<PAGE>

                                                                   Exhibit 10.62

                               SEVERANCE AGREEMENT

THIS AGREEMENT is entered into as of July 15, 2002, by and between Nancy E.
Wetherbee (the "Employee") and Essential Therapeutics, Inc., a Delaware
corporation (the "Company").

1.   Term of Agreement.
     This Agreement shall remain in effect from the date hereof until the
     earlier of:This Agreement shall remain in effect from the date hereof until
     the earlier of:
     a)  The date when the Employee's employment with the Company terminates for
         any reason not described in Section 6; or
     b)  The date when the Company has met all of its obligations under this
         Agreement following a Termination event as defined in Section 6 below.

2.   Definition of Change in Control.

     For all purposes under this Agreement, "Change in Control" shall mean (i) a
     merger, reorganization or other transaction or series of related
     transactions (other than financings) following which the shareholders of
     the Company do not own a majority of the capital stock of the surviving
     corporation or (ii) the sale of all or substantially all of the assets of
     the Company.

3.   Definition of Good Reason.

     For all purposes under this Agreement, "Good Reason" shall mean that the
     Employee:
     a)  Has been demoted or has incurred a material reduction in his authority
         or responsibility as an employee of the Company, including (without
         limitation) a reduction or elimination of his authority to approve
         expenditures or to hire, promote, demote or terminate subordinates;
     b)  Has incurred a reduction in his total compensation (including benefits)
         as an employee of the Company, other than pursuant to a Company-wide
         reduction of total compensation (including benefits) for employees of
         the Company generally; or
     c)  Has been notified that his principal place of work as an employee of
         the Company will be relocated by a distance of 50 miles or more.

4.   Definition of Cause.

         For all purposes under this Agreement, "Cause" shall mean:
     a)  A willful act by the Employee which constitutes misconduct or fraud and
         which is injurious to the Company; provided, however, that no act, or
         failure to act, by the Employee shall be considered "willful" unless
         committed

<PAGE>

         without good faith and without a reasonable belief that the act or
         omission was in the Company's best interest; or
     b)  Conviction of, or a plea of "guilty" or "no contest" to, a felony.

         The Board of Directors of the Company shall have sole discretion with
         respect to whether any act or failure to act constitutes "Cause" for
         purposes of this Agreement.

5.   Definition of Continuation Period.

     For all purposes under this Agreement, "Continuation Period" shall mean the
     period commencing on the date when the termination of the Employee's
     employment under Section 6 is effective and ending on the earlier of:
     a)  The date twelve (12) months after the date when the employment
         termination was effective; or
     b)  The date of the Employee's death.

6.   Entitlement to Severance Pay and Benefits.

     The employee shall be entitled to receive the severance pay described in
     Section 7 (the "Severance Pay") and the benefits described in Section 8
     from the Company if, and only if, one of the following events occurs (each
     a "Termination Event"):
     a)  Within the first 12-month period after the occurrence of a Change in
         Control, the Employee voluntarily resigns his employment for Good
         Reason; or
     b)  Within the first 12-month period after the occurrence of a Change in
         Control, the Company terminates the Employee's employment for any
         reason other than Cause.

7.   Amount of Severance Pay.

     During the Continuation Period, the Company shall pay the Employee
     Severance Pay at an annual rate equal to the Employee's base compensation
     at the annual rate in effect on the date when the termination of his
     employment with the Company is effective. Such amount shall be paid
     pro-rata at periodic intervals in accordance with the Company's standard
     procedures.

8.   Other Benefits

     a)  Stock options and Restricted Stock. All unvested stock options and
         shares of restricted stock granted to Employee by the Company shall
         vest immediately upon the occurrence of a Termination Event. The
         post-termination exercise grace period under the Employee's stock
         options shall commence at the end of the Continuation Period. The
         Employee represents that he has consulted or will consult a tax advisor
         regarding the impact of this Subsection a) on the tax treatment of
         incentive stock options and shares of restricted stock.

