UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

____________________________________________________

Form 10-Q

____________________________________________________

x Quarterly Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the quarterly period ended: June 30, 2023 or

o 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: 001-36066

____________________________________________________

PARATEK PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

____________________________________________________

Delaware	33-0960223
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

____________________________________________________

75 Park Plaza

Boston, MA 02116

(617) 807-6600

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive office)

____________________________________________________

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

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, par value $0.001 per share	PRTK	The Nasdaq Global 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 x No o

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 x No o

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	o	Accelerated filer	x
Non-accelerated filer	o	Smaller reporting company	x
Emerging growth company	o

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. o

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

As of July 31, 2023, there were 57,322,358 shares of the registrant's common stock, par value $0.001 per share, outstanding.

TABLE OF CONTENTS

		Page
PART I FINANCIAL INFORMATION
Item 1.	Financial Statements (unaudited)	2
	Condensed Consolidated Balance Sheets as of June 30, 2023 and December 31, 2022	2
	Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2023 and 2022	3
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2023 and 2022	4
	Condensed Consolidated Statements of Stockholders’ Equity (Deficit) for the Three Months Ended March 31, 2023 and 2022 and Three Months Ended June 30, 2023 and 2022	5
	Notes to Unaudited Condensed Consolidated Financial Statements	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	29
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	42
Item 4.	Controls and Procedures	42
PART II OTHER INFORMATION
Item 1.	Legal Proceedings	43
Item 1A.	Risk Factors	43
Item 6.	Exhibits	45
SIGNATURES		47

1

PART I – FINANCIAL INFORMATION

Item 1.    Financial Statements

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(in thousands, except for share and par value amounts)

(unaudited)

	June 30, 2023		December 31, 2022
Assets
Current assets
Cash and cash equivalents	$	42,685	$	34,248
Restricted cash	125		125
Accounts receivable, net	42,291		74,657
Inventories, net	11,413		16,565
Other receivables	220		3,381
Prepaid and other current assets	8,493		7,866
Total current assets	105,227		136,842
Fixed assets, net	554		616
Goodwill	829		829
Right-of-use assets	1,645		1,782
Long-term inventories, net	36,382		31,314
Other long-term assets	1,155		1,155
Total assets	$	145,792	$	172,538
Liabilities and Stockholders’ Deficit
Current liabilities
Accounts payable	$	2,951	$	5,308
Accrued expenses	34,803		31,210
Short-term debt	164,042		—
Other current liabilities	823		870
Total current liabilities	202,619		37,388
Long-term debt	94,285		256,946
Long-term lease liabilities	1,429		1,468
Accrued long-term compensation	46,565		45,325
Other liabilities	2,259		2,453
Total liabilities	$	347,157	$	343,580
Stockholders’ deficit
Preferred stock:
Undesignated preferred stock: $0.001 par value, 5,000,000 shares authorized; no shares issued and outstanding	—		—
Common stock, $0.001 par value; 200,000,000 shares authorized; 57,282,239 shares issued and outstanding as of June 30, 2023; and 200,000,000 shares authorized; 56,651,559 shares issued and outstanding as of December 31, 2022	57		56
Additional paid-in capital	763,723		759,351
Accumulated deficit	(965,145)		(930,449)
Total stockholders’ deficit	(201,365)		(171,042)
Total liabilities and stockholders’ deficit	$	145,792	$	172,538

See accompanying notes to unaudited condensed consolidated financial statements.

2

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations and Comprehensive Loss

(in thousands, except share and per share amounts)

(unaudited)

	Three Months Ended June 30,				Six Months Ended June 30,
	2023		2022		2023		2022
Product revenue, net	$	33,800	$	25,082	$	60,013	$	45,000
Government contract service revenue	3,620		1,896		5,301		4,068
Government contract grant revenue	1,931		2,082		4,084		4,182
Collaboration and royalty revenue	642		577		1,831		1,248
Net revenue	$	39,993	$	29,637	$	71,229	$	54,498
Expenses:
Cost of product revenue	4,368		4,878		10,612		8,372
Research and development	8,772		7,592		16,080		15,069
Selling, general and administrative	36,264		30,335		69,753		57,937
Total operating expenses	49,404		42,805		96,445		81,378
Loss from operations	(9,411)		(13,168)		(25,216)		(26,880)
Other income and expenses:
Interest income	252		133		473		240
Interest expense	(5,287)		(4,546)		(9,763)		(9,025)
Other (losses) gains, net	(56)		(38)		(78)		138
Net loss before provision for income taxes	$	(14,502)	$	(17,619)	$	(34,584)	$	(35,527)
Provision for income taxes	(51)		—		(111)		—
Net loss	(14,553)		(17,619)		(34,695)		(35,527)
Other comprehensive (loss)
Unrealized (loss) on available-for-sale securities, net of tax	—		(53)		—		(224)
Comprehensive loss	$	(14,553)	$	(17,672)	$	(34,695)	$	(35,751)
Basic and diluted net loss per common share	$	(0.25)	$	(0.33)	$	(0.61)	$	(0.67)
Weighted average common stock outstanding
Basic	57,282,239		53,023,350		57,093,876		53,310,091
Diluted	57,282,239		53,023,350		57,093,876		53,310,091

See accompanying notes to unaudited condensed consolidated financial statements.

3

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flows

(in thousands)

(unaudited)

	Six Months Ended June 30,
	2023		2022
Operating activities
Net loss	$	(34,695)	$	(35,527)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization and accretion	93		275
Stock-based compensation expense	4,372		6,354
Noncash interest expense	2,226		2,725
Changes in operating assets and liabilities
Accounts receivable, other receivables, prepaid, and other current assets	34,901		187
Inventories	84		(6,958)
Operating lease right-of-use asset	137		404
Accounts payable and accrued expenses	1,236		(923)
Operating lease liability	(39)		(455)
Accrued long-term compensation	1,241		—
Other liabilities and other assets	(242)		309
Net cash provided (used) by operating activities	9,314		(33,609)
Investing activities
Purchase of fixed assets	(32)		(36)
Purchase of marketable securities	—		(15,160)
Net cash used in investing activities	(32)		(15,196)
Financing activities
Proceeds from sale of common stock, net of costs	—		7,330
Proceeds from the employee stock purchase plan and stock options	—		488
Principal payments on long-term debt	(845)
Net cash (used) provided by financing activities	(845)		7,818
Net increase (decrease) in cash, cash equivalents and restricted cash	8,437		(40,987)
Cash, cash equivalents and restricted cash at beginning of period	34,373		80,617
Cash, cash equivalents and restricted cash at end of period	$	42,810	$	39,630
SUPPLEMENTAL DISCLOSURES OF CASH FLOW INFORMATION
Cash paid for interest	$	6,791	$	5,739
SUPPLEMENTAL DISCLOSURES OF NONCASH FINANCING ACTIVITIES
Paid in-kind interest included in accrued expenses	$	1,461	$	2,011

See accompanying notes to unaudited condensed consolidated financial statements.

4

Paratek Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

(in thousands, except share amounts)

(unaudited)

	Common Stock			Additional Paid-in Capital		Accumulated Deficit		Total Stockholders’ Deficit
	Shares	Amount
Balances at December 31, 2022	56,651,559	$	56	$	759,351	$	(930,449)	$	(171,042)
Vesting of restricted stock unit awards	630,680	1		—		—		1
Stock-based compensation expense	—	—		2,146		—		2,146
Net loss	—	—		—		(20,143)		(20,143)
Balances at March 31, 2023	57,282,239	$	57	$	761,497	$	(950,592)	$	(189,038)
Stock-based compensation expense	—	—		2,226		—		2,226
Net loss	—	—		—		(14,553)		(14,553)
Balances at June 30, 2023	57,282,239	$	57	$	763,723	$	(965,145)	$	(201,365)

	Common Stock			Additional Paid-in Capital		Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Total Stockholders’ Deficit
	Shares	Amount
Balances at December 31, 2021	51,711,809	$	52	$	739,053	$	(9)	$	(866,883)	$	(127,787)
Exercise of stock options	729	—		6		—		—		6
Issuance of common stock, net of expenses	884,230	1		3,090		—		—		3,091
Vesting of restricted stock unit awards	426,582	—		—		—		—		—
Employee stock purchase plan expense	—	—		36		—		—		36
Unrealized (loss) on available-for-sale securities, net of tax	—	—		—		(171)		—		(171)
Stock-based compensation expense	—	—		2,433		—		—		2,433
Net loss	—	—		—		—		(17,910)		(17,910)
Balances at March 31, 2022	53,023,350	$	53	$	744,618	$	(180)	$	(884,793)	$	(140,302)
Issuance of common stock, net of expenses	1,455,156	2		4,237		—		—		4,239
Employee stock purchase plan expense	—	—		29		—		—		29
Issuance of stock under the employee stock purchase plan	300,132	—		483		—		—		483
Unrealized gain on available-for-sale securities, net of tax	—	—		—		(53)		—		(53)
Stock-based compensation expense	—	—		3,856		—		—		3,856
Net loss	—	—		—		—		(17,619)		(17,619)
Balances at June 30, 2022	54,778,638	$	55	$	753,223	$	(233)	$	(902,412)	$	(149,367)

5

Paratek Pharmaceuticals, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

(unaudited)

1.    Description of the business

Paratek Pharmaceuticals, Inc., or the Company or Paratek, is a Delaware corporation with its corporate office in Boston, Massachusetts and an office in King of Prussia, Pennsylvania.

The Company is a commercial-stage biopharmaceutical company focused on the development and commercialization of novel life-saving therapies for life-threatening diseases or other public health threats for civilian, government and military use. The Company’s United States, or U.S., Food and Drug Administration, or FDA, approved commercial product, NUZYRA® (omadacycline), is a once-daily oral and intravenous antibiotic for the treatment of adult patients with community-acquired bacterial pneumonia, or CABP, and acute skin and skin structure infections, or ABSSSI, caused by susceptible pathogens. The Company retains worldwide commercial rights to omadacycline, with the exception in the People’s Republic of China, Hong Kong, Macau and Taiwan, where it has entered into a collaboration agreement with Zai Lab (Shanghai) Co., Ltd., or Zai. The National Medical Products Administration, or NMPA, of China approved NUZYRA for the treatment of adult patients with CABP and ABSSSI in December 2021. China’s National Healthcare Security Administration added the intravenous formulation of NUZYRA to the country's National Reimbursement Drug List for the treatment of CABP and ABSSSI in January 2023, resulting in millions of patients gaining access to this once daily broad-spectrum antibiotic.

SEYSARA® (sarecycline) is an FDA-approved product which the Company has exclusively licensed in the U.S. and the People’s Republic of China, Hong Kong and Macau, and Taiwan, certain rights to Almirall, LLC, or Almirall. SEYSARA is currently being marketed by Almirall in the U.S. as a once-daily oral therapy for the treatment of moderate to severe acne vulgaris. With respect to the Company’s technology as it relates to sarecycline, the Company retains development and commercialization rights in all countries other than the U.S. and the greater China region, and in February 2020, the Company exclusively licensed from Almirall certain technology owned or in-licensed by Almirall or its affiliates that is necessary or useful to develop or commercialize sarecycline outside of the U.S. Almirall plans to develop sarecycline for acne in China, with a submission to the NMPA expected in 2023, according to Almirall.

On June 6, 2023, the Company announced it had entered into a definitive agreement, or the Merger Agreement, to be acquired by Gurnet Point Capital, or Gurnet Point, and Novo Holdings A/S, or Novo Holdings, in a transaction valued at approximately $462.0 million, including the assumption of debt and assuming full payment of a Contingent Value Right, or CVR. This transaction is referred to herein as the Merger. Debt financing of $175.0 million for the Merger will be provided by funds managed by Oaktree Capital Management, L.P.

Under the terms of the Merger Agreement, Gurnet Point, a leading healthcare investment firm, and Novo Holdings, a holding and investment company responsible for managing the assets and wealth of the Novo Nordisk Foundation, will acquire all outstanding shares of Paratek for $2.15 per share in cash, plus a CVR of $0.85 per share payable upon the achievement of $320.0 million in U.S. NUZYRA net sales (excluding certain permitted deductions, payments under Paratek's contract with ASPR-BARDA, certain government payments and certain royalty revenue) in any calendar year ending on or prior to December 31, 2026.

The transaction, which our Board of Directors has unanimously approved, is subject to customary closing conditions, including approval by our stockholders and receipt of regulatory approvals. Following completion, Paratek will become a private company and will no longer be subject to the reporting requirements of the Securities Exchange Act of 1934, as amended, nor be traded on Nasdaq Global Market.

Between July 11, 2023 and July 27, 2023, the Company received eight demand letters, or the Demand Letters, each from a purported stockholder of the Company alleging to have identified purportedly materially misleading and incomplete statements in the preliminary proxy statement filed by the Company on June 30, 2023. Certain of the Demand Letters also purport to raise issues with aspects of the process that led to the Merger. Certain of those Demand Letters were served pursuant to Section 220 of the Delaware General Corporation Law and seek books and records of the Company related to the Merger. The Company believes the allegations asserted in the Demand Letters are without merit. Additional demand letters or lawsuits relating to the Merger may also be received and/or filed in the future.

The Company has incurred significant losses since inception in 1996. The Company has generated an accumulated deficit of $965.1 million through June 30, 2023 and may require substantial additional funding in connection with the

6

Company’s continuing operations to support clinical development and commercialization activities associated with NUZYRA. As of June 30, 2023, the Company had cash and cash equivalents of $42.7 million on hand.

The Company's current level of cash and cash equivalents may not be sufficient to fund operations for the next twelve months following the issuance of these financial statements. As a result, substantial doubt is deemed to exist regarding the Company’s ability to continue as a going concern for a period of one year from the issuance of these financial statements.

If the transaction with Gurnet Point and Novo Holdings is not consummated, the Company expects to finance future cash needs primarily through a combination of product sales, royalties, public or private equity offerings, debt or other structured financings, strategic partnership opportunities, government funding and active management of cash and expenses through operational efficiencies. With the Company’s convertible notes coming due on May 1, 2024, the Company believes it will need to successfully execute one or more financing transactions prior to that date or otherwise risk bankruptcy. The Company anticipates that any such financing transactions, if they could be completed, would likely be substantially dilutive to current Company stockholders. Further, to fund our future cash needs in absence of the transaction with Gurnet Point and Novo Holdings, the Company’s plans would require it to significantly reduce its workforce, including substantial reductions among the sales force, without materially negatively impacting the Company’s ability to generate sales of NUZYRA or to otherwise successfully operate its business. The Company also anticipates that an amendment to the convertible notes would likely require the grant of a security interest, thereby restricting the Company’s ability to raise debt financing in the future. There can be no assurance that the Company would be successful in securing additional funds on acceptable terms, or at all. If additional funds are not available, the Company may be forced to cease operations, significantly reduce operating expenses or delay, curtail, or eliminate one or more of its development programs or its business operations.

The accompanying consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and satisfaction of liabilities in the ordinary course of business. The consolidated financial statements do not include any adjustments relating to the recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might result from the outcome of this uncertainty.

The Company is subject to risks common to companies in the biopharmaceutical industry, including, but not limited to, risks of failure of preclinical studies and clinical trials, the need to obtain additional financing to fund the future commercialization of NUZYRA as well as the development of the Company’s product candidates, the need to obtain compliant product from third-party manufacturers, the need to obtain marketing approval for the Company’s product candidates, the need to successfully commercialize and gain market acceptance of product candidates, the risks of manufacturing product with an external supply chain, dependence on key personnel, and compliance with government regulations as well as the risks discussed in the "Risk Factors” section of the Company’s Annual Report on Form 10-K for the year ended December 31, 2022, or the 2022 Form 10-K, and in the Company’s other filings with the U.S. Securities and Exchange Commission, or the SEC.

2.    Summary of Significant Accounting Policies and Basis of Presentation

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or U.S. GAAP, as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB, and pursuant to the rules and regulations of the SEC.

The accompanying condensed consolidated financial statements are unaudited. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements as of and for the year ended December 31, 2022, and, in the opinion of management, reflect all normal recurring adjustments necessary for the fair presentation of the Company’s financial position as of June 30, 2023 and December 31, 2022, results of operations for the three and six month periods ended June 30, 2023 and June 30, 2022, cash flows for the six month periods ended June 30, 2023 and June 30, 2022 and changes in stockholders’ deficit for the three month periods ended March 31, 2023 and 2022 and three month periods ended June 30, 2023 and 2022.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2023. These unaudited interim condensed consolidated financial statements

7

should be read in conjunction with the audited consolidated financial statements as of and for the year ended December 31, 2022, and notes thereto, which are included in the Company’s 2022 Form 10-K.

Summary of Significant Accounting Policies

As of June 30, 2023, the Company’s significant accounting policies and estimates, which are detailed in the Company’s 2022 Form 10-K, have not changed.

