UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

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

For the quarterly period ended June 30, 2013

OR

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

For the transition period from              to             

Commission file number 001-34828

TRIUS THERAPEUTICS, INC.

(Exact name of registrant as specified in its charter)

Delaware	2834	20-1320630
(State or other jurisdiction of incorporation or organization)	(Primary Standard Industrial Classification Code Number)	(I.R.S. Employer Identification Number)

6310 Nancy Ridge Drive, Suite 105

San Diego, California 92121

(858) 452-0370

(Address, including zip code and telephone number, including

area code, of registrant’s principal executive offices)

(Former Name, Former Address and Former Fiscal Year, If Changed Since Last Report)

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  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted 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 and post such files).    Yes  x    No  ¨

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

Large accelerated filer	¨	Accelerated filer	x
Non-accelerated filer	¨ (do not check if a smaller reporting company)	Smaller reporting company	¨

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

The number of shares outstanding of the issuer’s common stock, par value $.0001 per share, as of August 1, 2013 was 48,268,557.

INDEX

		Page
Part I.	FINANCIAL INFORMATION		1
Item 1.	Financial Statements		1
	Balance Sheets as of June 30, 2013 (unaudited) and December 31, 2012		1
	Statements of Operations for the three and six months ended June 30, 2013 and 2012 (unaudited)		2
	Statements of Comprehensive Loss for the three and six months ended June 30, 2013 and 2012 (unaudited)		3
	Statements of Cash Flows for the six months ended June 30, 2013 and 2012 (unaudited)		4
	Notes to Financial Statements		5
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations		16
Item 3.	Quantitative and Qualitative Disclosures About Market Risk		24
Item 4.	Controls and Procedures		24
Part II.	OTHER INFORMATION		24
Item 1.	Legal Proceedings		24
Item 1A.	Risk Factors		24
Item 6.	Exhibits		45
SIGNATURES			47

PART I. FINANCIAL INFORMATION

Item 1. Financial Statements

Trius Therapeutics, Inc.

Balance Sheets

(In thousands except share data)

	June 30, 2013			December 31, 2012
	(unaudited)
Assets
Current assets:
Cash and cash equivalents	$	15,316		$	16,370
Short-term investments, available-for-sale		54,256			49,659
Accounts receivable		1,918			5,698
Prepaid expenses and other current assets		1,429			2,254
Total current assets		72,919			73,981
Property and equipment, net		836			990
Restricted cash		151			151
Other assets		149			152
Total assets	$	74,055		$	75,274
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable	$	5,420		$	6,761
Accrued liabilities		7,358			7,762
Common stock warrant liability		6,574			3,848
Current portion of deferred revenue		23			116
Total liabilities		19,375			18,487
Stockholders’ equity:
Preferred stock, $0.0001 par value; 10,000,000 shares authorized at June 30, 2013 and December 31, 2012; no shares issued and outstanding at June 30, 2013 and December 31, 2012		—			—
Common stock, $0.0001 par value; 200,000,000 shares authorized at June 30, 2013 and December 31, 2012; 48,047,472 and 40,661,360 shares issued and outstanding at June 30, 2013 and December 31, 2012, respectively		6			5
Additional paid-in capital		240,950			206,093
Accumulated other comprehensive income		6			9
Accumulated deficit		(186,282	)		(149,320	)
Total stockholders’ equity		54,680			56,787
Total liabilities and stockholders’ equity	$	74,055		$	75,274

See accompanying notes.

1

Trius Therapeutics, Inc.

Statements of Operations

(In thousands except per share data)

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2013			2012			2013			2012
Revenues:
Contract research	$	261		$	2,220		$	790		$	5,231
Collaborations		1,030			3,220			2,228			8,091
License		—			784			—			2,734
Total revenues		1,291			6,224			3,018			16,056
Operating expenses:
Research and development		14,683			16,379			27,228			33,225
General and administrative		5,543			3,311			10,047			6,315
Total operating expenses		20,226			19,690			37,275			39,540
Loss from operations		(18,935	)		(13,466	)		(34,257	)		(23,484	)
Other income (expense):
Interest income		8			7			19			7
Fair value adjustment of common stock warrant liability		(757	)		(955	)		(2,726	)		1,462
Other income (expense)		2			0			2			(3	)
Total other income (expense)		(747	)		(948	)		(2,705	)		1,466
Net loss	$	(19,682	)	$	(14,414	)	$	(36,962	)	$	(22,018	)
Net loss per share, basic and diluted	$	(0.41	)	$	(0.37	)	$	(0.79	)	$	(0.60	)
Weighted-average shares outstanding, basic and diluted		47,948			38,715			46,990			36,955

See accompanying notes.

2

Trius Therapeutics, Inc.

Statements of Comprehensive Loss

(In thousands)

(Unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2013			2012			2013			2012
Net loss	$	(19,682	)	$	(14,414	)	$	(36,962	)	$	(22,018	)
Unrealized gain (loss) on available-for-sale securities, net		(1	)		7			(3	)		(10	)
Comprehensive loss		(19,683	)	$	(14,407	)		(36,965	)	$	(22,028	)

See accompanying notes.

3

Trius Therapeutics, Inc.

Statements of Cash Flows

(In thousands)

(Unaudited)

	Six Months Ended June 30,
	2013			2012
Operating activities
Net loss	$	(36,962	)	$	(22,018	)
Adjustments to reconcile net loss to net cash used in operating activities
Depreciation and amortization		356			333
Gain on sale of capital equipment		(2	)		—
Share-based compensation		2,460			1,500
(Gain) loss on fair value adjustment of stock warrant liability		2,726			(1,462	)
Amortization of investment premiums		226			455
Changes in operating assets and liabilities:
Accounts receivable		3,781			(2,149	)
Prepaid expenses and other current assets		825			22
Accounts payable		(1,341	)		1,368
Accrued liabilities		(405	)		(1,378	)
Deferred revenue		(94	)		(197	)
Other assets		3			52
Net cash used in operating activities		(28,427	)		(23,474	)
Investing activities
Purchases of investments		(56,097	)		(55,948	)
Sales and maturities of investments		51,271			32,937
Purchases of property and equipment		(202	)		(221	)
Proceeds from sale of capital equipment		2			—
Net cash used in investing activities		(5,026	)		(23,232	)
Financing activities
Proceeds from issuance of common stock, net of offering costs		31,613			48,374
Proceeds from exercise of stock options and stock issuances under employee stock purchase plans		786			463
Net cash provided by financing activities		32,399			48,837
Net increase (decrease) in cash and cash equivalents		(1,054	)		2,131
Cash and cash equivalents at beginning of period		16,370			11,381
Cash and cash equivalents at end of period	$	15,316		$	13,512

See accompanying notes.

4

Trius Therapeutics, Inc.

NOTES TO FINANCIAL STATEMENTS

Note 1. Organization and Summary of Significant Accounting Policies

Organization

Trius Therapeutics, Inc., or the Company, is a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for serious infections. The Company was originally incorporated in California in June 2004 and reincorporated in Delaware in December 2007.

On July 30, 2013, the Company entered into an Agreement and Plan of Merger, or Merger Agreement, with Cubist Pharmaceuticals, Inc., a Delaware corporation, or Cubist, and BRGO Corporation, a Delaware corporation and a wholly owned subsidiary of Cubist, or Purchaser, pursuant to which, and on the terms and subject to the conditions thereof, among other things, Purchaser will commence a tender offer, or Offer, no later than August 13, 2013 to acquire all of the outstanding shares of common stock of the Company at a purchase price of (a) $13.50 per share in cash, or Closing Amount, without interest, plus (b) one non-transferrable contingent value right for each share of the Company’s common stock, each a CVR, which represents the contractual right to receive up to $2.00 per share upon the achievement of certain milestones, such amount together with the Closing Amount is referred to as the Offer Price, subject to any required withholding of taxes. Following the completion of the Offer and subject to the satisfaction or waiver of certain conditions set forth in the Merger Agreement, including, if required, receipt of approval by the stockholders of the Company, Purchaser will merge with and into the Company, with the Company surviving as a wholly owned subsidiary of Cubist, or the Merger.

Use of Estimates

The preparation of financial statements in conformity with United States generally accepted accounting principles, or GAAP, requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates.

Cash and Cash Equivalents

The Company considers all highly liquid investments with maturities of three months or less from the date of purchase to be cash equivalents.

Investments Available-for-Sale

Available-for-sale securities are carried at fair value, with the unrealized gains and losses reported in accumulated other comprehensive income (loss). The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity. The amortization of premiums and accretion of discounts is included in interest income. Realized gains and losses and declines in value judged to be other-than-temporary, if any, on available-for-sale securities are included in other income (expense). The cost of securities sold is based on the specific identification method. Interest and dividends on securities classified as available-for-sale are included in interest income.

Concentration of Credit Risk

Financial instruments, which potentially subject the Company to concentration of credit risk, consist primarily of cash and cash equivalents and marketable securities. The Company maintains deposits in federally insured financial institutions in excess of federally insured limits. Management believes that the Company is not exposed to significant credit risk due to the financial position of the depository institutions in which those deposits are held. Additionally, the Company has established guidelines regarding approved investments and maturities of investments, which are designed to maintain safety and liquidity.

Accounts Receivable

Accounts receivable at June 30, 2013 and December 31, 2012 represent amounts due under the Company’s Collaboration and License Agreement, or the Bayer Agreement, with Bayer Pharma AG, or Bayer, and from federal funding sources based upon federal contracts with the National Institute of Allergy and Infectious Diseases, or NIAID, a part of the National Institutes of Health, and Lawrence Livermore National Laboratory, or LLNL, a part of the U.S. Department of Energy’s National Nuclear Security Administration. The Company’s accounts receivable consists of both billed and unbilled amounts. The Company’s practice is to bill its customers and collaborators amounts for which the Company has been invoiced by third parties in the case of contract research or subcontractor costs or for internal costs incurred. Unbilled accounts receivable consist of expenses directly associated with the Company’s contracts that have been accrued at the end of the reporting period but have not been billed to its customers and collaborators.

Property and Equipment, Net

Property and equipment are stated at cost, less accumulated depreciation and amortization. Depreciation and amortization are calculated using the straight-line method over the estimated useful lives of the respective assets, generally three to seven years. Leasehold improvements are amortized over the shorter of the lease term or the estimated useful economic lives of the related assets.

Impairment of Long-Lived Assets

Long-lived assets consist of property and equipment, long-term investments and long term deposits. The Company will record impairment losses on long-lived assets used in operations when events and circumstances indicate that assets might be impaired and the undiscounted cash flows estimated to be generated by those assets are less than the carrying amount of those assets. While the Company’s current and historical operating losses and cash flows are indicators of impairment, the Company believes the future cash flows to be received support the carrying value of its long-lived assets and, accordingly, the Company has not recognized any impairment losses through June 30, 2013.

5

Restricted Cash

The Company’s corporate credit card arrangement requires that the Company maintain a deposit of $150,000 with the issuer of its credit cards. This security deposit is maintained in an interest bearing certificate of deposit and is recorded as restricted cash on the Balance Sheet.

Fair Value of Financial Instruments

The Company’s financial instruments consist of cash and cash equivalents, marketable securities, accounts receivable, accounts payable, accrued liabilities and warrants to purchase common stock. Fair value estimates of these instruments are made at a specific point in time based on relevant market information. These estimates may be subjective in nature and involve uncertainties and matters of significant judgment and therefore cannot be determined with precision. The carrying amount of cash and cash equivalents, accounts receivable, accounts payable, and accrued liabilities are generally considered to be representative of their respective fair values because of the short-term nature of those instruments. The fair value of marketable securities is based upon market prices quoted on the last day of the fiscal period. The fair value of the common stock warrants is determined using a Black-Scholes model.

Revenue Recognition

The Company’s revenues are derived from the Bayer Agreement and federal contracts. The Company recognizes revenues when all four of the following criteria are met: (1) persuasive evidence that an arrangement exists; (2) delivery of the products and/or services has occurred; (3) the selling price is fixed or determinable; and (4) collectability is reasonably assured.

The Company’s license and collaboration agreements contain multiple elements, including non-refundable upfront fees, payments for reimbursement of internal and third-party development and regulatory costs, payments associated with achieving specific milestones and royalties based on specified percentages of net product sales, if any. The Company considers a variety of factors in determining the appropriate method of revenue recognition under these arrangements, such as whether the elements are separable, whether there are determinable fair values and whether there is a unique earnings process associated with each element of a contract.

Revenue recognition for agreements with multiple deliverables is based on the individual units of accounting determined to exist in the agreement. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis.

The Company recognizes revenue according to the provisions of Accounting Standards Codification, or ASC, 605-25 Revenue Recognition—Multiple Element Arrangements . Consideration received from multiple-element arrangements is allocated at the inception of the agreement to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence, or VSOE, of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence of selling price exists, the Company uses its best estimate of the selling price for the deliverable.

The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance. Changes in the allocation of the sales price between delivered and undelivered elements can impact revenue recognition but do not change the total revenue recognized under an agreement.

Cash received in advance of services being performed is recorded as deferred revenue and recognized as revenue as services are performed over the applicable term of the agreement.

When a payment is specifically tied to a separate earnings process, revenues are recognized when the specific performance obligation associated with the payment is completed. Performance obligations typically consist of significant and substantive milestones pursuant to the related agreement. Revenues from milestone payments may be considered separable from funding for development and regulatory services because of the uncertainty surrounding the achievement of milestones for products in early stages of development. Accordingly, these payments are allowed to be recognized as revenue if and when the performance milestone is achieved if they are determined to be substantive milestones. Milestones do not include events that occur solely upon the passage of time or as a result of a counterparty’s performance.

When determining whether or not to account for transactions under the milestone method, the Company makes a determination at the inception of the agreement of whether or not each milestone is considered substantive. During this assessment process, the Company considers if achievement of the milestone is based in whole or in part on the Company’s performance or on the occurrence of a separate outcome resulting from the Company’s performance, if there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved, and if achievement will result in additional payments being due. In order for milestone consideration to be deemed substantive, it should:

1. Be commensurate with either the vendor’s performance to achieve the milestone or the enhancement of value of the item delivered as a result of the specific outcome resulting from the vendor’s performance to achieve the milestone.

2. Relate solely to past performance; and

3. Be reasonable relative to all deliverables and payment terms in the arrangement.

With respect to revenues derived from reimbursement of direct out-of-pocket expenses for research costs associated with federal contracts, where the Company acts as a principal, with discretion to choose suppliers, bears credit risk and performs part of the services required in the transaction, the Company records revenue for the gross amount of the reimbursement. The costs associated with these reimbursements are reflected as a component of research and development expense in the Statements of Operations.

6

Research and Development Expenses

Research and development expenses include related salaries, benefits, share-based compensation, costs to third-party contractors to perform research, conduct clinical trials and develop drug materials, research supplies, associated overhead expenses, facilities costs and license fees paid to third parties for use of their intellectual property. Research and development costs are expensed as incurred.

Patent Costs

Costs related to filing and pursuing patent applications are expensed as incurred, as recoverability of such expenditures is uncertain.

Operating Leases

The Company enters into operating leases primarily for office space. Minimum rents as defined in the Company’s lease agreements including rent escalations, rent holidays and rental concessions are recognized on the straight-line basis over the non-cancellable lease term. Payments made to or on behalf of the Company for leasehold improvement incentives are considered reductions in rental expense and are amortized on a straight-line basis over the non-cancellable lease term.

Share-Based Compensation

The Company accounts for share-based compensation by measuring and recognizing compensation expense for all share-based payments made to employees and directors based on estimated grant date fair values. The Company allocates compensation cost to reporting periods over each optionee’s requisite service period, which is generally the vesting period, and estimates the fair value of share-based awards to employees and directors using the Black-Scholes option valuation model. The Black-Scholes model requires the input of subjective assumptions, including volatility, the expected term and the fair value of the underlying common stock on the date of grant, among other inputs.

Stock options granted to non-employees are accounted for using the fair value approach. Stock options granted to non-employees are subject to periodic revaluation over their vesting terms.

Comprehensive Income (Loss)

Comprehensive income or loss consists of net income or loss and changes in equity during a period from transactions and other events and circumstances generated from non-owner sources.

Income Taxes

The Company uses the liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the difference between the financial reporting and the tax reporting basis of assets and liabilities and are measured using the enacted tax rates and laws that are expected to be in effect when the differences are expected to reverse. The Company provides a valuation allowance against net deferred tax assets unless, based upon the available evidence, it is more likely than not that the deferred tax assets will be realized. The Company has evaluated available evidence and concluded that the Company may not realize the benefit of its deferred tax assets; therefore a valuation allowance has been established for the full amount of the deferred tax assets at June 30, 2013 and December 31, 2012. The Company’s practice is to recognize interest and/or penalties related to income tax matters in income tax expense.

Unaudited Interim Financial Data

The accompanying balance sheet as of June 30, 2013, statements of operations for the three and six months ended June 30, 2013 and 2012, statements of comprehensive loss for the three and six months ended June 30, 2013 and 2012 and statements of cash flows for the six months ended June 30, 2013 and 2012 are unaudited. These unaudited financial statements have been prepared in accordance with the rules and regulations of the United States Securities and Exchange Commission, or SEC, for interim financial information. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. These financial statements should be read in conjunction with the audited financial statements and the accompanying notes for the year ended December 31, 2012 contained in the Company’s Annual Report on Form 10-K. The unaudited interim financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments (consisting of normal recurring adjustments) necessary to state fairly the Company’s financial position as of June 30, 2013 and the results of operations and comprehensive loss for the three and six months ended June 30, 2013 and 2012 and cash flows for the six months ended June 30, 2013 and 2012. The December 31, 2012 balance sheet included herein was derived from audited financial statements, but does not include all disclosures including notes required by GAAP for complete financial statements.

The financial data and other information disclosed in these notes to the financial statements related to the three and six months ended June 30, 2013 and 2012 are unaudited. Interim results are not necessarily indicative of results for an entire year.

Net Loss per Common Share

Basic net loss per share is calculated by dividing the net loss by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents. Diluted net loss per share is computed by dividing the net loss by the

7

weighted average number of common share equivalents outstanding for the period determined using the treasury-stock method. For purposes of this calculation, preferred stock, stock options and warrants 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.

The following table presents the computation of basic and diluted net loss per common share (in thousands, except per share data):

	Three Months Ended June 30,						Six Months Ended June 30,
	2013			2012			2013			2012
Net loss per share
Numerator
Net loss	$	(19,682	)	$	(14,414	)	$	(36,962	)	$	(22,018	)
Denominator
Weighted-average common shares outstanding		47,948			38,715			46,990			36,956
Less: Weighted-average shares subject to repurchase		—			—			—			(1	)
Denominator for basic and diluted net loss per share		47,948			38,715			46,990			36,955
Basic and diluted net loss per share	$	(0.41	)	$	(0.37	)	$	(0.79	)	$	(0.60	)

Potentially dilutive securities not included in the calculation of diluted net loss per common share because to do so would be anti-dilutive are as follows (in common equivalent shares):

	June 30,
	2013		2012
Common stock warrants		1,678,884		1,678,884
Common stock subject to repurchase		—		61
Common stock options		5,617,680		3,859,596
		7,296,564		5,538,541

Segments

The Company operates in only one segment. Management uses cash flows as the primary measure to manage its business and does not segment its business for internal reporting or decision making.

Note 2. Significant Agreements and Contracts

License Agreements

In January 2007, the Company entered into a license agreement whereby the Company acquired the rights to certain proprietary materials and information related to DA-7128 (now known as tedizolid phosphate) from Dong-A ST Co., Ltd. (as successor-in-interest to Dong-A Pharmaceutical Co., Ltd.), or Dong-A. Since the inception of the license agreement, $5.7 million in license fees and milestone payments have been paid to Dong-A. If certain development and regulatory approval milestones are achieved, the Company may be required to pay up to an additional $11.5 million to Dong-A. The agreement terminates upon the expiration of the last royalty term for a licensed product. Either party may terminate the agreement upon 90 days’ prior written notice to the other upon or after a material, uncured default by the other party. The Company may terminate the agreement by sending Dong-A 90 days’ advance written notice where the Company decides to discontinue development or commercialization of products for any reason. Dong-A may terminate the agreement by sending 90 days’ advance written notice to the Company in the event that the Company fails to meet specified development and commercialization efforts within specified time periods.

Contract Research

In September 2008, the Company entered into a five-year federal contract with NIAID under which the Company is advancing the development of a novel broad spectrum antibiotic. This was a cost reimbursement contract with total potential payments of up to $27.7 million. In February 2013, the Company was notified by NIAID that funding under the contract would not be extended beyond March 31, 2013. The Company discontinued contract activities on March 31, 2013. The Company recognized revenues under this contract as services were performed. Amounts received in advance of services performed have been recorded as deferred revenue until earned. The Company recorded revenues under this contract of $47,000 and $1.7 million for the three months ended June 30, 2013 and 2012, respectively, and $0.5 million and $3.2 million for the six months ended June 30, 2013 and 2012, respectively. Billed receivables due under the Company’s contract with NIAID at June 30, 2013 and December 31, 2012 were $77,000 and $503,000, respectively. Unbilled receivables were $0 and $123,000 at June 30, 2013 and December 31, 2012, respectively. From contract inception through June 30, 2013, the Company has recognized $25.6 million in revenues related to the research performed.

In April 2011, the Company entered into a three-year research contract with LLNL, a part of the U.S. Department of Energy’s National Nuclear Security Administration, for the development of novel antibiotics directed against Gram-negative multi-drug resistant

8

bacterial pathogens. This is a cost-plus-fixed-fee contract. In May 2013, the contract was amended to extend the contract for an additional year and increase the total potential payments the Company may receive in support of its development efforts from $3.0 million to $4.2 million. The Company recognizes revenue under this contract as the services are performed. Amounts received in advance of services performed are recorded as deferred revenue until earned. The Company recorded revenues under this contract of $0.2 million and $0.4 million for the three months ended June 30, 2013 and 2012, respectively, and $0.3 million and $0.7 million for the six months ended June 30, 2013 and 2012, respectively. LLNL can terminate the contract upon delivering notice to the Company for default or convenience. Upon receipt of a notice of termination, the Company must discontinue contract activities and LLNL must pay the Company a final settlement based on eligible expenses incurred under the contract. As of June 30, 2013, the Company has not received a notice of termination relative to contract activities. Billed receivables due under the Company’s contract with LLNL at June 30, 2013 and December 31, 2012 were $0 and $265,000, respectively. Unbilled receivables were $267,000 and $32,000 at June 30, 2013 and December 31, 2012, respectively. From contract inception through June 30, 2013, the Company has recognized $2.2 million in revenues related to the research performed.

In April 2010, the Company entered into a four-and-one-half-year federal contract with the Defense Threat Reduction Agency, or DTRA, an agency within the U.S. Department of Defense, for the development of novel antibiotics directed against Gram-negative bacterial pathogens. Due to programmatic priorities toward later stage programs, on May 3, 2012, DTRA elected not to exercise its option to extend funding under the contract with the Company and therefore, the contract was not extended beyond July 20, 2012. As a result, the Company chose to discontinue its marine natural products discovery program, which was solely funded by the DTRA contract. The Company recognized revenue under this contract as the services were performed. The Company recognized no revenue under this contract for the three and six months ended June 30, 2013 and recognized $0.2 million and $1.3 million in revenues for the three and six months ended June 30, 2012, respectively. There were no billed or unbilled receivables due under the Company’s contract with DTRA at June 30, 2013 or December 31, 2012. From contract inception through the termination of the contract in 2012, the Company recognized $7.3 million in revenues related to the research performed.

