PERSEPTIVE BIOSYSTEMS INC
SC 13D, 1997-02-20
LABORATORY ANALYTICAL INSTRUMENTS
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<PAGE>
 
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549


                                  SCHEDULE 13D


                   UNDER THE SECURITIES EXCHANGE ACT OF 1934
                             (AMENDMENT NO.   )/1/



                       Millennium Pharmaceuticals, Inc.
- -------------------------------------------------------------------------------
                               (Name of Issuer)

                         Common Stock, $.001 par value
- -------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                  0005999021
                      -----------------------------------
                                (CUSIP Number)

            Samuel P. Hunt, III, Esq., PerSeptive Biosystems, Inc.
                500 Old Connecticut Path, Framingham, MA 01701
- -------------------------------------------------------------------------------
(Name, Address and Telephone Number of Person Authorized to Receive Notices and
                                Communications)

                               February 10, 1997
            -------------------------------------------------------
            (Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report
the acquisition which is the subject of this Schedule 13D, and is filing this
schedule because of Rule 13d-1(b)(3) or (4), check the following box [  ].

       NOTE:  Six copies of this statement, including all exhibits, should be
   filed with the Commission.  See Rule 13d-1(a) for other parties to whom
   copies are to be sent.


- ---------------
/1/ The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter disclosures provided in a prior cover page.
                                        
     The information required on the remainder of this cover page shall not be
deemed to be "filed" for the purpose of Section 18 of the Securities Exchange
Act of 1934 ("Act") or otherwise subject to the liabilities of that section of
the Act but shall be subject to all other provisions of the Act (however, see
the Notes).
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 2 OF 8 PAGES
- ------------------------                                     ------------------
 
- ------------------------------------------------------------------------------
      NAME OF REPORTING PERSON
 1    S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

      PerSeptive Biosystems, Inc.   04-2987616

- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3
 

- ------------------------------------------------------------------------------
      SOURCE OF FUNDS*
 4    
      SC

- ------------------------------------------------------------------------------
      CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
 5    PURSUANT TO ITEMS 2(d) or 2(e)                                [_]      


- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 6    
      Delaware

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     7     
     NUMBER OF            1,612,582
 
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      8    
                          0
     OWNED BY
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     9     
    REPORTING             1,612,582
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH         10    
                          0
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
11    
      1,612,582

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*
12                                                                  [_]
       
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
13    
      5.6%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON*
14
      CO

- ------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!
          INCLUDE BOTH SIDES OF THE COVER PAGE, RESPONSES TO ITEMS 1-7
      (INCLUDING EXHIBITS) OF THE SCHEDULE, AND THE SIGNATURE ATTESTATION.

<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 3 OF 8 PAGES
- ------------------------                                     ------------------


ITEM 1.  SECURITY AND ISSUER

   This statement on Schedule 13D relates to the Common Stock, $.001 par value
per share (the "Common Stock"), of Millennium Pharmaceuticals, Inc., a Delaware
corporation (the "Issuer").   The principal executive offices of the Issuer are
located at 640 Memorial Drive, Cambridge, MA  02139-4815.

ITEM 2.  IDENTITY AND BACKGROUND

     (i) The name of the person filing this statement is PerSeptive Biosystems,
Inc., a Delaware corporation ("PerSeptive").

     (ii) The address of the principal office and principal business of 
PerSeptive is 500 Old Connecticut Path, Framingham, MA  01701.

     (iii)  PerSeptive and its subsidiaries develop, manufacture and market an
integrated line of proprietary advanced instrumentation systems and consumable
products for the purification, analysis and synthesis of biomolecules.

     (iv) Set forth in Schedule I is the name and present principal occupation
or employment and the name, principal business and address of any corporation or
other organization in which such employment is conducted, of each of
PerSeptive's directors and executive officers as of the date hereof.

     (v) During the past five years, neither PerSeptive, nor, to PerSeptive's
knowledge, any person named in Schedule I to this Schedule 13D has been
convicted in a criminal proceeding (excluding traffic violations or similar
misdemeanors).

     (vi) During the past five years, neither PerSeptive, nor, to PerSeptive's
knowledge, any person named in Schedule I to this Schedule 13D, was a party to a
civil proceeding of a judicial or administrative body of competent jurisdiction
as a result of which such person was or is subject to a judgment, decree or
final order enjoining future violations of or prohibiting or mandating activity
subject to Federal or state securities laws or finding any violation with
respect to such laws.

     (vii)  All of the directors and executive officers of PerSeptive named in
Schedule I are citizens of the United States.

