Document:

EXHIBIT 10.1

CHANGE IN CONTROL AGREEMENT

This Change in Control Agreement (the “Agreement”) is made as of October 10,
2006 between Senomyx, Inc.,
a Delaware corporation (the “Company”),
and R. Kent Snyder (“Employee”).

Whereas,
in order to provide an incentive for Employee to participate actively in the
affairs and maximize the value of the Company, the Company is willing to
provide Employee with certain benefits on the terms and conditions set forth
below.

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.             Accelerated Vesting of Options in the Event of
a Change in Control.  If (i) a Change in Control (defined below)
occurs and (ii) during the period beginning one (1) month prior to the
effective date of such Change in Control and ending thirty-six (36) months
after the effective date of such Change in Control, Employee’s employment with
the Company is terminated either (A) by the Company without Cause (defined
below) (not including death or Disability (as defined below)) or (B) by Employee for Good Reason (defined
below) (not including death or Disability), then, without further action by
Employee, the vesting applicable to all options to purchase shares of
the Company’s capital stock (“Options”)
and all shares of the Company’s capital stock which are subject to the Company’s
right to repurchase such shares (“Restricted Stock”)
held by Employee as of the effective date of such termination shall be
accelerated in full such that Employee shall have the right to exercise in
accordance with the terms thereof all or any portion of such Options
(notwithstanding any vesting schedule set forth in such Options) and any such Company
repurchase rights with respect to such Restricted Stock shall lapse in full.

2.             Severance Benefits in the Event of a Change in
Control.  In addition to the benefits set forth in Section
1, if (i) a Change in Control occurs and (ii) during the period
beginning one (1) month prior to the effective date of such Change in Control
and ending eighteen (18) months after the effective date of such Change in
Control, Employee’s employment with the Company is terminated either (A) by the
Company without Cause (not including death or Disability) or (B) by Employee for Good Reason (not including
death or Disability), then, without further action by Employee or the Company,
Employee shall be entitled to the benefits set forth below:

(a)           Employee
shall be entitled to receive a lump sum cash payment in an amount equal to one
hundred fifty percent (150%) of Employee’s Annual Pay (as defined below),
payable on the Effective Date specified in the Release (as defined below)
delivered by Employee to the Company following such Change in Control.  The foregoing payments shall be subject to
standard deductions and withholdings.

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(b)           Assuming
the Employee timely and accurately elects to continue his health insurance
benefits under the Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”), the Company
shall reimburse the Employee for the COBRA expenses he pays on behalf of
himself and his family until the earliest of (i) the end of the 12 month period
following Employee’s termination, (ii) the expiration of the Employee’s
continuation coverage under COBRA and any applicable state COBRA-like statute
that provides mandated continuation coverage or (iii) the date the Employee
becomes eligible for health insurance benefits of a subsequent employer.

3.             Release.  Notwithstanding the foregoing, the
Employee shall not receive any of the severance payments or benefits set forth
under Sections 1 and/or 2, unless upon Employee’s termination of employment,
the Employee furnishes the Company with an effective waiver and release of claims
(the “Release”) in a form acceptable to
the Company and substantially as attached hereto as Exhibit A.  If a majority of the Board of
Directors of the Company (the “Board”)
determines in good faith that the Employee has breached any provision of his Proprietary
Information and Inventions Agreement with the Company or any provision of this
Agreement, the Employment Agreement (as defined below) or the Release, the
Company shall be excused from the obligation to provide any severance payment
under Sections 1 and/or 2 and the Company shall be entitled to full recovery of
any severance payment already provided to the Employee under Sections 1 and/or
2.

4.             Definitions. 
For purposes of this Agreement, capitalized terms used herein
shall have the following meanings:

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

(b)           “Cause” means
the occurrence of any of the following: 
(i) the Employee’s commission of any felony or any crime involving
fraud, dishonesty or moral turpitude under the laws of the United States or any
state thereof; (ii) the Employee’s attempted commission of, or participation
in, a fraud or act of dishonesty against the Company; (iii) the Employee’s
intentional and material violation of any contract or agreement between the
Employee and the Company or any statutory duty owed to the Company; (iv) the
Employee’s unauthorized use or disclosure of the Company’s confidential
information or trade secrets or (v) the Employee’s gross misconduct.  The determination that a termination is for
Cause shall be made by the Company in its discretion.  Any determination by the Company that the
employment of the Employee was terminated by reason of dismissal without Cause
for the purposes of determining benefits under this Agreement shall have no
impact upon any determination of the rights or obligations of the Company or
such Employee for any other purpose.

