CUBIST PHARMACEUTICALS INC
10-K405, 1997-03-31
PHARMACEUTICAL PREPARATIONS
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               UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C. 20549
 
                                  FORM 10-K
 
                 FOR ANNUAL AND TRANSITION REPORTS PURSUANT TO
           SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 
/X/  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE 
     ACT OF 1934
     For the fiscal year ended: December 31, 1996
 
/ /  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES 
     EXCHANGE ACT OF 1934
     For the transition period from:       to
 
                         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, MA 02139
             (Address of principal executive offices and Zip Code)


                                 (617) 576-1999
                 (Registrant's telephone number, including area code)
 
              Securities registered pursuant to Section 12(b) of the Act:
                                        None
 
              Securities registered pursuant to Section 12(g) of the Act:
                          Common Stock, $.001 par value
                                  (Title of Class)
 
    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 / /
 
    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-X is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. /x/ 
 
    The aggregate market value of the registrant's common stock, $.001 par value
per share ("Common Stock"), held by non-affiliates of the registrant as of March
14, 1997 was approximately $55,422,808 based on 5,155,610 shares held by such
non-affiliates at the closing price of a share of Common Stock of $10.75 as
reported on the Nasdaq National Market on such date. Affiliates of the Company
(defined as officers, directors and owners of 10 percent or more of the
outstanding share of Common Stock) owned 4,392,741 shares of Common Stock
outstanding on such date. The number of outstanding shares of Common Stock of
the Company on March 14, 1997 was 9,548,351.
 
                      DOCUMENTS INCORPORATED BY REFERENCE

    Portions of the registrant's definitive Proxy Statement to be delivered 
to stockholders in connection with the Annual Meeting of Stockholders to be 
held on May 19, 1997 are incorporated by reference into Part III hereof. With 
the exception of the portions of such Proxy Statement expressly incorporated 
into this Annual Report on Form 10-K by reference, such Proxy Statement shall 
not be deemed filed as part of this Annual Report on Form 10-K.

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                          CUBIST PHARMACEUTICALS, INC.
                           ANNUAL REPORT ON FORM 10-K

                                TABLE OF CONTENTS

<TABLE>
<CAPTION>
ITEM                                                                                                     PAGE  
- ----                                                                                                   ------- 
<S>  <C>                                                                                               <C>     
                                      Part I                                                                         

 1   Business..........................................................................................    4   
 2   Description of Property...........................................................................   22   
 3   Legal Proceedings.................................................................................   22   
 4   Submission of Matters to a Vote of Security Holders...............................................   23   

                                      Part II                                                                  

 5   Market For Registrant's Common Stock and Related Stockholder Matters..............................   23   
 6   Selected Financial Data...........................................................................   24   
 7   Management's Discussion and Analysis of Financial Condition and Results of Operations.............   25   
 
 8   Financial Statements and Supplementary Data.......................................................   29   
 
 9   Changes in and Disagreements With Accountants on Accounting and Financial Disclosure..............   43   
 
                                      Part III                                                                 
 
10   Directors and Executive Officers of the Registrant................................................   43   
11   Executive Compensation............................................................................   43   
12   Security Ownership of Certain Beneficial Owners and Management....................................   43   
13   Certain Relationships and Related Transactions....................................................   43   

                                      Part IV

14   Exhibits, Financial Statement Schedules, and Reports on Form 8-K..................................   44   
     Signatures........................................................................................   47   

</TABLE>

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    Except for the historical information contained herein, this Annual 
Report on Form 10-K 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 this Annual Report on Form 10-K. 
The forward-looking statements contained herein represent the Company's 
judgment as of the date of this Annual Report on Form 10-K, and the Company 
cautions readers not to place undue reliance on such statements.

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                                     PART I

ITEM 1. BUSINESS
 
THE COMPANY
 
    Cubist Pharmaceuticals, Inc. ("Cubist" or the "Company") is a
biopharmaceutical company 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. Cubist's strategy for combating antiinfective drug
resistance is to identify novel intracellular targets essential for cell
function in bacteria and fungi, such as proteins, RNA or DNA, which if inhibited
by a drug would kill or attenuate the growth of the pathogen. Cubist selects
these targets based on a thorough understanding of their function, thereby
providing a foundation for assay development and identification of leads for
drug discovery.

OVERVIEW OF INFECTIOUS DISEASE AND DRUG RESISTANCE

    Infectious diseases are caused by bacteria and fungi present in the
environment that enter the body through the skin or mucous membranes of the
lungs, nasal passages or gastrointestinal tract, and overwhelm the body's immune
system. These pathogens then establish themselves in various tissues and organs
throughout the body and cause a number of serious and, in some cases, lethal
infections, including those of the bloodstream, heart, lung, liver and urinary
tract.
 
