debt issuance costs capitalized				$ 8,339,000
Net proceeds received				$ 400,000,000
Note Hedge Warrants
Notes Payable
Warrants strike price (in dollars per share) | $ / shares	$ 18.82			$ 21.50
Convertible Note Hedge
Notes Payable
Conversion price (in dollars per share) | $ / shares	$ 14.51			$ 16.58
Shares issuable upon conversion of debt (in shares) | shares				20,249,665
Convertible Senior Notes
Notes Payable
Debt issuance costs capitalized				$ 8,339,000		$ 5,004,000
2.25% Convertible Senior Notes due 2022 | Note Hedge Warrants
Notes Payable
Shares issuable upon conversion of debt (in shares) | shares	23,135,435
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued			335,700,000	$ 120,699,000		$ 335,699,000
Net proceed received			324,000,000.0
Fees and expenses			$ 11,700,000
Stated interest rate (as a percent)			2.25%		2.25%
Conversion rate, number of shares to be issued per	68.9172		60.3209
Principal amount used for debt instrument conversion ratio	$ 1,000		$ 1,000
Conversion price (in dollars per share) | $ / shares	$ 14.51		$ 16.58
Shares issuable upon conversion of debt (in shares) | shares	23,135,435		20,249,665
Number of trading days | D			20
Consecutive trading days | D			30
Minimum percentage of stock price			130.00%
Number of business days immediately after any five consecutive trading day period during the measurement period | D			5
Number of consecutive trading days before five business days during the measurement period | D			5
Repurchase price, as percentage of principal amount, if company undergoes change of control			100.00%
Maximum period of the sole remedy for event failures in the Indenture				180 days
Amortization period			7 years
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Minimum
Notes Payable
Percentage of aggregate principal amount payable, in case of event of default			25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Maximum
Notes Payable
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate			98.00%

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Notes Payable - 2.25% Convertible Senior Notes due 2022 - Future Minimum Payments (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Future minimum payments of Convertible senior notes
2019	$ 2,895
2020	7,216
2021	7,216
2022	126,556
2023	4,500
2024	203,750
Thereafter	204,500
Total future minimum payments under the convertible senior notes	556,633
Less: amounts representing interest	(35,934)
Less: unamortized debt discount	(109,685)
Less: unamortized debt issuance costs	(8,339)
Net carrying amount	402,675
Convertible Senior Notes
Future minimum payments of Convertible senior notes
Less: unamortized debt discount	(109,685)	$ (65,094)
Less: unamortized debt issuance costs	(8,339)	(5,004)
Net carrying amount	$ 402,675	$ 265,601

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Leases - Operating Leases - Summer Street Lease (Details) - USD ($) $ in Thousands		3 Months Ended	9 Months Ended
	Jun. 11, 2019	Sep. 30, 2019	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Operating leases
Restricted cash, noncurrent		$ 971	$ 971		$ 6,426
Operating lease right-of-use assets		$ 19,793	$ 19,793	$ 88,300
Weighted-average discount rate of operating leases (as a percent)		5.40%	5.40%
Operating lease cost		$ 6,244	$ 13,924
Summer Street Lease
Operating leases
Option to extend the term of the lease	true
Operating lease, renewal term	5 years
Annual rent escalation (as a percent)	2.00%
Restricted cash, noncurrent		1,000	1,000
Operating lease right-of-use assets		18,000	18,000
Lease liability, net of tenant improvement allowance reimbursement		$ 22,500	$ 22,500
Weighted-average discount rate of operating leases (as a percent)		5.80%	5.80%
Asset retirement obligation		$ 500	$ 500
Operating lease cost		$ 600	$ 800

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Inventory

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Inventory

6. Inventory

Inventory consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Raw Materials	$	1,134	$	—
Work in Progress		707		—
Finished Goods		457
	$	2,298	$	—

The Company’s inventory represents linaclotide API, drug product, and finished goods. The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified.

No impairment of inventory was recorded during the three and nine months ended September 30, 2019. The Company wrote down approximately $0.6 million and approximately $2.5 million related to lesinurad inventory and commercial supply purchase commitments during the three and nine months ended September 30, 2018, respectively, as a result of revised demand forecasts and the termination of the Lesinurad License. The adjustment was recorded as write-down of commercial supply to net realizable value and (settlement) loss on non-cancelable purchase commitments.

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Cyclerion Separation

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Cyclerion Separation

2. Cyclerion Separation

On April 1, 2019, Ironwood completed the Separation of Cyclerion. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019. Prior to the Separation on April 1, 2019, as described in Note 1, Nature of Business, Cyclerion was a wholly owned subsidiary of the Company. On March 30, 2019, the Company entered into certain agreements with Cyclerion relating to the Separation, including a separation agreement, a tax matters agreement, and an employee matters agreement.

Agreements with Cyclerion

The separation agreement with Cyclerion, dated as of March 30, 2019, sets forth, among other things, the Company’s agreements with Cyclerion regarding the principal actions to be taken in connection with the Separation, including the distribution, which was effective as of April 1, 2019. The separation agreement identifies assets transferred, liabilities assumed by and contracts assigned to each of Cyclerion and Ironwood as part of the Separation, and it provides for when and how these transfers, assumptions and assignments occur. The purpose of the separation agreement is to provide Cyclerion and Ironwood with assets to operate their respective businesses and retain or assume liabilities related to those assets.

The transfer of assets and liabilities to Cyclerion was effected through a contribution in accordance with the separation agreement as summarized below (in thousands):

		As of April 1, 2019
Assets:
Prepaid expenses and other current assets	$	1,169
Property and equipment, net		10,241
Other assets		21
	$	11,431
Liabilities:
Accrued research and development costs	$	5,673
Accrued expenses and other current liabilities		3,149
	$	8,822
Net Assets Transferred to Cyclerion	$	2,609

In addition, the Company received approximately $1.3 million during the three months ended September 30, 2019 associated with tenant improvement reimbursement provisions related to the Cyclerion lease in accordance with the separation agreement.

The tax matters agreement, dated as of March 30, 2019, governs each party’s rights, responsibilities and obligations with respect to taxes, including taxes, if any, incurred as a result of any failure of the Separation to qualify as tax-free. In general, if the parties incur tax liabilities in the event that the Separation is not tax-free, each party is expected to be responsible for any taxes imposed on Ironwood or Cyclerion that arise from the failure of the Separation to qualify as a transaction that is generally tax-free for U.S. federal income tax purposes, under Sections 355 and 368(a)(1)(D) and certain other relevant provisions of the Internal Revenue Code of 1986, as amended, to the extent that the failure to so qualify is attributable to an acquisition of stock or assets of, or certain actions, omissions or failures to act of, such party. If both Ironwood and Cyclerion are responsible for such failure, liability will be shared according to relative fault. U.S. tax otherwise resulting from the failure of the Separation to qualify as a transaction that is tax-free generally will be the responsibility of Ironwood. Each party otherwise agreed to indemnify the other party from and against any liability for taxes allocated to such party under the tax matters agreement and any taxes resulting from breach of any such party’s covenants under the tax matters agreement, the separation agreement, or any ancillary agreement entered into in connection with the Separation. Cyclerion agreed to certain covenants that contain restrictions intended to preserve the tax-free status of the distribution and certain related transactions.

The employee matters agreement, dated as of March 30, 2019, allocates assets, liabilities and responsibilities relating to the employment, compensation, and employee benefits of Ironwood and Cyclerion employees, and other related matters in connection with the Separation, including the treatment of outstanding Ironwood incentive equity awards. Pursuant to the employee matters agreement, the outstanding Ironwood equity awards held by Cyclerion and Ironwood employees were adjusted in connection with the Separation, with the intent to maintain, immediately following the Separation, the economic value of the awards. No incremental stock-based compensation expense was recognized during the three or nine months ended September 30, 2019 (Note 10).

Additionally, the Company entered into two transition services agreements and a development agreement with Cyclerion.

Pursuant to the transition service agreements, the Company is obligated to provide and is entitled to receive certain transition services related to corporate functions, such as finance, procurement, facilities and development. Services provided by the Company to Cyclerion will continue for an initial term of one to two years from the date of the Separation (as applicable), unless earlier terminated or extended according to the terms of the transition services agreement. Services provided by Cyclerion to the Company will continue for an initial term of one year from the date of the Separation, unless earlier terminated or extended according to the terms of such transition services agreement. Services received and performed are paid at a mutually agreed upon rate. Amounts for services provided to Cyclerion are recorded as other income and amounts for services provided by Cyclerion are recorded as selling, general and administrative expense and research and development expense, as applicable. During the three and nine months ended September 30, 2019, the Company recorded an insignificant amount and approximately $0.2 million as other income for services provided to Cyclerion, respectively. During each of the three and nine months ended September 30, 2019, the

Company recorded an insignificant amount in both selling, general and administrative expense and research and development expense for services provided by Cyclerion.

Pursuant to the development agreement, Cyclerion is obligated to provide the Company with certain research and development services with respect to certain of Ironwood’s products and product candidates, including MD-7246 and IW-3718. Such research and development activities are governed by a joint steering committee comprised of representatives from both Cyclerion and Ironwood. Services received are paid at a mutually agreed upon rate. The Company recorded approximately $1.4 million and approximately $3.0 million in research and development expenses under the development agreement during the three and nine months ended September 30, 2019, respectively.

Discontinued Operations

Upon Separation, the Company determined its sGC business qualified for discontinued operations accounting treatment in accordance with ASC 205-20. The following is a summary of expenses of Cyclerion for the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Costs and expenses:
Research and development		—		17,636		21,792		49,410
Selling, general and administrative		—		4,712		15,646		13,860
Restructuring expenses		—		180		—		1,086
Net loss from discontinued operations		—		22,528		37,438		64,356

There were no assets and liabilities related to discontinued operations as of September 30, 2019, as all balances were transferred to Cyclerion upon Separation. The following is a summary of assets and liabilities of discontinued operations as of December 31, 2018 (in thousands):

Assets:
Prepaid expenses and other current assets	$	847
Property and equipment, net		9,618
Other assets		25
	$	10,490
Liabilities:
Accounts payable	$	3,232
Accrued research and development costs		5,256
Accrued expenses and other current liabilities		7,251
	$	15,739

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Employee Stock Benefit Plans

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Employee Stock Benefit Plans

10. Employee Stock Benefit Plans

The Company has several share-based compensation plans under which stock options, restricted stock awards, restricted stock units (“RSUs”), and other share-based awards are available for grant to employees, officers, directors and consultants of the Company.

In May 2019, the Company’s stockholders approved the 2019 Equity Incentive Plan (the “2019 Equity Plan”) under which stock options, restricted stock awards, RSUs, and other stock-based awards may be granted to employees, officers, directors, or consultants of the Company. Under the 2019 Equity Plan, 10,000,000 shares of Class A common stock were initially reserved for issuance. As of September 30, 2019, 11,276,185 shares were available for future grant under the 2019 Equity Plan.

The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Research and development	$	1,208	$	2,974	$	5,306	$	8,446
Selling, general and administrative		4,312		7,643		19,832		19,708
Restructuring expenses		—		1,551		654		2,068
	$	5,520	$	12,168	$	25,792	$	30,222

During the three months ended March 31, 2018, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position, resulting in a modification to certain share-based payment awards. As a result of the modification, the Company recorded stock-based compensation expense of approximately $0.2 million to restructuring expenses during the three months ended March 31, 2018.

During the three months ended June 30, 2018, the Company initiated a reduction in headquarter-based workforce by approximately 40 employees associated with the Separation. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded approximately $1.0 million and $1.3 million of restructuring expenses during the three and nine months ended September 30, 2018, respectively.

During the three months ended September 30, 2018, the Company reduced its workforce by approximately 100 employees, primarily consisting of field-based sales representatives as a result of the termination of the Lesinurad License. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded share-based compensation expense of approximately $0.6 million to restructuring expenses during the three months ended September 30, 2018.

In February 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded no share-based compensation expense and approximately $0.7 million to restructuring expenses during the three and nine months ended September 30, 2019, respectively.

In April 2019, in connection with the Separation, all outstanding share-based payment awards were modified in accordance with the equity conversion-related provisions of the employee matters agreement. No share-based compensation expense was recognized in connection with these modifications. Additionally, modifications with respect to the Company’s Employee Stock Purchase Plan (“ESPP”) were made due to the change in share price as a result of the Separation. As a result of the modification to the ESPP, the Company recorded approximately $0.3 million of share-based compensation expense during the nine months ended September 30, 2019.

In connection with certain other modifications of share-based payment awards during the three and nine months ended September 30, 2019, the Company recognized approximately $0.2 million and approximately $2.8 million in share-based compensation expense, respectively.

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Nature of Business - Non-cancelable Operating Lease (Details) ft² in Thousands	Jun. 11, 2019 ft²
Summer Street Lease
Operating leases
Rentable area leased (in square feet)	39

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Nature of Business - Leases - Practical Expedients (Details)	9 Months Ended
	Sep. 30, 2019
Leases
Lease, Practical Expedients, Package	true
Lease, Practical Expedient, Lessor Single Lease Component	true

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Collaboration, License, Co-Promotion and Other Commercial Agreements - China, Hong Kong and Macau (Details) $ in Thousands	1 Months Ended		3 Months Ended		9 Months Ended
	Sep. 30, 2019 USD ($) installment	Oct. 31, 2012	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)
Collaboration, License and Co-Promotion Agreements
Revenue			$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue			130,524	54,194	273,998	188,487
Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue			643	10,257	28,114	24,494
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Collaborative arrangement, significant financing component, transaction price	$ 2,600		2,600		2,600
Net cost sharing offset or incremental expense related to research and development expense				800		800
Collaborative arrangement, expected interest income	2,600		2,600		2,600
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration and license agreements
Collaboration, License and Co-Promotion Agreements
Revenue			32,401		32,401
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Milestone payment to be received by company upon milestone achievement	90,000
Amount of non-contingent arrangement consideration	$ 35,000
Non-contingent consideration installments | installment	3
Percentage of tiered royalties	20.00%
Revenue			32,400		32,400
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, transition services agreement
Collaboration, License and Co-Promotion Agreements
Regulatory and administrative services initial term	2 years
AstraZeneca | China, Hong Kong, and Macau | Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue			643		646
AstraZeneca | China, Hong Kong, and Macau | Commercialization milestone | Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue				$ 0		$ 0
AstraZeneca | China, Hong Kong, and Macau | Commercialization milestone | Collaborative arrangement, collaboration agreements
Collaboration, License and Co-Promotion Agreements
Percentage of net loss from commercialization (as a percent)		55.00%
Pre-launch commercial services and supply chain services			$ 700		$ 1,200

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Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Commercial Efforts (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Collaboration, License and Co-Promotion Agreements
Revenue	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue	130,524	54,194	273,998	188,487
Collaborative arrangements, LINZESS | Allergan | U.S.
Collaboration, License and Co-Promotion Agreements
Revenue	84,565	52,261	223,831	182,675
Selling, general and administrative costs incurred by the Company	(9,129)	(10,915)	(29,764)	(33,556)
The Company's share of net profit	$ 75,436	$ 41,346	$ 194,067	$ 149,119

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Notes Payable - 0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 (Details)				1 Months Ended
	Aug. 12, 2019 USD ($)	Aug. 07, 2019 USD ($) $ / shares	Apr. 15, 2019 USD ($) $ / shares shares	Aug. 31, 2019 USD ($) D	Jun. 30, 2015 USD ($) D $ / shares shares	Sep. 30, 2019 USD ($)	Sep. 16, 2019	Dec. 31, 2018 USD ($)
Notes Payable
Payments for convertible note hedges				$ 25,200,000	$ 21,100,000
Repurchase price				100.00%
The percentage of aggregate principal amount of notes outstanding and payable in case of event of default under the agreement.				25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued					335,700,000	$ 120,699,000		$ 335,699,000
Net proceed received					324,000,000.0
Fees and expenses					$ 11,700,000
Stated interest rate (as a percent)					2.25%		2.25%
Conversion rate, number of shares to be issued per			68.9172		60.3209
Principal amount used for debt instrument conversion ratio			$ 1,000		$ 1,000
Initial conversion price (in dollars per share) | $ / shares			$ 14.51		$ 16.58
Shares issuable upon conversion of debt (in shares) | shares			23,135,435		20,249,665
Number of trading days | D					20
Consecutive trading days | D					30
Minimum percentage of stock price					130.00%
Number of business days immediately after any five consecutive trading day period during the measurement period | D					5
Number of consecutive trading days before five business days during the measurement period | D					5
Repurchase price, as percentage of principal amount, if company undergoes change of control					100.00%
Amortization period					7 years
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Minimum
Notes Payable
Percentage of aggregate principal amount payable, in case of event of default					25.00%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes | Maximum
Notes Payable
Percentage of the trading price to the product of the sale price of the entity's common stock and the conversion rate					98.00%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Net proceed received				$ 391,000,000.0
Fees and expenses				9,000,000.0
Conversion rate, number of shares to be issued per	74.6687
Principal amount used for debt instrument conversion ratio		$ 1,000		$ 1,000
Initial conversion price (in dollars per share) | $ / shares		$ 13.39
Conversion premium percentage on sale price of commonstock		37.50%
Share Price | $ / shares		$ 9.74
Number of consecutive trading days before five business days during the measurement period | D				5
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Calendar quarter commencing after December 31, 2019
Notes Payable
Number of trading days | D				20
Consecutive trading days | D				30
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Measurement period
Notes Payable
Number of business days immediately after any five consecutive trading day period during the measurement period | D				5
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Minimum | Calendar quarter commencing after December 31, 2019
Notes Payable
Minimum percentage of stock price				130.00%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes | Maximum | Measurement period
Notes Payable
Conversion premium percentage on sale price of commonstock				98.00%
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	$ 200,000,000.0			$ 200,000,000.0		200,000,000
Stated interest rate (as a percent)	0.75%
Amortization period				5 years
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued	$ 200,000,000.0			$ 200,000,000.0		$ 200,000,000
Stated interest rate (as a percent)	1.50%
Amortization period				7 years

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Leases - Operating Leases - Binney Street Lease (Details) $ in Thousands			1 Months Ended	3 Months Ended		9 Months Ended
	Jun. 11, 2019 USD ($) ft²	Apr. 01, 2019 ft²	Jan. 31, 2007 USD ($) ft²	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Jan. 01, 2019 USD ($)	Dec. 31, 2018 USD ($)
Operating leases
Restricted cash, noncurrent				$ 971		$ 971			$ 6,426
Operating lease right-of-use assets				19,793		19,793		$ 88,300
Lease liability				$ 32,594		$ 32,594		94,900
Weighted-average discount rate of operating leases (as a percent)				5.40%		5.40%
Operating lease cost				$ 6,244		$ 13,924
Sublease income						300
Binney Street Lease
Operating leases
Rentable area leased (in square feet) | ft²	108,000	108,000	223,000
Option to extend the term of the lease			true
Operating lease, renewal term			5 years
Annual rent escalation (as a percent)			3.00%
Restricted cash, noncurrent			$ 6,400
Operating lease right-of-use assets				1,800		1,800		87,700
Lease liability				9,700		9,700		$ 94,300
Surrendered space (in square feet) | ft²		114,000
Weighted-average discount rate of operating leases (as a percent)	4.00%	5.10%
Gain on modification of lease						3,200
Lease termination cost	$ 9,000
Operating lease cost				6,200		$ 14,300
Sublease income				$ 300
Rent expense					$ 2,500		$ 7,600

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Leases - Operating Leases - Vehicle fleet leases (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018	Apr. 30, 2018
Operating leases
Restricted cash, noncurrent	$ 971		$ 971		$ 6,426
Operating lease cost	6,244		13,924
Vehicles, 2018 Vehicle Leases
Operating leases
Operating lease, term						12 months
Operating lease, renewal term						1 month
Restricted cash, noncurrent						$ 1,300
Operating lease cost	$ 400	$ 400	$ 1,100	$ 400
Vehicles
Operating leases
Capital lease obligations					$ 0

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Accrued Expenses and Other Current Liabilities - Tabular Disclosure (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Accrued Expenses
Salaries	$ 1,703	$ 3,054
Accrued vacation	2,647	3,493
Accrued incentive compensation	8,647	13,867
Other employee benefits	1,340	1,883
Professional fees	5,177	1,735
Accrued interest	1,392	873
Restructuring accruals	432	2,885
Other	9,191	10,211
Total accrued expenses and other current liabilities	$ 30,529	$ 38,001

