ARQULE INC
SC 13G/A, 2000-02-14
PHARMACEUTICAL PREPARATIONS
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                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                  SCHEDULE 13G

                    UNDER THE SECURITIES EXCHANGE ACT OF 1934

                               (AMENDMENT NO. 3 )*


                                  ARQULE, INC.
             -------------------------------------------------------
                                (Name of Issuer)


                          COMMON STOCK, $.01 PAR VALUE
             -------------------------------------------------------
                         (Title of Class of Securities)


                                   00004269E1
             -------------------------------------------------------
                                 (CUSIP Number)


             -------------------------------------------------------
             (Date of Event Which Requires Filing of this Statement)

         Check the appropriate box to designate the rule pursuant to which this
Schedule is filed:

         [ ]  Rule 13d-1(b)
         [ ]  Rule 13d-1(c)
         [X]  Rule 13d-1(d)

         *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 the disclosures provided in a prior cover page.

         The information required in 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>   2

                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   2   OF   20   PAGES
           ----------                                       --        --


- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Atlas Venture Fund II, L.P.
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
        (SEE INSTRUCTIONS)                                            (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        Delaware Limited Partnership

- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  1,013,802 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 1,013,802 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,013,802 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        7.9%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        PN
- --------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 2 of 20 Pages

<PAGE>   3



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   3   OF   20   PAGES
           ----------                                       --        --


- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Atlas Venture Associates II, L.P.
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
        (SEE INSTRUCTIONS)                                            (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        Delaware Limited Partnership
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  1,013,802 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 1,013,802 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,013,802 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        7.9%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        PN
- --------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 3 of 20 Pages


<PAGE>   4



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   4   OF   20   PAGES
           ----------                                       --        --


- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Christopher J. Spray
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)     SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)     CITIZENSHIP OR PLACE OF ORGANIZATION

        United Kingdom

- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  589,191 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 589,191 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        589,191 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        4.6%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        IN
- --------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 4 of 20 Pages

<PAGE>   5



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   5   OF   20   PAGES
           ----------                                       --        --



- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Barry Fidelman
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        United States
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  589,191 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 589,191 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        589,191 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        4.6%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        IN
- --------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 5 of 20 Pages

<PAGE>   6



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   6   OF   20   PAGES
           ----------                                       --        --



- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Allan Ferguson
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        United States
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
         SHARES            (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  0 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 0 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        0 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        0%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        IN
- --------------------------------------------------------------------------------


                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 6 of 20 Pages


<PAGE>   7


                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   7   OF   20   PAGES
           ----------                                       --        --


- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Jean-Francois Formela
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        France
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
         SHARES            (6)   SHARED VOTING POWER
      BENEFICIALLY
       OWNED BY                  589,191 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 589,191 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        589,191 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        4.6%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        IN
- --------------------------------------------------------------------------------

                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 7 of 20 Pages

<PAGE>   8



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   8   OF   20   PAGES
           ----------                                       --        --



- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Atlas Venture Europe Fund B.V.
- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        The Netherlands
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  1,013,802 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 1,013,802 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,013,802 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        7.9%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        CO
- --------------------------------------------------------------------------------


                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 8 of 20 Pages

<PAGE>   9



                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE   9   OF   20   PAGES
           ----------                                       --        --



- --------------------------------------------------------------------------------
  (1)   NAMES OF REPORTING PERSONS
        I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY)

        Atlas InvesteringsGroep N.V.

- --------------------------------------------------------------------------------
  (2)   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
                                                                      (A)  [ ]
                                                                      (B)  [ ]
- --------------------------------------------------------------------------------
  (3)   SEC USE ONLY

- --------------------------------------------------------------------------------
  (4)   CITIZENSHIP OR PLACE OF ORGANIZATION

        The Netherlands
- --------------------------------------------------------------------------------
                           (5)   SOLE VOTING POWER

                                 0 shares
       NUMBER OF          ------------------------------------------------------
        SHARES             (6)   SHARED VOTING POWER
     BENEFICIALLY
       OWNED BY                  1,013,802 shares
         EACH             ------------------------------------------------------
       REPORTING           (7)   SOLE DISPOSITIVE POWER
      PERSON WITH
                                 0 shares
                          ------------------------------------------------------
                           (8)   SHARED DISPOSITIVE POWER

                                 1,013,802 shares
- --------------------------------------------------------------------------------
  (9)   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

        1,013,802 shares
- --------------------------------------------------------------------------------
 (10)   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
        CERTAIN SHARES (SEE INSTRUCTIONS)                                  [ ]

- --------------------------------------------------------------------------------
 (11)   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9

        7.9%
- --------------------------------------------------------------------------------
 (12)   TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

        CO
- --------------------------------------------------------------------------------


                     *SEE INSTRUCTIONS BEFORE FILLING OUT!

