**EXHIBIT10.41**

**CHANGE IN CONTROL AGREEMENT**

**THIS CHANGE IN CONTROL AGREEMENT** (the ***“Agreement”***) is made as of October10, 2006 between **SENOMYX, INC.**,a Delaware corporation (the ***“Company”***),and Sharon Wicker (***“Employee”***).

**WHEREAS**,in order to provide an incentive for Employee to participate actively in theaffairs and maximize the value of the Company, the Company is willing toprovide Employee with certain benefits on the terms and conditions set forthbelow.

**NOW THEREFORE,** for good and valuable consideration,the sufficiency of which is hereby acknowledged, Employee and the Company(each, a ***“Party,”*** and collectively,the ***“Parties”***) agree as follows:

**1.****             BENEFITS IN THE EVENT OF A CHANGE IN CONTROL**.  If(i) a Change in Control (defined below) occurs and (ii) during theperiod beginning one (1) month prior to the effective date of such Change inControl and ending eighteen (18) months after the effective date of such Changein Control, Employee’s employment with the Company is terminated either (A) bythe Company without Cause (defined below) (not including death orDisability (as defined below)) or (B) byEmployee for Good Reason (defined below) (not including death or Disability),then, without further action by Employee or the Company, Employee shall beentitled to the benefits set forth below:

**(a)****          **The vestingapplicable to all options to purchase shares of the Company’s capital stock (***“Options”***) and all shares of theCompany’s capital stock which are subject to the Company’s right to repurchasesuch shares (***“Restricted Stock”***) held byEmployee as of the effective date of such termination shall be accelerated infull such that Employee shall have the right to exercise in accordance with theterms thereof all or any portion of such Options (notwithstanding any vestingschedule set forth in such Options) and any such Company repurchase rights withrespect to such Restricted Stock shall lapse in full; and

**(b)****          **Employee shall beentitled to receive a lump sum cash payment in an amount equal to one hundredpercent (100%) of Employee’s Annual Pay (as defined below), payable on theEffective Date specified in the Release (as defined below) delivered byEmployee to the Company following such Change in Control.  The foregoing payments shall be subject tostandard deductions and withholdings.

**(c)****          **Assumingthe Employee timely and accurately elects to continue her health insurancebenefits under the Consolidated Omnibus Budget Reconciliation Act of 1985 (“***COBRA***”), the Companyshall reimburse the Employee for the COBRA expenses she pays on behalf ofhimself and her family until the earliest of (i) the end of the 12 month periodfollowing Employee’s termination, (ii) the expiration of the Employee’scontinuation coverage under COBRA and any applicable state COBRA-like statutethat provides mandated continuation coverage or (iii) the date the Employeebecomes eligible for health insurance benefits of a subsequent employer.

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**2.****             Release. **Notwithstanding the foregoing, theEmployee shall not receive any of the severance payments or benefits set forthunder Section 1, unless upon Employee’s termination of employment the Employeefurnishes the Company with an effective waiver and release of claims (the ***“Release”***) in a form acceptable tothe Company and substantially as attached hereto as **Exhibit A**.** **If a majority of the Board ofDirectors of the Company (the ***“Board”***)determines in good faith that the Employee has breached any provision of herProprietary Information and Inventions Agreement with the Company or anyprovision of this Agreement, the Employment Agreement (as defined below) or theRelease, the Company shall be excused from the obligation to provide anyseverance payment under Section 1 and the Company shall be entitled to fullrecovery of any severance payment already provided to the Employee underSection 1.

**3.****             DEFINITIONS. **For purposes of this Agreement, capitalized terms used hereinshall have the following meanings:

**(a)****           *“Annual Pay”***shall mean the sum of the Employee’s (i) base salary in effecton the date of termination and (ii) the last annual bonus paid to the Employeeby the Company prior to the date of termination.