<PAGE>

     b)  Group Insurance. At the commencement of the Continuation Period, the
         Employee (and, where applicable, his dependents) shall be entitled to
         convert his key employee long-term disability policy and group life
         insurance policy into individual policies pursuant to the terms of such
         policies. Should the Employee elect to convert either or both of such
         policies, the Company will pay the premiums for such policy or policies
         during the Continuation Period. At the commencement of the Continuation
         Period, the Employee shall be eligible to continue his group health
         continuation coverage under the Consolidated Omnibus Budget
         Reconciliation Act of 1986, and the Company will pay the premiums for
         such coverage during the Continuation Period. The foregoing
         notwithstanding, in the event that the Employee becomes eligible for
         comparable group insurance coverage in connection with new employment,
         the premium payments by the Company under this Subsection b) shall
         terminate immediately.

     c)  Outplacement Services. Upon the occurrence of a Termination Event, the
         Employee shall be entitled to reasonable outplacement services at the
         Company's expense. Such services shall be provided by a firm selected
         by the Employee from a list compiled by the Company and shall be
         limited to a period of six consecutive months.

9.   Limitation on Payments.

     a)  Basic Rule. Any other provision of this Agreement notwithstanding, the
         Company shall not be required to make any payment or property transfer
         to, or for the benefit of, the Employee (under this Agreement or
         otherwise) that would be nondeductible by the company by reason of
         Section 20G of the Internal Revenue Code of 1986, as amended (the
         "Code"), or that would subject the Employee to the excise tax described
         in Section 4999 of the Code. All calculations required by this Section
         9 shall be performed by the independent auditors retained by the
         Company most recently prior to the Change in Control (the "Auditors"),
         based on information supplied by the Company and the Employee, and
         shall be binding on the Company and the Employee. All fees and expenses
         of the Auditors shall be paid by the Company.

     b)  Reductions. If the amount of the aggregate payments or property
         transfers to the Employee must be reduced under this Section 9, then
         the Employee shall direct in which order the payments or transfers are
         to be reduced, but no change in the timing of any payment or transfer
         shall be made without the Company's consent. As a result of uncertainty
         in the application of sections 280G and 4999 of the Code at the time of
         an initial determination by the Auditors hereunder, it is possible that
         a payment will have been made by the Company that should not have been
         made (an "Overpayment"), or that an additional payment that will not
         have been made by the Company could have been made (an "Underpayment").
         IN the event that the Auditors, based upon

<PAGE>

         the assertion of a deficiency by the Internal Revenue Service against
         the Company or the Employee that the Auditors believe has a high
         probability of success, determine that an Overpayment has been made,
         such Overpayment shall be treated for all purposes as a loan to the
         Employee that he shall repay to the Company, together with interest at
         the applicable federal rate specified in section 7872(f)(2) of the
         Code; provided, however, that no amount shall be payable by the
         Employee to the company if and to the extent that such payment would
         not reduce the amount that is nondeductible under section 280G of the
         Code or is subject to an excise tax under section 4999 of the Code. In
         the event that the Auditors determine that an Underpayment has
         occurred, such Underpayment shall promptly be paid or transferred by
         the Company to, or for the benefit of, the Employee, together with
         interest at the applicable federal rate specified in section 7872(f)(2)
         of the Code.

10.  Non-solicitation.

         After the occurrence of a Termination Event, the Employee agrees that
         for a period of two years from the date of the Termination Event (the
         "Non-Solicitation Term") he will not directly or indirectly solicit for
         employment any employee of the Company who was employed by the Company
         at the time of the Occurrence of Termination Event and remains in the
         employment of the Company during the Non-Solicitation Term.

