EXHIBIT 3.3 CERTIFICATE OF AMENDMENT TO RESTATED CERTIFICATE OF INCORPORATION OF MICROCIDE PHARMACEUTICALS, INC. a Delaware Corporation Pursuant to (S)242 of the General Corporation Law of the State of Delaware Microcide Pharmaceuticals, Inc., a corporation organized and existing under the General Corporation Law of the State of Delaware (the "Corporation") does hereby certify: 1. The name of the Corporation is Microcide Pharmaceuticals, Inc. and was originally incorporated under the same name, and the original Certificate of Incorporation was filed with the Secretary of State of the State of Delaware on February 29, 1996. 2. The following amendment to the Restated Certificate of Incorporation of the corporation has been duly adopted in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware: Article I of the Restated Certificate of Incorporation is hereby amended to read in its entirety as follows: "ARTICLE I. The name of this corporation is Essential Therapeutics, Inc." 3. The capital of the corporation will not be reduced under or by reason of the foregoing amendment. IN WITNESS WHEREOF, Microcide Pharmaceuticals, Inc. has caused this Certificate to be executed by its duly authorized officer this 24th day of October, 2001. MICROCIDE PHARMACEUTICALS, INC. By: /s/ James E. Rurka -------------------------------------------- Name: James E. Rurka Title: President and Chief Executive Officer