                               Page 9 of 20 Pages

<PAGE>   10

                                  SCHEDULE 13G

CUSIP NO.  00004269E1                                 PAGE  10   OF   20   PAGES
           ----------                                       --        --


                                  SCHEDULE 13G

Item 1(a).        NAME OF ISSUER:  ArQule, Inc.

Item 1(b).        ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:
                  200 Boston Avenue, Medford, Massachusetts  02155.

Item 2(a).        NAMES OF PERSONS FILING: Atlas Venture Fund II, L.P., Atlas
                  Venture Associates II, L.P., Christopher J. Spray, Barry
                  Fidelman, Allan Ferguson, Jean-Francois Formela, Atlas Venture
                  Europe Fund B.V. and Atlas InvesteringsGroep N.V.

                  Atlas Venture Associates II, L.P. is the sole general partner
                  of Atlas Venture Fund II, L.P. Messrs. Spray, Fidelman and
                  Formela are the individual general partners of Atlas Venture
                  Associates II, L.P. Mr. Ferguson was formerly a general
                  partner of Atlas Venture Associates II, L.P. Atlas
                  InvesteringsGroep N.V. is the sole shareholder of Atlas
                  Venture Europe Fund B.V.

Item 2(b).        ADDRESS OF PRINCIPAL BUSINESS OFFICE OR, IF NONE, RESIDENCE:
                  The address of the principal business office of Atlas Venture
                  Fund II, L.P., Atlas Venture Associates II, L.P. and Messrs.
                  Spray, Fidelman, Ferguson and Formela is Atlas Venture, 222
                  Berkeley Street, Boston, Massachusetts 02116. The address of
                  the principal business office of Atlas Venture Europe Fund
                  B.V. and Atlas InvesteringsGroep N.V. is Atlas
                  InvesteringsGroep N.V., Naarderpoort 1, 1411 MA Naarden, The
                  Netherlands.

Item 2(c).        CITIZENSHIP: Atlas Venture Fund II, L.P. and Atlas Venture
                  Associates II, L.P. are each a limited partnership organized
                  under the laws of the State of Delaware. Messrs. Fidelman and
                  Ferguson are citizens of the United States. Mr. Spray is a
                  citizen of the United Kingdom. Mr. Formela is a citizen of
                  France. Atlas Venture Europe Fund B.V. and Atlas
                  InvesteringsGroep N.V. are each a corporation organized under
                  the laws of The Netherlands.

Item 2(d).        TITLE OF CLASS OF SECURITIES: Common Stock, $.01 par value.

Item 2(e).        CUSIP NUMBER: 00004269E1

Item 3.           IF THIS STATEMENT IS FILED PURSUANT TO RULES 13d-1(b), OR
                  13d-2(b) OR (c), CHECK WHETHER THE PERSON FILING IS A:

                  Not Applicable.

Item 4.           OWNERSHIP.

         (a)      Amount Beneficially Owned:

                  Each of Atlas Venture Fund II, L.P., Atlas Venture Associates
                  II, L.P., Atlas Venture Europe Fund B.V. and Atlas
                  InvesteringsGroep N.V. (individually an


                              Page 10 of 20 Pages

<PAGE>   11


                  "Entity" and collectively the "Entities") may be deemed to own
                  beneficially 1,013,802 shares of Common Stock as of December
                  31, 1999.

                  As of December 31, 1999, Atlas Venture Fund II, L.P. is the
                  record owner of 589,191 shares of Common Stock, Atlas
                  InvesteringsGroep N.V. is the record owner of 90,651 shares of
                  Common Stock and Atlas Venture Europe Fund B.V. is the record
                  owner of 333,960 shares of Common Stock (referred to as the
                  "Record Shares"). By virtue of the affiliate relationships
                  among the Entities, each Entity may be deemed to own
                  beneficially all of the Record Shares. Hence, each Entity may
                  be deemed to own beneficially 1,013,802 shares of Common
                  Stock.

         (b)      Percent of Class:

                  Atlas Venture Fund II, L.P.                    7.9%
                  Atlas Venture Associates II, L.P.              7.9%
                  Atlas Venture Europe Fund B.V.                 7.9%
                  Atlas InvesteringsGroep N.V.                   7.9%

         The foregoing percentages are calculated based on the 12,838,465 shares
         of Common Stock reported to be outstanding in a Quarterly Report on
         Form 10-Q for ArQule, Inc. for the Quarter Ended September 30, 1999, as
         adjusted pursuant to Rule 13d-3(d)(1).