ITEM 3.  SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION

   Pursuant to an Agreement and Plan of Merger dated January 20, 1997 (the
"Merger Agreement"), among the Issuer, CPI Acquisition Corp., a wholly-owned
subsidiary of the Issuer ("Merger Sub"), and ChemGenics Pharmaceuticals Inc.
("ChemGenics"), Merger Sub was merged with and into ChemGenics (the "Merger"),
with each share of the common stock, $.001 par per share, of ChemGenics (the
"ChemGenics Common Stock") (other than shares as to which appraisal rights have
been demanded and perfected in accordance with the Delaware General Corporation
Law), converted into the right to receive .2374 shares of common stock, $.001
par value per share, of the Issuer ("Issuer Common Stock").  Pursuant to the
Merger Agreement, PerSeptive received 1,612,582 shares of Issuer 
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 4 OF 8 PAGES
- ------------------------                                     ------------------


Common Stock in exchange for its ChemGenics Common Stock and cash in the amount
of $4,000,000 in exchange for certain other securities of ChemGenics.

   PerSeptive acquired its shares of ChemGenics Common Stock pursuant to a
Master Agreement (the "Master Agreement") dated as of May 7, 1996, as amended,
and a related License Agreement dated June 18, 1996, as amended, each such
agreement by and between PerSeptive (and certain of its subsidiaries) and
ChemGenics, whereby PerSeptive transferred certain assets and employees to
ChemGenics and granted ChemGenics a non-exclusive license to use PerSeptive's
technology for drug discovery purposes in exchange for shares of ChemGenics
Common Stock, warrants to purchase additional shares of ChemGenics Common Stock
exercisable until June 28, 2000, and a promissory note. Pursuant to the terms of
the Master Agreement, approximately 10% of the shares of ChemGenics Common Stock
issued to PerSeptive are subject to forfeiture if PerSeptive fails to perform 
certain obligations to ChemGenics. This forfeiture provision lapses with 
respect to one third of such shares on June 30, 1997 and on each of the next two
anniversaries thereof. After the Merger, these forfeiture provisions will
apply, in the same relative proportions, to PerSeptive's shares of Issuer
Common Stock.

ITEM 4.  PURPOSE OF TRANSACTION

     PerSeptive acquired the Issuer Common Stock pursuant to the Merger
Agreement described above.  Except as stated below, PerSeptive has no present
plans which relate to or would result in:

     (a) The acquisition by any person of additional securities of the Issuer,
         or the disposition of securities of the Issuer;

     (b) An extraordinary corporate transaction, such as a merger,
         reorganization or liquidation, involving the Issuer or any of its
         subsidiaries;

     (c) A sale or transfer of a material amount of assets of the Issuer or any
         of its subsidiaries;

     (d) Any change in the present board of directors or management of the
         Issuer, including any plans or proposals to change the number or term
         of directors or to fill any existing vacancies on the board;

     (e) Any material change in the present capitalization or dividend policy of
         the Issuer;

     (f) Any other material change in the Issuer's business or corporate
         structure;

     (g) Changes in the Issuer's charter, bylaws or instruments corresponding
         thereto or other actions which may impede the acquisition of control of
         the Issuer by any person;

     (h) Causing a class of securities of the Issuer to be delisted from a
         national securities exchange or to cease to be authorized to be quoted
         in an inter-dealer quotation system of a registered national securities
         association;

     (i) A class of equity securities of the Issuer becoming eligible for
         termination of registration pursuant to Section 12(g)(4) of the
         Securities Exchange Act of 1934; or

     (j) Any action similar to any of those enumerated above.
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 5 OF 8 PAGES
- ------------------------                                     ------------------


ITEM 5.  INTEREST IN SECURITIES OF THE ISSUER

   (a)   Amount Beneficially Owned:
              PerSeptive beneficially owns 1,612,582 shares of Issuer Common
              Stock.

         Percent of Class:
              PerSeptive owns 5.6% of Issuer Common Stock.

   (b)   Number of Shares as to which such person has:
          (i)    sole power to vote or direct the vote:  1,612,582 shares

          (ii)   shared power to vote or direct the vote: NOT APPLICABLE

          (iii)  sole power to dispose or to direct the disposition of:
                 1,612,582 shares

          (iv)   shared power to dispose or to direct the disposition of:
                 NOT  APPLICABLE
              

   (c)   Neither PerSeptive, nor, to PerSeptive's knowledge, any person named in
Schedule I, has affected any transaction in the Issuer Common Stock during the
past 60 days.

   (d)  Not applicable.

   (e)  Not applicable.