**(b)****           *“Cause”***means the occurrence of any of thefollowing:  (i) the Employee’s commissionof any felony or any crime involving fraud, dishonesty or moral turpitude underthe laws of the United States or any state thereof; (ii) the Employee’sattempted commission of, or participation in, a fraud or act of dishonestyagainst the Company; (iii) the Employee’s intentional and material violation ofany contract or agreement between the Employee and the Company or any statutoryduty owed to the Company; (iv) the Employee’s unauthorized use or disclosure ofthe Company’s confidential information or trade secrets or (v) the Employee’sgross misconduct.  The determination thata termination is for Cause shall be made by the Company in its discretion.  Any determination by the Company that theemployment of the Employee was terminated by reason of dismissal without Causefor the purposes of determining benefits under this Agreement shall have noimpact upon any determination of the rights or obligations of the Company orsuch Employee for any other purpose.

**(c)****           *“Change in Control”*** means the occurrence, in a singletransaction or in a series of related transactions, of any one or more of thefollowing events:

**(i)****           **any Exchange ActPerson (as defined in the Company’s Amended and Restated 2004 Equity IncentivePlan (the ***“Plan”***)) becomes the owner,directly or indirectly, of securities of the Company representing more thanfifty percent (50%) of the combined voting power of the Company’s thenoutstanding securities other than by virtue of a merger, consolidation orsimilar transaction.  Notwithstanding theforegoing, a Change in Control shall not be deemed to occur (A) on account ofthe acquisition of securities of the Company by an investor, any affiliatethereof or any other Exchange Act Person from the Company in a transaction orseries of related transactions the primary purpose of which is to obtainfinancing for the Company through the issuance of equity securities or (B)solely because the level of Ownership (as defined in the Plan) held by anyExchange Act Person (the “***SubjectPerson***”) exceeds the designated percentage threshold of theoutstanding voting securities as a result of a repurchase or other acquisitionof voting securities by the Company reducing the number of shares outstanding,provided that if a Change in Control would occur (but for the operation of

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this sentence) as a result of the acquisition ofvoting securities by the Company, and after such share acquisition, the SubjectPerson becomes the Owner of any additional voting securities that, assuming therepurchase or other acquisition had not occurred, increases the percentage ofthe then outstanding voting securities Owned by the Subject Person over thedesignated percentage threshold, then a Change in Control shall be deemed tooccur;

**(ii)****          **thereis consummated a merger, consolidation or similar transaction involving(directly or indirectly) the Company and, immediately after the consummation ofsuch merger, consolidation or similar transaction, the stockholders of theCompany immediately prior thereto do not Own, directly or indirectly, either(A) outstanding voting securities representing more than fifty percent (50%) ofthe combined outstanding voting power of the surviving Entity (as defined inthe Plan) in such merger, consolidation or similar transaction or (B) more thanfifty percent (50%) of the combined outstanding voting power of the parent ofthe surviving Entity in such merger, consolidation or similar transaction, ineach case in substantially the same proportions as their Ownership of theoutstanding voting securities of the Company immediately prior to suchtransaction;

**(iii)****        **thestockholders of the Company approve or the Board approves a plan of completedissolution or liquidation of the Company, or a complete dissolution orliquidation of the Company shall otherwise occur;

**(iv)****         **thereis consummated a sale, lease, license or other disposition of all orsubstantially all of the consolidated assets of the Company and itsSubsidiaries (as defined in the Plan), other than a sale, lease, license orother disposition of all or substantially all of the consolidated assets of theCompany and its Subsidiaries to an Entity, more than fifty percent (50%) of thecombined voting power of the voting securities of which are Owned bystockholders of the Company in substantially the same proportions as theirOwnership of the outstanding voting securities of the Company immediately priorto such sale, lease, license or other disposition; or

**(v)****           **individuals who,on the date of this Agreement, are members of the Board (the ***“Incumbent Board”***)cease for any reason to constitute at least a majority of the members of theBoard; *provided, however,* that ifthe appointment or election (or nomination for election) of any new Boardmember was approved or recommended by a majority vote of the members of theIncumbent Board then still in office, such new member shall, for purposes ofthis Agreement, be considered as a member of the Incumbent Board.

**(d)****          *****“Disability”*** shall mean Employee’sfailure or inability, for reasons of health, to perform Employee’s usual andcustomary duties on behalf of the Company in the usual and customary manner fora total of more than ninety (90) consecutive business days (excludingSaturdays, Sundays and holidays (days during which the Company is closed due toa recognized holiday)).