Collaborations

In July 2011, the Company entered into the Bayer Agreement under which the Company granted Bayer exclusive rights to commercialize the Company’s lead, novel antibiotic, tedizolid phosphate, in China, Japan and substantially all other countries in Asia, Africa, Latin America and the Middle East, excluding North and South Korea, which the Company refers to as the Bayer Licensed Territory. Under the Bayer Agreement, the Company retains full development and commercialization rights outside the Bayer Licensed Territory, including the United States, Canada and the European Union but excluding North and South Korea where Dong-A retained its rights. In exchange for development and commercialization rights in the Bayer Licensed Territory, Bayer paid the Company $25.0 million upfront and agreed to support approximately 25% of the future development costs of tedizolid required for global approval for treatment of acute bacterial skin and skin structure infections, or ABSSSI, and pneumonia, subject to certain adjustments and limitations. In addition, Bayer agreed to support 100% of the future development costs required for local approval in the Bayer Licensed Territory. The Company is also eligible to receive up to $69.1 million upon the achievement of certain development, regulatory, and commercial milestones and will receive double-digit royalties on net sales of tedizolid in the Bayer Licensed Territory. None of the payments that the Company has received from Bayer to date, whether recognized as revenue or deferred, are refundable even if the related program is not successful. Revenues recognized in connection with the Bayer Agreement were $1.0 million and $4.0 million for the three months ended June 30, 2013 and 2012, respectively, and $2.2 million and $10.8 million for the six months ended June 30, 2013 and 2012, respectively, as further discussed in Note 8.

Note 3. Investments in Marketable Securities

Investments classified as available-for-sale at June 30, 2013 and December 31, 2012 consisted of the following (in thousands):

	June 30, 2013		December 31, 2012
U.S. Treasury securities	$	54,256	$	49,659
Total available-for-sale investments	$	54,256	$	49,659

The following is a summary of investments classified as available-for-sale securities (in thousands):

	Amortized Cost		Gross Unrealized Gains (1)		Gross Unrealized Losses (1)		Aggregate Estimated Fair Value
June 30, 2013
U.S. Treasury securities with unrealized gains	$	53,250	$	6	$	—	$	53,256
U.S. Treasury securities with unrealized losses		1,000		—		—		1,000
Total available-for-sale securities	$	54,250	$	6	$	—	$	54,256
December 31, 2012
U.S. Treasury securities with unrealized gains	$	43,850	$	9	$	—	$	43,859
U.S. Treasury securities with unrealized losses		5,800		—		—		5,800
Total available-for-sale securities	$	49,650	$	9	$	—	$	49,659

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⁽¹⁾  Unrealized gains and losses on available-for-sale securities are included as a component of comprehensive loss. At June 30, 2013, there was one security in an unrealized loss position, and at December 31, 2012, there were three securities in an unrealized loss position. These unrealized losses were less than $1,000 individually and in the aggregate. These securities have not been in a continuous unrealized loss position for more than 12 months. The Company does not intend to sell these investments and it is not more likely than not that the Company will be required to sell these investments before recovery of their amortized cost basis which may be at maturity. The Company reviews its investments to identify and evaluate investments that have an indication of possible other-than-temporary impairment. Factors considered in determining whether a loss is other-than-temporary include the length of time and extent to which fair value has been less than the cost basis, the financial condition and near-term prospects of the investee, and the Company’s intent and ability to hold the investment for a period of time sufficient to allow for any anticipated recovery in market value.

The amortized cost and estimated fair value of debt securities classified as available-for-sale by contractual maturity at June 30, 2013 and December 31, 2012 are presented below (in thousands):

	Maturing in 12 months or less				Maturing in more than 12 months
	Amortized Cost		Estimated Fair Value		Amortized Cost		Estimated Fair Value
June 30, 2013
U.S. Treasury securities	$	54,250	$	54,256	$	—	$	—
Total available-for-sale securities	$	54,250	$	54,256	$	—	$	—
December 31, 2012
U.S. Treasury securities	$	49,650	$	49,659	$	—	$	—
Total available-for-sale securities	$	49,650	$	49,659	$	—	$	—

The proceeds from sales of available-for-sale securities during the three and six months ended June 30, 2013 were $2.0 million and $5.1 million, respectively, and resulted in realized gains of less than $1,000 during both periods. The proceeds from sales of available-for-sale securities during the three and six months ended June 30, 2012 were $3.6 million and $6.4 million, respectively, and resulted in realized gains of less than $1,000 during both periods.

Note 4. Fair Value Measurements

The Company’s financial instruments consist principally of cash and cash equivalents, marketable securities, accounts receivable, accounts payable, accrued liabilities, and warrant liabilities related to warrants to purchase common stock. Fair value measurements are classified and disclosed in one of the following three categories:

Level 1 —Quoted prices in active markets for identical assets or liabilities.

Level 2 —Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

Level 3 —Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Financial instruments measured at fair value as of June 30, 2013 and December 31, 2012 are classified below based on the three fair value hierarchy tiers described above (in thousands):

			Fair Value Measurements at Reporting Date Using
	Total		Level 1		Level 2		Level 3
June 30, 2013
Assets:
Money Market funds, included in cash equivalents	$	7,103	$	7,103	$	—	$	—
US Treasury securities, included in cash equivalents		4,703		4,703		—		—
U.S. Treasury securities, available-for-sale		54,256		0		54,256		—
Total	$	66,062	$	11,806	$	54,256	$	—
Liabilities:
Common stock warrant liability	$	6,574	$	—	$	—	$	6,574
Total	$	6,574	$	—	$	—	$	6,574
December 31, 2012
Assets:
Money Market funds, included in cash equivalents	$	13,464	$	13,464	$	—	$	—
U.S. Treasury securities, available-for-sale		49,659		0		49,659		—
Total	$	63,123	$	13,464	$	49,659	$	—
Liabilities:
Common stock warrant liability	$	3,848	$	—	$	—	$	3,848
Total	$	3,848	$	—	$	—	$	3,848

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The fair value of the common stock warrant liability was determined based on “Level 3” inputs and utilizing the Black-Scholes option pricing model. The following table presents activity for the common stock warrant liability measured at fair value using significant unobservable Level 3 inputs during the six months ended June 30, 2013 and 2012 (in thousands):

	Six Months Ended June 30,
	2013			2012
Beginning balance	$	(3,848	)	$	(7,124	)
Purchases		—			—
Issuances		—			—
Settlements		—			—
Gains (losses) included in other income (expense)		(2,726	)		1,462
Transfers (to) from Level 3		—			—
Ending balance	$	(6,574	)	$	(5,662	)

The Company performed an analysis to determine the sensitivity to changes in the unobservable input used in the calculation of the estimated fair value of the common stock warrant liability. If the volatility rate used in the calculation of the estimated fair value of the liability-classified common stock warrants at June 30, 2013 were to decrease by 10%, the liability would have decreased approximately $0.6 million. If the volatility rate were to increase by 10%, the liability would have increased approximately $0.6 million. These changes would have been recognized in the related component of other income (expense) in the Statements of Operations.

Note 5. Common Stock Warrants

Equity-classified warrants

During 2004, in connection with a financing arrangement, the Company issued warrants to purchase shares of its Series A-1 convertible preferred stock. Upon closing of the Company’s initial public offering, the warrants to purchase preferred stock converted into warrants to purchase common stock. At June 30, 2013, 16,384 warrants remain outstanding at a per share exercise price of $4.73.

Liability-classified warrants

On May 31, 2011, the Company closed a private placement transaction with certain accredited investors pursuant to which an aggregate of 1,662,500 warrants to purchase common stock were issued. Each warrant is exercisable in whole or in part for a period of five years commencing on November 27, 2011 at a per share exercise price of $8.50, subject to certain adjustments as specified in the warrant. The Company valued the warrants as derivative financial instruments as of the date of issuance and recorded them as a liability. The Company will continue to value the warrants at each reporting date, with any changes in fair value being recorded within other income (expense) in the Statements of Operations. The fair value of the warrants increased by approximately $2.7 million during the six months ended June 30, 2013 primarily due to the increase in the Company’s stock price since the December 31, 2012 measurement date. The warrants have been recorded at an estimated fair value of $6.6 million at June 30, 2013.

The determination that the warrants should be recorded as a liability is due to the fact that the warrants contain a net cash settlement provision under which the warrant holders may require the Company to purchase the warrants in exchange for a cash payment following the announcement of specified events defined as Fundamental Transactions involving the Company (e.g., merger, sale of all or substantially all assets, tender offer, or share exchange) or a Delisting, which is deemed to occur when the common stock is no longer listed on a national securities exchange. The net cash settlement provision requires use of the Black-Scholes model in calculating the cash payment value in the event of a Fundamental Transaction or a Delisting.

The net cash settlement value at the time of any future Fundamental Transaction or Delisting will depend upon the value of the following inputs at that time: the price per share of the Company’s common stock, the volatility of the Company’s common stock, the expected term of the warrant, the risk-free interest rate based on U.S. Treasury security yields, and the Company’s dividend yield. The warrant requires use of a volatility assumption equal to the greater of (i) 100%, (ii) the 30-day volatility determined as of the trading day immediately following announcement of a Fundamental Transaction or Delisting, or (iii) the arithmetic average of the 10, 30, and 50-day volatility determined as of the trading day immediately following announcement of a Fundamental Transaction or Delisting.

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The fair value of the warrants is determined using a Black-Scholes model. The valuation of warrants is subjective and is affected by changes in inputs to the valuation model including the price per share of the Company’s common stock, the historical volatility of the stock prices of the Company’s peer group, risk-free rates based on U.S. Treasury security yields, the expected term of the warrants and the Company’s dividend yield. Changes in these assumptions can materially affect the fair value estimate. The Company could ultimately pay amounts to settle the warrant under the net cash settlement value that are significantly different than the carrying value of the liability in the financial statements. The Company will continue to classify the estimated fair value of the warrants as a liability until the warrants are exercised, expire, or are amended in a way that would no longer require these warrants to be classified as a liability.

The fair value of the liability-classified common stock warrants was estimated using the Black-Scholes option pricing model based on the following assumptions at June 30, 2013:

Expected volatility	72%
Expected term (in years)	3.4
Risk-free interest rate	0.66%
Expected dividend yield	0%

Warrants Exercised and Outstanding

No warrants to purchase common stock were exercised during the six months ended June 30, 2013 or 2012. At June 30, 2013 and December 31, 2012, there were 1,678,884 common stock warrants outstanding all of which were exercisable. The common stock warrants outstanding will expire between two years and four years from June 30, 2013 and have a weighted average exercise price of $8.46.

Note 6. Common Stock Reserved for Issuance

The following table summarizes shares of common stock reserved for future issuance:

	June 30, 2013		December 31, 2012
Common stock warrants		1,678,884		1,678,884
Shares available for purchase under the 2010 Employee Stock Purchase Plan		442,471		314,218
Common stock options outstanding		5,617,680		3,902,682
Common stock options available for future grant		5,366,003		1,174,231
Total common shares reserved for issuance		13,105,038		7,070,015

Note 7. Share-based Compensation

The Company granted 1,834,500 stock options to certain employees of the Company with a weighted average exercise price of $6.42 per share during the six months ended June 30, 2013. The Company granted 1,463,500 stock options to certain employees and consultants of the Company with a weighted average exercise price of $5.02 per share during the six months ended June 30, 2012. The stock options granted by the Company had an exercise price equal to the closing market price of the Company’s common stock on the date of grant.

The following table summarizes stock option activity during the six months ended June 30, 2013:

	Shares			Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Term (years)		Aggregate Intrinsic Value (in thousands)
Options outstanding at December 31, 2012		3,902,682		$	4.25		8.00	$	3,726
Granted		1,834,500		$	6.42
Exercised		(95,230	)	$	2.98			$	402
Canceled		(24,272	)	$	7.49
Options outstanding at June 30, 2013		5,617,680		$	4.96		8.21	$	17,650
Options vested or expected to vest at June 30, 2013		5,596,727		$	4.96		8.21	$	17,607
Options exercisable at June 30, 2013		2,359,228		$	3.87		7.00	$	9,996

At June 30, 2013, there was approximately $12.5 million of total unrecognized compensation costs related to outstanding options granted which is expected to be recognized over a weighted average period of 2.88 years.

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The Company received cash from the exercise of stock options of $283,000 and $167,000 during the six months ended June 30, 2013 and 2012, respectively. Upon option exercise, the Company issues new shares of common stock.

Compensation cost for stock options granted to employees is based on the estimated grant date fair value and is recognized ratably over the vesting period of the applicable option. The estimated per share weighted average fair value of stock options granted to employees during the six months ended June 30, 2013 was $4.56.

As share-based compensation expense recognized is based on options ultimately expected to vest, the expense has been reduced for estimated forfeitures. The fair value of each employee option grant during the six months ended June 30, 2013 was estimated on the date of grant using the Black-Scholes option pricing model with the following weighted average assumptions:

	Six Months Ended June 30, 2013
Expected volatility	85%
Expected term (in years)	5.98
Risk-free interest rate	1.11%
Expected dividend yield	0%

Expected Volatility. The expected volatility rate used to value stock option grants is based on volatilities of a peer group of similar companies whose share prices are publicly available. The peer group was developed based on companies in the pharmaceutical and biotechnology industry in a similar stage of development to the Company.

Expected Term. The Company elected to utilize the “simplified” method for “plain vanilla” options to value stock option grants. Under this approach, the weighted-average expected life is presumed to be the average of the vesting term and the contractual term of the option.

Risk-free Interest Rate. The risk-free interest rate assumption was based on zero-coupon U.S. Treasury instruments that had terms consistent with the expected term of the Company’s stock option grants.

Expected Dividend Yield. The Company has never declared or paid any cash dividends and does not presently plan to pay cash dividends in the foreseeable future.

Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from estimates. The Company estimates forfeitures based on its historical experience. Groups of employees that have similar historical forfeiture behavior are considered separately for expense recognition.

2010 Employee Stock Purchase Plan (ESPP)

The following table shows the assumptions used to compute share-based compensation expense for the 2010 Employee Stock Purchase Plan, or the 2010 Purchase Plan, using the Black-Scholes option pricing model:

	Six Months Ended June  30,
	2013
Expected volatility	40%-80%
Expected term (in years)	0.5-2.0
Risk-free interest rate	0.09%-0.27%
Expected dividend yield	0%

During the six months ended June 30, 2013, approximately 122,000 shares of common stock were issued under the ESPP. The Company issues new shares of common stock on each ESPP purchase date.

Share-based Compensation Summary. Share-based compensation expense is recognized for stock options granted to employees and non-employees as well as employee participation in the 2010 Purchase Plan and has been reported in the Company’s Statements of Operations as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2013		2012		2013		2012
Research and development	$	730	$	374	$	1,350	$	700
General and administrative		648		427		1,110		800
Total	$	1,378	$	801	$	2,460	$	1,500

Since the Company had a net operating loss carryforward as of June 30, 2013, no excess tax benefits for the tax deductions related to share-based awards were recognized in the Statements of Operations. Additionally, no incremental tax benefits were recognized from stock options exercised during the six months ended June 30, 2013 and 2012 that would have resulted in a reclassification to reduce net cash provided by operating activities with an offsetting increase in net cash provided by financing activities.

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Note 8. Revenue Recognition Under Multiple Element Arrangements

In July 2011, the Company entered into the Bayer Agreement under which the Company granted Bayer exclusive rights to develop and commercialize the Company’s lead antibiotic, tedizolid phosphate in the Bayer Licensed Territory which includes China, Japan and substantially all other countries in Asia, Africa, Latin America and the Middle East, excluding North and South Korea. Under the Bayer Agreement, the Company has agreed to use commercially reasonable efforts to conduct those development and registration activities that are necessary to obtain regulatory approval of tedizolid phosphate for the treatment of ABSSSI and pneumonia in the United States, and Bayer has agreed to use commercially reasonable efforts to conduct those development and registration activities specific to the Bayer Licensed Territory that are necessary to obtain regulatory approval of tedizolid phosphate for the treatment of ABSSSI and pneumonia in major market countries in the Bayer Licensed Territory. The Company is responsible for all development and commercialization activities for tedizolid phosphate in the United States, Canada and the European Union and retains full development and commercialization rights outside the Bayer Licensed Territory, including the United States, Canada and the European Union but excluding North and South Korea where Dong-A retained its rights. In exchange for development and commercialization rights in the Bayer Licensed Territory, Bayer paid the Company $25.0 million upfront and agreed to support approximately 25% of the future development costs of tedizolid phosphate required for global approval for the treatment of ABSSSI and pneumonia, subject to certain adjustments and limitations. In addition, Bayer agreed to support 100% of the future development costs required for local approval in the Bayer Licensed Territory. The Company is also eligible to receive up to $69.1 million upon the achievement of certain development, regulatory and commercial milestones and will receive double-digit royalties on net sales of tedizolid phosphate in the Bayer Licensed Territory.

Pursuant to the accounting guidance under ASC 605-25, which governs revenue recognition for multiple element arrangements, the Company evaluated the two material non-contingent deliverables under the Bayer Agreement and determined that each meets the criteria for treatment as separate units of accounting, as follows:

• The license, referred to as the License, to develop and commercialize tedizolid in the Bayer Licensed Territory; and

• Certain Global Development Plan Services, referred to as Global Development Plan Services, which are expected to be conducted by the Company through 2018.

The Bayer Agreement requires that the Company manufacture and supply bulk drug product for commercial use for up to five years from the first commercial sale of tedizolid phosphate in the Bayer Licensed Territory. Since these manufacturing efforts are contingent upon regulatory approvals for commercialization and there were no firm orders for commercial supply at or near the execution of the agreement, this obligation is deemed a contingent deliverable and was not valued at the inception of the arrangement.

The Company allocated the estimated arrangement consideration based on the percentage of the relative selling price of each unit of accounting. The Company estimated the selling price of the License using the relief from royalty method income approach. The assumptions were based on the estimated after-tax income related to a hypothetical license agreement with a third-party pharmaceutical partner company, which would jointly develop tedizolid phosphate with the Company and hold the rights outside of the U.S., the European Union and Canada. The significant inputs used to determine the selling price were estimates of product sales in the licensed territory, the royalties to be received by the Company from these sales, contractual milestone payments to be received by the Company, total expenses expected to be incurred by the Company, the Company’s income tax rate in future years, and the discount rate used to discount the cash flows to their present values. If the Company’s best estimate of the selling price of the License had been less than the estimate made at the time of initial assessment, then less of the arrangement consideration would have been allocated to the License, while an equal amount would have been allocated to the Global Development Plan Services. If the amount allocated to the License had been less than the upfront payment, then that difference would not have been recorded immediately but would have been deferred until the future periods over which the Global Development Plan Services would be performed. Assuming a constant selling price for the Global Development Plan Services, if there was an assumed 10% decrease in the estimated selling price of the License, or approximately $2.9 million, the Company determined that this change in estimated selling price would have reduced the allocation of the initial arrangement consideration allocated to the License agreement by about $1.6 million.

The Company estimated the selling prices of the Global Development Plan Services using estimated development costs, which consist primarily of costs to be paid to third parties. The significant assumptions and inputs include estimated timeframes until approval of New Drug Applications, or NDAs, filed with the U.S. Food and Drug Administration, the number of internal hours to be spent performing these services, the estimated number of studies to be performed, the estimated number of patients to be included in the studies, the costs of clinical research organizations helping to conduct the studies, the estimated patient costs in conducting the studies, the estimated cost of drug product, the estimated regulatory costs of preparing NDA filings, and the estimated milestone payments to Dong-A, from whom the Company licensed tedizolid phosphate. If the selling price of the Global Development Plan Services were to increase, then more of the expected arrangement consideration would be allocated to the Global Development Plan Services, and an equal amount would be deducted from the License. Assuming a constant estimated selling price for the License and a 10% increase in the estimated selling price of the Global Development Plan Services, or approximately $4.5 million, then the Company would have allocated an additional $1.4 million of the initial arrangement consideration to the Global Development Plan Services, which would have been recorded over the period of performance of such services.

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Revenues recognized related to the Bayer Agreement were as follows (in thousands):

	License Revenue		Collaboration Revenue		Total Revenue
Three months ended June 30, 2013
Milestones	$	—	$	—	$	—
Global Development Plan Services		—		752		752
Bayer Licensed Territory Services		—		278		278
Total	$	—	$	1,030	$	1,030
Three months ended June 30, 2012
Milestones		784		1,216		2,000
Global Development Plan Services		—		1,562		1,562
Bayer Licensed Territory Services		—		442		442
Total	$	784	$	3,220	$	4,004

	License Revenue		Collaboration Revenue		Total Revenue
Six months ended June 30, 2013
Milestones	$	—	$	—	$	—
Global Development Plan Services		—		1,781		1,781
Bayer Licensed Territory Services		—		447		447
Total	$	—	$	2,228	$	2,228
Six months ended June 30, 2012
Milestones		2,734		4,266		7,000
Global Development Plan Services		—		3,272		3,272
Bayer Licensed Territory Services		—		553		553
Total	$	2,734	$	8,091	$	10,825

The Global Development Plan Services are expected to be performed into 2018, with no general right of return. From inception of the contract through June 30, 2013, the Company has provided certain Global Development Plan Services to Bayer. Under the Bayer Agreement, the Company is entitled to be reimbursed for certain costs associated with the performance of these services. At June 30, 2013, the Company calculated its percentage of completion estimate by taking its total actual costs for Global Development Plan Services since inception of the agreement and dividing it by the Company’s estimate of the expected total costs to be incurred to provide the Global Development Plan Services for the remainder of the Global Development Period. The expected arrangement consideration was multiplied by the percentage of completion to determine the maximum amount that could be recognized as revenue. Collaboration revenue was recognized for the lesser of (a) the total amounts billed and billable to Bayer for the Global Development Plan Services during the period, or (b) the product of the percentage of completion and the expected arrangement consideration less cumulative revenues previously recognized. For the three months ended June 30, 2013 and 2012, the Company recognized $0.8 million and $1.6 million, respectively, and for the six months ended June 30, 2013 and 2012, the Company recognized $1.8 million and $3.3 million, respectively, in collaboration revenues related to performance of Global Development Plan Services.

Development expenses incurred by the Company that pertain to the Global Development Plan Services are being charged to research and development expense. At Bayer’s election, the Company may perform certain services directly related to the Bayer Licensed Territory that are outside the scope of the Global Development Plan Services, or Bayer Licensed Territory Services. These services vary but may include contract research and intellectual property maintenance activities and are fully reimbursable to the Company. Expenses for these services are classified in the Statements of Operations on a basis consistent with the nature of the services. Amounts earned in connection with the performance of such services are recognized as collaboration revenues in the period the services are performed. The Company recognized collaboration revenues for the performance of Bayer Licensed Territory Services of $278,000 and $442,000 for the three months ended June 30, 2013 and 2012, respectively, and $447,000 and $553,000 for the six months ended June 30, 2013 and 2012, respectively.

At the inception of the Bayer Agreement, the Company was eligible to receive up to $69.1 million upon the achievement of certain development, regulatory and commercial events. Approximately $34.1 million of such payments that the Company may receive are related to the achievement of certain development and regulatory events and $35.0 million if certain commercial sales thresholds are met. The Company has determined that $19.1 million of the development and regulatory payments are based on its efforts. Since the inception of the collaboration and through June 30, 2013, the Company has earned $14.1 million in milestones for development and regulatory efforts, of which $12.1 million were deemed substantive given the payments were based solely on the Company’s past performance, the value created for the collaborator upon achievement of the events, and the relative reasonableness of the associated payments in relation to the collaboration consideration taken as a whole. The remaining $15.0 million of the development and regulatory payments and all $35.0 million of potential payments for the achievement of the commercial sales thresholds are based upon the efforts of Bayer.

Bayer has the ability to terminate the Bayer Agreement in its entirety by providing at least six months’ notice to the Company within the first two years of the Bayer Agreement. After two years, Bayer must provide at least 90 days’ notice. In addition, Bayer has the right to terminate the Bayer Agreement within 30 days of becoming aware of any material toxicity and/or material drug safety event or issue concerning tedizolid phosphate.

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Note 9. Stockholders’ Equity

Public Offering of Common Stock

In January 2013, the Company completed a public offering in which an aggregate of 7,169,135 shares of its common stock were sold at a purchase price of $4.75 per share. The Company raised a total of $31.6 million in net proceeds after deducting underwriting discounts and commissions of $2.0 million and offering expenses of $0.4 million.

