Exhibit 10.1


 


AMENDED
AND RESTATED CHANGE IN CONTROL AGREEMENT


 


This Amended and Restated Change in Control Agreement (the “Agreement”) is made as of December         ,
2008 (the “Effective Date”) between
Senomyx, Inc., a Delaware corporation (the “Company”),
and                           
(“Employee”).  This Agreement hereby amends and supersedes
in its entirety the Change in Control Agreement entered into by and between the
Company and Employee that was originally established in March 2008 (the “Prior Agreement”).


 


RECITALS


 


WHEREAS, the Company and the
Employee desire to amend and restate the Prior Agreement in its entirety to
clarify the application of Section 409A of the Internal Revenue Code to
Employee’s benefits provided under the Prior Agreement, effective as of the
Effective Date.


 


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 pay the insurer the applicable COBRA premiums on behalf of Employee and
his family (the “COBRA Payments”) until the
earliest of (i) the end of the 12 month period following Employee’s
termination, (ii) the expiration of the Employee’s 


 


1

















 


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. For the avoidance of doubt,
it is intended that the COBRA Payments are exempt from the application of Section 409A
of the Internal Revenue Code.


 


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 a waiver and release of claims  in a form acceptable to the Company and
substantially as attached hereto as Exhibit A
(the “Release”) within the applicable
time period set forth therein, but in no event later than forty-five (45) days
following termination of the Employee’s employment, and permits such Release to
become effective in accordance with its terms (such date, the “Release Effective Date”).  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, 


 


2

















 


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.


 


3

















 


(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.


 


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:  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.


 


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 


 


4

















 


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.


 


5.             APPLICATION
OF CODE SECTION 409A.


 


Notwithstanding anything to the contrary set forth herein, any payments
and benefits provided under this Agreement (the “Change
in Control Benefits”) that constitute “deferred compensation”
within the meaning of Section 409A of the Code and the regulations and
other guidance thereunder and any state law of similar effect (collectively “Section 409A”) shall not
commence in connection with Employee’s termination of employment unless and
until Employee has also incurred a “separation from service” (as such term is
defined in Treasury Regulation Section 1.409A-1(h) (“Separation From Service”), unless
the Company reasonably determines that such amounts may be provided to Employee
without causing Employee to incur the additional 20% tax under Section 409A.  Such determination by the Company shall be
made no later than ten (10) days following Employee’s termination of
employment.


 


Notwithstanding anything to the contrary set forth herein, if the
Company (or, if applicable, the successor entity thereto) determines that any
Change in Control Benefits constitute “deferred compensation” under Section 409A
and Employee is, on the termination of Employee’s service, a “specified
employee” of the Company or any successor entity thereto, as such term is
defined in Section 409A(a)(2)(B)(i) of the Code, then, solely to the
extent necessary to avoid the incurrence of the adverse personal tax
consequences under Section 409A, the timing of such Change in Control
Benefits payment shall be delayed until the earlier to occur of: (i) the
date that is six months and one day after Employee’s Separation From Service,
or (ii) the date of Employee’s death (such applicable date, the “Specified Employee Initial Payment Date”),
the Company (or the successor entity thereto, as applicable) shall pay to
Employee a lump sum amount equal to the sum of such Change in Control Benefits
payment that Employee would otherwise have received through the Specified
Employee Initial Payment Date if the payment of such Change in Control Benefits
had not been so delayed pursuant to this Section.


 


Notwithstanding any other payment schedule set forth in this Agreement,
none of the Change in Control Benefits will be paid or otherwise delivered
prior to the Release Effective Date. 
Except to the extent that payments may be delayed until the Specified
Employee Initial Payment Date pursuant to the preceding paragraph, on the first
regular payroll pay day following the Release Effective Date, the Company will
pay Employee the Change in Control Benefits 


 


5

















 


Employee would
otherwise have received under the Agreement on or prior to such date but for
the delay in payment related to the Release Effective Date.


 


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; provided,
however that any Change in Control Benefits payable in cash by the Company to
Employee pursuant to this Agreement shall be reduced (but not below zero) by
any severance benefits payable in cash by the Company to Employee under any
other policy, plan, program, agreement or arrangement, including, without
limitation, a contract between Employee and any entity, covering 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 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.


 


6

















 


IN WITNESS WHEREOF,
the undersigned have set their hand as of the date first above written.


 


	
  EMPLOYEE

  	
   

  	
  SENOMYX,
  INC.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  By:

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  Name:

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  Title:

  	
   

  
						



 


[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 Amended and Restated Change in Control Agreement dated December       ,
2008, between Senomyx, Inc. (the “Company”)
and                         
(“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: