TSRX / Trius Therapeutics Inc - Документы SEC, Годовой отчет, Доверенное заявление

TSRX / Trius Therapeutics Inc / KPCB PANDEMIC & BIO DEFENSE FUND LLC - SC 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 1)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K100 (CUSIP Number) December 31, 2013 (Date of Event Which Requir

- 15-12B

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 15 CERTIFICATION AND NOTICE OF TERMINATION OF REGISTRATION UNDER SECTION 12(g) OF THE SECURITIES EXCHANGE ACT OF 1934 OR SUSPENSION OF DUTY TO FILE REPORTS UNDER SECTIONS 13 AND 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934. Commission File Number 001-34828 Trius Therapeutics, Inc. (Exact name of registrant as specified in

- S-8 POS

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

- S-8 POS

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

- S-8 POS

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

TSRX / Trius Therapeutics Inc / CUBIST PHARMACEUTICALS INC - SC 13D/A Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 6) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

- POS AM

POS AM 1 a13-206772posam.htm POS AM As filed with the Securities and Exchange Commission on September 13, 2013 Registration No. 333-176621, 333-183673 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 POST-EFFECTIVE AMENDMENT NO. 1 TO FORM S-3 REGISTRATION STATEMENT NO. 333-176621 POST-EFFECTIVE AMENDMENT NO. 1 TO FORM S-3 REGISTRATION STATEMENT NO. 333-183673 UNDER THE SECUR

CUBIST PHARMACEUTICALS ANNOUNCES RESULTS OF TENDER OFFER FOR OUTSTANDING SHARES OF TRIUS THERAPEUTICS

EX-99.(A)(5)(H) 2 a13-1844418ex99da5h.htm EX-99.(A)(5)(H) Exhibit 99.(a)(5)(H) CUBIST PHARMACEUTICALS ANNOUNCES RESULTS OF TENDER OFFER FOR OUTSTANDING SHARES OF TRIUS THERAPEUTICS LEXINGTON, Mass. — September 11, 2013 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) today announced the results of Cubist’s tender offer to purchase all of the outstanding common shares of Trius Therapeutics, Inc. (NASD

- S-8 POS

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

- POS AM

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

- S-8 POS

As filed with the Securities and Exchange Commission on September 13, 2013 Registration No.

- SC 14D9

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14D-9 (Rule 14d-101) Solicitation/Recommendation Statement Under Section 14(d)(4) of the Securities Exchange Act of 1934 (Amendment No. 4) TRIUS THERAPEUTICS, INC. (Name of Subject Company) TRIUS THERAPEUTICS, INC. (Name of Person Filing Statement) Common Stock, $0.0001 par value per share (Title of Class of Securitie

CUBIST PHARMACEUTICALS ANNOUNCES RESULTS OF TENDER OFFER FOR OUTSTANDING SHARES OF TRIUS THERAPEUTICS

Exhibit 99.(a)(5)(H) CUBIST PHARMACEUTICALS ANNOUNCES RESULTS OF TENDER OFFER FOR OUTSTANDING SHARES OF TRIUS THERAPEUTICS LEXINGTON, Mass. — September 11, 2013 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) today announced the results of Cubist’s tender offer to purchase all of the outstanding common shares of Trius Therapeutics, Inc. (NASDAQ: TSRX) for $13.50 per share in cash, plus one Contingen

Changes in Control of Registrant, Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Material Modification to Rights of Security Holders, Unregistered Sales of Equity Securities, Notice of Delisting or Failure to Satisfy a Continued Listing Rule or Standard; Transfer of Listing, Financial Statements and Exhibits, Completion of Acquisition or Disposition of Assets - 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 11, 2013 Trius Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State or other jurisdiction of incorporation) (Commis

STATE of DELAWARE AMENDED AND RESTATED CERTIFICATE OF INCORPORATION TRIUS THERAPEUTICS, INC.

Exhibit 3.1 STATE of DELAWARE AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF TRIUS THERAPEUTICS, INC. 1. Name. The name of this corporation is Trius Therapeutics, Inc. 2. Registered Office and Agent. The registered office of this corporation in the State of Delaware is located at 1209 Orange Street in the City of Wilmington 19801, County of New Castle. The name of its registered agent at suc

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 6) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

AMENDED AND RESTATED BY-LAWS TRIUS THERAPEUTICS, INC. Section 1. LAW, CERTIFICATE OF INCORPORATION AND BY-LAWS

Exhibit 3.2 AMENDED AND RESTATED BY-LAWS OF TRIUS THERAPEUTICS, INC. Section 1. LAW, CERTIFICATE OF INCORPORATION AND BY-LAWS 1.1. These by-laws are subject to the certificate of incorporation of the corporation. In these by-laws, references to law, the certificate of incorporation and by-laws mean the law, the provisions of the certificate of incorporation and the by-laws as from time to time in

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 5) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

- SC 14D9/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14D-9 (Rule 14d-101) Solicitation/Recommendation Statement Under Section 14(d)(4) of the Securities Exchange Act of 1934 (Amendment No. 3) TRIUS THERAPEUTICS, INC. (Name of Subject Company) TRIUS THERAPEUTICS, INC. (Name of Person Filing Statement) Common Stock, $0.0001 par value per share (Title of Class of Securitie

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 4) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

CUBIST ANNOUNCES EXPIRATION OF HART-SCOTT-RODINO WAITING PERIOD FOR ACQUISITION OF TRIUS

Exhibit 99.(a)(5)(G) CUBIST ANNOUNCES EXPIRATION OF HART-SCOTT-RODINO WAITING PERIOD FOR ACQUISITION OF TRIUS Lexington, Mass. — August 29, 2013 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) and Trius Therapeutics, Inc. (NASDAQ: TSRX) today announced the expiration of the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976 (“HSR”) in connection with Cubist’s previously an