(c)           “Change in Control” means the occurrence, in a single
transaction or in a series of related transactions, of any one or more of the
following events:

(i)            any
Exchange Act Person (as defined in the Company’s Amended and Restated 2004
Equity Incentive Plan (the “Plan”))
becomes the owner, directly or indirectly, of securities of the Company
representing more than fifty percent (50%) of the combined voting 

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power of the Company’s then outstanding securities
other than by virtue of a merger, consolidation or similar transaction.  Notwithstanding the foregoing, a Change in
Control shall not be deemed to occur (A) on account of the acquisition of
securities of the Company by an investor, any affiliate thereof or any other
Exchange Act Person from the Company in a transaction or series of related
transactions the primary purpose of which is to obtain financing for the
Company through the issuance of equity securities or (B) solely because the
level of Ownership (as defined in the Plan) held by any Exchange Act Person
(the “Subject Person”)
exceeds the designated percentage threshold of the outstanding voting
securities as a result of a repurchase or other acquisition of 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 this
sentence) as a result of the acquisition of voting securities by the Company,
and after such share acquisition, the Subject Person becomes the Owner of any
additional voting securities that, assuming the repurchase or other acquisition
had not occurred, increases the percentage of the then outstanding voting
securities Owned by the Subject Person over the designated percentage
threshold, then a Change in Control shall be deemed to occur;

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

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

(iv)          there
is consummated a sale, lease, license or other disposition of all or
substantially all of the consolidated assets of the Company and its
Subsidiaries (as defined in the Plan), other than a sale, lease, license or
other disposition of all or substantially all of the consolidated assets of the
Company and its Subsidiaries to an Entity, more than fifty percent (50%) of the
combined voting power of the voting securities of which are Owned by
stockholders of the Company in substantially the same proportions as their
Ownership of the outstanding voting securities of the Company immediately prior
to 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 the
Board; provided, however, that if
the appointment or election (or nomination for election) of any new Board
member was approved or recommended by a majority vote of the members of the
Incumbent Board then still in office, such new member shall, for purposes of
this Agreement, be considered as a member of the Incumbent Board.

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

(e)           “Good Reason”
shall mean the occurrence 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, position or
responsibilities as in effect at any time within ninety (90) days preceding the
date of a Change in Control or at any time thereafter; (B) the assignment to
the Employee of any duties or responsibilities which are inconsistent with the
Employee’s status, title, position or responsibilities as in effect at any time
within ninety (90) days preceding the date of a Change in Control or at any
time thereafter; or (C) any removal of the Employee from or failure to
reappoint or reelect the Employee to any of such offices or positions (unless
such removal or failure to reappoint or reelect is (1) in connection with the
termination of the Employee’s employment for Cause, (2) as a result of the
Employee’s Disability or death, or (3) by the Employee other than as a result
of termination for Good Reason); (ii) a reduction in the Employee’s annual base
compensation; or (iii) the Company’s requiring the Employee to relocate to any
place outside a fifty (50) mile radius of the Employee’s current work site,
excluding in any event reasonably required travel on the business of the
Company or its affiliates. Notwithstanding the foregoing, in no event shall
Good Reason be satisfied solely because the Employee retains the same position
held prior to the Change in Control but in a distinct legal entity or business
unit of a larger entity following the Change in Control.

5.             Golden Parachute Taxes.  If any payment or benefit Employee would
receive pursuant to a Change in Control from the Company or otherwise (“Payments”) would (i) constitute a “parachute
payment” within the meaning of Section 280G of the Internal Revenue Code of
1986, as amended (the “Code”),
and (ii) but for this sentence, be subject to the excise tax imposed by Section
4999 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 no
portion of the Payment being subject to the Excise Tax or (y) the largest
portion, up to and including the total, of the Payment, whichever amount, after
taking into account all applicable federal, state and local employment taxes,
income taxes, and the Excise Tax (all computed at the highest applicable
marginal rate), results in Employee’s receipt, on an after-tax basis, of the
greater amount of the Payment notwithstanding that all or some portion of the
Payment may be subject to the Excise Tax. If a reduction in payments or
benefits constituting “parachute payments” is necessary so that the Payment
equals the Reduced Amount, reduction shall occur in the following order unless
Employee elects in writing a different order (provided,
however, that such election shall be subject to Company approval if
made on or after the date on which the event that triggers the Payment
occurs):  reduction of cash payments;
cancellation of accelerated vesting of stock awards; reduction of employee
benefits.  In the event that acceleration
of vesting of stock award compensation is to be reduced, such acceleration of
vesting shall be cancelled in the reverse order of the date of grant of
Employee’s stock awards unless Employee elects in writing a different order for
cancellation.

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The accounting firm engaged
by the Company for general audit purposes as of the day prior to the effective
date of the Change in Control shall perform the foregoing calculations.  If the accounting firm so engaged by the
Company is serving as accountant or auditor for the individual, entity or group
effecting the Change in Control, the Company shall appoint a nationally
recognized accounting firm to make the determinations required hereunder.  The Company shall bear all expenses with
respect to the determinations by such accounting firm required to be made
hereunder.

The accounting firm engaged to make the determinations
hereunder shall provide its calculations, together with detailed supporting
documentation, to the Company and Employee within fifteen (15) calendar days
after the date on which Employee’s right to a Payment is triggered (if
requested at that time by the Company or Employee) or such other time as
requested by the Company or Employee.  If
the accounting firm determines that no Excise Tax is payable with respect to a
Payment, either before or after the application of the Reduced Amount, it shall
furnish the Company and Employee with an opinion reasonably acceptable to
Employee that no Excise Tax will be imposed with respect to such Payment.  Any good faith determinations of the
accounting firm made hereunder shall be final, binding and conclusive upon the
Company and Employee.

6.             Application
of Code Section 409A.  If the Company determines that any of the Payments fail
to satisfy the distribution requirement of Section 409A(a)(2)(A) of the Code as
a result of Section 409A(a)(2)(B)(i) of the Code, the Payments shall be
accelerated to the minimum extent necessary so that such Payments are not
subject to the provisions of Section 409A(a)(1) of the Code (It is the
intention of the preceding sentence to apply the short-term deferral provisions
of Section 409A of the Code, and the regulations and other guidance thereunder,
to the Payments, and the payment
schedule as revised after the application of the preceding sentence shall be referred
to as the “Revised Payment Schedule”).  However, if there is no Revised Payment
Schedule 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 Payment
Schedule and instead shall be delayed to the minimum extent necessary so that
such benefits are not subject to the provisions of Section 409A(a)(1) of the
Code.  The Board may attach conditions to
or adjust the amounts paid pursuant to this Section 6 to
preserve, as closely as possible, the economic consequences that would have
applied in the absence of this Section 6;
provided, however, that no such
condition or adjustment shall result in the payments being subject to Section
409A(a)(1) of the Code.

7.             General Provisions.

(a)           This
Agreement shall be governed by the laws of the State of California (without
regard to principles of conflict of laws).

(b)           Any
notice, demand or request required or permitted to be given by either the
Company or Employee pursuant to the terms of this Agreement shall be in writing
and shall be deemed given when delivered personally or deposited in the U.S.
mail, First Class with postage prepaid, and addressed to the parties at such
addresses as have been previously furnished by the Parties or such other
address as a Party may request by notifying the other in writing.

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(c)           The
rights and obligations of Employee under this Agreement may not be transferred
or assigned without the prior written consent of the Company.

(d)           This
Agreement is meant to supplement the terms of stock option agreement(s) or
other agreement(s) pursuant to which Employee acquired the Options, as well as
any written employment agreement between the Company and Employee, including Employee’s
employment agreement with the Company dated June 2, 2003 (the “Employment Agreement”).  To the extent that the terms and conditions
of this Agreement regarding payment of severance benefits are inconsistent with
those found in the Employment Agreement, the terms and conditions of this
Agreement shall be controlling. 
Notwithstanding the foregoing, the parties acknowledge and agree that if
Employee is terminated without “cause” and the termination is not during the period beginning one (1) month prior
to the effective date of a Change in Control and ending eighteen (18) months
after the effective date of a Change in Control, the terms of the
Employment Agreement (including the definition of cause set forth therein)
shall govern the payment of any severance benefits to Employee in connection
with such termination.

