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                                                                  Exhibit 10.12

[LETTERHEAD FOR SENOMYX, INC.]


June 7, 2000

Klaus Gubernator
13434 Glencliff Way
San Diego, CA 92130

Telephone: (858) 350-8341


Dear Klaus:

It is my pleasure to provide you with this letter setting forth the
principal terms for you to join Senomyx, Inc., a Delaware corporation (the
"Company"), which is located in La Jolla, California.

POSITION:     Vice President of Chemistry. You will report to Mark Zoller,
              Vice President of Research.

COMPENSATION: Monthly compensation will be $16,667 per month, minus standard
              deductions and withholdings.

EQUITY:       Subject to approval by the Company's Board of Directors and
              pursuant to the terms of a separate Stock Option Agreement
              and the Company's Equity Incentive Plan, the Company will grant
              to you the right to purchase at fair market value 200,000
              shares (the "Shares") of the common stock of the Company.
              Assuming your continuous employment, the Shares will vest
              according to the following schedule: (i) twenty five
              percent (25%) of the total (50,000 shares) will vest upon the
              first anniversary of the commencement of your employment with
              the Company; (ii) one


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              forty-eighth (1/48) of the total (approximately 4,166 shares)
              will vest ratably on a monthly basis beginning at the end of the
              one year and will continue to vest over a three year period.

BENEFITS:     You will be eligible to participate in the Company's medical
              and dental benefit plans, as well as its 401(k) plan subject to
              the terms of the plans. Details about these benefit plans are
              available for your review. The Company may modify compensation
              and benefits from time to time as it deems necessary.

PAID TIME
OFF:          You will be entitled to 17 days per year of paid time off.

EMPLOYMENT
AT WILL:      Your employment with the Company is not for a guaranteed or
              definite period of time. Your employment will be at will, which
              means it may be terminated at any time by you or the Company
              with or without cause or advance notice.

SEVERANCE:    In the event your employment is terminated without Cause (as
              defined herein) then upon the Company's receipt from you of an
              effective Release and Waiver of Claims in the form attached
              hereto as Exhibit C, the Company will pay you your monthly base
              salary, minus standard deductions and withholdings, for a
              period of three (3) months from the date of termination.

              For purposes of this offer letter, Cause will be defined as:

              (i)    your repeated failure to satisfactorily perform your job
                     duties;

              (ii)   your failure to comply with all material applicable laws
                     in performing your job duties or in directing the conduct
                     of the Company's business;

              (iii)  your commission of any felony or intentionally fraudulent
                     or other act against the Company, or its affiliates,
                     employees, agents or customers which demonstrates your
                     untrustworthiness or lack of integrity;

              (iv)   your participation in any activity which is directly
                     competitive with or intentionally injurious to the
                     Company or any of its affiliates or which violates the
                     terms of your Proprietary Information and Inventions
                     Agreement; or

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              (v)    your commission of any fraud against the Company or any
                     of its affiliates or use or intentional appropriation for
                     your personal use or benefit of any funds or properties
                     of the Company not authorized by the Company's Board of
                     Directors to be so used or appropriated.

EMPLOYEE
HANDBOOK:     As a Company employee, you will be expected to abide by Company
              rules and regulations and acknowledge in writing that you have
              read the Company's Employee Handbook which will govern the
              terms and conditions of your employment. The Company's Employee
              Handbook may be modified from time to time at the sole
              discretion of the Company.

PROPRIETARY
INFORMATION
AND
INVENTIONS
AGREEMENT:    As a condition of employment, you will be required to sign and
              comply with the attached Proprietary Information and Inventions
              Agreement which, among other things, prohibits unauthorized use
              or disclosure of the Company's proprietary information.

THIRD PARTY
INFORMATION:  In your work for the Company, you agree that you will not make
              any unauthorized use or disclosure of any confidential or
              proprietary information governed by any agreement with any
              third party. You represent and warrant that your employment by
              the Company and your performance of your duties for the Company
              will not conflict with any prior agreement or relationship with
              any third party. You also agree that you will not enter into
              any agreement with any third party, either written or oral, in
              conflict with your duties to the Company. You acknowledge that:
              you have certain contractual obligations to your prior
              employers (e.g., your Noncompetition Agreement with E.I. du
              Pont de Nemours and Company); the Company expects you to abide
              by all lawful obligations under all such agreements; and the
              Company is not indemnifying you with regard to your obligations
              under such agreements. During your employment with the Company,
              you will be expected to use in the performance of your duties
              only that information generally known and used by persons with
              training and experience comparable to your own, information
              which is common knowledge in the industry or otherwise legally
              in the public domain, or which is otherwise provided or
              developed by the Company. Further, you agree not to bring onto
              the premises of the Company, nor to be in unauthorized
              possession or control of, any


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              unpublished documents or any property belonging to any former
              employer or any other party unless consented to in writing by
              that former employer or party.

WORKING
HOURS:        Normal working hours are from 8:00 a.m. to 5:00 p.m., Monday
              through Friday. As an exempt salaried employee, you will be
              expected to work additional hours as required by the nature of
              your work assignments.

ENTIRE
AGREEMENT:    This letter, together with your Proprietary Information and
              Inventions Agreement and the Employee Handbook, forms the
              complete and exclusive statement of the terms of your
              employment with the Company. The employment terms in this
              letter supersede any other agreements or promises made to you
              by anyone, whether oral or written, and they can only be
              modified or amended in a written agreement signed by you and a
              duly authorized Company officer.

START DATE:   June 14, 2000, or at another mutually agreeable date. This offer
              is subject to proof of United States Citizenship or other proof
              of employability in the United States and to the approval of the
              Board of Directors of Senomyx, Inc. and if not accepted by June
              9, 2000 it will lapse.

We are excited about Senomyx's prospects for success, and anticipate that your
contribution will substantially enhance our progress. I look forward to your
joining the Company, and to working with you as we develop our business.

Sincerely,


/s/  Paul A. Grayson
     Paul A. Grayson
     President and Chief Executive Officer

SIGNED AND AGREED TO:

/s/  Klaus Gubernator
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June 9, 2000
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(Date)

cc: Jean J. Lockhart

Exhibit A - Employee Proprietary Information and Inventions Agreement