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 3) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

- SC 14D9/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14D-9 (Rule 14d-101) Solicitation/Recommendation Statement Under Section 14(d)(4) of the Securities Exchange Act of 1934 (Amendment No. 2) TRIUS THERAPEUTICS, INC. (Name of Subject Company) TRIUS THERAPEUTICS, INC. (Name of Person Filing Statement) Common Stock, $0.0001 par value per share (Title of Class of Securitie

TSRX / Trius Therapeutics Inc / InterWest Partners IX, LP - SC 13D/A Activist Investment

SC 13D/A 1 d588556dsc13da.htm SC 13D/A SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 13D UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 1)* TRIUS THERAPEUTICS, INC. (Name of Issuer) Common Stock, $0.0001 par value per share (Title of Class of Securities) 89685K 10 0 (CUSIP Number) W. Stephen Holmes III InterWest Partners 2710 Sand Hill Road, Second Floor Menlo Park, CA

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 2) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

- SC 14D9/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14D-9 (Rule 14d-101) Solicitation/Recommendation Statement Under Section 14(d)(4) of the Securities Exchange Act of 1934 (Amendment No. 1) TRIUS THERAPEUTICS, INC. (Name of Subject Company) TRIUS THERAPEUTICS, INC. (Name of Person Filing Statement) Common Stock, $0.0001 par value per share (Title of Class of Securitie

- SC TO-T/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 1) TRIUS THERAPEUTICS, INC. (Name of Subject Company) BRGO CORPORATION (Name of Filing Persons (Offeror)) a wholly owned subsidiary of CUBIST PHARMACEUTICALS, INC. (Name of Filing Persons (Parent

AMENDMENT This Amendment (“Amendment”) is made as of July 1, 2013 (the “Effective Date”) and amends certain portions of the Mutual Non-Disclosure Agreement (the “Agreement”), dated as of July 24, 2012, by and between Trius Therapeutics, Inc. (“Trius”

Exhibit (d)(5) AMENDMENT This Amendment (“Amendment”) is made as of July 1, 2013 (the “Effective Date”) and amends certain portions of the Mutual Non-Disclosure Agreement (the “Agreement”), dated as of July 24, 2012, by and between Trius Therapeutics, Inc.

CUBIST PHARMACEUTICALS COMMENCES TENDER OFFER FOR ALL OUTSTANDING SHARES OF TRIUS THERAPEUTICS Tender Offer Consistent with Terms Announced on July 30, 2013

Exhibit (a)(5)(F) FOR IMMEDIATE RELEASE CUBIST PHARMACEUTICALS COMMENCES TENDER OFFER FOR ALL OUTSTANDING SHARES OF TRIUS THERAPEUTICS Tender Offer Consistent with Terms Announced on July 30, 2013 Lexington, Mass.

- SC TO-T

QuickLinks - Click here to rapidly navigate through this document UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.

Notice of Guaranteed Delivery for Tender of Shares of Common Stock TRIUS THERAPEUTICS, INC. $13.50 per share, plus one non-transferable contingent value right for each share, which represents the contractual right to receive up to $2.00 per share upo

QuickLinks - Click here to rapidly navigate through this document Exhibit (a)(1)(C) Notice of Guaranteed Delivery for Tender of Shares of Common Stock of TRIUS THERAPEUTICS, INC.

- SC 14D9

Use these links to rapidly review the document TABLE OF CONTENTS Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

[FORM OF SUMMARY ADVERTISEMENT]

EX-99.(A)(5)(E) 7 a2216365zex-99a5e.htm EX-99.(A)(5)(E) Exhibit (a)(5)(E) [FORM OF SUMMARY ADVERTISEMENT] This announcement is neither an offer to purchase nor a solicitation of an offer to sell securities. The Offer (as defined below) is made solely pursuant to the Offer to Purchase (as defined below), and the related Letter of Transmittal (as defined below), and is being made to all holders of S

Offer to Purchase All Outstanding Shares of Common Stock TRIUS THERAPEUTICS, INC. $13.50 per share, plus one non-transferable contingent value right for each share, which represents the contractual right to receive up to $2.00 per share upon the achi

QuickLinks - Click here to rapidly navigate through this document Exhibit (a)(1)(D) Offer to Purchase All Outstanding Shares of Common Stock of TRIUS THERAPEUTICS, INC.

Offer to Purchase All Outstanding Shares of Common Stock TRIUS THERAPEUTICS, INC. $13.50 per share, plus one non-transferable contingent value right for each share, which represents the contractual right to receive up to $2.00 per share upon the achi

QuickLinks - Click here to rapidly navigate through this document Exhibit (a)(1)(E) Offer to Purchase All Outstanding Shares of Common Stock of TRIUS THERAPEUTICS, INC.

MUTUAL NON-DISCLOSURE AGREEMENT THIS MUTUAL NON-DISCLOSURE AGREEMENT (the “Agreement”) is made effective as of July 24, 2012, by and between TRIUS THERAPEUTICS a Delaware corporation, and CUBIST PHARMACEUTICS, INC., a Delaware corporation, to assure

Exhibit (d)(4) MUTUAL NON-DISCLOSURE AGREEMENT THIS MUTUAL NON-DISCLOSURE AGREEMENT (the “Agreement”) is made effective as of July 24, 2012, by and between TRIUS THERAPEUTICS a Delaware corporation, and CUBIST PHARMACEUTICS, INC.