Principles of Consolidation

The accompanying unaudited condensed consolidated financial statements include the results of operations of Paratek Pharmaceuticals, Inc. and its wholly-owned subsidiaries, Paratek Pharma, LLC, Paratek Securities Corporation, Transcept Pharma, Inc., Paratek Ireland Limited, Paratek Royalty Corporation, Paratek Royalty Corporation II, PRTK SPV1 LLC and PRTK SPV2 LLC. All significant intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of the accompanying unaudited condensed consolidated financial statements in conformity with U.S. GAAP requires the Company to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses in the Company’s financial statements. On an ongoing basis, the Company evaluates its estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement (as defined below), manufacturing and clinical accruals, useful lives for depreciation and valuation allowances on deferred tax assets. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known by the Company’s management.

Segment and Geographic Information

Operating segments are defined as components of an enterprise engaging in business activities for which discrete financial information is available and regularly reviewed by the chief operating decision maker in deciding how to allocate resources and in assessing performance. The Company views its operations and manages its business in one operating segment.

Concentration of Credit Risk

Financial instruments that subject the Company to credit risk consist primarily of cash, restricted cash, and accounts receivable. The Company places its cash in an accredited financial institution and this balance is above federally insured amounts. The Company has no off-balance sheet concentrations of credit risk such as foreign currency exchange contracts, option contracts or other hedging arrangements.

Accounts receivable as of June 30, 2023 includes $38.8 million due from customers for sales of NUZYRA, net of prompt payment discounts, chargebacks, rebates and certain fees. Accounts receivable as of June 30, 2023 also includes $1.8 million of government contract service revenue earned under contract with the Biomedical Advanced Research and Development Authority, or the BARDA contract, $0.9 million of government contract grant revenue earned under the BARDA contract, and estimated revenue earned of $0.8 million of royalties on NUZYRA sales under the Zai Collaboration Agreement (as defined below), SEYSARA sales under the Almirall Collaboration Agreement (as defined below) and XERAVA TM (eravacycline) sales under the Tetraphase License Agreement (as defined below). Refer to Note 7, Government Contract Revenue for further information on the BARDA contract and to Note 8, License and Collaboration Agreements for further information on the Zai Collaboration Agreement, Almirall Collaboration Agreement and the Tetraphase License Agreement.

3.    Marketable Securities

The Company did not hold any marketable securities as of June 30, 2023 or December 31, 2022.

8

4.    Cash and Cash Equivalents and Restricted Cash

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the condensed consolidated statement of cash flows that sum to the total of the same such amounts shown in the condensed consolidated statement of cash flows (in thousands):

	June 30, 2023		June 30, 2022
Cash and cash equivalents	$	42,685	$	39,505
Short-term restricted cash	125		—
Long-term restricted cash	—		125
Total cash, cash equivalents and restricted cash shown on the condensed consolidated statement of cash flows	$	42,810	$	39,630

Short-term restricted cash

The Company leases its Boston, Massachusetts office space under a non-cancelable operating lease. In accordance with the lease, the Company had a cash-collateralized irrevocable standby letter of credit in the amount of $0.3 million at March 31, 2022, naming the landlord as beneficiary. The $0.3 million letter of credit was refunded to the Company in April 2022 under the terms of the original lease agreement. The Company executed an amendment to the existing lease agreement in April 2021. In accordance with the amendment, the cash-collateralized irrevocable standby letter of credit was reduced to an insignificant amount as of June 30, 2023. Refer to Note 14, Leases, for further details.

5.    Inventories

The following table presents inventories, net (in thousands):

	June 30, 2023		December 31, 2022
Raw materials	$	903	$	903
Work in process	35,670		30,007
Finished goods	11,222		16,969
Total inventories	$	47,795	$	47,879

When recorded, inventory reserves reduce the carrying value of inventories to their net realizable value. The Company reviews inventories on hand at least quarterly and records provisions for estimated excess, slow-moving and obsolete inventory, as well as inventory with a carrying value in excess of net realizable value. No inventory reserves existed as of June 30, 2023 and December 31, 2022.

6.    Net Loss Per Share

Basic net loss per share is calculated by dividing the net loss by the weighted-average number of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is computed by dividing the net loss by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method or the if-converted method, as applicable. For purposes of this calculation, shares of common stock issuable upon conversion of convertible debt, stock options, restricted stock units, or RSUs, warrants to purchase common stock, and shares issuable under the employee stock purchase plan are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive.

Common equivalent shares result from stock options and RSUs, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the employee stock purchase plan (the proceeds of which are then assumed to have been used to repurchase outstanding stock using the treasury stock method). The two-class method is used for outstanding warrants as it is considered to be a participating security, and it is more dilutive than the treasury stock method.

The Company was in a net loss position as of June 30, 2023 and June 30, 2022. The following outstanding shares

9

subject to stock options and RSUs, warrants to purchase shares of common stock, common stock issuable upon conversion of convertible debt and shares issuable under the Company’s employee stock purchase plan were antidilutive due to a net loss in the periods presented and, therefore, were excluded from the dilutive securities computation for the three and six months ended June 30, 2023 and 2022 as indicated below:

	June 30,
	2023	2022
Excluded potentially dilutive securities (1):
Common stock issuable under outstanding convertible notes	10,377,361	10,377,361
Shares subject to outstanding options to purchase common stock	1,347,183	2,119,588
Unvested restricted stock units	4,246,457	7,213,532
Shares subject to warrants to purchase common stock	426,866	426,866
Shares issuable under employee stock purchase plan	907,451	159,738
Totals	17,305,318	20,297,085

(1) The number of shares is based on the maximum number of shares issuable on exercise or conversion of the related securities as of June 30, 2023 and 2022. Such amounts have not been adjusted for the treasury-stock method or weighted-average outstanding calculations as required if the securities were dilutive.

7.    Government Contract Revenue

Biomedical Advanced Research and Development Authority

In December 2019, the Company entered into the BARDA contract, which is a five-year contract with an option to extend to ten years. The BARDA contract could result in payments to the Company of up to approximately $303.6 million and consists of a five-year base period-of-performance and a total contract period-of-performance (base period plus option exercises) of up to ten years. The BARDA contract supports the development of NUZYRA for the treatment of pulmonary anthrax, FDA post-marketing requirements, or PMRs, associated with the initial NUZYRA approval, and the ability for BARDA to procure up to 10,000 treatment courses of NUZYRA for use against potential biothreats. In September 2021, the Company and BARDA modified the original BARDA contract, herein referred to as the amended BARDA contract, to provide additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support a supplemental New Drug Application, or sNDA, to the FDA to include post-exposure prophylaxis, or PEP, in addition to the treatment of pulmonary anthrax, herein referred to as the amended option.

In July 2023, the Company and BARDA further modified the amended BARDA contract to provide new development milestones associated with the achievement of specific anthrax development milestones for the next BARDA procurement. BARDA and the Company have agreed the next procurement of NUZYRA anthrax treatment courses will be split into two equal procurements based on the achievement of specific development milestones toward both treatment and PEP indications of pulmonary anthrax.

The first of these procurements will be triggered by the delivery of positive top-line data from a dose-ranging efficacy study for PEP of inhalation anthrax in non-human primates, or NHPs. The second of these procurements will be triggered by BARDA's receipt of positive top-line data from a combination of two studies: a dose-ranging efficacy study in NHPs and a pivotal efficacy study in rabbits for the treatment of inhalation anthrax. The trigger for the final procurement of NUZYRA continues to be the Company's receipt of sNDA approval from the FDA for the treatment of inhalation anthrax.

Under the terms of the original BARDA contract, approximately $59.4 million was awarded to the Company by BARDA in December 2019 for the development of NUZYRA for the treatment of pulmonary anthrax and the purchase of an initial 2,500 treatment courses of NUZYRA. As part of this initial $59.4 million award, a $37.9 million procurement of NUZYRA was delivered to and accepted by BARDA in June 2021, and the amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the three months ended June 30, 2021. The Company has been periodically drawing down the remaining $21.5 million of the initial award based on costs incurred during the development program.

Two additional contractual services under the original BARDA contract were initiated by BARDA in March 2020 that awarded the Company approximately $76.8 million for reimbursement of existing FDA PMRs and approximately

10

$20.4 million for reimbursement of manufacturing-related requirements, which the Company has been drawing down based on costs incurred. This additional staged funding is expected to support all FDA PMRs associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study, and support the U.S. onshoring and security requirements of the Company’s manufacturing activities for NUZYRA.

BARDA initiated the amended option in September 2021 that expanded the development of NUZYRA under an FDA Animal Efficacy Rule development program to support an sNDA that will include PEP in addition to the treatment of pulmonary anthrax for a revised total of approximately $31.6 million.

A second procurement, the purchase of an additional 2,500 treatment courses of NUZYRA for a total of $36.4 million, was delivered to and accepted by BARDA in December 2022. The amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the three months ended December 31, 2022.

The remaining options under the amended BARDA contract include a maximum of approximately $79.0 million to provide for additional purchases of NUZYRA anthrax treatment courses, each of which may be exercised at BARDA’s discretion upon achievement of specific development milestones related to the anthrax treatment development program.

The BARDA contract contains a number of terms and conditions that are customary for government contracts of this nature, including provisions giving the government the right to terminate the contract at any time for its convenience.

The Company evaluated the BARDA contract under ASC, Topic 606, Revenue from Contracts with Customers, or ASC 606, and concluded that a portion of the arrangement represents a transaction with a customer. The Company identified five material promises under the BARDA contract: (i) research and development services performed for the treatment of pulmonary anthrax, (ii) the procurement of 2,500 treatment courses of NUZYRA, (iii) an option for services performed for the supplemental late-stage development of NUZYRA for treatment and prophylaxis of pulmonary anthrax, (iv) an option for services related to U.S. manufacturing onshoring and security requirements, which includes shelf-life stability extension work and regulatory activities that will benefit the manufacturing processes that support NUZYRA for the treatment of pulmonary anthrax, and (v) options to procure up to three tranches of up to 2,500 anthrax treatment courses of NUZYRA each.

In December 2019, the Company determined material promises (i) and (ii) above were performance obligations since they were distinct within the context of the contract as the services are separately identifiable from other promises within the arrangement. The Company also determined that for (i) and (ii) the transaction price included within the BARDA contract was equivalent to the standalone selling price of the services and the cost of the procurement.

The Company evaluated the material promises that contained option rights ((iii), (iv), and (v) above). The Company determined that (iii) and (iv) were not offered at a discount that is incremental to the range of discounts typically given for these goods and services, and therefore do not represent material rights. As such, options for additional services in (iii) and (iv) were not considered performance obligations at the outset of the arrangement. The Company also evaluated the future procurement option rights (v) and determined that those option rights represent a material right. As such, the optional additional NUZYRA procurements in (v) were considered performance obligations at the outset of the arrangement. The Company concluded that three performance obligations existed at the outset of the BARDA contract.

As the BARDA contract is partially within the scope of ASC 606 and partially within the scope of other guidance, the Company applied the guidance of ASC 606 to initially measure the parts of the contract to which ASC 606 is applicable. The total transaction price of the parts of the BARDA contract that existed at the outset of the contract that fall under ASC 606 was determined to be $63.6 million, inclusive of $4.2 million in variable consideration and was allocated to each of the three performance obligations based on the performance obligation’s estimated relative stand-alone selling prices. The transaction price was allocated as follows: $21.5 million to research and development services performed for the treatment of pulmonary anthrax in (i), which will be classified as government contract service revenue when recognized, $37.9 million to the procurement of 2,500 treatment courses of NUZYRA in (ii), which was classified as product revenue when recognized, and a total of $4.2 million to the options to procure up to three 2,500 treatment courses of NUZYRA in (v), which will be included within product revenue when recognized upon exercise and transfer of control of related treatment courses. The Company estimated the stand-alone selling price of the research and development services performed for the treatment of pulmonary anthrax based on the Company’s projected cost of providing the services plus an applicable profit margin commensurate with observable market data for similar services. The Company estimated the stand-alone selling price of the procurement of 2,500 treatment courses of NUZYRA based on historical pricing of the Company’s commercial products to similar customers. The Company estimated the stand-alone selling price

11

of the future procurement options based on the discount that the customer would obtain when exercising the option, adjusted for any discount that the customer could receive without entering into the contract, and the likelihood that the option will be exercised.

The Company’s performance obligations are either satisfied over time as work progresses or at a point in time.

The Company concluded that research and development services performed for the treatment of pulmonary anthrax in (i) would be recognized as government contract service revenue over time as the performance obligation is satisfied. Costs incurred represent work performed, which corresponds with, and thereby best depicts, the transfer of control to the customer. Types of contract costs include labor, material, and third-party services.

The product procurement performance obligations (ii) and, if any optional additional procurements are exercised from (v) above), generate revenue at a point in time, upon transfer of control of the product. As such, the related revenue for these performance obligations is recognized at a point in time as product revenue within the Company’s consolidated statement of operations. As of December 31, 2021, the product procurement performance obligation (ii) was completed and $37.9 million of product revenue was earned and recognized due to the delivery and acceptance of the first procurement under the BARDA contract.

In April 2020, BARDA exercised its option to obtain manufacturing-related services under material promise (iv) and the Company is treating these services as a separate $20.4 million contract for accounting purposes since manufacturing-related services were determined at the contract outset to be optional services that did not represent a material right. The Company’s manufacturing-related services are satisfied over time as work progresses.

In September 2021, BARDA exercised the amended option under the amended BARDA contract, to fund an FDA Animal Rule development program to support an sNDA to include PEP against, in addition to the treatment of, pulmonary anthrax. The Company is treating these services as a separate $31.6 million contract for accounting purposes since the completion of a late-stage development program was determined at the contract outset to be optional services that did not represent a material right. The additional services added as part of the amended option were distinct and the increased transaction price is reflective of the entity’s standalone selling prices of the additional promised services. The Company’s late-stage development program obligations are satisfied over time as work progresses. Research and development services performed under the amended option will be recognized as government contract service revenue over time as the performance obligation is satisfied.

The Company recognized $5.3 million and $4.1 million of government contract service revenue under the BARDA contract during the six months ended June 30, 2023 and June 30, 2022, respectively. The Company recognized $3.6 million and $1.9 million of government contract service revenue under the BARDA contract during the three months ended June 30, 2023 and June 30, 2022, respectively.

As of June 30, 2023, the aggregate amount of transaction price allocated to remaining performance obligations, excluding unexercised contract options, was $52.6 million. The Company expects to recognize this amount as revenue over the next three to six years.

The Company concluded that BARDA’s reimbursement for existing FDA PMRs associated with the initial NUZYRA approval was not within the scope of ASC 606 as BARDA is not receiving services as the Company’s customer. The Company estimated the consideration to be allocated to government contract grant revenue based on the consideration under the BARDA contract in excess of the estimated standalone selling prices for components of the BARDA contract accounted for under ASC 606. The Company recognizes the allocated consideration for BARDA’s reimbursement of existing FDA PMRs associated with the initial NUZYRA approval of $72.6 million as government contract grant revenue as the related reimbursable expenses are incurred.

The Company recognized $4.1 million and $4.2 million of government contract grant revenue under the BARDA contract during the six months ended June 30, 2023 and June 30, 2022, respectively. The Company recognized $1.9 million and $2.1 million of government contract grant revenue under the BARDA contract during the three months ended June 30, 2023 and June 30, 2022, respectively.

12

Contract Balances

Contract assets (i.e., unbilled accounts receivable) and/or contract liabilities (i.e., customer advances and deposits) may exist at the end of each reporting period under the BARDA contract. When amounts are received prior to performance obligations being satisfied, the amounts allocated to those performance obligations are reflected as contract liabilities on the consolidated balance sheets, as deferred revenue, until the performance obligations are satisfied.

As of June 30, 2023, $0.3 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet. As of December 31, 2022, $1.0 million of unbilled accounts receivable was recorded and is a component of accounts receivable, net on the Company’s condensed consolidated balance sheet.

As of June 30, 2023 and December 31, 2022, there was no deferred revenue recorded as a component of other current liabilities on the Company’s condensed consolidated balance sheet associated with the BARDA contract. The Company recognized the deferred revenue balance into net NUZYRA product revenue upon delivery of the second BARDA procurement in December 2022. In conjunction with the second NUZYRA procurement, the Company also recorded a $0.3 million contract asset, as a component of prepaid and other current assets, on the Company's consolidated balance sheet as of December 31, 2022. As of June 30, 2023, an insignificant net contract asset was recorded as a component of prepaid and other current assets on the Company's consolidated balance sheet.

8.    License and Collaboration Agreements

Tetraphase Pharmaceuticals, Inc.

In March 2019, Paratek and Tetraphase Pharmaceuticals, Inc., or Tetraphase, which later became a subsidiary of La Jolla Pharmaceutical Company, both of which are now a subsidiary of Innoviva, Inc, entered into a License Agreement, or the Tetraphase License Agreement. Under the terms of the Tetraphase License Agreement, Paratek granted to Tetraphase a non-exclusive, worldwide, royalty-bearing license, with the right to grant sublicenses, under certain Paratek patents, to develop, make, have, use, import, offer for sale and sell the licensed product, or XERAVATM, a drug for the treatment of complicated, intra-abdominal infections caused by bacteria, which was approved by the FDA in August 2018.