Committed Equity Line of Credit

In August 2012, the Company entered into a committed equity line of credit with Terrapin Opportunity, L.P., or Terrapin, pursuant to which the Company may sell up to the lesser of $25.0 million of its common stock or 7,757,607 shares of its common stock over an approximately 24-month period pursuant to the terms of a Common Stock Purchase Agreement, or the Terrapin Purchase Agreement. The Company is not obligated to utilize any portion of the facility. The Company will determine, at its sole discretion, the timing, the dollar amount and the price per share of each draw under this facility, subject to certain conditions. When and as the Company elects to utilize the facility by delivery of a draw down notice to Terrapin, the Company will issue shares to Terrapin at a discount ranging from 3.00% to 5.30% of the volume weighted average price of the Company’s common stock over a preceding period of trading days, or the Draw Down Period. The Terrapin Purchase Agreement also provides that from time to time, at the Company’s sole discretion, it may grant Terrapin an option to purchase additional shares of the Company’s common stock during each Draw Down Period for an amount of shares specified by the Company based on the trading price of its common stock. Upon Terrapin’s exercise of such an option, the Company will sell to Terrapin the shares subject to the option at a price equal to the greater of (i) the daily volume weighted average price of the Company’s common stock on the day Terrapin notifies the Company of its election to exercise its option or (ii) the threshold price for the option determined by the Company, in each case less a discount ranging from 3.00% to 5.30%. Terrapin is not required to purchase any shares at a pre-discounted purchase price below $1.00 per share, and any shares sold under this facility will be sold pursuant to a shelf registration statement declared effective by the SEC on September 11, 2012. The Terrapin Purchase Agreement will terminate on September 1, 2014.

The Company did not sell shares pursuant to the Terrapin Purchase Agreement during the six months ended June 30, 2013. Since entering into the Terrapin Purchase Agreement, the Company has sold 1,734,351 shares for net proceeds of $8.4 million.

Note 10. Commitments

The Company’s amended facility lease will expire on June 30, 2014 and the Company has options to extend the term of the lease for up to 36 additional months beyond the current termination date. In addition to the minimum lease payments, the Company is required to pay a pro-rata share of certain building expenses. Rent expense for the three months ended June 30, 2013 and 2012 was $214,000 and $198,000, respectively. Rent expense for the six months ended June 30, 2013 and 2012 was $416,000 and $380,000, respectively.

Note 11. Subsequent Events

On July 22, 2013, the Company entered into a Manufacturing Services Agreement, or Patheon Agreement, with Patheon Inc. and Patheon UK Limited, which are collectively referred to as Patheon. Under the terms of the Patheon Agreement, Patheon agreed to manufacture commercial quantities of both the oral tablet and intravenous lyophilized vial formulations of tedizolid phosphate.

The Company is not required to purchase any minimum quantity of tedizolid phosphate under the Patheon Agreement but the Company has agreed to purchase from Patheon not less than specified percentages of the Company’s and its licensees’ total annual commercial requirements of tedizolid phosphate, which vary depending upon the territory being supplied and whether such territory is in the commercial launch phase. The term of the Patheon Agreement continues until the date that is five years after the initial regulatory approval for the product candidate, and thereafter automatically continues for successive 24-month terms unless terminated by written notice at least 18 months prior to the end of the then-current term.

On July 30, 2013, the Company entered into the Merger Agreement with Cubist and BRGO Corporation, a Delaware corporation and a wholly owned subsidiary of Cubist, or Purchaser, pursuant to which, and on the terms and subject to the conditions thereof, among other things, Purchaser will commence the Offer no later than August 13, 2013 to acquire all of the outstanding shares of common stock of the Company for the Offer Price. Following the completion of the Offer and subject to the satisfaction or waiver of certain conditions set forth in the Merger Agreement, including, if required, receipt of approval by the stockholders of the Company, the Merger will be effected.

The obligation of Purchaser to purchase the shares of common stock of the Company tendered in the Offer is subject to the satisfaction or waiver of a number of conditions set forth in the Merger Agreement, including (i) that there shall have been validly tendered and not validly withdrawn a number of shares of common stock of the Company that represent one more than 50% of the total number of shares of common stock of the Company outstanding at the time of the expiration of the Offer (calculated on a fully-diluted basis), such amount is referred to as the Minimum Condition, and (ii) the expiration or termination of applicable waiting periods under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended. The consummation of the Offer is not subject to any financing condition.

At the effective time of the Merger, or Effective Time, the shares of common stock of the Company not purchased pursuant to the Offer (other than shares held by the Company, Cubist, Purchaser, any subsidiary of Cubist or by stockholders of the Company who have perfected their statutory rights of appraisal under Delaware law) will each be converted into the right to receive an amount in cash equal to the Closing Amount, without interest, plus a CVR, and subject to any required withholding of taxes. At the time Purchaser accepts, for the first time, for payment and pays for such number of shares of common stock of the Company validly tendered and not properly withdrawn as satisfies the Minimum Condition, or Offer Acceptance Time, each outstanding option to purchase shares of common stock of the Company issued pursuant to the Company’s equity incentive plans that is then outstanding and unexercised, whether or not vested, shall be cancelled and converted into the right to receive (i) a cash payment equal to (a) the excess, if any, of (x) the Closing Amount over (y) the exercise price payable per share of common stock of the Company under such option, multiplied by (b) the total number of shares of common stock of the Company subject to such option immediately prior to the Offer Acceptance Time (without regard to vesting) and (ii) CVRs with respect to the total number of shares of common stock of the Company subject to such option immediately prior to the Offer Acceptance Time (without regard to vesting). Prior to the initial expiration date of the Offer, the Company shall use commercially reasonable efforts to (i) provide holders of each outstanding and unexercised warrant of the Company with written notice of the Merger, including the effect of the Merger on such warrant, and (ii) assume the warrants issued in connection with the Company’s May 2011 private placement financing transaction.

On August 1, 2013, one putative class-action lawsuit (Bemis v. Trius Therapeutics, Inc., Case No. 37-2013-00060593-CU-SL-STL (the Complaint”)) was filed in Superior Court of the State of California, County of San Diego, against (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) Cubist Pharmaceuticals, Inc. and BRGO Corporation, collectively the Cubist Entities, arising out of the proposed acquisition of Trius by Cubist, or the Proposed Transaction. The Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

On August 6, 2013, another putative class-action lawsuit (Hurst v. Trius Therapeutics, Inc., (the “Second Complaint”)) was filed in the Superior Court of the State of California, County of San Diego, against: (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) the Cubist Entities. The Second Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Second Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Second Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, an award of damages, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

The outcome of this litigation cannot be predicted at this time and estimates of the financial effects, if any, cannot be made. The Company intends to vigorously defend against these claims.

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

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited financial statements and related notes included in this Quarterly Report on Form 1O-Q and the audited financial statements and notes thereto as of and for the year ended December 31, 2012 and the related Management’s Discussion and Analysis of Financial Condition and Results of Operations, both of which are contained in our Annual Report on Form 10-K filed by us with the Securities and Exchange Commission, or SEC, on March 13, 2013.

Forward-Looking Statements

The information in this discussion contains forward-looking statements and information within the meaning of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act, which are subject to the “safe harbor” created by those sections. These forward-looking statements include, but are not limited to, statements concerning our strategy, future operations, future financial position, future revenues, projected costs, prospects and plans and objectives of management. The words “anticipates”, “believes”, “estimates”, “expects”, “intends”, “may”, “plans”,

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“projects”, “will”, “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements that we make. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item IA, “Risk Factors” in this Quarterly Report on Form 10-Q and in our other filings with the SEC. The forward-looking statements are applicable only as of the date on which they are made, and we do not assume any obligation to update any forward-looking statements.

Overview

We are a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for serious infections. We are developing tedizolid phosphate, a novel antibiotic, for the treatment of serious Gram-positive bacterial infections, including those caused by methicillin-resistant staphylococcus aureus, or MRSA. Tedizolid phosphate is being developed for acute bacterial skin and skin structure infections, or ABSSSI, and pneumonia, and potentially for other indications. ABSSSI is the current classification for complicated skin and skin structure infections. In addition, we are discovering antibiotics for infections caused by Gram-negative bacteria using our structure-based discovery platform.

We have completed two Phase 3 clinical trials of tedizolid phosphate for the treatment of ABSSSI in which all primary and secondary endpoints were achieved. In December 2011, we reported top-line data from our first Phase 3 clinical trial, the ESTABLISH 1 (TR701-112) study, of the oral dosage form of tedizolid phosphate for the treatment of ABSSSI. In March 2013, we reported top-line results from our second Phase 3 clinical trial, the ESTABLISH 2 (TR701-113) study, which was an intravenous, or IV, to oral transition study for the treatment of ABSSSI. The U.S. Food and Drug Administration, or FDA, has designated tedizolid phosphate as a Qualified Infectious Disease Product, or QIDP, for the treatment of ABSSSI as well as for the treatment of pneumonia, which designation enables us to benefit from certain incentives for the development of new antibiotics, including priority review and eligibility for fast-track status. The QIDP designation was granted for each of the IV and oral dosage forms of tedizolid phosphate. We currently expect to submit a New Drug Application, or NDA, to the FDA, for tedizolid phosphate for the treatment of ABSSSI during the second half of 2013. Given the QIDP designation and if tedizolid phosphate is approved by the FDA, we could potentially commercially launch in the U.S. in the second half of 2014.

We also expect to initiate a Phase 3 program of tedizolid phosphate for the treatment of pneumonia using the same 200 mg, once daily dose of tedizolid phosphate that we tested for ABSSSI. We have met with the FDA, the European Medicines Agency, or EMA, as well as the China Food and Drug Administration, and have designed the protocol for the Phase 3 study consistent with their guidance and, subject to the acceptance of the protocol by the regulatory agencies, we plan to initiate the study in the second half of 2013.

In January 2013, we raised approximately $31.6 million in net proceeds from a public offering of our common stock in which we sold 7,169,135 shares at an offering price of $4.75 per share.

We also continue to fund the preclinical research for our Gyrase-B program, including Investigational New Drug, or IND, enabling studies. Our Gyrase-B research program had been substantially funded by our contract with the National Institute of Allergy and Infectious Disease, or NIAID. We plan to seek additional external funding for the long-term advancement of the program. If our preclinical activities for the Gyrase-B program are successful, we plan to file an IND application in 2014.

In July 2011, we signed a collaboration and license agreement with Bayer Pharma AG, or Bayer, under which we granted Bayer exclusive rights to develop and commercialize tedizolid phosphate in China, Japan and substantially all other countries in Asia, Africa, Latin America and the Middle East, excluding North and South Korea, which we refer to as the Bayer Licensed Territory.

As of June 30, 2013, we had an accumulated deficit of $186.3 million. These losses have resulted principally from costs incurred in connection with research and development activities, including the costs of clinical trial activities associated with tedizolid phosphate, license fees and general and administrative expenses. In the event the Agreement and Plan of Merger with Cubist Pharmaceuticals, Inc. and BRGO Corporation is not completed, we expect to continue to incur operating losses for the next several years as we pursue the clinical development and commercialization of tedizolid phosphate and work to discover and develop additional product candidates through our research and discovery program. As a result, we will seek to fund our operations through public or private equity or debt financings or other sources, such as collaborations and government contracts. Our failure to raise capital as and when needed would have a negative impact on our financial condition and our ability to pursue our business strategies.

Financial Obligations Related to the License of Tedizolid Phosphate

In January 2007, we entered into a license agreement with Dong-A ST Co., Ltd. (as successor-in-interest to Dong-A Pharmaceutical Co., Ltd.), or Dong-A, pursuant to which we acquired an exclusive license to certain patent applications and other intellectual property related to the oral and injectable forms of tedizolid phosphate to develop and commercialize licensed products, including tedizolid phosphate, outside of Korea. We have the right to grant sublicenses to third parties.

Since the inception of the license agreement, $5.7 million in license fees and milestone payments have been paid to Dong-A. In addition, we may be required to make up to an aggregate of $11.5 million in additional payments, upon the achievement of specified development and regulatory approval milestones. We are also obligated to pay Dong-A mid-single digit tiered royalties on net sales of tedizolid phosphate.

Agreement and Plan of Merger

On July 30, 2013, we entered into an Agreement and Plan of Merger, or Merger Agreement, with Cubist Pharmaceuticals, Inc., a Delaware corporation, or Cubist, and BRGO Corporation, a Delaware corporation and a wholly owned subsidiary of Cubist, or Purchaser, pursuant to which, and on the terms and subject to the conditions thereof, among other things, Purchaser will commence a tender offer, or Offer, no later than August 13, 2013 to acquire all of the outstanding shares of our common stock at a purchase price of (a) $13.50 per share in cash, or the Closing Amount, without interest, plus (b) one non-transferrable contingent value right for each share of our common stock, each a CVR, which represents the contractual right to receive up to $2.00 per share upon the achievement of certain milestones, such amount together with the Closing Amount is referred to as the Offer Price, subject to any required withholding of taxes. Following the completion of the Offer and subject to the satisfaction or waiver of certain conditions set forth in the Merger Agreement, including, if required, receipt of approval by our stockholders, Purchaser will merge with and into us, with us surviving as a wholly owned subsidiary of Cubist, or the Merger.

The obligation of Purchaser to purchase the shares of our common stock tendered in the Offer is subject to the satisfaction or waiver of a number of conditions set forth in the Merger Agreement, including (i) that there shall have been validly tendered and not validly withdrawn a number of shares of our common stock that represent one more than 50% of the total number of shares of our common stock outstanding at the time of the expiration of the Offer (calculated on a fully-diluted basis), such amount is referred to as the Minimum Condition, and (ii) the expiration or termination of applicable waiting periods under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended. The consummation of the Offer is not subject to any financing condition.

At the effective time of the Merger, or Effective Time, the shares of our common stock not purchased pursuant to the Offer (other than shares held by us, Cubist, Purchaser, any subsidiary of Cubist or by our stockholders who have perfected their statutory rights of appraisal under Delaware law) will each be converted into the right to receive an amount in cash equal to the Closing Amount, without interest, plus a CVR, and subject to any required withholding of taxes. At the time Purchaser accepts, for the first time, for payment and pays for such number of shares of our common stock validly tendered and not properly withdrawn as satisfies the Minimum Condition, or Offer Acceptance Time, each outstanding option to purchase shares of our common stock issued pursuant to our equity incentive plans that is then outstanding and unexercised, whether or not vested, shall be cancelled and converted into the right to receive (i) a cash payment equal to (a) the excess, if any, of (x) the Closing Amount over (y) the exercise price payable per share of our common stock under such option, multiplied by (b) the total number of shares of our common stock subject to such option immediately prior to the Offer Acceptance Time (without regard to vesting) and (ii) CVRs with respect to the total number of shares of our common stock subject to such option immediately prior to the Offer Acceptance Time (without regard to vesting). Prior to the initial expiration date of the Offer, we shall use commercially reasonable efforts to (i) provide holders of each of our outstanding and unexercised warrants with written notice of the Merger, including the effect of the Merger on such warrant, and (ii) assume the warrants issued in connection with our May 2011 private placement financing transaction.

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Financial Overview

Revenues

We have recognized $90.2 million of revenues from inception through June 30, 2013. We have derived substantially all of our revenues from our collaboration and license agreement with Bayer, government contracts, small business innovation research grants funded by the National Institutes of Health, and collaborations with other third parties for the research and development of certain preclinical programs. We have no products approved for sale, and we have not generated any revenues from product sales. We expect to recognize revenues from our government contracts as well as through our license and collaboration agreement with Bayer. We continue to pursue government contract funding for our nonclinical, preclinical and clinical programs. If our development efforts for any of our product candidates result in clinical success and regulatory approval, we may generate revenues from those product candidates.

Research and Development Expenses

The majority of our operating expenses to date have been for research and development activities related to tedizolid phosphate and our preclinical and nonclinical programs. Research and development expenses consist of: (1) expenses incurred under agreements with contract research organizations, or CROs, and investigative sites, which conduct a substantial portion of our nonclinical and preclinical studies, and all of our clinical trials; (2) employee-related expenses, which include salaries, benefits and share-based compensation; (3) payments to third-party manufacturers, which produce our active pharmaceutical ingredient, or API, and finished product; (4) license fees paid to third parties for use of their intellectual property; (5) facilities, depreciation and other allocated expenses, which include direct and allocated expenses for rent and maintenance of facilities and equipment, depreciation of leasehold improvements and equipment and laboratory and other supplies; and (6) payments to consultants.

The following table presents our research and development expenses for the periods indicated (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2013		2012		2013		2012
Clinical and nonclinical research and development (including manufacturing)	$	12,873	$	13,511	$	23,655	$	27,156
Preclinical research and development		1,810		2,868		3,573		6,069
Total	$	14,683	$	16,379	$	27,228	$	33,225

At this time, due to the inherently unpredictable nature of preclinical, nonclinical and clinical development and given the early stage of our preclinical programs, we are unable to estimate with any certainty the costs we will incur in the continued development of tedizolid phosphate and our preclinical programs for potential commercialization. Clinical development timelines, the probability of success and development costs can differ materially from expectations. While we are currently focused on advancing tedizolid phosphate and our preclinical programs, our future research and development expenses will depend on the clinical success of each product candidate that we develop, as well as ongoing assessments of the commercial potential of such product candidates. We expect to incur increased research and development expenses as we continue our Phase 3 clinical programs for tedizolid phosphate. In addition, we expect to incur significant research and development costs as we perform additional clinical trials necessary to obtain regulatory approval of tedizolid phosphate for additional indications, as well as to advance our preclinical programs.

The costs of clinical trials may vary significantly over the life of a project owing to but not limited to the following:

• Per patient trial costs;

• The number of sites included in the trials;

• The countries in which the trials are conducted;

• The length of time required to enroll eligible patients;

• The number of patients that participate in the trials;

• The number of doses that patients receive;

• The cost of comparative agents used in trials;

• The drop-out or discontinuation rates of patients;

• Potential additional safety monitoring or other studies requested by regulatory agencies;

• The duration of patient follow-up; and

• The efficacy and safety profile of the product candidate.

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General and Administrative Expenses

General and administrative expenses consist primarily of salaries and related expenses for personnel in administration, finance, commercial strategy, legal and business development. Other significant expenses include professional fees for general legal services, legal expenses to pursue patent protection of our intellectual property, accounting fees, director fees, directors’ and officers’ insurance premiums, fees for investor relations services, share-based compensation and allocated facility costs. We expect our general and administrative expense to increase as we continue to build our corporate infrastructure, particularly our commercial group, as we pursue approval of our first commercial product and in support of continued development of tedizolid phosphate and our preclinical programs. These increases likely will include additional salaries and related expenses, consultant fees, and expenses related to enhanced business systems.

Interest Income

Interest income consists of interest earned on our cash, cash equivalents and investments in marketable securities.

Income Taxes

We assess income tax positions and record tax benefits for all years subject to examination based upon our evaluation of the facts, circumstances and information available at the reporting date. For those tax positions where there is a greater than 50% likelihood that a tax benefit will be sustained, we have recorded the largest amount of tax benefit that may potentially be realized upon ultimate settlement with a taxing authority that has full knowledge of all relevant information. For those income tax positions where there is less than 50% likelihood that a tax benefit will be sustained, no tax benefit has been recognized in the financial statements.

We have federal and state net operating loss carryforwards and federal and state research and development tax credit carryforwards. Under Section 382/383 of the Internal Revenue Code of 1986, as amended, or the Internal Revenue Code, substantial changes in our ownership may limit the amount of net operating loss carryforwards and development tax credit carryforwards that could be utilized annually in the future to offset taxable income. Any such annual limitation may significantly reduce the utilization of the net operating losses and tax credits before they expire. After a public offering of common stock in January 2012, we performed an analysis under Section 382 through January 31, 2012 and determined that an “ownership change” had occurred, but the resulting annual limitation does not have a material impact on our ability to use our net operating loss and tax credit carryforwards. After our public offering in January 2013, we updated our Section 382 analysis and determined that it would not result in an additional “ownership change.” In each period since our inception, we have recorded a valuation allowance for the full amount of our net deferred tax asset, as the realization of such net deferred tax asset is uncertain.

Change in Fair Value of Common Stock Warrants Liability

We have issued warrants to purchase our common stock that may require us to purchase unexercised warrants for a cash amount equal to their fair value following the announcement of specified events defined as Fundamental Transactions involving us (e.g., merger, sale of all or substantially all assets, tender offer, or share exchange) or a delisting, which is deemed to occur when the common stock is no longer listed on a national securities exchange. The cash settlement provisions require use of the Black-Scholes model in calculating the cash payment value in the event of a Fundamental Transaction or a delisting. As a consequence of these provisions, the warrants are classified as a liability on our balance sheets. The cash settlement value at the time of any future Fundamental Transaction or delisting will depend upon the value of the following inputs at that time: the price per share of our common stock, the volatility of our common stock, the expected term of the warrant, the risk-free interest rate based on U.S. Treasury security yields, and our dividend yield.

The fair value of the warrants is determined using a Black-Scholes model. The valuation of warrants is subjective and is affected by changes in inputs to the valuation model including the price per share of our common stock, the historical volatility of the stock prices of our peer group, risk-free rates based on U.S. Treasury security yields, the expected term of the warrants and our dividend yield. Changes in these assumptions can materially affect the fair value estimate. We could ultimately incur amounts to settle the warrant at a cash settlement value that is significantly different than the carrying value of the liability on our financial statements. We will continue to classify the fair value of the warrants as a liability until the warrants are exercised, expire, or are amended in a way that would no longer require these warrants to be classified as a liability. Changes in the fair value of the common stock warrants liability are recognized as a component of other income (expense) in the statements of operations.

Critical Accounting Policies and Significant Judgments and Estimates

Our management’s discussion and analysis of financial condition and results of operations is based on our financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. The preparation of these financial statements requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenues and expenses during the reporting periods. On an ongoing basis, we evaluate our estimates and judgments related to revenues earned under our contracts, preclinical, nonclinical and clinical development costs and drug manufacturing costs (research and development expense), and share-based compensation. 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. Actual results may differ from these estimates under different assumptions or conditions.

We discussed accounting policies and assumptions that involve a higher degree of judgment and complexity within Note 1 to our financial statements in our Annual Report on Form 10-K for the year ended December 31, 2012. There have been no material changes to our critical accounting policies and estimates as disclosed in our Annual Report on Form 10-K for the year ended December 31, 2012.

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Results of Operations

Comparison of the Three Months Ended June 30, 2013 and 2012

Revenues

The following table summarizes our revenues for the three months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Three Months Ended June 30,				$ Change			% Change
	2013		2012
Contract research	$	261	$	2,220	$	(1,959	)		(88	)%
Collaborations		1,030		3,220		(2,190	)		(68	)%
License fees		—		784		(784	)		(100	)%
Total	$	1,291	$	6,224		(4,933	)		(79	)%

Contract research revenues decreased for the three months ended June 30, 2013 as compared to the three months ended June 30, 2012 primarily due to reduced research for our Gram-negative pathogen program under our contract with NIAID. NIAID elected to discontinue funding for research under the contract beyond March 31, 2013. In addition, our contract research revenues decreased from the comparable period in 2012 because we no longer receive funding for our marine natural products research program that was previously being funded under our contract with the Defense Threat Reduction Agency, or DTRA. DTRA elected not to extend funding under the contract beyond July 2012.

License fees and collaboration revenues for the three months ended June 30, 2013 and 2012 relate to activities performed under our collaboration and license agreement with Bayer. The decrease in license and collaboration revenues as compared to the prior year was primarily due to the fact that we earned a $2.0 million milestone payment upon achieving 25% patient enrollment in our second Phase 3 clinical trial for tedizolid phosphate in ABSSSI during the three months ended June 30, 2012. We earned no milestone payments under our collaboration and license agreement with Bayer during the three months ended June 30, 2013.

Research and Development Expenses

The following table summarizes our research and development expenses for the three months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Three Months Ended June 30,				$ Change			% Change
	2013		2012
Research and development expenses	$	14,683	$	16,379	$	(1,696	)		(10	)%

During the three months ended June 30, 2013 our research and development costs related primarily to clinical and nonclinical expenses for tedizolid phosphate, drug product manufacturing, and expenses incurred in connection with the preparation for the submission of regulatory applications for tedizolid phosphate. Clinical trial expenses decreased from the comparable period in 2012 as there were fewer studies ongoing during the three months ended June 30, 2013 since we have shifted our activities towards the preparation of our NDA. In addition, our research and development costs included expenses resulting from research under our government contracts and other preclinical activities. Expenses related to our government contracts decreased as research under our contract with NIAID concluded in the first quarter of 2013. Furthermore, there were no expenses from our marine natural products research program in 2013 as this program was discontinued in May 2012 after DTRA’s election not to exercise its option to extend funding under the contract.