    Antiinfective drugs have, in many cases, proven highly successful in
controlling the serious morbidity and mortality that accompany these infections.
These drugs work by chemically binding to specific targets in a bacterial or
fungal pathogen, thereby inhibiting a cell function essential to its survival.
Currently available antiinfective drugs can be divided into the following four
broad categories, according to the type of essential cell function they inhibit:
(i) protein synthesis (e.g., tetracyclines, macrolides and aminoglycosides),
(ii) cell wall and membrane synthesis (e.g., penicillins, cephalosporins,
carbapenems, glycopeptides and polyenes), (iii) nucleic acid synthesis (e.g.,
fluoroquinolones) and (iv) cell metabolism (e.g., trimethoprim, sulfonamides,
azoles and allylamines).

    Recently, there has been a rise in the incidence of infectious diseases
caused by bacteria and fungi that have developed resistance to existing
antiinfective drugs. This phenomenon has been well documented in the medical
literature. A number of serious pathogens such as Staphylococcus aureus,
Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium,
Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, Mycobacterium
tuberculosis, Candida albicans, Aspergillus fumigatus and Aspergillus flavus
have shown significant evidence of drug resistance.

    The increasing prevalence of antiinfective drug resistance is a natural
outcome of the use and overuse of antiinfective drugs. When bacteria or fungi
are exposed to an antiinfective drug, the drug kills or attenuates the growth of
the susceptible pathogen. However, any variant in the bacterial population that
has spontaneously undergone a genetic change that confers drug

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resistance will have a selective growth advantage, which is known in 
evolutionary terms as natural selection. Thus, the antiinfective drug does 
not technically cause the resistance but creates a situation in which the 
resistant pathogen can multiply in the presence of the drug, increasing the 
population approximately a millionfold in a day and quickly becoming the 
predominant microorganism. These resistant bacteria can then spread rapidly 
from the infected patient to healthy individuals.

    Bacteria and fungi have evolved multiple resistance mechanisms against
currently available categories of antiinfective drugs. These mechanisms include:
(i) utilization of an enzyme to alter the drug's structure by creating or
destroying chemical bonds, (ii) modification of the cell membrane to block entry
of the drug, (iii) utilization of a protein to pump the drug out of their cells
before the drug binds to the target and (iv) alteration of the target to
significantly limit the ability of the antiinfective drug to bind to the target.
Bacteria and fungi change the target by mutation of the target's protein
sequence, by chemical modification of the target structure or by the acquisition
of a new gene from another pathogen that substitutes for the target function.
 
    Traditional drug discovery approaches have not met the challenge posed by
drug-resistant pathogens. To date, biology-based approaches have attempted to
identify compounds that kill or attenuate the growth of the pathogen using
whole-cell screening assays. This approach is limited because compounds that
could effectively inhibit a target function inside the cell, but are unable to
penetrate cell membranes, are not identified by whole-cell screening assays.
Thus, entire classes of effective inhibitors of intracellular targets, which
could be modified by medicinal chemistry to penetrate cell membranes, have
potentially been overlooked. Chemistry-based approaches have focused on
chemically modifying the molecular structure of existing antiinfective drugs or
combining existing antiinfective drugs with another agent (an antibiotic
potentiator) to circumvent established drug resistance mechanisms. Despite the
introduction of second and third generation antiinfective drugs, certain
pathogens, such as vancomycin-resistant strains of Enterococcus faecium, have
developed resistance to all currently available drugs.

    For decades, antiinfective drug discovery research has utilized only a fixed
number of targets and chemical structures thereby limiting the ability of these
approaches to identify new classes of drugs effective against drug-resistant
bacteria and fungi. During the past 20 years, these traditional approaches have
identified only one new chemical class of antiinfective drugs. Cubist believes
that the identification of new drug classes inhibiting new targets will prove to
be a more effective approach to the problem of antiinfective drug resistance.

THE CUBIST APPROACH

    Cubist is identifying new targets in bacteria or fungi which if inhibited by
a drug would disrupt an essential cell function and thereby kill or attenuate
the growth of the pathogen, allowing it to be cleared by the immune system. This
rational, target-based approach represents a distinct departure from traditional
strategies to develop antiinfective drugs. The Company expects that drugs
inhibiting these new targets would be immediately effective against currently
drug-resistant

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bacteria and fungi since these pathogens have not had an opportunity to 
evolve resistance specific to these new drugs.