The terms of the Tetraphase License Agreement provide for Tetraphase to pay Paratek royalties at a low single digit percent on net product revenues of the licensed product sold in the U.S. Tetraphase’s obligation to pay royalties with respect to the licensed product shall be retroactive to the date of the first commercial sale of the licensed product in the U.S., which occurred in February 2019. La Jolla is currently selling XERAVATM (Eravacycline) in the U.S.

The Tetraphase License Agreement will continue until the expiration of and payment by Tetraphase of all Tetraphase's payment obligations, which is when there are no longer any valid claims of the licensed Paratek patents that would be infringed, in the absence of a license, by a manufacture, use, or sales of the licensed product. The principal licensed patent under the Tetraphase License Agreement is expected to expire in October 2023.

In accordance with the Company’s revenue recognition policy, the Company recognized an insignificant amount of royalty revenue during the three and six months ended June 30, 2023 and June 30, 2022 under the Tetraphase License Agreement.

Zai Lab (Shanghai) Co., Ltd.

In April 2017, Paratek Bermuda Ltd., a former wholly-owned subsidiary of Paratek Pharmaceuticals, Inc., and Zai entered into a License and Collaboration Agreement, or the Zai Collaboration Agreement. On December 18, 2019, Paratek Bermuda Ltd. assigned its rights under the Zai Collaboration Agreement to Paratek Pharmaceuticals, Inc. Under the terms of the Zai Collaboration Agreement, Paratek granted Zai an exclusive license to develop, manufacture and commercialize omadacycline, or the licensed product, in the People’s Republic of China, Hong Kong, Macau and Taiwan, or the Zai territory, for all human therapeutic and preventative uses other than biodefense. Zai is responsible for the development, manufacturing and commercialization of the licensed product in the Zai territory, at its sole cost with certain assistance from Paratek.

Under the terms of the Zai Collaboration Agreement, Paratek earned an upfront cash payment of $7.5 million in April 2017, $5.0 million upon approval by the FDA of a NDA submission in the CABP indication in October 2018,

13

$3.0 million upon submission of the first regulatory approval application for a licensed product in the People’s Republic of China in December 2019, and a $6.0 million milestone payment upon regulatory approval of omadacycline for the treatment of adults with ABSSSI and CABP in the People’s Republic of China in December 2021. Paratek is also eligible to receive up to $40.5 million in potential future commercial milestone payments. The terms of the Zai Collaboration Agreement also provide for Zai to pay Paratek tiered royalties at a low double digit to mid-teen percent on net sales of the licensed product in the Zai territory.

The Zai Collaboration Agreement will continue, on a region-by-region basis, until the expiration of and payment by Zai of all Zai’s payment obligations, which is until the later of: (i) the abandonment, expiry or final determination of invalidity of the last valid claim within the Paratek patents that covers the licensed product in the region in the Zai territory in the manner that Zai or its affiliates or sublicensees exploit the licensed product or intend for the licensed product to be exploited; or (ii) 2032, the eleventh anniversary of the first commercial sale of such licensed product in such region.

The Company evaluated the Zai Collaboration Agreement under ASC 606. The Company determined that there were six material promises under the Zai Collaboration Agreement: (i) an exclusive license to develop, manufacture and commercialize omadacycline in the Zai territory, (ii) the initial technology transfer (iii) a transfer of certain materials and materials know-how, (iv) optional manufacturing services, (v) optional regulatory support and (vi) optional commercialization support. The Company determined that the exclusive license and initial technology transfer were not distinct from one another, as the license has limited value without the transfer of the Company’s technology, which will allow Zai to develop the manufacturing process and commercialize omadacycline in the Zai territory in the timeline anticipated under the agreement. Without the technology transfer, Zai would incur additional costs to recreate the Company’s know-how. Therefore, the license and initial technology transfer are combined as a single performance obligation. The transfer of materials is a single distinct performance obligation. The Company evaluated the option rights for manufacturing services, regulatory support and commercialization support to determine whether they represent or include material rights to Zai and concluded that the options were not issued at a discount, and therefore do not represent material rights. As such, they are not considered performance obligations at the outset of the arrangement.

Based on these assessments, the Company determined that two performance obligations existed at the outset of the Zai Collaboration Agreement: (i) the exclusive license combined with the initial technology transfer and (ii) the transfer of certain materials. The Company has recognized $21.5 million in milestone revenue, as described above, under the Zai Collaboration Agreement as of June 30, 2023. The performance obligation to deliver the license was satisfied in 2017 and research and development services were completed by December 2021. Milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. Therefore, the $6.0 million milestone payment upon regulatory approval of NUZYRA in the People’s Republic of China was recognized in December 2021.

As of June 30, 2023 and December 31, 2022 there was no deferred revenue recorded as a component of other current liabilities on the Company’s condensed consolidated balance sheet associated with the Zai Collaboration Agreement.

Almirall, LLC

In July 2007, the Company and Warner Chilcott Company, Inc. (which became a part of Allergan plc, or Allergan), entered into a collaborative research and license agreement under which the Company granted Allergan an exclusive license to research, develop, manufacture and commercialize tetracycline products for use in the U.S. for the treatment of acne and rosacea. In September 2018, Allergan assigned to Almirall, its rights under the collaboration agreement, or the Almirall Collaboration Agreement. Since Allergan did not exercise its development option with respect to the treatment of rosacea prior to initiation of a Phase 3 trial for the product, the license grant to Allergan, which was assigned to Almirall, converted to a non-exclusive license for the treatment of rosacea as of December 2014.

Under the terms of the Almirall Collaboration Agreement, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize tetracycline compounds that are specified in the agreement for the treatment of acne. The Company has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compounds in the U.S. for the treatment of acne, and Almirall has agreed during the term of the Almirall Collaboration Agreement not to directly or indirectly develop or commercialize any tetracycline compound included as part of the agreement for any use other than as provided in the Almirall Collaboration Agreement.

In February 2020, the Company finalized a license agreement with Almirall granting the Company exclusive rights to develop, manufacture and commercialize sarecycline outside of the U.S., including rights of reference to Almirall’s

14

clinical data thus formalizing the Company’s rights to develop, manufacture and commercialize sarecycline in the rest of the world. In connection with that license, the Company then exclusively licensed Almirall pursuant to the Almirall China License Agreement, the rights to develop, manufacture and commercialize sarecycline in the greater China region. Almirall currently holds a nonexclusive license to develop and commercialize sarecycline for the treatment of rosacea in the U.S., and in the U.S., Paratek cannot grant rights on back-up compounds, lead candidate(s), or products licensed to Almirall for rosacea.

The Almirall Collaboration Agreement contains two performance obligations: (i) an exclusive license to research, develop and commercialize tetracycline products for use in the U.S. for the treatment of acne and non-exclusive rights to rosacea and (ii) research and development services. The performance obligation to deliver the license was satisfied upon execution of the Almirall Collaboration Agreement in July 2007. All research and development services were completed by December 2010. The options provided to Almirall for additional development services do not provide Almirall with a material right as these services will not be provided at a significant or incremental discount. As such, the option services are not performance obligations. As the performance obligation to deliver the license was satisfied in 2007 and research and development services were completed by December 2010, all subsequent milestone payments are recognized as revenue when the risk of significant reversal is resolved, generally when the milestone event occurs. The Company recognized all Almirall milestones in prior years. There are no milestones left to be recognized under the Almirall Collaboration Agreement.

Almirall is also obligated to pay the Company tiered royalties, ranging from the mid-single digits to the low double digits, based on net sales of tetracycline compounds developed under the Almirall Collaboration Agreement, with a standard royalty reduction post patent expiration for such product for the remainder of the royalty term.

Royalty payments are recognized when the sales occur. During the six months ended June 30, 2023 and June 30, 2022, the Company recognized $0.6 million and $0.9 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. During the three months ended June 30, 2023 and June 30, 2022, the Company recognized $0.1 million and $0.4 million of royalty revenue, respectively, for sales of SEYSARA in the U.S. by Almirall under the Almirall Collaboration Agreement. Royalty revenue recognized for sales of SEYSARA in the U.S. is estimated using third-party data and an approximation of discounts and allowances to calculate net product sales, to which the Company then applies the applicable royalty percentage specified in the Almirall Collaboration Agreement. Differences between actual and estimated royalty revenues are adjusted for in the period in which they become known, which is expected to be the following quarter.

In February 2020, the Company entered into (i) an ex-U.S. license agreement with Almirall, or the Ex-U.S. License, which grants the Company an exclusive license in and to certain technology owned or in-licensed by Almirall or its affiliates in order to research, develop, manufacture and commercialize sarecycline for the treatment of acne in all countries other than the U.S. and (ii) a license agreement with Almirall that is specific to the greater China region, or the China License, under which we granted to Almirall an exclusive license in and to certain technology owned or in-licensed by the Company or its affiliates in order to research, develop and commercialize sarecycline for the treatment of acne in the greater China region.

Under the terms of the China License, Almirall is responsible for and is obligated to use commercially reasonable efforts to develop and commercialize sarecycline for the treatment of acne, including requirements to (i) file an Investigational New Drug Application (or analogous foreign submission) for sarecycline for the treatment of acne in the greater China region in calendar year 2020, (ii) receive regulatory approval for sarecycline for the treatment of acne in the greater China region within seven years following such submission and (iii) commercialize sarecycline for the treatment of acne in the greater China region within eighteen months after obtaining regulatory approval. If Almirall does not satisfy the diligence requirements set forth in subclauses ii or iii above, we may terminate the China License.

In connection with the Ex-U.S. License, the Company pays Almirall, on a country-by-country and product-by-product basis, (i) for eight years following the first commercial sale of a sarecycline product in a country, a royalty in the middle-single digits on its or its affiliates’ nets sales of sarecycline products outside of the U.S., subject to certain standard reductions, and (ii) for fifteen years following the first commercial sale of a sarecycline product in a country, a percentage of the consideration (e.g., milestones, royalties) we receive from sublicensees in connection with developing and commercializing sarecycline outside of the U.S., which ranges from one-fifth to one-half of such consideration, subject to certain standard reductions. In connection with the China License, for fifteen years following the first commercial sale of a sarecycline product in China, Almirall pays the Company a royalty in the high-single digits on their, their affiliates’ or their sublicensees’ net sales of sarecycline products in the greater China region, subject to certain standard reductions.

15

Tufts University

In February 1997, the Company and Tufts University, or Tufts, entered into a license agreement under which the Company acquired an exclusive license to certain patent applications and other intellectual property of Tufts related to the drug resistance field to develop and commercialize products for the treatment or prevention of bacterial or microbial diseases or medical conditions in humans or animals or for agriculture. The Company subsequently entered into eleven amendments to that agreement, or collectively the Tufts License Agreement, to include patent applications filed after the effective date of the original license agreement, to exclusively license additional technology from Tufts, to expand the field of the agreement to include disinfectant applications, and to change the royalty rate and percentage of sublicense income paid by the Company to Tufts under sublicense agreements with specified sublicensees. The Company is obligated under the Tufts License Agreement to provide Tufts with annual diligence reports and a business plan and to meet certain other diligence milestones. The Company has the right to grant sublicenses of the licensed rights to third parties, which will be subject to the prior approval of Tufts unless the proposed sublicensee meets a certain net worth or market capitalization threshold. The Company is primarily responsible for the preparation, filing, prosecution and maintenance of all patent applications and patents covering the intellectual property licensed under the Tufts License Agreement at its sole expense. The Company has the first right, but not the obligation, to enforce the licensed intellectual property against infringement by third parties.

The Company issued Tufts 1,024 shares of the Company’s common stock on the date of execution of the original license agreement, and the Company was required to make certain payments of up to $0.3 million to Tufts upon the achievement by products developed under the agreement of specified development and regulatory approval milestones. The Company made a payment of $50,000 to Tufts for achieving the first milestone following commencement of the Phase 3 clinical trial for omadacycline and a payment of $100,000 to Tufts for achieving the second milestone following its first marketing application submitted in the U.S. The third, and final, payment of $150,000 became due upon FDA approval of omadacycline in October 2018. The Company is also obligated to pay Tufts a minimum royalty payment in the amount of $25,000 per year. In addition, the Company is obligated to pay Tufts royalties based on gross sales of products, as defined in the agreement, ranging in the low single digits depending on the applicable field of use for such product sale. If the Company enters into a sublicense under the agreement, based on the applicable field of use for such product, the Company will be obligated to pay Tufts (i) a percentage, ranging from 10% to 14% (ten percent to fourteen percent) for compounds other than omadacycline, and a percentage in the single digits for the compound omadacycline, of that portion of any sublicense issue fees or maintenance fees received by the Company that are reasonably attributable to the sublicense of the rights granted to the Company under the Tufts License Agreement and (ii) the lesser of (a) a percentage, ranging from the low tens to the high twenties based on the applicable field of use for such product, of the royalty payments made to the Company by the sublicensee or (b) the amount of royalty payments that would have been paid by the Company to Tufts if it had sold the product.

Unless terminated earlier, the Tufts License Agreement will expire at the same time as the last-to-expire patent in the patent rights licensed to the Company under the agreement and after any such expiration the Company will continue to have an exclusive, fully-paid-up license to such intellectual property licensed from Tufts. Tufts has the right to terminate the agreement upon 30 days’ notice should the Company fail to make a material payment under the Tufts License Agreement or commit a material breach of the agreement and not cure such failure or breach within such 30-day period, or if, after the Company has started to commercialize a product under the Tufts License Agreement, the Company ceases to carry on its business for a period of 90 consecutive days. The Company has the right to terminate the Tufts License Agreement at any time upon 180 days’ notice.

During the six months ended June 30, 2023 and June 30, 2022, the Company incurred $0.9 million and $0.7 million of royalty expense, respectively, under the Tufts License Agreement. During the three months ended June 30, 2023 and June 30, 2022, the Company incurred $0.5 million and $0.4 million of royalty expense, respectively, under the Tufts License Agreement.

16

Past Collaborations

Novartis International Pharmaceutical Ltd.

In September 2009, the Company and Novartis International Pharmaceutical Ltd., or Novartis, which merged into Novartis Pharma AG, a wholly owned subsidiary of Novartis AG, entered into a Collaborative Development, Manufacture and Commercialization License Agreement, or the Novartis Agreement, which provided Novartis with a global, exclusive patent and technology license for the development, manufacturing and marketing of omadacycline. The Novartis Agreement was terminated by Novartis without cause in June 2011 and the termination was effective 60 days later. The Company and Novartis subsequently entered in a letter agreement in January 2012, or the Novartis Letter Agreement, as amended, pursuant to which we reconciled shared development costs and expenses and granted Novartis a right of first negotiation with respect to commercialization rights of omadacycline following approval of omadacycline from the FDA, European Medicines Agency, or EMA, or any regulatory agency, but only to the extent the Company had not previously granted such commercialization rights related to omadacycline to another third-party as of any such approval. The Company also agreed to pay Novartis a 0.25% royalty, to be paid from net sales received by the Company in any country following the launch of omadacycline in that country and continuing until the later of expiration of the last active valid patent claim covering such product in the country of sale and 10 years from the date of first commercial sale in such country. The first royalty payment became payable as of March 31, 2019. The amended Novartis Letter Agreement resulted in a long-term liability in the amount of $2.3 million and $2.5 million as of June 30, 2023 and December 31, 2022, respectively, included within “Other Liabilities” on the Company’s consolidated balance sheet. In addition, short-term liabilities of $0.4 million and $0.4 million included within “Other Current Liabilities” on our consolidated balance sheets as of June 30, 2023 and December 31, 2022, respectively, represent the portion of royalty payments due to Novartis within twelve months of each balance sheet date. There are no other payment obligations under the Novartis Agreement or the amended Novartis Letter Agreement.

For additional information related to these agreements, as well as the Company’s other significant collaborative agreements, please read Note 6, License and Collaboration Agreements, to the consolidated financial statements included within the Company’s 2022 Form 10-K.

9.    Capital Stock

On May 17, 2021, the Company entered into an At-the-Market Sales Agreement, or the Sales Agreement, with BTIG, LLC, or BTIG, under which it may offer and sell its common stock having aggregate sales proceeds of up to $50.0 million from time to time through BTIG as its sales agent. Sales of the Company’s common stock through BTIG, if any, will be made by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415(a)(4) under the Securities Act of 1933, as amended, including without limitation sales made directly on the Nasdaq Global Market or any other existing trading market for its common stock. BTIG will use commercially reasonable efforts to sell the Company’s common stock from time to time, based upon instructions from the Company (including any price, time or size limits or other customary parameters or conditions the Company may impose). The Company will pay BTIG a commission of 3% of the gross sales proceeds of any common stock sold through BTIG under the Sales Agreement. The Company has also provided BTIG with customary indemnification rights.