(e)           Any
Party’s failure to enforce any provision or provisions of this Agreement shall
not in any way be construed as a waiver of any such provision or provisions,
nor prevent any Party from thereafter enforcing each and every other provision
of this Agreement.  The rights granted
the Parties herein are cumulative and shall not constitute a waiver of any
Party’s right to assert all other legal remedies available to it under the
circumstances.

(f)            Employee
agrees upon request to execute any further documents or instruments necessary
or desirable to carry out the purposes or intent of this Agreement.

(g)           In
case any provision of this Agreement shall be invalid, illegal or
unenforceable, the validity, legality and enforceability of the remaining
provisions shall not in any way be affected or impaired.

(h)           This
Agreement, in whole or in part, may be modified, waived or amended upon the
written consent of the Company and Employee.

(i)            This
Agreement may be executed in one or more counterparts, each of which shall be
deemed an original, but all of which shall constitute one instrument.

[THE REMAINDER OF THIS
PAGE INTENTIONALLY LEFT BLANK]

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In
Witness Whereof, the undersigned have set their hand as of the date
first above written.

 

	
  EMPLOYEE

  	
   

  	
  SENOMYX, INC.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  /s/ R. Kent Snyder

  	
   

  	
  By:

  	
  /s/ Harry J. Leonhardt

  
	
   

  	
   

  	
   

  
	
  R. Kent Snyder

  	
   

  	
  Name:

  	
   Harry J. Leonhardt

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  Title:

  	
   Senior Vice President, General

  
	
   

  	
   

  	
   

  	
  Counsel and Corporate Secretary

  
						

 

[SIGNATURE PAGE TO
CHANGE IN CONTROL AGREEMENT]

 

EXHIBIT A

RELEASE AND WAIVER OF CLAIMS

In
consideration of the payments and other benefits set forth in the Change in
Control Agreement dated October 10, 2006, between Senomyx, Inc. (the “Company”) and R. Kent Snyder (“Employee”), to which this form is
attached, Employee hereby furnishes the Company with the following release and
waiver.

Employee
hereby releases, and forever discharges the Company, its officers, directors,
agents, employees, stockholders, successors, assigns and affiliates, of and
from any and all claims, liabilities, demands, causes of action, costs,
expenses, attorneys’ fees, damages, indemnities and obligations of every kind
and nature, in law, equity, or otherwise, known and unknown, suspected and
unsuspected, disclosed and undisclosed, arising at any time prior to and
including Employee’s employment termination date with respect to any claims
relating to Employee’s employment and the termination of Employee’s employment,
including but not limited to, claims pursuant to any federal, state or local
law relating to employment, including, but not limited to, discrimination
claims, claims under the California Fair Employment and Housing Act, and the
Federal Age Discrimination in Employment Act of 1967, as amended (“ADEA”), the Federal Americans with
Disabilities Act or claims for wrongful termination, breach of the covenant of
good faith, contract claims, tort claims, and wage or benefit claims, including
but not limited to, claims for salary, bonuses, commissions, stock, stock
options, vacation pay, fringe benefits, severance pay or any form of
compensation.  Notwithstanding the above, this Release and
Waiver does not release any claims Employee may have (i) for indemnification
pursuant to and in accordance with the applicable statutes and the applicable
terms of the charters, articles of incorporation or bylaws of the Company or
under any indemnification agreements or insurance coverage, (ii) in vested
pension and retirement benefits under the terms of qualified employee pension
benefit plans, (iii) for accrued benefits under the terms of applicable
employment agreements or employee benefit plans, and (iv) for any claims under
any state Workers’ Compensation laws and any state unemployment benefits laws.

Employee
also acknowledges that Employee has read and understood Section 1542 of the
California Civil Code which reads as follows: 
“A general release does not extend to claims which the creditor does not
know or suspect to exist in his favor at the time of executing the release,
which if known by him must have materially affected his settlement with the
debtor.”  Employee hereby expressly
waives and relinquishes all rights and benefits under that section and any law
of any jurisdiction of similar effect with respect to any claims Employee may
have against the Company.