Letter of Transmittal To Tender Shares of Common Stock TRIUS THERAPEUTICS, INC. $13.50 per share, plus one non-transferable contingent value right for each share, which represents the contractual right to receive up to $2.00 per share upon the achiev

QuickLinks - Click here to rapidly navigate through this document Exhibit (a)(1)(B) Letter of Transmittal To Tender Shares of Common Stock of TRIUS THERAPEUTICS, INC.

OFFER TO PURCHASE FOR CASH All Outstanding Shares of Common Stock TRIUS THERAPEUTICS, INC. $13.50 per share, plus one non-transferable contingent value right for each share, which represents the contractual right to receive up to $2.00 per share upon

QuickLinks - Click here to rapidly navigate through this document Exhibit (a)(1)(A) OFFER TO PURCHASE FOR CASH All Outstanding Shares of Common Stock of TRIUS THERAPEUTICS, INC.

JOINT FILING AGREEMENT

Exhibit 1 JOINT FILING AGREEMENT In accordance with Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree that this Statement on Schedule 13D (including any amendments thereto) relating to the beneficial ownership of Common Stock, $0.

TSRX / Trius Therapeutics Inc / CUBIST PHARMACEUTICALS INC - SC 13D Activist Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. )* TRIUS THERAPEUTICS, INC. (Name of Issuer) Common Stock, $0.0001 par value per share (Title of Class of Securities) 89685K100 (CUSIP Number) Thomas J. DesRosier Senior Vice President, Chief Legal Officer, General Counsel and Secretary Cubist Pharmaceutical

TRIUS THERAPEUTICS, INC. SEVERANCE BENEFIT PLAN

EXHIBIT 10.3 TRIUS THERAPEUTICS, INC. SEVERANCE BENEFIT PLAN Section 1. INTRODUCTION. The Trius Therapeutics, Inc. Severance Benefit Plan (the “Plan”) was established effective August 11, 2011 (the “Effective Date”). The purpose of the Plan is to provide for the payment of severance benefits to certain eligible employees of Trius Therapeutics, Inc. (the “Company”) whose employment with the Company

Quarterly Report - FORM 10-Q

Form 10-Q Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

Financial Statements and Exhibits, Results of Operations and Financial Condition - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): August 6, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commiss

TRIUS THERAPEUTICS REPORTS SECOND QUARTER 2013 FINANCIAL RESULTS

EX-99.1 Exhibit 99.1 TRIUS THERAPEUTICS REPORTS SECOND QUARTER 2013 FINANCIAL RESULTS San Diego, CA, August 6, 2013 – Trius Therapeutics, Inc. (NASDAQ: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for serious infections, announced today its financial results for the second quarter ended June 30, 2013. Recent Events On July

Dear Dr. XXX;

Date Dear Dr. XXX; Earlier this week, Cubist announced our planned acquisitions of both Trius Therapeutics and Optimer Pharmaceuticals. As a key infectious disease expert, we thought it important to convey this information to you directly. The prospects of continuing the development and potential commercialization of tedizolid (Trius) and the marketing of DIFICID (Optimer) reaffirms Cubist’s missi

- SC TO-C

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(D)(1) OR SECTION 13(E)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 TRIUS THERAPEUTICS, INC. (Name Of Subject Company (Issuer)) BRGO CORPORATION CUBIST PHARMACEUTICALS, INC. (Names of Filing Persons (Offerors)) Common Stock, par value $0.0001 per share (Title of Class of Securit

- SC TO-C

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE TO TENDER OFFER STATEMENT UNDER SECTION 14(D)(1) OR SECTION 13(E)(1) OF THE SECURITIES EXCHANGE ACT OF 1934 TRIUS THERAPEUTICS, INC. (Name Of Subject Company (Issuer)) BRGO CORPORATION CUBIST PHARMACEUTICALS, INC. (Names of Filing Persons (Offerors)) Common Stock, par value $0.0001 per share (Title of Class of Securit

- 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of Report (Date of earliest event reported) July 30, 2013 CUBIST PHARMACEUTICALS, INC. (Exact name of registrant as specified in charter) Delaware 0-21379 22-3192085 (State or Other Jurisdiction of Incorporation) (Commission Fil

TENDER AND VOTING AGREEMENT

Exhibit 10.2 TENDER AND VOTING AGREEMENT THIS TENDER AND VOTING AGREEMENT (this “Agreement”) dated July 30, 2013, is entered into between Cubist Pharmaceuticals, Inc., a Delaware corporation (“Parent”), BRGO Corporation, a Delaware corporation and direct or indirect wholly owned subsidiary of Parent (“Purchaser”), and [ ] (“Stockholder”), with respect to (i) the shares of common stock, par value $

TENDER AND VOTING AGREEMENT

EX-2.2 Exhibit 2.2 TENDER AND VOTING AGREEMENT THIS TENDER AND VOTING AGREEMENT (this “Agreement”) dated July 30, 2013, is entered into between Cubist Pharmaceuticals, Inc., a Delaware corporation (“Parent”), BRGO Corporation, a Delaware corporation and direct or indirect wholly owned subsidiary of Parent (“Purchaser”), and [ ] (“Stockholder”), with respect to (i) the shares of common stock, par v

CONTINGENT VALUE RIGHTS AGREEMENT

Exhibit 10.1 CONTINGENT VALUE RIGHTS AGREEMENT THIS CONTINGENT VALUE RIGHTS AGREEMENT, dated as of [·], 2013 (this “Agreement”), is entered into by and between Cubist Pharmaceuticals, Inc., a Delaware corporation (“Parent”), and Broadridge Corporate Issuer Solutions, Inc., a Pennsylvania corporation, as Rights Agent. RECITALS WHEREAS, Parent, BRGO Corporation, a Delaware corporation (“Sub”), and T