The Company is not obligated to make any sales of common stock under the Sales Agreement. The offering of shares of the Company’s common stock pursuant to the Sales Agreement will terminate upon the earlier of (i) the sale of all common stock subject to the Sales Agreement, or (ii) termination of the Sales Agreement in accordance with its terms.

As of July 31, 2023, $23.3 million remains available for sale under the Sales Agreement.

On May 9, 2023, the Company filed a registration statement on Form S-3 with the SEC to sell certain of its securities in an aggregate amount of up to $250.0 million. As of July 31, 2023, $250.0 million remains available on this shelf registration statement.

17

10.    Accrued Expenses

Accrued expenses consist of the following (in thousands):

	June 30,		December 31,
	2023		2022
Accrued sales allowances	$	14,823	$	9,555
Accrued compensation	6,997		11,339
Accrued interest	2,401		2,392
Accrued commercial	2,693		2,668
Accrued inventory	20		327
Accrued contract research	2,164		1,989
Accrued professional fees	609		702
Accrued manufacturing	527		826
Accrued other	606		1,132
Accrued legal costs	3,963		280
Total	$	34,803	$	31,210

11.    Fair Value Measurements

Financial instruments, including cash, cash equivalents, restricted cash, money market funds, U.S. treasury securities, accounts receivable, accounts payable, and accrued expenses are carried on the condensed consolidated financial statements at amounts that approximate fair value. The fair value of the Company’s long-term debt is determined using current applicable rates for similar instruments as of the balance sheet date. The fair value of the Company’s debt (including the Notes as defined in Note 13, Debt), was $256.5 million as of June 30, 2023 and $227.2 million as of December 31, 2022. The fair value of the Company’s debt was determined using Level 2 inputs. Fair values are based on assumptions concerning the amount and timing of estimated future cash flows and assumed discount rates, reflecting varying degrees of perceived risk.

There were no financial assets and liabilities measured at fair value as of June 30, 2023 and December 31, 2022.

12.    Stock-Based and Incentive Compensation

Stock-based Compensation

The following table presents stock-based compensation expense included in the Company’s condensed consolidated statements of operations and comprehensive income (loss) (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2023		2022		2023		2022
Research and development expense	$	308	$	515	$	614	$	692
Selling, general and administrative expense	1,918		3,371		3,758		5,662
Total stock-based compensation expense	$	2,226	$	3,886	$	4,372	$	6,354

Stock-based compensation expense is estimated as of the grant date based on the fair value of the award and is recognized as expense over the requisite service period, which generally represents the vesting period. The Company

18

estimates the fair value of its stock options using the Black-Scholes option-pricing model. The weighted-average assumptions used to determine the fair value of the stock option grants is as follows:

	Six Months Ended June 30,
	2023		2022
Volatility	66.6	%	62.2	%
Risk-free interest rate	3.8	%	2.3	%
Expected dividend yield	0.0	%	0.0	%
Expected life of options (in years)	6.1		5.9

Stock Plan Activity

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Equity Incentive Plan, or the 2015 Plan, which was approved by Company stockholders at the annual meeting of stockholders held on June 9, 2015. As of June 30, 2023, there are 4,545,170 shares available for future issuance under the 2015 Plan.

The Company recognizes the stock-based compensation expense of awards subject to performance-based vesting conditions over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance using the accelerated attribution method. A change in the requisite service period that does not change the estimate of the total stock-based compensation expense (i.e., it does not affect the grant-date fair value or quantity of awards to be recognized) is recognized prospectively over the remaining requisite service period.

During the six months ended June 30, 2023, the Company’s Board of Directors granted 140,000 RSUs to directors of the Company under the 2015 Plan. The RSU awards granted to directors of the Company during the six months ended June 30, 2023, are subject to time-based vesting over a period of one year.

Performance-based RSU, or PRSU, awards granted to certain executives and employees of the Company in prior years remained outstanding and probable as of June 30, 2023, and will vest as follows: 15/55 of the February 2020 grants will vest on achievement of certain clinical milestones related to NUZYRA, and 25/55 and 10/55 of the March 2021 grants will vest on certain net product revenue achievements and on achievement of certain clinical milestones related to NUZYRA, respectively.

The Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2015 Inducement Plan, or the 2015 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 360,000 shares of common stock solely for the grant of inducement stock options to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. The Company has not made any grants under the 2015 Inducement Plan since December 31, 2015. Although the Company does not currently anticipate the issuance of additional grants under the 2015 Inducement Plan, as of June 30, 2023, 341,500 shares remain available for grant under that plan, as well as any shares underlying outstanding stock options that may become available for grant pursuant to the plan’s terms. It is therefore possible that the Company may, based on the business and recruiting needs of the Company, issue additional stock options under the 2015 Inducement Plan.

In June 2017, the Company’s Board of Directors adopted the Paratek Pharmaceuticals, Inc. 2017 Inducement Plan, or the 2017 Inducement Plan, in accordance with Nasdaq Rule 5635(c)(4), reserving 550,000 shares of common stock solely for the grant of inducement stock options to employees entering into employment or returning to employment after a bona fide period of non-employment with the Company. In October 2018 and March 2022, the Company’s Board of Directors approved the reserve of an additional 500,000 shares and 750,000 shares, respectively, for the 2017 Inducement Plan, for a total of 1,800,000 shares reserved for issuance under it.

During the six months ended June 30, 2023, the Company’s Board of Directors granted 8,400 stock options and 7,000 RSU awards to employees of the Company under the 2017 Inducement Plan. The stock option awards are generally subject to time-based vesting over a period of one to four years. The RSU awards are generally subject to time-based vesting, with 100% of the shares of common stock subject to the RSU award vesting three years from the grant date. As of June 30, 2023, 773,085 shares remain available for grant under the 2017 Inducement Plan, as well as any shares underlying awards that may become available for grant pursuant to the plan’s terms.

19

Stock Options

A summary of stock option activity for the six months ended June 30, 2023 is as follows:

	Number of Shares	Weighted Average Exercise Price		Weighted Average Remaining Contractual Term (in years)	Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2022	1,374,152	$	11.14	5.84
Granted	8,400	$	1.99
Exercised	—	$	—
Cancelled or forfeited	(35,369)	$	6.61
Outstanding at June 30, 2023	1,347,183	$	11.20	5.31	$	—
Exercisable at June 30, 2023	1,124,469	$	12.67	4.68	$	—

The total intrinsic value of stock options granted, cancelled or forfeited was insignificant for the six months ended June 30, 2023.

Restricted Stock Units

A summary of RSU activity for the six months ended June 30, 2023 is as follows:

	Number of Shares	Weighted Average Grant Date Fair Value
Unvested balance at December 31, 2022	4,752,538	$	5.10
Granted	147,000	2.05
Released	(630,680)	4.38
Forfeited	(22,401)	3.51
Unvested balance at June 30, 2023	4,246,457	$	5.11

Total unrecognized stock-based compensation expense for all stock-based awards was $6.8 million as of June 30, 2023. This amount will be recognized over a weighted-average period of 1.14 years.

2009 Employee Stock Purchase Plan

In June 2009, at the annual meeting of stockholders, the stockholders of the Company approved the 2009 Employee Stock Purchase Plan, or the 2009 ESPP. As of June 30, 2023, 36,539 shares were available for issuance under the 2009 ESPP. Since the merger involving privately-held Paratek Pharmaceuticals, Inc. and Transcept Pharmaceuticals, Inc., the Company has not made the 2009 ESPP available to employees.

2018 Employee Stock Purchase Plan

The Company’s Board of Directors adopted, and in June 2018 Company’s stockholders approved, the Paratek Pharmaceuticals, Inc. 2018 Employee Stock Purchase Plan, or the 2018 ESPP. The 2018 ESPP was amended in October 2018 to change the commencement dates of the offering periods. The maximum aggregate number of shares of the Company’s common stock that may be purchased under the 2018 ESPP is 943,294 shares, or the ESPP Share Pool, subject to adjustment as provided for in the 2018 ESPP. The ESPP Share Pool represented 3% of the total number of shares of our common stock outstanding as of March 31, 2018. The 2018 ESPP allows eligible employees to purchase shares during certain offering periods, which will be six-month periods commencing June 1 and ending November 30 and commencing December 1 and ending May 31 of each year. The first offering under the 2018 ESPP was December 1, 2018. On June 6, 2023, the Company's stockholders approved the Amended and Restated Employee Stock Purchase Plan, which increased

20

the number of authorized shares of common stock under the plan from 943,294 to 1,793,067 shares. As of June 30, 2023, 870,912 shares remained available for issuance under the 2018 ESPP.

Revenue Performance Incentive Plan

On October 4, 2018, the Company adopted the Revenue Performance Incentive Plan, or the Plan, to grant performance-based cash incentive awards to key employees and consultants of the Company. The Plan provides for an incentive pool of up to $50.0 million, plus accrued interest during the period between the awards’ vesting date and payment dates. Each participant will be allocated a percentage of the incentive pool.

The incentive pool will be divided into two equal tranches with the first tranche vesting upon the Company’s achievement of cumulative net product revenues over $300.0 million by December 31, 2025, or Tranche 1, and the second tranche vesting upon the Company’s achievement of cumulative product revenues over $600.0 million by December 31, 2026, or Tranche 2. Participants will vest annually in each tranche of their awards in four equal installments on December 31, 2019, December 31, 2020, December 31, 2021, and December 31, 2022, subject to their continued employment with the Company through the applicable vesting date. Participants subsequently added to the plan, will vest on a weighted basis over three years, subject to their continued employment with the Company through the applicable vesting date. Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant who has remained in continuous employment with the Company through December 31, 2022 will be 100% vested in the applicable tranche. In the event of a change of control of the Company prior to December 31, 2026, participants whose employment has terminated prior to such date will be eligible for payouts under the Plan based on the then-vested portion of their awards, and participants who have remained employed through the change of control will be deemed to have time vested in full in each tranche of their awards.

Upon the achievement of a Tranche 1 or Tranche 2 milestone (but not a deemed achievement in connection with a change of control), each participant’s payout in respect of the applicable tranche of his or her award will equal (a) the participant’s then-vested percentage, multiplied by (b) $25 million, multiplied by (c) the participant’s individual percentage allocation of the incentive pool.

If a change of control occurs prior to December 31, 2026, and the Tranche 1 milestone was not achieved prior to the change of control, the Tranche 1 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 50% and (2) the cumulative product revenues as of the change of control, divided by $300.0 million. If a change of control occurs prior to December 31, 2026, and the Tranche 2 milestone was not achieved prior to the change of control, the Tranche 2 milestone will be deemed to be achieved at a percentage equal to the greater of (1) 30% and (2) the cumulative product revenues as of the change of control, divided by $600.0 million. A participant’s payout in respect of each tranche of his or her award in a change of control will equal (1) the participant’s then-vested percentage of such tranche, multiplied by (2) the percentage of that tranche’s milestone that has been achieved or is deemed to have been achieved, multiplied by (3) $25.0 million, multiplied by (4) the participant’s individual percentage allocation of the incentive pool.

The Tranche 1 milestone vested on January 31, 2023, upon the Company's achievement of cumulative net product revenues over $300.0 million. Amounts payable from the achievement of the Tranche 1 milestone will be paid in a lump-sum in the first quarter of 2026 and amounts that become payable upon achievement of the Tranche 2 milestone will be paid in a lump-sum in the first quarter of 2027. In the event of a change of control, any portion of the incentive pool that is earned, but unpaid, or deemed earned in connection with the change of control will be paid at the time of the change of control.

If a change of control occurs prior to the achievement of either or both of the Tranche 1 and Tranche 2 milestones, the awards will remain outstanding and the remaining unpaid portion of the incentive pool applicable to the Tranche 1 or Tranche 2 milestone, as applicable, will be paid following the achievement of either such milestone at the time or times the awards would otherwise be paid out. Any successor in interest to the Company upon or following a change of control will be required to assume all obligations under the Plan.

Awards may be paid out in cash or in a combination of cash and registered securities of equal value (based on the Company’s 20-day trailing average closing common stock price), with the portion paid in registered securities not to exceed 50% of the aggregate payment amount with respect to each tranche; provided, however, that any amounts that are immediately payable on closing with respect to an award in connection with a change in control will be paid in cash.

21

The Company recognizes the compensation cost over the requisite service period, to the extent achievement of the performance condition is deemed probable relative to targeted performance. The performance condition under Tranche 1 of the Plan was deemed probable during 2021. The performance condition under Tranche 2 was deemed probable during 2022. Accordingly, approximately $0.6 million of compensation expense was recognized during the six months ended June 30, 2023. Compensation expense of $0.5 million was recognized during the six months ended June 30, 2022. Compensation cost of $45.9 million and $45.3 million is included in accrued long-term compensation in the Company’s consolidated balance sheet as of June 30, 2023 and December 31, 2022, respectively. Accrued interest of $0.7 million is included in accrued long-term compensation in the Company's consolidated balance sheet as of June 30, 2023. No accrued interest existed as of December 31, 2022 as the achievement of the Tranche 1 milestone occurred during the six months ended June 30, 2023.

13.    Debt

Long-Term Debt

R-Bridge Loan Agreement

On December 31, 2020, or the Closing Date, the Company, through its wholly-owned subsidiary PRTK SPV2 LLC, a Delaware limited liability company, or the Subsidiary, entered into a royalty and revenue interest-backed loan agreement, or the R-Bridge Loan Agreement, with an affiliate of R-Bridge Healthcare Investment Advisory, Ltd., or the R-Bridge Lender. Pursuant to the terms of the R-Bridge Loan Agreement, the Subsidiary borrowed a $60.0 million term loan, secured by, and repaid with proceeds from, (i) royalties from the Zai Collaboration Agreement, and such royalties, or the Royalty Interest, and (ii) a revenue interest based on the Company’s U.S. sales of NUZYRA in an initial amount of two and a half percent (2.5%), which amount may adjust under certain circumstances up to five percent (5%), of the Company’s net U.S. sales, subject to an annual cap of $10.0 million, which may adjust under certain circumstances to $12.0 million, or the Revenue Interest.

Under the R-Bridge Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 7.0%, increasing to an annual rate of 10% during the continuance of any event of default. Payments of the obligations outstanding under the R-Bridge Loan Agreement are made quarterly out of the Royalty Interest payments and Revenue Interest payments received by the Subsidiary during such quarter, or the Collection Amount. On each payment date, after payment of certain expenses, the Collection Amount shall be applied first to accrued interest, with any excess up to $15.0 million per annum applied to repay principal until the balance is fully repaid, and any shortfalls being capitalized and added to the principal balance of the loan. Amounts in excess of the $15.0 million annual cap shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement. Following repayment in full of the loan, the first $15.0 million per annum in Collection Amount shall be paid to the Company and any amounts in excess shall be shared between the Company and the R-Bridge Lender based on a formula set out in the R-Bridge Loan Agreement.

Prior to the eighth (8th) anniversary of the Closing Date, the R-Bridge Loan Agreement will automatically terminate once the Subsidiary has paid to the R-Bridge Lender, in the form of regularly scheduled payments or as a voluntary prepayment, a capped amount of $114.0 million, less principal, interest and certain fee payments through the date of such prepayment, or the Capped Amount. From and after the eighth (8th) anniversary of the Closing Date, the Revenue Interest can be terminated by payment of the Capped Amount, but the Royalty Interest payments shall continue until maturity of the R-Bridge Loan Agreement on December 31, 2032, at which time, the outstanding principal amount of the loan, if any, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash by the Subsidiary.

The Company’s subsidiary, PRTK SPV1 LLC, a Delaware limited liability company and owner of the Subsidiary’s capital stock, has entered into a Pledge and Security Agreement in favor of the R-Bridge Lender, pursuant to which the Subsidiary’s obligations under the R-Bridge Loan Agreement are secured by PRTK SPV1 LLC’s pledge of all of the Subsidiary’s capital stock.

The R-Bridge Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The R-Bridge Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Zai Collaboration Agreement; and permitting any additional liens on the collateral provided to the R-Bridge Lender under the

22

R-Bridge Loan Agreement. As of June 30, 2023, the Company was in compliance with all covenants under the R-Bridge Loan Agreement.

An ancillary agreement executed by the Company and the Subsidiary in respect of the Revenue Interest, contains negative covenants applicable to the Company, including restrictions on the sale or transfer of our assets related to NUZYRA and giving rise to the Revenue Interest, each subject to the exceptions set forth therein.

The R-Bridge Loan Agreement contains customary defined events of default, upon which any outstanding principal, unpaid interest, and other obligations of the Subsidiary, shall be immediately due and payable by the Subsidiary. These include: failure to pay any principal or interest when due; failure to pay the Capped Amount when due following a non-qualified change of control of the Company, any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured breach of our representations, warranties or covenants under an ancillary agreement executed by the Company and the Subsidiary in respect of the Royalty Interest; any termination of the Zai Collaboration Agreement; and certain bankruptcy or insolvency events. No events of default had occurred under the R-Bridge Loan Agreement through June 30, 2023.