THE CUBIST PROGRAMS

    Cubist's initial focus is on the identification and development of 
targets that are involved in the fundamental process of protein synthesis. 
This process involves a sequential order of well-established, enzymatic 
events that leads to the incorporation of amino acids into proteins. 
Antiinfective drugs, such as tetracyclines and erythromycin, that work by 
inhibiting protein synthesis at the ribosome (a cellular component which is 
the site of incorporation of amino acids into proteins) have been 
successfully developed and commercialized. There are, however, several 
classes of essential enzyme targets that function independently of the 
ribosome during protein synthesis and that have not yet been exploited as 
effective drug targets. The Company's programs address targets in the areas 
of: (i) Synthetases, (ii) Ribonuclease P, (iii) Amidotransferase and (iv) 
Elongation Factors. These enzyme targets are essential for the survival of 
both bacterial and fungal pathogens. The Company believes that these targets 
will enable the development of clinically useful antiinfective drugs against 
susceptible and drug-resistant pathogens.

    THE SYNTHETASE PROGRAM

    Synthetases are enzymes that play a fundamental role in protein synthesis in
all living organisms. In most organisms, there are 20 essential aminoacyl-tRNA
synthetases, one for each amino acid, which charge its specific amino acid to a
transfer RNA molecule ("tRNA") forming an amino acid-charged tRNA. These charged
tRNAs then interact with messenger RNA ("mRNA") at the ribosome to incorporate
the amino acid into the protein being synthesized. Inhibition of any one of the
20 aminoacyl-tRNA synthetases from any bacterial or fungal pathogen, at the
amino acid or tRNA binding sites, would disrupt protein production, thereby
killing or attenuating the growth of the pathogen. As a result, large numbers of
targets, each with multiple sites of inhibition, are available to Cubist for
drug discovery.
 
    The Company has developed over 100 proprietary aminoacyl-tRNA synthetase
targets and related assays that are currently being utilized in the discovery
and characterization of leads in its Synthetase Program. These aminoacyl-tRNA
synthetase targets were cloned or purified from Streptococcus pneumoniae,
Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Haemophilus
influenzae, Mycobacterium tuberculosis and Helicobacter pylori bacteria, Candida
albicans and Pneumocystis carinii fungi and cultured human cells.
 
    Through a combination of automated, high-throughput screening and a rational
drug design approach, Cubist has identified several proprietary leads that
inhibit certain aminoacyl-tRNA synthetases. These leads are currently being
optimized to improve stability, potency, selectivity, whole cell activity and
efficacy in animal models in an effort to identify clinical development
candidates.

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    THE RIBONUCLEASE P PROGRAM

    The Company's Ribonuclease P Program focuses on the discovery of
antiinfective drugs that inhibit ribonuclease P ("RNase P"), an essential target
in the process of protein synthesis. All tRNAs are initially synthesized as
immature tRNA molecules which are cleaved to the required functional size and
structure by an essential enzyme, RNase P. Inhibition of RNase P will thus
prevent the maturation of tRNA molecules, an essential step in protein
synthesis, thereby killing or attenuating the growth of the pathogen.

    Cubist has cloned, sequenced and expressed the genes encoding both the
protein and the RNA components of RNase P from certain bacteria. Recombinant
RNase P enzymes that have demonstrated the ability to cleave immature tRNA serve
as the foundation for biological assays. The Company has developed an automated
in vitro enzyme assay for high-throughput screening to identify inhibitors of
bacterial RNase P and is currently screening for the identification of such
inhibitors.

    THE AMIDOTRANSFERASE PROGRAM

    The Company's Amidotransferase Program focuses on the discovery of
antiinfective drugs that inhibit glutamine amidotransferase ("AdTase"), an
essential target in the process of protein synthesis. Certain bacteria have only
19 of the 20 required aminoacyl-tRNA synthetases and lack glutamine-tRNA
synthetase. These bacteria still require all 20 amino acids for protein
synthesis and therefore have developed a two-step process to compensate for the
lack of glutamine aminoacyl-tRNA synthetase. In step one, glutamate-tRNA
synthetase attaches glutamate to both glutamate-tRNA and glutamine-tRNA. In step
two, AdTase modifies the glutamate that is charged to the glutamine-tRNA into
glutamine, the appropriate amino acid. The now correctly charged tRNA can
incorporate the amino acid glutamine into the growing protein chain. Inhibiting
AdTase activity would thus limit the synthesis of all proteins that require
glutamine, thereby killing or attenuating the growth of the pathogen.

    The Company has established that AdTase activity is present in certain
bacteria, including Staphylococcus aureus and Enterococcus faecalis. The Company
has developed an assay to monitor the function of this enzyme. Cubist is
currently adapting this assay for automated, high-throughput screening and
expects to commence screening for the identification of inhibitors of AdTase
activity upon completion of such adaptation.