General and Administrative Expenses

The following table summarizes our general and administrative expenses for the three months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Three Months Ended June 30,				$ Change		% Change
	2013		2012
General and administrative expenses	$	5,543	$	3,311	$	2,232		67	%

The increase in general and administrative expenses was primarily due to additional market planning activities as we prepare for the expected commercial launch of tedizolid phosphate.

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Other Income (Expense)

The following table summarizes our other income (expense) for the three months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Three Months Ended June 30,						$ Change			% Change
	2013			2012
Interest income	$	8		$	7		$	1			14	%
Fair value adjustment of common stock warrant liability		(757	)		(955	)		(198	)		(21	)%
Other income (expense)		2			—			2			—
Total Other Income (Expense)	$	(747	)	$	(948	)		(201	)		(21	)%

Other income and expense for the three months ended June 30, 2013 and 2012 resulted primarily from the remeasurement of the estimated fair value of the common stock warrant liability. This liability was recorded upon the issuance of warrants in connection with our private placement in May 2011 and is remeasured at each reporting date with changes in estimated fair value recognized as other income or expense.

Comparison of the Six Months Ended June 30, 2013 and 2012

Revenues

The following table summarizes our revenues for the six months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Six Months Ended June 30,				$ Change			% Change
	2013		2012
Contract research	$	790	$	5,231	$	(4,441	)		(85	)%
Collaborations		2,228		8,091		(5,863	)		(72	)%
License fees		—		2,734		(2,734	)		(100	)%
Total	$	3,018	$	16,056		(13,038	)		(81	)%

Contract research revenues decreased for the six months ended June 30, 2013 as compared to the six months ended June 30, 2012 primarily due to reduced research for our Gram-negative pathogen program under our NIAID contract. NIAID elected to discontinue funding for research under the contract beyond March 31, 2013. In addition, our contract research revenues decreased from the comparable period in 2012 because we no longer receive funding for our marine natural products research program that was previously being funded under our contract with DTRA. In May 2012, we were notified of DTRA’s election not to extend funding under the contract.

License and collaboration revenues for the six months ended June 30, 2013 and 2012 relate to activities performed under our collaboration and license agreement with Bayer. The decrease in license and collaboration revenues as compared to the prior year was primarily due to the fact that we earned a $5.0 million milestone payment upon successfully completing our first Phase 3 clinical trial for tedizolid phosphate in ABSSSI and a $2.0 million milestone payment upon achieving 25% patient enrollment in our second Phase 3 clinical trial for tedizolid phosphate in ABSSSI during the six months ended June 30, 2012. We earned no milestone payments under our collaboration and license agreement with Bayer during the six months ended June 30, 2013.

Research and Development Expenses

The following table summarizes our research and development expenses for the six months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Six Months Ended June 30,				$ Change			% Change
	2013		2012
Research and development expenses	$	27,228	$	33,225	$	(5,997	)		(18	)%

During the six months ended June 30, 2013 our research and development costs related primarily to clinical and nonclinical expenses for tedizolid phosphate, drug product manufacturing, and expenses incurred in connection with the preparation for the submission of regulatory applications for tedizolid phosphate. Clinical trial expenses decreased from the comparable period in 2012 as there were fewer studies ongoing during the six months ended June 30, 2013. In addition, our research and development costs included expenses resulting from research under our government contracts and other preclinical activities. Expenses related to our government contracts decreased as research under our contract with NIAID wound down during the six months ended June 30, 2013. Furthermore, there were no expenses from our marine natural products research program during the six months ended June 30, 2013 as this program was discontinued in May 2012 after DTRA elected not to extend funding under the contract beyond July 2012.

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General and Administrative Expenses

The following table summarizes our general and administrative expenses for the six months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Six Months Ended June 30,				$ Change		% Change
	2013		2012
General and administrative expenses	$	10,047	$	6,315	$	3,732		59	%

The increase in general and administrative expenses was primarily due to additional market planning activities as we prepare for the expected commercial launch of tedizolid phosphate.

Other Income (Expense)

The following table summarizes our other income (expense) for the six months ended June 30, 2013 and 2012 (in thousands, except percentages):

	Six Months Ended June 30,						$ Change			% Change
	2013			2012
Interest income	$	19		$	7		$	12			171	%
Other income (expense)		2			(3	)		5			167	%
Fair value adjustment of common stock warrant liability		(2,726	)		1,462			(4,188	)		(286	)%
Total Other Income (Expense)	$	(2,705	)	$	1,466			(4,171	)		(285	)%

Other income and expense for the six months ended June 30, 2013 and 2012 resulted primarily from the remeasurement of the estimated fair value of the common stock warrant liability. This liability was recorded upon the issuance of warrants in connection with our private placement in May 2011 and is remeasured at each reporting date with changes in estimated fair value recognized as other income or expense.

Liquidity and Capital Resources

On July 30, 2013, we entered into the Merger Agreement with Cubist and Purchaser, pursuant to which, and on the terms and subject to the conditions thereof, among other things, Purchaser will commence the Offer no later than August 13, 2013 to acquire all of the outstanding shares of our common stock for the Offer Price. Following the completion of the Offer and subject to the satisfaction or waiver of certain conditions set forth in the Merger Agreement, including, if required, receipt of approval by the stockholders of the Company, the Merger will be effected.

We have incurred losses since our inception and we anticipate that we will continue to incur losses for at least the next several years. In the event we are unable to complete the proposed merger with Cubist, we expect that our operating expenses will continue to increase and, as a result, we will need additional capital to fund our operations, which we may obtain from financings, research funding, collaborations, contract revenues or other sources.

Since our inception, we have funded our operations principally through the receipt of funds from the placement of equity securities, convertible notes payable, collaboration fees under our partnership with Bayer, contract research funding under our government contracts, license and research grants. As of June 30, 2013, we had cash, cash equivalents and investments of approximately $69.6 million. Cash in excess of immediate requirements is invested in accordance with our investment policy primarily with a view to liquidity and capital preservation. As of June 30, 2013, our funds are held in cash, money market funds and United States Treasury securities.

	Six Months Ended June 30,
	2013			2012
	(In thousands)
Cash Flows from Continuing Operations:
Net cash used in operating activities	$	(28,427	)	$	(23,474	)
Net cash used in investing activities		(5,026	)		(23,232	)
Net cash provided by financing activities		32,399			48,837
Net increase (decrease) in cash and cash equivalents	$	(1,054	)	$	2,131

During the six months ended June 30, 2013 and 2012, our operating activities used cash of $28.4 million and $23.5 million, respectively, primarily resulting from our net losses and changes in our working capital accounts. During the six months ended June 30, 2013 and 2012, our investing activities used cash of $5.0 million and $23.2 million, respectively, primarily due to purchases of investments in excess of proceeds from sales and maturities of investments. During the six months ended June 30, 2013, financing activities provided cash of $32.4 million which was primarily derived from proceeds received from our public offering of common stock in January 2013 from which we raised a total of $31.6 million in net proceeds after deducting underwriting discounts, commissions and offering expenses. During the six months ended June 30, 2012, financing activities provided cash of $48.8 million which was primarily derived from proceeds received from our public offering of common stock in January 2012 from which we raised a total of $48.4 million in net proceeds after deducting underwriting discounts, commissions and offering expenses.

Operating Capital Requirements

We anticipate that we will continue to incur net losses for the next several years as we incur expenses for our clinical and nonclinical studies for tedizolid phosphate, complete preclinical studies and initiate clinical development of our preclinical programs, build commercial capabilities and expand our corporate infrastructure. We may not be able to complete the development and initiate commercialization of these programs if, among other things, our preclinical research and clinical trials are not successful, the FDA does not approve tedizolid phosphate or any other product candidates arising out of our current preclinical programs when we expect, or at all, or funding under our government contracts is discontinued.

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On August 30, 2012, we entered into a committed equity line of credit with Terrapin Opportunity, L.P., or Terrapin, under which we may sell up to the lesser of $25.0 million of common stock or 7,757,607 shares of our common stock over an approximately 24-month period pursuant to a Common Stock Purchase Agreement, or the Terrapin Purchase Agreement. We are not obligated to utilize any of the facility and we remain free to enter into and consummate other equity and debt financing transactions. We will determine, at our sole discretion, the timing, the dollar amount and the price per share of each draw under this facility, subject to certain conditions. When and as we elect to use the facility, we will issue shares to Terrapin at a discount ranging from 3.00% to 5.30% of the volume weighted average price of our common stock over a preceding period of trading days. Terrapin is not required to purchase any shares at a pre-discounted purchase price below $1.00 per share. Any shares sold under this facility will be sold pursuant to a shelf registration statement declared effective by the SEC on September 11, 2012. In October 2012, we sold 612,133 shares of our common stock under the Terrapin Purchase Agreement and received net proceeds of $3.4 million after deducting expenses of $0.1 million. In December 2012, we sold 1,122,218 shares of our common stock under the Terrapin Purchase Agreement and received net proceeds of $4.9 million after deducting expenses of $0.1 million.

On January 24, 2013, we completed a public offering of common stock in which we sold 7,169,135 shares of common stock at an offering price of $4.75 per share. We raised approximately $31.6 million in net proceeds after deducting underwriting discounts and commissions of $2.0 million and offering expenses of $0.4 million.

We believe that we have sufficient cash and cash equivalents to fund our operations through the estimated time that we expect to receive a response from the FDA on our NDA for tedizolid phosphate. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. Our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement and involves risks and uncertainties, and actual results could vary as a result of a number of factors, including the factors discussed in Part II, Item 1A, “Risk Factors.”

In the event we are unable to complete the proposed Merger, we do not anticipate that our existing working capital alone will be sufficient to fund our operations through the successful development and commercialization of tedizolid phosphate or any other products we develop. As a result, we will need to raise additional capital to fund our operations and continue to conduct clinical and nonclinical activities to support potential regulatory approval of tedizolid phosphate and any other product candidates. To raise additional capital, we may seek to sell additional equity or convertible debt securities or incur indebtedness. The sale of additional equity and debt securities may result in additional dilution to our stockholders. If we raise additional funds through the issuance of debt securities or preferred stock, these securities could have rights senior to those of our common stock and could contain covenants that would restrict our operations. We may also seek funding through collaborations or other similar arrangements with third parties.

Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products, we are unable to estimate the exact amount of our working capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

• The progress of our tedizolid phosphate clinical program, including expenses to support the clinical trials;

• The costs and timing of regulatory approvals;

• Our progress in advancing our preclinical programs through preclinical development into clinical trials;

• The costs and timing of clinical and commercial manufacturing supply arrangements for our product candidates;

• The costs of establishing sales or distribution capabilities;

• The success of the commercialization of our products;

• Our ability to maintain existing, and be awarded new, government research contracts;

• Our ability to maintain our current collaboration and license agreement with Bayer and establish potential future strategic collaborations, including licensing and other arrangements; and

• The costs involved in enforcing or defending patent claims or other intellectual property rights.

Off-Balance Sheet Arrangements

We do not have any off-balance sheet arrangements.

Contractual Obligations

The following table summarizes our outstanding contractual obligations as of payment due date by period at June 30, 2013:

	Payment by Period
	Total		Less Than 1 Year		1 -3 Years		3-5 Years		More Than 5 Years
	(In thousands)
Operating leases	$	780	$	780	$	—	$	—	$	—

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Under our license agreement with Dong-A, we may be required to make up to an aggregate of $11.5 million in additional payments to Dong-A upon the achievement of specified development and regulatory approval milestones. We are unable at this time to estimate with certainty the amount or timing of future costs we will incur under this agreement.

Recent Accounting Pronouncements

Occasionally, new accounting standards are issued or proposed by the Financial Accounting Standards Board, or other standard-setting bodies that we adopt by the effective date specified within the standard. Unless otherwise discussed, standards that do not require adoption until a future date are not expected to have a material impact on our financial statements upon adoption.

Item 3. Qualitative and Quantitative Disclosures About Market Risk

Our cash equivalents and available-for-sale investments consisted of money market funds and debt instruments of agencies of the U.S. government at June 30, 2013. The investments in these financial instruments are made in accordance with an investment policy approved by our board of directors which specifies the categories, allocations, and ratings of securities we may consider for investment. The primary objective of our investment activities is to preserve principal while at the same time maximizing the income we receive without significantly increasing risk. Some of the financial instruments that we invest in could be subject to market risk. This means that a change in prevailing interest rates may cause the value of the instruments to fluctuate. For example, if we purchase a security that was issued with a fixed interest rate and the prevailing interest rate later rises, the value of that security will probably decline. To minimize this risk, we intend to maintain a portfolio which may include cash, cash equivalents and investment securities available-for-sale in a variety of securities which may include money market funds, government and non-government debt securities and commercial paper, all with various maturity dates. Based on our current investment portfolio, we do not believe that our results of operations would be materially impacted by an immediate change of 10% in interest rates.

We do not hold or issue derivatives, derivative commodity instruments or other financial instruments for speculative trading purposes. Further, we do not believe our cash equivalents and investment securities have significant risk of default or illiquidity. We made this determination based on discussions with our investment advisors and a review of our holdings. While we believe our cash equivalents and investment securities do not contain excessive risk, we cannot provide absolute assurance that in the future our investments will not be subject to adverse changes in market value. All of our investments are held at fair value.

Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures

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

Changes in Internal Control

As required by Rule 13a-15(d) and Rule 15d-15(d) of the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation of the internal control over financial reporting to determine whether any changes occurred during the period covered by this Quarterly Report on Form 10-Q that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Based on that evaluation, our principal executive officer and principal financial officer concluded no such changes during the period covered by this Quarterly Report on Form 10-Q materially affected, or were reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

On August 1, 2013, one putative class-action lawsuit (Bemis v. Trius Therapeutics, Inc., Case No. 37-2013-00060593-CU-SL-STL (the Complaint”)) was filed in Superior Court of the State of California, County of San Diego, against (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) Cubist Pharmaceuticals, Inc. and BRGO Corporation, collectively the Cubist Entities, arising out of the proposed acquisition of Trius by Cubist, or the Proposed Transaction. The Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

On August 6, 2013, another putative class-action lawsuit (Hurst v. Trius Therapeutics, Inc., (the “Second Complaint”)) was filed in the Superior Court of the State of California, County of San Diego, against: (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) the Cubist Entities. The Second Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Second Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Second Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, an award of damages, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

The Company intends to vigorously defend against these claims. The outcome of this litigation cannot be predicted at this time and any outcome in favor of the plaintiffs could have a significant adverse effect on the Proposed Transaction, our financial condition, and our results of operations.

Item 1A. Risk Factors

You should consider carefully the following information about the risks described below, together with the other information contained in this Quarterly Report and in our other public filings in evaluating our business. The risk factors set forth below with an asterisk (*) next to the title contain changes to the description of the risk factors associated with our business previously disclosed in Item 1A. of our annual report on Form 10-K for the year ended December 31, 2012. Additional risks and uncertainties that we are unaware of may also become important factors that affect us. If any of the following risks actually occurs, our business, financial condition, results of operations and future growth prospects would likely be materially and adversely affected. In these circumstances, the market price of our common stock would likely decline. With the exception of the risks relating to the proposed Offer and Merger, the risks described below relate to our continued operation as a stand alone entity.

Risks Related to the Proposed Offer and Merger

If a sufficient number of shares are not tendered pursuant to the pending Offer, the Offer and Merger may not be completed and our business could be impaired.*

If Cubist and Purchaser acquire at least 90% of our issued and outstanding shares pursuant to the Offer, the Merger can be effected as a “short form merger” under Delaware law. A short form merger would enable Cubist and Purchaser to complete the acquisition of us without any action on the part of the other holders of our shares. If Cubist and Purchaser satisfy the Minimum Condition for completion of the Offer but do not acquire 90% of the issued and outstanding shares pursuant to the Offer (including through the exercise of a top-up option and any subsequent offering period), we will be required to hold a stockholders’ meeting in order to obtain the approval of our stockholders to consummate the Merger. Although this would not prevent the Merger from occurring because Cubist and Purchaser would control a sufficient number of our shares to approve the Merger, it would delay the completion of the Merger and could create uncertainty for us and our business could be adversely affected. If less than the required minimum number of shares are tendered, then neither the Offer nor the Merger may be completed and this could also cause significant uncertainty for us and our business could be severely and adversely affected.

Our executive officers and directors may have interests that are different from, or in addition to, those of our stockholders generally.*

Our executive officers and directors may have interests in the Offer and the Merger that are different from, or are in addition to, those of our stockholders generally. These interests include direct or indirect ownership of our common stock and stock options and the potential receipt of change in control payments by certain executive officers in connection with the proposed Offer and Merger.

Failure to complete the pending Offer and Merger could adversely affect our stock price and our future business and operations.*

The Offer is subject to customary closing conditions and is contingent upon the tender of a sufficient number of shares held by our current stockholders pursuant to the Offer and clearance under US antitrust laws. Neither we, Cubist nor Purchaser can assure you that the Offer will be consummated. In the event that the Offer and Merger is not consummated, we will be subject to significant costs, including legal, accounting and advisory fees related to the Offer and the Merger, which must be paid even if the Offer is not completed, and the payment of a termination fee under certain circumstances. If the Offer is not consummated, the market price of our common stock may decline to the extent that the current market price of our common stock reflects a positive market assumption that the Merger will be completed. In addition, if the Offer is not completed, we may fail to retain key employees who have sought and obtained different employment in anticipation of the Offer and Merger being completed.

We are subject to litigation initiated in connection with the tender offer and proposed merger with Cubist, which could be time consuming and divert our resources and the attention of our management.*

On August 1, 2013, one putative class-action lawsuit (Bemis v. Trius Therapeutics, Inc., Case No. 37-2013-00060593-CU-SL-STL) was filed in Superior Court of the State of California, County of San Diego, against (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) Cubist Pharmaceuticals, Inc. and BRGO Corporation, collectively the Cubist Entities, arising out of the proposed acquisition of Trius by Cubist, or the Proposed Transaction. The Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

On August 6, 2013, another putative class-action lawsuit (Hurst v. Trius Therapeutics, Inc., (the “Second Complaint”)) was filed in the Superior Court of the State of California, County of San Diego, against: (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) the Cubist Entities. The Second Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Second Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Second Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, an award of damages, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

The Company intends to vigorously defend against these claims. The outcome of this litigation cannot be predicted at this time and any outcome in favor of the plaintiffs could have a significant adverse effect on the Proposed Transaction, our financial condition, and our results of operations.

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Risks Related to Our Financial Condition and Capital Requirements

We have incurred significant operating losses since inception and anticipate that we will incur continued losses for the foreseeable future. We may never become profitable.*

As of June 30, 2013, we had an accumulated deficit of $186.3 million. We have funded, and plan to continue to fund, our operations from the sale of our securities, through research funding and from collaboration and license payments, including payments under the Bayer collaboration. However, we have generated no revenues from product sales to date. We expect that the uncertainty of our ability to achieve milestones under the Bayer collaboration and any other collaboration agreements we may enter into in the future and the timing of those payments will lead to significant fluctuations in our earnings and profitability. However, even with these funds, we expect to continue to incur substantial additional operating losses for the next several years as we advance tedizolid phosphate and our preclinical programs. In addition, if we obtain regulatory approval for tedizolid phosphate, we may incur significant sales, marketing, licensing and outsourced manufacturing expenses. As a result, we expect to continue to incur significant and increasing losses for the foreseeable future. Because of the numerous risks and uncertainties associated with developing and commercializing pharmaceutical drugs, we are unable to predict the extent of any future losses. We may never successfully commercialize any products and thus may never have any significant future revenues or achieve and sustain profitability.

We have limited sources of revenues and have not to date generated any revenues from product sales.*

We are a biopharmaceutical company with no products approved for commercial sale. To date, substantially all of our revenues have been derived from federal contract and grant revenues and fees for development and regulatory services from license or collaboration agreements, and we have not generated any revenues from product sales. Our ability to generate future revenues from product sales depends heavily on our success in:

• Successfully advancing the development of tedizolid phosphate for the treatment of ABSSSI;

• Obtaining United States and/or foreign regulatory approvals for tedizolid phosphate;

• Commercializing tedizolid phosphate and any other product candidates for which we obtain FDA approval, including by building a hospital-directed sales force and/or collaborating with third parties;

• Achieving broad market acceptance of tedizolid phosphate in the medical community and with third-party payers;

• Pursuing clinical development of tedizolid phosphate for the treatment of pneumonia and potentially for other indications;

• Generating a pipeline of innovative product candidates using our drug discovery platform or through licensing strategies;

• Maintaining our current federal contracts that support our current drug discovery efforts and obtaining new federal contracts to help pay for future drug discovery efforts; and

• Maintaining our collaboration and license agreement with Bayer to support our continuing development and regulatory efforts for tedizolid phosphate for the treatment of ABSSSI and pneumonia.

Tedizolid phosphate will require extensive additional clinical study and evaluation, regulatory approval in multiple jurisdictions, substantial investment and significant marketing efforts before we generate any revenues from product sales. We are not permitted to market or promote tedizolid phosphate, or any other antibiotic product candidates that we develop, before we obtain regulatory approval from the FDA or comparable foreign regulatory authorities. If we do not obtain regulatory approval for and successfully commercialize tedizolid phosphate, we may not generate any revenues from product sales, and we may not be able to continue our operations. Even if we successfully obtain regulatory approval to market tedizolid phosphate, our revenues are dependent upon the size of the markets in the territories for which we obtain regulatory approval and have commercial rights, as well as our ability to gain market acceptance and achieve commercial success. If we do not generate revenues, or the markets for the treatment of ABSSSI are not as significant as we estimate, our business and prospects will be materially harmed.

If we fail to obtain additional financing, we may not be able to complete the development and commercialization of tedizolid phosphate or any other product candidates.*

Our operations have consumed substantial amounts of cash since our inception. In the event that we do not complete the Merger, we expect to continue to spend substantial amounts to:

• Complete the development of tedizolid phosphate for the treatment of ABSSSI;

• Launch and commercialize tedizolid phosphate and any other product candidates for which we obtain regulatory approval, including by building a hospital-directed sales force and/or collaborating with third parties;

• Pursue clinical development of tedizolid phosphate for the treatment of pneumonia and potentially for other indications; and

• Continue our discovery and development programs to advance our preclinical product pipeline.

In May 2011, we completed a private placement, raising $28.0 million in net proceeds. In July 2011, we signed a collaboration agreement with Bayer where they agreed to pay us $25.0 million in upfront fees, and agreed to support approximately 25% of our development costs of tedizolid phosphate for ABSSSI and pneumonia, pay us up to $69.1 million upon the achievement of certain milestones, and pay us royalties on net sales of tedizolid phosphate in the Bayer Licensed Territory. In addition, Bayer agreed to pay for 100% of the development efforts in the Bayer Licensed Territory. In January 2012, we completed a public offering, raising $48.4 million in net proceeds. In August 2012, we entered into a committed equity line of credit under which we may sell up to $25.0 million of our common stock from time to time to Terrapin over a 24-month period. To date, we have received aggregate net proceeds of $8.4 million under the committed equity line of credit. In January 2013, we completed a public offering, raising $31.6 million in net proceeds. We expect that the net proceeds from the sale of our common stock, revenues under our Bayer collaboration and our existing cash and cash

25

equivalents, together with interest thereon, will be sufficient to fund our capital requirements through the estimated time that we expect to receive a response from the FDA on our NDA for tedizolid phosphate. However, changing circumstances may cause us to consume capital significantly faster than we currently anticipate, and we may need to spend more money than currently expected because of circumstances beyond our control. For example, our clinical trials may encounter technical, enrollment or other issues that could cause our development costs to increase more than we expected. We may also need to raise additional funds sooner if we choose to initiate clinical trials more rapidly than we presently anticipate. In any event, we expect that we will require additional capital to obtain regulatory approval of and to commercialize tedizolid phosphate, and we expect the costs and duration of a Phase 3 program required for approval for the treatment of pneumonia to exceed those for the treatment of ABSSSI. Securing additional financing will require a substantial amount of time and attention from our management and may divert a disproportionate amount of its attention away from our day-to-day activities, which may adversely affect our management’s ability to conduct our day-to-day operations. In addition, we cannot guarantee that future financing will be available in sufficient amounts or on terms acceptable to us, if at all. If we are unable to raise additional capital when required or on acceptable terms, we may be required to:

• Significantly delay, scale back or discontinue the development or commercialization of tedizolid phosphate or our preclinical programs;

• Seek collaborators for one or more of our current or future product candidates at an earlier stage than otherwise would be desirable or on terms that are less favorable than might otherwise be available; or

• Relinquish or license on unfavorable terms, our rights to technologies or product candidates that we otherwise would seek to develop or commercialize ourselves.