Employee
acknowledges that, among other rights, Employee is waiving and releasing any
rights Employee may have under ADEA, that this waiver and release is knowing
and voluntary, and that the consideration given for this waiver and release is
in addition to anything of value to which Employee was already entitled as an
employee of the Company.  Employee
further acknowledges that Employee has been advised, as required by the Older
Workers Benefit Protection Act, that: 
(a) the waiver and release granted herein does not relate to claims
which may arise after this release and waiver is executed; (b) Employee
has the right to consult with an attorney prior to executing this release and
waiver (although Employee may choose voluntarily not to do so); and (c) if
on the date of execution of this release and waiver Employee is age 40 or 

 

older, then
(I) Employee has twenty-one (21) days from the date Employee receives this
release and waiver, in which to consider this release and waiver (although
Employee may choose voluntarily to execute this release and waiver earlier);
and (II) Employee has seven (7) days following the execution of this
release and waiver to revoke Employee’s consent to this release and
waiver.  This release and waiver shall be
effective as of the date of execution hereof; provided that if on the date of
execution of this release and waiver Employee is age 40 or older, then this
release and waiver shall not be effective until the foregoing seven (7) day
revocation period has expired.  The date
as of which this release and waiver is effective as aforesaid shall be deemed
the “Effective Date” hereof.

	
  Date:

  	
   

  	
   

  	
  By:

  	
   

  
	
   

  	
   

  	
  R. Kent SnyderEXHIBIT 10.2

CHANGE IN CONTROL AGREEMENT

This Change in Control Agreement (the “Agreement”) is made as of October 10,
2006 between Senomyx, Inc.,
a Delaware corporation (the “Company”),
and Mark J. Zoller (“Employee”).

Whereas,
in order to provide an incentive for Employee to participate actively in the
affairs and maximize the value of the Company, the Company is willing to
provide Employee with certain benefits on the terms and conditions set forth
below.

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 the
period beginning one (1) month prior to the effective date of such Change in
Control and ending eighteen (18) months after the effective date of such Change
in Control, Employee’s employment with the Company is terminated either (A) by
the Company without Cause (defined below) (not including death or
Disability (as defined below)) or (B) by
Employee for Good Reason (defined below) (not including death or Disability),
then, without further action by Employee or the Company, Employee shall be
entitled to the benefits set forth below:

(a)           The vesting
applicable to all options to purchase shares of the Company’s capital stock (“Options”) and all shares of the
Company’s capital stock which are subject to the Company’s right to repurchase
such shares (“Restricted Stock”) held by
Employee as of the effective date of such termination shall be accelerated in
full such that Employee shall have the right to exercise in accordance with the
terms thereof all or any portion of such Options (notwithstanding any vesting
schedule set forth in such Options) and any such Company repurchase rights with
respect to such Restricted Stock shall lapse in full; and

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

(c)           Assuming
the Employee timely and accurately elects to continue his health insurance
benefits under the Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”), the Company
shall reimburse the Employee for the COBRA expenses he pays on behalf of
himself and his family until the earliest of (i) the end of the 12 month period
following Employee’s termination, (ii) the expiration of the Employee’s
continuation coverage under COBRA and any applicable state COBRA-like statute
that provides mandated continuation coverage or (iii) the date the Employee
becomes eligible for health insurance benefits of a subsequent employer.

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2.             Release.  Notwithstanding the foregoing, the
Employee shall not receive any of the severance payments or benefits set forth
under Section 1, unless upon Employee’s termination of employment the Employee
furnishes the Company with an effective waiver and release of claims (the “Release”) in a form acceptable to
the Company and substantially as attached hereto as Exhibit A.  If a majority of the Board of
Directors of the Company (the “Board”)
determines in good faith that the Employee has breached any provision of his
Proprietary Information and Inventions Agreement with the Company or any
provision of this Agreement or the Release, the Company shall be excused from
the obligation to provide any severance payment under Section 1 and the Company
shall be entitled to full recovery of any severance payment already provided to
the Employee under Section 1.