    THE ELONGATION FACTORS PROGRAM

    The Company's Elongation Factors Program focuses on the discovery of
antiinfective drugs that inhibit elongation factors Tu (EF-Tu) and Ts (EF-Ts),
essential protein targets in the process of protein synthesis. EF-Tu transports
amino acid-charged tRNA to the ribosome and also plays a role in the continuing
synthesis of proteins. During this process EF-Tu becomes inactivated and its

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reactivation requires a second elongation factor, EF-Ts. A crystal structure of
EF-Tu associated with some of its substrates including EF-Ts, has been defined.
Inhibition of either EF-Tu or EF-Ts activity will inhibit protein synthesis and
kill or attenuate the growth of the pathogen.

    Cubist has cloned, sequenced and expressed the genes encoding the EF-Tu and
EF-Ts proteins. Cubist is currently developing an assay for automated,
high-throughput screening of inhibitors of EF-Tu and EF-Ts activity.

    OTHER TARGET DISCOVERY PROGRAMS

    The Company is currently utilizing genomic information to develop additional
biological screening assays for drug discovery. Strategically, the Company will
continue to investigate targets involved in protein synthesis and will seek to
broaden its focus to include additional targets outside of this area.

DRUG DISCOVERY TECHNOLOGIES

    The Cubist drug discovery process consists of four primary steps as part of
an integrated platform: (i) target identification and validation, (ii) assay
development, (iii) lead identification and (iv) lead optimization.

    Target Identification and Validation-the use of microbial genomics and
functional genetics to identify multiple targets for drug discovery. The Company
uses a rational target selection approach which incorporates microbial genomics
and functional genetics to identify and characterize targets. To be selected for
entry into a drug discovery program, targets must be: (i) essential for the life
of the pathogen, so that inhibition of the target's natural function will kill
or attenuate the growth of the pathogen, (ii) functionally characterized for
assay development prior to high-throughput screening and (iii) structurally
divergent between bacteria or fungi and humans so that the pathogen target can
be selectively inhibited.

    Assay Development-the use of molecular biology, biochemistry and enzymology
to characterize targets and validate high-throughput screening assays.
Established molecular biology tools enable Cubist to rapidly clone, sequence,
express and purify multiple targets. Cubist then utilizes enzymology and
biochemistry techniques to functionally characterize targets. By characterizing
these targets, Cubist can develop robust, sensitive high-throughput screening
assays. The Company utilizes these assays to identify inhibitors. Cubist employs
proprietary screens to provide a quantitative description of potency, spectrum
and selectivity. In addition, the Company's enzymology studies identify reaction
mechanisms that provide the basis for rational drug design.

    Lead Identification-the use of high-throughput screening of small molecule
libraries, combinatorial chemistry and rational drug design to identify
potential drug candidates. Cubist has implemented automation and robotics,
together with other enhancement techniques, to perform high-throughput screening
of compound libraries in order to identify novel inhibitors.

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Novel inhibitors are further characterized using Cubist's secondary screens 
consisting of increasingly stringent selection criteria (such as spectrum and 
selectivity) to identify drug candidates with the greatest potential for 
successful development.

    Molecules used in the Cubist screening program currently originate from four
sources: (i) Cubist's proprietary rational design chemistry programs, (ii)
Cubist's proprietary combinatorial chemistry programs, (iii) academic and
industrial collaborations and (iv) commercial sources.

    The Cubist combinatorial chemistry program generates two types of libraries,
general and lead-specific. The general libraries are designed to provide Cubist
with a diversity of molecular structures which can be used in conjunction with
high-throughput screening to identify novel lead compounds which inhibit
selected targets. Cubist constructs lead-specific libraries based on principles
of rational drug design using structural templates demonstrated to interact with
the aminoacyl-tRNA synthetases. Cubist's proprietary general and lead-specific
libraries are being used to identify new lead inhibitors of the aminoacyl-tRNA
synthetases and other enzyme targets.

    Lead Optimization-the use of medicinal chemistry, high speed analoging and
pre-clinical evaluation to enhance pharmaceutical properties. Cubist optimizes
lead compounds, which have been identified by its high-throughput screening and
rational drug design approaches, through the iterative use of medicinal
chemistry and in vitro biological assays to enhance pharmaceutical properties.
These lead compounds first enter a high-speed chemical analoging program which
generates large numbers of structurally-related compounds. These analogs are
then evaluated for their (i) spectrum of inhibitory potency against a given
enzyme from a variety of pathogens, (ii) selectivity of the pathogen against the
human enzyme, (iii) inhibitory potency against multiple targets from a single
pathogen to identify a compound that could inhibit more than one target and (iv)
spectrum of activity against whole cells, including drug-resistant strains, to
determine potential clinical indication. Cubist subsequently evaluates, in
animal models, drug candidates exhibiting suitable potency, spectrum and
selectivity to determine their pharmacological and toxicological properties.