**(e)****          *****“Good Reason”*** shall mean theoccurrence of any of the following events or conditions:  (i) (A) a change in the Employee’s status,title, position or responsibilities (including reporting responsibilities)which represents an adverse change from the Employee’s status, title, positionor responsibilities as in effect at any time within ninety (90) days precedingthe date of a 

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Change in Control or at any time thereafter; (B) theassignment to the Employee of any duties or responsibilities which areinconsistent with the Employee’s status, title, position or responsibilities asin effect at any time within ninety (90) days preceding the date of a Change inControl or at any time thereafter; or (C) any removal of the Employee from orfailure to reappoint or reelect the Employee to any of such offices orpositions (unless such removal or failure to reappoint or reelect is (1) inconnection with the termination of the Employee’s employment for Cause, (2) asa result of the Employee’s Disability or death, or (3) by the Employee otherthan as a result of termination for Good Reason); (ii) a reduction in theEmployee’s annual base compensation; or (iii) the Company’s requiring theEmployee to relocate to any place outside a fifty (50) mile radius of theEmployee’s current work site, excluding in any event reasonably required travelon the business of the Company or its affiliates. Notwithstanding theforegoing, in no event shall Good Reason be satisfied solely because theEmployee retains the same position held prior to the Change in Control but in adistinct legal entity or business unit of a larger entity following the Changein Control.

**4.****             GOLDEN PARACHUTE TAXES.**  If any payment or benefit Employee wouldreceive pursuant to a Change in Control from the Company or otherwise (***“Payments”***) would (i) constitute a “parachutepayment” within the meaning of Section 280G of the Internal Revenue Code of1986, as amended (the ***“Code”***),and (ii) but for this sentence, be subject to the excise tax imposed by Section4999 of the Code (the ***“Excise Tax”***),then such Payments shall be equal to the Reduced Amount.  The ***“Reduced Amount”***shall be either (x) the largest portion of the Payment that would result in noportion of the Payment being subject to the Excise Tax or (y) the largestportion, up to and including the total, of the Payment, whichever amount, aftertaking into account all applicable federal, state and local employment taxes,income taxes, and the Excise Tax (all computed at the highest applicablemarginal rate), results in Employee’s receipt, on an after-tax basis, of thegreater amount of the Payment notwithstanding that all or some portion of thePayment may be subject to the Excise Tax. If a reduction in payments orbenefits constituting “parachute payments” is necessary so that the Paymentequals the Reduced Amount, reduction shall occur in the following order unlessEmployee elects in writing a different order (*provided,however,* that such election shall be subject to Company approval ifmade on or after the date on which the event that triggers the Paymentoccurs):  reduction of cash payments;cancellation of accelerated vesting of stock awards; reduction of employeebenefits.  In the event that accelerationof vesting of stock award compensation is to be reduced, such acceleration ofvesting shall be cancelled in the reverse order of the date of grant ofEmployee’s stock awards unless Employee elects in writing a different order forcancellation.

The accounting firm engagedby the Company for general audit purposes as of the day prior to the effectivedate of the Change in Control shall perform the foregoing calculations.  If the accounting firm so engaged by theCompany is serving as accountant or auditor for the individual, entity or groupeffecting the Change in Control, the Company shall appoint a nationallyrecognized accounting firm to make the determinations required hereunder.  The Company shall bear all expenses withrespect to the determinations by such accounting firm required to be madehereunder.

The accounting firm engaged to make the determinationshereunder shall provide its calculations, together with detailed supportingdocumentation, to the Company and Employee within fifteen (15) calendar daysafter the date on which Employee’s right to a Payment is

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triggered (if requested at that time by the Company orEmployee) or such other time as requested by the Company or Employee.  If the accounting firm determines that noExcise Tax is payable with respect to a Payment, either before or after theapplication of the Reduced Amount, it shall furnish the Company and Employeewith an opinion reasonably acceptable to Employee that no Excise Tax will beimposed with respect to such Payment. Any good faith determinations of the accounting firm made hereundershall be final, binding and conclusive upon the Company and Employee.