AGREEMENT AND PLAN OF MERGER TRIUS THERAPEUTICS, INC., a Delaware corporation; CUBIST PHARMACEUTICALS, INC., a Delaware corporation; and BRGO CORPORATION, a Delaware corporation Dated as of July 30, 2013

Exhibit 2.1 AGREEMENT AND PLAN OF MERGER among: TRIUS THERAPEUTICS, INC., a Delaware corporation; CUBIST PHARMACEUTICALS, INC., a Delaware corporation; and BRGO CORPORATION, a Delaware corporation Dated as of July 30, 2013 TABLE OF CONTENTS Page Section 1. THE OFFER 2 1.1 The Offer 2 1.2 Company Actions 4 1.4 Merger Without Meeting of Stockholders 5 1.4 Directors 5 1.5 Top-Up Option 7 Section 2. M

AGREEMENT AND PLAN OF MERGER TRIUS THERAPEUTICS, INC., a Delaware corporation; CUBIST PHARMACEUTICALS, INC., a Delaware corporation; and BRGO CORPORATION, a Delaware corporation Dated as of July 30, 2013 TABLE OF CONTENTS Page Section 1. THE OFFER 2

EX-2.1 Exhibit 2.1 AGREEMENT AND PLAN OF MERGER among: TRIUS THERAPEUTICS, INC., a Delaware corporation; CUBIST PHARMACEUTICALS, INC., a Delaware corporation; and BRGO CORPORATION, a Delaware corporation Dated as of July 30, 2013 TABLE OF CONTENTS Page Section 1. THE OFFER 2 1.1 The Offer 2 1.2 Company Actions 4 1.4 Merger Without Meeting of Stockholders 5 1.4 Directors 5 1.5 Top-Up Option 7 Secti

Entry into a Material Definitive Agreement, Financial Statements and Exhibits - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of Report (Date of Earliest Event Reported): July 30, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commissi

Safe Harbor Statement 2 This presentation and statements in this conference call regarding the proposed transactions contain forward-looking statements. Any statements contained herein which do not describe historical facts, including but not limited

Planned Acquisitions of Trius Therapeutics and Optimer Pharmaceuticals Accelerating Cubist’s Global Leadership in Acute Care July 30, 2013 Exhibit 99.

CUBIST PHARMACEUTICALS, INC. Moderator: Eileen McIntyre July 30, 2013 6:00 p.m. EST

CUBIST PHARMACEUTICALS, INC. 07-30-13/6:00 p.m. EST The following is a transcript of an investor presentation given by Cubist Pharmaceuticals, Inc. (“Cubist”) on July 30, 2013, in connection with the Cubist’s proposed acquisitions of Trius Therapeutics, Inc. (“Trius”) and Optimer Pharmaceuticals, Inc. (“Optimer”) Important Additional Information about the Potential Trius Transaction will be Filed

CONTINGENT VALUE RIGHTS AGREEMENT

EX-2.3 Exhibit 2.3 CONTINGENT VALUE RIGHTS AGREEMENT THIS CONTINGENT VALUE RIGHTS AGREEMENT, dated as of [—], 2013 (this “Agreement”), is entered into by and between Cubist Pharmaceuticals, Inc., a Delaware corporation (“Parent”), and Broadridge Corporate Issuer Solutions, Inc., a Pennsylvania corporation, as Rights Agent. RECITALS WHEREAS, Parent, BRGO Corporation, a Delaware corporation (“Sub”),

- SC14D9C

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14D-9 (Rule 14d-101) Solicitation/Recommendation Statement Under Section 14(d)(4) of the Securities Exchange Act of 1934 TRIUS THERAPEUTICS, INC. (Name of Subject Company) TRIUS THERAPEUTICS, INC. (Name of Person Filing Statement) Common Stock, $0.0001 par value per share (Title of Class of Securities) 89685K100 (CUSI

CUBIST PHARMACEUTICALS TO ACQUIRE TRIUS THERAPEUTICS Adds Highly Complementary, Late-Stage Antibiotic Candidate, Tedizolid, and Bolsters Cubist’s Global Leadership in the Acute Care/Hospital Environment

Exhibit 99.1 CUBIST PHARMACEUTICALS TO ACQUIRE TRIUS THERAPEUTICS Adds Highly Complementary, Late-Stage Antibiotic Candidate, Tedizolid, and Bolsters Cubist’s Global Leadership in the Acute Care/Hospital Environment Lexington, Mass., and San Diego, Calif. — July 30, 2013 — Cubist Pharmaceuticals, Inc. (NASDAQ: CBST) and Trius Therapeutics, Inc. (NASDAQ: TSRX) today announced that they have signed

- 8-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of Report (Date of earliest event reported) July 30, 2013 CUBIST PHARMACEUTICALS, INC. (Exact name of registrant as specified in charter) Delaware 0-21379 22-3192085 (State or Other Jurisdiction of Incorporation) (Commission Fil

Entry into a Material Definitive Agreement - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 22, 2013 Trius Therapeutics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-34828 20-1320630 (State or Other Jurisdiction of Incorporation) (Co

TRIUS THERAPEUTICS, INC. 2010 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: FEBRUARY 9, 2010 APPROVED BY THE STOCKHOLDERS: FEBRUARY 9, 2010 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 APPROVED BY THE STOCKHOLDERS: MAY 21, 2013 TERMINA