3.             Definitions. 
For purposes of this Agreement, capitalized terms used herein
shall have the following meanings:

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

(b)           “Cause” means the occurrence of any of the
following:  (i) the Employee’s commission
of any felony or any crime involving fraud, dishonesty or moral turpitude under
the laws of the United States or any state thereof; (ii) the Employee’s
attempted commission of, or participation in, a fraud or act of dishonesty
against the Company; (iii) the Employee’s intentional and material violation of
any contract or agreement between the Employee and the Company or any statutory
duty owed to the Company; (iv) the Employee’s unauthorized use or disclosure of
the Company’s confidential information or trade secrets or (v) the Employee’s
gross misconduct.  The determination that
a termination is for Cause shall be made by the Company in its discretion.  Any determination by the Company that the
employment of the Employee was terminated by reason of dismissal without Cause
for the purposes of determining benefits under this Agreement shall have no
impact upon any determination of the rights or obligations of the Company or
such Employee for any other purpose.

(c)           “Change in Control” means the occurrence, in a single
transaction or in a series of related transactions, of any one or more of the
following events:

(i)            any Exchange Act
Person (as defined in the Company’s Amended and Restated 2004 Equity Incentive
Plan (the “Plan”)) becomes the owner,
directly or indirectly, of securities of the Company representing more than
fifty percent (50%) of the combined voting power of the Company’s then
outstanding securities other than by virtue of a merger, consolidation or
similar transaction.  Notwithstanding the
foregoing, a Change in Control shall not be deemed to occur (A) on account of
the acquisition of securities of the Company by an investor, any affiliate
thereof or any other Exchange Act Person from the Company in a transaction or
series of related transactions the primary purpose of which is to obtain
financing for the Company through the issuance of equity securities or (B)
solely because the level of Ownership (as defined in the Plan) held by any
Exchange Act Person (the “Subject
Person”) exceeds the designated percentage threshold of the
outstanding voting securities as a result of a repurchase or other acquisition
of 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 of
voting securities by the Company, and after such share acquisition, the Subject
Person becomes the Owner of any additional voting securities that, assuming the
repurchase or other acquisition had not occurred, increases the percentage of
the then outstanding voting securities Owned by the Subject Person over the designated
percentage threshold, then a Change in Control shall be deemed to occur;

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

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

(iv)          there
is consummated a sale, lease, license or other disposition of all or
substantially all of the consolidated assets of the Company and its
Subsidiaries (as defined in the Plan), other than a sale, lease, license or
other disposition of all or substantially all of the consolidated assets of the
Company and its Subsidiaries to an Entity, more than fifty percent (50%) of the
combined voting power of the voting securities of which are Owned by
stockholders of the Company in substantially the same proportions as their
Ownership of the outstanding voting securities of the Company immediately prior
to 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 the
Board; provided, however, that if
the appointment or election (or nomination for election) of any new Board
member was approved or recommended by a majority vote of the members of the
Incumbent Board then still in office, such new member shall, for purposes of
this Agreement, be considered as a member of the Incumbent Board.

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

(e)           “Good Reason” shall mean the
occurrence 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, position
or responsibilities as in effect at any time within ninety (90) days preceding
the date of a 

 3
  
 

 

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

4.             Golden Parachute Taxes.  If any payment or benefit Employee would
receive pursuant to a Change in Control from the Company or otherwise (“Payments”) would (i) constitute a “parachute
payment” within the meaning of Section 280G of the Internal Revenue Code of
1986, as amended (the “Code”),
and (ii) but for this sentence, be subject to the excise tax imposed by Section
4999 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 no
portion of the Payment being subject to the Excise Tax or (y) the largest
portion, up to and including the total, of the Payment, whichever amount, after
taking into account all applicable federal, state and local employment taxes,
income taxes, and the Excise Tax (all computed at the highest applicable
marginal rate), results in Employee’s receipt, on an after-tax basis, of the
greater amount of the Payment notwithstanding that all or some portion of the
Payment may be subject to the Excise Tax. If a reduction in payments or
benefits constituting “parachute payments” is necessary so that the Payment
equals the Reduced Amount, reduction shall occur in the following order unless
Employee elects in writing a different order (provided,
however, that such election shall be subject to Company approval if
made on or after the date on which the event that triggers the Payment
occurs):  reduction of cash payments;
cancellation of accelerated vesting of stock awards; reduction of employee
benefits.  In the event that acceleration
of vesting of stock award compensation is to be reduced, such acceleration of
vesting shall be cancelled in the reverse order of the date of grant of
Employee’s stock awards unless Employee elects in writing a different order for
cancellation.