**5.****            ****APPLICATIONOF CODE SECTION 409A****.**  If the Company determines that any of the Payments****failto satisfy the distribution requirement of Section 409A(a)(2)(A) of the Code asa result of Section 409A(a)(2)(B)(i) of the Code, the Payments shall beaccelerated to the minimum extent necessary so that such Payments are notsubject to the provisions of Section 409A(a)(1) of the Code (It is theintention of the preceding sentence to apply the short-term deferral provisionsof Section 409A of the Code, and the regulations and other guidance thereunder,to the Payments, and the paymentschedule as revised after the application of the preceding sentence shall bereferred to as the ***“Revised Payment Schedule”***).  However, if there is no Revised PaymentSchedule that would avoid the application of Section 409A(a)(1) of the Code,the payment of such benefits shall not be paid pursuant to a Revised PaymentSchedule and instead shall be delayed to the minimum extent necessary so thatsuch benefits are not subject to the provisions of Section 409A(a)(1) of theCode.  The Board may attach conditions toor adjust the amounts paid pursuant to this Section 5****topreserve, as closely as possible, the economic consequences that would haveapplied in the absence of this Section5; *provided, however,* thatno such condition or adjustment shall result in the payments being subject toSection 409A(a)(1) of the Code.

**6.****             GENERAL PROVISIONS.**

**(a)****          **This Agreementshall be governed by the laws of the State of California (without regard toprinciples of conflict of laws).

**(b)****          **Any notice, demandor request required or permitted to be given by either the Company or Employeepursuant to the terms of this Agreement shall be in writing and shall be deemedgiven when delivered personally or deposited in the U.S. mail, First Class withpostage prepaid, and addressed to the parties at such addresses as have beenpreviously furnished by the Parties or such other address as a Party mayrequest by notifying the other in writing.

**(c)****          **The rights andobligations of Employee under this Agreement may not be transferred or assignedwithout the prior written consent of the Company.

**(d)****          **This Agreement ismeant to supplement the terms of stock option agreement(s) or otheragreement(s) pursuant to which Employee acquired the Options, as well as anywritten employment agreement between the Company and Employee, includingEmployee’s employment agreement with the Company dated March 13, 2006 (the ***“Employment Agreement”****)*.  To the extent thatthe terms and conditions of this Agreement regarding payment of severancebenefits are inconsistent with those found in the Employment Agreement, theterms and conditions of this Agreement shall be controlling.  Notwithstanding the foregoing, the partiesacknowledge and agree that if Employee is terminated without “cause” and thetermination is not

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during the period beginning one(1) month prior to the effective date of a Change in Control and endingeighteen (18) months after the effective date of a Change in Control, the termsof the Employment Agreement (including the definition of cause set forththerein) shall govern the payment of any severance benefits to Employee inconnection with such termination.

**(e)****          **Any Party’s failureto enforce any provision or provisions of this Agreement shall not in any waybe construed as a waiver of any such provision or provisions, nor prevent anyParty from thereafter enforcing each and every other provision of thisAgreement.  The rights granted theParties herein are cumulative and shall not constitute a waiver of any Party’sright to assert all other legal remedies available to it under thecircumstances.

**(f)****           **Employee agreesupon request to execute any further documents or instruments necessary ordesirable to carry out the purposes or intent of this Agreement.

**(g)****          **In case anyprovision of this Agreement shall be invalid, illegal or unenforceable, thevalidity, legality and enforceability of the remaining provisions shall not inany way be affected or impaired.

**(h)****          **This Agreement, inwhole or in part, may be modified, waived or amended upon the written consentof the Company and Employee.

**(i)****           **This Agreement maybe executed in one or more counterparts, each of which shall be deemed anoriginal, but all of which shall constitute one instrument.