If we are unable to raise additional capital in sufficient amounts or on terms acceptable to us, we may not be able to maintain our collaboration and license agreement with Bayer and we will be prevented from pursuing discovery, development and commercialization efforts and our ability to generate revenues and achieve or sustain profitability will be substantially harmed. In addition, if the United States government stops funding our preclinical programs or we are unable to enter into new government funding contracts , we may not be able to continue our preclinical programs, and our business and prospects may be materially harmed.

To raise additional funds to support our business operations, we may sell additional equity or convertible debt securities, which would result in dilution to our stockholders, or incur indebtedness which could result in restrictive covenants that adversely impact the operation of our business.*

The sale of additional equity would result, and the issuance of convertible debt securities would likely result, in the issuance of additional shares of our capital stock and dilution to our stockholders. The incurrence of indebtedness would result in increased fixed payment obligations and could also result in certain restrictive covenants, such as limitations on our ability to incur additional debt, limitations on our ability to acquire, sell or license intellectual property rights and other operating restrictions that could adversely impact our ability to conduct our business.

The timing of the milestone and royalty payments we are required to make to Dong-A is uncertain and could adversely affect our cash flows and results of operations.*

In January 2007, we entered into a license agreement with Dong-A pursuant to which we acquired an exclusive license to certain patent applications and other intellectual property related to the oral and injectable forms of tedizolid phosphate to develop and commercialize licensed products, including tedizolid phosphate, outside of Korea. In addition to milestone payments we have already made to Dong-A, we have an obligation to make up to an aggregate of $11.5 million in additional payments upon achievement of specified development and regulatory approval milestones. We are also required to pay Dong-A mid-single digit tiered royalties on net sales of tedizolid phosphate. The timing of our achievement of these events and corresponding milestone payments to Dong-A is subject to factors relating to the clinical and regulatory development and commercialization of tedizolid phosphate, many of which are beyond our control. We may become obligated to make a milestone payment when we do not have the cash on hand to make such payment, which could require us to delay our clinical trials, curtail our operations, scale back our planned commercialization and marketing efforts or seek funds to meet these obligations on terms unfavorable to us. In addition, if we are unable to make any payment to Dong-A when due or if we fail to use commercially reasonable efforts to achieve certain development and commercialization milestones within the timeframes required by our license agreement with Dong-A, Dong-A has the right to terminate the license agreement and all of our rights to develop and commercialize tedizolid phosphate upon 90 days written notice of our failure to make any such payment or to timely achieve the specified development and commercialization milestones.

The timing of the milestone and royalty payments we are entitled to receive from Bayer is uncertain and could adversely affect our cash flows and results of operations.

The timing of the up to $55.0 million remaining that we are entitled to receive upon the achievement of certain milestones under our collaboration and license agreement with Bayer is inherently uncertain. The receipt of milestone payments under the Bayer collaboration and license agreement can have a significant impact on our cash flows and results of operations for the periods of time in which such payments are made. However, while receipt of milestone and royalty payments would result in significant income, the absence of collaboration revenues in subsequent quarters could result in significant reductions in net income and could cause our stock price to drop.

Our limited operating history makes it difficult to evaluate our business and prospects.*

We were incorporated in 2004. Our operations to date have been limited to organizing and staffing our company, conducting product development activities for tedizolid phosphate and performing research and development with respect to our preclinical programs. We have not yet demonstrated an ability to obtain regulatory approval for or commercialize a product candidate. Consequently, any predictions about our future performance may not be as accurate as they could be if we had a history of successfully achieving regulatory approval of and commercializing pharmaceutical products.

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Risks Related to our Business

We are heavily dependent on the success of tedizolid phosphate, which is still under development. We cannot assure you that we will obtain regulatory approval for tedizolid phosphate. If we fail to obtain regulatory approval for tedizolid phosphate, our business will be materially harmed.*

To date, we have not marketed, distributed or sold any products. Our near-term prospects are substantially dependent on our ability to develop and commercialize tedizolid phosphate. To date, we have completed two Phase 3 studies, two Phase 2 studies and fifteen Phase 1 studies of tedizolid phosphate. In October 2009, we completed our end of Phase 2 meeting with the FDA. Based on the feedback and guidance we received from the FDA as well as the Special Protocol Assessment, or SPA, agreement we reached with the FDA on the protocol for our ESTABLISH 1 clinical trial of tedizolid phosphate for the treatment of ABSSSI, we conducted our ESTABLISH 1 Phase 3 clinical trial of tedizolid phosphate. We completed our ESTABLISH 1 Phase 3 trial in ABSSSI and, in December 2011, announced the positive results on both the early endpoints used by the FDA and the post-treatment assessment used by EMA. In addition, we obtained a SPA agreement for our ESTABLISH 2 Phase 3 clinical trial of tedizolid phosphate and, in March 2013, announced the achievement of all primary and secondary endpoints established by the FDA and EMA. We plan to use both Phase 3 trials as a basis for our NDA and Marketing Authorization Application submissions, seeking approvals to commercialize the IV and oral dosage forms of tedizolid phosphate for the treatment of ABSSSI. Additional clinical safety and special population Phase 1 clinical trials necessary for registration have also been performed. We cannot commercialize tedizolid phosphate prior to obtaining FDA approval. However, tedizolid phosphate is susceptible to the risks of failure inherent at any stage of drug development, including the appearance of adverse events, or AEs, failure to maintain efficacy across a broad population of patients and the FDA’s determination that a drug product is not approvable. We cannot assure you that our clinical trials for tedizolid phosphate will be completed timely or at all, or that we will be able to obtain FDA or EMA approvals for this product candidate, and we expect that the costs and duration of a Phase 3 program required for approval for the treatment of pneumonia to exceed those for the treatment of ABSSSI. If we are not able to commercialize tedizolid phosphate for ABSSSI or for any other indications, we will not be able to generate product revenues in the foreseeable future, or at all. Tedizolid phosphate is the only product candidate for which we have conducted clinical trials, and we cannot be certain that we will advance any other product candidates into clinical trials. As a company, we have never obtained regulatory approval for or commercialized a drug. It is possible that the FDA may refuse to accept our NDA for substantive review or may conclude after review of our data that our application is insufficient to obtain regulatory approval of tedizolid phosphate. If the FDA does not accept or approve our NDA, it may require that we conduct additional clinical, preclinical or manufacturing validation studies and submit that data before it will reconsider our application. Depending on the extent of these or any other FDA required studies, approval of any NDA or application that we submit may be delayed by several years, or may require us to expend more resources than we have available. In addition, increased scrutiny by the United States Congress of the FDA’s approval process, particularly in our areas of focus, may significantly delay or prevent regulatory approval, as well as impose more stringent product labeling and post-marketing testing and other requirements. Any delay in obtaining, or an inability to obtain, regulatory approvals would prevent us from commercializing tedizolid phosphate, generating revenues and achieving and sustaining profitability. It is also possible that additional studies, if performed and completed, may not be considered sufficient by the FDA to approve our NDA. If any of these outcomes occur, we may be forced to abandon our NDA for tedizolid phosphate, which would materially adversely affect our business and could potentially cause us to cease operations.

Clinical trials involve a lengthy and expensive process with an uncertain outcome, and results of earlier studies and trials may not be predictive of future trial results.*

Clinical testing is expensive and can take many years to complete, and its outcome is highly uncertain. Failure can occur at any time during the clinical trial process due to inadequate performance of a drug or inadequate adherence by patients or investigators to clinical trial protocols, leading to poor data quality. The results of preclinical studies and early clinical trials of product candidates may not be predictive of the results of later-stage clinical trials. Investigational drugs in later stages of clinical trials may fail to show the desired safety and efficacy traits despite having progressed satisfactorily through preclinical studies and initial clinical testing. A number of companies in the pharmaceutical and biotechnology industries, including those with greater resources and experience than us, have suffered significant setbacks even after seeing promising results in earlier clinical trials. Despite the results reported in clinical trials for tedizolid phosphate so far, we do not know whether any other clinical and nonclinical studies we may conduct will demonstrate adequate efficacy and safety to result in regulatory approval to market tedizolid phosphate.

The FDA regulatory approval process is lengthy, time consuming and inherently unpredictable, and if we are ultimately unable to obtain regulatory approval for tedizolid phosphate, our business will be substantially harmed.*

The time required to obtain approval for commercialization from the FDA and similar foreign authorities is unpredictable but typically takes many years following the commencement of clinical trials, depending upon numerous factors, and we expect that our Phase 3 program of tedizolid phosphate for the treatment of pneumonia will be of longer duration than our Phase 3 program for the treatment of ABSSSI. In addition, approval policies, regulations, or the type and amount of clinical data necessary to obtain regulatory approval may change during the course of a product candidate’s clinical development.

We may fail to obtain regulatory approval for tedizolid phosphate or any other product candidate for many reasons, including the following:

• We may not be able to demonstrate to the satisfaction of the FDA or comparable foreign regulatory authorities that a product candidate is safe and effective for any indication;

• The results of clinical trials may not meet the level of statistical significance required by the FDA or comparable foreign regulatory authorities for approval;

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• The FDA or comparable foreign regulatory authorities may disagree with the design or implementation of our clinical trials;

• We may not be able to demonstrate that a product candidate’s clinical and other benefits outweigh its safety risks;

• We may not be able to demonstrate that a product candidate provides an advantage over current standard of care, future competitive therapies in development, or over placebo in any indications for which the FDA requires a placebo-controlled trial;

• The FDA or comparable foreign regulatory authorities may disagree with our interpretation of data from preclinical studies or clinical trials;

• The FDA or comparable foreign regulatory authorities may not accept data generated at our clinical trial sites, including as a result of pre-approval inspections of us, our CROs or clinical sites;

• The data collected from clinical trials of any product candidates that we develop may not be sufficient to support the submission of an NDA or other submission or to obtain regulatory approval in the United States or elsewhere;

• The FDA or comparable foreign regulatory authorities may fail to approve the manufacturing processes or facilities of third-party manufacturers with which we or our collaborators enter into agreements for clinical and commercial supplies; and

• The approval policies or regulations of the FDA or comparable foreign regulatory authorities may significantly change in a manner rendering our clinical data insufficient for approval.

This lengthy approval process as well as the unpredictability of future clinical trial results may result in our failing to obtain regulatory approval to market tedizolid phosphate or any future product candidates, which would significantly harm our business, results of operations and prospects.

Delays in clinical trials are common and have many causes, and any such delays could result in increased costs to us and jeopardize or delay our ability to obtain regulatory approval and commence product sales as currently contemplated.*

We may experience delays in clinical trials of our product candidates. To date, tedizolid phosphate has completed two Phase 3 studies for the treatment of ABSSSI. We have conducted additional safety, pharmacology and special population clinical studies necessary for registration. We intend to use both of our Phase 3 studies as a basis to submit an NDA and EMA submission for the approval of the IV and oral dosage forms of tedizolid phosphate for the treatment of ABSSSI. We also expect to initiate a Phase 3 program of tedizolid phosphate for the treatment of pneumonia, and we may in the future perform clinical studies of tedizolid phosphate for other indications. We do not know whether our planned clinical trials will begin on time, need to be redesigned, enroll a sufficient number of patients or be completed on schedule, if at all. Clinical trials can be delayed for a variety of reasons, including the following:

• Delays in obtaining regulatory approval to commence a trial;

• Delays in reaching agreement with the FDA on any SPAs we submit;

• Imposition of a clinical hold following an inspection of our clinical trial operations or trial sites by the FDA or other regulatory authorities;

• Delays in reaching agreement on acceptable terms with prospective CROs and clinical trial sites;

• Delays in obtaining required institutional review board approval at each clinical trial site;

• Delays in recruiting suitable patients to participate in a clinical trial;

• Delays in having patients complete participation in a trial or return for post-treatment follow-up;

• Clinical trial sites dropping out of a trial to the detriment of enrollment;

• Time required to add new sites;

• Delays in obtaining sufficient supplies of clinical trial materials; or

• Delays resulting from negative or equivocal findings of a data safety monitoring board, or DSMB, for a clinical trial.

Patient enrollment, a significant factor in the timing of clinical trials, is affected by many factors, including the size and nature of the patient population, enrollment criteria imposed by the FDA, the proximity of patients to clinical sites, the eligibility criteria for participating in the trial, the design of the clinical trial, competing clinical trials and clinicians’ and patients’ perceptions as to the potential advantages of the drug being studied in relation to other available therapies, including any new drugs that may be approved for the indications we are investigating. For example, we could encounter delays in our clinical trials of tedizolid phosphate if participating physician investigators encounter unresolved ethical issues associated with enrolling patients in clinical trials of tedizolid phosphate in lieu of prescribing approved antibiotics that have established safety and efficacy profiles. Furthermore, we rely on CROs and clinical trial sites to ensure the proper and timely conduct of our clinical trials and while we have agreements governing their committed activities, we have limited influence over their actual performance. Any delays in completing our clinical trials could increase our costs, slow down our product development and approval process and jeopardize our ability to commence product sales and generate revenues.

We may be required to suspend or discontinue clinical trials due to adverse side effects or other safety risks that could preclude approval of tedizolid phosphate or any of our future product candidates.*

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Our clinical trials may be suspended at any time for a number of reasons. A clinical trial may be suspended or terminated by us, our collaborators, the FDA or other regulatory authorities due to a failure to conduct the clinical trial in accordance with regulatory requirements or our clinical protocols, unforeseen safety issues including adverse side effects, failure to demonstrate a benefit from using the investigational drug, changes in governmental regulations or administrative actions, lack of adequate funding to continue the clinical trial, or negative or equivocal findings of a DSMB, an Institutional Review Board or an Independent Ethics Committee for a clinical trial. We may voluntarily suspend or terminate our clinical trials if at any time we believe that they present an unacceptable risk to participants. In addition, regulatory agencies may order the temporary or permanent discontinuation of our clinical trials at any time if they believe that the clinical trials are not being conducted in accordance with applicable regulatory requirements or that they present an unacceptable safety risk to participants. If we elect or are forced to suspend or terminate any clinical trial of any product candidates that we develop, the commercial prospects of such product candidates will be harmed and our ability to generate product revenues, if at all, from any of these product candidates will be delayed or eliminated. Any of these occurrences may harm our business, financial condition and prospects significantly.

To date, the drug-related adverse events experienced by patients while being treated with tedizolid phosphate were mostly mild or moderate side effects that included nausea, diarrhea, vomiting and headache. However future clinical trials will involve broader populations and could reveal a higher prevalence or different severity of these or other side effects. In such an event, our trials could be suspended or terminated and the FDA or comparable foreign regulatory authorities could order us to cease further development of or deny approval of tedizolid phosphate for any or all targeted indications. Any of these occurrences may harm our business and prospects significantly.

The SPAs for our Phase 3 studies of tedizolid phosphate do not guarantee any particular outcome from regulatory review of our Phase 3 studies.*

The FDA’s SPA process creates a written agreement between the sponsoring company and the FDA regarding clinical trial design and data analysis and other clinical trial issues that can be used to support approval of a product candidate. The SPA is intended to provide assurance that if the agreed upon clinical trial protocols are followed, the clinical trial endpoints are achieved, and there is a favorable risk-benefit profile, the data may serve as the primary basis for an efficacy claim in support of an NDA. However, SPA agreements are not a guarantee of an approval of a product candidate or any permissible claims about the product candidate. In particular, SPAs are not binding on the FDA if previously unrecognized public health concerns arise during the performance of the clinical trial, other new scientific developments regarding product candidate safety or efficacy arise or if the sponsoring company fails to comply with the agreed upon clinical trial protocols. We do not know how the FDA will interpret the commitments under the agreed upon SPAs, how it will interpret the data and results or whether it will approve tedizolid phosphate for the treatment of ABSSSI or any other indication. In addition, although the FDA has provided us with feedback as to the adequacy of the proposed size of our safety population to support an NDA, it may require us to conduct additional clinical trials. As a result, we cannot guarantee any particular outcome from regulatory review of our Phase 3 studies.

We rely on third parties to conduct our clinical trials. If these third parties do not successfully carry out their contractual duties or meet expected deadlines, we may be delayed in obtaining or ultimately not be able to obtain regulatory approval for or commercialize tedizolid phosphate or any other product candidates.*

We have relied and plan to continue to rely upon CROs to monitor and manage data for our on-going clinical programs for tedizolid phosphate as well as the execution of our preclinical and nonclinical studies, and control only certain aspects of our CROs’ activities. Nevertheless, we are responsible for ensuring that each of our studies is conducted in accordance with the applicable protocol, legal, regulatory and scientific standards and our reliance on the CROs does not relieve us of our regulatory responsibilities. We and our CROs are required to comply with the FDA’s current good clinical practices, or cGCPs, which are regulations and guidelines enforced by the FDA for all of our products in clinical development. The FDA enforces these cGCPs through periodic inspections of trial sponsors, principal investigators and clinical trial sites. If we or our CROs fail to comply with applicable cGCPs, the clinical data generated in our clinical trials may be deemed unreliable, and the FDA may require us to perform additional clinical trials before approving our marketing applications. We cannot assure you that, upon inspection, the FDA will determine that any of our clinical trials comply with cGCPs. In addition, our clinical trials will require an adequately large number of test subjects to evaluate the safety and effectiveness of tedizolid phosphate. Accordingly, if our CROs fail to comply with these regulations or recruit a sufficient number of patients, the FDA may require us to repeat clinical trials, which would delay the regulatory approval process. In addition, our CROs are not our employees, and we cannot control whether or not they devote sufficient time and resources to our on-going clinical, nonclinical and preclinical programs. These CROs may also have relationships with other commercial entities, including our competitors, for whom they may also be conducting clinical studies or other drug development activities, which could harm our competitive position. If our CROs do not successfully carry out their contractual duties or obligations or meet expected deadlines, if they need to be replaced, or if the quality or accuracy of the clinical data they obtain is compromised due to the failure to adhere to our clinical protocols or regulatory requirements, or for other reasons, our clinical trials may be extended, delayed or terminated, and we may not be able to obtain regulatory approval for or successfully commercialize tedizolid phosphate or any other product candidates that we develop. As a result, our financial results and the commercial prospects for tedizolid phosphate and any other product candidates that we develop would be harmed, our costs could increase and our ability to generate revenues could be delayed or diminished.

We plan to maintain our relationships with existing CROs and enter into agreements with additional CROs to obtain additional resources and expertise in an attempt to accelerate our progress with regard to on-going clinical, nonclinical and preclinical programs and specifically, the initiation of our Phase 3 clinical trial program for tedizolid phosphate for the treatment of pneumonia and potentially for other indications. Switching or entering into new relationships with CROs involves substantial cost and requires extensive management time and focus. In addition, there is a natural transition period when a new CRO commences work. As a result, delays occur, which can materially impact our ability to meet our desired clinical development timelines. Though we carefully manage our relationships with our CROs, there can be no assurance that we will not encounter similar challenges or delays in the future or that these delays or challenges will not have a material adverse impact on our operating results, financial condition or future prospects.

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Our dependence upon third parties for the manufacture and supply of tedizolid phosphate and any future product candidates and products may cause delays in, or prevent us from, successfully developing and commercializing products.*

We do not currently have nor do we plan to implement the infrastructure or capability internally to manufacture tedizolid phosphate for use in the conduct of our clinical trials. We employ the services of Albany Molecular Research, Inc., or AMRI, to produce tedizolid phosphate API and Patheon, Inc., or Patheon, to produce the solid oral and sterile IV tedizolid phosphate finished products. We have entered into clinical supply master services agreements with AMRI and Patheon for our short-term clinical supply needs, but we do not have any other agreements for the clinical supply of tedizolid phosphate or any future product candidates with AMRI, Patheon or any other third party.

With respect to the manufacturing for our commercial scale products, we have entered into a worldwide agreement with Patheon to supply the commercial quantities of solid oral and sterile IV tedizolid phosphate bulk and finished products that we expect to require to support the markets in which we and our licensors, including Bayer, intend to commercialize the product, subject to regulatory approval. However, tedizolid phosphate is a new chemical entity that has never been produced at commercial scale, and, as such, there are underlying risks associated with its manufacture, which could include cost overruns, new impurities, difficulties in scaling up or reproducing manufacturing processes and lack of timely availability of raw materials. Any of these risks may prevent or delay us from successfully developing and commercializing tedizolid phosphate. Reliance on third-party manufacturers entails many risks, including regulatory compliance and quality assurance, the possibility of breach of the manufacturing agreement by the third party because of factors beyond our control and the possibility of termination or nonrenewal of the agreement by the third party, based on its own business priorities, at a time that is costly or damaging to us.

Our third-party manufacturers are required to comply with applicable FDA current good manufacturing practice, or cGMP, regulations. In addition, our manufacturers will be subject to ongoing periodic unannounced inspections by the FDA and corresponding state and foreign agencies for compliance with cGMPs and similar regulatory requirements. These regulations cover all aspects of the manufacturing, testing, quality control and record keeping relating to our product candidates. We do not have control over our manufacturers’ compliance with these regulations and standards. Failure by any of our manufacturers to comply with applicable regulations could result in sanctions being imposed on us, including fines, injunctions, civil penalties, failure to grant approval to market our product candidates, delays, suspensions or withdrawals of approvals, operating restrictions, and interruptions in supply and criminal prosecutions, any of which could significantly and adversely affect our business.

We could also experience manufacturing delays if our third-party manufacturers give greater priority to the supply of other products over our product candidates. If AMRI, Patheon or any alternate supplier of bulk or finished drug product, experiences any significant difficulties in its respective manufacturing processes for tedizolid phosphate API or bulk or finished drug product, we could experience significant interruptions in the supply of tedizolid phosphate. Our inability to coordinate the efforts of our third-party manufacturing partners, or the lack of capacity available at our third-party manufacturing partners, could impair our ability to supply tedizolid phosphate at the levels required for successful commercialization. If our current suppliers are unable or unwilling to perform under their agreements, we could experience significant interruptions in the supply of tedizolid phosphate because of the significant regulatory requirements that we would need to satisfy in order to qualify a new tedizolid phosphate API or bulk or finished drug product supplier.

If for any reason we are unable to use our currently available supply of tedizolid phosphate, the inability to acquire additional quantities of tedizolid phosphate in a timely manner from third parties could delay clinical trials of tedizolid phosphate or result in product shortages and prevent us from developing and commercializing tedizolid phosphate in a cost-effective manner or on a timely basis.

The failure to maintain our collaboration with Bayer or the failure of Bayer to perform its obligations under this collaboration, could negatively impact our business.*

Pursuant to the terms of our collaboration and license agreement with Bayer, we granted to Bayer exclusive rights to develop and commercialize tedizolid phosphate in the Bayer Licensed Territory. Consequently, our ability to generate any revenues from tedizolid phosphate in the Bayer Licensed Territory depends on our ability to maintain our collaboration with Bayer and Bayer’s ability to obtain regulatory approvals for and to successfully commercialize tedizolid phosphate in the Bayer Licensed Territory. We have limited control over the amount and timing of resources that Bayer will dedicate to these efforts.

We are subject to a number of other risks associated with our collaboration and license agreement with Bayer, including:

• Bayer has the right to terminate the Agreement within 30 days of becoming aware of any material toxicity and/or material drug safety event or issue concerning tedizolid.

