<PAGE>   1
                                                                   Exhibit 10.54



            AMENDMENT TO COLLABORATIVE RESEARCH AND LICENSE AGREEMENT
            ---------------------------------------------------------


     This Amendment ("Amendment") dated March 20, 1997, by and among American
Home Products Corporation, a Delaware corporation, represented by its
Wyeth-Ayerst Laboratories Division ("Wyeth-Ayerst") and ChemGenics
Pharmaceuticals Inc., a Delaware corporation (the "Company") amends that certain
Collaborative Research and License Agreement dated November 1, 1996 by and
between Wyeth-Ayerst and the Company (the "License Agreement").

     WHEREAS Wyeth-Ayerst has been advised that the Company has executed an
Agreement and Plan of Merger dated January 20, 1997 by and among the Company,
Millennium Pharmaceuticals, Inc., a Delaware corporation ("Millennium") and CPI
Acquisition Corp., a Delaware corporation and a wholly-owned subsidiary of
Millennium ("CPI") pursuant to which, among other things, CPI will be merged
(the "Merger") with and into the Company and the Company will become a
wholly-owned subsidiary of Millennium.

     WHEREAS, Wyeth-Ayerst is a party to that certain Series E Preferred Stock
Purchase Agreement dated November 27, 1996 by and among Wyeth-Ayerst, the
Company and certain other stockholders a party thereto (the "Purchase
Agreement");

     WHEREAS, the License Agreement and the Purchase Agreement provide that,
unless the License Agreement has been terminated, Wyeth-Ayerst may become
obligated to purchase additional shares of capital stock of the Company (the
"Additional Equity Investments").

     WHEREAS, in connection with the Merger, Wyeth-Ayerst, the Company and
Millennium have heretofore entered into an Amendment, Consent and Waiver dated
as of January 18, 1997 pursuant to which the parties have agreed to modify the
terms and conditions of the Additional Equity Investments set forth in the
License Agreement and Purchase Agreement.

     NOW, THEREFORE, in consideration of the foregoing premises and other good
and valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereby agree as follows:


     1. Section 3.1 of the License Agreement is deleted in its entirety and a
new Section 3.1 is inserted in lieu thereof which reads as follows:


<PAGE>   2



        "3.1 Equity Investments
             ------------------

        WYETH-AYERST will make two equity investments in CHEMGENICS in
        accordance with the terms of a Series E Preferred Stock Purchase
        Agreement of even date herewith (the "Stock Purchase Agreement"):

        1.   $5 million on the Effective Date of this Agreement.

        2.   $3 million as set forth in Section 1.03 (b) of the Stock Purchase
             Agreement."

     2. The Agreement, as supplemented and modified by this Amendment, together
with the other writings referred to in the Agreement or delivered pursuant
thereto which form a part thereof, contains the entire Agreement among the
parties with respect to the subject matter thereof and amends, restates and
supersedes all prior and contemporaneous arrangements or understandings with
respect thereto.

     3. From and after the effective date of this Amendment, each reference in
the Agreement to "this agreement," "hereunder," "hereof," "herein" or words of
like import, and each reference to the other documents entered into in
connection with the Agreement shall mean and be a reference to the Agreement as
amended hereby. Except as specifically amended above, the Agreement shall remain
in full force and effect and is hereby ratified and confirmed.

     4. This Amendment shall be governed by and construed in accordance with the
laws of the State of New Jersey, U.S.A., without regard to the application of
principles of conflicts of law.

     5. This Amendment may be executed in any number of counterparts, and each
such counterpart shall be deemed to be an original instrument, but all such
counterparts together shall constitute but one agreement.

     IN WITNESS WHEREOF, the parties hereto have executed this Amendment to
Collaborative Research and License Agreement on the date first written above.

                                                 CHEMGENICS PHARMACEUTICALS INC.


                                                 By: /s/ Barry A. Berkowitz
                                                    ----------------------------
                                                      Barry A. Berkowitz
                                                      President

                                       -2-

<PAGE>   3



                                                 AMERICAN HOME PRODUCTS
                                                 CORPORATION
                                                 ACTING THROUGH ITS
                                                 WYETH-AYERST LABORATORIES
                                                 DIVISION


                                                 By: /s/ Gerald A. Jibilian
                                                    ----------------------------
                                                 Name: Gerald A. Jibilian
                                                      --------------------------
                                                 Title: Vice President
                                                       -------------------------

     The undersigned hereby agrees to and acknowledges the foregoing as of the
date first written above:


MILLENNIUM PHARMACEUTICALS, INC.


By: /s/ Steven H. Holtzman
   --------------------------------
Name: Steven H. Holtzman
     ------------------------------
Title: Chief Business Officer
      -----------------------------



                                       -3-