EX-99.1 Exhibit 99.1 TRIUS THERAPEUTICS, INC. 2010 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: FEBRUARY 9, 2010 APPROVED BY THE STOCKHOLDERS: FEBRUARY 9, 2010 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 APPROVED BY THE STOCKHOLDERS: MAY 21, 2013 TERMINATION DATE: FEBRUARY 8, 2020 1. GENERAL. (a) Successor to and Continuation of Prior Plan. The Plan is intended as the successor to

- FORM S-8

FORM S-8 As filed with the Securities and Exchange Commission on June 5, 2013 Registration No.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits, Other Events, Submission of Matters to a Vote of Security Holders - FORM 8-K

FORM 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of Report (Date of Earliest Event Reported): May 21, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commissio

TRIUS THERAPEUTICS, INC. 2010 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: FEBRUARY 9, 2010 APPROVED BY THE STOCKHOLDERS: FEBRUARY 9, 2010 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 APPROVED BY THE STOCKHOLDERS: MAY 21, 2013 TERMINA

Exhibit 99.1 TRIUS THERAPEUTICS, INC. 2010 EQUITY INCENTIVE PLAN ADOPTED BY THE BOARD OF DIRECTORS: FEBRUARY 9, 2010 APPROVED BY THE STOCKHOLDERS: FEBRUARY 9, 2010 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 APPROVED BY THE STOCKHOLDERS: MAY 21, 2013 TERMINATION DATE: FEBRUARY 8, 2020 1. GENERAL. (a) Successor to and Continuation of Prior Plan. The Plan is intended as the successor to and con

TRIUS THERAPEUTICS, INC. AMENDED AND RESTATED 2010 NON-EMPLOYEE DIRECTORS’ STOCK OPTION PLAN AMENDED AND RESTATED ON AUGUST 11, 2011 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 AMENDED BY THE BOARD OF DIRECTORS: MAY 21, 2013

EX-99.2 Exhibit 99.2 TRIUS THERAPEUTICS, INC. AMENDED AND RESTATED 2010 NON-EMPLOYEE DIRECTORS’ STOCK OPTION PLAN AMENDED AND RESTATED ON AUGUST 11, 2011 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2013 AMENDED BY THE BOARD OF DIRECTORS: MAY 21, 2013 1. GENERAL. (a) Eligible Option Recipients. The persons eligible to receive Options are the Non-Employee Directors of the Company. (b) Purpose. The C

Financial Statements and Exhibits, Results of Operations and Financial Condition - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): May 7, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commission

TRIUS THERAPEUTICS REPORTS FIRST QUARTER 2013 FINANCIAL RESULTS

EX-99.1 Exhibit 99.1 TRIUS THERAPEUTICS REPORTS FIRST QUARTER 2013 FINANCIAL RESULTS San Diego, CA, May 7, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for serious infections, announced today its financial results for the first quarter ended March 31, 2013. “After successfully compl

- DEF 14A

DEF 14A SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

TRIUS APPOINTS SETH FISCHER TO ITS BOARD OF DIRECTORS Risa Stack Announces Planned Departure from the Trius Board

EX-99.1 Exhibit 99.1 TRIUS APPOINTS SETH FISCHER TO ITS BOARD OF DIRECTORS Risa Stack Announces Planned Departure from the Trius Board San Diego, CA, April 3, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX) announced today the appointment of Seth H. Z. Fischer to its Board of Directors. Mr. Fischer was the former Company Group Chairman Johnson & Johnson, Worldwide Franchise Chairman Cordis Corporat

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): April 1, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commissi

TRIUS ANNOUNCES POSITIVE RESULTS FROM ESTABLISH 2 STUDY OF TEDIZOLID IN SEVERE SKIN INFECTIONS Tedizolid met all primary and secondary efficacy outcomes designated by the FDA and EMA NDA filing expected second half of this year

EX-99.1 Exhibit 99.1 TRIUS ANNOUNCES POSITIVE RESULTS FROM ESTABLISH 2 STUDY OF TEDIZOLID IN SEVERE SKIN INFECTIONS Tedizolid met all primary and secondary efficacy outcomes designated by the FDA and EMA NDA filing expected second half of this year San Diego, CA, March 25, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX) today announced top-line results from its ESTABLISH 2 Phase 3 clinical trial of

The Future of Anti-Infectives

The Future of Anti-Infectives ESTABLISH 2 Top Line Data Release March 25, 2013 Exhibit 99.

Financial Statements and Exhibits, Other Events - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 25, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commiss

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 7, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commission file n

- FORM S-8

Form S-8 As filed with the Securities and Exchange Commission on March 13, 2013 Registration No.

TRIUS THERAPEUTICS REPORTS 2012 FOURTH QUARTER AND FULL YEAR 2012 FINANCIAL RESULTS

EX-99.1 Exhibit 99.1 TRIUS THERAPEUTICS REPORTS 2012 FOURTH QUARTER AND FULL YEAR 2012 FINANCIAL RESULTS San Diego, CA, March 12, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for serious infections, announced today its financial results for the fourth quarter and year ended December

Financial Statements and Exhibits, Results of Operations and Financial Condition - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 12, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commiss

TSRX / Trius Therapeutics Inc / WELLINGTON MANAGEMENT GROUP LLP - DISCLOSURE DOCUMENT Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K100 (CUSIP Number) December 31, 2012 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which thi

TSRX / Trius Therapeutics Inc / Versant Side Fund III, L.P. - SC 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 3)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K10 (CUSIP Number) December 31, 2012 (Date of Event

4,224,700 Shares Common Stock

Prospectus Supplement Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.