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Leases - Operating Leases - Future Minimum Lease Payments - ASC 842 (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Future minimum lease payments
2019	$ 9,729
2020	1,146
2021	3,128
2022	3,129
2023	3,065
2024 and thereafter	21,170
Total future minimum lease payments	$ 41,367

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Notes Payable - 2.25% Convertible Senior Notes due 2022 - Balances (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Aug. 31, 2019	Aug. 12, 2019	Dec. 31, 2018	Jun. 30, 2015
Liability component:
Long-term Debt, Gross	$ 556,633
Less: unamortized debt discount	(109,685)
Less: unamortized debt issuance costs	(8,339)
Net carrying amount	402,675
Convertible Senior Notes
Liability component:
Less: unamortized debt discount	(109,685)			$ (65,094)
Less: unamortized debt issuance costs	(8,339)			(5,004)
Net carrying amount	402,675			265,601
Equity component	112,309			114,199
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Liability component:
Aggregate principal amount of notes issued	120,699			335,699	$ 335,700
Equity component	19,807			$ 114,199
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Liability component:
Aggregate principal amount of notes issued	200,000	$ 200,000	$ 200,000
Equity component	41,152
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Liability component:
Aggregate principal amount of notes issued	200,000	$ 200,000	$ 200,000
Equity component	$ 51,350

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Cyclerion Separation - Summary of Assets and Liabilities Held for Disposition (Details) - Discontinued Operations, Disposed of by Means Other than Sale, Spinoff - sGC Business - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Assets:
Prepaid expenses and other current assets		$ 847
Property and equipment, net		9,618
Other assets		25
Assets	$ 0	10,490
Liabilities:
Accounts payable		3,232
Accrued research and development costs		5,256
Accrued expenses and other current liabilities		7,251
Liabilities	$ 0	$ 15,739

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Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 139,231	$ 173,172
Accounts receivable, net	2,017	20,991
Related party accounts receivable, net	94,553	59,959
Inventory, net	2,298
Prepaid expenses and other current assets	11,863	10,216
Restricted cash	7,676	1,250
Current assets of discontinued operations		847
Total current assets	257,638	266,435
Restricted cash, net of current portion	971	6,426
Accounts receivable, net of current portion	32,398
Property and equipment, net	11,381	7,652
Operating lease right-of-use assets	19,793
Convertible note hedges	11,357	41,020
Goodwill	785	785
Other assets	20	89
Non-current assets of discontinued operations		9,643
Total assets	334,343	332,050
Current liabilities:
Accounts payable	4,505	14,891
Related party accounts payable, net	1,593
Accrued research and development costs	4,956	2,963
Accrued expenses and other current liabilities	30,529	38,001
Capital lease obligations		73
Current portion of deferred rent		252
Current portion of 2026 Notes		47,554
Current portion of operating lease liabilities	9,934
Current portion of contingent consideration		51
Current liabilities of discontinued operations		15,739
Deferred revenue	1,278
Total current liabilities	52,795	119,524
Capital lease obligations, net of current portion		158
Deferred rent, net of current portion		6,308
Note hedge warrants	8,768	33,763
Convertible senior notes	402,675	265,601
Operating lease liabilities, net of current portion	22,660
Operating lease liabilities, net of current portion	22,660
2026 Notes, net of current portion		100,537
Other liabilities	492	2,530
Commitments and contingencies
Stockholders' deficit:
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding
Class A common stock, $0.001 par value, 500,000,000 shares authorized and 156,808,126 issued and outstanding at September 30, 2019 and 500,000,000 shares authorized and 154,414,691 shares issued and outstanding at December 31, 2018	157	154
Additional paid-in capital	1,466,886	1,394,603
Accumulated deficit	(1,620,090)	(1,591,128)
Total stockholders' deficit	(153,047)	(196,371)
Total liabilities and stockholders' deficit	$ 334,343	$ 332,050

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Collaboration, License, Co-Promotion and Other Commercial Agreements - Summary (Details) - USD ($) $ in Thousands	3 Months Ended			9 Months Ended
	Sep. 30, 2019	Dec. 31, 2018	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Revenue	$ 131,167		$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Revenues:
Revenue	130,524		54,194	273,998	188,487
Collaborative arrangement, co-promotion agreements
Revenues:
Revenue				2,600
Collaborative arrangement, other agreements
Revenues:
Revenue	346		465	1,616	1,273
Sale of active pharmaceutical ingredient
Revenues:
Revenue	643		10,257	28,114	24,494
Allergan | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue	1,363	$ 1,300	750	2,602	2,250
Allergan | Sale of active pharmaceutical ingredient
Revenues:
Revenue			756		756
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue	85,107		52,724	225,390	184,133
Allergan | North America | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	85,107		52,724	225,390	184,133
Allergan | Europe and Other | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	526		255	1,208	831
AstraZeneca | China, Hong Kong, and Macau | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	32,401			32,401
AstraZeneca | China, Hong Kong, and Macau | Sale of active pharmaceutical ingredient
Revenues:
Revenue	643			646
Astellas Pharma Inc. | Japan | Collaborative arrangement, collaboration and license agreements
Revenues:
Revenue	10,059			10,059
Astellas Pharma Inc. | Japan | Sale of active pharmaceutical ingredient
Revenues:
Revenue	0		$ 9,501	27,468	$ 23,738
Alnylam | Collaborative arrangement, co-promotion agreements
Revenues:
Revenue	$ 722			$ 722

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Condensed Consolidated Statements of Stockholders' Deficit - USD ($) $ in Thousands	Class A common stock Common Stock	Class B common stock Common Stock	Additional paid-in capital	Accumulated deficit	Accumulated other comprehensive income (loss)	Total
Balance at Dec. 31, 2017	$ 137	$ 14	$ 1,318,536	$ (1,308,760)	$ (79)	$ 9,848
Balance (in shares) at Dec. 31, 2017	136,465,526	13,983,762
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to share-based awards and employee stock purchase plan	$ 1		6,193			6,194
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	882,448	272,146
Issuance of common stock awards (in shares)	162
Conversion of Class B common stock to Class A common stock (in shares)	258,551	(258,551)
Share-based compensation expense related to share-based awards and employee stock purchase plan			9,062			9,062
Unrealized gains (losses) on available-for-sale securities / short-term investments					(12)	(12)
Net income (loss)				(43,144)		(43,144)
Balance at Mar. 31, 2018	$ 138	$ 14	1,333,791	(1,351,904)	(91)	(18,052)
Balance (in shares) at Mar. 31, 2018	137,606,687	13,997,357
Balance at Dec. 31, 2017	$ 137	$ 14	1,318,536	(1,308,760)	(79)	9,848
Balance (in shares) at Dec. 31, 2017	136,465,526	13,983,762
Increase (Decrease) in Stockholders' Equity
Unrealized gains (losses) on available-for-sale securities / short-term investments						70
Net income (loss)						(266,875)
Balance at Sep. 30, 2018	$ 140	$ 14	1,378,195	(1,575,635)	(9)	(197,295)
Balance (in shares) at Sep. 30, 2018	139,805,308	13,976,855
Balance at Mar. 31, 2018	$ 138	$ 14	1,333,791	(1,351,904)	(91)	(18,052)
Balance (in shares) at Mar. 31, 2018	137,606,687	13,997,357
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to share-based awards and employee stock purchase plan	$ 1		12,865			12,866
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	989,830	129,501
Issuance of common stock awards (in shares)	130,045
Conversion of Class B common stock to Class A common stock (in shares)	134,367	(134,367)
Share-based compensation expense related to share-based awards and employee stock purchase plan			10,568			10,568
Unrealized gains (losses) on available-for-sale securities / short-term investments					47	47
Net income (loss)				(49,380)		(49,380)
Balance at Jun. 30, 2018	$ 139	$ 14	1,357,224	(1,401,284)	(44)	(43,951)
Balance (in shares) at Jun. 30, 2018	138,860,929	13,992,491
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options, employee stock purchase plan and restricted stock units	$ 1		8,319			8,320
Issuance of common stock upon exercise of stock options, employee stock purchase plan and restricted stock units (in shares)	621,420	307,051
Issuance of common stock awards (in shares)	272
Conversion of Class B common stock to Class A common stock (in shares)	322,687	(322,687)
Share-based compensation expense related to share-based awards and employee stock purchase plan			12,652			12,652
Unrealized gains (losses) on available-for-sale securities / short-term investments					35	35
Net income (loss)				(174,351)		(174,351)
Balance at Sep. 30, 2018	$ 140	$ 14	1,378,195	(1,575,635)	$ (9)	(197,295)
Balance (in shares) at Sep. 30, 2018	139,805,308	13,976,855
Balance at Dec. 31, 2018	$ 154		1,394,603	(1,591,128)		(196,371)
Balance (in shares) at Dec. 31, 2018	154,414,691
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to share-based awards and employee stock purchase plan	$ 2		3,486			3,488
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	1,210,858
Share-based compensation expense related to share-based awards and employee stock purchase plan			14,988			14,988
Net income (loss)				(59,284)		(59,284)
Balance at Mar. 31, 2019	$ 156		1,413,077	(1,650,412)		(237,179)
Balance (in shares) at Mar. 31, 2019	155,625,549
Balance at Dec. 31, 2018	$ 154		1,394,603	(1,591,128)		(196,371)
Balance (in shares) at Dec. 31, 2018	154,414,691
Increase (Decrease) in Stockholders' Equity
Net income (loss)						(26,353)
Balance at Sep. 30, 2019	$ 157		1,466,886	(1,620,090)		(153,047)
Balance (in shares) at Sep. 30, 2019	156,808,126
Balance at Mar. 31, 2019	$ 156		1,413,077	(1,650,412)		(237,179)
Balance (in shares) at Mar. 31, 2019	155,625,549
Increase (Decrease) in Stockholders' Equity
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations			1,801			1,801
Issuance of common stock upon exercise of stock options and employee stock purchase plan, net of cancellations (in shares)	621,588
Share-based compensation expense related to share-based awards and employee stock purchase plan			6,337			6,337
Share-based compensation expense related to share-based awards and employee stock purchase plan (in shares)	195,195
Dividend of sGC business				(2,609)		(2,609)
Net income (loss)				12,283		12,283
Balance at Jun. 30, 2019	$ 156		1,421,215	(1,640,738)		(219,367)
Balance (in shares) at Jun. 30, 2019	156,442,332
Increase (Decrease) in Stockholders' Equity
Issuance of common stock related to share-based awards and employee stock purchase plan	$ 1		1,859			1,860
Issuance of common stock related to share-based awards and employee stock purchase plan (in shares)	364,102
Share-based compensation expense related to share-based awards and employee stock purchase plan			5,520			5,520
Share-based compensation expense related to share-based awards and employee stock purchase plan (in shares)	1,692
Equity component of convertible senior notes			92,502			92,502
Equity component of issuance costs for convertible senior notes			(2,092)			(2,092)
Equity component of the partial repurchase of the 2022 Convertible Notes			(26,959)			(26,959)
Purchase of capped calls			(25,159)			(25,159)
Net income (loss)				20,648		20,648
Balance at Sep. 30, 2019	$ 157		$ 1,466,886	$ (1,620,090)		$ (153,047)
Balance (in shares) at Sep. 30, 2019	156,808,126

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Employee Stock Benefit Plans - Share-based Compensation Reflected in the Consolidated Statement of Operations (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Employee Stock Benefit Plans
Share-based compensation expense	$ 5,520	$ 12,168	$ 25,792	$ 30,222
Research and development
Employee Stock Benefit Plans
Share-based compensation expense	1,208	2,974	5,306	8,446
Selling, general and administrative
Employee Stock Benefit Plans
Share-based compensation expense	$ 4,312	7,643	19,832	19,708
Restructuring expenses
Employee Stock Benefit Plans
Share-based compensation expense		$ 1,551	$ 654	$ 2,068

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Fair Value of Financial Instruments - Change in Level 3 - Convertible Note Hedges (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2019 USD ($)
Change in Level 3 Assets
Balance at beginning of period	$ 41,020
Cash settlement (received) paid upon early termination of derivatives	(28,909)
Change in fair value, recorded as a component of gain (loss) on derivatives	(754)
Balance at end of period	$ 11,357

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Fair Value of Financial Instruments - Measured on Recurring Basis (Details) - Recurring basis - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Assets:
Convertible note hedges	$ 11,357	$ 41,020
Total assets measured at fair value	150,364	214,113
Liabilities:
Note hedge warrants	8,768	33,763
Contingent consideration		51
Total liabilities measured at fair value	8,768	33,814
Money market funds
Assets:
Cash and cash equivalents	101,207	142,218
Repurchase agreements
Assets:
Cash and cash equivalents	37,800	30,875
Quoted Prices in Active Markets for Identical Assets (Level 1)
Assets:
Total assets measured at fair value	139,007	173,093
Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds
Assets:
Cash and cash equivalents	101,207	142,218
Quoted Prices in Active Markets for Identical Assets (Level 1) | Repurchase agreements
Assets:
Cash and cash equivalents	37,800	30,875
Significant Unobservable Inputs (Level 3)
Assets:
Convertible note hedges	11,357	41,020
Total assets measured at fair value	11,357	41,020
Liabilities:
Note hedge warrants	8,768	33,763
Contingent consideration		51
Total liabilities measured at fair value	$ 8,768	$ 33,814

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Notes Payable - 2.25% Convertible Senior Notes due 2022, 0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 (Details) - USD ($) $ in Millions	1 Months Ended
	Aug. 31, 2019	Jun. 30, 2015	Sep. 30, 2019	Sep. 29, 2019
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Debt Instruments [Abstract]
Debt issuance costs incurred		$ 11.7
Debt issuance costs allocated to equity components		4.0
Debt issuance costs allocated to liability components		$ 7.7
Debt instrument term		7 years
Effective interest rate on liability components			9.37%	9.34%
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Debt Instruments [Abstract]
Debt issuance costs incurred	$ 9.0
Debt issuance costs allocated to equity components	2.1
Debt issuance costs allocated to liability components	$ 6.9
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Debt Instruments [Abstract]
Debt instrument term	5 years
Effective interest rate on liability components			6.10%
1.50% Convertible Senior Notes due 2026
Debt Instruments [Abstract]
Effective interest rate on liability components			6.50%
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Debt Instruments [Abstract]
Debt instrument term	7 years

XML

Fair Value of Financial Instruments - Nonrecurring Fair Value Measurements - Intangible Assets (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018
Impairment of Intangible Assets (Excluding Goodwill) [Abstract]
Impairment of intangible assets	$ 151,794	$ 151,794

XML

Workforce Reduction - General Information (Details) $ in Thousands					3 Months Ended			9 Months Ended
	Feb. 07, 2019 employee	Aug. 16, 2018 employee	Jun. 27, 2018 item employee	Jan. 30, 2018 employee	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Mar. 31, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)
Restructuring expenses
Restructuring expenses					$ (166)	$ 10,102		$ 3,652	$ 14,010
Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								3,198
Reduction in Field-based Workforce, January 30, 2018
Workforce Reduction
Number of employees eliminated | employee				60
Restructuring expenses
Employee severance, benefits and related costs							$ 2,400
Reduction in Headquarter-based Workforce, June 27, 2018
Workforce Reduction
Number of new business | item			2
Number of employees expected to be eliminated | employee			40
Restructuring expenses
Employee severance, benefits and related costs						2,500			4,000
Reduction in Headquarter-based Workforce, June 27, 2018 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								16
Reduction in Workforce, Termination of Lesinurad License Agreement, August 16, 2018
Workforce Reduction
Number of employees eliminated | employee		100
Number of employees expected to be eliminated | employee		100
Restructuring expenses
Employee severance, benefits and related costs						$ 7,600			$ 7,600
Reduction in Workforce, February 7, 2019
Workforce Reduction
Number of employees expected to be eliminated | employee	35
Restructuring expenses
Employee severance, benefits and related costs					$ (200)			3,700
Reduction in Workforce, February 7, 2019 | Employee severance, benefits and related costs
Restructuring expenses
Restructuring expenses								$ 3,182

XML

Inventory (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of Inventory

Inventory consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Raw Materials	$	1,134	$	—
Work in Progress		707		—
Finished Goods		457
	$	2,298	$	—

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Cyclerion Separation (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Summary of assets and liabilities transferred in separation

		As of April 1, 2019
Assets:
Prepaid expenses and other current assets	$	1,169
Property and equipment, net		10,241
Other assets		21
	$	11,431
Liabilities:
Accrued research and development costs	$	5,673
Accrued expenses and other current liabilities		3,149
	$	8,822
Net Assets Transferred to Cyclerion	$	2,609

Summary of the discontinued operations

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Costs and expenses:
Research and development		—		17,636		21,792		49,410
Selling, general and administrative		—		4,712		15,646		13,860
Restructuring expenses		—		180		—		1,086
Net loss from discontinued operations		—		22,528		37,438		64,356

Assets:
Prepaid expenses and other current assets	$	847
Property and equipment, net		9,618
Other assets		25
	$	10,490
Liabilities:
Accounts payable	$	3,232
Accrued research and development costs		5,256
Accrued expenses and other current liabilities		7,251
	$	15,739

XML

Workforce Reduction (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of charges made to the reduction in field-based workforce

The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the three and nine months ended September 30, 2019 (in thousands):

	Amounts								Amounts
	Accrued at								Accrued at
	December 31, 2018		Charges		Amount Paid		Adjustments		September 30, 2019
Employee severance, benefits and related costs
June 2018 Reduction		696		16		(689)		(23)		—
August 2018 Reduction		1,756		—		(1,708)		(48)		—
February 2019 Reduction		—		3,182		(2,765)		(89)		328
Total	$	2,452	$	3,198	$	(5,162)	$	(160)	$	328
Contract related costs
August 2018 Reduction	$	433	$	—		(287)		(42)	$	104
Total	$	433	$	—	$	(287)	$	(42)	$	104

XML

Nature of Business - Segment Information (Details) - segment	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Segment Information
Number of reportable segments	1	1	1	1

XML

Nature of Business - New Accounting Pronouncements (Details)	Sep. 30, 2019
Accounting Standards Update 2016-02
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Jan. 01, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2016-13
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2017-04
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-07
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Mar. 31, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-09
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	true
Change in Accounting Principle, Accounting Standards Update, Adoption Date	Mar. 31, 2019
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-13
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-15
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false
Accounting Standards Update 2018-17
New Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Change in Accounting Principle, Accounting Standards Update, Early Adoption	false

XML

Leases

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Leases

8. Leases

Effective January 1, 2019, the Company adopted ASC 842 using the optional transition method. The Company’s lease portfolio for the nine months ended September 30, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment.

Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the three and nine months ended September 30, 2019 are as follows (in thousands):

	Three Months Ended		Nine Months Ended
	September 30,		September 30,
	2019		2019
Operating lease cost during period, net(1)	$	6,244		13,924
Variable lease payments		654		1,308
Short-term lease cost		375		1,143
Total lease cost	$	7,273		16,375

(1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the nine months ended September 30, 2019. Sublease income relates to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019.

Supplemental cash flow information related to leases for the periods reported is as follows:

	Nine Months Ended
	September 30,
	2019
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands)	$	88,299
Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands)		(40,427)
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands)		(34,440)
Right-of-use assets obtained in exchange for new operating lease liabilities(1) (in thousands)		18,452
Cash paid for amounts included in the measurement of lease liabilities (in thousands)		8,869
Weighted-average remaining lease term of operating leases (in years)		8.0
Weighted-average discount rate of operating leases		5.4	%

(1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease.

Future minimum lease payments under non-cancelable operating leases under ASC 842 as of September 30, 2019 are as follows (in thousands):

	Operating
	Lease
	Payments
2019(1)	$	9,729
2020		1,146
2021		3,128
2022		3,129
2023		3,065
2024 and thereafter		21,170
Total future minimum lease payments		41,367
Less: present value adjustment		8,773
Operating lease liabilities at September 30, 2019		32,594
Less: current portion of operating lease liabilities		9,934
Operating lease liabilities, net of current portion	$	22,660

(1) Amounts are for the three months ending December 31, 2019.