COLLABORATIVE AGREEMENTS

    The Company has entered into agreements based on certain targets within the
Synthetase Program with Bristol-Myers Squibb Company ("Bristol-Myers Squibb"),
Merck & Co., Inc. ("Merck") and Pfizer Inc. ("Pfizer") to screen the
collaborators' respective compound libraries against certain aminoacyl-tRNA
synthetase targets. These collaborations are expected to provide the Company
with funding, research and development resources, and access to libraries of
diverse compounds and clinical development, manufacturing and commercialization
capabilities. Through December 31, 1996, the Company's collaborative partners
have provided the Company with $5.6 million of funding in the form of research
support payments, technology licensing fees and a milestone payment and with a
$4.0 million equity investment.

    BRISTOL-MYERS SQUIBB

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    In June 1996, Cubist and Bristol-Myers Squibb entered into a 
Collaborative Research and License Agreement (the "Bristol-Myers Squibb 
Agreement") pursuant to which they agreed to collaborate to discover and 
develop novel antiinfective drugs from leads obtained by screening six of 
Cubist's aminoacyl-tRNA synthetase targets against Bristol-Myers Squibb's 
compound library. In connection with the collaboration, Bristol-Myers Squibb 
has made a $4.0 million equity investment in Cubist, has made a $1.0 million 
milestone payment and has made research support payments to Cubist. See 
"Management's Discussion and Analysis of Financial Condition and Results of 
Operations--Results of Operations." Under the terms of the Bristol-Myers 
Squibb Agreement, Cubist is entitled to receive additional research support 
payments and, if certain milestones are achieved, additional milestone 
payments from Bristol-Myers Squibb. Cubist has granted to Bristol-Myers 
Squibb an exclusive worldwide license to commercialize drugs resulting from 
this collaboration. The development, manufacture and worldwide sale of drugs 
resulting from the collaboration will be conducted by Bristol-Myers Squibb, 
and Cubist will be entitled to receive royalties on the worldwide sales of 
any drug developed and commercialized from this collaboration.

    MERCK

    In June 1996, the Company and Merck entered into a Collaborative Research
and License Agreement (the "Merck Agreement") pursuant to which they agreed to
collaborate to discover and develop novel antiinfective drugs from leads
obtained by screening three of Cubist's aminoacyl-tRNA synthetase targets
against Merck's compound library. In connection with the collaboration, Merck
has made research support payments and has paid technology licensing fees to
Cubist. See "Management's Discussion and Analysis of Financial Condition and
Results of Operations--Results of Operations." Under the terms of the Merck
Agreement, Cubist is entitled to receive additional research support payments
and, if certain milestones are achieved, milestone payments from Merck. Cubist
has granted Merck an exclusive worldwide license to commercialize drugs
resulting from this collaboration. The development, manufacture and worldwide
sale of drugs resulting from the collaboration will be conducted by Merck, and
the Company will be entitled to receive royalties on the worldwide sales of any
drug developed and commercialized from this collaboration.

    PFIZER

    In December 1995, the Company and Pfizer entered into a Research
Collaboration Agreement (the "Pfizer Agreement") pursuant to which they agreed
to collaborate to discover and develop novel antiinfective drugs from leads
obtained by screening six of Cubist's aminoacyl-tRNA synthetase targets against
Pfizer's compound library. In connection with the collaboration, Pfizer has made
research support payments and has paid technology licensing fees to Cubist. See
"Management's Discussion and Analysis of Financial Condition and Results of
Operations--Results of Operations." Under the terms of the Pfizer Agreement,
Cubist is entitled to receive additional research support payments and, if
certain milestones are achieved, milestone payments and a $5.0 million equity
investment from Pfizer. Cubist has granted Pfizer an exclusive

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worldwide license to commercialize drugs resulting from this collaboration. 
The development, manufacture and sale of drugs worldwide resulting from the 
collaboration will be conducted by Pfizer, and the Company will be entitled 
to receive royalties on the worldwide sales of any drug developed and 
commercialized from this collaboration.

    OTHER COLLABORATIONS

    To obtain additional compound libraries for further expansion of the
Company's internal drug discovery programs, Cubist has entered into screening
agreements with ArQule, Inc., Genzyme Corporation, Pharmacopeia, Inc. and
Terrapin Technologies, Inc. pursuant to which Cubist screens such party's
compound libraries against Cubist's proprietary targets. If a lead is identified
as a result of such screening activities, Cubist has a right of first
negotiation with the owner of such lead to enter into a drug development and
commercialization collaboration.

