SECURITIES AND EXCHANGE COMMISSION
                              Washington, D.C. 20549
 
                                   FORM 10-Q
 
 X   Quarterly report under Section 13 or 15(d) of the Securities Exchange Act
- ---  of 1934
 
For the period ended March 31, 1997
 
                                       OR
 
- ---  Transition report pursuant to Section 13 or 15 (d) of the Securities
     Exchange Act of 1934
 
                         Commission file number 0-21379
 
                          CUBIST PHARMACEUTICALS, INC.
              (Exact name of registrant as specified in its charter) 

          Delaware                                         22-3192085
 (State or other jurisdiction of                        (I.R.S. Employer
  incorporation or organization)                        Identification No.)

                               24 Emily Street
                     Cambridge, Massachusetts 02139 
                 (Address of principal executive offices)

                                (617) 576-1999 
             (Registrant's telephone number, including area code)
 
                                    None
                 (Former name, former address and former
                  fiscal year, if changed since last report)
 
    Indicate by check mark whether the registrant (1) has filed all reports 
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 
1934 during the preceding 12 months (or for such shorter period that the 
registrant was required to file such reports), and (2) has been subject to 
such filing requirements for the past 90 days. Yes  X  No
                                                   ---    ---
 
    As of May 1, 1997, there were 9,556,395 shares outstanding of the 
Company's common stock, $0.001 per value per share.
 
                                       

                          CUBIST PHARMACEUTICALS, INC.
 
                                     INDEX
 

   ITEM                                                             PAGE
  NUMBER                                                           NUMBER
  ------                                                           ------

PART I.    FINANCIAL INFORMATION
 
  Item 1.  Condensed Financial Statements
 
               Condensed Balance Sheets as of March 31, 1997 
               and December 31, 1996.............................    3
 
               Condensed Statements of Operations for the three 
               months ended March 31, 1997 and 1996..............    4
 
               Condensed Statements of Cash Flows for the three 
               months ended March 31, 1997 and 1996..............    5
 
               Notes to the Unaudited Condensed Financial 
               Statements........................................    6
 
  Item 2.  Management's Discussion and Analysis of Financial 
            Condition and Results of Operations..................    7
 
PART II.   OTHER INFORMATION
 
  Item 6.  Exhibits and Reports on Form 8-K.......................   10
 
           Signature..............................................   11

                                       2

                         PART I--FINANCIAL INFORMATION
 
ITEM 1. CONDENSED FINANCIAL STATEMENTS
 
                          CUBIST PHARMACEUTICALS, INC.
                             CONDENSED BALANCE SHEETS
                                    UNAUDITED
 


                                                                   MARCH 31,    DECEMBER 31,
                                                                     1997           1996
                                                                 -------------  -------------
                                                                          
ASSETS
Current Assets:
 Cash and cash equivalents......................................  $  3,892,300  $  19,329,353
 Short-term investments.........................................    10,635,801           --
 Accounts receivable............................................       505,267        505,267
 Prepaid expenses and other current assets......................       426,322        286,642
                                                                 -------------  -------------
 Total current assets...........................................    15,459,690     20,121,262
Property and equipment.........................................      5,216,912      4,898,538
 Less: Accumulated depreciation and amortization................    (1,956,114)    (1,741,152)
                                                                 -------------  -------------
 Property and equipment, net....................................     3,260,798      3,157,386
Long-term investments..........................................      2,565,297           --
Other assets...................................................        183,799        173,799
                                                                 -------------  -------------
   Total assets................................................  $  21,469,584  $  23,452,447
                                                                 -------------  -------------
                                                                 -------------  -------------
LIABILITIES AND STOCKHOLDERS' EQUITY
Current Liabilities:
 Accounts payable............................................... $     533,152  $     741,409
 Accrued expenses...............................................       395,973        484,732
 Deferred revenue...............................................        42,300        126,900
 Current portion of long-term debt..............................       193,760        188,062
 Current portion of capital lease obligations...................       549,865        559,767
                                                                 -------------  -------------
   Total current liabilities...................................      1,715,050      2,100,870
Long-term debt, net of current portion.........................        240,604        291,683
Long-term capital lease obligation, net of current portion.....        804,868        761,284
                                                                 -------------  -------------
   Total liabilities...........................................      2,760,522      3,153,837
                                                                 -------------  -------------
Commitments
Stockholders' Equity:
Common Stock--$.001 par value; authorized: 25,000,000 shares,
  1997 and 1996; issued: 9,554,759 shares, 1997 and 9,544,373
  shares, 1996.................................................          9,555          9,544
Additional paid-in capital.....................................     36,021,423     36,019,608
Accumulated deficit............................................    (17,321,916)   (15,730,542)
                                                                 -------------  -------------
   Total stockholders' equity..................................     18,709,062     20,298,610
                                                                 -------------  -------------
   Total liabilities and stockholders' equity..................  $  21,469,584  $  23,452,447
                                                                 -------------  -------------
                                                                 -------------  -------------