11.  Successors.

     a)  Company's Successors. The Company shall require any successor (whether
         direct or indirect and whether by purchase lease, merger,
         consolidation, liquidation or otherwise) to all or substantially all of
         the Company's business and/or assets, by an agreement in substance and
         form satisfactory to the Employee, to assume this Agreement and to
         agree expressly to perform this Agreement in the same manner and to the
         same extent as the Company would be required to perform it in the
         absence of a succession. For all purposes under this Agreement, the
         Term "Company" shall include any successor to the Company's business
         and/or assets which executes and delivers the assumption agreement
         described in this Subsection (a) or which becomes bound by this
         Agreement by operation of law.

     b)  Employee's Successors. This Agreement and all rights of the Employee
         hereunder shall inure to the benefit of, and be enforceable by, the
         Employee's personal or legal representatives, executors,
         administrators, successors, heirs, distributes, devisees and legatees.

12.  Miscellaneous Provisions.

     a)  Notice. Notices and all other communications contemplated by this
         Agreement shall be in writing and shall be deemed to have been duly
         given

<PAGE>

         when personally delivered or when mailed by U.S. registered or
         certified mail, return receipt requested and postage prepaid. In the
         case of the Employee, mailed notices shall be addressed to him at the
         home address, which he most recently communicated to the Company in
         writing. In the case of the company, mailed notices shall be addressed
         to its corporate headquarters, and all notices shall be directed to
         the attention of its Secretary.

     b)  Waiver. No provision of this Agreement shall be modified, waived or
         discharge unless the modification, waiver or discharge is agreed to in
         writing and signed by the Employee and by an authorized officer of the
         Company (other than the Employee). No waiver by either party of any
         breach of, or of compliance with, any condition or provision of this
         Agreement by the other party shall be considered a waiver of any other
         condition or provision or of the same condition or provision at another
         time.

     c)  Whole Agreement. No agreements, representations or understandings
         (whether oral or written and whether express or implied) which are not
         expressly set forth in this Agreement have been made or entered into by
         either party with respect to the subject matter hereof.

     d)  No Setoff; Withholding Taxes. There shall be no right of setoff or
         counterclaim, with respect to any claim, debt or obligation, against
         payments to the Employee under this Agreement. All payments made under
         this Agreement shall be subject to reduction to reflect taxes required
         to be withheld by law.

     e)  Choice of Law. The validity or unenforceability of any provision or
         provisions of the Agreement shall not affect the validity or
         enforceability of any other provision hereof, which shall remain in
         full force and effect.

     f)  Severability. The invalidity or unenforceability of any other provision
         hereof, which shall remain in full force and effect.

     g)  Potential Pooling Transactions. In the event the Board determines that
         the acceleration of options pursuant to Sections 8(a) above would
         preclude accounting for a proposed business transaction involving a
         Change in Control as a "Pooling of Interests" but the Board otherwise
         desires to approve and account for such transaction as a "Pooling of
         Interests," the acceleration of options described in Sections 8(a)
         above shall be null and void, and the Company shall enter into a
         consulting agreement with the employee covering services and
         compensation to be determined by the parties at that time. Such
         agreement shall be for a period of three years and shall not be subject
         to earlier termination unless by mutual consent of the parties.

     h)  Arbitration. Except as otherwise provided in Section 9, any dispute or
         controversy arising under or in connection with this Agreement shall be

<PAGE>

         settled exclusively by arbitration in San Jose, California, in
         accordance with the rules of the American Arbitration Association then
         in effect. Judgment may be entered on the arbitrator's award in any
         court having jurisdiction. Punitive damages shall not be awarded.

     i)  No Assignment of Benefits. The rights of any person to payments or
         benefits under this Agreement shall not be made subject to option or
         assignment, either by voluntary or involuntary assignment or by
         operation of law, including (without limitation) bankruptcy,
         garnishment, attachment or other creditor's process, and any action in
         violation of this subsection (i) shall be void.

     j)  Employment Taxes. All payments made pursuant to this Agreement will be
         subject to withholding of applicable income and employment taxes.

Counterparts. This Agreement may be executed in counterparts, each of which
shall be deemed an original but all of which together will constitute one and
the same instrument.

                                                Essential Therapeutics, Inc.


                                                _______________________________
                                                By:

                                                Title:


                                                Nancy E. Wetherbee


                                                _______________________________