PATENTS AND PROPRIETARY TECHNOLOGY

    The Company seeks to protect its cloned targets, assays, organic synthetic
processes, lead compounds, screening technology and certain other technology by,
among other things, filing, or causing to be filed on its behalf, patent
applications. Cubist has 11 pending U.S. patent applications and one pending
international patent application. To date, the Company has received a notice of
allowance for four of these U.S. applications covering isolated recombinant
nucleic acids encoding tRNA synthetases and processes of making such
synthetases. In addition, Cubist has licensed three U.S. patents. There can be
no assurance that patents will be granted with respect to any of the Company's
pending patent applications or with respect to any patent applications filed by
the Company in the future.

    The commercial success of the Company will depend in part on not infringing
patents or proprietary rights of others. There can be no assurance that the
Company will be able to obtain a license to any third-party technology it may
require to conduct its business or that if obtainable, such technology can be
licensed at reasonable cost. Failure by the Company to obtain a license to
technology that it may require to utilize its technologies or commercialize its
products may have a material adverse effect on the Company's business, operating
results and financial condition. In some cases, litigation or other proceedings
may be necessary to defend against or assert claims of infringement, to enforce
patents issued to the Company, to protect trade secrets, know-how or other
intellectual property rights owned by the Company, or to determine the scope and
validity of the proprietary rights of third parties. Any potential litigation
could result in substantial costs to and diversion of resources by the Company
and could have a material adverse effect on the Company's business, operating
results and financial condition. There can be no assurance that any of the
Company's issued or licensed patents would ultimately be held valid or that
efforts to defend any of its patents, trade secrets, know-how or other
intellectual property rights would be successful. An adverse outcome in any such
litigation or proceeding could subject the Company to significant liabilities,
require the Company to cease using the subject technology or require the Company
to license the subject technology from the third party, all of which could have
a material adverse effect on the Company's business, operating results and
financial condition.


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    Much of the know-how of importance to the Company's technology and many of
its processes are dependent upon the knowledge, experience and skills, which are
not patentable, of key scientific and technical personnel. To protect its rights
to and to maintain the confidentiality of trade secrets and proprietary
information, the Company requires employees, Scientific Advisory Board members,
consultants and collaborators to execute confidentiality and invention
assignment agreements upon commencement of a relationship with the Company.
These agreements prohibit the disclosure of confidential information to anyone
outside the Company and require disclosure and assignment to the Company of
ideas, developments, discoveries and inventions made by employees, advisors,
consultants and collaborators. There can be no assurance, however, that these
agreements will not be breached or that the Company's trade secrets or
proprietary information will not otherwise become known or developed
independently by others.

GOVERNMENT REGULATION

    OVERVIEW

    The development, manufacture and marketing of drugs (including antibiotics)
developed by the Company or its collaborative partners are subject to regulation
by numerous governmental agencies in the United States, principally the Food and
Drug Administration ("FDA"), by state and local governments, and in some
instances by foreign governments. Pursuant to the Federal Food, Drug, and
Cosmetic Act and the regulations promulgated thereunder (the "FDC Act"), the FDA
regulates the pre-clinical and clinical trials, safety, effectiveness,
manufacture, labeling, storage, distribution, and promotion of drugs. Product
development and approval within the FDA regulatory framework usually takes a
significant number of years, involves the expenditure of substantial capital
resources and is uncertain.

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    U.S. Regulatory Process

    Before testing in the United States of any compounds with potential 
therapeutic value in human test subjects may begin, stringent government 
requirements for preclinical data must be satisfied. Pre-clinical testing 
includes both in vitro and in vivo laboratory evaluation and characterization 
of the safety and efficacy of a drug and its formulation. Pre-clinical 
testing results obtained from studies in several animal species, as well as 
from in vitro studies, are submitted to the FDA as part of an investigational 
new drug application ("IND") and are reviewed by the FDA prior to the 
commencement of human clinical trials. These pre-clinical data must provide 
an adequate basis for evaluating both the safety and the scientific rationale 
for the initial (Phase I) studies in human volunteers. Unless the FDA objects 
to an IND, the IND becomes effective 30 days following its receipt by the 
FDA. Once trials have commenced, the FDA may stop the trials by placing them 
on "clinical hold" because of concerns about, for example, the safety of the 
product being tested.

    Clinical trials involve the administration of the drug to healthy human 
volunteers or to patients under the supervision of a qualified investigator, 
usually a physician, pursuant to an FDA-reviewed protocol. Human clinical 
trials are typically conducted in three sequential phases, although the 
phases may overlap with one another. Clinical trials must be conducted under 
protocols that detail the objectives of the study, the parameters to be used 
to monitor safety and the efficacy criteria to be evaluated. Each protocol 
must be submitted to the FDA as part of the IND.