TRIUS THERAPEUTICS, INC. PRICES PUBLIC OFFERING OF COMMON STOCK

Press Release dated January 18, 2013 Exhibit 99.2 TRIUS THERAPEUTICS, INC. PRICES PUBLIC OFFERING OF COMMON STOCK San Diego, CA, January 18, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX) today announced the pricing of an underwritten public offering of 6,300,000 shares of its common stock at a price to the public of $4.75 per share. The gross proceeds to Trius from this offering are expected to b

Entry into a Material Definitive Agreement, Financial Statements and Exhibits - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 17, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commi

TRIUS THERAPEUTICS, INC. ANNOUNCES PROPOSED PUBLIC OFFERING OF COMMON STOCK

Press Release dated January 17, 2013 Exhibit 99.1 TRIUS THERAPEUTICS, INC. ANNOUNCES PROPOSED PUBLIC OFFERING OF COMMON STOCK San Diego, CA, January 17, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX) today announced that it intends to offer and sell shares of its common stock in an underwritten public offering. Citigroup and Leerink Swann are acting as joint book-running managers and Baird is acti

2,075,300 Shares Common Stock

Prospectus Supplement Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.

6,300,000 Shares TRIUS THERAPEUTICS, INC. Common Stock, par value $0.0001 per share UNDERWRITING AGREEMENT

Underwriting Agreement Exhibit 1.1 6,300,000 Shares TRIUS THERAPEUTICS, INC. Common Stock, par value $0.0001 per share UNDERWRITING AGREEMENT January 17, 2013 CITIGROUP GLOBAL MARKETS INC. LEERINK SWANN LLC As Representatives of the several Underwriters, c/o Citigroup Global Markets Inc. 388 Greenwich Street New York, NY 10013 c/o Leerink Swann LLC One Federal Street, 37th Floor Boston, MA 02110 D

SUBJECT TO COMPLETION, DATED JANUARY 17, 2013

Preliminary Prospectus Supplement Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.

SUBJECT TO COMPLETION, DATED JANUARY 17, 2013

Preliminary Prospectus Supplement Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.

Financial Statements and Exhibits, Results of Operations and Financial Condition, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 7, 2013 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commission file

TEDIZOLID RECEIVES QUALIFIED INFECTIOUS DISEASE PRODUCT (QIDP) DESIGNATION FROM FDA FDA’s action expedites regulatory review process of the new drug application (NDA)

Trius Therapeutics, Inc. Press Release Exhibit 99.1 TEDIZOLID RECEIVES QUALIFIED INFECTIOUS DISEASE PRODUCT (QIDP) DESIGNATION FROM FDA FDA’s action expedites regulatory review process of the new drug application (NDA) San Diego, CA, January 7, 2013 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery and development of innovative antibiotics for serious

Financial Statements and Exhibits - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): December 12, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Comm

TRIUS THERAPEUTICS, INC. 1,122,218 SHARES OF COMMON STOCK

Prospectus Supplement No. 3 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration Statement No. 333-176621 PROSPECTUS SUPPLEMENT NO. 3 (To Prospectus dated September 15, 2011, as supplemented by Prospectus Supplement dated August 31, 2012) TRIUS THERAPEUTICS, INC. 1,122,218 SHARES OF COMMON STOCK This Prospectus Supplement No. 3 supplements the prospectus dated September 15, 2011, as sup

Financial Statements and Exhibits, Results of Operations and Financial Condition - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): November 5, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commi

TRIUS THERAPEUTICS REPORTS 2012 THIRD QUARTER FINANCIAL RESULTS

Press Release Exhibit 99.1 TRIUS THERAPEUTICS REPORTS 2012 THIRD QUARTER FINANCIAL RESULTS San Diego, CA, November 5, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections, announced today its financial results for the third quarter ended September 30, 2012 an

TRIUS THERAPEUTICS, INC. 612,133 SHARES OF COMMON STOCK

Prospectus Supplement No. 2 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration Statement No. 333-176621 PROSPECTUS SUPPLEMENT NO. 2 (To Prospectus dated September 15, 2011, as supplemented by Prospectus Supplement dated August 31, 2012) TRIUS THERAPEUTICS, INC. 612,133 SHARES OF COMMON STOCK This Prospectus Supplement No. 2 supplements the prospectus dated September 15, 2011, as suppl

Financial Statements and Exhibits, Other Events - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 9, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commis

$77,000,000 TRIUS THERAPEUTICS, INC. Common Stock Preferred Stock Debt Securities

424b3 Table of Contents Filed Pursuant to Rule 424(b)(3) Registration No. 333-183673 PROSPECTUS $77,000,000 TRIUS THERAPEUTICS, INC. Common Stock Preferred Stock Debt Securities Warrants From time to time, we may offer our common stock, preferred stock, debt securities and/or warrants, either individually or in combination, in one or more offerings in amounts, at prices and on terms that we will d

COMMON STOCK PURCHASE AGREEMENT DATED AS OF AUGUST 30, 2012 BY AND BETWEEN TRIUS THERAPEUTICS, INC. TERRAPIN OPPORTUNITY, L.P. TABLE OF CONTENTS Article I PURCHASE AND SALE OF COMMON STOCK 1 Section 1.1 Purchase and Sale of Stock 1 Section 1.2 Effect