• Bayer may not comply with applicable regulatory guidelines with respect to developing or commercializing tedizolid phosphate, which could adversely impact future development or sales of tedizolid phosphate in the Bayer Licensed Territory and elsewhere;

• We and Bayer could disagree as to current or future development plans for tedizolid phosphate for the treatment of ABSSSI or pneumonia and Bayer may delay clinical trials or stop a clinical trial;

• There may be disputes between us and Bayer, including disagreements regarding the collaboration and license agreement, that may result in (1) the delay of or failure to achieve regulatory and commercial objectives that would result in milestone or royalty payments, (2) the delay or termination of any future development or commercialization of tedizolid phosphate for the treatment of ABSSSI or pneumonia, and/or (3) costly litigation or arbitration that diverts our management’s attention and resources;

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• Bayer may not provide us with timely and accurate information regarding supply forecasts, which could adversely impact our ability to comply with our supply obligations to Bayer and manage our own inventory of tedizolid phosphate, as well as our ability to generate accurate financial forecasts;

• Business combinations or significant changes in Bayer’s business strategy may adversely affect Bayer’s ability or willingness to perform its obligations under our collaboration agreement;

• We may not be able to raise additional capital in sufficient amounts or on terms acceptable to us, or business combinations or significant changes in our business strategy may adversely affect our ability or willingness to perform our obligations under our collaboration agreement;

• The royalties we are eligible to receive from Bayer may be reduced or eliminated based upon Bayer’s and our ability to maintain or defend our intellectual property rights and the presence of generic competitors in the Bayer Licensed Territory;

• Limitations on our or an acquirer’s ability to maintain or pursue development or commercialization of products that are competitive with tedizolid phosphate could deter a potential acquisition of us that our stockholders may otherwise view as beneficial; and

• If Bayer is unsuccessful in obtaining regulatory approvals for or commercializing tedizolid phosphate in the Bayer Licensed Territory, we may not receive certain additional milestone payments or any royalty payments under the collaboration and license agreement and our business prospects and financial results may be materially harmed.

The collaboration and license agreement is subject to early termination, including through Bayer’s right to terminate without cause upon advance notice to us. If the agreement is terminated early, we may not be able to find another collaborator for the further development and commercialization of tedizolid phosphate in the Bayer Licensed Territory on acceptable terms, or at all, and we may be unable to pursue continued development and commercialization of tedizolid phosphate in the Bayer Licensed Territory on our own.

In the event we are unable to complete the proposed Merger, we may enter into additional collaboration and license agreements for the development and commercialization of tedizolid phosphate or other of our drug candidates, and may be similarly dependent on the performance of third parties with similar risk.

Other than our collaboration and license agreement with Bayer, we may not be able to enter into acceptable agreements to develop and commercialize tedizolid phosphate or, if needed, adequately build our own marketing and sales capabilities.*

We intend to pursue the development and commercialization of tedizolid phosphate through strategic arrangements with third parties, such as our collaboration and license agreement with Bayer. We may be unable to enter into additional arrangements outside of the Bayer Licensed Territory. In addition, there can be no guarantee that Bayer or any other parties that we may enter into strategic arrangements with will be successful or generate more revenues than we could obtain by developing and commercializing tedizolid phosphate on our own. If we are unable to enter into additional strategic arrangements for tedizolid phosphate or develop an effective international sales force, our ability to generate product revenues would be limited, which would adversely affect our business, financial condition, results of operations and prospects. If we are unable to enter into such arrangements for development of tedizolid phosphate in areas outside of the Bayer Licensed Territory, we may need to develop our own marketing and sales force to market tedizolid phosphate in these territories, for which currently we do not have sufficient funds. There is no guarantee that we will be able to develop an effective international sales force to successfully commercialize tedizolid phosphate or any other future products in these markets. If we cannot commercialize tedizolid phosphate in any territory that represents a significant market opportunity, our ability to achieve and sustain profitability will be substantially limited.

If the FDA does not approve the manufacturing facilities of AMRI, Patheon or any future manufacturing partners for commercial production, we may not be able to commercialize tedizolid phosphate.

After we submit our NDA to the FDA and before approval of tedizolid phosphate, the facilities used by AMRI, Patheon and any of our future manufacturers to manufacture tedizolid phosphate must be approved by the FDA. We do not control the manufacturing process of tedizolid phosphate and are completely dependent on these third-party manufacturing partners for compliance with the FDA’s requirements for manufacture of tedizolid phosphate API and finished product. If our manufacturers cannot successfully manufacture material that conforms to our specifications and the FDA’s strict regulatory requirements, they will not be able to secure FDA approval for their manufacturing facilities. If the FDA does not approve these facilities for the commercial manufacture of tedizolid phosphate, we may need to find alternative manufacturing facilities, which would result in significant delays of up to several years in obtaining FDA approval for tedizolid phosphate.

If approved, tedizolid phosphate will face competition from less expensive generic versions of branded antibiotics of competitors and, if we are unable to differentiate the benefits of tedizolid phosphate over these less expensive alternatives, we may never generate meaningful product revenues.*

Generic antibiotic therapies are typically sold at lower prices than branded antibiotics and are generally preferred by hospital formularies and managed care providers of health services. We anticipate that, if approved, tedizolid phosphate will face increasing competition in the form of generic versions of branded products of competitors that have lost or will lose their patent exclusivity. For example, tedizolid phosphate, if approved, will initially face competition from the inexpensive generic forms of vancomycin that are currently available and, in the future, would face additional competition from a generic form of linezolid when licenses to the patents covering it are expected to commence in 2015, or earlier if the patents are successfully challenged. If we are unable to demonstrate to physicians and payers that the key differentiating features of tedizolid phosphate translate to overall clinical benefit or lower cost of care, we may not be able to compete with generic antibiotics.

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We face significant competition from other biotechnology and pharmaceutical companies and our operating results will suffer if we fail to compete effectively.*

The biotechnology and pharmaceutical industries are intensely competitive and subject to rapid and significant technological change. We have competitors both in the United States and internationally, including major multinational pharmaceutical companies, established biotechnology companies, specialty pharmaceutical and generic drug companies and universities and other research institutions. Many of our competitors have greater financial and other resources, such as larger research and development staff and more experienced marketing and manufacturing organizations. As a result, these companies may obtain regulatory approval more rapidly than we are able and may be more effective in selling and marketing their products as well. Smaller or early-stage companies may also prove to be significant competitors, particularly through collaborative arrangements with large, established companies. Our competitors may succeed in developing, acquiring or licensing on an exclusive basis, technologies and drug products that are more effective or less costly than tedizolid phosphate or any other drug candidate that we are currently developing or that we may develop, which could render our products obsolete and noncompetitive.

The competition in the market for antibiotics is intense. If approved, tedizolid phosphate will face competition from commercially available antibiotics such as vancomycin, marketed as a generic by Abbott Laboratories and others; teicoplanin, marketed as Targocid ^® by Sanofi Aventis and as a generic by others; daptomycin, marketed by Cubist Pharmaceuticals, Inc. as Cubicin^®; linezolid, marketed by Pfizer Inc. as Zyvox^®; ceftaroline, marketed by Forest Laboratories, Inc. and AstraZeneca PLC as Teflaro^®; ceftobiprole, under development by Basilea Pharmaceutica AG; quinupristin/dalfopristin, marketed by King Pharmaceuticals, Inc, a subsidiary of Pfizer, as Synercid^®; tigecycline, marketed by Pfizer as Tygacil^®; and telavancin, marketed by Theravance, Inc. as Vibativ^®. Vancomycin has been a widely used and well known antibiotic for over 50 years and is sold in a relatively inexpensive generic IV form. Vancomycin, daptomycin, linezolid, telavancin, tigecycline, quinupristin/dalfopristin and ceftaroline are all approved treatments for serious Gram-positive infections such as complicated skin and skin structure infections, or cSSSI or ABSSSI. Additionally, daptomycin is an approved treatment for bacteremia, linezolid is an approved treatment for pneumonia and vancomycin is an approved treatment for both bacteremia and pneumonia. In addition, if approved, tedizolid phosphate may face additional competition from antibiotics currently in clinical development. Other antibiotics currently in development include CEM-102, under development by Cempra Pharmaceuticals, Inc., dalbavancin, under development by Durata Therapeutics, Inc., delafloxacin and radezolid, both under development by Rib-X Pharmaceuticals, Inc., NXL-103, under development by AstraZeneca PLC, oritavancin, under development by The Medicines Company, PTK 0796, under development by Paratek Pharmaceuticals, Inc., BC-3781, under development by Nabrivia, GSK1322322, under development by GlaxoSmithKline, AFN-1252, under development by Affinium Pharmaceuticals, Inc. and JNJ-Q2, under development by Furiex Pharmaceuticals, Inc., which, if approved, would compete in the antibiotic market and would target indications such as ABSSSI. In addition, tedizolid phosphate may face competition from drug candidates currently in clinical development and drug candidates that could receive regulatory approval before tedizolid phosphate in countries outside the United States and the European Union, or EU. If we are unable to obtain regulatory approval of tedizolid phosphate for some or all of the indications for which our competitors are approved, or if we are unable to demonstrate the advantages of tedizolid phosphate over competing drugs and drug candidates, we will not be able to successfully commercialize tedizolid phosphate and our results of operations will suffer.

Established pharmaceutical companies may also invest heavily to accelerate discovery and development of novel compounds or to in-license novel compounds that could make tedizolid phosphate or any other product candidates that we develop obsolete. As a result of all of these factors, our competitors may succeed in obtaining patent protection and/or FDA approval or discovering, developing and commercializing antibiotics before we do.

Coverage and adequate reimbursement may not be available for tedizolid phosphate or any other product candidates that we develop, which could make it difficult for us to sell our products profitably.*

Market acceptance and sales of tedizolid phosphate or any other product candidates that we develop will depend on reimbursement policies and may be affected by future healthcare reform measures. Government authorities, hospital formularies and third-party payers, such as private health insurers and health maintenance organizations, decide which drugs they will pay for and establish reimbursement levels. We cannot be sure that coverage and adequate reimbursement will be available for tedizolid phosphate or any other product candidates that we develop. Also, we cannot be sure that coverage decisions or reimbursement amounts will not reduce the demand for, or the price of, our products. In addition, third-party payers may implement prior authorizations which may lead to a decrease in sales of our future products. If coverage or reimbursement is not available or is available only to limited levels or extensive prior authorizations are introduced, we may not be able to successfully commercialize tedizolid phosphate or any other product candidates that we develop.

In the U.S., the EU and other potentially significant markets for our product candidates, government authorities and third-party payers are increasingly attempting to limit or regulate the price of medical products and services, particularly for new and innovative products and therapies, which has resulted in lower average selling prices. Further, the increased emphasis on managed healthcare in the U.S. and on country and regional pricing and reimbursement controls in the EU will put additional pressure on product pricing, reimbursement and usage, which may adversely affect our future product sales and results of operations. These pressures can arise from rules and practices of managed care groups, judicial decisions and governmental laws and regulations related to Medicare, Medicaid and healthcare reform, pharmaceutical reimbursement policies and pricing in general.

The United States and some foreign jurisdictions are considering or have enacted a number of additional legislative and regulatory proposals to change the healthcare system in ways that could affect our ability to sell our products profitably. Among policy makers and payers in the United States and elsewhere, there is significant interest in promoting changes in healthcare systems with the stated goals of containing healthcare costs, improving quality and/or expanding access. In the United States, the pharmaceutical industry has been a particular focus of these efforts and has been significantly affected by major legislative initiatives.

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In the United States, the Medicare Prescription Drug, Improvement, and Modernization Act of 2003, also called the Medicare Modernization Act, or MMA, changed the way Medicare covers and pays for pharmaceutical products. The legislation established Medicare Part D, which expanded Medicare coverage for outpatient prescription drug purchases by the elderly but provided authority for limiting the number of drugs that will be covered in any therapeutic class. The MMA also introduced a new reimbursement methodology based on average sales prices for physician-administered drugs.

In March 2010, the Patient Protection and Affordable Care Act, as amended by the Health Care and Education Affordability Reconciliation Act, or collectively PPACA, became law. PPACA substantially changes the way healthcare is financed by both governmental and private insurers and significantly affects the pharmaceutical industry. Among other cost containment measures, the PPACA establishes: an annual, nondeductible fee on any entity that manufactures or imports certain branded prescription drugs and biologic agents; a new Medicare Part D coverage gap discount program; and a new formula that increases the rebates a manufacturer must pay under the Medicaid Drug Rebate Program. In the future, there may continue to be additional proposals relating to the reform of the U.S. healthcare system, some of which could further limit the prices we are able to charge for our products, or the amounts of reimbursement available for our products.

The availability of numerous generic antibiotics at lower prices than branded antibiotics, such as tedizolid phosphate if it were approved for commercial introduction, may also substantially reduce the likelihood or levels of reimbursement for tedizolid phosphate. We expect to experience pricing pressures in connection with the sale of tedizolid phosphate and any other products that we develop, due to the trend toward managed healthcare, the increasing influence of health maintenance organizations and additional legislative proposals. If we fail to successfully secure and maintain coverage and adequate reimbursement for our products or are significantly delayed in doing so, we will have difficulty achieving market acceptance of our products and our business will be harmed.

The commercial success of tedizolid phosphate and any other product candidates that we develop, if approved in the future, will depend upon attaining significant market acceptance of these products among physicians and payers.*

We have never commercialized a product candidate for any indication. Even if tedizolid phosphate or any other product candidates that we develop are approved by the appropriate regulatory authorities for marketing and sale, physicians may not prescribe our approved products, which would prevent us from generating revenues or becoming profitable. Market acceptance of tedizolid phosphate and any other product candidates that we develop by physicians and payers will depend on a number of factors, many of which are beyond our control, including:

• The clinical indications for which the product is approved;

• Acceptance by physicians and payers of each product as a safe and effective treatment;

• The cost of treatment in relation to alternative treatments, including numerous generic drug products, such as vancomycin;

• The relative convenience, ease of administration and acceptance by physicians and payers of tedizolid phosphate in the treatment of the indications for which it is approved;

• The availability and efficacy of competitive drugs;

• The extent to which the product is approved for inclusion on formularies of hospitals and managed care organizations;

• The extent to which bacteria develop resistance to any antibiotic product candidates that we develop, thereby limiting its efficacy in treating or managing infections;

• Whether the product is designated under physician treatment guidelines as a first-line therapy or as a second- or third-line therapy for particular infections;

• The availability of coverage and adequate reimbursement by third parties, such as insurance companies and other healthcare payers, and/or by government healthcare programs, including Medicare and Medicaid;

• Limitations or warnings contained in a product’s approved labeling;

• Prevalence and severity of adverse side effects; and

• The ability to develop convincing health economics and outcomes research.

Even if the medical community accepts that tedizolid phosphate is safe and efficacious for its approved indications, physicians may not immediately be receptive to the use of tedizolid phosphate or may be slow to adopt it as an accepted treatment. In addition, even though we believe tedizolid phosphate has significant advantages, we cannot assure you that any labeling approved by the health authority will contain claims that tedizolid phosphate is safer or more effective than linezolid, or that will permit us to promote tedizolid phosphate as being superior to linezolid or any other competing products. Moreover, in the future, as has happened with other antibiotics, bacteria could over time develop resistance to tedizolid phosphate, particularly if it becomes widely used, which would render it less effective and therefore less appealing to physicians. If tedizolid phosphate is approved but does not achieve an adequate level of acceptance by physicians and payers, we may not generate sufficient or any revenues from this product candidate and we may not become profitable. In addition, our efforts to educate the medical community and third-party payers on the benefits of tedizolid phosphate may require significant resources and may never be successful.

We currently have limited marketing capabilities and no sales organization and have no experience in marketing drug products. If we are unable to establish effective marketing and sales capabilities or enter into agreements with third parties to market and sell our products after they are approved, we may not be able to generate product revenues.

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We currently have limited marketing capabilities and do not have a sales organization or distribution capabilities. In order to commercialize any products, we must build our marketing, sales, distribution, managerial and other non-technical capabilities or make arrangements with third parties to perform these services. Outside of Korea and the Bayer Licensed Territory, we own exclusive rights to commercialize tedizolid phosphate worldwide, and we contemplate establishing our own sales force or seeking third-party partners to sell tedizolid phosphate in those territories. We have partnered with Bayer in the Bayer Licensed Territory and will be reliant on them to develop and commercialize tedizolid phosphate in the Bayer Licensed Territory. The establishment and development of our own sales force to market any products we may develop will be expensive and time consuming and could delay any product launch, and we cannot be certain that we will be able to successfully develop this capability. We, Bayer for the Bayer Licensed Territory and any potential future third-party commercialization partners will also have to compete with other pharmaceutical and biotechnology companies to recruit, hire, train and retain marketing and sales personnel.

In addition, we may not be able to enter into collaboration and license arrangements with third parties to sell tedizolid phosphate on favorable terms or at all. If we fail to enter into marketing arrangements for our products and are unable to develop an effective international sales force, our ability to generate revenue would be limited as a significant portion of the market opportunity for tedizolid phosphate and any other product candidates we develop is likely to be in international markets. To the extent we rely on third parties to commercialize our approved products whether within or outside the United States, we will receive less revenues than if we commercialized these products ourselves. In international markets in particular, we would have little or no control over the sales efforts of any other third parties involved in our commercialization efforts. In the event we are unable to develop our own marketing and sales force or collaborate with a third-party marketing and sales organization, we would not be able to commercialize tedizolid phosphate or any other product candidates that we develop, which would negatively impact our ability to generate product revenues.

Even if the FDA approves tedizolid phosphate, adverse effects discovered after approval could limit the commercial profile of any approved label.

If we obtain regulatory approval for tedizolid phosphate or any other product candidate that we develop, and we or others later discover, after approval and use in an increasing number of patients for longer periods of time, that our products could have adverse effect profiles that limit their usefulness or require their withdrawal (whether or not the therapies showed the adverse effect profile in Phase 1 through Phase 3 clinical trials), a number of potentially significant negative consequences could result, including:

• Regulatory authorities may withdraw their approval of the product;

• Regulatory authorities may require the addition of labeling statements, such as warnings or contraindications;

• We may be required to change the way the product is administered, conduct additional clinical studies, implement a burdensome risk evaluation and mitigation strategy, or REMS, or restrict the distribution of the product;

• We could be sued and held liable for harm caused to patients; and

• Our reputation may suffer.

Any of these events could prevent us from maintaining market acceptance of the affected product candidate and could substantially increase the costs of commercializing our product candidates.

If we are not successful in attracting and retaining highly qualified personnel, including our current senior executive team, we may not be able to successfully implement our business strategy.*

Our ability to compete in the highly competitive biotechnology and pharmaceuticals industries depends in large part upon our ability to attract and retain highly qualified managerial, scientific and medical personnel. We are highly dependent on our executive team. In order to induce these and other valuable employees to remain with us, we have provided stock options that vest over time. The value to employees of stock options is significantly affected by movements in our stock price that we cannot control and may at any time be insufficient to counteract more lucrative offers from other companies.

Our scientific team has expertise in many different aspects of drug discovery and development. We conduct our operations at our facility in San Diego, California. This region is headquarters to many other biopharmaceutical companies and many academic and research institutions and, as a result, competition for skilled personnel in our market is very intense and competition for experienced research scientists and development personnel may limit our ability to hire and retain highly qualified personnel on acceptable terms or at all.

Despite our efforts to retain valuable employees, members of our management, scientific and medical teams may terminate their employment with us on short notice given the announcement of the Merger. While we have employment agreements with all of our employees, these employment arrangements provide for at-will employment, which means that any of our employees could leave our employment at any time, with or without notice. The loss of the services of any of our executive officers or other key employees could potentially harm our business, operating results or financial condition. Our success also depends on our ability to continue to attract, retain and motivate highly skilled junior, mid-level and senior managers as well as junior, mid-level and senior scientific and medical personnel.

Other biotechnology and pharmaceutical companies with which we compete for qualified personnel have greater financial and other resources, different risk profiles and a longer history in the industry than we do. They also may provide more diverse opportunities and better chances for career advancement. Some of these characteristics may be more appealing to high quality candidates than what we have to offer. If we are unable to continue to attract and retain high quality personnel, the rate and success at which we can discover, develop and commercialize drug candidates will be limited.

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We will need to grow our organization, and we may experience difficulties in managing this growth, which could disrupt our operations.*

As of August 1, 2013, we employed 94 full time employees. As our development and commercialization plans and strategies develop, we expect to expand our employee base for managerial, operational, sales, marketing, financial and other resources. Future growth would impose significant added responsibilities on members of management, including the need to identify, recruit, maintain, motivate and integrate additional employees. Also, our management may need to divert a disproportionate amount of its attention away from our day-to-day activities and devote a substantial amount of time to managing these growth activities. We may not be able to effectively manage the expansion of our operations which may result in weaknesses in our infrastructure, give rise to operational mistakes, loss of business opportunities, loss of employees and reduced productivity among remaining employees. Our expected growth could require significant capital expenditures and may divert financial resources from other projects, such as the development of additional product candidates. If our management is unable to effectively manage our expected growth, our expenses may increase more than expected, our ability to generate and/or grow revenues could be reduced and we may not be able to implement our business strategy. Our future financial performance and our ability to commercialize tedizolid phosphate and our other product candidates and compete effectively will depend, in part, on our ability to effectively manage any future growth.

If we fail to develop tedizolid phosphate for additional indications, our commercial opportunity will be limited.

To date, we have focused primarily on the development of tedizolid phosphate for the treatment of ABSSSI. A key element of our strategy is to pursue clinical development of tedizolid phosphate for pneumonia and potentially for other indications. Although we believe there is large commercial opportunity for the treatment of ABSSSI alone, our ability to generate and grow revenues will be highly dependent on our ability to successfully develop and commercialize tedizolid phosphate for the treatment of additional indications. The development of tedizolid phosphate for additional indications is prone to the risks of failure inherent in drug development and we cannot provide you any assurance that we will be able to successfully advance any of these programs through the development process. Even if we receive FDA approval to market tedizolid phosphate for the treatment of any additional indications, we cannot assure you that any such indications will be successfully commercialized, widely accepted in the marketplace or more effective than other commercially available alternatives. If we are unable to successfully develop and commercialize tedizolid phosphate for additional indications, our commercial opportunity will be limited and our business prospects will suffer.

Even if we obtain FDA approval of tedizolid phosphate or any other product candidate we develop, we or Bayer may never obtain approval or commercialize our products outside of the United States, which would limit our ability to realize their full market potential.*

In order to market any products outside of the United States, we and Bayer in the Bayer Licensed Territory must establish and comply with numerous and varying regulatory requirements of other countries regarding safety and efficacy. Clinical trials conducted in one country may not be accepted by regulatory authorities in other countries, and regulatory approval in one country does not mean that regulatory approval will be obtained in any other country. Approval procedures vary among countries and can involve additional product testing and validation and additional administrative review periods. Seeking foreign regulatory approvals could result in significant delays, difficulties and costs for us and require additional preclinical studies or clinical trials which would be costly and time consuming. Regulatory requirements can vary widely from country to country and are in many cases subject to the post hoc discretion of regulatory authorities, which requirements could delay or prevent the introduction of our products in those countries. For example, certain countries require minimum trial sizes for clinical studies and certain other countries require minimum numbers of patients enrolled in such trials in such countries, and we may not be able to meet or satisfy such requirements. Satisfying these and other regulatory requirements is costly, time consuming, uncertain and subject to unanticipated delays. In addition, our or Bayer’s failure to obtain regulatory approval in any country may delay or have negative effects on the process for regulatory approval in other countries. We do not have any product candidates approved for sale in any jurisdiction, including international markets, and we do not have experience in obtaining regulatory approval in international markets. If we or Bayer fail to comply with regulatory requirements in our international markets or to obtain and maintain required approvals, our target market will be reduced and our ability to realize the full market potential of our products will be harmed.

If we fail to develop and commercialize product candidates other than tedizolid phosphate, we may not be able to grow our business or sustain profitability.