The accounting firm engaged
by the Company for general audit purposes as of the day prior to the effective
date of the Change in Control shall perform the foregoing calculations.  If the accounting firm so engaged by the
Company is serving as accountant or auditor for the individual, entity or group
effecting the Change in Control, the Company shall appoint a nationally
recognized accounting firm to make the determinations required hereunder.  The Company shall bear all expenses with
respect to the determinations by such accounting firm required to be made
hereunder.

The accounting firm engaged to make the determinations
hereunder shall provide its calculations, together with detailed supporting
documentation, to the Company and Employee within fifteen (15) calendar days
after the date on which Employee’s right to a Payment is 

 4
  
 

 

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

5.             Application
of Code Section 409A.  If the Company determines that any of the Payments fail
to satisfy the distribution requirement of Section 409A(a)(2)(A) of the Code as
a result of Section 409A(a)(2)(B)(i) of the Code, the Payments shall be
accelerated to the minimum extent necessary so that such Payments are not
subject to the provisions of Section 409A(a)(1) of the Code (It is the
intention of the preceding sentence to apply the short-term deferral provisions
of Section 409A of the Code, and the regulations and other guidance thereunder,
to the Payments, and the payment
schedule as revised after the application of the preceding sentence shall be
referred to as the “Revised Payment Schedule”).  However, if there is no Revised Payment
Schedule 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 Payment
Schedule and instead shall be delayed to the minimum extent necessary so that
such benefits are not subject to the provisions of Section 409A(a)(1) of the
Code.  The Board may attach conditions to
or adjust the amounts paid pursuant to this Section 5 to
preserve, as closely as possible, the economic consequences that would have
applied in the absence of this Section
5; provided, however, that
no such condition or adjustment shall result in the payments being subject to
Section 409A(a)(1) of the Code.

6.             General Provisions.

(a)           This Agreement
shall be governed by the laws of the State of California (without regard to
principles of conflict of laws).

(b)           Any notice, demand
or request required or permitted to be given by either the Company or Employee
pursuant to the terms of this Agreement shall be in writing and shall be deemed
given when delivered personally or deposited in the U.S. mail, First Class with
postage prepaid, and addressed to the parties at such addresses as have been
previously furnished by the Parties or such other address as a Party may
request by notifying the other in writing.

(c)           The rights and
obligations of Employee under this Agreement may not be transferred or assigned
without the prior written consent of the Company.

(d)           This Agreement is
meant to supplement the terms of stock option agreement(s) or other
agreement(s) pursuant to which Employee acquired the Options, as well as any
written employment agreement between the Company and Employee.

(e)           Any Party’s failure
to enforce any provision or provisions of this Agreement shall not in any way
be construed as a waiver of any such provision or provisions, nor prevent any
Party from thereafter enforcing each and every other provision of this
Agreement.  The rights 

 5
  
 

 

granted the Parties herein are cumulative and shall
not constitute a waiver of any Party’s right to assert all other legal remedies
available to it under the circumstances.

(f)            Employee agrees
upon request to execute any further documents or instruments necessary or
desirable to carry out the purposes or intent of this Agreement.

(g)           In case any
provision of this Agreement shall be invalid, illegal or unenforceable, the
validity, legality and enforceability of the remaining provisions shall not in
any way be affected or impaired.

(h)           This Agreement, in
whole or in part, may be modified, waived or amended upon the written consent
of the Company and Employee.

(i)            This Agreement may
be executed in one or more counterparts, each of which shall be deemed an
original, but all of which shall constitute one instrument.

[THE REMAINDER OF THIS
PAGE INTENTIONALLY LEFT BLANK]

 6
  

 

In
Witness Whereof, the undersigned have set their hand as of
the date first above written.

	
  EMPLOYEE

  	
  SENOMYX, INC.

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ Mark J.
  Zoller, Ph.D.