At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands):

	Operating
	Lease
	Payments
2019	$	18,736
2020		18,312
2021		18,863
2022		19,365
2023		19,818
2024 and thereafter		22,118
Total future minimum lease payments	$	117,212

Summer Street Lease (current headquarters)

On June 11, 2019, the Company entered into the Summer Street Lease, a non-cancelable operating lease with MA-100 Summer Street Owner, L.L.C. (the “Summer Street Landlord”) for the Summer Street Property. The Summer Street Property began serving as the Company’s headquarters beginning in October 2019, replacing its prior headquarters at 301 Binney Street in Cambridge, Massachusetts. The Summer Street Lease terminates on June 11, 2030 and includes an option to extend the term of the lease for an additional five years at a market base rental rate, a 2% annual rent escalation, free rent periods, and a tenant improvement allowance. The rent expense for the Summer Street Property, inclusive of the escalating rent payments and lease incentives, is recognized on a straight-line basis over the lease term. Additionally, the Summer Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $1.0 million, which is collateralized by a money market account recorded as restricted cash on the Company’s condensed consolidated balance sheets as of September 30, 2019.

At lease inception, the Company recorded a right-of-use asset and a lease liability associated with the Summer Street Lease using an incremental borrowing rate of approximately 5.8%. At September 30, 2019, the balance of the right-of-use asset for the Summer Street Lease was approximately $18.0 million. At September 30, 2019, the balance of the lease liability for the Summer Street Lease was approximately $22.5 million.

The Company recorded an asset retirement obligation in connection with the estimated future costs related to the removal of certain leasehold improvements at the Summer Street Property upon termination of the lease. The balance of the Company’s asset retirement obligation for the Summer Street Lease was approximately $0.5 million as of September 30, 2019.

Lease cost related to the Summer Street Lease recorded during the three and nine months ended September 30, 2019 was approximately $0.6 million and $0.8 million, respectively.

Binney Street Lease (prior headquarters)

The Company rented office space at 301 Binney Street, Cambridge, Massachusetts (“Binney Street Property”) under a non-cancelable operating lease, entered into in January 2007, as amended (“Binney Street Lease”) through October 2019. The Binney Street Property previously served as the Company’s headquarters but was replaced by the Summer Street Property in October 2019, as discussed above.

Prior to the modifications discussed below, the term of the Binney Street Lease was through January 31, 2025 for approximately 223,000 square feet of laboratory and office space. The Binney Street Lease included an option to extend the term of the lease for an additional five years at a market base rental rate, a 3% annual rent escalation, free rent periods, a tenant improvement allowance, and an option to extend the term of the lease for an additional five years at a market base rental rate. The rent expense for the Binney Street Lease, inclusive of the escalating rent payments, lease incentives and free rent periods, was to be recognized on a straight-line basis over the lease term through January 2025. Additionally, the Binney Street Lease required a letter of credit to secure the Company’s obligations under the lease agreement of approximately $6.4 million, which is recorded as restricted cash.

As of January 1, 2019, in conjunction with the adoption of ASC 842, the Company recorded a right-of-use asset of approximately $87.7 million and a lease liability of approximately $94.3 million associated with the Binney Street Lease.

On April 1, 2019, the Company modified its lease with BMR-Rogers Street LLC (“Binney Street Landlord”), to reduce its leased premises to approximately 108,000 rentable square feet of office space on the first and third floors. The surrendered portion of approximately 114,000 rentable square feet on the first and second floor of the building is now occupied by Cyclerion under a direct lease between Cyclerion and the Binney Street Landlord. As a result of the modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 5.1% in accordance with ASC 842, and recognized a gain of approximately $3.2 million, recorded as operating expenses on its condensed consolidated statement of operations. The Company elected to determine the proportionate reduction in the right-of-use asset based on the reduction to the lease liability and will apply that methodology consistently to all comparable modifications that decrease the scope of the lease.

On June 11, 2019, the Company entered into a lease termination agreement (the “Lease Termination”) with the Binney Street Landlord to terminate the Company’s existing lease for approximately 108,000 square feet of office space. The Lease Termination was effective during the fourth quarter of 2019 in exchange for an approximately $9.0 million payment to the Binney Street Landlord. The Company determined that the Lease Termination would be accounted for as a lease modification that reduces the term of the existing lease. As a result of this modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 4.0%.

At September 30, 2019, the balances of the right-of-use asset and lease liability for the Binney Street Lease were approximately $1.8 million and approximately $9.7 million, respectively.

Lease cost related to the Binney Street Lease recorded during the three months ended September 30, 2019 was approximately $6.2 million. Lease cost related to the Binney Street Lease recorded during the nine months ended September 30, 2019 was approximately $14.3 million, net of sublease income of approximately $0.3 million. Under ASC 840, rent expense related to the Binney Street Lease recorded during the three and nine months ended September 30, 2018 was approximately $2.5 million and $7.6 million, respectively.

Data center colocation lease

The Company rents space for its data center at a colocation in Boston, Massachusetts under a non-cancelable operating lease (the “Data Center Lease”). The Data Center Lease contains various provisions, including a 4% annual rent escalation. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term through August 2022. The Company recorded a right-of-use asset of approximately $0.6 million, and a lease liability of approximately $0.6 million associated with the Data Center Lease upon adoption of ASC 842. During the

three months ended March 31, 2019, the Company migrated its data management process to a cloud-based services system, rendering its current data center technology and assets obsolete. As a result, the Company considered the right-of-use asset associated with the Data Center Lease to be impaired. The Company recorded a charge of approximately $0.5 million to selling, general, and administrative expenses on its condensed consolidated statement of operations as a result of the impairment during the three months ended March 31, 2019.

At September 30, 2019, the lease liability associated with the Data Center Lease was approximately $0.5 million, and the right-of-use asset remained fully impaired. The incremental borrowing rate for the outstanding Data Center Lease obligation upon adoption of ASC 842 was approximately 6.0%.

Under ASC 842, the lease costs related to the Data Center Lease were insignificant for each of the three and nine months ended September 30, 2019. Under ASC 840, rent expenses related to the Data Center Lease were insignificant for each of the three and nine months ended September 30, 2018.

Vehicle fleet leases

During April 2018, the Company entered into a master services agreement containing 12-month leases (the “2018 Vehicle Leases”) for certain vehicles within its fleet for its field-based sales force and medical science liaisons. These leases are classified as short-term in accordance with the practical expedient in ASC 842. The 2018 Vehicle Leases expire at varying times beginning in June 2019, with a monthly renewal provision. In accordance with the terms of the 2018 Vehicle Leases, the Company maintains a letter of credit securing its obligation under the lease agreements of $1.3 million, which is collateralized by a money market account recorded as restricted cash.

Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million and approximately $1.1 million for the three and nine months ended September 30, 2019, respectively. Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million for each of the three and nine months ended September 30, 2018.

Prior to the adoption of ASC 842, during 2018, the Company had certain ongoing vehicle leases for its field-based sales force and medical science liaisons (the “2015 Vehicle Leases”). These leases were classified as capital leases under ASC 840. The 2015 Vehicle Leases expired at varying times through December 2018. In connection with entering into the 2018 Vehicle Leases, all of the 2015 Vehicle Leases were terminated through December 31, 2018. At December 31, 2018, the Company had no remaining capital lease obligations related to the 2015 Vehicle Leases.

Other leases

Prior to the adoption of ASC 842, the Company entered into leases for certain computer and office equipment that expired in 2018. These leases were classified as capital leases under ASC 840. At December 31, 2018, the Company had approximately $0.2 million in capital lease obligations. At December 31, 2018, the weighted average interest rate on the outstanding capital lease obligations was approximately 3.4%.

XML

Collaboration, License, Co-Promotion and Other Commercial Agreements

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Collaboration, License, Co-Promotion and Other Commercial Agreements

4. Collaboration, License, Co-Promotion and Other Commercial Agreements

For the three and nine months ended September 30, 2019, the Company had linaclotide collaboration agreements with Allergan for North America and AstraZeneca for China, including Hong Kong and Macau, as well as linaclotide license agreements with Astellas for Japan and with Allergan for the Allergan License Territory. The Company also had agreements with Allergan to co-promote VIBERZI in the U.S. and Alnylam to perform disease awareness activities for AHP and, if givosiran is approved by the FDA, future sales detailing activities of a product containing givosiran. The following table provides amounts included in the Company’s condensed consolidated statements of operations as collaborative arrangements revenue and sale of active pharmaceutical ingredient (“API”) attributable to transactions from these arrangements (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
Collaborative Arrangements Revenue	2019		2018		2019		2018
Linaclotide Collaboration Agreements:
Allergan (North America)	$	85,107	$	52,724	$	225,390	$	184,133
Allergan (Europe and other)		526		255		1,208		831
AstraZeneca (China, including Hong Kong and Macau)		32,401		—		32,401		—
Astellas (Japan)		10,059		—		10,059		—
Co-Promotion and Other Agreements:
Allergan (VIBERZI)		1,363		750		2,602		2,250
Alnylam (givosiran)		722		—		722		—
Other		346		465		1,616		1,273
Total collaborative arrangements revenue	$	130,524	$	54,194	$	273,998	$	188,487
Sale of API (1)
Linaclotide License Agreements:
Astellas (Japan)	$	—	$	9,501	$	27,468	$	23,738
AstraZeneca (China, including Hong Kong and Macau)		643		—		646		—
Other (1)		—		756		—		756
Total sale of API	$	643	$	10,257	$	28,114	$	24,494

(1) During the three months ended September 30, 2018, the Company recorded approximately $0.8 million in revenue related to the sale of API to Allergan.

Accounts receivable, net and related party accounts receivable, net included approximately $129.0 million related to collaborative arrangements revenue and sale of API as of September 30, 2019, net of approximately $3.8 million related to related party accounts payable.

As of September 30, 2019, there were no impairment indicators for the accounts receivable recorded.

Linaclotide Agreements

Collaboration Agreement for North America with Allergan

In September 2007, the Company entered into a collaboration agreement with Allergan to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in North America. Under the terms of this collaboration agreement, the Company received a non-refundable, upfront licensing fee and shares equally with Allergan all development costs as well as net profits or losses from the development and sale of linaclotide in the U.S. The Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Allergan is solely responsible for the further development, regulatory approval and commercialization of linaclotide in those countries and funding any costs. The collaboration agreement for North America also includes contingent milestone payments, as well as a contingent equity investment, based on the achievement of specific development and commercial milestones. At September 30, 2019, $205.0 million in license fees and all six development milestone payments had been received by the Company, as well as a $25.0 million equity investment in the Company’s capital stock (Note 11). The Company can also achieve up to $100.0 million in a sales-related milestone if certain conditions are met, which will be recognized as

collaborative arrangements revenue when it is probable that a significant reversal of revenue would not occur and the associated constraints have been lifted.

As a result of the research and development cost-sharing provisions of the linaclotide collaboration for North America, the Company offset approximately $0.9 million and approximately $6.5 million in incremental research and development costs during the three and nine months ended September 30, 2019, respectively, and offset approximately $2.5 million and approximately $5.8 million in incremental research and development costs during the three and nine months ended September 30, 2018, respectively, to reflect the obligations of each party under the collaboration to bear half of the development costs incurred.

The Company and Allergan began commercializing LINZESS in the U.S. in December 2012. The Company receives 50% of the net profits and bears 50% of the net losses from the commercial sale of LINZESS in the U.S. Net profits or net losses consist of net sales of LINZESS to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. LINZESS net sales are calculated and recorded by Allergan and may include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions. If either party provided fewer calls on physicians in a particular year than it was contractually required to provide, such party’s share of the net profits would be adjusted as set forth in the collaboration agreement for North America. The Company has completed its obligations under the terms of the commercial agreement with Allergan, pursuant to which it promoted CANASA, and these adjustments to the share of the net profits have been eliminated, in full, in 2018 and all subsequent years.

The Company evaluated this collaboration arrangement under ASC 606, Revenue from Contracts with Customers (“ASC 606”) and concluded that all development-period performance obligations had been satisfied as of September 2012. However, the Company has determined that there are three remaining commercial-period performance obligations, which include the sales detailing of LINZESS, participation in the joint commercialization committee, and approved additional trials. The consideration remaining includes cost reimbursements in the U.S., as well as commercial sales-based milestones and net profit and loss sharing payments based on net sales in the U.S. Additionally, the Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Royalties, commercial sales-based milestones, and net profit and loss sharing payments will be recorded as collaborative arrangements revenue or expense in the period earned, in accordance with the sales-based royalty exception, as these payments relate predominately to the license granted to Allergan. The Company records royalty revenue in the period earned based on royalty reports from its partner, if available, or based on the projected sales and historical trends. The cost reimbursements received from Allergan during the commercialization period will be recognized as billed in accordance with the right-to-invoice exemption, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period.

Under the Company’s collaboration agreement with Allergan for North America, LINZESS net sales are calculated and recorded by Allergan and include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions, as noted above. These amounts include the use of estimates and judgments, which could be adjusted based on actual results in the future. The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis less commercial expenses and presents the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. This treatment is in accordance with the Company’s revenue recognition policy, given that the Company is not the primary obligor and does not have the inventory risks in the collaboration agreement with Allergan for North America. The Company relies on Allergan to provide accurate and complete information related to net sales of LINZESS in accordance with U.S. generally accepted accounting principles in order to calculate its settlement payments to and from Allergan and record collaboration expense or collaborative arrangements revenue, as applicable. 

From time to time, in accordance with the terms of the collaboration with Allergan for North America, the Company engages an independent certified public accounting firm to review the accuracy of the financial reporting from Allergan to the Company. In connection with such a review during the three months ended September 30, 2018, Allergan reported to the Company an approximately $59.3 million negative adjustment to LINZESS net sales. Such adjustment related to the cumulative difference between certain previously estimated LINZESS gross-to-net sales reserves and allowances made by Allergan during the years ended December 31, 2015, 2016 and 2017, and subsequent actual payments made. This adjustment was primarily associated with estimated governmental and contractual rebates, as reported by Allergan. Accordingly, upon receiving this information from Allergan, the Company recorded a change in

accounting estimate to reduce collaborative arrangements revenue by approximately $29.7 million during the three months ended September 30, 2018 related to the Company’s share of this adjustment.

The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the three and nine months ended September 30, 2019 and 2018 as follows (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.	$	84,565	$	52,261	$	223,831	$	182,675
Royalty revenue		542		463		1,559		1,458
Total collaborative arrangements revenue	$	85,107	$	52,724	$	225,390	$	184,133

The collaborative arrangements revenue recognized in the three and nine months ended September 30, 2019 and 2018 primarily represents the Company’s share of the net profits and net losses on the sale of LINZESS in the U.S.

The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.(1)(2)	$	84,565	$	52,261	$	223,831	$	182,675
Selling, general and administrative costs incurred by the Company(1)		(9,129)		(10,915)		(29,764)		(33,556)
The Company’s share of net profit	$	75,436	$	41,346	$	194,067	$	149,119

(1) Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and nine months ended September 30, 2019 and 2018.

In May 2014, CONSTELLA became commercially available in Canada and in June 2014, LINZESS became commercially available in Mexico. The Company records royalties on sales of CONSTELLA in Canada and LINZESS in Mexico in the period earned. The Company recognized approximately $0.5 million and approximately $1.6 million of combined royalty revenues from Canada and Mexico during the three and nine months ended September 30, 2019, respectively. The Company recognized approximately $0.5 million and approximately $1.5 million of combined royalty revenues from Canada and Mexico during the three and nine months ended September 30, 2018, respectively.

License Agreement with Allergan (All countries other than the countries and territories of North America, China, including Hong Kong and Macau, and Japan)

In April 2009, the Company entered into a license agreement with Almirall, S.A. (“Almirall”) to develop and commercialize linaclotide in Europe (including the Commonwealth of Independent States and Turkey) for the treatment of IBS-C, CIC and other GI conditions (the “European License Agreement”). In accordance with the European License Agreement, the Company granted Almirall a right to access its U.S. Phase III clinical trial data for the purposes of supporting European regulatory approval. Additionally, the Company was required to participate on a joint development committee during linaclotide’s development period and is required to participate in a joint commercialization committee while linaclotide is commercially available. In October 2015, Almirall transferred its exclusive license to develop and commercialize linaclotide in Europe to Allergan.

Additionally, in October 2015, the Company and Allergan separately entered into an amendment to the European License Agreement relating to the development and commercialization of linaclotide in Europe. Pursuant to the terms of the amendment, (i) certain sales-based milestones payable to the Company under the European License Agreement were modified to increase the total milestone payments such that, when aggregated with certain commercial launch milestones, they could total up to $42.5 million, (ii) the royalties payable to the Company during the term of the European License Agreement were modified such that the royalties based on sales volume in Europe begin in the mid-single digit percent and escalate to the upper-teens percent by calendar year 2019, and (iii) Allergan assumed

responsibility for the manufacturing of linaclotide API for Europe from the Company, as well as the associated costs. The Company concluded that the 2015 amendment to the European License Agreement was not a modification to the linaclotide collaboration agreement with Allergan for North America.

In January 2017, concurrently with entering into the commercial agreement as described below in Commercial Agreement with Allergan, the Company and Allergan entered into an amendment to the European License Agreement (the “2017 Amendment”). The European License Agreement, as amended (the “Allergan License Agreement”), extended the license to develop and commercialize linaclotide in all countries other than China, including Hong Kong and Macau, Japan, and the countries and territories of North America. On a country-by-country and product-by-product basis in such additional territory, Allergan is obligated to pay the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient in the upper-single digits for five years following the first commercial sale of a linaclotide product in a country, and in the low-double digits thereafter. The royalty rate for products in the expanded territory will decrease, on a country-by-country basis, to the lower-single digits, or cease entirely, following the occurrence of certain events. Allergan also is obligated to assume certain purchase commitments for quantities of linaclotide API under the Company’s agreements with third-party API suppliers. The amendment to the European License Agreement did not modify any of the milestones or royalty terms related to Europe.

Prior to the adoption of ASC 606, the Company concluded that the 2017 Amendment was a material modification to the European License Agreement; however, this modification did not have a material impact on the Company's condensed consolidated financial statements as there was no deferred revenue associated with the European License Agreement. The Company also concluded that the 2017 Amendment was not a material modification to the linaclotide collaboration agreement with Allergan for North America.

In evaluating the terms of the 2009 European License Agreement under ASC 606, the Company determined that there are no remaining performance obligations as of September 2012. However, the Company continues to be eligible to receive consideration in the form of commercial launch milestones, sales-based milestones, and royalties.

The commercial launch milestones, sales-based milestones and royalties under the European License Agreement have historically been recognized as revenue as earned. Under ASC 606, the Company applied the sales-based royalty exception to royalties and sales-based milestones, as these payments relate predominantly to the license granted to Allergan (formerly Almirall). Accordingly, the royalties and sales-based milestones are recorded as revenue in the period earned. The Company records royalties on sales of CONSTELLA in Europe in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends. The commercial launch milestones are recognized as revenue when it is probable that a significant reversal of revenue would not occur and the associated constraint has been lifted.

Additionally, the Company evaluated the terms of the 2017 Amendment under ASC 606 and determined that it would be treated as a separate contract given that it adds a distinct good or service at an amount that reflects standalone selling price. The Company determined that all performance obligations in the 2017 Amendment were satisfied in January 2017 when the license for the additional territory was transferred. The Company continues to receive royalties under this agreement, which are recorded in the period earned pursuant to the sales-based royalty exception, as they related predominantly to the license granted to Allergan.

The Company recognized approximately $0.5 million and approximately $1.2 million of royalty revenue from the European License Agreement during the three and nine months ended September 30, 2019, respectively, and recognized approximately $0.2 million and approximately $0.8 million during the three and nine months ended September 30, 2018, respectively.

License Agreement for Japan with Astellas

In November 2009, the Company entered into a license agreement with Astellas, as amended, to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in Japan (the “2009 License Agreement with Astellas”). Astellas is responsible for all activities relating to development, regulatory approval and commercialization in Japan as well as funding the associated costs and the Company is required to participate on a joint development committee over linaclotide’s development period. During the year ended December 31, 2017, the Company and Astellas entered into a commercial API supply agreement (the “Astellas Commercial Supply Agreement”). Pursuant to the Astellas Commercial Supply Agreement, the Company sells linaclotide API supply to Astellas at a contractually defined rate and recognizes related revenue as sale of API. Under the 2009 License Agreement with Astellas, the Company received royalties which escalated based on sales volume, beginning in the low-twenties percent, less the transfer price paid for the API included in the product sold and other contractual deductions.