A key element of our strategy is to develop and commercialize a portfolio of new product candidates in addition to tedizolid phosphate. As a significant part of this strategy, we intend to develop and commercialize additional products and product candidates through our proprietary drug discovery platform. The success of this strategy depends upon our ability to leverage this platform to identify optimal bacterial targets and subsequently design small molecule inhibitors against these targets leading to the development of differentiated new antibiotics.

We cannot be certain that we will be successful in our efforts to identify and develop additional differentiated new antibiotics or that any of our product candidates we do identify will produce commercially viable drugs that safely and effectively treat infectious diseases or other diseases. To date, our proprietary discovery platform has yielded certain candidates that are advancing into IND enabling studies. While these candidates hold significant promise in treating serious infections, they might fail to advance to clinical development or might fail in clinical trials to show the desirable pharmacokinetics, safety and efficacy needed to advance to a product. In addition, research and discovery programs to identify new disease targets and product candidates require substantial technical, financial and human resources whether or not we ultimately identify any candidates. To date, our discovery programs have been largely funded by United States government grants and research contracts. If we are unable to maintain existing funding or secure additional funding for these programs and/or continue to devote the other technical and human resources to them, our ability to continue these programs will be adversely affected.

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Any product candidate we do successfully identify may require substantial additional development efforts prior to commercial sale, including preclinical studies, extensive clinical testing and approval by the FDA and applicable foreign regulatory authorities. All product candidates are susceptible to the risks of failure that are inherent in pharmaceutical product development, including the possibility that the product candidate will not be shown to be sufficiently safe and/or effective for approval by regulatory authorities. In addition, we cannot assure you that any such products that are approved will be manufactured or produced economically, successfully commercialized, widely accepted in the marketplace or more effective than other commercially available alternatives.

If we are unable to develop suitable potential product candidates through internal research and discovery programs or otherwise by obtaining rights to novel therapeutics from third parties, our business and prospects will suffer.

A variety of risks associated with our international business relationships could materially adversely affect our business.

We have entered into a collaboration and license agreement with Bayer in the Bayer Licensed Territory and may enter into other agreements with third parties who will market tedizolid phosphate elsewhere. Consequently, we expect that we will be subject to additional risks related to entering into international business relationships, including:

• Differing regulatory requirements for drug approvals in foreign countries;

• Potentially reduced protection for intellectual property rights;

• The potential for so-called parallel importing, which is what happens when a local seller, faced with high or higher local prices, opts to import goods from a foreign market (with low or lower prices) rather than buying them locally;

• Unexpected changes in tariffs, trade barriers and regulatory requirements;

• Economic weakness, including inflation, or political instability in particular foreign economies and markets;

• Compliance with tax, employment, immigration and labor laws for employees living or traveling abroad;

• Foreign taxes, including withholding of payroll taxes;

• Foreign currency fluctuations, which could result in increased operating expenses and reduced revenues, and other obligations incident to doing business in another country;

• Workforce uncertainty in countries where labor unrest is more common than in the United States;

• Production shortages resulting from any events affecting raw material supply or manufacturing capabilities abroad; and

• Business interruptions resulting from geo-political actions, including war and terrorism, or natural disasters including earthquakes, typhoons, floods and fires.

These and other risks may materially adversely affect our ability to attain or sustain profitable operations.

Risks Related to Our Industry

We are subject to extensive and costly government regulation.

Antibiotics, including those we are developing and plan to develop in the future, are subject to extensive and rigorous domestic government regulation including regulation by the FDA, the Centers for Medicare and Medicaid Services, other divisions of the United States Department of Health and Human Services, the United States Department of Justice, state and local governments and their respective foreign equivalents. The FDA regulates the research, development, preclinical and clinical testing, manufacture, safety, effectiveness, record-keeping, reporting, labeling, storage, approval, advertising, promotion, sale, distribution, import and export of biopharmaceutical products. If any products we or our partners develop are tested or marketed abroad, they will also be subject to extensive regulation by foreign governments, whether or not we have obtained FDA approval for a given product and its uses. Such foreign regulation may be equally or more demanding than corresponding United States regulation.

Government regulation substantially increases the cost and risk of researching, developing, manufacturing and selling the products that we are developing.

New and future legislation, and/or regulations and policies adopted by the FDA or other regulatory health authorities, in addition to findings in ongoing and future clinical and nonclinical studies, may increase the time and cost required for us to conduct and complete clinical trials for tedizolid phosphate or other product candidates that we develop.*

The FDA revised its existing guidance for industry entitled, “Uncomplicated and Complicated Skin and Skin Structure Infections—Developing Antimicrobial Drugs for Treatment” (Final July 1998) and issued “Guidance for Industry Acute Bacterial Skin and Skin Structure Infections: Developing Drugs for Treatment (Draft August 2010). It is not known when the FDA will issue its final guidance on ABSSSI. In addition in March 2010, the FDA released draft guidance entitled “Guidance for Industry Non-Inferiority Clinical Trials.” This guidance document is relevant to our Phase 3 clinical program because our Phase 3 clinical trials use a non-inferiority trial design. It is not known when the FDA will issue a final guidance document or whether the final guidance will differ significantly from the draft guidance. In January 2012, the EMA issued its finalized revision to the “Guideline on the Evaluation of Medicinal Products Indicated for the Treatment of Bacterial Infections.” In July 2012, the EMA issued a draft addendum to the Note for Guidance on Evaluation of New Anti-bacterial Medicinal Products that addresses indication specific guidance. The timing for the issuance of the EMA finalized addendum, as well as its contents, is

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not known. In November 2010, the FDA issued draft guidance entitled “Guidance for Industry Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated Bacterial Pneumonia: Developing Drugs for Treatment.” It is not known when the FDA will issue final HABP guidance.

Along with the information in the draft guidance for ABSSSI, we have received input from the FDA regarding specific changes that are being contemplated. Based on this input, we know that the enrollment criteria for patients in our Phase 3 clinical trials for treatment of ABSSSI was different than those that were applicable under the July 1998 guidance regarding cSSSI. As a result, we needed to enroll patients with a different proportion of infection types than we enrolled in our completed Phase 2 clinical trial for the treatment of cSSSI. In addition, the draft guidance recommends a change in the time at which the clinical cure is tested relative to the end of antibiotic therapy. As part of the SPA procedure, we reached agreement with the FDA on the appropriate endpoints.

While we have received information from the FDA regarding certain aspects that have been incorporated into the draft guidance, we will not know the potential impact that any finalized guidance, should it be issued, may have on the design and conduct of our planned Phase 3 clinical trials and supportive studies or on the FDA’s approval of ABSSSI or any other indication for which we are seeking or may seek approval, which could potentially significantly increase the time and cost required for us to conduct and complete these trials if size and scope were to be modified. Additionally, changes in regulatory requirements due to the adoption by the FDA and/or any foreign health authorities of new legislation, regulation, or policies may require us to amend clinical trial protocols or add new clinical trials to comply with these changes. Such amendments to existing protocols and/or clinical trial applications or the need for new ones, may impact the cost, timing and completion of the clinical trials.

Even if we obtain regulatory approval for tedizolid phosphate or any of our future product candidates, we will still face extensive regulatory requirements and our products may face future development and regulatory difficulties.*

Even if regulatory approval in the United States is obtained, the FDA may still impose significant restrictions on a product’s indicated uses or marketing or impose ongoing requirements for potentially costly post-approval studies or post-market surveillance. For example, the labeling ultimately approved for tedizolid phosphate, if any, may include restrictions on use. Tedizolid phosphate or any of our other product candidates will also be subject to ongoing FDA requirements governing the labeling, packaging, storage, distribution, safety surveillance, advertising, promotion, record-keeping and reporting of safety and other post-market information. The holder of an approved NDA is subject to obligations to monitor and report AEs and instances of the failure of a product to meet the specifications in the NDA. Application holders must submit new or supplemental applications and obtain FDA approval for certain changes to the approved product, product labeling or manufacturing process. Application holders must also submit advertising and other promotional material to the FDA and report on ongoing clinical trials. New legal requirements have also been enacted to require disclosure of clinical trial results on publicly available databases.

In addition, manufacturers of drug products and their facilities are subject to continual review and periodic inspections by the FDA and other regulatory authorities for compliance with current good manufacturing practices regulations. If we or a regulatory agency discovers problems with the facility where the product is manufactured, a regulatory agency may impose restrictions on that product, the manufacturing facility or us, including requiring recall or withdrawal of the product from the market or suspension of manufacturing. The FDA and other regulatory authorities may also revisit the risk-benefit profile of an approved product if, for example, previously unknown problems with a product, such as AEs of unanticipated severity or frequency arise. In such circumstances, the FDA or other regulatory authorities may withdraw approval, require new warnings or other labeling changes to limit use of the drug, impose new study or monitoring requirements or require that we establish a REMS. Advertising and promotional materials must comply with FDA rules in addition to other potentially applicable federal and state laws. Our relationships with healthcare providers will be subject to federal and state requirements prohibiting or requiring the disclosure of payments or items of value given to potential prescribers of our products. For example, as part of PPACA, pharmaceutical manufacturers must report certain gifts and payments to physicians beginning in 2014. These reports will then be placed on a public database. Failure to so report could subject companies to significant financial penalties.

The distribution of product samples to physicians must comply with the requirements of the Prescription Drug Marketing Act. Sales, marketing and scientific/educational grant programs must comply with the anti-fraud and abuse provisions of the Social Security Act, the False Claims Act and similar state laws, each as amended. Pricing and rebate programs must comply with the Medicaid rebate requirements of the Omnibus Budget Reconciliation Act of 1990 and the Veteran’s Health Care Act of 1992, each as amended. If products are made available to authorized users of the Federal Supply Schedule of the General Services Administration, additional laws and requirements apply. All of these activities are also potentially subject to federal and state consumer protection and unfair competition laws. If we or Bayer fail to comply with applicable regulatory requirements, a regulatory agency may:

• Issue warning letters or untitled letters asserting that we are in violation of the law;

• Seek an injunction or impose civil or criminal penalties or monetary fines;

• Suspend or withdraw regulatory approval;

• Suspend any ongoing clinical trials;

• Refuse to approve pending applications or supplements to applications filed by us;

• Suspend or impose restrictions on operations, including costly new manufacturing requirements or exclusions from doing business with federal or state programs;

• Seize or detain products, refuse to permit the import or export of products, or require us to initiate a product recall; or

• Refuse to allow us to enter into supply contracts, including government contracts.

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Any government investigation of alleged violations of law could require us to expend significant time and resources in response, and could generate negative publicity.

The occurrence of any event or penalty described above may inhibit our ability to commercialize our products and generate revenues.

If we fail to comply with federal and state healthcare laws, including fraud and abuse and health information privacy and security laws, we could face substantial penalties and our business, results of operations, financial condition and prospects could be adversely affected.

As a pharmaceutical company, even though we do not and will not control referrals of healthcare services or bill directly to Medicare, Medicaid or other third-party payers, certain federal and state healthcare laws and regulations pertaining to fraud and abuse and patients’ rights are and will be applicable to our business. We could be subject to healthcare fraud and abuse and patient privacy regulation by both the federal government and the states in which we conduct our business. The laws that may affect our ability to operate include:

• the federal Anti-Kickback Statute, which constrains our marketing practices, educational programs, pricing policies, and relationships with healthcare providers or other entities, by prohibiting, among other things, soliciting, receiving, offering or paying remuneration, directly or indirectly, to induce, or in return for, either the referral of an individual or the purchase or recommendation of an item or service reimbursable under a federal healthcare program, such as the Medicare and Medicaid programs;

• federal civil and criminal false claims laws and civil monetary penalty laws, which prohibit, among other things, individuals or entities from knowingly presenting, or causing to be presented, claims for payment from Medicare, Medicaid, or other third-party payers that are false or fraudulent;

• the federal Health Insurance Portability and Accountability Act of 1996, or HIPAA, which created new federal criminal statutes that prohibit executing a scheme to defraud any healthcare benefit program or making false statements relating to healthcare matters;

• HIPAA, as amended by the Health Information Technology for Economic and Clinical Health Act of 2009 and its implementing regulations, which imposes certain requirements relating to the privacy, security and transmission of individually identifiable health information; and

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

Because of the breadth of these laws and the narrowness of available statutory and regulatory exceptions, it is possible that some of our business activities could be subject to challenge under one or more of such laws. To the extent that any of our product candidates is ultimately sold in a foreign country, we may be subject to similar foreign laws and regulations. If we or our operations are found to be in violation of any of the laws described above or any other governmental regulations that apply to us, we may be subject to penalties, including civil and criminal penalties, damages, fines, imprisonment, exclusion of products from reimbursement under U.S. federal or state healthcare programs, and the curtailment or restructuring of our operations. Any penalties, damages, fines, curtailment or restructuring of our operations could materially adversely affect our ability to operate our business and our financial results. Although compliance programs can mitigate the risk of investigation and prosecution for violations of these laws, the risks cannot be entirely eliminated. Any action against us for violation of these laws, even if we successfully defend against it, could cause us to incur significant legal expenses and divert our management’s attention from the operation of our business. Moreover, achieving and sustaining compliance with applicable federal and state privacy, security and fraud laws may prove costly.

Product liability lawsuits could divert our resources, result in substantial liabilities and reduce the commercial potential of our products.

The risk that we may be sued on product liability claims is inherent in the development of pharmaceutical products. Our products and the clinical trials using our product candidates may expose us to product liability claims and possible adverse publicity. These lawsuits may divert our management from pursuing our business strategy and may be costly to defend. In addition, if we are held liable in any of these lawsuits, we may incur substantial liabilities and may be forced to limit or forgo further development and commercialization of those products.

Although we maintain general liability and product liability insurance with limits of $2 million and $10 million, respectively, this insurance may not fully cover potential liabilities. The cost of any product liability litigation or other proceeding, even if resolved in our favor, could be substantial. In addition, inability to obtain or maintain sufficient insurance coverage at an acceptable cost or to otherwise protect against potential product liability claims could prevent or inhibit the development and commercial production and sale of our products, which could adversely affect our business, operating results and financial condition.

If we use hazardous and biological materials in a manner that causes injury or violates applicable law, we may be liable for damages.

Our research and development activities involve the controlled use of potentially hazardous substances, including chemical, biological and radioactive materials and viruses. In addition, our operations produce hazardous waste products. Federal, state and local laws and regulations in the United States govern the use, manufacture, storage, handling and disposal of hazardous materials. Although we believe that our procedures for use, handling, storing and disposing of these materials comply with legally prescribed standards, we may incur significant additional costs to comply with applicable laws in the future. We also cannot predict the impact on our business of new or

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amended environmental laws or regulations, or any changes in the way existing and future laws and regulations are interpreted or enforced. Also, even if we are in compliance with applicable laws, we cannot completely eliminate the risk of contamination or injury resulting from hazardous materials and we may incur liability as a result of any such contamination or injury. In the event of an accident, we could be held liable for damages or penalized with fines, and the liability could exceed our resources. If we fail to comply with applicable requirements, we could incur substantial costs, including civil or criminal fines and penalties, clean-up costs, or capital expenditures for control equipment or operational changes necessary to achieve or maintain compliance. Compliance with applicable environmental laws and regulations is expensive, and current or future environmental regulations may impair our research, development and production efforts, which could harm our business, operating results and financial condition.

Risks Related to our Intellectual Property

Our ability to pursue the development and commercialization of tedizolid phosphate depends upon the continuation of our license from Dong-A.

Our license agreement with Dong-A provides us with a worldwide exclusive license to develop and sell tedizolid phosphate outside of Korea. If we are unable to make the required milestone and royalty payments under the license agreement, if we do not continue to use commercially reasonable efforts to achieve certain development and commercialization milestones for tedizolid phosphate within the timeframes required by the license agreement or if we otherwise materially breach the license agreement, our rights to develop and commercialize tedizolid phosphate would terminate and revert to Dong-A. In addition, either we or Dong-A may terminate the license agreement upon an uncured material breach of the license agreement for 90 days. If our license agreement with Dong-A were terminated, we would lose our rights to develop and commercialize tedizolid phosphate, which would materially and adversely affect our business, results of operations and future prospects.

If our efforts to protect the proprietary nature of the intellectual property related to tedizolid phosphate and our other product candidates are not adequate, we may not be able to compete effectively in our market.*

We rely upon a combination of patents, trade secret protection and confidentiality agreements to protect the intellectual property related to tedizolid phosphate and our other product candidates. Any involuntary disclosure to or misappropriation by third parties of our confidential proprietary information could enable competitors to quickly duplicate or surpass our technological achievements, thus eroding our competitive position in our market.

The strength of patents in the biotechnology and pharmaceutical field involves complex legal and scientific questions and can be uncertain and our commercial success will depend on our ability to obtain patents and maintain adequate protection for tedizolid phosphate and other product candidates in the United States and other countries. Through our license agreement with Dong-A, we currently license issued United States utility patents, a pending United States utility patent application and issued and pending foreign national and regional counterpart patent applications covering various aspects of tedizolid and tedizolid phosphate. In addition, we own pending and issued United States utility patent applications and pending foreign national and regional counterpart patent applications directed to aspects of tedizolid phosphate discovered by our scientists. The patent applications that we licensed or have filed on our own may fail to result in issued patents in the United States or in foreign countries. Even if the patents do successfully issue, third parties may challenge the patents. Further, the future patents to which we have rights based on our agreement with Dong-A, or that we file on our own, may be too narrow to prevent third parties from developing or designing around these patents. If the sufficiency of the breadth or strength of protection provided by the patent applications we licensed or own with respect to tedizolid phosphate or the patents we pursue related to any of our other product candidates is threatened, it could dissuade companies from collaborating with us to develop, and threaten our ability to commercialize, tedizolid phosphate and our other product candidates. Further, if we encounter delays in our clinical trials, the period of time during which we could market our drug candidates under patent protection would be reduced. In addition, we do not know whether:

• We or Dong-A were the first to make the inventions covered by each of our pending or issued patent applications or our licensed pending or issued patent applications;

• We or Dong-A were the first to file patent applications for these inventions;

• Others will independently develop similar or alternative technologies or duplicate any of our technologies;

• Any of our or Dong-A’s pending patent applications will result in issued patents;

• Any of our or Dong-A’s patents, once issued, will be valid or enforceable;

• Any patents issued to us or Dong-A will provide us with any competitive advantages, or will be challenged by third parties;

• We will develop additional proprietary technologies that are patentable;

• The patents of others will have an adverse effect on our business; or

• Our unissued patents in the Bayer Licensed Territory will ever issue, and if they do not issue, this could adversely affect our collaboration and license agreement with Bayer.

In addition to the protection afforded by patents, we rely on trade secret protection and confidentiality agreements to protect proprietary know-how that is not patentable, for processes for which patents are difficult to enforce and for any other elements of our drug discovery program that involve proprietary know-how, information and technology that is not covered by patents. Although we require all of our employees, consultants, advisors and third parties who have access to our proprietary know-how, information and technology to enter into confidentiality agreements, we cannot be certain that this know-how, information and technology will not be disclosed or that competitors will not otherwise gain access to our trade secrets or independently develop substantially equivalent information and techniques.

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Our and Dong-A’s ability to obtain patents is highly uncertain because, to date, some legal principles remain unresolved, there has not been a consistent policy regarding the breadth or interpretation of claims allowed in patents in the United States and the specific content of patents and patent applications that are necessary to support and interpret patent claims is highly uncertain due to the complex nature of the relevant legal, scientific and factual issues. Changes in either patent laws or interpretations of patent laws in the United States and other countries may diminish the value of our intellectual property or narrow the scope of our patent protection. For example, on September 16, 2011, the Leahy-Smith America Invents Act, or the Leahy-Smith Act, was signed into law. The Leahy-Smith Act includes a number of significant changes to United States patent law. These include provisions that affect the way patent applications will be prosecuted and may also affect patent litigation. The United States Patent and Trademark Office, or USPTO, has developed new and untested regulations and procedures to govern the full implementation of the Leahy-Smith Act, and many of the substantive changes to patent law associated with the Leahy-Smith Act, and in particular, the first to file provisions, became effective in March 2013. The Leahy-Smith Act has also introduced procedures making it easier for third-parties to challenge issued patents, as well as to intervene in the prosecution of patent applications. Finally, the Leahy-Smith Act contains new statutory provisions that still require the USPTO to issue new regulations for their implementation and it may take the courts years to interpret the provisions of the new statute. Accordingly, it is too early to tell what, if any, impact the Leahy-Smith Act will have on the operation of our business and the protection and enforcement of our intellectual property. However, the Leahy-Smith Act and its implementation could increase the uncertainties and costs surrounding the prosecution of our patent applications and the enforcement or defense of our issued patents. An inability to obtain, enforce and defend patents covering our proprietary technologies would materially and adversely affect our business prospects and financial condition.

Further, the laws of some foreign countries do not protect proprietary rights to the same extent as the laws of the United States. As a result, we may encounter significant problems in protecting and defending our intellectual property both in the United States and abroad. For example, if the issuance to us or Dong-A, in a given country, of a patent covering an invention is not followed by the issuance, in other countries, of patents covering the same invention, or if any judicial interpretation of the validity, enforceability, or scope of the claims in, or the written description or enablement in, a patent issued in one country is not similar to the interpretation given to the corresponding patent issued in another country, our ability to protect our intellectual property in those countries may be limited. Changes in either patent laws or in interpretations of patent laws in the United States and other countries may materially diminish the value of our intellectual property or narrow the scope of our patent protection. If we are unable to prevent material disclosure of the intellectual property related to our technologies to third parties, we will not be able to establish or, if established, maintain a competitive advantage in our market, which could materially adversely affect our business, operating results and financial condition.

Obtaining and maintaining our patent protection depends on compliance with various procedural, document submission, fee payment and other requirements imposed by governmental patent agencies, and our patent protection could be reduced or eliminated for non-compliance with these requirements.

Periodic maintenance fees, renewal fees, annuity fees and various other governmental fees on patents and/or applications will be due to be paid to the USPTO and various foreign governmental patent agencies in several stages over the lifetime of the patents and/or applications. We have systems in place to remind us to pay these fees, and we employ an outside firm, Computer Patent Annuities, to pay these fees due to foreign patent agencies. The USPTO and various foreign governmental patent agencies require compliance with a number of procedural, documentary, fee payment and other similar provisions during the patent application process. We employ reputable law firms and other professionals to help us comply, and in many cases, an inadvertent lapse can be cured by payment of a late fee or by other means in accordance with the applicable rules. However, there are situations in which noncompliance can result in abandonment or lapse of the patent or patent application, resulting in partial or complete loss of patent rights in the relevant jurisdiction. In such an event, our competitors might be able to enter the market and this circumstance would have a material adverse effect on our business.

We have not yet registered our trademarks in all of our potential markets, and failure to secure those registrations could adversely affect our business.*

The TRIUS THERAPEUTICS mark has been registered in the United States, Canada, Australia, European Community, India, Japan, China, New Zealand and Singapore for use in connection with pharmaceutical research and development services and for anti-infective and antibacterial pharmaceutical preparations for the treatment of infections. We are not aware of any third party opposition or cancellation proceedings against the TRIUS THERAPEUTICS mark. We cannot be sure that our pending trademark applications will ultimately mature into registrations.

Third-party claims of intellectual property infringement may prevent or delay our drug discovery and development efforts.

Our commercial success depends in part on our avoiding infringement of the patents and proprietary rights of third parties. Third parties may assert that we are employing their proprietary technology without authorization. There may be third-party patents with claims to materials, methods of manufacture or methods for treatment related to the use or manufacture of tedizolid phosphate and/or our other product candidates. Our commercial success depends in part on our avoiding infringement of the patents and proprietary rights of third parties. If any third-party patents were held by a court of competent jurisdiction to cover the tedizolid phosphate manufacturing process, any molecules formed during the tedizolid phosphate manufacturing process or the final tedizolid phosphate product for any use thereof, the holders of any such patents may be able to block our ability to commercialize tedizolid phosphate unless we obtained a license under the applicable patent or patents, or until such patents expire. We cannot predict whether we would be able to obtain a license on commercially reasonable terms, if at all. Any inability to obtain such a license under the applicable patents on commercially reasonable terms, or at all, may have a material adverse effect on our ability to commercialize tedizolid phosphate until such patents expire.