         (c) Number of shares as to which such person has:

                  (i)      sole power to vote or to direct the vote:

                           0 shares as to each reporting person

                 (ii)      shared power to vote or to direct the vote:

                           Atlas Venture Fund II, L.P.          1,013,802 shares
                           Atlas Venture Associates II, L.P.    1,013,802 shares
                           Atlas Venture Europe Fund B.V.       1,013,802 shares
                           Atlas InvesteringsGroep N.V.         1,013,802 shares

                (iii)      sole power to dispose or to direct the disposition
                           of:

                           0 shares as to each reporting person

                 (iv)      shared power to dispose or to direct the disposition
                           of:

                           Atlas Venture Fund II, L.P.          1,013,802 shares
                           Atlas Venture Associates II, L.P.    1,013,802 shares
                           Atlas Venture Europe Fund B.V.       1,013,802 shares
                           Atlas InvesteringsGroep N.V.         1,013,802 shares

         Each of the reporting persons expressly disclaims beneficial ownership
         of any shares of Common Stock of ArQule, Inc., except in the case of
         (i) Atlas Venture Fund II, L.P. for


                              Page 11 of 20 Pages

<PAGE>   12


         the 589,191 shares which it holds of record, (ii) Atlas
         InvesteringsGroep N.V. for the 90,651 shares which it holds of record,
         and (iii) Atlas Venture Europe Fund B.V. for the 333,960 shares which
         it holds of record.

Item 5.           OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS.

                  [x] In their capacities as individual general partners of
                  Atlas Venture Associates II, L.P., each of Messrs. Spray,
                  Fidelman and Formela may be deemed to own beneficially 589,191
                  shares of Common Stock as of December 31, 1999, which is five
                  percent or less of the Common Stock of ArQule, Inc. Mr.
                  Ferguson may be deemed to own beneficially no shares of Common
                  Stock as of December 31, 1999.

Item 6.           OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER
                  PERSON.

                  Not Applicable.

Item 7.           IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
                  ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING
                  COMPANY.

                  Not Applicable.

Item 8.           IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP.

                  Not Applicable. The reporting persons expressly disclaim
                  membership in a "group" as defined in Rule 13d-1(b)(1)(ii)(J).

Item 9.           NOTICE OF DISSOLUTION OF GROUP.

                  Not Applicable.

Item 10.          CERTIFICATIONS.

                  Not Applicable. This statement on Schedule 13G is not filed
                  pursuant to Rule 13d-1(b) or Rule 13d-1(c).

                              Page 12 of 20 Pages

<PAGE>   13



                                   SIGNATURES

         After reasonable inquiry and to the best of our knowledge and belief,
we certify that the information set forth in this statement is true, complete
and correct. We also hereby agree to file this statement jointly pursuant to the
Agreement listed on EXHIBIT 1 hereto.

Dated:  February 10, 2000

ATLAS VENTURE FUND II, L.P.              ATLAS INVESTERINGSGROEP N.V.

By: Atlas Venture Associates II, L.P.
                                         By:                  *
                                             -----------------------------------
                                             Hans Bosman,
                                             Managing Director
By:               *
    -----------------------------
    Christopher J. Spray,
    General Partner
                                                            *
                                         ---------------------------------------
                                         Christopher J. Spray
ATLAS VENTURE ASSOCIATES II, L.P.

                                                            *
                                         ---------------------------------------
By:               *                      Allan Ferguson
    -----------------------------
    Christopher J. Spray,
    General Partner                                         *
                                         ---------------------------------------
                                         Barry Fidelman

ATLAS VENTURE EUROPE FUND B.V.

By: Atlas InvesteringsGroep N.V.                            *
                                         ---------------------------------------
                                         Jean-Francois Formela
By:               *
    -----------------------------
    Hans Bosman,
    Managing Director



*   The undersigned attorney-in-fact, by signing her name below, does hereby
    sign this statement on behalf of the above indicated filers pursuant to
    Powers of Attorney filed hereto as EXHIBIT 2.


    /s/ Jeanne Larkin Henry
    -----------------------------
    Jeanne Larkin Henry
    Attorney-in-fact


                              Page 13 of 20 Pages

<PAGE>   14



                                                                       EXHIBIT 1
                                    AGREEMENT

         Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934,
the undersigned hereby agree that only one statement containing the information
required by Schedule 13G need be filed with respect to the ownership by each of
the undersigned of shares of Common Stock of ArQule, Inc.

         This agreement may be executed in any number of counterparts, each of
which shall be deemed an original.

         EXECUTED this 10th day of February, 2000.

ATLAS VENTURE FUND II, L.P.              ATLAS INVESTERINGSGROEP N.V.