Under the 2009 License Agreement with Astellas, the Company received an up-front licensing fee of $30.0 million and three development milestone payments that totaled up to $45.0 million, which were recognized as revenue prior to the adoption of ASC 606 on January 1, 2018.

The Company had evaluated the terms of the 2009 License Agreement with Astellas under ASC 606 and determined that there were no remaining performance obligations as of the adoption of ASC 606.

Additionally, under the terms of the Astellas Commercial Supply Agreement, the Company determined it had an ongoing performance obligation to supply API. Upon adoption of ASC 606, product revenue is recognized when the customer obtains control of the Company’s product, which occurs at a point in time, typically upon shipment of the product to the customer. This results in earlier revenue recognition than the Company’s historical accounting.

On August 1, 2019, the Company and Astellas amended and restated the 2009 License Agreement with Astellas (the “Amended Astellas License Agreement”). This amendment is considered a modification to the 2009 License Agreement with Astellas and is accounted for as a new and separate contract. Under the terms of this Amended Astellas License Agreement, the Company will no longer be responsible for the supply of linaclotide API to Astellas, and Astellas will be responsible for its own supply of linaclotide API for sale in Japan, beginning in 2020. Astellas has committed to purchase certain quantities of linaclotide API from the Company in 2019.

In connection with the execution of the Amended Astellas License Agreement, Astellas paid the Company a non-refundable upfront payment of $10.0 million in August 2019. Further, beginning in 2020, Astellas will, in lieu of the royalty payment terms set forth in the 2009 License Agreement with Astellas, pay royalties to the Company at rates beginning in the mid-single digit percent and escalating to low-double-digit percent, based on aggregate annual net sales in Japan of products containing linaclotide API. These royalty payments will be subject to reduction following the expiration of certain licensed patents and the occurrence of generic competition in Japan. The Company will continue to supply linaclotide API for Japan during 2019 at a contractually defined rate. Additionally, Astellas will reimburse the Company for the Company’s performance of adverse event reporting services at a fixed monthly rate until such services are terminated.

The Company identified the following performance obligations under the Amended Astellas License Agreement:

● delivery of the expanded license of intellectual property, including the applicable manufacturing know-how,

● obligation to supply linaclotide API for 2019, and

● adverse event reporting services.

The Company allocated the $10.0 million upfront payment to the delivery of the expanded license of intellectual property and recognized it as collaborative arrangements revenue at contract inception. The Company allocated the approximately $20.4 million in remaining purchase orders for API to the obligation to supply linaclotide API to Astellas for 2019. Consideration for the supply of linaclotide API will be recognized over the performance period using an output method as linaclotide API is shipped to Astellas. Consideration allocated to the adverse event reporting services will be recognized as such services are provided over the performance period using an output method based on the amount to which the Company has a right to invoice.

Royalties on sales of LINZESS in Japan relate predominantly to the license granted to Astellas. Accordingly, the Company applies the sales-based royalty exception and records royalties on sales of LINZESS in Japan in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends.

The Company recognized $10.0 million in collaborative arrangements revenue during the three and nine months ended September 30, 2019 related to the upfront fee associated with the execution of the Amended Astellas License Agreement. The Company recognized no revenue and approximately $27.5 million from the sale of API to Astellas under the Amended License Agreement, the 2009 License Agreement with Astellas and the Astellas Commercial Supply Agreement during the three and nine months ended September 30, 2019, respectively, and recognized approximately $9.5 million and approximately $23.7 million during the three and nine months ended September 30, 2018, respectively. The royalties on sales of LINZESS in Japan did not exceed the transfer price of API sold and other contractual deductions during each of the periods presented. The Company recognized an insignificant amount of collaborative arrangements revenue related to adverse event reporting services in each of the three and nine months ended September 30, 2019.

Collaboration Agreement for China (including Hong Kong and Macau) with AstraZeneca

In October 2012, the Company entered into a collaboration agreement with AstraZeneca to co-develop and co-commercialize linaclotide in the AstraZeneca License Territory (the “AstraZeneca Collaboration Agreement”). The collaboration provided AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the AstraZeneca License Territory. The parties shared responsibility for continued development and commercialization of linaclotide under a joint development plan and a joint commercialization plan, respectively, with AstraZeneca having primary responsibility for the local operational execution. In September 2019, the Company and AstraZeneca entered into an amendment and restatement of the AstraZeneca Collaboration Agreement (the “Amended AstraZeneca Agreement”), under which AstraZeneca obtained the exclusive right to develop, manufacture and commercialize products containing linaclotide in the AstraZeneca License Territory (the “AstraZeneca License”).

Prior to the execution of the Amended AstraZeneca Agreement, the Company identified the following performance obligations under the AstraZeneca Collaboration Agreement:
​

● research, development and regulatory services pursuant to the development plan (“R&D Services”),

● Joint Development Committee (“JDC”) services,

● obligation to supply clinical trial material, and

● Joint Commercialization Committee (“JCC”) services.

Under the AstraZeneca Collaboration Agreement, the Company shared development costs with AstraZeneca, with AstraZeneca incurring 55% of the net losses from the development and commercialization of linaclotide in the AstraZeneca License Territory. Payments from AstraZeneca with respect to both research and development and selling, general and administrative costs incurred by the Company prior to the commercialization of linaclotide in the AstraZeneca License Territory were recorded as a reduction in expense, in accordance with the Company’s policy. Development costs incurred by the Company that pertained to the joint development plan and subsequent amendments to the joint development plan, as approved by the JDC, were recorded as research and development expense as incurred. Payments to AstraZeneca were recorded as incremental research and development expense.

During the three and nine months ended September 30, 2019, the Company incurred no costs and offset an insignificant amount of costs related to R&D Services and JDC Services, respectively, under the AstraZeneca Collaboration Agreement. During the three and nine months ended September 30, 2018, the Company offset an insignificant amount of costs and approximately $0.8 million, respectively, related to R&D Services and JDC Services. During the three and nine months ended September 30, 2019, the Company recognized an insignificant amount of revenue related to sale of linaclotide drug product and API under the AstraZeneca Collaboration Agreement. The Company recorded no revenue related to sale of linaclotide drug product and API during each of the three and nine months ended September 30, 2018. Additionally, the Company incurred approximately $0.7 million and approximately $1.2 million in costs related to pre-launch commercial services and supply chain services during the three and nine months ended September 30, 2019, respectively.

Under the Amended AstraZeneca Agreement, the Company will receive non-contingent payments totaling $35.0 million in three installments through 2024. In addition, AstraZeneca may be required to make milestone payments totaling up to $90.0 million contingent on the achievement of certain sales targets and will be required to pay tiered royalties to the Company at rates beginning in the mid-single-digit percent and increasing up to twenty percent based on the aggregate annual net sales of products containing linaclotide in the AstraZeneca License Territory. In connection with the Amended AstraZeneca Agreement, the Company and AstraZeneca entered into a transition services agreement (“AstraZeneca TSA”) and an amended commercial supply agreement (“AstraZeneca CSA”). Under the terms of the AstraZeneca TSA, the Company will provide certain regulatory and administrative services for a term of approximately two years from the date of execution, unless earlier terminated or extended according to the terms of the transition services agreement. Services performed are paid at a mutually agreed upon rate. Amounts for AstraZeneca TSA services are recorded as collaborative arrangements revenue. Under the terms of the AstraZeneca CSA, the Company will supply linaclotide API, drug product and finished goods for the Licensed Territory through no later than March 31, 2020 at predetermined rates.

The Company evaluated the Amended AstraZeneca Agreement in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the Amended AstraZeneca Agreement were identified:

● delivery of the AstraZeneca License,

● AstraZeneca TSA services, and

● supply of linaclotide API, drug product and finished goods under the AstraZeneca CSA.

The Company determined that the non-contingent payments should be allocated to the delivery of the AstraZeneca License. The non-contingent payments totaling $35.0 million will be paid in installments through 2024. The Company determined that the performance obligation related to the transfer of the AstraZeneca License was satisfied as of the execution date of the Amended AstraZeneca Agreement. As a portion of the payments relating to the transfer of the AstraZeneca License are due significantly after the performance obligation was satisfied, the Company adjusted its transaction price for the significant financing component of approximately $2.6 million. Accordingly, the Company recognized approximately $32.4 million relating to the delivery of the AstraZeneca license as collaborative arrangements revenue during the three months ended September 30, 2019 and will recognize the approximately $2.6 million relating to the significant financing component as interest income through 2024. Consideration allocated to the AstraZeneca TSA services will be recognized as collaborative arrangements revenue as such services are provided over the performance period using an output method based on the amount to which the Company has a right to invoice. Consideration for the supply of linaclotide API, drug product and finished goods under the AstraZeneca CSA will be recognized over the performance period using an output method as linaclotide API, drug product and finished goods are shipped to AstraZeneca.

During each of the three and nine months ended September 30, 2019, the Company recognized approximately $32.4 million in collaborative arrangements revenue related to the Amended AstraZeneca License, of which approximately $32.4 million related to the delivery of the AstraZeneca License and an insignificant amount related to the AstraZeneca TSA services. During each of the three and nine months ended September 30, 2019, the Company recognized approximately $0.6 million of sale of API on its condensed consolidated statement of operations, relating to the supply of linaclotide drug product and finished goods under the AstraZeneca CSA.

Co-Promotion and Other Agreements

Co-Promotion Agreements with Allergan

In January 2017, concurrently with entering into the amendment to the European License Agreement, the Company and Allergan entered into an agreement under which the adjustments to the Company’s or Allergan’s share of the net profits under the share adjustment provision of the collaboration agreement for linaclotide in North America relating to the contractually required calls on physicians in each year were eliminated, in full, in 2018 and all subsequent years (the “Commercial Agreement”). Pursuant to the Commercial Agreement, Allergan appointed the Company, on a non-exclusive basis, to promote CANASA, approved for the treatment of ulcerative proctitis in the U.S. for approximately two years through February 2019. Under the terms of the Commercial Agreement, the Company was obligated to perform third position sales details and offer samples of such products to gastroenterology prescribers who were on the then-current call panel for LINZESS to which the Company was providing first or second position details.

On a product-by-product basis, Allergan paid the Company a royalty in the mid-teens on incremental sales of CANASA above a mutually agreed upon sales baseline. The Company discontinued its promotion of CANASA on December 31, 2018.

Upon adoption of ASC 606, the Company evaluated the commercial agreement and the amendment to the European License Agreement under the contract combination and contract modification guidance in ASC 606. The Company determined that the agreements should be accounted for as separate contracts because each agreement adds distinct goods or services at an amount that reflects standalone selling price. The Company concluded that the CANASA sales detailing deliverable under ASC 605 was also considered a performance obligation in accordance with ASC 606. Accordingly, the Company recorded royalties on sales of CANASA and any estimated detailing shortfall penalty over the period of performance for the sales details; collaborative arrangements revenue was recognized when it was probable that a significant reversal of revenue would not occur and the associated constraint has been lifted. The Company estimated sales detailing royalties based on royalty reports from its partner, if available, or the projected sales and historical trends. At the inception of the arrangement, the consideration associated with the agreement comprised of royalties and a sales detailing shortfall penalty are fully constrained. During each of the three and nine months ended September 30, 2018, the Company did not recognize royalty revenue related to the Commercial Agreement with Allergan for sales of CANASA.

In December 2017, the Company and Allergan entered into an amendment to the commercial agreement with Allergan (the “VIBERZI Amendment”), as described below, to include the VIBERZI promotional activities through December 31, 2018. Under the terms of the VIBERZI Amendment, the Company’s clinical sales specialists detailed VIBERZI in the second position to the same health care practitioners to whom they detailed LINZESS in the first position and provided certain medical education services. The Company had the potential to achieve a milestone payment of up to $7.5 million based on the net sales of VIBERZI during 2018 and was compensated approximately $3.0 million over the term of the agreement for its medical education initiatives. The Company evaluated the VIBERZI Amendment in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the VIBERZI Amendment were identified:

● sales detailing of VIBERZI in either first or second position, and

● medical education services.

The sales-based milestone payment was recognized as collaborative arrangements revenue when it was probable that a significant reversal of revenue would not occur and the associated constraint had been lifted. During the three months ended December 31, 2018, the Company determined the sales-based milestone payment was no longer constrained and recognized approximately $1.3 million in collaborative arrangements revenue. The consideration related to medical education events of approximately $3.0 million was recognized over the period of performance that medical education services are provided. During the three and nine months ended September 30, 2018, the Company recognized approximately $0.8 million and approximately $2.3 million of collaborative arrangements revenue, respectively, related to VIBERZI medical education services. In December 2018 and in March 2019, the Company extended the VIBERZI Amendment through April 2019.

In April 2019, the Company entered into a new agreement with Allergan to perform sales detailing activities for VIBERZI, effective April 1, 2019 through December 31, 2019 (the “VIBERZI Promotion Agreement”). Under the terms of the VIBERZI Promotion Agreement, the Company’s clinical sales specialists will continue detailing VIBERZI in the second position to the same health care practitioners to whom they detail LINZESS in the first position. The Company has the potential to achieve a milestone payment of up to approximately $4.2 million based on the number of VIBERZI prescription extended units filled over the term of the agreement. The Company will be compensated based on the number of VIBERZI sales details performed, up to a maximum amount of approximately $4.1 million over the term of the agreement. In accordance with ASC 606, the VIBERZI Promotion Agreement will be accounted for as a separate contract as it contains distinct services at an amount that reflects standalone selling price, incremental to past agreements. The Company identified the performance of VIBERZI second position sales details as the sole performance obligation under the agreement.

The milestone payment will be recognized as collaborative arrangements revenue when it is probable that a significant reversal of revenue will not occur and the associated constraint has been lifted. As of September 30, 2019, the Company determined the milestone payment was fully constrained. The compensation related to the VIBERZI sales

details is recognized over the term of the agreement using an output method based on estimated amounts for which the Company has the right to invoice based on the number of sales details performed during the associated period. During each of the three and nine months ended September 30, 2019, the Company recognized approximately $1.4 million and approximately $2.6 million of collaborative arrangements revenue related to VIBERZI sales details, respectively.

Disease Education and Promotional Agreement with Alnylam

On August 9, 2019, the Company and Alnylam entered into a disease education and promotional agreement for Alnylam’s investigational RNAi therapeutic givosiran for the potential treatment of AHP (the “Alnylam Agreement”). As of September 30, 2019, givosiran was not yet approved by the FDA. Under the terms of the agreement, the Company’s sales force will perform disease awareness activities and, if givosiran is approved by the FDA, future sales detailing activities of a product containing givosiran to gastroenterologists and health care practitioners to whom they detail LINZESS in the first position.

The Company is entitled to receive service fees, payable by Alnylam quarterly, totaling up to $9.5 million over the term of the agreement, which is approximately three years. The Company also is eligible to receive a royalty based on a percentage of net sales of an FDA-approved product containing givosiran that are directly attributable to the Company’s promotional efforts. The Company identified the following performance obligation under the Alnylam Agreement:

● performance of disease education activities for AHP and performance of sales details for an FDA-approved product containing givosiran (together “Givosiran Education and Promotion Activities”).

The Company allocated the service fees to the performance of Givosiran Education and Promotion Activities and recognizes collaborative arrangements revenue over the term of the agreement as the services are performed using an output method based on the amount to which the Company has a right to invoice. Royalties will be recognized as collaborative arrangements revenue using an output method for Givosiran Education and Promotion Activities based on the amount to which the Company has a right to invoice when the associated constraints have been lifted. At contract inception, the royalty revenue is fully constrained because givosiran has not yet been approved by the FDA.

During each of the three and nine months ended September 30, 2019, the Company recognized approximately $0.7 million in collaborative arrangements revenue related to the service fees. As of September 30, 2019, the Company had a deferred revenue balance of approximately $1.3 million related to the Givosiran Education and Promotion Activities performed in accordance with the Alnylam Agreement. The Company did not recognize any royalty revenue related to the Alnylam Agreement as revenue remains fully constrained.

Other Collaboration and License Agreements

The Company has other collaboration and license agreements that are not individually significant to its business. Pursuant to the terms of one agreement, the Company was required to pay $7.5 million for development milestones, all of which had been paid as of September 30, 2019. The Company may also be required to pay up to $18.0 million for regulatory milestones, none of which had been paid as of September 30, 2019. Pursuant to the terms of another license agreement, the Company recognized no revenue and approximately $0.5 million in collaborative arrangements revenue during the three and nine months ended September 30, 2019, respectively, related to a nonrefundable upfront payment. The Company is eligible to receive up to $63.5 million in development and sales-based milestones, as well as a royalty as a percentage of net sales of a product, under the terms of this agreement. The Company recorded no research and development expenses associated with the Company’s other collaboration and license agreements during each of the three and nine months ended September 30, 2019. The Company recorded approximately $5.0 million in research and development expenses associated with the Company’s other collaboration and license agreements during each of the three and nine months ended September 30, 2018.

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Notes Payable - 8.375% Notes due 2026 - General Information (Details) - USD ($) $ in Thousands		1 Months Ended		3 Months Ended	9 Months Ended
	Sep. 23, 2016	Sep. 30, 2019	Aug. 31, 2019	Sep. 30, 2019	Sep. 30, 2019	Sep. 16, 2019	Dec. 31, 2018	Jun. 30, 2015
Notes Payable
Proceeds from partial termination of convertible note hedges and warrants			$ 3,200		$ 3,174
Loss on extinguishment of debt				$ 30,977	30,977
Equity component of convertible senior notes				92,502
Debt issuance costs capitalized		$ 8,339		8,339	8,339
Convertible Senior Notes
Notes Payable
Debt issuance costs capitalized		$ 8,339		$ 8,339	$ 8,339		$ 5,004
8.375% Notes due 2026 | Notes Payable
Notes Payable
Aggregate principal amount of notes issued	$ 150,000
Stated interest rate (as a percent)	8.375%	8.375%		8.375%	8.375%
Debt redeemed/repurchased						$ 116,500
Debt redemption/repurchase price						$ 123,000
Loss on extinguishment of debt	$ 7,600	$ 31,000
Debt issuance costs capitalized	$ 500
Percentage of net sales to determine quarterly payments (as a percent)					7.50%
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued		$ 120,699		$ 120,699	$ 120,699		$ 335,699	$ 335,700
Stated interest rate (as a percent)						2.25%		2.25%
Debt redeemed/repurchased			215,000			$ 215,000
Debt redemption/repurchase price			227,300
Loss on extinguishment of debt			23,400
Equity component of convertible senior notes			$ (27,000)

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Leases - Lease Cost (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Lease cost
Operating lease cost during period	$ 6,244	$ 13,924
Variable lease payments	654	1,308
Short-term lease cost	375	1,143
Total lease cost	$ 7,273	16,375
Sublease income		$ 300

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Leases - Operating Leases - Future Minimum Lease Payments - ASC 840 (Details) $ in Thousands	Dec. 31, 2018 USD ($)
Future minimum lease payments
2019	$ 18,736
2020	18,312
2021	18,863
2022	19,365
2023	19,818
2024 and thereafter	22,118
Total future minimum lease payments	$ 117,212

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Notes Payable - 2.25% Convertible Senior Notes due 2022 - Total Interest Expense (Details) - 2.25% Convertible Senior Notes due 2022 - Convertible Senior Notes - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Interest Expense
Contractual interest expense	$ 1,780	$ 1,889	$ 5,557	$ 5,665
Amortization of debt issuance costs	301	249	856	712
Amortization of debt discount	4,460	3,900	12,699	11,450
Total interest expense	$ 6,541	$ 6,038	$ 19,112	$ 17,827

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Collaboration, License, Co-Promotion and Other Commercial Agreements - Other Collaborations and License Agreements (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Collaboration, License and Co-Promotion Agreements
Research and development	$ 27,551	$ 29,158	$ 88,507	$ 72,821
Collaborative arrangement, co-promotion and other agreements
Collaboration, License and Co-Promotion Agreements
Revenue related to nonrefundable upfront payments	0		500
Collaborative arrangement, co-promotion and other agreements | Development and sales milestones
Collaboration, License and Co-Promotion Agreements
Maximum payment receivable under the milestone	63,500		63,500
Collaborative arrangement, other agreements
Collaboration, License and Co-Promotion Agreements
Research and development	$ 0	$ 5,000	0	$ 5,000
Collaborative arrangement, other agreements | Development milestones
Collaboration, License and Co-Promotion Agreements
Contingent milestone payable			7,500
Collaborative arrangement, other agreements | Regulatory milestones
Collaboration, License and Co-Promotion Agreements
Contingent milestone payable			18,000
Milestone payment made			$ 0