ITEM 6.  CONTRACTS, ARRANGEMENTS, UNDERSTANDINGS OR RELATIONSHIPS
         WITH RESPECT TO SECURITIES OF THE ISSUER

   Pursuant to the terms of the Merger Agreement, the Issuer has agreed to file
with the Securities and Exchange Commission ("SEC") a resale registration
statement on Form S-3 (or other appropriate form) registering the shares of
Issuer Common Stock issued pursuant to the Merger Agreement. Pursuant to a
letter agreement (the "Letter Agreement") dated February 3, 1997 by and between
PerSeptive and the Issuer, PerSeptive has agreed that, during the period
commencing at the Effective Time (as defined in the Merger Agreement) and ending
on the date that such registration statement is filed by the Issuer and declared
effective by the SEC (the "Date of Effectiveness"), PerSeptive shall not sell,
exchange, transfer, assign, pledge, dispose of or engage in any transaction,
including a transaction or arrangement that reduces the risk of loss by short
sale, hedging or otherwise, of any Issuer Common Stock issued and delivered
pursuant to the Merger Agreement. During the period commencing on the Date of
Effectiveness and ending July 31, 1997 and the period beginning August 1, 1997
and ending September 30, 1997, the foregoing prohibition shall apply with
respect to fifty percent (50%) and twenty-five percent (25%), respectively, of
the Issuer Common Stock issued and delivered to PerSeptive pursuant to the
Merger Agreement. After September 30, 1997, the foregoing prohibition shall have
no further force and effect.
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 6 OF 8 PAGES
- ------------------------                                     ------------------

   Except as described above, to PerSeptive's knowledge, there are no contracts,
arrangements, understandings or relationships (legal or otherwise) among the
persons named in Item 2 and between such persons and any person with respect to
any securities of the Issuer, including but not limited to transfer or voting of
any of the securities, finder's fees, joint ventures, loan or option
arrangements, puts or calls, guarantees of profits, division of profits or loss,
or the giving or withholding of proxies.

ITEM 7.  MATERIAL TO BE FILED AS EXHIBITS
<TABLE>
<CAPTION>
 
Exhibit No.        Description
- -----------        -----------
<S>               <C>
   
   1               Letter Agreement dated February 3, 1997 by and between 
                   PerSeptive Biosystems, Inc. and Millennium Pharmaceuticals, 
                   Inc.
 
</TABLE>
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 7 OF 8 PAGES
- ------------------------                                     ------------------


  After reasonable inquiry and to the best of my knowledge and belief, I certify
that the information set forth in this statement is true, complete and current.

Date:  February 20, 1997            PERSEPTIVE BIOSYSTEMS, INC.



                                    /s/ John F. Smith
                                    --------------------------------------
                                    John F. Smith
                                    President
<PAGE>
 
                                  SCHEDULE 13D
- ------------------------                                     ------------------
CUSIP NO.    0005999021                                       PAGE 8 OF 8 PAGES
- ------------------------                                     ------------------

<TABLE>
<CAPTION>
 
 
                                                          SCHEDULE I
                                                          ----------
 
                                                      Name and Address of
                                                      Corporation or Other
                             Principal Occupation     Organization in Which
Name                         or Employment            Employed
- ----                         ----------------------   ------------------------ 
<S>                          <C>                      <C>
 
Noubar B. Afeyan, Ph.D.      Chief Executive          PerSeptive Biosystems,
                             Officer, Director and    Inc.
                             Chairman of the Board    500 Old Connecticut Path
                                                      Framingham, MA 01701
 
John F. Smith                President and Director   PerSeptive Biosystems,
                                                      Inc.
                                                      500 Old Connecticut Path
                                                      Framingham, MA 01701

Thomas G. Ruane              Senior Vice President,   PerSeptive Biosystems,
                             Chief Financial          Inc.
                             Officer and Treasurer    500 Old Connecticut Path
                                                      Framingham, MA 01701
 
Bruce J. Ryan                Director                 Amdahl Corporation
                                                      1250 East Arques Avenue
                                                      (M/S 104)
                                                      P.O. Box 3470
                                                      Sunnyvale, OH  94088-3470

Daniel I.C. Wang, Ph.D.      Director                 Massachusetts Institute
                                                      of Technology
                                                      18 Vassar Street
                                                      Building 20A
                                                      Room 207
                                                      Cambridge, MA 02139

Edwin M. Kania, Jr.          Director                 One Liberty Ventures
                                                      One Liberty Square
                                                      Boston, MA 02109

William F. Pounds, Ph.D.     Director                 MIT Sloan School of
                                                      Management
                                                      50 Memorial Drive E52-472
                                                      Cambridge, MA 02142
</TABLE>

<PAGE>
 
                           LOCK-UP LETTER AGREEMENT


February 3, 1997



Millennium Pharmaceuticals, Inc.
640 Memorial Drive
Cambridge, MA  02139-4815

     Re:  ChemGenics Pharmaceuticals Inc.