The Company raised approximately $58.3 million in net proceeds in connection with the R-Bridge Loan Agreement, comprised of the $60.0 million term loan funded at execution, net of $1.1 million in lender fees accounted for as debt discount and $0.6 million in direct and incremental third-party expenses accounted for as debt issuance costs. The net proceeds of the term loan, together with cash on hand, was used to prepay in full all obligations outstanding under our loan arrangement with Hercules Capital, Inc.

The accounting for the R-Bridge Loan Agreement requires the Company to make certain estimates and assumptions, particularly about future royalties under the Zai Collaboration Agreement and sales of NUZYRA in the U.S. Such estimates and assumptions are utilized in determining the expected repayment term, amortization period of the debt discount and issuance costs, accretion of interest expense and classification between current and long-term portions of amounts outstanding. The Company amortizes the debt discount and issuance costs to interest expense over the expected term of the arrangement using the interest method based on projected cash flows. Similarly, the Company classifies as current debt for the R-Bridge Loan Agreement, amounts that are expected to be repaid during the succeeding twelve months after the reporting period end. However, the repayment of amounts due under the R-Bridge Loan Agreement is variable because the cash flows to be utilized for periodic payments is a function of amounts received by the Company with respect to the Royalty Interest and the Revenue Interest. Accordingly, the estimates of the magnitude and timing of amounts to be available for debt service are subject to significant variability and thus, subject to significant uncertainty. Therefore, these estimates and assumptions are likely to change, which may result in future adjustments to the portion of the debt that is classified as a current liability, the amortization of debt discount and issuance costs and the accretion of interest expense.

The amount of principal to be repaid in each of the five succeeding years is not fixed and determinable.

Other amounts that may become due and payable under the R-Bridge Loan Agreement, including amounts shared between the parties with respect to cash flows received in excess of pre-defined thresholds, are recognized as additional interest expense when they become probable and estimable.

The following table summarizes the impact of the R-Bridge Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2023 and December 31, 2022 (in thousands):

	June 30, 2023		December 31, 2022
Principal debt including paid-in-kind interest	$	58,960	$	59,806
Unamortized debt discount and issuance costs	(1,071)		(1,205)
Carrying value	$	57,889	$	58,601

In accordance with the terms of the R-Bridge Loan Agreement, the Company repaid approximately $0.8 million of the outstanding principal balance during the six months ended June 30, 2023, comprised of the excess of the Collection Amount over accrued interest on the loan for the six months ended June 30, 2023.

23

The Company recognized coupon interest expense of $2.1 million and $2.2 million, and an insignificant amount of amortization expense on debt issuance costs, on the R-Bridge Loan Agreement for the six months ended June 30, 2023 and June 30, 2022, respectively. The Company recognized coupon interest expense of $1.1 million, and an insignificant amount of amortization expense on debt issuance costs, on the R-Bridge Loan Agreement for each of the three months ended June 30, 2023 and June 30, 2022.

Royalty-Backed Loan Agreement

On February 25, 2019, the Company, through its wholly-owned subsidiary Paratek Royalty Corporation, or the Subsidiary, entered into a royalty-backed loan agreement, or the Royalty-Backed Loan Agreement, with Healthcare Royalty Partners III, L.P., or HCRP. Pursuant to the terms of the Royalty-Backed Loan Agreement, upon the satisfaction of the conditions precedent set forth therein, the Subsidiary borrowed a $32.5 million loan, which was secured by, and will be repaid based upon, royalties from the Almirall Collaboration Agreement. On May 1, 2019, the Company received $27.8 million, net of $0.5 million lender discount, $0.2 million in lender expenses incurred, and $4.0 million that was deposited into an interest reserve account. The Company also paid $1.2 million in other lender fees related to the Royalty-Backed Loan Agreement.

Under the Royalty-Backed Loan Agreement, the outstanding principal balance will bear interest at an annual rate of 12.0%. Payments of interest under the Royalty-Backed Loan Agreement are made quarterly out of the Almirall Collaboration Agreement royalty payments received since the immediately preceding payment date. On each interest payment date, any royalty payments in excess of accrued interest on the loan will be used to repay the principal of the loan until the balance is fully repaid and any royalty shortfalls will be capitalized and added to the principal balance of the loan. In addition, the Subsidiary will make up-front payments to HCRP of (i) a 1.5% fee and (ii) up to $300,000 for HCRP’s expenses. The Royalty-Backed Loan Agreement matures on May 1, 2029, at which time, if not earlier repaid in full, the outstanding principal amount of the loan, together with any accrued and unpaid interest, and all other obligations then outstanding, shall be due and payable in cash. The Company has entered into a Pledge and Security Agreement in favor of HCRP, pursuant to which the Subsidiary’s obligations under the Royalty-Backed Loan Agreement are secured by a pledge of all of the Company’s holdings of the Subsidiary’s capital stock.

The Royalty-Backed Loan Agreement contains certain customary affirmative covenants, including those relating to: use of proceeds; maintenance of books and records; financial reporting and notification; compliance with laws; and protection of Company intellectual property. The Royalty-Backed Loan Agreement also contains certain customary negative covenants, barring the Subsidiary from: certain fundamental transactions; issuing dividends and distributions; incurring additional indebtedness outside of the ordinary course of business; engaging in any business activity other than related to the Almirall Collaboration Agreement; and permitting any additional liens on the collateral provided to HCRP under the Royalty-Backed Loan Agreement.

The Royalty-Backed Loan Agreement contains customary defined events of default, upon which any outstanding principal and unpaid interest shall be immediately due and payable. These include: failure to pay any principal or interest when due; any uncured breach of a representation, warranty or covenant; any uncured failure to perform or observe covenants; any uncured cross default under a material contract; any uncured breach of the Company’s representations, warranties or covenants under its Contribution and Servicing Agreement with the Subsidiary; any termination of the Almirall Collaboration Agreement; and certain bankruptcy or insolvency events.

The following table summarizes the impact of the Royalty-Backed Loan Agreement on the Company’s condensed consolidated balance sheets at June 30, 2023 and December 31, 2022 (in thousands):

	June 30, 2023		December 31, 2022
Principal debt including paid-in-kind interest	$	37,849	$	36,388
Unamortized debt issuance costs	(1,453)		(1,532)
Carrying value	$	36,396	$	34,856

During the six months ended June 30, 2023, $1.5 million of paid-in-kind interest was capitalized and added to the principal balance of the loan, which represents the shortfall between the interest owed, and the Almirall Collaboration Agreement royalty payments received.

24

The Company recognized coupon interest expense of $2.2 million and $2.0 million for the six months ended June 30, 2023 and June 30, 2022, respectively, and an insignificant amount of amortization expense on the debt issuance costs on the Royalty-Backed Loan Agreement for each of the six months ended June 30, 2023 and June 30, 2022. The Company recognized coupon interest expense of $1.1 million and $1.0 million, for the three months ended June 30, 2023 and June 30, 2022, respectively, and an insignificant amount of amortization expense on debt issuance costs, on the Royalty-Backed Loan Agreement for each of the three months ended June 30, 2023 and June 30, 2022.

Short-Term Debt

Convertible Senior Subordinated Notes

On April 18, 2018, the Company entered into a Purchase Agreement, or the Purchase Agreement, with several initial purchasers, or the Initial Purchasers, for whom Merrill Lynch, Pierce, Fenner & Smith Incorporated and Leerink Partners LLC acted as representatives, relating to the sale of $135.0 million aggregate principal amount of 4.75% Convertible Senior Subordinated Notes due 2024, or the Notes, to the Initial Purchasers. The Company also granted the Initial Purchasers an option to purchase up to an additional $25.0 million aggregate principal amount of Notes, which was exercised in full on April 20, 2018.

The Purchase Agreement includes customary representations, warranties and covenants. Under the terms of the Purchase Agreement, the Company agreed to indemnify the Initial Purchasers against certain liabilities.

In addition, J. Wood Capital Advisors LLC, the Company’s financial advisor, purchased $5.0 million aggregate principal amount of Notes in a separate, concurrent private placement on the same terms as other investors.

The Notes were issued by the Company on April 23, 2018, pursuant to an Indenture, dated as of such date, or the Indenture, between the Company and U.S. Bank National Association, as trustee, or the Trustee. The Notes bear cash interest at the annual rate of 4.75%, payable on November 1 and May 1 of each year, beginning on November 1, 2018, and mature on May 1, 2024 unless earlier repurchased, redeemed or converted. The Company will settle conversions of the Notes through delivery of shares of common stock of the Company, in accordance with the terms of the Indenture. The initial conversion rate for the Notes is 62.8931 shares of common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the Notes, which is equal to an initial conversion price of approximately $15.90 per share, representing a conversion premium of approximately 20% above the closing price of the common stock of $13.25 per share on April 18, 2018.

Holders of the Notes may convert all or any portion of their Notes, in multiples of $1,000 principal amount, at their option at any time prior to the close of business on the second scheduled trading day immediately preceding the stated maturity date.

The Company may redeem for cash all or part of the Notes, at its option, on or after May 6, 2021, if the last reported sale price of the Company’s common stock has been at least 130% of the conversion price then in effect for at least 20 trading days (whether or not consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption at a redemption price equal to 100% of the principal amount of the Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date.

If the Company experiences a fundamental change, as described in the Indenture, prior to the maturity date of the Notes, holders of the 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 maturity date of the Notes and following a notice of redemption 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 or redemption.

The Indenture provides for customary events of default. In the case of an event of default with respect to the Notes arising from specified events of bankruptcy or insolvency, all outstanding Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the Notes under the Indenture occurs or is continuing, the Trustee or holders of at least 25% in aggregate principal amount of the then outstanding Notes may declare the principal amount of the Notes to be immediately due and payable.

25

After deducting costs incurred of $6.0 million, the Company raised net proceeds from the issuance of long-term convertible debt of $159.0 million in April 2018. All costs were deferred and are being amortized over the life of the Notes at an effective interest rate of 5.47% and recorded as additional interest expense.

The Company evaluated the conversion feature and determined it was not within the scope of ASC 815 and therefore is not required to be accounted for separately. The Company concluded that the embedded conversion option is not subject to separate accounting pursuant to either the cash conversion guidance or the beneficial conversion feature guidance. Under the general conversion guidance in ASC 470, Debt, all of the proceeds received from the Notes was recorded as a liability on the condensed consolidated balance sheet.

The following table summarizes the impact of the Notes on the Company’s condensed consolidated balance sheets at June 30, 2023 and December 31, 2022 (in thousands):

	June 30, 2023		December 31, 2022
Principal debt	$	165,000	$	165,000
Unamortized debt issuance costs	(958)		(1,511)
Carrying value	$	164,042	$	163,489

The Company recognized coupon interest expense of $3.9 million for each of the six months ended June 30, 2023 and June 30, 2022, and amortization expense on the debt issuance costs of $0.6 million and $0.5 million on the Notes for the six months ended June 30, 2023 and June 30, 2022, respectively. The Company recognized coupon interest expense of $2.0 million and amortization expense on the debt issuance costs of $0.3 million for each of the three months ended June 30, 2023 and June 30, 2022.

Debt issuance costs are presented on the consolidated balance sheet as a direct deduction from the related debt liability rather than capitalized as an asset in accordance with ASU No. 2015-03, Interest - Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs.

Long-term debt on the Company’s consolidated balance sheets at June 30, 2023 includes the carrying value of the R-Bridge Loan Agreement and the Royalty-Backed Loan Agreement. Long-term debt on the Company's consolidated balance sheets at December 31, 2022 includes the carrying value of the R-Bridge Loan Agreement, the Notes and the Royalty-Backed Loan Agreement. Short-term debt on the Company's consolidated balance sheets at June 30, 2023 includes the carrying value of the Notes. The Company had no short-term debt on its consolidated balance sheet at December 31, 2022.

14.    Leases

Operating Leases

The Company leases its Boston, Massachusetts and King of Prussia, Pennsylvania office spaces under non-cancelable operating leases expiring in 2023 and 2026, respectively.

The Company executed an amendment to the existing lease agreement on its Boston office space in April 2021. The amended lease agreement released 8,104 rentable square feet of office space and extended the lease term for the remaining 4,153 rentable square feet of office space through August 2023 for an additional commitment of $0.4 million. In accordance with the amendment, a cash-collateralized irrevocable standby letter of credit for the lease was reduced to an insignificant amount as of June 30, 2023. In July 2023, the Company extended its lease agreement on its Boston office space on a month-to-month basis, commencing on September 1, 2023.

The Company executed an amended lease agreement on its King of Prussia office space in November 2022. The amended lease agreement extended the lease term through September 2026 for an additional commitment of $1.2 million.

The total operating lease liability is presented on the Company’s condensed consolidated balance sheet based on maturity dates. Approximately $0.4 million of the total operating liabilities is classified under “Other Current Liabilities” for the portion due within twelve months of June 30, 2023, and $1.4 million is classified under “Long-Term Lease Liability”.

26

15.    Income Taxes

The Company recorded an insignificant provision for income taxes for the three and six months ended June 30, 2023 and no provision for income taxes for the three and six months ended June 30, 2022.

Deferred tax assets and deferred tax liabilities are recognized based on temporary differences between the financial reporting and tax bases of assets and liabilities using statutory rates. Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets, which are comprised principally of net operating loss carryforwards and research and development credits. Under the applicable accounting standards, management has considered the Company’s history of losses and concluded that it is more likely than not that the Company will not recognize the benefits of federal and state deferred tax assets. Accordingly, a full valuation allowance has been established against the Company’s otherwise recognizable net deferred tax assets.

16.    Product Revenue

To date, the Company’s only source of product revenue has been from NUZYRA product sales beginning in February 2019 when NUZYRA launched in the U.S. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories (in thousands):

	Chargebacks, discounts and fees		Government and other rebates		Returns		Patient assistance		Total
Balance at December 31, 2022	$	1,409	$	7,552	$	413	$	181	$	9,555
Provision related to current period sales	5,527		21,760		626		851		28,764
Adjustment related to prior period sales	154		556		608		—		1,318
Credit or payments made during the period	(4,727)		(18,106)		(1,039)		(942)		(24,814)
Balance at June 30, 2023	$	2,363	$	11,762	$	608	$	90	$	14,823

17.    Commitments and Contingencies

In the ordinary course of business, the Company is from time to time involved in lawsuits, claims, investigations, proceedings, and threats of litigation relating to intellectual property, commercial arrangements, employment and other matters. While the outcome of these proceedings and claims cannot be predicted with certainty, as of June 30, 2023, the Company was not party to any legal or arbitration proceedings that may have, or have had in the recent past, significant effects on the Company’s financial position. No governmental proceedings are pending or, to the Company’s knowledge, contemplated against the Company. The Company is not a party to any material proceedings in which any director, member of executive management or affiliate of the Company is either a party adverse to the Company or the Company’s subsidiaries or has a material interest adverse to the Company or the Company’s subsidiaries.

In July 2021, the Company entered into a supply agreement with CARBOGEN AMCIS AG, or Carbogen, that provides for the terms and conditions under which Carbogen will manufacture and supply to the Company the active pharmaceutical ingredient for the Company’s omadacycline product in bulk quantities, or the Carbogen Product. Under this agreement, the Company is responsible for the cost and supply of crude omadacycline that Carbogen requires to manufacture the Carbogen Product and perform related services. The Company is obligated to initially pay Carbogen an amount in the high six-digit U.S. dollar range per batch of Carbogen Product that the Company orders, and the price may be adjusted in accordance with the terms of the agreement. The Company may also request that Carbogen perform certain services related to the Carbogen Product, for which the Company will pay reasonable compensation to Carbogen.

The agreement will remain in effect for a fixed initial term. If neither party has provided notice of its intent to terminate the agreement prior to the end of the initial term, then the Agreement will automatically be extended for a fixed period of time. The agreement may be terminated under certain circumstances, including by either party delivering notice of termination following the initial term, or by either party due to a material uncured breach by the other party or the other party’s insolvency.

In November 2016, the Company entered into a manufacturing and services agreement, or MSA, with CIPAN, which was later amended and restated in April 2018, and further amended in February 2019, December 2019, July 2020, December 2020, January 2022, and February 2023, collectively, the CIPAN Agreements. The CIPAN Agreements provide

27

the terms and conditions under which CIPAN will manufacture and supply to the Company increased quantities of minocycline starting material and crude omadacycline, or the CIPAN Products, for purification into omadacycline and, subsequently, for use in the Company’s products that contain omadacycline tosylate as the active pharmaceutical ingredient.

Additionally, the CIPAN Agreements included an investment by the Company in a new facility area to increase the manufacturing capacity for production of crude omadacycline. The Company was required to make advance payments to CIPAN upon completion of certain milestones within the CIPAN Agreements.