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Collaboration, License, Co-Promotion and Other Commercial Agreements - European and Other Territories (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Oct. 31, 2015	Sep. 30, 2012
Collaboration, License and Co-Promotion Agreements
Revenue	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue	130,524	54,194	$ 273,998	188,487
License | Allergan
Collaboration, License and Co-Promotion Agreements
Royalty percentage, five years following the first commercial sale			upper-single digits
Annual royalty			5 years
Royalty percentage, thereafter			low-double digits
Royalty percentage, expanded territory			lower-single digits
License | Allergan | Europe
Collaboration, License and Co-Promotion Agreements
Remaining milestone payment due upon the amendment to the license agreement					$ 42,500
Revenue remaining performance obligation						$ 0
Royalty | Allergan | Europe
Collaboration, License and Co-Promotion Agreements
Revenue	$ 500	$ 200	$ 1,200	$ 800

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Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Change in Accounting Estimate (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Change in accounting estimate
Revenue	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Change in accounting estimate
Revenue	130,524	54,194	273,998	188,487
Collaborative arrangements revenue | Allergan | North America
Change in accounting estimate
Revenue	85,107	52,724	225,390	184,133
Collaborative arrangements, LINZESS | Allergan | North America
Change in accounting estimate
Revenue	$ 84,565	52,261	$ 223,831	$ 182,675
Sales Returns and Allowances | Allergan
Change in accounting estimate
Revenue		59,300
Sales Returns and Allowances | Collaborative arrangements, LINZESS | Allergan | North America | Collaborative arrangement, collaboration and license agreements
Change in accounting estimate
Revenue		$ 29,700

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Employee Stock Benefit Plans - Share-based Compensation Expense (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Employee Stock Benefit Plans
Share-based compensation expense, other modifications	$ 0.2	$ 2.8

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Fair Value of Financial Instruments - Notes Payable (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 16, 2019	Aug. 31, 2019	Aug. 12, 2019	Dec. 31, 2018	Sep. 23, 2016	Jun. 30, 2015
Notes Payable | 8.375% Notes due 2026
Fair value disclosures
Stated interest rate (as a percent)	8.375%					8.375%
Debt Instrument, Repurchased Face Amount		$ 116,500
Aggregate principal amount of notes issued						$ 150,000
Notes Payable | 8.375% Notes due 2026 | Significant Unobservable Inputs (Level 3)
Fair value disclosures
Estimated fair value					$ 148,200
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022
Fair value disclosures
Stated interest rate (as a percent)		2.25%					2.25%
Debt Instrument, Repurchased Face Amount		$ 215,000	$ 215,000
Aggregate principal amount of notes issued	$ 120,699				335,699		$ 335,700
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	120,000				$ 315,000
Convertible Senior Notes | 0.75% Convertible Senior Notes due 2024
Fair value disclosures
Stated interest rate (as a percent)				0.75%
Aggregate principal amount of notes issued	200,000		200,000	$ 200,000
Convertible Senior Notes | 0.75% Convertible Senior Notes due 2024 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	185,900
Convertible Senior Notes | 1.50% Convertible Senior Notes due 2026
Fair value disclosures
Stated interest rate (as a percent)				1.50%
Aggregate principal amount of notes issued	200,000		$ 200,000	$ 200,000
Convertible Senior Notes | 1.50% Convertible Senior Notes due 2026 | Significant Other Observable Inputs (Level 2)
Fair value disclosures
Estimated fair value	$ 183,600

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Fair Value of Financial Instruments - Assumptions - Convertible Note Hedges (Details)	Sep. 30, 2019 $ / shares Y	Dec. 31, 2018 $ / shares Y
Fair Value of Financial Instruments
Derivative asset, valuation technique	us-gaap:ValuationTechniqueOptionPricingModelMember	us-gaap:ValuationTechniqueOptionPricingModelMember
Measurement Input, Risk Free Interest Rate
Fair Value of Financial Instruments
Derivative asset, measurement input	0.016	0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative asset, measurement input | Y	2.7	3.5
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative asset, measurement input	8.59	10.36
Measurement Input, Exercise Price
Fair Value of Financial Instruments
Derivative asset, measurement input	14.51	16.58
Measurement Input, Price Volatility
Fair Value of Financial Instruments
Derivative asset, measurement input	0.478	0.438
Measurement Input, Expected Dividend Rate
Fair Value of Financial Instruments
Derivative asset, measurement input	0	0

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Notes Payable - Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes (Details) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended
	Aug. 31, 2019 USD ($) $ / shares $ / item shares	Sep. 30, 2019 USD ($)
Capped Calls
Purchase of capped calls		$ 25,159
Equity component of issuance costs for convertible senior notes		$ 2,092
Capped Calls
Capped Calls
Payment made to enter into Capped Calls	$ 25,200
Strike price (in dollars per share) | $ / shares	$ 13.39
Cap price | $ / item	17.05
Percentage of cap premium (as a percent)	75.00%
Number of shares covered by capped calls (in shares) | shares	29,867,480
Purchase of capped calls	$ 25,000
Equity component of issuance costs for convertible senior notes	$ 200

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Cyclerion Separation - General Information (Details) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2019 USD ($)	Sep. 30, 2019 USD ($) agreement
Cyclerion Separation
Initial term of service, low end of range		1 year
Initial term of service, high end of range		2 years
Incremental stock-based compensation expense	$ 0.0	$ 0.0
Transition services agreements | agreement		2
Transition Service Agreement [Member]
Cyclerion Separation
Other Income		$ 0.2
Affiliated Entity
Cyclerion Separation
Tenant improvement reimbursement provisions	1.3	1.3
Affiliated Entity | Research and development | Development Agreement [Member]
Cyclerion Separation
Expense for service provided by related party	$ 1.4	$ 3.0

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Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Total revenues	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Cost and expenses:
Cost of revenues, excluding amortization of acquired intangible assets	506	4,616	12,862	11,288
Write-down of commercial supply and inventory to net realizable value and (settlement) loss on non-cancellable purchase commitments	(3,530)	(1,589)	(3,530)	247
Research and development	27,551	29,158	88,507	72,821
Selling, general and administrative	40,919	50,536	133,260	169,252
Amortization of acquired intangible assets		1,159		8,111
Gain on fair value remeasurement of contingent consideration		(33,519)		(31,045)
Gain on lease modification			(3,169)
Restructuring expenses	(166)	10,102	3,652	14,010
Impairment of intangible assets		151,794		151,794
Total cost and expenses	65,280	212,257	231,582	396,478
Income (loss) from operations	65,887	(146,571)	70,530	(180,531)
Other (expense) income:
Interest expense	(10,457)	(9,482)	(29,479)	(28,138)
Interest and investment income	893	741	2,297	2,154
(Loss) gain on derivatives	(4,766)	3,489	(1,494)	3,996
Loss on extinguishment of debt	(30,977)		(30,977)
Other income	68		208
Other expense, net	(45,239)	(5,252)	(59,445)	(21,988)
Net income (loss) from continuing operations	20,648	(151,823)	11,085	(202,519)
Net loss from discontinued operations		(22,528)	(37,438)	(64,356)
Net income (loss)	$ 20,648	$ (174,351)	$ (26,353)	$ (266,875)
Net income (loss) per share from continuing operations-basic and diluted (in dollars per share)	$ 0.13	$ (0.99)	$ 0.07	$ (1.33)
Net loss per share from discontinued operations-basic and diluted (in dollars per share)		(0.15)	(0.24)	(0.42)
Net income (loss) per share-basic and diluted (in dollars per share)	$ 0.13	$ (1.14)	$ (0.17)	$ (1.75)
Weighted average number of common shares-basic and diluted (in shares)	156,436	153,227	155,752	152,143
Collaborative arrangements revenue
Revenues:
Total revenues	$ 130,524	$ 54,194	$ 273,998	$ 188,487
Product revenue, net
Revenues:
Total revenues		1,235		2,966
Sale of active pharmaceutical ingredient
Revenues:
Total revenues	$ 643	$ 10,257	$ 28,114	$ 24,494

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Net Income (Loss) Per Share - Potentially Dilutive Securities (Details) - shares shares in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	67,480	64,754
Employee stock options
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	17,889	20,860
Shares subject to repurchase
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	182	97
Restricted stock units
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	2,838	3,238
Shares subject to issuance under Employee Stock Purchase Plan
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	67	59
Note Hedge Warrants
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	8,318	20,250
2.25% Convertible Senior Notes due 2022
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	8,318	20,250
0.75% Convertible Senior Notes due 2024
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	14,934
1.50% Convertible Senior Notes due 2026
Potentially dilutive securities
Total potentially dilutive securities excluded from the computation of diluted weighted average shares outstanding (in shares)	14,934

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Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - General Information (Details) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($) item payment	Sep. 30, 2018 USD ($)
Sales milestones
Collaboration, License and Co-Promotion Agreements
Sales-related milestone if certain conditions are met	$ 100.0		$ 100.0
Allergan
Collaboration, License and Co-Promotion Agreements
Equity investment in the entity's capital stock			25.0
Net cost sharing offset or incremental expense related to research and development expense	0.9		$ 6.5
Cost sharing amount, reduction to research and development		$ 2.5		$ 5.8
Remaining commercial-period performance obligations | item			3
Allergan | Development and sales milestones
Collaboration, License and Co-Promotion Agreements
Cumulative license fees and development milestone payments received	$ 205.0		$ 205.0
Allergan | Development milestones
Collaboration, License and Co-Promotion Agreements
Number of milestone payments received | payment			6
Allergan | Sales milestones
Collaboration, License and Co-Promotion Agreements
Percentage of net profit from commercialization (as a percent)			50.00%
Percentage of net loss from commercialization (as a percent)			50.00%

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Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2018
Reconciliation of cash, cash equivalents, and restricted cash to the condensed consolidated balance sheets
Cash and cash equivalents	$ 139,231	$ 141,562
Restricted cash	8,647	7,676
Total cash, cash equivalents, and restricted cash	$ 147,878	$ 149,238

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Leases (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of components of lease cost and supplemental cash flow information

Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the three and nine months ended September 30, 2019 are as follows (in thousands):

	Three Months Ended		Nine Months Ended
	September 30,		September 30,
	2019		2019
Operating lease cost during period, net(1)	$	6,244		13,924
Variable lease payments		654		1,308
Short-term lease cost		375		1,143
Total lease cost	$	7,273		16,375

(1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the nine months ended September 30, 2019. Sublease income relates to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019.

Supplemental cash flow information related to leases for the periods reported is as follows:

	Nine Months Ended
	September 30,
	2019
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands)	$	88,299
Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands)		(40,427)
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands)		(34,440)
Right-of-use assets obtained in exchange for new operating lease liabilities(1) (in thousands)		18,452
Cash paid for amounts included in the measurement of lease liabilities (in thousands)		8,869
Weighted-average remaining lease term of operating leases (in years)		8.0
Weighted-average discount rate of operating leases		5.4	%

(1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease.

Schedule of future minimum lease payments under non-cancelable operating leases - ASC 842

Future minimum lease payments under non-cancelable operating leases under ASC 842 as of September 30, 2019 are as follows (in thousands):

	Operating
	Lease
	Payments
2019(1)	$	9,729
2020		1,146
2021		3,128
2022		3,129
2023		3,065
2024 and thereafter		21,170
Total future minimum lease payments		41,367
Less: present value adjustment		8,773
Operating lease liabilities at September 30, 2019		32,594
Less: current portion of operating lease liabilities		9,934
Operating lease liabilities, net of current portion	$	22,660

(1) Amounts are for the three months ending December 31, 2019.

Schedule of future minimum lease payments under non-cancelable operating leases - ASC 840

At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands):

	Operating
	Lease
	Payments
2019	$	18,736
2020		18,312
2021		18,863
2022		19,365
2023		19,818
2024 and thereafter		22,118
Total future minimum lease payments	$	117,212

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Collaboration, License, Co-Promotion and Other Commercial Agreements (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of revenue attributable to transactions from collaboration and license arrangements

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
Collaborative Arrangements Revenue	2019		2018		2019		2018
Linaclotide Collaboration Agreements:
Allergan (North America)	$	85,107	$	52,724	$	225,390	$	184,133
Allergan (Europe and other)		526		255		1,208		831
AstraZeneca (China, including Hong Kong and Macau)		32,401		—		32,401		—
Astellas (Japan)		10,059		—		10,059		—
Co-Promotion and Other Agreements:
Allergan (VIBERZI)		1,363		750		2,602		2,250
Alnylam (givosiran)		722		—		722		—
Other		346		465		1,616		1,273
Total collaborative arrangements revenue	$	130,524	$	54,194	$	273,998	$	188,487
Sale of API (1)
Linaclotide License Agreements:
Astellas (Japan)	$	—	$	9,501	$	27,468	$	23,738
AstraZeneca (China, including Hong Kong and Macau)		643		—		646		—
Other (1)		—		756		—		756
Total sale of API	$	643	$	10,257	$	28,114	$	24,494

(1) During the three months ended September 30, 2018, the Company recorded approximately $0.8 million in revenue related to the sale of API to Allergan.

Allergan

Table Text Blocks

Schedule of revenue attributable to transactions from collaboration and license arrangements

The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the three and nine months ended September 30, 2019 and 2018 as follows (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.	$	84,565	$	52,261	$	223,831	$	182,675
Royalty revenue		542		463		1,559		1,458
Total collaborative arrangements revenue	$	85,107	$	52,724	$	225,390	$	184,133

Schedule of amount recorded by the Company for share of net loss related to collaborative arrangement

The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Collaborative arrangements revenue related to sales of LINZESS in the U.S.(1)(2)	$	84,565	$	52,261	$	223,831	$	182,675
Selling, general and administrative costs incurred by the Company(1)		(9,129)		(10,915)		(29,764)		(33,556)
The Company’s share of net profit	$	75,436	$	41,346	$	194,067	$	149,119

(1) Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and nine months ended September 30, 2019 and 2018.

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Workforce Reduction

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Workforce Reduction

12. Workforce Reduction

On January 30, 2018, the Company commenced an initiative to evaluate the optimal mix of investments for the lesinurad franchise. As part of this effort, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position. During the three months ended March 31, 2018, the Company substantially completed the implementation of this reduction in field-based workforce and, in accordance with ASC Topic 420, Exit or Disposal Activities (“ASC 420”), recorded approximately $2.4 million of costs in its condensed consolidated statement of operations.

On June 27, 2018, the Company determined the initial organizational designs of the two new businesses, including employees’ roles and responsibilities, in connection with the Separation. As part of this process, the Company initiated a reduction in its headquarter-based workforce by approximately 40 employees. During the three and nine months ended September 30, 2019, the Company recorded an insignificant amount of costs in connection with this workforce reduction. During the three and nine months ended September 30, 2018, the Company recorded approximately $2.5 million and $4.0 million, respectively, of costs in connection with the reduction in workforce in

accordance with ASC 420. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

On August 16, 2018, the Company initiated a reduction in its workforce by approximately 100 employees, primarily consisting of field-based sales representatives in connection with the termination of the Lesinurad License. During the three and nine months ended September 30, 2019, the Company did not record any restructuring costs related to this workforce reduction. During each of the three and nine months ended September 30, 2018, the Company recorded approximately $7.6 million of costs in connection with the reduction in workforce. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

On February 7, 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. During the three and nine months ended September 30, 2019, the Company reversed approximately $0.2 million and recorded approximately $3.7 million, respectively, of costs that are reflected in the condensed consolidated statement of operations as restructuring expenses.

The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the three and nine months ended September 30, 2019 (in thousands):

	Amounts								Amounts
	Accrued at								Accrued at
	December 31, 2018		Charges		Amount Paid		Adjustments		September 30, 2019
Employee severance, benefits and related costs
June 2018 Reduction		696		16		(689)		(23)		—
August 2018 Reduction		1,756		—		(1,708)		(48)		—
February 2019 Reduction		—		3,182		(2,765)		(89)		328
Total	$	2,452	$	3,198	$	(5,162)	$	(160)	$	328
Contract related costs
August 2018 Reduction	$	433	$	—		(287)		(42)	$	104
Total	$	433	$	—	$	(287)	$	(42)	$	104

During the three and nine months ended September 30, 2019, the Company reversed approximately $0.2 million and recorded approximately $3.7 million in restructuring expenses, respectively, and recorded approximately $10.1 million and approximately $14.0 million in restructuring expenses during the three and nine months ended September 30, 2018, respectively.

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Related Party Transactions (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Sep. 30, 2009	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Related Party Transactions
Accounts payable from related party		$ 1,593		$ 1,593
Investor | Allergan
Related Party Transactions
Accounts receivable		94,400		94,400		$ 60,000
Investor | Allergan | Convertible preferred stock
Related Party Transactions
Shares sold (in shares)	2,083,333
Board of Directors member
Related Party Transactions
Fees paid to related party		800	$ 800	2,000	$ 2,600
Amount of insurance premium paid to the insurance provider		1,700	$ 2,900	5,800	$ 9,200
Accounts payable from related party		0		0		$ 0
Net of accounts receivable		$ 1,300		$ 1,300

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Workforce Reduction - Restructuring Expenses (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Restructuring expenses
Restructuring expenses	$ (166)	$ 10,102	$ 3,652	$ 14,010

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Fair Value of Financial Instruments - Capped Calls in connection with issuance of 2024 Convertible Notes and the 2026 Convertible Notes (Details) - Capped Calls	1 Months Ended
	Aug. 31, 2019 $ / shares $ / item shares
Capped Calls
Number of shares covered by capped calls (in shares) | shares	29,867,480
Strike price (in dollars per share) | $ / shares	$ 13.39
Cap price | $ / item	17.05

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Fair Value of Financial Instruments - Assumptions - Note Hedge Warrants (Details) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2019 USD ($) Y $ / shares	Sep. 30, 2019 USD ($) Y $ / shares	Sep. 16, 2019 USD ($)	Aug. 31, 2019 USD ($)	Dec. 31, 2018 $ / shares Y
Fair Value of Financial Instruments
(Loss) gain on derivatives	$ 4.8
Derivative liability, valuation technique	us-gaap:ValuationTechniqueOptionPricingModelMember	us-gaap:ValuationTechniqueOptionPricingModelMember			us-gaap:ValuationTechniqueOptionPricingModelMember
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Fair Value of Financial Instruments
Debt redeemed/repurchased			$ 215.0	$ 215.0
Debt redemption/repurchase price				$ 227.3
Warrants
Fair Value of Financial Instruments
(Loss) gain on derivatives	$ (4.8)	$ (1.5)
Measurement Input, Risk Free Interest Rate
Fair Value of Financial Instruments
Derivative liability, measurement input	0.016	0.016			0.025
Measurement Input, Expected Term
Fair Value of Financial Instruments
Derivative liability, measurement input | Y	3.3	3.3			4.1
Measurement Input, Share Price
Fair Value of Financial Instruments
Derivative liability, measurement input | $ / shares	8.59	8.59			10.36
Measurement Input, Exercise Price
Fair Value of Financial Instruments
Derivative liability, measurement input | $ / shares	18.82	18.82			21.50
Measurement Input, Price Volatility
Fair Value of Financial Instruments
Derivative liability, measurement input	0.465	0.465			0.436
Measurement Input, Expected Dividend Rate
Fair Value of Financial Instruments
Derivative liability, measurement input	0	0			0

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Employee Stock Benefit Plans - Equity Plan (Details) - 2019 Equity Plan	May 31, 2019 shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares reserved for issuance (in shares)	10,000,000
Shares available for future grant (in shares)	11,276,185

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Collaboration, License, Co-Promotion and Other Commercial Agreements - Accounts Receivable (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Accounts receivable, net
Accounts payable from related party	$ 1,593
Collaborative arrangements and active pharmaceutical ingredient
Accounts receivable, net
Accounts receivable, net and related party accounts receivable, net, net of related party accounts payable	129,000
Accounts payable from related party	$ 3,800

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Nature of Business

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Nature of Business

1. Nature of Business

Overview

Ironwood Pharmaceuticals, Inc. (“Ironwood” or the “Company”) is a gastrointestinal (“GI”) focused healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. The Company is advancing innovative product opportunities in areas of large unmet need, capitalizing on its proven development and commercial capabilities and its deep expertise in GI diseases. On April 1, 2019, the Company completed its tax-free spin-off of its soluble guanylate cyclase (“sGC”) business into a separate publicly traded company, Cyclerion Therapeutics, Inc. (“Cyclerion”).