Ladies and Gentlemen:

     The undersigned, at the date hereof, is the owner of (or has the right
to direct the disposition of) 6,792,679 shares (excluding shares issuable
upon the exercise of options or warrants*, whether or not presently
exercisable) (the "Shares") of common stock, par value $.001 per share (the
"Common Stock") of ChemGenics Pharmaceuticals Inc. (the "Company").  The
undersigned understands that Millennium Pharmaceuticals, Inc. (the "Buyer")
and CPI Acquisition Corp., a wholly-owned subsidiary of the Buyer (the
"Transitory Subsidiary") have entered into an Agreement and Plan of Merger
(the "Merger Agreement") with the Company, pursuant to which the Transitory
Subsidiary will be merged (the "Merger") with and into the Company and the
outstanding shares of capital stock of the Company will be converted into
an aggregate of 4,783,688 shares of common stock of the Buyer (the "Merger
Shares").  Following the Merger, all options to purchase shares of
ChemGenics' Common Stock will be converted into options (the "Options") to
purchase shares of common stock of the Buyer (the "Option Shares"),
although the number and price of the shares subject to each Option will be
adjusted based upon the conversion rate set forth in the Merger Agreement.
Merger Shares and Option Shares are collectively referred to herein as
"Buyer Shares."

     The undersigned agrees that, during the period commencing at the
Effective Time (as defined in the Merger Agreement) and ending on the date
that the Registration Statement on Form S-3 (or other appropriate form)
filed by the Buyer is declared effective by the Securities and Exchange
Commission (the "Date of Effectiveness"), the undersigned shall not sell,
exchange, transfer, assign, pledge, dispose of or engage in any
transaction, including a transaction of arrangement that reduces the risk
of loss by short sale, hedging or otherwise, any of the Buyer Shares issued
and delivered to the undersigned pursuant to the Merger or the exercise of
options.  During the period commencing on the Date of Effectiveness and
ending July 31, 1997, the foregoing prohibition shall apply with respect to
fifty percent (50%) of the Buyer Shares issued and delivered to the
undersigned pursuant to the Merger or upon the exercise of Options.  During
the period beginning August 1, 1997 and ending September 30, 1997, the
foregoing prohibition shall apply with respect to twenty-five percent (25%)
of the Buyer Shares issued and delivered to the undersigned pursuant to the
Merger or upon the exercise of Options.  After September 30, 1997, the
foregoing prohibition shall have no further force or effect.

     Notwithstanding the foregoing, if the undersigned is an individual, he
may transfer any or all of the Buyer Shares either during his or her
lifetime or on death by gift, will or intestate succession to his or her
immediate family or to a trust the beneficiaries of which are exclusively
the undersigned and/or a member or members of his or her immediate family;
and if the undersigned is a partnership, the
<PAGE>
 
 partnership may transfer any Buyer Shares to a partner of such partnership
 or a retired partner of such partnership who retires after the date hereof,
 or to the estate of any such partner or retired partner, and any partner
 who is an individual may transfer Buyer Shares by gift, will or intestate
 succession to his or her immediate family; and if the undersigned is a
 corporation, the corporation may transfer Buyer Shares to any stockholder
 of such corporation pursuant to a duly declared dividend and any
 stockholder who is an individual may transfer Buyer Shares by gift, will or
 intestate succession to his or her immediate family; provided, however,
                                                      --------  ------- 
 that in any such case it shall be a condition to the transfer that the
 transferee execute an agreement stating that the transferee is receiving
 and holding the Buyer Shares subject to the provisions of this letter
 agreement, and there shall be no further transfer of such Buyer Shares
 except in accordance with this letter agreement.

      For purposes of this letter agreement, "immediate family" shall mean
 spouse and lineal descendant, father, mother, brother or sister of the
 transferor or his spouse.

                                    Sincerely,

                                    PERSEPTIVE BIOSYSTEMS, INC.

                                    By: /s/ Noubar B. Afeyan
                                        ---------------------------------
                                    Signature of Security Holder


                                    PerSeptive Biosystems, Inc.
                                    -------------------------------------
                                    Print Exact Name of Security Holder


                                    (If Security Holder is an Entity)


                                    Noubar B. Afeyan, Ph.D.
                                    ------------------------------------

                                    Print Name of Signatory

                                    CEO
                                    ------------------------------------
                                    Print Title of Signatory

                                                                 


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