<PAGE>   1
[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.

                                                                 EXHIBIT 10.93

                          SECOND AMENDMENT TO AGREEMENT


        This is the second amendment to the Research Collaboration and License
Agreement between MERCK & CO., INC., a corporation organized and existing under
the laws of New Jersey ("MERCK") and ARRIS PHARMACEUTICAL CORPORATION, a
corporation organized and existing under the laws of Delaware, now known as AxyS
Pharmaceuticals, Inc. ("AxyS") made as of November 6, 1996 (the "Agreement").
The purpose of this second amendment is to extend the Research Program Term in
accordance with Section 2.8 of the Agreement, and to amend Section 1.23(a)(iv)
of the Agreement.

        1. In accordance with Section 2.8 of the Agreement, the Research Program
Term is extended for one additional year, through November 5, 1999. Reference is
made to Section 5.2(C) of the Agreement. The parties agree that a [*] will be
required during the period [*] and that [*] will be required during the [*] the
Research Program Term, i.e., from [*], the [*].

        2. Attachment 2.1 setting forth the Research Program is hereby amended
to include the additional research work set forth on the attachment to this
second amendment.

        3. Section 1.23(a)(iv) is hereby amended to read in its entirety as
follows:

        [*]

        4. Capitalized terms used and not otherwise defined herein shall have
the respective meanings set forth in the Agreement. The Agreement, together with
the first amendment dated February 9, 1998, and this second amendment, contain
entire understanding of the parties with respect to their subject matter. All
express or implied agreements and understandings, either oral or written,
heretofore made are expressly merged in and made a part of the Agreement as
amended by the first and second amendments. The Agreement and its amendments may
be amended, or any term thereof modified, only by a written instrument duly
executed by both parties hereto.

IN WITNESS WHEREOF, the parties have executed this Amendment as of November 5,
1998.

MERCK & CO., INC.                           AxyS Pharmaceutical, Inc.


By:   /s/ Bennett Shapiro                   By:   /s/Daniel Petree
    ------------------------------              ------------------------------
    Bernard W. Shapiro, M.D.                    Daniel H. Petree
    Executive Vice President                    President &
    Merck Research Laboratories                 Chief Operating Officer



<PAGE>   2

                                 ATTACHMENT 2.1

                                RESEARCH PROGRAM

                                       [*]



[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.



<PAGE>   3

                                  APPENDIX A-1

                                       [*]


[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.



<PAGE>   4

                                  APPENDIX A-2

                                       [*]



[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.



<PAGE>   5

                                   APPENDIX B

                                       [*]


[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.



<PAGE>   6

                                  APPENDIX C-1

                                       [*]


[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.



<PAGE>   7

                                  APPENDIX C-2

                                       [*]


[*] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.