The term of the CIPAN Agreements will continue throughout the term that the Company receives benefit from the new facility area. The Company may renew the CIPAN Agreements for additional periods and can terminate the CIPAN Agreements at any time by delivery, within a certain time period, of prior written notice to CIPAN. Following the first renewal term, CIPAN may terminate the MSA in its entirety by delivery, within a certain time period, of prior written notice to the Company.

Under the CIPAN Agreements, the Company will purchase product in batches from CIPAN in quantities to be set forth on purchase orders submitted to CIPAN, within a certain time period, prior to the requested date of delivery. The Company will provide CIPAN with a rolling forecast with a best estimate of the quantities that will be ordered each month.

18.    Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption.

In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, or ASU 2016-13. The FASB subsequently issued amendments to ASU 2016-13, which have the same effective date and transition date of January 1, 2023. These standards require that credit losses be reported using an expected losses model rather than the incurred losses model that is currently used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, these standards now require allowances to be recorded instead of reducing the amortized cost of the investment. These standards limit the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases. Based on the composition of our investment portfolio, accounts receivable and other financial assets, current market conditions and historical credit loss activity, the adoption of these standards does not have a material effect on the Company’s consolidated balance sheet, consolidated statements of operation and comprehensive loss and related disclosures.

28

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

You should read the following discussion and analysis of our financial condition and results of operations in conjunction with our unaudited condensed consolidated financial statements and related notes included in Part I, Item 1 of this Quarterly Report on Form 10-Q. All references to “Paratek,” “we,” “us,” “our” or the “Company” in this Quarterly Report on Form 10-Q mean Paratek Pharmaceuticals, Inc. and our subsidiaries.

This discussion contains certain forward-looking statements that involve risks and uncertainties. We make such forward-looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. Forward-looking statements are identified by words such as “believe,” “will,” “may,” “estimate,” “continue,” “anticipate,” “intend,” “should,” “plan,” “expect,” “predict,” “could,” “potential,” “potentially” or the negative of these terms or similar expressions. You should read these statements carefully because they discuss future expectations, contain projections of future results of operations or financial condition, or state other “forward- looking” information. These statements relate to our future plans, objectives, expectations, intentions and financial performance and the assumptions that underlie these statements. These forward-looking statements are subject to certain risks and uncertainties that could cause actual results to differ materially from those anticipated in the forward-looking statements. Factors that might cause such a difference include, but are not limited to, those discussed in the “Risk Factors” section of our Annual Report on Form 10-K for the year ended December 31, 2022, as filed with the U.S. Securities and Exchange Commission, or the SEC, on March 16, 2023, or the 2022 Form 10-K. Forward-looking statements are based on our management’s beliefs and assumptions and on information currently available to our management. These statements, like all statements in this report, speak only as of their date, and except as required by law, we undertake no obligation to update or revise these statements in light of future developments. We caution investors that our business and financial performance are subject to substantial risks and uncertainties.

Company Overview

We are a commercial-stage biopharmaceutical company focused on the development and commercialization of novel life-saving therapies for life-threatening diseases or other public health threats for civilian, government and military use. Our United States, or U.S., Food and Drug Administration, or FDA, approved commercial product, NUZYRA® (omadacycline) is a once-daily oral and intravenous antibiotic for the treatment of adult patients with community-acquired bacterial pneumonia, or CABP, and acute skin and skin structure infections, or ABSSSI, caused by susceptible pathogens. We retain worldwide commercial rights to omadacycline, with the exception in the People’s Republic of China, Hong Kong, Macau and Taiwan, where we have entered into a collaboration agreement with Zai Lab (Shanghai) Co., Ltd., or Zai. The National Medical Products Administration, or NMPA, of China approved NUZYRA for the treatment of adult patients with CABP and ABSSSI in December 2021. China's National Healthcare Security Administration added the intravenous formulation of NUZYRA to the country's National Reimbursement Drug List for treatment of CABP and ABSSSI in January 2023, resulting in millions of patients gaining access to this once daily broad-spectrum antibiotic.

SEYSARA® (sarecycline) is an FDA-approved product that we have exclusively licensed in the U.S. and the People’s Republic of China, Hong Kong, Macau and Taiwan, certain rights to Almirall, LLC, or Almirall. SEYSARA is currently being marketed by Almirall in the U.S. as a once-daily oral therapy for the treatment of moderate to severe acne vulgaris. With respect to our technology as it relates to sarecycline, we retain development and commercialization rights in all countries other than the U.S., the People's Republic of China, Hong Kong, Macau and Taiwan, and in February 2020, we exclusively licensed from Almirall certain technology owned or in-licensed by Almirall or its affiliates that is necessary or useful to develop or commercialize sarecycline outside of the U.S. Almirall plans to develop sarecycline for acne in China, with a submission to the NMPA expected in 2023, according to Almirall.

We believe that NUZYRA has the potential to become the primary choice of physicians for use as a once-daily broad-spectrum monotherapy oral and IV antibiotic for ABSSSI, CABP and other serious community-acquired bacterial infections where resistance is of concern. NUZYRA is used in the emergency room, hospital, and community care settings. We have designed NUZYRA to provide potential advantages over existing antibiotics, including activity against resistant bacteria, broad-spectrum antibacterial activity, oral and IV formulations with once-daily dosing, and no dosing adjustments for patients on concomitant medications and a generally safe and well-tolerated profile. NUZYRA also has the potential to be used as a once-daily oral and IV antibiotic for the treatment of non-tuberculous mycobacteria, or NTM, and pulmonary anthrax, where it could be suitable for both the treatment and post-exposure prophylaxis, or PEP, of anthrax as a priority medical countermeasure.

29

In December 2019, we entered into the BARDA contract, which is a five-year contract with an option to extend to ten years. The BARDA contract could result in payments to the Company of up to approximately $303.6 million and consists of a five-year base period-of-performance and a total contract period-of-performance (base period plus option exercises) of up to ten years. The BARDA contract supports the development of NUZYRA for the treatment of pulmonary anthrax, FDA post-marketing requirements, or PMRs, associated with the initial NUZYRA approval, and the ability for BARDA to procure up to 10,000 treatment courses of NUZYRA for use against potential biothreats. In September 2021, we and BARDA modified the original BARDA contract, herein referred to as the amended BARDA contract, to provide additional funding to expand the development of NUZYRA under an FDA Animal Efficacy Rule development program to support a sNDA to the FDA to include PEP in addition to the treatment of pulmonary anthrax, herein referred to as the amended option.

In July 2023, we and BARDA further modified the amended BARDA contract to provide new development milestones associated with the achievement of specific anthrax development milestones for the next BARDA procurement of NUZYRA® (omadacycline). We and BARDA have agreed the next procurement of NUZYRA anthrax treatment courses will be split into two equal procurements based on the achievement of specific development milestones toward both treatment and PEP indications of pulmonary anthrax.

The first of these procurements will be triggered by the delivery of positive top-line data from a dose-ranging efficacy study for PEP of inhalation anthrax in non-human primates, or NHPs. We expect this data to be available in the first quarter of 2024. The second of these procurements will be triggered by BARDA's receipt of positive top-line data from a combination of two studies: a dose-ranging efficacy study in NHPs and a pivotal efficacy study in rabbits for the treatment of inhalation anthrax, which we anticipate could be available as early as the fourth quarter of 2024. The trigger for the final procurement of NUZYRA continues to be our receipt of sNDA approval from the FDA for the treatment of inhalation anthrax. We will provide further specificity on these timelines as the anthrax development program progresses.

Under the terms of the original BARDA contract, approximately $59.4 million was awarded to us by BARDA in December 2019 for the development of NUZYRA for the treatment of pulmonary anthrax and the purchase of an initial 2,500 treatment courses of NUZYRA. As part of this initial $59.4 million award, a $37.9 million procurement of NUZYRA was delivered to and accepted by BARDA in June 2021, and the amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the second quarter of 2021. The Company has been periodically drawing down the remaining $21.5 million of the initial award based on costs incurred during the development program.

Two additional contractual services under the original BARDA contract were initiated by BARDA in March 2020 that awarded us approximately $76.8 million for reimbursement of existing FDA PMRs and approximately $20.4 million for reimbursement of manufacturing-related requirements, which the Company has been drawing down based on costs incurred. This additional staged funding is expected to support all FDA PMRs associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study, and support the U.S. onshoring and security requirements of our manufacturing activities for NUZYRA.

BARDA initiated the amended option in September 2021 that expanded the development of NUZYRA under an FDA Animal Efficacy Rule development program to support an sNDA that will include PEP in addition to the treatment of pulmonary anthrax for a revised total of approximately $31.6 million.

The second procurement, the purchase of an additional 2,500 treatment courses of NUZYRA for a total of $36.4 million, was delivered to and accepted by BARDA in December 2022. The amount earned from this procurement was recognized in net U.S. sales of NUZYRA during the fourth quarter of 2022.

The remaining government options under the amended BARDA contract include a maximum of approximately $79.0 million to provide for two additional purchases of NUZYRA anthrax treatment courses, each of which may be exercised at BARDA’s discretion upon achievement of specific development milestones related to the anthrax treatment development program.

We continue to make significant progress in the pulmonary anthrax development program under the amended BARDA contract. Several omadacycline PK studies have been completed in rabbits and in non-human primates to derive the doses to be tested in upcoming pilot efficacy, or dose range finding, studies for the treatment of inhalation anthrax in both rabbits and non-human primates. The first oral omadacycline PK study in non-human primates was also completed marking the initiation of the development program for the post exposure prophylaxis indication. We completed the first Animal Rule pilot efficacy study in 2022, which revealed that all three doses of omadacycline demonstrated one-hundred

30

percent efficacy; all animals survived at day 45 which is the primary endpoint in an anthrax treatment model during which all non-treated animals died by Day 3.

In addition, we have evaluated minimum inhibitory concentrations, or MICs, of omadacycline against more than 130 anthrax strains. In these in vitro studies, omadacycline continued to demonstrate potent MICs and is considered effective against all anthrax isolates that were tested, including a strain resistant to doxycycline and a strain resistant to ciprofloxacin. Omadacycline MIC values in all of these strains remained unchanged and consistent with very potent in vitro activity which was not impacted in either of these resistant anthrax strains.

Together with BARDA, we also continue to advance our efforts to onshore the manufacturing of NUZYRA to the U.S. We have completed the knowledge transfer and development stage of our manufacturing process for the active pharmaceutical ingredient, or API, of omadacycline to our U.S. onshoring partners and are currently in the engineering stage of the initiative. We have completed knowledge transfer and the initiation of the process development work for production of vials. U.S.-based commercial supply production of tablets was implemented in 2022 and we anticipate U.S.-produced vials will be available by 2024.

The breadth of the utility of NUZYRA as a countermeasure against bioterrorism was affirmed when NUZYRA was added to the Center for Disease Control and Prevention's updated report, "Antimicrobial Treatment and Prophylaxis of Plague: Recommendations for Naturally Acquired Infections and Bioterrorism Response" in July 2021. Accordingly, NUZYRA is now listed as an alternative agent for the treatment, pre-exposure prophylaxis, and postexposure prophylaxis of primary bubonic and pharyngeal plague infections in adults 18 years of age and over.

We continue to pursue a number of other life-cycle opportunities for NUZYRA. In May 2021, the FDA approved our supplemental new drug application, or sNDA, for the oral-only loading dose regimen for patients diagnosed with CABP, based upon the results of a study that demonstrated an oral-only loading dose regimen has a comparable PK profile to the approved IV loading dose regimen in patients with CABP that was established in the Phase 3 CABP registration study.

Additionally, we have also discussed trial designs and potential registration pathways with the FDA to determine the efficacy and safety of omadacycline in patients afflicted with NTM, which are environmental organisms that can be found in soil, dust, and water, including natural and municipal water sources. Infection occurs when a person is exposed to NTM organisms. NTM can form difficult-to-eliminate biofilms, which are collections of microorganisms that stick to each other, and adhere to surfaces in moist environments. Although severe infection can affect the lymph nodes, skin, soft tissues, bones, and joints, the vast majority of NTM infection cases are pulmonary. The diagnosis of NTM infection is often delayed due to the constellation of non-specific symptoms and a lack of disease state awareness by clinicians.

NTM is a rare and orphan disease with no FDA-approved therapies in the U.S. In August 2021, the FDA granted orphan drug designation for NUZYRA for the treatment of NTM infections caused by Mycobacterium abscessus, or MAB, and Mycobacterium avium complex, or MAC. In October 2021, we initiated a double-blinded, placebo-controlled, randomized monotherapy Phase 2b clinical study for the treatment of MAB patients who are not receiving other treatments. The study size will be approximately 75 subjects randomized in a 1.5 to 1 ratio and therapy will last for 12 weeks with an efficacy endpoint assessment at that time point. Due to the small numbers of patients with this rare disease, we expect this study will complete enrollment by the end of 2023.

The FDA granted Fast Track designation for the oral and IV formulations of NUZYRA for the treatment of NTM caused by both MAB and MAC in July 2022. We hosted an Investor Day in October 2022 that updated investors on the global market opportunity for NTM in both MAB and MAC, and laid the foundation for ex-U.S. partnering discussions. This event highlighted the significant global unmet medical need for patients suffering from this chronic, rare and life-threatening pulmonary disease and summarized key takeaways from our ongoing scientific program in NTM that includes the first randomized, placebo-controlled Phase 2b study being conducted in patients with NTM pulmonary disease caused by MAB. In February 2023, we held our fifth meeting in the last 12 months with the Pharmaceuticals and Medical Devices Agency, or PMDA, and have aligned on the registration program for NTM abscessus in Japan. The completion of this regulatory process is an important milestone in creating momentum in our ongoing discussions with potential partners in this country. Additionally, the European Medicines Agency, or EMA, Committee for Orphan Medicinal Products, or COMP, recommended a positive opinion for orphan medicinal product designation for NUZYRA for the treatment of NTM lung disease in June 2023. The European Commission officially designated NUZYRA as an orphan medicinal product in July 2023.

On June 6, 2023, we announced that we had entered into a definitive agreement, or the Merger Agreement, to be acquired by Gurnet Point Capital, or Gurnet Point, and Novo Holdings A/S, or Novo Holdings, in a transaction valued at

31

approximately $462.0 million, including the assumption of debt and assuming full payment of a Contingent Value Right CVR. This transaction is referred to herein as the Merger. Debt financing of $175.0 million for this transaction will be provided by funds managed by Oaktree Capital Management, L.P.

Under the terms of the Merger Agreement, Gurnet Point, a leading healthcare investment firm, and Novo Holdings, a holding and investment company responsible for managing the assets and wealth of the Novo Nordisk Foundation, will acquire all of our outstanding shares for $2.15 per share in cash, plus a CVR of $0.85 per share payable upon the achievement of $320.0 million in U.S. NUZYRA net sales (excluding certain permitted deductions, payments under our contract with ASPR-BARDA, certain government payments and certain royalty revenue) in any calendar year ending on or prior to December 31, 2026.

The transaction, which our Board of Directors has unanimously approved, is expected to close in the third quarter of 2023, subject to customary closing conditions, including approval by our stockholders and receipt of regulatory approvals. Following completion, we will become a private company and will no longer be subject to the reporting requirements of the Securities Exchange Act of 1934, as amended, nor be traded on Nasdaq Global Market.

Between July 11, 2023 and July 27, 2023, the Company received eight demand letters, or the Demand Letters, each from a purported stockholder of the Company alleging to have identified purportedly materially misleading and incomplete statements in the preliminary proxy statement filed by the Company on June 30, 2023. Certain of the Demand Letters also purport to raise issues with aspects of the process that led to the Merger. Certain of those Demand Letters were served pursuant to Section 220 of the Delaware General Corporation Law and seek books and records of the Company related to the Merger. The Company believes the allegations asserted in the Demand Letters are without merit. Additional demand letters or lawsuits relating to the Merger may also be received and/or filed in the future.

To date, we have devoted a substantial amount of our resources to research and development efforts, including conducting clinical trials for omadacycline, protecting our intellectual property and providing selling, general and administrative support for these operations. We began generating revenue from product sales in February 2019; as such, we have historically financed our operations primarily through sales of our common stock, debt financings, strategic collaborations, and grant funding.

We have incurred significant losses since our inception in 1996. Our accumulated deficit at June 30, 2023 was $965.1 million and our net loss for the six months ended June 30, 2023 was $34.7 million. A substantial amount of our net losses resulted from costs incurred in connection with our research and development programs and selling, general and administrative costs associated with our operations. The net losses and negative operating cash flows incurred to date, together with expected future losses, have had, and likely will continue to have, an adverse effect on our stockholders’ deficit and working capital. The amount of future net losses will depend, in part, on the rate of future growth of our expenses and our ability to generate offsetting revenue. We expect to continue to incur significant expenses and operating losses for the next several years.