The Company’s commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation (“IBS-C”), or chronic idiopathic constipation (“CIC”), in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms.

Linaclotide is available under the trademarked name LINZESS^® (linaclotide) to adult men and women suffering from IBS-C or CIC in the United States (the “U.S.”) and Mexico and to adult men and women suffering from IBS-C in Japan. Linaclotide is available under the trademarked name CONSTELLA^® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries.

The Company has strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. The Company and its partner, Allergan plc (together with its affiliates, “Allergan”), began commercializing LINZESS in the U.S. in December 2012. Under the Company’s collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party and the resulting amount is shared equally between the Company and Allergan. Allergan also has an exclusive license from the Company to develop and commercialize linaclotide in all countries other than China, including Hong Kong and Macau, Japan and the countries and territories of North America (the “Allergan License Territory”). On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS.

Astellas Pharma Inc. (“Astellas”), the Company’s partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adults with chronic constipation in Japan. On August 1, 2019, the Company amended and restated its license agreement with Astellas. Beginning in 2020, the Company will no longer be responsible for the supply of linaclotide active pharmaceutical ingredient (“API”) to Astellas (Note 4).

In October 2012, the Company and AstraZeneca AB (together with its affiliates, “AstraZeneca”), entered into a collaboration agreement to co-develop and co-commercialize linaclotide in China, including Hong Kong and Macau (the “AstraZeneca License Territory”). In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. On September 16, 2019, the Company amended its existing collaboration agreement with AstraZeneca. As of September 16, 2019, AstraZeneca has the exclusive right to develop, manufacture, and commercialize products containing linaclotide in the AstraZeneca License Territory (Note 4).

The Company and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations, and formulations to assess its potential to treat various conditions. In June 2019, the Company announced positive topline data from its Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C.

The Company and Allergan are advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain-relieving agent for patients suffering from abdominal pain associated with certain GI diseases. There are an estimated 16 million Americans who suffer from symptoms of IBS with diarrhea (“IBS-D”), according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, the Company and Allergan initiated a Phase II clinical trial evaluating MD-7246 in adult patients with IBS-D.

The Company is advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of persistent gastroesophageal reflux disease (“GERD”). There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al. in Gut; a Lieberman HCP Survey, 2019; a Lieberman GI patient landscape survey, 2010; a survey conducted by American Gastroenterological Association; and 2019 U.S. census data. In June 2018, the Company initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

The Company periodically enters into co-promotion agreements to maximize its salesforce productivity, such as its co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D. In August 2019, the Company entered into a disease education and promotional agreement with Alnylam Pharmaceuticals, Inc. (“Alnylam”) for Alnylam’s givosiran, an investigational RNAi therapeutic for the treatment of patients with acute hepatic porphyria (“AHP”). Under the agreement, the Company will perform disease awareness activities related to AHP and, if givosiran is approved by the U.S. Food and Drug Administration (“FDA”), future sales detailing activities of a product containing givosiran (Note 4).

On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into Cyclerion (the “Separation”). The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of all outstanding shares of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019 (Note 2).

On June 11, 2019, the Company entered into a non-cancelable operating lease (the “Summer Street Lease”) for approximately 39,000 square feet of office space on the 23^rd floor of 100 Summer Street, Boston, Massachusetts (the “Summer Street Property”). The Summer Street Property became the Company’s new headquarters in October 2019, replacing its prior headquarters at 301 Binney Street (Note 8).

In August 2019, the Company issued $200.0 million in aggregate principal amount of 0.75% Convertible Senior Notes due 2024 (the “2024 Convertible Notes”) and $200.0 million in aggregate principal amount of 1.50% Convertible Senior Notes due 2026 (the “2026 Convertible Notes”). The Company received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and the 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million.

The proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used in August 2019 to pay the cost of associated capped call transactions (the “Capped Calls”) and to repurchase $215.0 million aggregate principal amount of the existing 2.25% Convertible Senior Notes due 2022 (the “2022 Convertible Notes”). The proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes were also used to redeem all of the outstanding principal balance of the 8.375% Notes due 2026 (the “2026 Notes”) on September 16, 2019 (Note 9). The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. During the three months ended September 30, 2019, the Company recognized a loss on extinguishment of debt of approximately $31.0 million related to the redemption of the 2026 Notes and the partial repurchase of the 2022 Convertible Notes.

Basis of Presentation

The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”).

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of September 30, 2019, and the results of its operations for the three and nine months ended September 30, 2019 and 2018, its statements of stockholders’ deficit for the three and nine months ended September 30, 2019 and 2018, and its cash flows for the nine months ended September 30, 2019 and 2018. The results of operations for the three and nine months ended September 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period.

The Company has presented its sGC business as discontinued operations in its condensed consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly (Note 2). For periods following the Separation, the Company continues to report financial results under one business segment.

Principles of Consolidation

The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of September 30, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent, publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation.

Use of Estimates

The preparation of condensed consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance and repurchase of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Reclassifications of Prior Period Financial Statements

Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation.

Summary of Significant Accounting Policies

The Company’s significant accounting policies are described in Note 2, Summary of Significant Accounting Policies, in the 2018 Annual Report on Form 10-K. During the nine months ended September 30, 2019, the Company adopted the following additional significant accounting policies:

Discontinued Operations

During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations (“ASC 205-20”). Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements.

Leases

Effective January 1, 2019, the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and nine months ended September 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases (“ASC 840”). Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary.

The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s condensed consolidated financial statements.

As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include:

● Accounting policy election to use the short-term lease exception by asset class;

● Election of the practical expedient package during transition, which includes:

o An entity need not reassess whether any expired or existing contracts are or contain leases.

o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

o An entity need not reassess initial direct costs for any existing leases.

Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

The Company’s lease portfolio for the three and nine months ended September 30, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s condensed consolidated balance sheets. As of September 30, 2019, the Company did not have any finance leases.

Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company.

Derivative Assets and Liabilities

In June 2015, in connection with the issuance of the 2022 Convertible Notes, the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 12). In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, the Company terminated its Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging (“ASC 815”).

These derivatives are recorded as assets or liabilities at fair value each reporting period and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of the Company’s Class A common stock on the date of valuation, time to maturity of the derivative instruments, the strike prices of the derivative instruments, the risk-free interest rate, and the volatility of the Company’s Class A common stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. Subject to customary anti-dilution and certain other adjustments, the Capped Calls cover the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met.

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (the “FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as set forth below, the Company did not adopt any new accounting pronouncements during the three and nine months ended September 30, 2019 that had a material effect on its condensed consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which supersedes the lease accounting requirements in ASC 840 and most industry-specific guidance with ASC 842. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, lease arrangements exceeding a 12-month term must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation are recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization and interest expense for financing leases. The balance sheet amounts recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. ASU 2016-02 is effective for fiscal

years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. Subsequent to the issuance of ASU 2016-02, the FASB issued ASU No. 2018-10, Leases (Topic 842), Codification Improvements (“ASU 2018-10”), ASU No. 2018-11, Leases (Topic 842), Targeted Improvements (“ASU 2018-11”), and ASU No. 2019-01 Leases (Topic 842), Codification Improvements (“ASU 2019-01”) to provide additional guidance for the adoption of Topic 842. ASU 2018-10 clarifies certain provisions and corrects unintended applications of the guidance, such as the rate implicit in a lease, impairment of the net investment in a lease, lessee reassessment of lease classifications, lessor reassessment of lease term and purchase options, variable payments that depend on an index or rate and certain transition adjustments. The amendments in ASU 2018-11 allow for an additional transition method, whereby at the adoption date the entity recognizes a cumulative-effect adjustment to the opening balance of retained earnings in the period of adoption, while the comparative period disclosures continue recognition under ASC 840. Additionally, ASU 2018-11 includes a practical expedient for separating contract components for lessors. The Company adopted ASC 842 using the optional transition method outlined in ASU 2018-11 as of January 1, 2019. The adoption of ASC 842 resulted in the recognition of operating lease right-of-use assets of approximately $88.3 million and corresponding lease liabilities of approximately $94.9 million. The adoption of these ASUs did not have a material impact on the Company’s results of operations; however, the adoption resulted in significant changes to the Company’s financial statement disclosures.

In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”). ASU 2016-13 will change how companies account for credit losses for most financial assets and certain other instruments. For trade receivables, loans and held-to-maturity debt securities, companies will be required to recognize an allowance for credit losses rather than reducing the carrying value of the asset. Subsequent to the issuance of ASU 2016-13, the FASB issued ASU No. 2019-04, Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments (“ASU 2019-04”) and ASU No. 2019-05, Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief (“ASU 2019-05”) to provide additional guidance on the adoption of ASU 2016-13. ASU 2019-04 added Topic 326, Financial Instruments—Credit Losses, and made several amendments to the codification and also modified the accounting for available-for-sale debt securities. ASU 2019-05 provides targeted transition relief by providing an option to irrevocably elect the fair value option for certain financial assets previously measured at amortized cost basis. ASU 2016-13, ASU 2019-04 and ASU 2019-05 are effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have on the Company’s financial position and results of operations.

In January 2017, the FASB issued ASU No. 2017-04, Intangibles—Goodwill and Other (Topic 350) (“ASU 2017-04”) to simplify the accounting for goodwill impairment by removing Step 2 of the goodwill impairment test. ASU 2017-04 is effective for fiscal years beginning after December 15, 2019. Early adoption is permitted. The Company is evaluating the potential impact that the adoption of ASU 2017-04 may have on the Company’s financial position and results of operations.

In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) (“Topic 718”): Improvements to Nonemployee Share-Based Payment Accounting (“ASU 2018-07”). ASU 2018-07 expands the scope of Topic 718 to include share-based payment transactions for acquiring goods and services from non-employees, and as a result, the accounting for share-based payments to non-employees will be substantially aligned. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within that fiscal year. Early adoption is permitted but not earlier than an entity’s adoption date of Topic 606. The Company adopted this standard during the three months ended March 31, 2019. The adoption of ASU 2018-07 did not have a material impact on the Company’s financial position and results of operations.

In July 2018, the FASB issued ASU 2018-09, Codification Improvements (“ASU 2018-09”). The amendments in ASU 2018-09 affect a wide variety of Topics in the FASB codification and apply to all reporting entities within the scope of the affected accounting guidance. The Company has evaluated ASU 2018-09 in its entirety and determined that the amendments related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, are the only provisions that currently apply to the Company. The amendments in ASU 2018-09 related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, clarify that an entity should recognize excess tax benefits related to stock compensation transactions in the period in which the amount of the deduction is determined. The amendments in ASU 2018-09 related to Topic 718-740 are effective for fiscal years beginning after December 15, 2018, with early adoption permitted. The Company adopted this standard during the three months ended March 31, 2019. The adoption of this standard did not have a material impact on the Company’s financial position and results of operations.

In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirement for Fair Value Measurement (“ASU 2018-13”) which amends the disclosure requirements for fair value measurements. The amendments in ASU 2018-13 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-13 may have on the Company’s financial position and results of operations.

In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement that is a Service Contract (a consensus of the FASB Emerging Issues Task Force) (“ASU 2018-15)” which provides additional guidance on the accounting for costs of implementation activities performed in a cloud computing arrangement that is a service contract. The amendments in ASU 2018-15 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-15 may have on the Company’s financial position and results of operations.

In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities (“ASU 2018-17”). The update is intended to improve general purpose financial reporting by considering indirect interests held through related parties in common control arrangements on a proportional basis for determining whether fees paid to decision makers and service providers are variable interests. The amendments in ASU 2018-17 will be effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-17 may have on the Company’s financial position and results of operations.

In July 2019, the FASB issued ASU No. 2019-07, Disclosure Update and Simplification and Investment Company Reporting Modernization (“ASU 2019-07”). The update is intended to simplify disclosure requirements to reflect the amendments of various Securities and Exchange Commission (“SEC”) disclosure requirements that the SEC determined were redundant, duplicative, overlapping, outdated or superseded and is effective upon issuance. The adoption of ASU 2019-07 did not have a material impact on the Company’s financial position, results of operations, or financial statement disclosures.

No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption.

XML

Document and Entity Information - $ / shares	9 Months Ended
	Sep. 30, 2019	Oct. 25, 2019
Document and Entity Information [Abstract]
Entity Central Index Key	0001446847
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2019
Document Transition Report	false
Entity File Number	001-34620
Entity Registrant Name	IRONWOOD PHARMACEUTICALS INC
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3404176
Entity Address, Address Line One	100 Summer Street
Entity Address, Address Line Two	Suite 2300
Entity Address, City or Town	Boston
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02110
City Area Code	617
Local Phone Number	621-7722
Title of 12(b) Security	Class A common stock, $0.001 par value
Entity Listing, Par Value Per Share	$ 0.001
Trading Symbol	IRWD
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		156,818,126
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Amendment Flag	false

XML

Cyclerion Separation - Separation Agreement (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Apr. 01, 2019	Dec. 31, 2018
Assets:
Prepaid expenses and other current assets	$ 11,863		$ 10,216
Property and equipment, net	11,381		7,652
Other assets	20		89
Total assets	334,343		332,050
Liabilities:
Accrued research and development costs	4,956		2,963
Accrued expenses and other current liabilities	$ 30,529		$ 38,001
Cyclerion Therapeutics, Inc.
Assets:
Prepaid expenses and other current assets		$ 1,169
Property and equipment, net		10,241
Other assets		21
Total assets		11,431
Liabilities:
Accrued research and development costs		5,673
Accrued expenses and other current liabilities		3,149
Liabilities		8,822
Net Assets Transferred to Cyclerion		$ 2,609

XML

Condensed Consolidated Statements of Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Condensed Consolidated Statements of Comprehensive Income (Loss)
Net income (loss)	$ 20,648	$ (174,351)	$ (26,353)	$ (266,875)
Other comprehensive income:
Unrealized gains on available-for-sale securities		35		70
Total other comprehensive income		35		70
Comprehensive income (loss)	$ 20,648	$ (174,316)	$ (26,353)	$ (266,805)

XML

Net Income (Loss) Per Share - Notes Payable (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018	Jun. 30, 2015
Convertible Senior Notes | 2.25% Convertible Senior Notes due 2022
Notes Payable
Aggregate principal amount of notes issued	$ 120,699	$ 335,699	$ 335,700

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Fair Value of Financial Instruments (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of assets and liabilities measured at fair value on a recurring basis

The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands):

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	September 30, 2019		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	101,207	$	101,207	$	—	$	—
Repurchase agreements		37,800		37,800		—		—
Convertible Note Hedges		11,357		—		—		11,357
Total assets measured at fair value	$	150,364	$	139,007	$	—	$	11,357
Liabilities:
Note Hedge Warrants	$	8,768	$	—	$	—	$	8,768
Total liabilities measured at fair value	$	8,768	$	—	$	—	$	8,768

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	December 31, 2018		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	142,218	$	142,218	$	—	$	—
Repurchase agreements		30,875		30,875		—		—
Convertible Note Hedges		41,020		—		—		41,020
Total assets measured at fair value	$	214,113	$	173,093	$	—	$	41,020
Liabilities:
Note Hedge Warrants	$	33,763	$	—	$	—	$	33,763
Contingent Consideration		51		—		—		51
Total liabilities measured at fair value	$	33,814	$	—	$	—	$	33,814

Schedule of assumptions used in fair market valuations

The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of September 30, 2019 and December 31, 2018:

	Nine Months Ended						Year Ended
	September 30,						December 31,
	2019						2018
	Convertible			Note Hedge			Convertible			Note Hedge
	Note Hedges			Warrants			Note Hedges			Warrants
Risk-free interest rate (1)		1.6	%		1.6	%		2.5	%		2.5	%
Time to maturity		2.7			3.3			3.5			4.1
Stock price (2)	$	8.59		$	8.59		$	10.36		$	10.36
Strike price (3)	$	14.51		$	18.82		$	16.58		$	21.50
Common stock volatility (4)		47.8	%		46.5	%		43.8	%		43.6	%
Dividend yield		—	%		—	%		—	%		—	%

(1) Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants.

(2) The closing price of the Company’s Class A common stock on the last trading day of the quarter ended September 30, 2019 and December 31, 2018, respectively.

(3) As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 9).

(4) Expected volatility based on historical volatility of the Company’s Class A common stock.

(5) The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero.

Schedule of the change in Level 3 convertible note derivatives

The following table reflects the change in the Company’s Level 3 Convertible Note Hedges and Note Hedge Warrants from December 31, 2018 through September 30, 2019 (in thousands):

	Convertible		Note Hedge
	Note Hedges		Warrants
Balance at December 31, 2018	$	41,020	$	(33,763)
Cash settlement (received) paid upon early termination of derivatives		(28,909)		25,735
Change in fair value, recorded as a component of gain (loss) on derivatives		(754)		(740)
Balance at September 30, 2019	$	11,357	$	(8,768)

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Nature of Business (Policies)

9 Months Ended

Sep. 30, 2019

Policy Text Blocks

Basis of Presentation

Basis of Presentation

The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”).

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of September 30, 2019, and the results of its operations for the three and nine months ended September 30, 2019 and 2018, its statements of stockholders’ deficit for the three and nine months ended September 30, 2019 and 2018, and its cash flows for the nine months ended September 30, 2019 and 2018. The results of operations for the three and nine months ended September 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period.

The Company has presented its sGC business as discontinued operations in its condensed consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly (Note 2). For periods following the Separation, the Company continues to report financial results under one business segment.

Principles of Consolidation

Principles of Consolidation

The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of September 30, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent, publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation.

Use of Estimates

Use of Estimates

The preparation of condensed consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance and repurchase of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Reclassifications of Prior Period Financial Statements

Reclassifications of Prior Period Financial Statements

Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation.

Discontinued Operations

Discontinued Operations

During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations (“ASC 205-20”). Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements.

Leases

Leases

Effective January 1, 2019, the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and nine months ended September 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases (“ASC 840”). Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary.

The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s condensed consolidated financial statements.

As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include:

● Accounting policy election to use the short-term lease exception by asset class;

● Election of the practical expedient package during transition, which includes:

o An entity need not reassess whether any expired or existing contracts are or contain leases.

o An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

o An entity need not reassess initial direct costs for any existing leases.

Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

The Company’s lease portfolio for the three and nine months ended September 30, 2019 includes: leases for its prior and current headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s condensed consolidated balance sheets. As of September 30, 2019, the Company did not have any finance leases.

Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company.

Derivative Assets and Liabilities

Derivative Assets and Liabilities

In June 2015, in connection with the issuance of the 2022 Convertible Notes, the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 12). In connection with the partial repurchase of the 2022 Convertible Notes in August 2019, the Company terminated its Convertible Note Hedges and Note Hedge Warrants proportionately. These instruments are derivative financial instruments under ASC Topic 815, Derivatives and Hedging (“ASC 815”).

These derivatives are recorded as assets or liabilities at fair value each reporting period and the fair value is determined using the Black-Scholes option-pricing model. The changes in fair value are recorded as a component of other (expense) income in the consolidated statements of operations. Significant inputs used to determine the fair value include the price per share of the Company’s Class A common stock on the date of valuation, time to maturity of the derivative instruments, the strike prices of the derivative instruments, the risk-free interest rate, and the volatility of the Company’s Class A common stock. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants in future periods.

In August 2019, in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. Subject to customary anti-dilution and certain other adjustments, the Capped Calls cover the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met.