    Phase I clinical trials represent the initial administration of the 
investigational drug to a small group of healthy human subjects or, more 
rarely, to a group of selected patients with the targeted disease or 
disorder. The goal of Phase I clinical trials is typically to test for safety 
(adverse effects), dose tolerance, absorption, biodistribution, metabolism, 
excretion and clinical pharmacology and, if possible, to gain early evidence 
regarding efficacy.

    Phase II clinical trials involve a small sample of the actual intended 
patient population and seek to assess the efficacy of the drug for specific 
targeted indications, to determine dose tolerance and the optimal dose range 
and to gather additional information relating to safety and potential adverse 
effects.

    Once an investigational drug is found to have some efficacy and an 
acceptable safety profile in the targeted patient population, Phase III 
clinical trials are initiated to establish further clinical safety and 
efficacy of the investigational drug in a broader sample of the general 
patient population at geographically dispersed study sites in order to 
determine the overall risk-benefit ratio of the drug and to provide an 
adequate basis for product labeling. The Phase III clinical development 
program consists of expanded, large-scale studies of patients with the target 
disease or disorder, to obtain definitive statistical evidence of the 
efficacy and safety of the proposed product and dosage regimen. All of the 
phases of clinical studies must be conducted in conformance with the FDA's 
bioresearch monitoring regulations.

                                       13
<PAGE>

    All data obtained from a comprehensive development program including 
research and product development, manufacturing, pre-clinical and clinical 
trials and related information are submitted in a new drug application 
("NDA") to the FDA and the corresponding agencies in other countries for 
review and approval. In addition to reports of the trials conducted under the 
IND application, the NDA includes information pertaining to the preparation 
of the new drug or antibiotic, analytical methods, details of the manufacture 
of finished products and proposed product packaging and labeling. Although 
the FDC Act requires the FDA to review NDAs within 180 days of their filing, 
in practice longer times may be required. The FDA also frequently requests 
that additional information be submitted, requiring significant additional 
review time. Any proposed product of the Company likely would be subject to 
demanding and time-consuming NDA approval procedures in virtually all 
countries where marketing of the products is intended. These regulations 
define not only the form and content of safety and efficacy data regarding 
the proposed product but also impose specific requirements regarding 
manufacture of the product, quality assurance, packaging, storage, 
documentation and recordkeeping, labeling, advertising and marketing 
procedures.

    The FDA has developed two "fast track" policies for certain new drugs, 
one policy for expedited development and review, and one policy for 
accelerated approval. The expedited review policy applies to new drug 
therapies, including antibiotics, that are intended to treat persons with 
life-threatening and severely-debilitating illnesses, especially where no 
satisfactory alternative therapy exists. The FDA has defined 
"severely-debilitating" to mean diseases or conditions that cause major 
irreversible morbidity. During the developmental stage of drugs that qualify, 
the FDA expedites consultation and review of these experimental therapies.
 
     The FDA's accelerated approval policy applies to certain new drug or 
antibiotic products that have been studied for their safety and effectiveness 
in treating serious or life-threatening illnesses and that provide 
"meaningful therapeutic benefit to patients over existing treatments." This 
accelerated approval, or fast track approach, is generally limited to new 
drugs or antibiotics that treat patients that are unresponsive to, or 
intolerant of, available therapy, or when there is improved patient response 
over currently available therapy. The accelerated approval policy is further 
limited to drugs for which the predictive value of the surrogate endpoint, in 
terms of clinical outcome, has not been established. At the time of approval, 
the FDA may grant approval on a surrogate endpoint or an effect on a clinical 
endpoint other than survival or irreversible morbidity. The FDA may impose 
certain restrictions on distribution, limiting its use to certain facilities 
or specialty-trained physicians or making its use contingent on the 
performance of certain specified medical procedures. Postmarketing studies 
(Phase IV trials) are usually required to further affirm safety and/or 
efficacy. However, if an acceptable clinical endpoint has been established, 
the drug must be evaluated for approval under the traditional (non-fast 
track) approach.

    The Company is also subject to regulation under other federal laws and 
regulation under state and local laws, including laws relating to 
occupational safety, laboratory practices, the use, handling and disposition 
of radioactive materials, environmental protection and hazardous substance 
control. Although the Company believes that its safety procedures for 
handling and disposing of radioactive compounds and other hazardous materials 
used in its research and

                                       14
<PAGE>

development activities comply with the standards prescribed by federal, state 
and local regulations, the risk of accidental contamination or injury from 
these materials cannot be completely eliminated. In the event of any such 
accident, the Company could be held liable for any damages that result and 
any such liability could exceed the resources of the Company.