[THE REMAINDER OF THIS PAGEINTENTIONALLY LEFT BLANK]

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**INWITNESS WHEREOF,** the undersigned have set their hand as ofthe date first above written.
| **Employee**     | **Senomyx, Inc.** |
|------------------|-------------------|
| ** **       |              |
| ** **       |              |
| /s/Sharon Wicker |              | By: |      /s/Kent Snyder |   |
|             |              |
| Sharon Wicker    | Name:             |   Kent Snyder |   |
|             |              |
|             | Title:            |     President and CEO |   |
|                  |                   |  |  |  |  |  |

 

[SIGNATURE PAGE TOCHANGE IN CONTROL AGREEMENT]

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**EXHIBIT A**

**RELEASE AND WAIVER OF CLAIMS**

Inconsideration of the payments and other benefits set forth in the Change inControl Agreement dated October 10, 2006, between Senomyx, Inc. (the ***“Company”***) and Sharon Wicker (***“Employee”***), to which this form isattached, Employee hereby furnishes the Company with the following release andwaiver.

Employeehereby releases, and forever discharges the Company, its officers, directors,agents, employees, stockholders, successors, assigns and affiliates, of andfrom any and all claims, liabilities, demands, causes of action, costs,expenses, attorneys’ fees, damages, indemnities and obligations of every kindand nature, in law, equity, or otherwise, known and unknown, suspected andunsuspected, disclosed and undisclosed, arising at any time prior to andincluding Employee’s employment termination date with respect to any claimsrelating to Employee’s employment and the termination of Employee’s employment,including but not limited to, claims pursuant to any federal, state or locallaw relating to employment, including, but not limited to, discriminationclaims, claims under the California Fair Employment and Housing Act, and theFederal Age Discrimination in Employment Act of 1967, as amended (***“ADEA”***), the Federal Americans withDisabilities Act or claims for wrongful termination, breach of the covenant ofgood faith, contract claims, tort claims, and wage or benefit claims, includingbut not limited to, claims for salary, bonuses, commissions, stock, stockoptions, vacation pay, fringe benefits, severance pay or any form ofcompensation.  Notwithstanding the above, this Release andWaiver does not release any claims Employee may have (i) for indemnificationpursuant to and in accordance with the applicable statutes and the applicableterms of the charters, articles of incorporation or bylaws of the Company orunder any indemnification agreements or insurance coverage, (ii) in vestedpension and retirement benefits under the terms of qualified employee pensionbenefit plans, (iii) for accrued benefits under the terms of applicableemployment agreements or employee benefit plans, and (iv) for any claims underany state Workers’ Compensation laws and any state unemployment benefits laws.

Employeealso acknowledges that Employee has read and understood Section 1542 of theCalifornia Civil Code which reads as follows: “A general release does not extend to claims which the creditor does notknow or suspect to exist in her favor at the time of executing the release,which if known by him must have materially affected her settlement with thedebtor.”  Employee hereby expresslywaives and relinquishes all rights and benefits under that section and any lawof any jurisdiction of similar effect with respect to any claims Employee mayhave against the Company.

Employeeacknowledges that, among other rights, Employee is waiving and releasing anyrights Employee may have under ADEA, that this waiver and release is knowingand voluntary, and that the consideration given for this waiver and release isin addition to anything of value to which Employee was already entitled as anemployee of the Company.  Employeefurther acknowledges that Employee has been advised, as required by the OlderWorkers Benefit Protection Act, that: (a) the waiver and release granted herein does not relate to claimswhich may arise after this release and waiver is executed; (b) Employeehas the right to consult with an attorney prior to executing this release andwaiver (although Employee may choose voluntarily not to do so); and (c) ifon the date of execution of this release and waiver Employee is age 40 or

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older, then(I) Employee has twenty-one (21) days from the date Employee receives thisrelease and waiver, in which to consider this release and waiver (althoughEmployee may choose voluntarily to execute this release and waiver earlier);and (II) Employee has seven (7) days following the execution of thisrelease and waiver to revoke Employee’s consent to this release andwaiver.  This release and waiver shall beeffective as of the date of execution hereof; provided that if on the date ofexecution of this release and waiver Employee is age 40 or older, then this releaseand waiver shall not be effective until the foregoing seven (7) day revocationperiod has expired.  The date as of whichthis release and waiver is effective as aforesaid shall be deemed the “EffectiveDate” hereof.
| Date:  |   |   |          | By:    |   |   |
|--------|--------|--------|---------------|--------|--------|--------|
|   |   |   | Sharon Wicker |   |

 

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