Business Update Regarding COVID-19

The COVID-19 pandemic continues to negatively impact public health and economic conditions around the world and is continuing to affect health care institutions and patient access. Certain COVID-19 related restrictions on in-person promotional access to some health care institutions remain and the overall impact of COVID-19 restrictions on the health care and hospital environments could restrict the full potential of NUZYRA’s growth. The length of time and full extent to which the business and healthcare effects of the COVID-19 pandemic will directly or indirectly impact our business, results of operations and financial condition will depend on future developments that are uncertain.

For additional information on the various risks posed by the COVID-19 pandemic, refer to Item 3. Quantitative and Qualitative Disclosures About Market Risk and Item 1A. Risk Factors included in the 2022 Form 10-K.

Financial Operations Overview

Product Revenue, Net

Product revenue, net, is recognized when earned on sales of NUZYRA, which was approved by the FDA in October 2018 and launched in the U.S. in February 2019. NUZYRA is sold principally to a limited number of specialty distributors and specialty pharmacy providers in the U.S. These customers subsequently resell our product to health care providers or

32

dispense the product to patients. In addition to distribution agreements with customers, we enter into arrangements with health care providers and payers that provide for government mandated and/or privately negotiated rebates, chargebacks and discounts with respect to the purchase of our product. Product revenue is recognized net of reserves for all variable consideration, including rebates, chargebacks, discounts and product returns.

Under the terms of the BARDA contract, BARDA can procure up to 10,000 anthrax treatment courses of NUZYRA. As of June 30, 2023, the first two of four 2,500 treatment courses of NUZYRA have been purchased by BARDA. The product procurement performance obligations generate revenue at a point in time, which is upon transfer of control of the product. As such, the related revenue for these performance obligations is recognized at a point in time as product revenue within our consolidated statement of operations. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

Government Contract Service Revenue

Government contract service revenue is recognized when earned under our BARDA contract and represents the reimbursement by BARDA of costs incurred by us for work performed to develop NUZYRA for the treatment of pulmonary anthrax and for the U.S. onshoring of NUZYRA manufacturing plus a small fixed administrative fee. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

Government Contract Grant Revenue

The allocated consideration of government contract grant revenue is recognized when earned under our BARDA contract and represents the reimbursement by BARDA of costs incurred by us for FDA post-marketing requirements, or PMRs, associated with the approval of NUZYRA, including CABP and pediatric studies, as well as a five-year post-marketing bacterial surveillance study. Refer to Note 7, Government Contract Revenue to the interim condensed consolidated financial statements included in this report for further discussion of the BARDA contract and related revenue recognition.

Collaboration and Royalty Revenue

Collaboration and royalty revenue are recognized when revenue is earned under our collaboration and license agreements. Refer to Note 8, License and Collaboration Agreements to the interim condensed consolidated financial statements included in this report for further discussion of the collaboration agreements and the related revenue recognition.

Cost of Product Revenue

Cost of product revenue represents the cost of the product itself, labor and overhead, and any reserve for excess or obsolete inventory, as well as stability studies and inventory scrap. Cost of product revenue also represents royalties owed on net sales of NUZYRA.

Research and Development Expense

Research and development expenses consisted primarily of costs directly incurred by us for the development of our product candidates, which include:

•expenses incurred under agreements with clinical research organizations, or CROs, and investigative sites that conduct our clinical trials;

•the cost of acquiring and manufacturing preclinical and clinical study materials and developing manufacturing processes;

•direct employee-related expenses, including salaries, benefits, travel and stock-based compensation expense of our research and development personnel;

•allocated facilities, depreciation, and other expenses, which include rent and maintenance of facilities, insurance and other supplies; and

33

•costs associated with preclinical activities and regulatory compliance.

Research and development expenses also include gross reimbursable costs incurred related to research and development services performed for the treatment of pulmonary anthrax, services performed for U.S. manufacturing onshoring and security requirements, and services performed for FDA PMRs under the BARDA contract.

Research and development costs are expensed as incurred. Costs for certain development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and our clinical sites.

We cannot determine with certainty the duration and completion costs of the current or future clinical trials of our product candidates or if, when, or to what extent we will generate revenues from the commercialization and sale of any of our products or product candidates for which we or any partner obtain regulatory approval, such as NUZYRA and SEYSARA. Aside from the FDA approval of NUZYRA and SEYSARA in the U.S., we or our partners may never succeed in achieving regulatory approval for any of our other product candidates. The duration, costs and timing of clinical trials and development of our product candidates depend on a variety of factors, including:

•the scope, rate of progress, and expense of our ongoing, as well as any additional, clinical trials and other research and development activities;

•future clinical trial results;

•potential changes in government regulation; and

•the timing and receipt of any regulatory approvals.

A change in the outcome of any of these variables with respect to the development of a product candidate could mean a significant change in the costs and timing associated with the development of that therapeutic candidate. For example, if the FDA, or another regulatory authority, were to require us to conduct clinical trials beyond those that we currently anticipate will be required for the completion of the clinical development of product candidates, or if we experience significant delays in the enrollment in any clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

We manage certain activities, such as clinical trial operations, manufacture of clinical trial material, and preclinical animal toxicology studies, through third-party contract organizations. The only costs we track by each product candidate are external costs such as services provided to us by CROs, manufacturing of preclinical and clinical drug product, and other outsourced research and development expenses. We do not assign or allocate to individual development programs internal costs such as salaries and benefits, facilities costs, lab supplies and the costs of preclinical research and studies except as required by the BARDA contract. Our research and development expenses for omadacycline and other projects during the three and six months ended June 30, 2023 and 2022 are as follows:

	Three Months Ended June 30,				Six Months Ended June 30,
(in thousands)	2023		2022		2023		2022
Omadacycline costs	$	6,268	$	4,986	$	10,833	$	10,067
Other research and development costs	2,504		2,606		5,247		5,002
Total	$	8,772	$	7,592	$	16,080	$	15,069

Selling, General and Administrative Expense

Selling, general and administrative expenses consist principally of compensation costs for our sales force, commercial support personnel, and medical affairs professionals, as well as personnel in executive and other administrative functions. Other selling, general and administrative expenses include marketing, trade, and other commercial costs and distribution fees for the sale of NUZYRA and professional fees for legal, consulting and accounting services.

Interest Income

Interest income represents interest earned on our money market funds and marketable securities.

34

Interest Expense

Interest expense represents interest incurred on the R-Bridge Loan Agreement, the Notes, and the Royalty-Backed Loan Agreement (each as defined in Note 13, Long-Term Debt to the interim condensed consolidated financial statements), as well as the adjustment of our marketable securities to amortized cost.

Results of Operations

Comparison of the three months ended June 30, 2023 and 2022

	Three Months Ended June 30,
(in thousands)	2023		2022		$ Change
Product revenue, net	$	33,800	$	25,082	$	8,718
Government contract service revenue	3,620		1,896		1,724
Government contract grant revenue	1,931		2,082		(151)
Collaboration and royalty revenue	642		577		65
Net revenue	$	39,993	$	29,637	$	10,356
Expenses:
Cost of product revenue	4,368		4,878		(510)
Research and development	8,772		7,592		1,180
Selling, general and administrative	36,264		30,335		5,929
Total operating expenses	49,404		42,805		6,599
Loss from operations	(9,411)		(13,168)		3,757
Other income and expenses:
Interest income	252		133		119
Interest expense	(5,287)		(4,546)		(741)
Other (losses) gains, net	(56)		(38)		(18)
Net loss before provision for income taxes	$	(14,502)	$	(17,619)	$	3,117
Provision for income taxes	(51)		—		(51)
Net loss	(14,553)		(17,619)		3,066

Product Revenue, Net

Net product revenue recognized on sales of NUZYRA in the U.S. was $33.8 million and $25.1 million for the three months ended June 30, 2023 and June 30, 2022, respectively. The increase in net product revenue is primarily the result of an increase in sales volume due to higher customer demand during the three months ended June 30, 2023.

Government Contract Service Revenue

Government contract service revenue earned under our BARDA contract was $3.6 million and $1.9 million for the three months ended June 30, 2023 and June 30, 2022, respectively. The increase in government contract service revenue was primarily due to additional work performed under the anthrax development program.

Government Contract Grant Revenue

Government contract grant revenue earned under our BARDA contract was $1.9 million and $2.1 million for the three months ended June 30, 2023 and June 30, 2022, respectively. Government contract grant revenue recognized in both periods represents the reimbursement under the BARDA contract of costs incurred for our on-going post-marketing required clinical studies.

35

Collaboration and Royalty Revenue

Collaboration and royalty revenue was $0.6 million for each of the three months ended June 30, 2023 and June 30, 2022. Royalty revenue recognized primarily reflects royalty revenues earned on sales of NUZYRA in China and on sales of SEYSARA in the United States.

Cost of Product Revenue

Cost of product revenue was $4.4 million for the three months ended June 30, 2023, compared to $4.9 million for the three months ended June 30, 2022. The decrease is primarily the result of a decrease in product samples distributed, partially offset by an increase in NUZYRA product sales during the three months ended June 30, 2023.

Research and Development Expense

Research and development expenses were $8.8 million for the three months ended June 30, 2023, compared to $7.6 million for the three months ended June 30, 2022. The increase in research and development expenses was primarily due to the timing of costs incurred for activities reimbursed under the BARDA contract.

We anticipate an increase in research and development expenses in future periods as we continue development of NUZYRA for the treatment of and PEP against pulmonary anthrax, continue the work on our FDA post-marketing requirements, and continue the onshoring of our manufacturing process, the majority of which is reimbursable under the BARDA contract. We will also incur additional spend as we continue exploring pathways for NTM indications.

Selling, General and Administrative Expense

Selling, general and administrative expenses were $36.3 million for the three months ended June 30, 2023, compared to $30.3 million for the three months ended June 30, 2022. The increase is primarily the result of costs incurred in connection with the potential acquisition of Paratek by Gurnet Point and Novo Holdings, as well as higher sales and marketing costs.

We expect a modest increase in selling, general and administrative expenses in future periods in support of our expansion into the community setting and other commercial activities, as well as the continued costs of operating as a public company if the transaction with Gurnet Point and Novo Holdings is not consummated. This will include costs for travel, in-person training events and sales meetings, executing marketing and promotional programs, engaging consultants, legal and other professional fees, and other operating expenses.

Other Income and Expenses

Interest expense for the three months ended June 30, 2023 represents interest incurred on the Notes of $2.2 million, the Royalty-Backed Loan Agreement of $1.2 million, the R-Bridge Loan Agreement of $1.1 million, and interest on the Revenue Performance Incentive Plan of $0.7 million. Interest income for the three months ended June 30, 2023 represents interest earned on our money market funds.

Interest expense for the three months ended June 30, 2022 represents interest incurred on the Notes of $2.2 million, the R-Bridge Loan Agreement of $1.2 million, and the Royalty-Backed Loan Agreement of $1.1 million, and insignificant interest expense related to money market funds and marketable securities. Interest income for the three months ended June 30, 2022 represents interest earned on our money market funds and marketable securities.

36

Comparison of the Six Months Ended June 30, 2023 and 2022

	Six Months Ended June 30,
(in thousands)	2023		2022		$ Change
Product revenue, net	$	60,013	$	45,000	$	15,013
Government contract service revenue	5,301		4,068		1,233
Government contract grant revenue	4,084		4,182		(98)
Collaboration and royalty revenue	1,831		1,248		583
Net revenue	$	71,229	$	54,498	$	16,731
Expenses:
Cost of product revenue	10,612		8,372		2,240
Research and development	16,080		15,069		1,011
Selling, general and administrative	69,753		57,937		11,816
Total operating expenses	96,445		81,378		15,067
Income (loss) from operations	(25,216)		(26,880)		1,664
Other income and expenses:
Interest income	473		240		233
Interest expense	(9,763)		(9,025)		(738)
Other gains (losses), net	(78)		138		(216)
Net loss before provision for income taxes	$	(34,584)	$	(35,527)	$	943
Provision for income taxes	(111)		0		(111)
Net loss	(34,695)		(35,527)		832

Product Revenue, Net

Net product revenue recognized on sales of NUZYRA in the U.S. was $60.0 million and $45.0 million for the six months ended June 30, 2023 and June 30, 2022, respectively. The increase in net product revenue is primarily the result of an increase in sales volume due to higher customer demand during the six months ended June 30, 2023.

Government Contract Service Revenue

Government contract service revenue earned under our BARDA contract was $5.3 million and $4.1 million for the six months ended June 30, 2023 and June 30, 2022, respectively. The increase in government contract service revenue is primarily due to the timing of work performed under the anthrax development program.

Government Contract Grant Revenue

Government contract grant revenue earned under our BARDA contract was $4.1 million and $4.2 million during the six months ended June 30, 2023 and June 30, 2022, respectively. Government contract grant revenue recognized in both periods represents the reimbursement under the BARDA contract of costs incurred for our on-going post-marketing required clinical studies.

Collaboration and Royalty Revenue

Collaboration and royalty revenue was $1.8 million and $1.2 million for the six months ended June 30, 2023 and June 30, 2022, respectively. Royalty revenue recognized primarily reflects royalty revenues earned on sales of NUZYRA in China and on sales of SEYSARA in the United States. The increase in collaboration and royalty revenue is primarily the result of an increase on initial sales of NUZYRA in China.

37

Cost of Product Revenue

Cost of product revenue was $10.6 million for the six months ended June 30, 2023, compared to $8.4 million for the six months ended June 30, 2022. The increase is primarily the result of an increase in NUZYRA product sales during the six months ended June 30, 2023.

Research and Development Expense

Research and development expenses were $16.1 million for the six months ended June 30, 2023, compared to $15.1 million for the six months ended June 30, 2022. The increase in research and development expenses was primarily due to costs for activities reimbursed under the BARDA contract, analytical testing, and other non-clinical studies.

We anticipate an increase in research and development expenses in future periods as we continue development of NUZYRA for the treatment of and PEP against pulmonary anthrax, continue the work on our FDA post-marketing requirements, and continue the onshoring of our manufacturing process, the majority of which is reimbursable under the BARDA contract. We will also incur additional spend as we continue exploring pathways for NTM indications.

Selling, General and Administrative Expense

Selling, general and administrative expenses were $69.8 million for the six months ended June 30, 2023, compared to $57.9 million for the six months ended June 30, 2022. The increase is primarily the result of costs incurred in connection with the potential acquisition of Paratek by Gurnet Point and Novo Holdings, as well as higher sales and marketing costs.

We expect a modest increase in selling, general and administrative expenses in future periods in support of our expansion into the community setting and other commercial activities, as well as the continued costs of operating as a public company if the transaction with Gurnet Point and Novo Holdings is not consummated. This will include costs for travel, in-person training events and sales meetings, executing marketing and promotional programs, engaging consultants, legal and other professional fees, and other operating expenses.

Other Income and Expenses

Interest expense for the six months ended June 30, 2023 represents interest incurred on the Notes of $4.5 million, the Royalty-Backed Loan Agreement of $2.3 million, the R-Bridge Loan Agreement of $2.2 million, and interest on the Revenue Performance Incentive Plan of $0.7 million. Interest income for the six months ended June 30, 2023 represents interest earned on our money market funds and marketable securities.

Interest expense for the six months ended June 30, 2022 represents interest incurred on the Notes of $4.4 million, the R-Bridge Loan Agreement of $2.3 million, the Royalty-Backed Loan Agreement of $2.1 million, and insignificant interest expense related to our money market funds and marketable securities. Interest income for the six months ended June 30, 2022 represents interest earned on our money market funds and marketable securities.

38

Liquidity and Capital Resources

On May 9, 2023, we filed a registration statement on Form S-3 with the SEC to sell certain of our securities in an aggregate amount of up to $250.0 million. As of July 31, 2023, $250.0 million remains available on this shelf registration statement. On May 17, 2021, we entered into an At-the-Market Sales Agreement, or the Sales Agreement, with BTIG, LLC, or BTIG, under which we may offer and sell our common stock having aggregate sales proceeds of up to $50.0 million from time to time through BTIG as our sales agent. Sales of our common stock through BTIG, if any, will be made by any method permitted by law deemed to be an “at the market offering” as defined in Rule 415(a)(4) under the Securities Act of 1933, as amended, including without limitation sales made directly on the Nasdaq Global Market or any other existing trading market for its common stock. BTIG will use commercially reasonable efforts to sell our common stock from time to time, based upon instructions (including any price, time or size limits or other customary parameters or conditions we may impose). We will pay BTIG a commission of 3% of the gross sales proceeds of any common stock sold through BTIG under the Sales Agreement. As of July 31, 2023, $23.3 million remains available for sale under the Sales Agreement.

We have used and we intend to continue to use the net proceeds from the above offerings of our common stock and the Notes, as well as other current and retired long-term debt agreements, together with our existing capital resources and future NUZYRA product sales, government contract revenue and royalty revenue, to fund our ongoing company operations, including clinical studies of omadacycline, NUZYRA commercial operations, and for working capital and other general corporate purposes. Refer to Note 13, Debt, for further details on our loan agreements, which include the R-Bridge Loan Agreement, the Notes, and the Royalty-Backed Loan Agreement.