By: Atlas Venture Associates II, L.P.
                                         By:                  *
                                             -----------------------------------
                                             Hans Bosman,
                                             Managing Director
By:               *
    -----------------------------
    Christopher J. Spray,
    General Partner
                                                            *
                                         ---------------------------------------
                                         Christopher J. Spray
ATLAS VENTURE ASSOCIATES II, L.P.

                                                            *
                                         ---------------------------------------
By:               *                      Allan Ferguson
    -----------------------------
    Christopher J. Spray,
    General Partner                                         *
                                         ---------------------------------------
                                         Barry Fidelman

ATLAS VENTURE EUROPE FUND B.V.

By: Atlas InvesteringsGroep N.V.                            *
                                         ---------------------------------------
                                         Jean-Francois Formela
By:               *
    -----------------------------
    Hans Bosman,
    Managing Director


*   The undersigned attorney-in-fact, by signing her name below, does hereby
    sign this statement on behalf of the above indicated filers pursuant to
    Powers of Attorney filed hereto as EXHIBIT 2.


    /s/ Jeanne Larkin Henry
    -----------------------------
    Jeanne Larkin Henry
    Attorney-in-fact


                              Page 14 of 20 Pages

<PAGE>   15



                                                                       EXHIBIT 2
                                POWER OF ATTORNEY


         KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below hereby constitutes and appoints each and any of Christopher J.
Spray and Jeanne Larkin Henry his true and lawful attorney-in-fact and agent,
with full power of substitution and resubstitution, for him and in his name,
place and stead, in any and all capacities (until revoked in writing) to sign
any and all instruments, certificates and documents required to be executed on
behalf of himself individually or on behalf of each or any of Atlas Venture
Fund, L.P., Atlas Venture Associates, L.P., Atlas Venture Partners III, B.V.,
Atlas Venture Fund II, L.P., Atlas Venture Associates II, L.P., Atlas Venture
Europe Fund B.V., Atlas InvesteringsGroep N.V., and Atlas Venture Beheer II B.V.
pursuant to sections 13 and 16 of the Securities Exchange Act of 1934, as
amended (the "Exchange Act"), and any and all regulations promulgated
thereunder, and to file the same, with all exhibits thereto, and any other
documents in connection therewith, with the Securities and Exchange Commission,
and with any other entity when and if such is mandated by the Exchange Act or by
the By-laws of the National Association of Securities Dealers, granting unto
said attorney-in-fact and agent full power and authority to do and perform each
and every act and thing requisite and necessary fully to all intents and
purposes as he might or could do in person thereby ratifying and confirming all
that said attorney-in-fact and agent, or his substitute or substitutes, may
lawfully do or cause to be done by virtue hereof.





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                              Page 15 of 20 Pages


<PAGE>   16



      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.



                                            /s/ Christopher J. Spray
                                            ------------------------------------
                                            Christopher J. Spray


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Christopher
J. Spray, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. LeBlanc
                                            ------------------------------------
                                            Notary Public

                                            My commission expires:  July 3, 1998



                              Page 16 of 20 Pages

<PAGE>   17


         IN WITNESS WHEREOF, this Power of Attorney has been signed as of the
31st day of January, 1997.



                                            /s/ Allan Ferguson
                                            ------------------------------------
                                            Allan Ferguson


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Allan
Ferguson, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. LeBlanc
                                            ------------------------------------
                                            Notary Public

                                            My commission expires:  July 3, 1998



                              Page 17 of 20 Pages



<PAGE>   18


      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.



                                            /s/ Barry Fidelman
                                            ------------------------------------
                                            Barry Fidelman


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Barry
Fidelman, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. LeBlanc
                                            ------------------------------------
                                            Notary Public

                                            My commission expires:  July 3, 1998



                              Page 18 of 20 Pages

<PAGE>   19


      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 31st
day of January, 1997.



                                            /s/ Jean-Francois Formela
                                            ------------------------------------
                                            Jean-Francois Formela


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Jean-Francois
Formela, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                               /s/ Elizabeth  A. LeBlanc
                                            ------------------------------------
                                            Notary Public

                                            My commission expires:  July 3, 1998





                              Page 19 of 20 Pages

<PAGE>   20



      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 7th
day of February, 2000.



                                            /s/ Hans Bosman
                                            ------------------------------------
                                            Hans Bosman


Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 7th day of February, 2000, before me personally came Hans
Bosman, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.


[Notary Seal]                           /s/ Ann M. Grummitt
                                        ------------------------------------
                                        Notary Public

                                        My commission expires:  November 6, 2003





                              Page 20 of 20 Pages







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