New Accounting Pronouncements

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (the “FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as set forth below, the Company did not adopt any new accounting pronouncements during the three and nine months ended September 30, 2019 that had a material effect on its condensed consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which supersedes the lease accounting requirements in ASC 840 and most industry-specific guidance with ASC 842. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, lease arrangements exceeding a 12-month term must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation are recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization and interest expense for financing leases. The balance sheet amounts recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. ASU 2016-02 is effective for fiscal

years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. Subsequent to the issuance of ASU 2016-02, the FASB issued ASU No. 2018-10, Leases (Topic 842), Codification Improvements (“ASU 2018-10”), ASU No. 2018-11, Leases (Topic 842), Targeted Improvements (“ASU 2018-11”), and ASU No. 2019-01 Leases (Topic 842), Codification Improvements (“ASU 2019-01”) to provide additional guidance for the adoption of Topic 842. ASU 2018-10 clarifies certain provisions and corrects unintended applications of the guidance, such as the rate implicit in a lease, impairment of the net investment in a lease, lessee reassessment of lease classifications, lessor reassessment of lease term and purchase options, variable payments that depend on an index or rate and certain transition adjustments. The amendments in ASU 2018-11 allow for an additional transition method, whereby at the adoption date the entity recognizes a cumulative-effect adjustment to the opening balance of retained earnings in the period of adoption, while the comparative period disclosures continue recognition under ASC 840. Additionally, ASU 2018-11 includes a practical expedient for separating contract components for lessors. The Company adopted ASC 842 using the optional transition method outlined in ASU 2018-11 as of January 1, 2019. The adoption of ASC 842 resulted in the recognition of operating lease right-of-use assets of approximately $88.3 million and corresponding lease liabilities of approximately $94.9 million. The adoption of these ASUs did not have a material impact on the Company’s results of operations; however, the adoption resulted in significant changes to the Company’s financial statement disclosures.

In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”). ASU 2016-13 will change how companies account for credit losses for most financial assets and certain other instruments. For trade receivables, loans and held-to-maturity debt securities, companies will be required to recognize an allowance for credit losses rather than reducing the carrying value of the asset. Subsequent to the issuance of ASU 2016-13, the FASB issued ASU No. 2019-04, Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments (“ASU 2019-04”) and ASU No. 2019-05, Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief (“ASU 2019-05”) to provide additional guidance on the adoption of ASU 2016-13. ASU 2019-04 added Topic 326, Financial Instruments—Credit Losses, and made several amendments to the codification and also modified the accounting for available-for-sale debt securities. ASU 2019-05 provides targeted transition relief by providing an option to irrevocably elect the fair value option for certain financial assets previously measured at amortized cost basis. ASU 2016-13, ASU 2019-04 and ASU 2019-05 are effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have on the Company’s financial position and results of operations.

In January 2017, the FASB issued ASU No. 2017-04, Intangibles—Goodwill and Other (Topic 350) (“ASU 2017-04”) to simplify the accounting for goodwill impairment by removing Step 2 of the goodwill impairment test. ASU 2017-04 is effective for fiscal years beginning after December 15, 2019. Early adoption is permitted. The Company is evaluating the potential impact that the adoption of ASU 2017-04 may have on the Company’s financial position and results of operations.

In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) (“Topic 718”): Improvements to Nonemployee Share-Based Payment Accounting (“ASU 2018-07”). ASU 2018-07 expands the scope of Topic 718 to include share-based payment transactions for acquiring goods and services from non-employees, and as a result, the accounting for share-based payments to non-employees will be substantially aligned. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within that fiscal year. Early adoption is permitted but not earlier than an entity’s adoption date of Topic 606. The Company adopted this standard during the three months ended March 31, 2019. The adoption of ASU 2018-07 did not have a material impact on the Company’s financial position and results of operations.

In July 2018, the FASB issued ASU 2018-09, Codification Improvements (“ASU 2018-09”). The amendments in ASU 2018-09 affect a wide variety of Topics in the FASB codification and apply to all reporting entities within the scope of the affected accounting guidance. The Company has evaluated ASU 2018-09 in its entirety and determined that the amendments related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, are the only provisions that currently apply to the Company. The amendments in ASU 2018-09 related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, clarify that an entity should recognize excess tax benefits related to stock compensation transactions in the period in which the amount of the deduction is determined. The amendments in ASU 2018-09 related to Topic 718-740 are effective for fiscal years beginning after December 15, 2018, with early adoption permitted. The Company adopted this standard during the three months ended March 31, 2019. The adoption of this standard did not have a material impact on the Company’s financial position and results of operations.

In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirement for Fair Value Measurement (“ASU 2018-13”) which amends the disclosure requirements for fair value measurements. The amendments in ASU 2018-13 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-13 may have on the Company’s financial position and results of operations.

In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement that is a Service Contract (a consensus of the FASB Emerging Issues Task Force) (“ASU 2018-15)” which provides additional guidance on the accounting for costs of implementation activities performed in a cloud computing arrangement that is a service contract. The amendments in ASU 2018-15 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-15 may have on the Company’s financial position and results of operations.

In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities (“ASU 2018-17”). The update is intended to improve general purpose financial reporting by considering indirect interests held through related parties in common control arrangements on a proportional basis for determining whether fees paid to decision makers and service providers are variable interests. The amendments in ASU 2018-17 will be effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-17 may have on the Company’s financial position and results of operations.

In July 2019, the FASB issued ASU No. 2019-07, Disclosure Update and Simplification and Investment Company Reporting Modernization (“ASU 2019-07”). The update is intended to simplify disclosure requirements to reflect the amendments of various Securities and Exchange Commission (“SEC”) disclosure requirements that the SEC determined were redundant, duplicative, overlapping, outdated or superseded and is effective upon issuance. The adoption of ASU 2019-07 did not have a material impact on the Company’s financial position, results of operations, or financial statement disclosures.

No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption.

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Notes Payable (Tables)

9 Months Ended

Sep. 30, 2019

Table Text Blocks

Schedule of outstanding Convertible Note

The Company’s outstanding balances for the Convertible Senior Notes as of September 30, 2019 and December 31, 2018 consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Liability component:
Principal:
2022 Convertible Notes	$	120,699	$	335,699
2024 Convertible Notes		200,000		—
2026 Convertible Notes		200,000		—
Less: unamortized debt discount		(109,685)		(65,094)
Less: unamortized debt issuance costs		(8,339)		(5,004)
Net carrying amount	$	402,675	$	265,601
Equity Component:
2022 Convertible Notes	$	19,807	$	114,199
2024 Convertible Notes		41,152		—
2026 Convertible Notes		51,350		—
Total Equity component	$	112,309	$	114,199

Schedule of interest expense related to Convertible Notes

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Contractual interest expense	$	1,780	$	1,889	$	5,557	$	5,665
Amortization of debt issuance costs		301		249		856		712
Amortization of debt discount		4,460		3,900		12,699		11,450
Total interest expense	$	6,541	$	6,038	$	19,112	$	17,827

Schedule of future minimum payments details of debt

Future minimum payments under the Convertible Senior Notes as of September 30, 2019 are as follows (in thousands):

2019(1)	$	2,895
2020		7,216
2021		7,216
2022		126,556
2023		4,500
2024		203,750
Thereafter		204,500
Total future minimum payments under the convertible senior notes		556,633
Less: amounts representing interest		(35,934)
Less: unamortized debt discount		(109,685)
Less: unamortized debt issuance costs		(8,339)
Convertible senior notes balance	$	402,675

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Nature of Business - Leases - Recognition of Assets and Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019
Leases
Operating lease right-of-use assets	$ 19,793	$ 88,300
Lease liabilities	$ 32,594	$ 94,900

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Employee Stock Benefit Plans (Tables)

9 Months Ended

Sep. 30, 2019

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Share-based compensation expense reflected in the condensed consolidated statements of operations

The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Research and development	$	1,208	$	2,974	$	5,306	$	8,446
Selling, general and administrative		4,312		7,643		19,832		19,708
Restructuring expenses		—		1,551		654		2,068
	$	5,520	$	12,168	$	25,792	$	30,222

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Nature of Business - Notes Payable (Details) - USD ($) $ in Thousands		1 Months Ended		3 Months Ended	9 Months Ended
	Sep. 23, 2016	Sep. 30, 2019	Aug. 31, 2019	Sep. 30, 2019	Sep. 30, 2019	Sep. 16, 2019	Aug. 12, 2019	Dec. 31, 2018	Jun. 30, 2015
Notes Payable
Loss on extinguishment of debt				$ 30,977	$ 30,977
Equity component of the partial repurchase of the 2022 Convertible Notes				(26,959)
Convertible Senior Notes
Notes Payable
Net proceed received			$ 391,000
2.25% Convertible Senior Notes due 2022 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued		$ 120,699		120,699	120,699			$ 335,699	$ 335,700
Stated interest rate (as a percent)						2.25%			2.25%
Fees and expenses									$ 11,700
Debt redeemed/repurchased			215,000			$ 215,000
Debt redemption/repurchase price			227,300
Loss on extinguishment of debt			23,400
Initial debt issuance costs			2,800
0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Fees and expenses			9,000
0.75% Convertible Senior Notes due 2024 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued		200,000	200,000	200,000	200,000		$ 200,000
Stated interest rate (as a percent)							0.75%
1.50% Convertible Senior Notes due 2026 | Convertible Senior Notes
Notes Payable
Aggregate principal amount of notes issued		$ 200,000	$ 200,000	$ 200,000	$ 200,000		$ 200,000
Stated interest rate (as a percent)							1.50%
8.375% Notes due 2026 | Notes Payable
Notes Payable
Aggregate principal amount of notes issued	$ 150,000
Stated interest rate (as a percent)	8.375%	8.375%		8.375%	8.375%
Debt redeemed/repurchased						116,500
Debt redemption/repurchase price						$ 123,000
Loss on extinguishment of debt	$ 7,600	$ 31,000

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Notes Payable

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Notes Payable

9. Notes Payable

8.375% Notes due 2026

On September 23, 2016, the Company closed a direct private placement, pursuant to which the Company issued $150.0 million in aggregate principal amount of 8.375% notes due 2026 on January 5, 2017. The Company capitalized approximately $0.5 million of debt issuance costs, which were netted against the carrying value of the 2026 Notes. Proceeds from the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes were used, in part, to redeem the outstanding principal balance of the 2026 Notes in September 2019. The Company retired the 2026 Notes, which had an outstanding aggregate principal balance of approximately $116.5 million, for a redemption price of approximately $123.0 million. The redemption of the 2026 Notes resulted in a loss on extinguishment of debt of approximately $7.6 million related to the prepayment premium and write-off of the remaining 2026 Notes, the unamortized debt issuance costs, and the unamortized debt discount.

The 2026 Notes had an annual interest rate of 8.375%, with interest payable March 15, June 15, September 15 and December 15 of each year (each an “8.375% Payment Date”), which began June 15, 2017. Principal of the 2026 Notes was payable on the 8.375% Payment Dates beginning March 15, 2019 through the redemption of the 2026 Notes. From March 15, 2019, the Company made quarterly payments on the 2026 Notes equal to the greater of (i) 7.5% of net sales of linaclotide in the U.S. for the preceding quarter (the “8.375% Synthetic Royalty Amount”) and (ii) accrued and unpaid interest on the 2026 Notes (the “8.375% Required Interest Amount”). Principal on the 2026 Notes was due to be repaid in an amount equal to the 8.375% Synthetic Royalty Amount minus the 8.375% Required Interest Amount, when this is a positive number, until the principal had been paid in full.

Convertible Senior Notes

2.25% Convertible Senior Notes due 2022

In June 2015, the Company issued approximately $335.7 million aggregate principal amount of the 2022 Convertible Notes. The Company received net proceeds of approximately $324.0 million from the sale of the 2022 Convertible Notes, after deducting fees and expenses of approximately $11.7 million. The Company used approximately $21.1 million of the net proceeds from the sale of the 2022 Convertible Notes to pay the net cost of the Convertible Note Hedges (after such cost was partially offset by the proceeds to the Company from the sale of the Note Hedge Warrants), as described below.

The 2022 Convertible Notes are governed by an indenture (the “2022 Indenture”) between the Company and U.S. Bank National Association, as the trustee. The 2022 Convertible Notes are senior unsecured obligations and bear cash interest at the annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. The 2022 Convertible Notes will mature on June 15, 2022, unless earlier converted or repurchased. The Company may settle conversions of the 2022 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A common stock of the Company or a combination of cash and shares of Class A common stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the 2022 Indenture). The initial conversion rate for the 2022 Convertible Notes was 60.3209 shares of Class A common stock (subject to adjustment as provided for in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes, which was equal to an initial conversion price of approximately $16.58 per share and 20,249,665 shares.

In connection with the Separation in April 2019, the conversion rate under the 2022 Indenture was adjusted to equal 68.9172 shares of Ironwood Class A common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equal to an adjusted conversion price of approximately $14.51 per share and 23,135,435 shares.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes in August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes.

Holders of the 2022 Convertible Notes may convert their 2022 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2021 in multiples of $1,000 principal amount, only under the following circumstances:

● during any calendar quarter commencing after the calendar quarter ending on September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s Class A common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the 2022 Convertible Notes on each applicable trading day;

● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in the 2022 Indenture) per $1,000 principal amount of the 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s Class A common stock and the conversion rate for the 2022 Convertible Notes on each such trading day; or

● upon the occurrence of specified corporate events described in the 2022 Indenture.

On or after December 15, 2021, until the close of business on the second scheduled trading day immediately preceding June 15, 2022, holders may convert their 2022 Convertible Notes, in multiples of $1,000 principal amount, at the option of the holder regardless of the foregoing circumstances.

If a make-whole fundamental change, as described in the 2022 Indenture, occurs and a holder elects to convert its 2022 Convertible Notes in connection with such make-whole fundamental change, such holder may be entitled to an increase in the conversion rate as described in the 2022 Indenture. The Company may not redeem the 2022 Convertible Notes prior to the maturity date and no “sinking fund” is provided for by the 2022 Convertible Notes, which means that the Company is not required to periodically redeem or retire the 2022 Convertible Notes. Upon the occurrence of certain fundamental changes involving the Company, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest.

The 2022 Indenture does not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The 2022 Indenture provides for customary events of default. In the case of an event of default with respect to the 2022 Convertible Notes arising from specified events of bankruptcy or insolvency, all outstanding 2022 Convertible Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the 2022 Convertible Notes under the 2022 Indenture occurs or is continuing, the trustee or holders of at least 25% in aggregate principal amount of the then outstanding 2022 Convertible Notes may declare the principal amount of the 2022 Convertible Notes to be immediately due and payable. Notwithstanding the foregoing, the 2022 Indenture provides that, upon the Company’s election, and for up to 180 days, the sole remedy for an event of default relating to certain failures by the Company to comply with certain reporting covenants in the 2022 Indenture consists exclusively of the right to receive additional interest on the 2022 Convertible Notes.

In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2022 Convertible Notes by allocating the proceeds between the liability component and the embedded conversion option, or equity component, due to the Company’s ability to settle the 2022 Convertible Notes in cash, its Class A common stock, or a combination of cash and Class A common stock at the option of the Company. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The equity component of the 2022 Convertible Notes was recognized as a debt discount and represents the difference between the gross proceeds from the issuance of the 2022 Convertible Notes and the fair value of the liability of the 2022 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over seven years, or the expected life of the 2022 Convertible Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes in August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes were repurchased at a premium totaling approximately $227.3 million. Accordingly, the Company recognized a loss on extinguishment of debt of approximately $23.4 million related to the prepayment premium and proportional write-off of the 2022 Convertible Notes unamortized debt issuance costs and unamortized debt discount. Additionally, the repurchase resulted in a reduction to additional paid-in capital by approximately $27.0 million related to the equity component of the 2022 Convertible Notes.

0.75% Convertible Senior Notes due 2024 and 1.50% Convertible Senior Notes due 2026

In August 2019, the Company issued $200.0 million aggregate principal amount of the 2024 Convertible Notes and $200.0 million aggregate principal amount of the 2026 Convertible Notes. The Company received net proceeds of approximately $391.0 million from the sale of the 2024 Convertible Notes and 2026 Convertible Notes, after deducting fees and expenses of approximately $9.0 million. The Company used approximately $25.2 million of the net proceeds from the sale of the 2024 Convertible Notes and 2026 Convertible Notes to pay the net cost of the Capped Calls, as described below. For purposes of this section, “Notes” refer to the 2024 Convertible Notes and the 2026 Convertible Notes, collectively.

The 2024 Convertible Notes and 2026 Convertible Notes were issued by the Company on August 12, 2019, pursuant to separate Indentures, each dated as of such date (each an “Indenture” and together the “Indentures”), between the Company and U.S. Bank National Association, as trustee (the “Trustee”). The 2024 Convertible Notes will bear cash interest at the annual rate of 0.75% and the 2026 Convertible Notes will bear cash interest at the annual rate of 1.50%, each payable on June 15 and December 15 of each year, beginning on December 15, 2019. The 2024 Convertible Notes will mature on June 15, 2024 and the 2026 Convertible Notes will mature on June 15, 2026, unless earlier converted or repurchased. The Company will settle conversions of the 2024 Convertible Notes and 2026 Convertible Notes through payment or delivery, as the case may be, of cash, shares of Class A common stock of the Company or a combination of cash and shares of Class A common stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the applicable Indenture). The initial conversion rate for each of the 2024 Convertible Notes and the 2026 Convertible Notes is 74.6687 shares of Class A common stock (subject to adjustment as provided for in the applicable Indenture) per $1,000 principal amount of the 2024 Convertible Notes and 2026 Convertible Notes, which is equal to an initial conversion price of approximately $13.39 per share, representing a conversion premium of approximately 37.5% above the last reported sale price of Class A common stock of $9.74 per share on August 7, 2019.

Holders of the 2024 Convertible Notes and 2026 Convertible Notes may convert their Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, in multiples of $1,000 principal amount, only under the following circumstances:

● during any calendar quarter commencing after the calendar quarter ending on December 31, 2019 (and only during such calendar quarter), if the last reported sale price of Class A common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the Notes on each applicable trading day;

● during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in each Indenture) per $1,000 principal amount of Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of Class A common stock and the conversion rate for the Notes on each such trading day; or

● upon the occurrence of specified corporate events described in each Indenture.

On or after December 15, 2023, with respect to the 2024 Convertible Notes, and December 15, 2025, with respect to the 2026 Convertible Notes, until the close of business on the second scheduled trading day immediately preceding the applicable maturity date, the holders of the Notes may convert their Notes, in multiples of $1,000 principal amount, regardless of the foregoing conditions.

If the Company experiences a fundamental change, as described in the Indentures, prior to the maturity date of the respective Notes, holders of such Notes will, subject to specified conditions, have the right, at their option, to require the Company to repurchase for cash all or a portion of their Notes at a repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any, to, but not including, the fundamental change repurchase date. In addition, following certain corporate events that occur prior to the applicable maturity date of the Notes, the Company will increase the conversion rate for a holder who elects to convert its Notes in connection with such corporate event.

The Indentures do not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The Indentures provide for customary events of default. In the case of an event of default with respect to a series of Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes of such series will become due and payable immediately without further action or notice. If any other event of default with respect to a series of Notes under the relevant Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes of such series may declare the principal amount of such Notes to be immediately due and payable.

In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2024 Convertible Notes and the 2026 Convertible Notes by allocating the proceeds between the liability components and the embedded conversion options, or equity components, due to the Company’s ability to settle the 2024 Convertible Notes and the 2026 Convertible Notes in cash, its Class A common stock, or a combination of cash and Class A common stock at the option of the Company. The carrying amount of the respective liability components were calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The respective equity components of the 2024 Convertible Notes and the 2026 Convertible Notes were recognized as a debt discount and represent the difference between the gross proceeds from the issuance of the 2024 Convertible Notes and 2026 Convertible Notes and the fair value of the liability of the 2024 Convertible Notes and 2026 Convertible Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over approximately five and seven years, or the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes, respectively. The respective equity components are not remeasured as long as they continue to meet the conditions for equity classification.

The Company’s outstanding balances for the Convertible Senior Notes as of September 30, 2019 and December 31, 2018 consisted of the following (in thousands):

	September 30, 2019		December 31, 2018
Liability component:
Principal:
2022 Convertible Notes	$	120,699	$	335,699
2024 Convertible Notes		200,000		—
2026 Convertible Notes		200,000		—
Less: unamortized debt discount		(109,685)		(65,094)
Less: unamortized debt issuance costs		(8,339)		(5,004)
Net carrying amount	$	402,675	$	265,601
Equity Component:
2022 Convertible Notes	$	19,807	$	114,199
2024 Convertible Notes		41,152		—
2026 Convertible Notes		51,350		—
Total Equity component	$	112,309	$	114,199

In connection with the issuance of the 2022 Convertible Notes, the Company incurred approximately $11.7 million of debt issuance costs, which primarily consisted of initial purchasers’ discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $4.0 million were recorded as a reduction to additional paid-in capital upon issuance. The portion of these costs allocated to the liability components totaling approximately $7.7 million were recorded as a reduction in the carrying value of the debt on the balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2022 Convertible Notes. In connection with the partial repurchase of the 2022 Convertible Notes, the Company recorded a loss on extinguishment of debt of approximately $23.4 million, of which approximately $2.8 million related to the initial debt issuance costs.