 
    The accompanying notes are an integral part of the unaudited condensed
financial statements.
 
                                       3

                          CUBIST PHARMACEUTICALS, INC.
                        CONDENSED STATEMENTS OF OPERATIONS
                                    UNAUDITED
 


                                                                       THREE MONTHS ENDED
                                                                           MARCH 31,
                                                                  ----------------------------
                                                                           
                                                                      1997           1996
                                                                  -------------  -------------
Sponsored research revenues.....................................  $     834,600  $      53,667
Operating expenses:
 Research and development........................................     2,011,273      1,523,259
 General and administrative......................................       645,469        376,665
                                                                  -------------  -------------
   Total operating expenses.....................................      2,656,742      1,899,924
Interest income.................................................        286,779         25,044
Interest expense................................................        (56,011)       (52,014)
                                                                  -------------  -------------
Net loss........................................................  ($  1,591,374) ($  1,873,227)
                                                                  -------------  -------------
                                                                  -------------  -------------
Net loss per common share.......................................  ($       0.17) ($       1.02)
                                                                  -------------  -------------
                                                                  -------------  -------------
Weighted average number of common shares........................      9,547,771      1,832,534
                                                                  -------------  -------------
                                                                  -------------  -------------

 
    The accompanying notes are an integral part of the unaudited condensed
financial statements.
 
                                       4

                          CUBIST PHARMACEUTICALS, INC.
                        CONDENSED STATEMENTS OF CASH FLOWS
                                    UNAUDITED
 


                                                                       THREE MONTHS ENDED
                                                                           MARCH 31,
                                                                  ----------------------------
                                                                      1997           1996
                                                                  -------------  -------------
                                                                           
Cash Flows from operating activities:
 Net loss........................................................  $ (1,591,374)  $ (1,873,227)
 Adjustments to reconcile net loss to net cash provided by/ (used
  in) operating activities:
  Depreciation and amortization...................................      225,943        152,932
  Changes in assets and liabilities:
   Accounts receivable.............................................        --          988,000
   Prepaid expenses and other current assets....................       (164,043)        11,926
   Other assets.................................................        (10,000)        (5,000)
   Accounts payable and accrued expenses........................       (297,015)        99,921
   Deferred revenue.............................................        (84,600)          --
                                                                  -------------  -------------
    Total adjustments...........................................       (329,715)     1,247,779
                                                                  -------------  -------------
Net cash provided by/(used in) operating activities.............     (1,921,089)      (625,448)
Cash flows from investing activities:
 Purchase of fixed assets........................................      (311,611)      (112,532)
 Leasehold improvements..........................................        (6,763)          --
 Purchase of short-term investments..............................   (10,635,801)          --
 Redemption of short-term investments............................          --        1,006,569
 Purchase of long-term investments...............................    (2,540,934)          --
                                                                  -------------  -------------
Net cash provided by/(used in) investing activities.............    (13,495,109)       894,037
Cash flows from financing activities:
 Issuance of stock...............................................        (9,156)         2,151
 Repayments of debt..............................................       (45,381)       (40,274)
 Proceeds from capital lease financing...........................       185,665         26,687
 Principal payments of capital lease obligations.................      (151,983)      (114,651)
                                                                  -------------  -------------
Net cash provided by/(used in) financing activities.............        (20,855)      (126,087)
                                                                  -------------  -------------
Net increase (decrease) in cash and cash equivalents............    (15,437,053)       142,502
Cash and cash equivalents, beginning of period..................     19,329,353      2,049,555
                                                                  -------------  -------------
Cash and cash equivalents, end of period........................  $   3,892,300  $   2,192,057
                                                                  -------------  -------------
                                                                  -------------  -------------
Supplemental disclosures of cash flow information:
  Cash paid during the year for interest........................  $      56,011  $      52,014