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In addition, third parties may obtain patents in the future and claim that use of our technologies infringes upon these patents. Furthermore, parties making claims against us may obtain injunctive or other equitable relief, which could effectively block our ability to further develop and commercialize one or more of our product candidates. Defense of these claims, regardless of their merit, would involve substantial litigation expense and would be a substantial diversion of employee resources from our business. In the event of a successful claim of infringement against us, we may have to pay substantial damages, obtain one or more licenses from third parties or pay royalties. In addition, even in the absence of litigation, we may need to obtain licenses from third parties to advance our research or allow commercialization of tedizolid phosphate or any of our other product candidates. We may fail to obtain any of these licenses at a reasonable cost or on reasonable terms, if at all. In that event, we would not be able to further develop and commercialize such product candidates, which could harm our business significantly.

We may be required to file lawsuits or take other actions to protect or enforce our patents or the patents of our licensors, which could be expensive and time consuming.

Competitors may infringe our patents or the patents of our licensors. To counter infringement or unauthorized use, we may be required to file infringement claims, which can be expensive and time-consuming. In addition, in an infringement proceeding, a court may decide that a patent of ours or our licensors is not valid or is unenforceable, or may refuse to stop the other party from using the technology at issue on the grounds that our patents, or those of Dong-A, do not cover the technology in question. An adverse result in any litigation or defense proceedings could put one or more of our patents, or those of Dong-A, at risk of being invalidated, held unenforceable or interpreted narrowly and could put our patent applications, or those of Dong-A, at risk of not issuing.

Interference proceedings brought by the USPTO may be necessary to determine the priority of inventions with respect to our patent applications or those of our collaborators or licensors. Litigation or interference proceedings may fail and, even if successful, may result in substantial costs and distract our management. We may not be able to prevent, alone or with our licensors, misappropriation of our proprietary rights, particularly in countries where the laws may not protect those rights as fully as in the United States.

Issued patents may be challenged during reexamination proceedings brought by a third party or the USPTO, or in foreign countries, during post-grant opposition proceedings or invalidation appeal proceedings. These proceedings may result in loss of patent claims, adverse changes to the scope of the claims and may result in substantial costs and distract our management.

Furthermore, because of the substantial amount of discovery required in connection with intellectual property litigation, there is a risk that some of our confidential information could be compromised by disclosure during this type of litigation. In addition, if securities analysts or investors perceive public announcements of the results of hearings, motions or other interim proceedings or developments to be negative, the price of our common stock could drop.

We may be subject to claims that our employees have wrongfully used or disclosed alleged trade secrets of their former employers.

As is common in the biotechnology and pharmaceutical industries, we employ individuals who were previously employed at other biotechnology or pharmaceutical companies, including our competitors or potential competitors. We may be subject to claims that these employees, or we, have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. Even if we are successful in defending against these claims, litigation could result in substantial costs and be a distraction to management.

Risks Related to Our United States Government Contracts and Grants

If we do not receive all of the funds under our sponsored research contracts or are unable to generate additional revenues from additional contracts, we may be forced to suspend or terminate one or more of our preclinical programs.*

Substantially all of our contract research revenues that have supported our preclinical programs have been derived from United States government grants and our government contracts. There can be no assurances that our contracts will continue or that we will be able to enter into new contracts with the United States government to support our preclinical programs. The process of obtaining government contracts is lengthy and uncertain and we will have to compete with other companies and institutions for each contract. Further, changes in government budgets and agendas may result in a decreased and de-prioritized emphasis on supporting the discovery and development of biodefense products in our preclinical programs. In such event, the sponsors of our research programs may not be required to continue funding our existing contracts. In February 2013, we were notified by NIAID that they would not be extending funding under the contract beyond March 31, 2013 and that we will not be eligible to drawdown against the remaining amounts available under the contract. In the near term, we will continue to fund our Gyrase-B program.

Due to the decline of federal tax receipts and substantial increase in the federal deficit, the United States government may be forced or choose to reduce or delay spending in the biodefense field, which could decrease the likelihood of our receipt of future government contract revenues.

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United States government agencies have special contracting requirements that give them the ability to unilaterally control our contracts.*

United States government contracts typically contain unfavorable termination provisions and are subject to audit and modification by the government at its sole discretion, which will subject us to additional risks. These risks include the ability of the United States government to unilaterally:

• Audit and object to our NIAID, DTRA or Lawrence Livermore National Laboratory, or LLNL, contract-related costs and fees, and require us to reimburse all such costs and fees;

• Suspend or prevent us for a set period of time from receiving new contracts or extending our existing contracts based on violations or suspected violations of laws or regulations;

• Cancel, terminate or suspend our contracts based on violations or suspected violations of laws or regulations;

• Terminate our contracts if in the government’s best interest, including if funds become unavailable to the applicable governmental agency;

• Reduce the scope and value of our contracts; and

• Change certain terms and conditions in our contracts.

The United States government will be able to terminate each of its contracts with us, either for its best interests or if we default by failing to perform in accordance with or to achieve the milestones set forth in the contract schedules and terms. Termination-for-convenience provisions generally enable us to recover only our costs incurred or committed and settlement expenses on the work completed prior to termination. In February 2013, we were notified by NIAID that they would not be extending funding under the contract beyond March 31, 2013 and that we will not be eligible to drawdown against the remaining amounts available under the contract after that date. Except for the amount of services received by the government, termination-for-default provisions do not permit these recoveries and would make us liable for excess costs incurred by the United States government in procuring undelivered items from another source.

The United States government’s determination to award any contracts may be challenged by an interested party, such as another bidder, at the United States Government Accountability Office, or the GAO, or in federal court. If such a challenge is successful, our LLNL contract or any future contract we may be awarded may be terminated.*

The laws and regulations governing the procurement of goods and services by the United States government provide procedures by which other bidders and interested parties may challenge the award of a government contract. If we are awarded a government contract, such challenges or protests could be filed even if there are not any valid legal grounds on which to base the protest. If any such protests are filed, the government agency may decide to suspend our performance under the contract while such protests are being considered by the GAO or the applicable federal court, thus potentially delaying delivery of payment. In addition, we could be forced to expend considerable funds to defend any potential award. If a protest is successful, the government may be ordered to terminate any one or more of our contracts and reselect bids. The government agencies with which we have contracts could even be directed to award a potential contract to one of the other bidders.

Our business is subject to audit by the United States government, including under our contracts with NIAID, DTRA and LLNL, and a negative audit could adversely affect our business.

United States government agencies such as the Department of Health and Human Services, or DHHS, the Defense Contract Audit Agency, or the DCAA, routinely audit and investigate government contractors and recipients of Federal grants. These agencies review a contractor’s performance under its contracts, cost structure and compliance with applicable laws, regulations and standards.

The DHHS and the DCAA also review the adequacy of, and a contractor’s compliance with, its internal control systems and policies, including the contractor’s purchasing, property, estimating, compensation and management information systems. Any costs found to be improperly allocated to a specific contract will not be reimbursed, while such costs already reimbursed must be refunded. If an audit uncovers improper or illegal activities, we may be subject to civil and criminal penalties and administrative sanctions, including:

• Termination of contracts;

• Forfeiture of profits;

• Suspension of payments;

• Fines; and

• Suspension or prohibition from conducting business with the United States government.

In addition, we could suffer serious reputational harm if allegations of impropriety were made against us, which could cause our stock price to decrease.

Laws and regulations affecting government contracts make it more costly and difficult for us to successfully conduct our business.

We must comply with numerous laws and regulations relating to the formation, administration and performance of government contracts, which can make it more difficult for us to retain our rights under our government contracts. These laws and regulations affect how we conduct business with government agencies. Among the most significant government contracting regulations that affect our business are:

• The Federal Acquisition Regulations, or FAR, and agency-specific regulations supplemental to the FAR, which comprehensively regulate the procurement, formation, administration and performance of government contracts;

• The business ethics and public integrity obligations, which govern conflicts of interest and the hiring of former government employees, restrict the granting of gratuities and funding of lobbying activities and incorporate other requirements such as the Anti-Kickback Act and Foreign Corrupt Practices Act;

• Export and import control laws and regulations; and

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• Laws, regulations and executive orders restricting the use and dissemination of information classified for national security purposes and the exportation of certain products and technical data.

Foreign governments typically also have laws and regulations governing contracts with their respective agencies. These foreign laws and regulations affect how we and our customers conduct business and, in some instances, impose added costs on our business. Any changes in applicable laws and regulations could restrict our ability to maintain our existing government contracts and obtain new contracts, which could limit our ability to conduct our business and materially adversely affect our revenues and results of operations.

Agreements with government agencies may lead to claims against us under the Federal False Claims Act, and these claims could result in substantial fines and other penalties.

The biopharmaceutical industry is, and in recent years has been, under heightened scrutiny as the subject of government investigations and enforcement actions. Our government contracts are subject to substantial financial penalties under the Federal Civil Monetary Penalties Act and the Federal Civil False Claims Act. Under the False Claims Act’s “whistleblower” provisions, private enforcement of fraud claims against businesses on behalf of the United States government has increased due in part to amendments to the False Claims Act that encourage private individuals to sue on behalf of the government. These whistleblower suits, known as qui tam actions, may be filed by private individuals, including present and former employees. The False Claims Act statute provides for treble damages and civil penalties between $5,500 and $11,000 for each separate false claim. If our operations are found to be in violation of any of these laws, or any other governmental regulations that apply to us, we may be subject to penalties, including civil and criminal penalties, damages, fines, exclusion of our products from the Medicare and Medicaid programs, and the curtailment or restructuring of our operations. Any penalties, damages, fines, exclusions, curtailment, or restructuring of our operations could adversely affect our ability to operate our business and our financial results.

Risks Related to Ownership of Our Common Stock

The market price of our common stock may be highly volatile, and you may not be able to resell your shares at or above your purchase price.*

We cannot assure you that an active trading market for our common stock will develop or persist, and, as of August 1, 2013 our executive officers, directors, 5% shareholders and their affiliates own approximately 28% of our common stock, which may further reduce trading activity in our common stock. You may not be able to sell your shares quickly or at the market price if trading in our common stock is not active.

The trading price of our common stock is likely to be volatile. Our stock price could be subject to wide fluctuations in response to a variety of factors, including the following:

• Risks related to our pending Offer and Merger;

• Adverse results or delays in clinical trials;

• Any delay in filing our NDA for tedizolid phosphate and any adverse development or perceived adverse development with respect to the FDA’s review of the NDA, including without limitation the FDA’s issuance of a “refusal to file” letter or a request for additional information;

• Failure to successfully commercialize tedizolid phosphate, develop additional product candidates and commercialize additional product candidates;

• Changes in laws or regulations applicable to our products, including but not limited to clinical trial requirements for approvals;

• Unanticipated serious safety concerns related to the use of tedizolid phosphate or any of our other product candidates;

• A decision to initiate a clinical trial, not to initiate a clinical trial or to terminate an existing clinical trial;

• Inability to obtain adequate product supply for tedizolid phosphate or any other approved drug product, or the inability to do so at acceptable prices;

• Adverse regulatory decisions;

• Introduction of new products, services or technologies offered by us or our competitors;

• Failure to meet or exceed revenue and financial projections we provide to the public;

• Actual or anticipated variations in quarterly operating results;

• Failure to meet or exceed the estimates and projections of the investment community;

• The perception of the pharmaceutical industry by the public, legislatures, regulators and the investment community;

• General market conditions and overall fluctuations in United States equity markets;

• Developments concerning our sources of manufacturing supply and our future international commercialization partners;

• Announcements of significant acquisitions, strategic partnerships, joint ventures or capital commitments by us or our competitors;

• Disputes or other developments relating to proprietary rights, including patents, litigation matters and our ability to obtain patent protection for our technologies;

• Additions or departures of key scientific or management personnel;

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• Issuances of debt or equity securities;

• Significant lawsuits, including patent or stockholder litigation;

• Changes in the market valuations of similar companies;

• Sales of our common stock by us or our stockholders in the future;

• Trading volume of our common stock; and

• Other events or factors, many of which are beyond our control.

In addition, the stock market in general, and the Nasdaq Global Market and biotechnology companies in particular, have experienced extreme price and volume fluctuations that have often been unrelated or disproportionate to the operating performance of these companies. Broad market and industry factors may negatively affect the market price of our common stock, regardless of our actual operating performance.

Our principal stockholders and management own a significant percentage of our stock and will be able to exert significant influence over matters subject to stockholder approval.*

As of August 1, 2013, our executive officers, directors, 5% stockholders and their affiliates own approximately 28% of our outstanding voting stock. Therefore, these stockholders may have the ability to influence us through this ownership position. For example, these stockholders may be able to significantly influence elections of directors, amendments of our organizational documents, or approval of any merger, sale of assets, or other major corporate transaction. This may prevent or discourage unsolicited acquisition proposals or offers for our common stock that you may feel are in your best interest as one of our stockholders.

Sales of a substantial number of shares of our common stock in the public market by our existing stockholders could cause our stock price to fall.

Sales of a substantial number of shares of our common stock in the public market or the perception that these sales might occur, could depress the market price of our common stock and could impair our ability to raise capital through the sale of additional equity securities. We are unable to predict the effect that sales may have on the prevailing market price of our common stock.

Certain holders of shares of our common stock are entitled to rights with respect to the registration of their shares under the Securities Act. Registration of these shares under the Securities Act would result in the shares becoming freely tradable without restriction under the Securities Act, except for shares held by our affiliates as defined in Rule 144 under the Securities Act. Any sales of securities by these stockholders could have a material adverse effect on the trading price of our common stock.

Future sales and issuances of our common stock or rights to purchase common stock, including pursuant to our equity incentive plans, could result in additional dilution of the percentage ownership of our stockholders and could cause our stock price to fall.*

We expect that significant additional capital will be needed in the future to continue our planned operations. To the extent we raise additional capital by issuing equity securities, our stockholders may experience substantial dilution. We may sell common stock, convertible securities or other equity securities in one or more transactions at prices and in a manner we determine from time to time. If we sell common stock, convertible securities or other equity securities in more than one transaction, investors may be materially diluted by subsequent sales. Such sales may also result in material dilution to our existing stockholders, and new investors could gain rights superior to our existing stockholders.

Pursuant to our 2010 Equity Incentive Plan, or the 2010 Plan, and our 2010 Non-Employee Directors’ Stock Option Plan, or the 2010 Directors’ Plan, our management is authorized to grant stock options to our employees, directors and consultants. Our board of directors approved an amendment to the 2010 Plan, which was subsequently approved by stockholders at our 2013 annual meeting of stockholders, to eliminate automatic annual increases to the number of shares available for future grant under the 2010 Plan. However, in connection with that amendment, the total number of shares available for future grant under the 2010 Plan was increased by 5,100,000 shares. The number of shares available for future grant under our 2010 Directors’ Plan will automatically increase each year by an amount equal to the lesser of the aggregate number of shares of common stock subject to options granted during the immediately preceding calendar year or 150,000 shares, subject to the ability of our board of directors to take action to reduce the size of such increase in any given year. Our board of directors approved an amendment to the 2010 Directors’ Plan, which was subsequently approved by stockholders at our 2013 annual meeting of stockholders, to eliminate such automatic annual increases under the 2010 Directors’ Plan immediately following the increase in shares that takes effect on January 1, 2015.

Pursuant to our 2010 Employee Stock Purchase Plan, or the 2010 Purchase Plan, rights to purchase common stock are granted to our employees. The number of shares reserved for issuance under our 2010 Purchase Plan will automatically increase each year by an amount equal to the least of 1% of the total number of shares of our common stock outstanding on December 31 of the preceding calendar year or 250,000 shares, subject to the ability of our board of directors to take action to reduce the size of such increase in any given year.

We registered the increased number of shares available for issuance under our 2010 Plan. Currently, we plan to register the increased number of shares available for issuance under our 2010 Directors’ Plan and 2010 Purchase Plan each year. Unless our board of directors elects not to increase the number of shares available for future grant each year, our stockholders may experience additional dilution, which could cause our stock price to fall.

We are at risk of securities class action litigation.

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In the past, securities class action litigation has often been brought against a company following a decline in the market price of its securities. This risk is especially relevant for us because biotechnology and biopharmaceutical companies have experienced significant stock price volatility in recent years.

On August 1, 2013, one putative class-action lawsuit (Bemis v. Trius Therapeutics, Inc., Case No. 37-2013-00060593-CU-SL-STL (the Complaint”)) was filed in Superior Court of the State of California, County of San Diego, against (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) Cubist Pharmaceuticals, Inc. and BRGO Corporation, collectively the Cubist Entities, arising out of the proposed acquisition of Trius by Cubist, or the Proposed Transaction. The Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

On August 6, 2013, another putative class-action lawsuit (Hurst v. Trius Therapeutics, Inc., (the “Second Complaint”)) was filed in the Superior Court of the State of California, County of San Diego, against: (a) the Company; (b) each member of the Company’s board of directors (including its chief executive officer); and (3) the Cubist Entities. The Second Complaint alleges that the Company’s directors breached their fiduciary duties in connection with the proposed acquisition of the Company by the Cubist Entities, and that the other defendants aided and abetted these alleged breaches of fiduciary duty. Specifically, the Second Complaint asserts that the Company’s directors breached their fiduciary duties to the Company’s public stockholders by, among other things, (i) agreeing to sell the Company to the Cubist Entities at an unfair price; (ii) implementing an unfair process; and (iii) agreeing to certain provisions of the merger agreement that are alleged to favor the Cubist Entities and deter alternative bids. The Second Complaint seeks an injunction against the consummation of the merger and rescission of the Merger Agreement to the extent already implemented, an award of damages, and an award of costs and expenses, including a reasonable allowance for attorneys’ and experts’ fees.

The Company intends to vigorously defend against these claims. The outcome of this litigation cannot be predicted at this time and any outcome in favor of the plaintiffs could have a significant adverse effect on the Proposed Transaction, our financial condition, and our results of operations.

Our ability to use our net operating loss carryforwards and certain other tax attributes may be limited.

Under Section 382 of the Internal Revenue Code, if a corporation undergoes an “ownership change” (generally defined as a greater than 50% change in its equity ownership over a three year period), the corporation’s ability to use its pre-change net operating loss carryforwards and other pre-change tax attributes (such as research tax credits) to offset its post-change income may be limited. After a public offering of common stock in January 2012, we performed an analysis under Section 382 through January 31, 2012 and determined that an “ownership change” had occurred, but the resulting annual limitation does not have a material impact on our ability to use our net operating loss and tax credit carryforwards. After our public offering in January 2013, we updated our Section 382 analysis and determined that it would not result in an additional “ownership change.” We may experience additional ownership changes in the future as a result of subsequent shifts in our stock ownership. If this were to occur, our ability to use our net operating loss carryforwards to offset United States federal taxable income may be subject to limitations, which could potentially result in increased future tax liability to us.

We do not intend to pay dividends on our common stock so any returns will be limited to the value of our stock.

We have never declared or paid any cash dividend on our common stock. We currently anticipate that we will retain future earnings for the development, operation and expansion of our business and do not anticipate declaring or paying any cash dividends for the foreseeable future. Any return to stockholders will therefore be limited to the appreciation of their stock.

Some provisions of our charter documents and Delaware law may have anti-takeover effects that could discourage an acquisition of us by others, even if an acquisition would be beneficial to our stockholders and may prevent attempts by our stockholders to replace or remove our current management.

Provisions in our amended and restated certificate of incorporation and bylaws, as well as provisions of Delaware law, could make it more difficult for a third party to acquire us or increase the cost of acquiring us, even if doing so would benefit our stockholders or remove our current management. These provisions include:

• Authorizing the issuance of “blank check” preferred stock, the terms of which may be established and shares of which may be issued without stockholder approval;

• Limiting the removal of directors by the stockholders;

• Creating a staggered board of directors;

• Prohibiting stockholder action by written consent, thereby requiring all stockholder actions to be taken at a meeting of our stockholders;

• Eliminating the ability of stockholders to call a special meeting of stockholders;

• Permitting our board of directors to accelerate the vesting of outstanding option grants upon certain transactions that result in a change of control; and

• Establishing advance notice requirements for nominations for election to the board of directors or for proposing matters that can be acted upon at stockholder meetings.

These provisions may frustrate or prevent any attempts by our stockholders to replace or remove our current management by making it more difficult for stockholders to replace members of our board of directors, which is responsible for appointing the members of our management. In addition, we are subject to Section 203 of the Delaware General Corporation Law, which generally prohibits a Delaware corporation from engaging in any of a broad range of business combinations with an interested stockholder for a period of three years following the date on which the stockholder became an interested stockholder, unless such transactions are approved by our board of directors. This provision could have the effect of delaying or preventing a change of control, whether or not it is desired by or beneficial to our stockholders. Further, other provisions of Delaware law may also discourage, delay or prevent someone from acquiring us or merging with us.

Item 6. Exhibits

EXHIBIT INDEX

Exhibit No:	Description
2.1(4)	Agreement and Plan of Merger, dated July 30 2013, by and among Trius Therapeutics, Inc., Cubist Pharmaceuticals, Inc. and BRGO Corporation.
3.1(1)	Amended and Restated Certificate of Incorporation.
3.2(1)	Amended and Restated Bylaws.
4.1(1)	Form of Common Stock Certificate.
4.2(1)	Warrant issued by Trius Therapeutics, Inc. on November 1, 2004 to Forsythe Biotechnology Group, Inc.
4.3(2)	Amended and Restated Investor Rights Agreement dated March 19, 2008, as amended, among Trius Therapeutics, Inc. and certain of its stockholders.

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4.4(3)	Form of Warrant issued pursuant to the Securities Purchase Agreement dated May 24, 2011, among Trius Therapeutics, Inc. and the Purchasers listed therein.
4.5(3)	Form of Registration Rights Agreement dated May 24, 2011, among Trius Therapeutics, Inc. and the Purchasers listed therein.
10.1(5)	2010 Equity Incentive Plan, as amended
10.2(5)	Amended and Restated 2010 Non-Employee Directors’ Stock Option Plan
10.3	Severance Benefit Plan, as amended
31.1	Certification of Principal Executive Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.
31.2	Certification of Principal Financial Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.
32.1	Certification of Principal Executive Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
32.2	Certification of Principal Financial Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
101.INS**	XBRL Instance Document
101.SCH**	XBRL Taxonomy Extension Schema Document
101.CAL**	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF**	XBRL Taxonomy Definition Linkbase Document
101.LAB**	XBRL Taxonomy Extension Label Linkbase Document
101.PRE**	XBRL Taxonomy Extension Presentation Linkbase Document

(1) Incorporated herein by reference to Trius Therapeutics, Inc.’s Registration Statement on Form S-1 (File No. 333-162945), as amended, filed with the Securities and Exchange Commission.

(2) Incorporated by reference to Trius Therapeutics, Inc.’s Registration Statement on Form S-1 (File No. 333-175050), filed with the Securities and Exchange Commission on June 21, 2011.

(3) Incorporated herein by reference to Trius Therapeutics, Inc.’s Current Report on Form 8-K (File No. 001-34828), filed with the Securities and Exchange Commission on May 25, 2011.

(4) Incorporated herein by reference to Trius Therapeutics, Inc.’s Current Report on Form 8-K (File No. 001-34828), filed with the

Securities and Exchange Commission on August 1, 2013.

(5) Incorporated herein by reference to Trius Therapeutics, Inc.’s Current Report on Form 8-K (File No. 001-34828), filed with the

Securities and Exchange Commission on May 24, 2013.

** Pursuant to applicable securities laws and regulations, we are deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and are not subject to liability under any anti-fraud provisions of the federal securities laws as long as we have made a good faith attempt to comply with the submission requirements and promptly amend the interactive data files after becoming aware that the interactive data files fail to comply with the submission requirements. Users of this data are advised that, pursuant to Rule 406T, these interactive data files are deemed not filed and otherwise are not subject to liability.

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SIGNATURES

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

	Trius Therapeutics, Inc.
Date: August 7, 2013	By:	/S/    JEFFREY STEIN
		Jeffrey Stein, Ph.D. President, Chief Executive Officer and Director (Principal Executive Officer)
Date: August 7, 2013	By:	/S/    JOHN P. SCHMID
		John P. Schmid Chief Financial Officer (Principal Financial Officer)

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