As of June 30, 2023, we had cash and cash equivalents of $42.7 million.

The following table summarizes our cash provided by and used in operating, investing and financing activities (in thousands):

	Six Months Ended June 30,
(in thousands)	2023		2022
Net cash provided (used) by operating activities	$	9,314	$	(33,609)
Net cash used in investing activities	$	(32)	$	(15,196)
Net cash (used) provided by financing activities	$	(845)	$	7,818

Operating Activities

Net cash provided by operating activities was $9.3 million for the six months ended June 30, 2023, compared to net cash used in operating activities of $33.6 million for the six months ended June 30, 2022. The change in net cash used in operating activities primarily consists of our net losses adjusted for non-cash items and changes in components of operating assets and liabilities as follows:

–for the six months ended June 30, 2023, a net loss of $34.7 million was adjusted for non-cash items, including stock-based compensation expense of $4.4 million, non-cash interest expense of $2.2 million, and a net decrease of $37.3 million due to changes in operating assets and liabilities. The significant items in the change in operating assets and liabilities include a net decrease in accounts receivable, other receivables, prepaid, and other current assets of $34.9 million, partially offset by a decrease in accounts payable and accrued expenses, accrued long-term compensation, inventories, and other liabilities and other assets of $2.3 million.

–for the six months ended June 30, 2022, a net loss of $35.5 million was adjusted for non-cash items including stock-based compensation expense of $6.4 million and non-cash interest expense of $2.7 million and a net increase of $7.4 million due to changes in operating assets and liabilities. The significant items in the change in operating assets and liabilities include a net increase in accounts payable and accrued expenses, inventories, and other liabilities and other assets of $8.0 million, offset by a decrease in accounts receivable, other receivables, prepaid, and other current assets of $0.2 million.

39

Investing Activities

Net cash used in investing activities during the six months ended June 30, 2023 consists of insignificant purchases of fixed assets.

Net cash used in investing activities during the six months ended June 30, 2022 consists of $15.2 million in purchases of maturities of marketable securities.

Financing Activities

Net cash used in financing activities during the six months ended June 30, 2023 consists of $0.8 million in a principal repayment of long-term debt under our R-Bridge Loan Agreement.

Net cash provided by financing activities during the six months ended June 30, 2022 consists of $7.3 million in net proceeds raised through the sale of shares of our common stock under the Sales Agreement and $0.5 million in proceeds received from the ESPP.

Future Funding Requirements

We began generating revenue from product sales when we launched NUZYRA in the U.S. in February 2019. We also began earning royalties on net sales of SEYSARA in the U.S. when Almirall launched the product in January 2019 and on net sales of NUZYRA in the greater China region when Zai launched the product in December 2021. Our future funding requirements will depend on our ability to generate continued revenue from sales of NUZYRA, and our partners, Almirall and Zai's, ability to generate continued revenue from sales of SEYSARA and NUZYRA, respectively. We do not expect to generate any other revenue unless and until our SEYSARA greater China region partner, Almirall, obtains regulatory approval of and commercializes its respective product in the greater China region. We will require substantial additional funding to meet FDA PMRs for NUZYRA, which we expect to continue to be funded through the BARDA contract. Additional resources will also be needed to support and accelerate the commercialization of NUZYRA, fund the development of omadacycline in other indications, including NTM, and to advance the development of potential other product candidates, and such funding may not be available on favorable terms or at all. BARDA’s procurements of NUZYRA will also be an important component to satisfying future funding requirements.

We expect to continue to incur significant expenditures and operating losses for the next few years as we:

•conduct additional clinical trials of omadacycline;

•seek regulatory approvals for additional indications for omadacycline, such as omadacycline for the treatment of NTM;

•continue to augment our sales, marketing and distribution infrastructure to commercialize NUZYRA and increase our manufacturing capacity and capabilities to satisfy demand;

•support our planned commercialization efforts;

•build product inventory; and

•service and pay down our debt.

As of June 30, 2023, we had $42.7 million of cash and cash equivalents on hand. Our current level of cash and cash equivalents may not be sufficient to fund operations for the next twelve months following the issuance of the financial statements included in this Quarterly Report on Form 10-Q. As a result, there is substantial doubt regarding our ability to continue as a going concern for a period of one year from the date of this filing.

We have based this estimate on assumptions that may prove to be wrong, and we could use our available capital resources sooner than we currently expect. Because of the numerous risks and uncertainties associated with the development and commercialization of our pharmaceutical products, especially given the constraints on in-person promotion of NUZYRA and reduced access to prescribers due to restrictions in access to hospitals during the COVID-19 pandemic, and the unknown extent to which we will maintain existing or enter into new collaborations with third parties to participate in the development and commercialization of our product and product candidates, we are unable to estimate with certainty the amounts of increased capital outlays and operating expenditures that we will require to fund our

40

continuing operations, including for our clinical development programs and commercialization efforts for NUZYRA. Our future capital requirements will depend on many factors, including:

•the progress of clinical development of omadacycline in additional indications, including NTM and pulmonary anthrax;

•the costs and timing of commercialization activities for NUZYRA;

•product revenue received from commercial sales of NUZYRA;

•royalty revenue received from commercial sales of SEYSARA by Almirall;

•timing and amount of actual reimbursements and NUZYRA purchases under the BARDA contract;

•the ability of Zai to develop, manufacture and commercialize omadacycline in the Zai territory;

•the number and characteristics of other product candidates that we may pursue;

•the scope, progress, timing, cost and results of research, preclinical development and clinical trials;

•the costs, timing and outcome of seeking, obtaining, maintaining and expanding FDA and non-U.S. regulatory approvals;

•the costs associated with manufacturing and maintaining high quality sales, marketing and distribution capabilities;

•our ability to maintain, expand and defend the scope of our intellectual property portfolio, including the amount and timing of any payments we may be required to make in connection with the licensing, filing, defense and enforcement of any patents or other intellectual property rights;

•our need and ability to hire additional management, scientific, commercial, operations and medical personnel;

•the effect of competing products that may limit market penetration of our products;

•our need to implement additional internal systems and infrastructure, including financial and reporting systems;

•resources required to develop and implement policies and processes to promote ongoing compliance with applicable healthcare laws and regulations;

•costs required to ensure that our and our partners’ business arrangements with third parties comply with applicable healthcare laws and regulations;

•the economic and other terms, timing and success of our existing collaboration and licensing arrangements and any collaboration, licensing or other arrangements into which we may enter in the future, including the timing of receipt of any milestone or royalty payments under such arrangements; and

•the effect of the COVID-19 pandemic on the economy generally and on our business and operations specifically, including our sales of NUZYRA, sales by our collaboration partners with respect to which we are entitled to royalties, our third-party manufacturers and supply chain, our research and development efforts, our clinical trials and our employees.

Critical Accounting Policies and Estimates

Our management’s discussion and analysis of our financial condition and results of operations are based on our financial statements, which have been prepared in accordance with generally accepted accounting principles of the United States of America. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses and the disclosure of contingent liabilities in our financial statements. On an ongoing basis, we evaluate our estimates and judgments, including those related to, among other items, accounts receivable and related reserves, inventory and related reserves, goodwill, accrued sales allowances, net product revenue, government contract service revenue, government contract grant revenue, collaboration and royalty revenue, leases, stock-

41

based compensation arrangements, amortization of the debt discount and issuance costs under the R-Bridge Loan Agreement, manufacturing and clinical accruals, useful lives for depreciation and amortization of long-lived assets and valuation allowances on deferred tax assets. We base our estimates on historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Our actual results may differ from these estimates under different assumptions or conditions.

Recent Accounting Pronouncements

Refer to Note 18, Recent Accounting Pronouncements, to our Condensed Consolidated Financial Statements in this Quarterly Report on Form 10-Q.

Item 3.    Quantitative and Qualitative Disclosures about Market Risks

Our cash and cash equivalents balance as of June 30, 2023 consisted of cash and cash equivalents. Our primary exposure to market risk is interest income sensitivity, which is affected by changes in the general level of interest rates, including interest rate changes resulting from the impact of the COVID-19 pandemic. However, a sudden change in interest rates would not have a material effect on the fair market value of our cash and cash equivalents balance. 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 cash and cash equivalents balance.

We engage CROs and contract manufacturers on a global scale. We may be subject to fluctuations in foreign currency rates in connection with certain of these agreements. We currently do not hedge any such foreign currency exchange rate risk. Transactions denominated in currencies other than U.S. dollars are recorded based on exchange rates at the time such transactions arise and were less than 5.0% of total liabilities as of June 30, 2023.

Item 4.    Controls and Procedures

Management’s Evaluation of our Disclosure Controls and Procedures

We maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Securities Exchange Act of 1934, as amended, is (1) recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms and (2) accumulated and communicated to our management, including our principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure.

As of June 30, 2023, our management, with the participation of our principal executive officer and principal financial officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended). Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Our principal executive officer and principal financial officer have concluded based upon the evaluation described above that, as of June 30, 2023, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting

During the three months ended June 30, 2023, there have been no changes in our internal control over financial reporting, as such term is defined in Rules 13a-15(f) and 15(d)-15(f) promulgated under the Securities Exchange Act of 1934, as amended, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

42

PART II – OTHER INFORMATION

Item 1.    Legal Proceedings

Information in response to this Item is incorporated herein by reference from Note 17, Commitments and Contingencies, to our Condensed Consolidated Financial Statements in this Quarterly Report on Form 10-Q.

Item 1A.    Risk Factors

There have been no material changes from the risk factors set forth in our 2022 Form 10-K, other than the following:

The announcement and pendency of the transactions contemplated by the Merger Agreement may adversely affect our business, financial condition and results of operations.

Uncertainty about the effect of the transactions contemplated by the Merger Agreement on our employees, customers, and other parties may have an adverse effect on our business, financial condition and results of operation regardless of whether the Merger is completed. These risks to our business include the following, all of which could be exacerbated by a delay in the completion of the Merger:

•the impairment of our ability to attract, retain, and motivate our employees, including key personnel;

•the diversion of management’s attention from our ongoing business operations;

•difficulties maintaining relationships with associates, customers, manufacturers, other business partners or governmental entities;

•restrictions during the pendency of the proposed transaction that may impact our ability to pursue certain business opportunities or strategic transactions;

•litigation relating to the Merger and the costs related thereto; and

•the incurrence of significant costs, expenses, and fees for professional services and other transaction costs in connection with the proposed transaction.

Failure to consummate the Merger within the expected timeframe or at all could have a material adverse impact on our business, financial condition and results of operations.

There can be no assurance that the Merger will be consummated. The consummation of the proposed Merger is subject to certain conditions, including: (i) no order, injunction or decree issued by any court or other governmental body, and no statute, rule, regulation, order, injunction, or decree will have been enacted, entered, promulgated, or enforced (and continue to be in effect) by any governmental body that prohibits, enjoins, restricts, prevents or makes illegal the consummation of the transactions contemplated by the Merger Agreement; and (ii) approval of the adoption of the Merger Agreement by the holders of a majority of the outstanding shares of common stock entitled to vote on such matters at a stockholders’ meeting duly called and held for such purpose; and (iii) the expiration of the applicable waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976.

The Merger Agreement also contains certain termination rights. Upon termination of the Merger Agreement in accordance with its terms, under certain circumstances, we will be required to pay a termination fee in an amount equal to $4.9 million. In addition, in the event that the Merger Agreement is terminated due to a failure of the holders of a majority of the outstanding shares of common stock to approve the adoption of the Merger Agreement, we will be requirement to make a reimbursement payment to a subsidiary owned by Gurnet Point for fees and expenses incurred in connection with the Merger Agreement and the transactions contemplated thereby in an amount not to exceed $1.75 million.

A failed transaction may result in negative publicity and a negative impression of us among our customers, in the investment community or business community generally. Further, any disruptions to our business resulting from the announcement and pendency of the proposed Merger, including any adverse changes in our relationships with our customers, partners, suppliers and employees, could continue or accelerate in the event of a failed transaction. In addition, if the proposed Merger is not completed, and there are no other parties willing and able to acquire the Company at a price of $2.15 per share (and an equivalently valued CVR) or higher, on terms acceptable to us, the share price of our common stock will likely decline to the extent that the current market price of our common stock reflects an assumption that the proposed Merger will be completed. Also, we have incurred, and will continue to incur, significant costs, expenses and fees

43

for professional services and other transaction costs in connection with the proposed Merger, for which we will have received little or no benefit if the proposed Merger is not completed. Many of these fees and costs will be payable by us even if the proposed Merger is not completed and may relate to activities that we would not have undertaken other than to complete the proposed Merger.

In addition, if the Merger is not consummated, our board, in assessing our, operations, prospects, strategic and short- and long-term operating plans, assets, liabilities, financial condition, believes there is a high risk of insolvency if we continue to operate independently and pursue our business on a standalone basis. With our convertible notes coming due on May 1, 2024, we believe we will need to successfully execute one or more financing transactions prior to that date or otherwise risk bankruptcy. We anticipate that any such financing transactions, if they could be completed, would likely be substantially dilutive to our current stockholders. Our plans would also require us to reduce our workforce by at least 30%, including substantial reductions among the sales force, without materially negatively impacting our ability to generate sales of NUZYRA or to otherwise successfully operate our business. We also anticipate that an amendment to the convertible notes would require the grant of a security interest, thereby restricting our ability to raise debt financing in the future. Finally, there can be no assurance that we would be successful in securing additional funds on acceptable terms, or at all. If additional funds are not available, we may be forced to cease operations, significantly reduce operating expenses or delay, curtail, or eliminate one or more of our development programs or our business operations.

44

Item 6.    Exhibits

EXHIBIT INDEX

		Incorporated by Reference
Exhibit No.	Exhibit Description	Schedule/ Form	File Number	Exhibit	Filing Date
2.1†	Agreement and Plan of Merger, dated as of June 6, 2023, by and among the Company, Resistance Acquisition, Inc. and Resistance Merger Sub, Inc.	Form 8-K	001-36066	2.1	June 7, 2023
3.1	Amended and Restated Certificate of Incorporation.	Form 8-K	001-36066	3.1	October 31, 2014
3.2	Certificate of Amendment of Amended and Restated Certificate of Incorporation.	Form 8-K	001-36066	3.2	October 31, 2014
3.3	Certificate of Elimination of Series A Junior Participating Preferred Stock	Form 8-K	001-36066	3.1	July 24, 2015
3.4	Certificate of Amendment to the Amended and Restated Certificate of Incorporation.	Form 10-Q	001-36066	3.4	August 9, 2021
3.5	Amended and Restated Bylaws.	Form 8-K	001-36066	3.1	March 14, 2023
4.1	Specimen Common Stock Certificate.	Form S-3	333-201458	4.2	January 12, 2015
4.2	Form of Warrant Agreement issued to Hercules Capital, Inc.	Form 8-K	001-36066	4.1	June 29, 2017
4.3	Warrant Agreement issued to Hercules Capital, Inc.	Form 10-Q	001-36066	4.5	August 2, 2018
4.4	Warrant Agreement, dated as of August 5, 2020 issued to Hercules Capital, Inc.	Form 10-Q	001-36066	4.9	August 10, 2020
31.1*	Certification of the Company’s Chief Executive Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities and Exchange Act of 1934, as amended, pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2*	Certification of the Company’s Principal Financial Officer pursuant to Rule 13a-14(a) and Rule 15d-14(a) of the Securities and Exchange Act of 1934, as amended, pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1*	Certification of the Company’s Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2*	Certification of the Company’s Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS*	Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.

45

		Incorporated by Reference
Exhibit No.	Exhibit Description	Schedule/ Form	File Number	Exhibit	Filing Date
101.SCH*	Inline XBRL Taxonomy Extension Schema Document.
101.CAL*	Inline XBRL Taxonomy Extension Calculation Linkbase Document.
101.DEF*	Inline XBRL Taxonomy Extension Definition Linkbase Document.
101.LAB*	Inline XBRL Taxonomy Extension Labels Linkbase Document.
101.PRE*	Inline XBRL Taxonomy Extension Presentation Linkbase Document.
104*	Cover Page Interactive Data File (embedded within the Inline XBRL document)

_________________________

* Filed herewith.

† Certain exhibits and schedules have been omitted pursuant to Item 601(b)(2) of Regulation S-K. The Company agrees to furnish supplementally to the Securities and Exchange Commission a copy of any omitted exhibits or schedules upon request.

46

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized, on the 3rd day of August 2023.

Paratek Pharmaceuticals, Inc.
By:	/s/ Evan Loh M.D.
	Evan Loh M.D.
	Chief Executive Officer (Principal Executive Officer)
By:	/s/ Sarah Higgins
	Sarah Higgins
	Vice President, Finance (Principal Financial and Accounting Officer)

47