The Company determined the expected life of the 2022 Convertible Notes was equal to their seven-year term. The effective interest rate on the liability components of the 2022 Convertible Notes for the period from the date of issuance through June 30, 2019 was 9.34%. From the date of the partial repurchase of the 2022 Convertible Notes in

August 2019 through September 30, 2019, the effective interest rate on the liability component of the 2022 Convertible Notes was 9.37%.

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company incurred approximately $9.0 million of debt issuance costs, which primarily consisted of initial purchaser’s discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $2.1 million were recorded as a reduction to additional paid-in capital. The portion of these costs allocated to the liability components totaling approximately $6.9 million were recorded as a reduction in the carrying value of the debt on the balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes.

The Company determined the expected life of the 2024 Convertible Notes and the 2026 Convertible Notes was equal to their approximately five and seven-year terms, respectively. The effective interest rates on the liability components of the 2024 Convertible Notes and the 2026 Convertible Notes for the period from the date of issuance through September 30, 2019 was 6.1% and 6.5%, respectively.

The following table sets forth total interest expense recognized related to the 2022 Convertible Notes, 2024 Convertible Notes, and 2026 Convertible Notes during the three and nine months ended September 30, 2019 and 2018 (in thousands):

	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2019		2018		2019		2018
Contractual interest expense	$	1,780	$	1,889	$	5,557	$	5,665
Amortization of debt issuance costs		301		249		856		712
Amortization of debt discount		4,460		3,900		12,699		11,450
Total interest expense	$	6,541	$	6,038	$	19,112	$	17,827

Future minimum payments under the Convertible Senior Notes as of September 30, 2019 are as follows (in thousands):

2019(1)	$	2,895
2020		7,216
2021		7,216
2022		126,556
2023		4,500
2024		203,750
Thereafter		204,500
Total future minimum payments under the convertible senior notes		556,633
Less: amounts representing interest		(35,934)
Less: unamortized debt discount		(109,685)
Less: unamortized debt issuance costs		(8,339)
Convertible senior notes balance	$	402,675

(1) Amounts are for the three months ending December 31, 2019.

Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Convertible Notes

To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2022 Convertible Notes, the Company entered into the Convertible Note Hedges covering 20,249,665 shares of the Company’s Class A common stock in connection with the issuance of the 2022 Convertible Notes. The Convertible Note Hedges had an initial exercise price of $16.58 per share, subject to adjustment upon the occurrence of certain corporate events or transactions, and were exercisable if the 2022 Convertible Notes were converted. In connection with the adjustment to the conversion rate of the 2022 Indenture, the exercise price of the Convertible Note Hedges and the Note Hedge Warrants were adjusted to $14.51 per share and $18.82 per share, respectively (Note 5). If upon conversion of the 2022 Convertible Notes, the price of the Company’s Class A common stock is above the exercise price of the

Convertible Note Hedges, the counterparties are obligated to deliver shares of the Company’s Class A common stock and/or cash with an aggregate value approximately equal to the difference between the price of the Company’s Class A common stock at the conversion date and the exercise price, multiplied by the number of shares of the Company’s Class A common stock related to the Convertible Note Hedge being exercised.

Concurrently with entering into the Convertible Note Hedges, the Company also sold Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments. The strike price of the Note Hedge Warrants was initially $21.50 per share, subject to adjustment, and such warrants are exercisable over the 150 trading day period beginning on September 15, 2022. In connection with the Separation in April 2019, the exercise price was adjusted to $18.82 per share and the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. The Note Hedge Warrants could have a dilutive effect on the Class A common stock to the extent that the market price per share of the Company’s Class A common stock exceeds the applicable strike price of such warrants.

The Convertible Note Hedges and the Note Hedge Warrants are separate transactions entered into by the Company and are not part of the terms of the 2022 Convertible Notes. Holders of the 2022 Convertible Notes and the Note Hedge Warrants do not have any rights with respect to the Convertible Note Hedges. The Company paid approximately $91.9 million for the Convertible Note Hedges and recorded this amount as a long-term asset on its condensed consolidated balance sheet. The Company received approximately $70.8 million for the Note Hedge Warrants and recorded this amount as a long-term liability, resulting in a net cost to the Company of approximately $21.1 million.

In August 2019, concurrently with the repurchase of $215.0 million aggregate principal amount of the 2022 Convertible Notes, the Company terminated the respective portion of the Convertible Note Hedges and Note Hedge Warrants. The Company received approximately $3.2 million related to net termination payments from the counterparties of the Convertible Note Hedges and Note Hedge Warrants. During the three months ended September 30, 2019, the Company recorded approximately $4.8 million in loss on derivatives as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and change in fair value over the period.

The Convertible Note Hedges and Note Hedge Warrants are accounted for as derivative assets and liabilities, respectively, in accordance with ASC Topic 815, Derivatives and Hedging (Note 5).

Capped Calls with Respect to 2024 Convertible Notes and 2026 Convertible Notes

To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into separate Capped Calls in connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes. The Company paid the counterparties approximately $25.2 million to enter into the Capped Calls.

The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have a cap price of approximately $17.05 per share, representing an approximately 75% premium over the last reported sale price of the Class A common stock as of August 7, 2019, which cap price is subject to certain adjustments under the terms of the Capped Calls. The Capped Calls cover 29,867,480 shares of Class A common stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes.

The Capped Calls are expected generally to reduce the potential dilution to the Class A common stock upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes in the event that the market price per share of Class A common stock, as measured under the terms of the Capped Calls, is greater than the strike price of the Capped Calls as adjusted pursuant to the anti-dilution adjustments. If, however, the market price per share of Class A common stock, as measured under the terms of the Capped Calls, exceeds the cap price of the Capped Calls, there would nevertheless be dilution upon conversion of the 2024 Convertible Notes and the 2026 Convertible Notes to the extent that such market price exceeds the cap price of the Capped Calls.

The Capped Calls are separate transactions entered into by and between the Company and the Capped Calls counterparties and are not part of the terms of the 2024 Convertible Notes or the 2026 Convertible Notes. Holders of the

2024 Convertible Notes and the 2026 Convertible Notes do not have any rights with respect to the Capped Calls. These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met. The Company recorded a reduction to additional paid-in capital of approximately $25.0 million related to the premium payments for the Capped Calls. Additionally, the Company recorded an approximately $0.2 million reduction to equity related to transaction costs incurred in connection with the Capped Calls.

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Fair Value of Financial Instruments

9 Months Ended

Sep. 30, 2019

Disclosure Text Block

Fair Value of Financial Instruments

5. Fair Value of Financial Instruments

The tables below present information about the Company’s assets that are measured at fair value on a recurring basis as of September 30, 2019 and December 31, 2018 and indicate the fair value hierarchy of the valuation techniques

the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize observable inputs such as quoted prices in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are either directly or indirectly observable, such as quoted prices for similar instruments in active markets, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.

The Company’s investment portfolio may include fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company apply other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare valuations. In addition, model processes are used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data. The Company validates the prices provided by its third-party pricing services by obtaining market values from other pricing sources and analyzing pricing data in certain instances. The Company also invests in certain reverse repurchase agreements which are collateralized by deposits in the form of Government Securities and Obligations for an amount not less than 102% of their principal amount. The Company does not record an asset or liability for the collateral as the Company is not permitted to sell or re-pledge the collateral. The collateral has at least the prevailing credit rating of U.S. Government Treasuries and Agencies. The Company utilizes a third-party custodian to manage the exchange of funds and ensure the collateral received is maintained at 102% of the reverse repurchase agreements principal amount on a daily basis.

The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands):

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	September 30, 2019		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	101,207	$	101,207	$	—	$	—
Repurchase agreements		37,800		37,800		—		—
Convertible Note Hedges		11,357		—		—		11,357
Total assets measured at fair value	$	150,364	$	139,007	$	—	$	11,357
Liabilities:
Note Hedge Warrants	$	8,768	$	—	$	—	$	8,768
Total liabilities measured at fair value	$	8,768	$	—	$	—	$	8,768

			Fair Value Measurements at Reporting Date Using
			Quoted Prices in		Significant Other		Significant
			Active Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
	December 31, 2018		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash and cash equivalents:
Money market funds	$	142,218	$	142,218	$	—	$	—
Repurchase agreements		30,875		30,875		—		—
Convertible Note Hedges		41,020		—		—		41,020
Total assets measured at fair value	$	214,113	$	173,093	$	—	$	41,020
Liabilities:
Note Hedge Warrants	$	33,763	$	—	$	—	$	33,763
Contingent Consideration		51		—		—		51
Total liabilities measured at fair value	$	33,814	$	—	$	—	$	33,814

There were no transfers between fair value measurement levels during each of the three and nine months ended September 30, 2019 or 2018.

Cash equivalents, accounts receivable, related party accounts receivable, prepaid expenses and other current assets, accounts payable, related party accounts payable, accrued expenses and other current liabilities, the current portion of capital lease obligations, deferred rent, deferred revenue and operating lease obligations at September 30, 2019 and December 31, 2018 are carried at amounts that approximate fair value due to their short-term maturities.

Convertible Note Hedges and Note Hedge Warrants

The Company’s Convertible Note Hedges and the Note Hedge Warrants are recorded as derivative assets and liabilities, and are classified as Level 3 under the fair value hierarchy. These derivatives are not actively traded and are valued using the Black-Scholes option-pricing model which requires the use of subjective assumptions. Significant inputs used to determine the fair value as of September 30, 2019 included the price per share of the Company’s Class A common stock, time to maturity of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, expected volatility of the Company’s Class A common stock, and expected dividend yield. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants.

In April 2019, the Company announced an adjustment to the conversion rate applicable to the 2022 Convertible Notes, effective April 15, 2019 (Note 9).

In August 2019, the Company repurchased $215.0 million aggregate principal amount of the 2022 Convertible Notes, which triggered a partial termination of the outstanding Convertible Note Hedges and Note Hedge Warrants. During the three and nine months ended September 30, 2019, the Company recorded a loss of approximately $4.8 million and approximately $1.5 million on derivatives, respectively, as a result of the partial termination of the Convertible Note Hedges and Note Hedge Warrants and the change in fair value of the remaining Convertible Note Hedges and Note Hedge Warrants during the quarter (Note 9).

The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of September 30, 2019 and December 31, 2018:

	Nine Months Ended						Year Ended
	September 30,						December 31,
	2019						2018
	Convertible			Note Hedge			Convertible			Note Hedge
	Note Hedges			Warrants			Note Hedges			Warrants
Risk-free interest rate (1)		1.6	%		1.6	%		2.5	%		2.5	%
Time to maturity		2.7			3.3			3.5			4.1
Stock price (2)	$	8.59		$	8.59		$	10.36		$	10.36
Strike price (3)	$	14.51		$	18.82		$	16.58		$	21.50
Common stock volatility (4)		47.8	%		46.5	%		43.8	%		43.6	%
Dividend yield		—	%		—	%		—	%		—	%

(1) Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants.

(2) The closing price of the Company’s Class A common stock on the last trading day of the quarter ended September 30, 2019 and December 31, 2018, respectively.

(3) As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 9).

(4) Expected volatility based on historical volatility of the Company’s Class A common stock.

(5) The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero.

The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting period and changes in fair value are recorded in other expense, net within the Company’s condensed consolidated statements of operations. Gains and losses for these derivative financial instruments are presented separately in the Company’s condensed consolidated statements of cash flows.

The following table reflects the change in the Company’s Level 3 Convertible Note Hedges and Note Hedge Warrants from December 31, 2018 through September 30, 2019 (in thousands):

	Convertible		Note Hedge
	Note Hedges		Warrants
Balance at December 31, 2018	$	41,020	$	(33,763)
Cash settlement (received) paid upon early termination of derivatives		(28,909)		25,735
Change in fair value, recorded as a component of gain (loss) on derivatives		(754)		(740)
Balance at September 30, 2019	$	11,357	$	(8,768)

Convertible Senior Notes

In June 2015, the Company issued approximately $335.7 million aggregate principal amount of its 2022 Convertible Notes. In August 2019, the Company repurchased $215.0 million aggregate principal amount of its 2022 Convertible Notes. Additionally, in August 2019, the Company issued $200.0 million aggregate principal amount of its 2024 Convertible Notes and $200.0 million aggregate principal amount of its 2026 Convertible Notes. The Company separately accounted for the liability and equity components of each of the 2022 Convertible Notes, 2024 Convertible Notes, and 2026 Convertible Notes, and together the Convertible Senior Notes, by allocating the proceeds between the liability component and equity component (Note 9). The fair value of the respective Convertible Senior Notes, which differs from their carrying value, is influenced by interest rates, the price of the Company’s Class A common stock and the volatility thereof, and the prices for the respective Convertible Senior Notes observed in market trading, which are Level 2 inputs.

The estimated fair value of the 2022 Convertible Notes was approximately $120.0 million and approximately $315.0 million as of September 30, 2019 and December 31, 2018, respectively. The estimated fair value of the 2024 Convertible Notes was approximately $185.9 million as of September 30, 2019. The estimated fair value of the 2026 Convertible Notes was approximately $183.6 million as of September 30, 2019.

Capped Calls

In connection with the issuance of the 2024 Convertible Notes and the 2026 Convertible Notes, the Company entered into the Capped Calls with certain financial institutions. The Capped Calls cover 29,867,480 shares of Class A common stock (subject to anti-dilution and certain other adjustments), which is the same number of shares of Class A common stock that initially underlie the 2024 Convertible Notes and the 2026 Convertible Notes. The Capped Calls have an initial strike price of approximately $13.39 per share, which corresponds to the initial conversion price of the 2024 Convertible Notes and the 2026 Convertible Notes and is subject to anti-dilution adjustments generally similar to those applicable to the 2024 Convertible Notes and the 2026 Convertible Notes, and have a cap price of approximately $17.05 per share (Note 9). These instruments meet the conditions outlined in ASC 815 to be classified in stockholders’ deficit and are not subsequently remeasured as long as the conditions for equity classification continue to be met (Note 1).

8.375% Notes Due 2026

In September 2016, the Company closed a direct private placement pursuant to which the Company issued $150.0 million in aggregate principal amount of the 2026 Notes in January 2017. The outstanding principal balance of the 2026 Notes was redeemed in September 2019 (Note 9). The estimated fair value of the 2026 Notes was approximately $148.2 million as of December 31, 2018. This valuation was calculated using a discounted cash flow estimate of expected interest and principal payments and was determined using Level 3 inputs, including significant estimates related to expected LINZESS sales and a discount rate equivalent to market participant interest rates.

Nonrecurring fair value measurements – Intangible Assets

On August 2, 2018, the Company delivered to AstraZeneca notice of termination of the lesinurad license agreement for the development, manufacture, and commercialization of products in the U.S. containing lesinurad as an active ingredient (the “Lesinurad License”). During the three months ended September 30, 2018, the Company recorded an approximately $151.8 million impairment charge related to its acquired intangible assets. The impairment assessment

performed utilized the revised projected revenue and net cash flows assumed through the termination of the lesinurad license agreement, resulting in an impairment of the full carrying value of the intangible assets.

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Leases - Other Leases (Details) - Computer and office equipment, under capital lease $ in Millions	Dec. 31, 2018 USD ($)
Capital leases
Capital lease obligations	$ 0.2
Weighted average interest rate on the outstanding capital lease obligations (as a percent)	3.40%

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Accrued Expenses and Other Current Liabilities - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Accrued Expenses
Other accrued expenses	$ 9,191		$ 9,191		$ 10,211
Move activities	4,000		4,000
Unbilled inventories	1,200		1,200
Other accrued expenses contracted services	700		700
Recorded settlement			3,500
Write-down of inventory	0	$ 2,500	0
Lesinurad
Accrued Expenses
Write-down of inventory		$ 600
Commercial and Sample Supply Commitments
Accrued Expenses
Write-down of inventory				$ 2,500
Write-down of excess non-cancellable sample purchase commitments					1,400
Commercial and Sample Supply Commitments | Linaclotide
Accrued Expenses
Accrued non-cancelable purchase	4,000		4,000
Commercial and Sample Supply Commitments | Linaclotide | Accrued Expenses and Other Current Liabilities
Accrued Expenses
Accrual for non-cancellable purchase commitments					$ 2,500
Commercial and Sample Supply Commitments | Linaclotide | Other Current Liabilities
Accrued Expenses
Accrued non-cancelable purchase	$ 2,500		$ 2,500

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Leases - Operating Leases - Operating Lease Obligations (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019
Operating lease obligations
Total future minimum lease payments	$ 41,367
Less: present value adjustment	8,773
Operating lease liabilities	32,594	$ 94,900
Less: current portion of operating lease obligations	9,934
Operating lease liabilities, net of current portion	$ 22,660

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Notes Payable - 2.25% Convertible Senior Notes due 2022 - Additional Information (Details) - 2.25% Convertible Senior Notes due 2022 - Convertible Senior Notes - USD ($) $ in Millions	1 Months Ended
	Jun. 30, 2015	Sep. 30, 2019	Sep. 29, 2019
Notes Payable
Debt issuance costs incurred	$ 11.7
Debt issuance costs allocated to equity components	4.0
Debt issuance costs allocated to liability components	$ 7.7
Debt instrument term	7 years
Effective interest rate on liability components		9.37%	9.34%

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Collaboration, License, Co-Promotion and Other Commercial Agreements - Japan (Details) $ in Thousands		1 Months Ended	3 Months Ended		9 Months Ended		12 Months Ended
	Aug. 01, 2019 USD ($)	Nov. 30, 2009 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Dec. 31, 2017 USD ($) payment	Dec. 31, 2016 USD ($)
Collaboration, License and Co-Promotion Agreements
Revenue			$ 131,167	$ 65,686	$ 302,112	$ 215,947
Astellas Pharma Inc. | Japan
Collaboration, License and Co-Promotion Agreements
Up-front fee received		$ 30,000
Astellas Pharma Inc. | Japan | Additional development milestones
Collaboration, License and Co-Promotion Agreements
Number of milestone payments | payment							3
Total milestone payments to be received							$ 45,000
Collaborative arrangements revenue
Collaboration, License and Co-Promotion Agreements
Revenue			130,524	54,194	273,998	188,487
Collaborative arrangement, collaboration and license agreements | Astellas Pharma Inc. | Japan
Collaboration, License and Co-Promotion Agreements
Revenue			10,059		10,059
Revenue remaining performance obligation	$ 20,400
Non-refundable upfront payment	$ 10,000
Collaborative arrangement, collaboration and license agreements, upfront fee | Astellas Pharma Inc. | Japan
Collaboration, License and Co-Promotion Agreements
Revenue			10,000		10,000
Sale of active pharmaceutical ingredient
Collaboration, License and Co-Promotion Agreements
Revenue			643	10,257	28,114	24,494
Sale of active pharmaceutical ingredient | Astellas Pharma Inc. | Japan
Collaboration, License and Co-Promotion Agreements
Revenue			$ 0	$ 9,501	$ 27,468	$ 23,738
Revenue remaining performance obligation								$ 0

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Collaboration, License, Co-Promotion and Other Commercial Agreements - North America - Collaborative Arrangements Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Revenue	$ 131,167	$ 65,686	$ 302,112	$ 215,947
Collaborative arrangements revenue
Revenues:
Revenue	130,524	54,194	273,998	188,487
Allergan | North America | Collaborative arrangements revenue
Revenues:
Revenue	85,107	52,724	225,390	184,133
Allergan | North America | Collaborative arrangements, LINZESS
Revenues:
Revenue	84,565	52,261	223,831	182,675
Allergan | North America | Royalty
Revenues:
Revenue	$ 542	$ 463	$ 1,559	$ 1,458

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Fair Value of Financial Instruments - General Information (Details)	Sep. 30, 2019
Fair Value of Financial Instruments
Threshold percentage of collateralized value (as a percent)	102.00%