  	
   

  	
  By:

  	
  /s/ Kent Snyder

  	
   

  
	
   

  	
   

  
	
  Mark J. Zoller,
  Ph.D.

  	
  Name:

  	
   Kent Snyder

  	
   

  
	
   

  	
   

  
	
   

  	
  Title:

  	
   President and Chief Executive Officer

  	
   

  
							

 

[SIGNATURE PAGE TO CHANGE
IN CONTROL AGREEMENT]

Exhibit A

RELEASE AND WAIVER OF CLAIMS

In
consideration of the payments and other benefits set forth in the Change in
Control Agreement dated October 10, 2006, between Senomyx, Inc. (the “Company”) and Mark J. Zoller (“Employee”), to which this form is
attached, Employee hereby furnishes the Company with the following release and
waiver.

Employee
hereby releases, and forever discharges the Company, its officers, directors,
agents, employees, stockholders, successors, assigns and affiliates, of and
from any and all claims, liabilities, demands, causes of action, costs,
expenses, attorneys’ fees, damages, indemnities and obligations of every kind
and nature, in law, equity, or otherwise, known and unknown, suspected and
unsuspected, disclosed and undisclosed, arising at any time prior to and
including Employee’s employment termination date with respect to any claims
relating to Employee’s employment and the termination of Employee’s employment,
including but not limited to, claims pursuant to any federal, state or local
law relating to employment, including, but not limited to, discrimination
claims, claims under the California Fair Employment and Housing Act, and the
Federal Age Discrimination in Employment Act of 1967, as amended (“ADEA”), the Federal Americans with
Disabilities Act or claims for wrongful termination, breach of the covenant of
good faith, contract claims, tort claims, and wage or benefit claims, including
but not limited to, claims for salary, bonuses, commissions, stock, stock
options, vacation pay, fringe benefits, severance pay or any form of
compensation.  Notwithstanding the above, this Release and
Waiver does not release any claims Employee may have (i) for indemnification
pursuant to and in accordance with the applicable statutes and the applicable
terms of the charters, articles of incorporation or bylaws of the Company or
under any indemnification agreements or insurance coverage, (ii) in vested
pension and retirement benefits under the terms of qualified employee pension
benefit plans, (iii) for accrued benefits under the terms of applicable
employment agreements or employee benefit plans, and (iv) for any claims under
any state Workers’ Compensation laws and any state unemployment benefits laws.

Employee
also acknowledges that Employee has read and understood Section 1542 of the
California Civil Code which reads as follows: 
“A general release does not extend to claims which the creditor does not
know or suspect to exist in his favor at the time of executing the release,
which if known by him must have materially affected his settlement with the
debtor.”  Employee hereby expressly
waives and relinquishes all rights and benefits under that section and any law
of any jurisdiction of similar effect with respect to any claims Employee may
have against the Company.

Employee
acknowledges that, among other rights, Employee is waiving and releasing any
rights Employee may have under ADEA, that this waiver and release is knowing
and voluntary, and that the consideration given for this waiver and release is
in addition to anything of value to which Employee was already entitled as an
employee of the Company.  Employee
further acknowledges that Employee has been advised, as required by the Older
Workers Benefit Protection Act, that: 
(a) the waiver and release granted herein does not relate to claims
which may arise after this release and waiver is executed; (b) Employee
has the right to consult with an attorney prior to executing this release and
waiver (although Employee may choose voluntarily not to do so); and (c) if
on the date of execution of this release and waiver Employee is age 40 or 

older, then
(I) Employee has twenty-one (21) days from the date Employee receives this
release and waiver, in which to consider this release and waiver (although
Employee may choose voluntarily to execute this release and waiver earlier);
and (II) Employee has seven (7) days following the execution of this
release and waiver to revoke Employee’s consent to this release and
waiver.  This release and waiver shall be
effective as of the date of execution hereof; provided that if on the date of
execution of this release and waiver Employee is age 40 or older, then this
release and waiver shall not be effective until the foregoing seven (7) day
revocation period has expired.  The date
as of which this release and waiver is effective as aforesaid shall be deemed
the “Effective Date” hereof.

 

	
  Date:

  	
   

  	
   

  	
  By:

  	
   

  	
   

  
	
   

  	
  Mark J. Zoller, Ph.D.

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