ARQULE INC
SC 13G/A, 1998-02-13
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1
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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. 1 )*


                                  ArQule, Inc.
         ----------------------------------------------------------
                                (Name of Issuer)


                          Common Stock, $.01 par value
         ----------------------------------------------------------
                         (Title of Class of Securities)


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


         *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 1 of 22 Pages


<PAGE>   2

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 2 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Atlas Venture Fund II, L.P.
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             1,185,004 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          1,185,004 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        1,185,004 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        10.0%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        PN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 2 of 22 Pages


<PAGE>   3

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 3 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Atlas Venture Associates II, L.P.
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             1,185,004 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          1,185,004 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        1,185,004 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        10.0%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        PN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 3 of 22 Pages


<PAGE>   4

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 4 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Christopher J. Spray
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             670,056 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          670,056 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        670,056 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        5.6%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        IN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 4 of 22 Pages




<PAGE>   5
                                  

CUSIP NO. 00004269E1                 13G                      PAGE 5 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Barry Fidelman
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             670,056 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          670,056 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        670,056 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        5.6%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        IN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 5 of 22 Pages


<PAGE>   6

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 6 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Allan Ferguson
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             670,056 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          670,056 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        670,056 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        5.6%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        IN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 6 of 22 Pages


<PAGE>   7

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 7 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Jean-Francois Formela
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             670,056 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          670,056 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        670,056 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        5.6%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        IN
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 7 of 22 Pages



<PAGE>   8

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 8 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Atlas Venture Europe Fund B.V.
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             1,185,004 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          1,185,004 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        1,185,004 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        10.0%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        CO
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 8 of 22 Pages


<PAGE>   9

                                  

CUSIP NO. 00004269E1                 13G                      PAGE 9 OF 22 PAGES
          ----------                                              ---  ----

- --------------------------------------------------------------------------------
1.      NAME OF REPORTING PERSON
        S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON

        Atlas InvesteringsGroep N.V.
- --------------------------------------------------------------------------------
2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*      (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             1,185,004 shares
       EACH        -------------------------------------------------------------
    REPORTING      7.     SOLE DISPOSITIVE POWER
      PERSON              
       WITH               0 shares
                   -------------------------------------------------------------
                   8.     SHARED DISPOSITIVE POWER
                          
                          1,185,004 shares
- --------------------------------------------------------------------------------
9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
        
        1,185,004 shares
- --------------------------------------------------------------------------------
10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
        SHARES*                                                      [ ]

- --------------------------------------------------------------------------------
11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
        
        10.0%
- --------------------------------------------------------------------------------
12.     TYPE OF REPORTING PERSON*
        
        CO
- --------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!



                               Page 9 of 22 Pages



<PAGE>   10



                                  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,
                 Ferguson and Formela are the individual general partners 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), CHECK WHETHER THE PERSON FILING IS A:

                 (a)   [ ]   Broker or Dealer registered under Section 15 of the
                             Securities Exchange Act of 1934 (the "Act").

                 (b)   [ ]   Bank as defined in Section 3(a)(6) of the Act.

                 (c)   [ ]   Insurance Company as defined in Section 3(a)(19) of
                             the Act.

                 (d)   [ ]   Investment Company registered under Section 8 of
                             the Investment Company Act of 1940.




                               Page 10 of 22 Pages
<PAGE>   11


                 (e)   [ ]   Investment Adviser registered under Section 203 of 
                             the Investment Advisers Act of 1940.

                 (f)   [ ]   Employee Benefit Plan, Pension Fund which is 
                             subject to the provisions of the Employee
                             Retirement Income Security Act of 1974 or Endowment
                             Fund; see Rule 13d-1(b)(1)(ii)(F) of the Act.

                 (g)   [ ]   Parent Holding Company, in accordance with 
                             Rule 13d-1(b)(ii)(G) of the Act.

                 (h)   [ ]   Group, in accordance with Rule 13d-1(b)(1)(ii)(H) 
                             of the Act.

                 None.

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 "Entity" and
                 collectively the "Entities") may be deemed to own beneficially
                 1,185,004 shares of Common Stock as of December 31, 1997. Each
                 of Messrs. Spray, Fidelman, Ferguson and Formela may be deemed
                 to own beneficially 670,056 shares of Common Stock as of
                 December 31, 1997.

                 As of December 31, 1997, Atlas Venture Fund II, L.P. is the
                 record owner of 670,056 shares of Common Stock, Atlas
                 InvesteringsGroep N.V. is the record owner of 127,759 shares of
                 Common Stock and Atlas Venture Europe Fund B.V. is the record
                 owner of 387,189 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 1,185,004 shares of Common Stock.
                 In their capacities as individual general partners of Atlas
                 Venture Associates II, L.P., each of Messrs. Spray, Fidelman,
                 Ferguson and Formela may be deemed to own beneficially 670,056
                 shares of Common Stock.

