AUTOIMMUNE INC
SC 13D/A, 1999-11-08
BIOLOGICAL PRODUCTS, (NO DIAGNOSTIC SUBSTANCES)
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<PAGE>

                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549

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

                                  SCHEDULE 13D
                                 (RULE 13d-101)

         INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO 13d-
             1(a) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2(a)

                               (AMENDMENT NO. 1)(1)

                                 AUTOIMMUNE INC.
                                ----------------
                                (Name of Issuer)

                                  COMMON STOCK
                                  ------------
                         (Title of Class of Securities)

                                   052776 10 1
                                   -----------
                                 (CUSIP Number)

                                   Hope Flack
                                BVF Partners L.P.
                       227 West Monroe Street, Suite 4800
                             Chicago, Illinois 60606
                                 (312) 263-7777
                  ---------------------------------------------
                  (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                November 1, 1999
                                ----------------
             (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.

                         (Continued on following pages)

- -----------------------
(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 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>



CUSIP NO. 052776 10 1               13D               Page 2 of 7 Pages
- ------------------------------              -----------------------------------



     1       NAME OF REPORTING PERSONS
             I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                      BIOTECHNOLOGY VALUE FUND, L.P.

     2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                            (a) /X/  (b)  / /

     3       SEC USE ONLY

     4       SOURCE OF FUNDS*
                      WC

     5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
             REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                      / /

     6       CITIZENSHIP OR PLACE OF ORGANIZATION
                      DELAWARE

         NUMBER OF                7       SOLE VOTING POWER
          SHARES                                   -0-
       BENEFICIALLY
         OWNED BY                 8       SHARED VOTING POWER
           EACH                                  836,625
         REPORTING
        PERSON WITH               9       SOLE DISPOSITIVE POWER
                                                   -0-

                                  10      SHARED DISPOSITIVE POWER
                                                 836,625

     11      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING
             PERSON
                      836,625

     12      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
             CERTAIN SHARES*                                              / /

     13      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                      5.0%

     14      TYPE OF REPORTING PERSON*
                      PN


                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



<PAGE>

CUSIP NO. 052776 10 1               13D               Page 3 of 7 Pages
- ------------------------------              -----------------------------------

     1        NAME OF REPORTING PERSONS
              I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                       BVF PARTNERS L.P.

     2        CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                            (a) /X/  (b)  / /

     3        SEC USE ONLY

     4        SOURCE OF FUNDS*
                       OO

     5        CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
              REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                     / /

     6        CITIZENSHIP OR PLACE OF ORGANIZATION
                       DELAWARE

         NUMBER OF                7       SOLE VOTING POWER
          SHARES                                   -0-
       BENEFICIALLY
         OWNED BY                 8       SHARED VOTING POWER
           EACH                                    1,476,100
         REPORTING
        PERSON WITH               9       SOLE DISPOSITIVE POWER
                                                   -0-

                                  10      SHARED DISPOSITIVE POWER
                                                   1,476,100

     11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING
              PERSON
                       1,476,100

     12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
              CERTAIN SHARES*                                             / /

     13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                       8.9%

     14       TYPE OF REPORTING PERSON*
                       PN


                     * SEE INSTRUCTIONS BEFORE FILLING OUT!


<PAGE>

CUSIP NO. 052776 10 1               13D               Page 4 of 7 Pages
- ------------------------------              -----------------------------------

      1       NAME OF REPORTING PERSONS
              I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)
                       BVF INC.

      2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                            (a) /X/  (b)  / /

      3       SEC USE ONLY

      4       SOURCE OF FUNDS*
                       WC, OO

      5       CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS
              REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)                     / /

      6       CITIZENSHIP OR PLACE OF ORGANIZATION
                       DELAWARE

         NUMBER OF                7       SOLE VOTING POWER
          SHARES                                   -0-
       BENEFICIALLY
         OWNED BY                 8       SHARED VOTING POWER
           EACH                                    1,476,100
         REPORTING
        PERSON WITH               9       SOLE DISPOSITIVE POWER
                                                   -0-

                                 10       SHARED DISPOSITIVE POWER
                                                   1,476,100

     11       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING
              PERSON
                       1,476,100

     12       CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
              CERTAIN SHARES*                                             / /

     13       PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)
                       8.9%

     14       TYPE OF REPORTING PERSON*
                       IA, CO


                     * SEE INSTRUCTIONS BEFORE FILLING OUT!



<PAGE>

CUSIP NO. 052776 10 1               13D               Page 5 of 7 Pages
- ------------------------------              -----------------------------------


         Amendment No. 1 (the "Amendment") to the Statement on Schedule 13D
dated September 8, 1998 (as so amended, the "Statement"), is filed with the
Securities and Exchange Commission on behalf of Biotechnology Value Fund,
L.P., a Delaware limited partnership ("BVF"), BVF Partners L.P., a Delaware
limited partnership ("Partners"), and BVF Inc., a Delaware corporation ("BVF
Inc.") and, together with BVF and Partners, the "Reporting Persons") with
respect to the Common Stock, par value $0.01 per share (the "Stock"), of
Autoimmune Inc. ("Autoimmune"). The principle office of Autoimmune is located
at 128 Spring Street, Lexington, MA 02173.