Common Stock Purchase Agreement Exhibit 10.1 COMMON STOCK PURCHASE AGREEMENT DATED AS OF AUGUST 30, 2012 BY AND BETWEEN TRIUS THERAPEUTICS, INC. AND TERRAPIN OPPORTUNITY, L.P. TABLE OF CONTENTS Article I PURCHASE AND SALE OF COMMON STOCK 1 Section 1.1 Purchase and Sale of Stock 1 Section 1.2 Effective Date; Settlement Dates 1 Section 1.3 Reservation of Common Stock 2 Section 1.4 Current Report; Pr

TRIUS THERAPEUTICS, INC. , As Warrant Agent FORM OF PREFERRED STOCK WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Deliv

Form of Preferred Stock Warrant Agreement and Warrant Certificate Exhibit 4.14 TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF PREFERRED STOCK WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Delivery of Warrant Certificates 1 1.3 Issuance of Warrant Certificates

TRIUS THERAPEUTICS, INC. , As Warrant Agent FORM OF DEBT SECURITIES WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Deliv

Exhibit 4.15 TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF DEBT SECURITIES WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Delivery of Warrant Certificates 1 1.3 Issuance of Warrant Certificates 2 ARTICLE 2 WARRANT PRICE, DURATION AND EXERCISE OF WARRANTS 2 2.1

Entry into a Material Definitive Agreement, Financial Statements and Exhibits

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 30, 2012 Trius Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 000-34828 20-1320630 (State or other jurisdiction of incorporation) (

TRIUS THERAPEUTICS, INC. COMMON STOCK

PROSPECTUS SUPPLEMENT Table of Contents Filed Pursuant to Rule 424(b)(5) Registration Statement No.

TRIUS THERAPEUTICS, INC., Dated as of [ ], 20 Senior Debt Securities TABLE OF CONTENTS PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 3 Section

Form of Senior Debt Indenture Exhibit 4.9 TRIUS THERAPEUTICS, INC., Issuer AND [Trustee], Trustee INDENTURE Dated as of [ ], 20 Senior Debt Securities TABLE OF CONTENTS PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 3 Section 2.01 Designation and Terms of Securities 3 Section 2.02 Form of Secu

- FORM S-3

Table of Contents As filed with the Securities and Exchange Commission on August 31, 2012 Registration No.

TRIUS THERAPEUTICS, INC., Dated as of [ ], 20 Subordinated Debt Securities TABLE OF CONTENTS PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 3 Se

EX-4.10 3 d403616dex410.htm FORM OF SUBORDINATED DEBT INDENTURE Exhibit 4.10 TRIUS THERAPEUTICS, INC., Issuer AND [Trustee], Trustee INDENTURE Dated as of [ ], 20 Subordinated Debt Securities TABLE OF CONTENTS PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 3 Section 2.01 Designation and Terms

TRIUS THERAPEUTICS, INC. , As Warrant Agent FORM OF COMMON STOCK WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Delivery

Form of Common Stock Warrant Agreement and Warrant Certificate Exhibit 4.13 TRIUS THERAPEUTICS, INC. and , As Warrant Agent FORM OF COMMON STOCK WARRANT AGREEMENT Dated As Of TABLE OF CONTENTS ARTICLE 1 ISSUANCE OF WARRANTS AND EXECUTION AND DELIVERY OF WARRANT CERTIFICATES 1 1.1 Issuance of Warrants 1 1.2 Execution and Delivery of Warrant Certificates 1 1.3 Issuance of Warrant Certificates 2 ARTI

TRIUS THERAPEUTICS SECURES A $25 MILLION COMMITTED EQUITY FINANCING FACILITY WITH TERRAPIN OPPORTUNITY, L.P.

Press Release Exhibit 99.1 TRIUS THERAPEUTICS SECURES A $25 MILLION COMMITTED EQUITY FINANCING FACILITY WITH TERRAPIN OPPORTUNITY, L.P. San Diego, CA, August 31, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX) announced today that it has obtained a committed equity financing facility under which it may sell up to $25 million of its registered common stock to Terrapin Opportunity, L.P., over a 24-mo

Statement of Computation of Ratios Year Ended December 31, Six Months Ended June 30, 2012 2007 2008 2009 2010 2011 (In thousands, except ratio amounts) Earnings: Net loss $ (8,748 ) $ (20,791 ) $ (22,681 ) $ (23,863 ) $ (18,250 ) $ (22,018 ) Add: Fix

Statement of Computation of Ratios Exhibit 12.1 Statement of Computation of Ratios Year Ended December 31, Six Months Ended June 30, 2012 2007 2008 2009 2010 2011 (In thousands, except ratio amounts) Earnings: Net loss $ (8,748 ) $ (20,791 ) $ (22,681 ) $ (23,863 ) $ (18,250 ) $ (22,018 ) Add: Fixed charges 237 485 663 4,039 202 127 Earnings as defined $ (8,511 ) $ (20,306 ) $ (22,018 ) $ (19,824

TRIUS THERAPEUTICS REPORTS 2012 SECOND QUARTER FINANCIAL RESULTS

Press Release Exhibit 99.1 TRIUS THERAPEUTICS REPORTS 2012 SECOND QUARTER FINANCIAL RESULTS San Diego, CA, August 6, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections, announced today its financial results for the second quarter ended June 30, 2012 and pro

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): August 6, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commission file

Submission of Matters to a Vote of Security Holders - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 Date of Report (Date of Earliest Event Reported): May 22, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commissio

TSRX / Trius Therapeutics Inc / Versant Side Fund III, L.P. - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 3)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K10 (CUSIP Number) December 31, 2011 (Date of Event

TRIUS THERAPEUTICS REPORTS FIRST QUARTER 2012 FINANCIAL RESULTS

Press Release Exhibit 99.1 TRIUS THERAPEUTICS REPORTS FIRST QUARTER 2012 FINANCIAL RESULTS San Diego, CA, May 8, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections, announced today its financial results for the first quarter ended March 31, 2012 and provide

Termination of a Material Definitive Agreement, Financial Statements and Exhibits, Results of Operations and Financial Condition

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): May 3, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commission

- DEFINITIVE PROXY STATEMENT

Definitive Proxy Statement SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): April 6, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commissi

- FORM S-8

Form S-8 As filed with the Securities and Exchange Commission on March 14, 2012 Registration No.