         (b)     Percent of Class:

                 Atlas Venture Fund II, L.P.                 10.0%
                 Atlas Venture Associates II, L.P.           10.0%
                 Christopher J. Spray                         5.6%
                 Barry Fidelman                               5.6%
                 Allan Ferguson                               5.6%
                 Jean-Francois Formela                        5.6%
                 Atlas Venture Europe Fund B.V.              10.0%
                 Atlas InvesteringsGroep N.V.                10.0%




                               Page 11 of 22 Pages


<PAGE>   12

         The foregoing percentages are calculated based on the 11,888,909 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, 1997.

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

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

                        0 shares for each reporting person

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

                        Atlas Venture Fund II, L.P.            1,185,004 shares
                        Atlas Venture Associates II, L.P.      1,185,004 shares
                        Christopher J. Spray                     670,056 shares
                        Barry Fidelman                           670,056 shares
                        Allan Ferguson                           670,056 shares
                        Jean-Francois Formela                    670,056 shares
                        Atlas Venture Europe Fund B.V.         1,185,004 shares
                        Atlas InvesteringsGroep N.V.           1,185,004 shares

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

                        0 shares for each reporting person

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

                        Atlas Venture Fund II, L.P.            1,185,004 shares
                        Atlas Venture Associates II, L.P.      1,185,004 shares
                        Christopher J. Spray                     670,056 shares
                        Barry Fidelman                           670,056 shares
                        Allan Ferguson                           670,056 shares
                        Jean-Francois Formela                    670,056 shares
                        Atlas Venture Europe Fund B.V.         1,185,004 shares
                        Atlas InvesteringsGroep N.V.           1,185,004 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 the 670,056 shares which it holds
         of record , (ii) Atlas InvesteringsGroep N.V. for the 127,759 shares
         which it holds of record, and (iii) Atlas Venture Europe Fund B.V. for
         the 387,189 shares which it holds of record.

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

                 Not Applicable

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

                 Not Applicable.




                               Page 12 of 22 Pages


<PAGE>   13

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)(ii)(H).

Item 9.          NOTICE OF DISSOLUTION OF GROUP.

                 Not Applicable.

Item 10.         CERTIFICATION.

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






                               Page 13 of 22 Pages
<PAGE>   14



                                   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 6, 1998

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

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

                                                               *
                                             -----------------------------------
By:               *                          Barry Fidelman
    ---------------------------------
    Christopher J. Spray,
    General Partner
                                                               *
                                             -----------------------------------
                                             Allan Ferguson
ATLAS VENTURE EUROPE FUND B.V.

By: Atlas InvesteringsGroep N.V.                               *
                                             -----------------------------------
                                             Jean-Francois Formela

By:               *
    ---------------------------------
    Michiel de Haan,
    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 22 Pages


<PAGE>   15



                                                                       Exhibit 1
                                                                       ---------

                                    AGREEMENT

         Pursuant to Rule 13d-1(f)(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 6th day of February, 1998.

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

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

                                                               *
                                             -----------------------------------
By:               *                          Barry Fidelman
    ---------------------------------
    Christopher J. Spray,
    General Partner
                                                               *
                                             -----------------------------------
                                             Allan Ferguson
ATLAS VENTURE EUROPE FUND B.V.

By: Atlas InvesteringsGroep N.V.                               *
                                             -----------------------------------
                                             Jean-Francois Formela

By:               *
    ---------------------------------
    Michiel de Haan,
    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 15 of 22 Pages


<PAGE>   16



                                                                       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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                      [SIGNATURE PAGE FOLLOWS IMMEDIATELY]











                               Page 16 of 22 Pages


<PAGE>   17



      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 17 of 22 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 22 Pages
<PAGE>   19


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



                                             /s/ Michiel de Haan
                                             -----------------------------------
                                             Michiel de Haan



Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Michiel de
Haan, 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 22 Pages
<PAGE>   20


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



                                             /s/ Evert Smid
                                             -----------------------------------
                                             Evert Smid



Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Evert Smid,
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 20 of 22 Pages
<PAGE>   21


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



                                             /s/ Allan R. Ferguson
                                             -----------------------------------
                                             Allan R. Ferguson



Commonwealth of Massachusetts)
                             ) ss:
County of Suffolk            )

      On this 31st day of January, 1997, before me personally came Allan R.
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 21 of 22 Pages
<PAGE>   22



      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 22 of 22 Pages



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