 
    The accompanying notes are an integral part of the unaudited condensed
financial statements.
 
                                       5

                          CUBIST PHARMACEUTICALS, INC.
             NOTES TO THE UNAUDITED CONDENSED FINANCIAL STATEMENTS
 
NOTE A. NATURE OF BUSINESS
 
    Cubist Pharmaceuticals, Inc. ("Cubist" or the "Company") is a 
biopharmaceutical company founded in May 1992 and is engaged in the research, 
development and commercialization of novel classes of antiinfective drugs to 
treat infectious diseases caused by bacteria and fungi, primarily those 
resistant to existing antiinfective drugs. Cubist has established multiple 
technology licenses and collaborations, has established a network of advisors 
and collaborators and is located in Cambridge, Massachusetts.
 
NOTE B. ACCOUNTING POLICIES
 
BASIS OF PRESENTATION
 
    The accompanying unaudited condensed financial statements reflect all 
adjustments, consisting of normal recurring adjustments, which are necessary, 
in the opinion of management, for a fair presentation of the results of the 
interim periods presented. Interim results are not necessarily indicative of 
results for a full year. These unaudited condensed financial statements do 
not include all information and footnote disclosures required by generally 
accepted accounting principles and therefore should be read in conjunction 
with the Company's audited financial statements and related footnotes for the 
year ended December 31, 1996 which are included in the Company's Annual 
Report on Form 10-K. Such Annual Report on Form 10-K was filed by the Company 
with the Securities and Exchange Commission (the "Commission") on March 31, 
1997.
 
NET LOSS PER COMMON SHARE
 
    The net loss per common share is computed based upon the weighted average 
number of common shares and common equivalent shares (using the treasury 
stock method) outstanding after certain adjustments described below. Common 
equivalent shares are not included in the per share calculations where the 
effect of their inclusion would be anti-dilutive, except that, in accordance 
with Securities and Exchange Commission Staff Accounting Bulletin No. 83, all 
common and common equivalent shares issued during the twelve-month period 
prior to the filing of the initial public offering, even when anti-dilutive, 
have been included in the calculation as if they were outstanding for all 
periods, using the treasury stock method and the initial public offering 
price of $6.00 per share.
 
    Effective December 31, 1997, the Company will adopt Statement of 
Financial Accounting Standards No. 128 (SFAS 128) "Earnings per Share", which 
will require the disclosure of Basic Earnings per Common Share and Diluted 
Basic Earnings per Common Share for all periods presented. Early application 
of SFAS 128 is not allowed, but pro forma disclosure is allowed. The Company 
does not expect this to have a material impact on the earnings per share 
computation.
 
NOTE C. SUBSEQUENT EVENT
 
COLLABORATIVE AGREEMENT
 
    In May 1997, the company entered into a collaborative research agreement 
with Novalon Pharmaceutical Corporation. Under the terms of the agreement, 
the Company will purchase a minority equity stake in Novalon for $1,000,000. 
In addition, the Company will make research support payments and pay 
royalties on sales of products developed using the Novalon technology. 
Novalon has also granted Cubist an exclusive six month option to acquire all 
the outstanding assets of Novalon in an equity-based transaction.
 
                                       6

                          CUBIST PHARMACEUTICALS, INC.
 
ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION
        AND RESULTS OF OPERATIONS
 
    Except for the historical information contained herein, this quarterly 
report on Form 10-Q may contain "forward-looking statements" within the 
meaning of Section 27A of the Securities Act of 1933 and Section 21E of the 
Securities Exchange Act of 1934, including, but not limited to, (i) 
statements about the adequacy of the Company's cash, cash equivalents, other 
capital resources, interest income and future revenues due under the 
Company's collaborative agreements to fund its operating expenses and capital 
requirements as currently planned through mid-1998 and (ii) certain 
statements identified or qualified by words such as "likely", "will", 
"suggests", "may", "would", "could", "should", "expects", "anticipates", 
"estimates", "plans", "projects", "believes", or similar expressions (and 
variants of such words or expressions). Investors are cautioned that 
forward-looking statements are inherently uncertain. Actual performance and 
results of operations may differ materially from those projected or suggested 
in the forward-looking statements due to certain risks and uncertainties, 
including, but not limited to, the risks and uncertainties described or 
discussed in the section "Risk Factors" in the Company's Annual Report on 
Form 10-K for the fiscal year ended December 31, 1996. The forward-looking 
statements contained herein represent the Company's judgment as of the date 
of this quarterly report on Form 10-Q, and the Company cautions readers not 
to place undue reliance on such statements.
 
OVERVIEW
 
    Since its incorporation on May 1, 1992 and commencement of operations in 
February 1993, Cubist has been engaged in the research, development and 
commercialization of novel antiinfective drugs to treat infectious diseases 
caused by bacteria and fungi, primarily those resistant to existing 
antiinfective drugs. The Company has a limited history of operations and has 
experienced significant operating losses since inception. The Company expects 
to incur significant additional operating losses over the next several years 
and expects cumulative losses to increase substantially due to expanded 
research and development efforts, pre-clinical and clinical trials and 
development of manufacturing, marketing and sales capabilities.
 
    A key element of the Company's strategy is to enhance certain of its drug 
discovery and development programs and to fund its capital requirements, in 
part, by entering into collaborative agreements with major pharmaceutical 
companies. To date, the Company has entered into collaborative agreements 
based specifically on its aminoacyl-tRNA synthetase program with 
Bristol-Myers Squibb, Merck and Pfizer. Under the collaborative agreements, 
the Company is entitled to receive research support payments, technology 
licensing fees and, if certain drug development milestones are achieved, 
milestone payments. In addition, the Company will be entitled to receive 
royalties on worldwide sales of any drug developed and commercialized from 
these collaborations.
 
RESULTS OF OPERATIONS
 
THREE MONTHS ENDED MARCH 31, 1997 AND 1996

    REVENUES.  Total revenues in the three months ended March 31, 1997 were 
$835,000 compared to $54,000 in the three months ended March 31, 1996, an 
increase of $781,000 or 1,446.3%. The revenue recognized in the three months 
ended March 31, 1997 consisted of research support funding from the 
Bristol-Myers Squibb and Merck collaborations. In the three months ended 
March 31, 1996, total revenues consisted entirely of SBIR Phase I grant 
funding.
 
                                       7



    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development 
expenses in the three months ended March 31, 1997 were $2,011,000 compared to 
$1,523,000 in the three months ended March 31, 1996, an increase of $488,000 
or 32.0%. The increase was largely due to increased costs related to 
additional personnel and purchases of laboratory research supplies that are 
required by such additional personnel.
 
    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses 
in the three months ended March 31, 1997 were $645,000 compared to $377,000 
in the three months ended March 31, 1996, an increase of $268,000 or 71.1%. 
The increase was largely due to: increased costs related to expenses for 
additional personnel and recruiting; expenses for directors and officers 
insurance which did not exist prior to the Company's initial public offering; 
and increased legal expenses.
 
    INTEREST INCOME AND EXPENSE.  Interest income in the three months ended 
March 31, 1997 was $287,000 compared to $25,000 in three months ended, March 
31, 1996, an increase of $262,000 or 1,048.0%. The increase in interest 
income was due primarily to a higher average cash, cash equivalent and 
investment balance during the three months ended March 31, 1997 as compared 
to the three months ended March 31, 1996. Interest expense in the three 
months ended March 31, 1997 was $56,000 as compared to $52,000 during the 
three months ended March 31, 1996.
 