Financial Statements and Exhibits, Results of Operations and Financial Condition - FORM 8-K

FORM 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 13, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commiss

TRIUS THERAPEUTICS REPORTS FOURTH QUARTER AND YEAR END 2011 FINANCIAL

PRESS RELEASE DATED MARCH 13, 2012 Exhibit 99.1 TRIUS THERAPEUTICS REPORTS FOURTH QUARTER AND YEAR END 2011 FINANCIAL RESULTS San Diego, CA, March 13, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections, announced today its financial results for the fourth q

-

Comment and Response Letter VIA EDGAR AND FEDERAL EXPRESS February 17, 2012 United States Securities and Exchange Commission Division of Corporation Finance Mail Stop 4720 100 F Street, N.

TSRX / Trius Therapeutics Inc / WELLINGTON MANAGEMENT GROUP LLP - DISCLOSURE DOCUMENT Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K100 (CUSIP Number) December 31, 2011 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which thi

TSRX / Trius Therapeutics Inc / WELLINGTON MANAGEMENT GROUP LLP - DISCLOSURE DOCUMENT Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K100 (CUSIP Number) January 31, 2012 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this

TSRX / Trius Therapeutics Inc / Versant Side Fund III, L.P. - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 2)* Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K10 (CUSIP Number) December 31, 2011 (Date of Event

8,600,000 Shares TRIUS THERAPEUTICS, INC. Common Stock, par value $0.0001 per share UNDERWRITING AGREEMENT

Underwriting Agreement Exhibit 1.1 8,600,000 Shares TRIUS THERAPEUTICS, INC. Common Stock, par value $0.0001 per share UNDERWRITING AGREEMENT January 26, 2012 CITIGROUP GLOBAL MARKETS INC. PIPER JAFFRAY & CO. As Representatives of the several Underwriters, c/o Citigroup Global Markets Inc. 388 Greenwich Street New York, NY 10013 c/o Piper Jaffray & Co. U.S. Bancorp Center 800 Nicollet Mall Minneap

8,600,000 Shares Common Stock

Final Prospectus Supplement Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No.

TRIUS THERAPEUTICS, INC. PRICES PUBLIC OFFERING OF COMMON STOCK

Press Release dated January 26, 2012 Exhibit 99.2 TRIUS THERAPEUTICS, INC. PRICES PUBLIC OFFERING OF COMMON STOCK San Diego, CA, January 26, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX) today announced the pricing of an underwritten public offering of 8,600,000 shares of its common stock at a price to the public of $5.25 per share. The gross proceeds to Trius from this offering are expected to b

TRIUS THERAPEUTICS, INC. ANNOUNCES PROPOSED PUBLIC OFFERING OF COMMON STOCK

Press Release dated January 25, 2012 Exhibit 99.1 TRIUS THERAPEUTICS, INC. ANNOUNCES PROPOSED PUBLIC OFFERING OF COMMON STOCK San Diego, CA, January 25, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX) today announced that it intends to offer and sell shares of its common stock in an underwritten public offering. Citigroup and Piper Jaffray & Co. are acting as joint book-running managers. The offeri

Entry into a Material Definitive Agreement, Financial Statements and Exhibits - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 26, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commi

SUBJECT TO COMPLETION, DATED JANUARY 25, 2012

Preliminary Prospectus Supplement Table of Contents The information in this preliminary prospectus supplement is not complete and may be changed.

Other Events - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 25, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commi

TRIUS EARNS $5 MILLION MILESTONE PAYMENT FROM BAYER FOR SUCCESSFUL COMPLETION OF FIRST PHASE 3 TRIAL OF TEDIZOLID

Press Release Exhibit 99.1 TRIUS EARNS $5 MILLION MILESTONE PAYMENT FROM BAYER FOR SUCCESSFUL COMPLETION OF FIRST PHASE 3 TRIAL OF TEDIZOLID San Diego, CA, January 23, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX) announced today that it has earned a $5 million milestone payment from Bayer HealthCare for the achievement of all efficacy and safety objectives in the TR701-112 Phase 3 pivotal study

Financial Statements and Exhibits, Other Events - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 23, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commi

TSRX / Trius Therapeutics Inc / SOFINNOVA VENTURE PARTNERS VII L P - AMENDED TRANSACTION REPORT Activist Investment

SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13D (RULE 13d-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(a) (AMENDMENT NO. 2) Trius Therapeutics, Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 89685K100 (CUSIP Number) Nathalie Auber Sofinnova Ventures, Inc. 2800 Sand Hill Ro

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Response Letter January 13, 2012 United States Securities and Exchange Commission Division of Corporation Finance Mail Stop 4720 100 F Street, N.

Financial Statements and Exhibits, Other Events - FORM 8-K

Form 8-K UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K Current Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 3, 2012 TRIUS THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-34828 20-1320630 (State of incorporation or organization) (Commis

Tedizolid 112 Trial: Top Line Results

Slide presentation dated January 3, 2012 1 Tedizolid 112 Trial: Top Line Results Update January 3, 2012 Exhibit 99.