Item 3 is hereby amended to read in its entirety as follows:

ITEM 3.        SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

         Since September 1, 1999, Partners, in its capacity as general
partner of BVF, has purchased on behalf of such limited partnership an
aggregate number of 194,900 shares of the Stock for an aggregate
consideration of $124,319.50, utilizing funds provided by BVF from its
working capital pursuant to the terms of its limited partnership agreement
with Partners. In addition, Partners, in its capacity as investment manager
with respect to certain managed accounts, has purchased on behalf of such
managed accounts an aggregate number of 69,500 shares of the Stock for an
aggregate consideration of $62,467.50, utilizing funds under management by
Partners pursuant to investment manager agreements between Partners and such
managed accounts.

Item 5 is hereby amended to read in its entirety as follows:

ITEM 5.        INTEREST IN SECURITIES OF THE ISSUER.

         (a)   BVF beneficially owns 836,625 shares of the Stock, Partners
beneficially owns 1,476,100 shares of the Stock, and BVF Inc. beneficially
owns 1,476,100 shares of the Stock, approximately 5.0%, 8.9% and 8.9%,
respectively, of the aggregate number of shares outstanding as of July 31,
1999 (as reported in Autoimmune's most recent quarterly statement on Form
10-Q).

         (b)   BVF shares voting and dispositive power over the 836,625
shares of the Stock it beneficially owns with Partners. Partners and BVF Inc.
share voting and dispositive power over the 1,476,100 shares of the Stock
they beneficially own with, in addition to BVF, the managed accounts on whose
behalf Partners, as investment manager, purchased such shares. The managed
accounts on whose behalf Partners owns shares of the Stock are Investment 10
L.L.C., an Illinois limited liability company ("ILL10") and Biotechnology
Value Fund, Ltd., a Cayman Islands Corporation ("BVF Ltd."). Together, ILL10
and BVF Ltd. are referred to herein as the "Accounts." The Accounts
specialize in holding biotechnology stocks for investment purposes and the
business address of each is BVF Partners L.P., 227 West Monroe Street, Suite
4800, Chicago, Illinois 60606.

<PAGE>


CUSIP NO. 052776 10 1               13D               Page 6 of 7 Pages
- ------------------------------              -----------------------------------


         (c)   Exhibit B attached hereto contains information as to all
transactions in the Stock by the Reporting Persons in the last sixty (60) days.
All such transactions were made for cash in open market, over-the-counter
transactions. No other transactions in the Stock have been effected by the
Reporting Persons in the last sixty (60) days.

         (d)   The Accounts are entitled to receive dividends and any sale
proceeds with respect to the Stock in proportion to their respective ownership
interests therein.

Item 7 is hereby amended to read in its entirety as follows:

ITEM 7.        MATERIAL TO BE FILED AS EXHIBITS.

         Exhibit A - Agreement Regarding Joint Filing

         Exhibit B - Transactions in the Stock by the Reporting Persons during
the past sixty (60) days.


<PAGE>

CUSIP NO. 052776 10 1               13D               Page 7 of 7 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
correct.

Dated: November 05, 1999.

                  BIOTECHNOLOGY VALUE FUND, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By:     /s/ Mark N. Lampert
                                            ----------------------
                                            Mark N. Lampert
                                            President


                  BVF PARTNERS L.P.

                  By:      BVF Inc., its general partner


                           By:      /s/ Mark N. Lampert
                                    ---------------------
                                    Mark N. Lampert
                                    President


                  BVF INC.


                  By:      /s/ Mark N. Lampert
                           ---------------------
                           Mark N. Lampert
                           President



<PAGE>

                                    EXHIBIT A

                        AGREEMENT REGARDING JOINT FILING

         The undersigned, Biotechnology Value Fund, L.P., a Delaware limited
partnership, and BVF Partners L.P., a Delaware limited partnership, and BVF
Inc., a Delaware corporation, hereby agree and acknowledge that the Amendment
containing the information required by Schedule 13D, to which this Agreement is
attached as an exhibit, is filed on behalf of each of them. The undersigned
further agree that any further amendments or supplements thereto shall also be
filed on behalf of each of them.

Dated:  November 05, 1999.

                  BIOTECHNOLOGY VALUE FUND, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By:     /s/ Mark N. Lampert
                                            ----------------------
                                            Mark N. Lampert
                                            President


                  BVF PARTNERS L.P.

                  By:      BVF Inc., its general partner


                           By:      /s/ Mark N. Lampert
                                    ---------------------
                                    Mark N. Lampert
                                    President


                  BVF INC.


                  By:      /s/ Mark N. Lampert
                           ---------------------
                           Mark N. Lampert
                           President



<PAGE>


                                                              EXHIBIT B

         TRANSACTIONS IN THE STOCK BY THE REPORTING PERSONS
                    DURING THE PAST SIXTY DAYS

<TABLE>
<CAPTION>

Trade Date       By              For the          Quantity          Price per        Type of Trade       Broker
- ----------       --              -------          --------          ---------        -------------       ------
                                Account of                           Share
                                ----------                           -----
<S>             <C>             <C>                <C>               <C>              <C>                 <C>
09/01/99        BVF             Partners           70,000            $0.9400           Purchase            INET
09/01/99        ILL10           Partners           16,000            $0.9400           Purchase            INET
09/01/99        BVF Ltd.        Partners           40,000            $0.9400           Purchase            INET
09/27/99        BVF             Partners           15,000            $0.6290           Purchase            INET
09/27/99        BVF Ltd.        Partners           13,500            $0.6250           Purchase            INET
10/25/99        BVF             Partners           84,900            $0.4300           Purchase            CANT
11/01/99        BVF             Partners           25,000            $0.4375           Purchase            HRZG
</TABLE>

    INET     =        Instinet
    CANT     =        Cantor Fitzgerald
    HRZG     =        Herzog, Hein & Geduld





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