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                                                                  Exhibit 10.45


                         ChemGenics Pharmaceuticals Inc.
                               One Kendall Square
                                  Building 300
                               Cambridge, MA 02139


                                              November 22, 1996


PerSeptive Biosystems, Inc.
500 Old Connecticut Path
Framingham, MA 01701

Gentlemen:

         Reference is made to the Master Agreement dated May 7, 1996 and to the
Warrant (the "Warrant") for the purchase for 4,896,335 shares of Common Stock of
ChemGenics Pharmaceuticals Inc. ("ChemGenics") issued to PerSeptive Biosystems,
Inc. ("PerSeptive") on June 28, 1996. ChemGenics has described to PerSeptive a
proposed transaction between ChemGenics and American Home Products Corporation,
represented by its Wyeth-Ayerst Laboratories Division ("Wyeth-Ayerst") in which
ChemGenics and Wyeth-Ayerst will enter into a Collaborative Research and License
Agreement, Stock Purchase Agreement and Standstill Agreement (collectively, the
"Wyeth-Ayerst Transaction"). For good and valuable consideration, the receipt
and sufficiency of which are hereby acknowledged, PerSeptive and ChemGenics have
agreed as follows:

1.       Contingent upon the closing of the Wyeth-Ayerst Transaction, ChemGenics
         and PerSeptive agree to modify and amend Section 8.07 of the Master
         Agreement to terminate PerSeptive's rights under the second sentence
         thereof with the effect that PerSeptive shall not, after the closing of
         the Wyeth-Ayerst Transaction, have the right to rescind the Master
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         Agreement and the other agreements, documents and instruments entered
         into in connection therewith or to unwind the collaboration established
         by such agreements and other documents.

2.       PerSeptive agrees that, notwithstanding the terms of the Warrant, or
         any other document or agreement entered into in connection therewith,
         PerSeptive will at no time exercise the Warrant in a manner which would
         cause the shares of Common Stock owned by PerSeptive to be more than
         49.9% of all outstanding equity securities of ChemGenics (treating any
         convertible securities issued by ChemGenics as having been converted).
         ChemGenics agrees that, in the event the foregoing restriction prevents
         PerSeptive from exercising any or all of the Warrant at the time of its
         expiration on June 28, 2000, the expiration date of the portion of the
         Warrant which cannot be exercised shall be extended for a six-month
         period through December 28, 2000; and if such restriction prevents the
         exercise of all or part of the Warrant at that extended date, the
         execution date of the portion which cannot be exercised shall be
         continued for an additional six months, which opportunity to extend the
         exercise date of the Warrant shall continue in increments of six months
         until such time as the foregoing restriction no longer prevents the
         full exercise of the Warrant.

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         If the foregoing accurately sets forth our understanding, please so
signify by signing and returning a duplicate copy of this letter, whereupon it
will take effect as an amendment to both the Master Agreement and the Warrant in
accordance with the terms thereof.

                                           Very truly yours,

                                           CHEMGENICS PHARMACEUTICALS INC.


                                           By: /s/ Barry A. Berkowitz
                                               -----------------------
                                               Chief Executive Officer


ACCEPTED AND AGREED:

PERSEPTIVE BIOSYSTEMS, INC.


By: /s/ Noubar B. Afeyan
    -----------------------
    Chairman and
    Chief Executive Officer


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