    NET LOSS.  The net loss during the three months ended March 31, 1997 was 
$1,591,000 compared to $1,873,000 during the three months ended March 31, 
1996, a decrease of $282,000 or 15.1%. The decrease was primarily due to the 
increased revenues associated with the Bristol-Myers Squibb, and Merck 
collaborations, which were offset only in part by additional expenses 
incurred to support the advancement of the Company's internal research 
programs.
 
LIQUIDITY AND CAPITAL RESOURCES
 
    Since inception, the Company has financed its operations through the sale 
of equity securities, equipment financing, sponsored research revenues, 
license revenues and interest earned on invested capital. The Company's total 
cash, cash equivalent and investments balance at March 31, 1997 was 
$17,093,000 compared to $19,329,000 at December 31, 1996. For the three 
months ended March 31, 1997, the Company received $835,000 in sponsored 
research payments.
 
    Through March 31, 1997, the Company's collaborative partners have 
provided the Company with $3.8 million of research support payments and $4.0 
million in an equity investment. There can be no assurance that the Company 
will receive any additional funding from any of the Company's collaborative 
partners.
 
    As of March 31, 1997, the Company had invested an aggregate of $5,217,000 
(of which $318,000 was invested during the three months then ended) in 
property and equipment, primarily in facility renovations and laboratory 
equipment under capital leases. The obligations under capital leases at March 
31, 1997 were $1,355,000. Minimum annual principal payments due under capital 
leases total $770,000 in 1997. Principal payments decline each year 
thereafter until expiration in 2001. The Company made principal payments 
under its capital lease obligations of $152,000 in the three months ended on 
March 31, 1997. The Company expects its capital expenditures in 1997 to be 
approximately $1,000,000 consisting of laboratory and other equipment 
purchases.

    The Company believes that its existing cash, cash equivalents, other capital
resources, interest income and future revenues which may become due under the
Bristol-Myers Squibb, Merck and Pfizer collaborative agreements, will be
sufficient to fund its operating expenses and capital requirements as currently
planned through mid-1998.
 
                                       8



EARNINGS PER SHARE
 
    Effective December 31, 1997, the Company will adopt Statement of 
Financial Accounting Standards 128 (SFAS 128) "Earnings per Share", which 
will require the disclosure of Basic Earnings per Common Share and Diluted 
Basic Earnings per Common Share for all periods presented. Early application 
of SFAS 128 is not allowed, but pro forma disclosure is allowed. The Company 
does not expect this to have a material impact on the earnings per share 
computation.

                                       9


 
                           PART II--OTHER INFORMATION
 
ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K
 
    (a) Exhibits 
        10.1--Acquisition Option Agreement, dated May 5, 1997, by and
              among Novalon Pharmaceutical Corporation, certain stockholders 
              of Novalon Pharmaceutical Corporation, and the Applicant 
        10.2--Series B Convertible Preferred Stock Purchase Agreement, dated 
              May 5, 1997, by and between Novalon Pharmaceutical Corporation 
              and the Applicant 
          11--Statement of Computation of Earnings Per Share 
          27--Financial Data Schedule
 
    (b) Reports on Form 8-K
 
    No reports on Form 8-K were filed by the Company during the quarter ended 
March 31, 1997.

                                    10


 
                                   SIGNATURE
 
    Pursuant to the requirements of the Securities Exchange Act of 1934, the 
registrant has duly caused this report to be signed on its behalf by the 
undersigned, thereunto duly authorized.
 
                          CUBIST PHARMACEUTICALS, INC.
 
May 14, 1997              By:  /s/ Thomas A. Shea
                              -------------------------------
                                   Thomas A. Shea
                                   Director of Finance 
                                   & Administration and Treasurer
                                   (Authorized Officer and Principal
                                   Finance and Accounting Officer)

                                    11