COMPETITION

    The biotechnology and pharmaceutical industries are intensely competitive
and subject to rapid and significant technological change. Competitors of the
Company in the United States and elsewhere are numerous and include, among
others, major, multinational pharmaceutical and chemical companies, specialized
biotechnology firms and universities and other research institutions. Many of
these competitors employ greater financial and other resources, including larger
research and development staffs and more effective marketing and manufacturing
organizations, than the Company or its collaborative partners. Acquisitions of
ocmpeting companies and potential competitors by large pharmaceutical companies
or others could enhance financial, marketing and other resources available to
such competitors. As a result of academic and government institutions becoming
increasingly aware of the commercial value of their research findings, such
institutions are more likely to enter into exclusive licensing agreements with
commercial enterprises, including competitors of the Company, to market
commercial products. There can be no assurance that the Company's competitors
will not succeed in developing technologies and drugs that are more effective or
less costly than any which are being developed by the Company or which would
render the Company's technology and future drugs obsolete and noncompetitive.

    In addition, some of the Company's competitors have greater experience 
than the Company in conducting pre-clinical and clinical trials and obtaining 
FDA and other regulatory approvals. Accordingly, the Company's competitors 
may succeed in obtaining FDA or other regulatory approvals for drug 
candidates more rapidly than the Company. Companies that complete clinical 
trials, obtain required regulatory agency approvals and commence commercial 
sale of their drugs before their competitors may achieve a significant 
competitive advantage, including certain patent and FDA marketing exclusivity 
rights that would delay the Company's ability to market certain products. 
There can be no assurance that drugs resulting from the Company's research 
and development efforts, or from the joint efforts of the Company and its 
collaborative partners, will be able to compete successfully with 
competitors' existing products or products under development or that they 
will obtain regulatory approval in the United States or elsewhere.

EMPLOYEES

    As of March 14, 1997, the Company had 57 full-time employees, 47 of whom 
were engaged in research and development and 10 of whom were engaged in 
management, administration and finance. Doctorates are held by 22 of the 
Company's employees. The Company's employees are not covered by a collective 
bargaining agreement. The Company has

                                       15
<PAGE>

never experienced an employment-related work stoppage and considers its 
employee relations to be good.

EXECUTIVE OFFICERS OF THE REGISTRANT

     The executive officers of the Company are as follows:

<TABLE>
<CAPTION>

NAME                                        AGE    POSITION
- ------------------------                    ----   -----------------------------------------------------
<S>                                         <C>    <C>

Scott M. Rocklage, Ph.D. ..................   42    President, Chief Executive Officer and Director     
Francis P. Tally, M.D. ....................   56    Vice President, Drug Development and Medical Affairs
Arthur F. Kluge, Ph.D. ....................   52    Vice President of Chemistry                         
Thomas A. Shea.............................   37    Director of Finance & Administration, Treasurer     
</TABLE>

    Dr. Rocklage has served as President and Chief Executive Officer and as a 
member of the Board of Directors of the Company since July 1994. From 1990 to 
1994, Dr. Rocklage served as President and Chief Executive Officer of Nycomed 
Salutar, Inc., a diagnostic imaging company. From 1992 to 1994, he also 
served as President and Chief Executive Officer and Chairman of Nycomed 
Interventional, Inc., a medical device company. From 1986 to 1990, he served 
in various positions at Salutar, Inc., a diagnostic imaging company and was 
responsible for designing and implementing research and development programs 
that resulted in three drug products in human clinical trials, including the 
approved drug Omniscan. Dr. Rocklage received his B.S. in Chemistry from the 
University of California, Berkeley and his Ph.D. in Chemistry from the 
Massachusetts Institute of Technology.

    Dr. Tally has served as Vice President of Drug Development since January 
1997. From March 1995 to January 1997, he served the Company as Vice 
President of Research and Development. From 1986 to 1995, Dr. Tally served as 
Executive Director of Infectious Disease, Molecular Biology and Natural 
Products Research at the Lederle Laboratories of American Cyanamid/American 
Home Products, where he was responsible for worldwide clinical studies for 
piperacillin/tazobactam which was registered for sales in Europe in 1992, 
approved by the FDA in 1993 and marketed as Zosyn. From 1975 to 1986, he 
served as Senior Physician in Infectious Disease at the New England Medical 
Center and Associate Professor of Medicine at Tufts Medical Center. Dr. Tally 
received his A.B. in Biology from Providence College and his M.D. from George 
Washington University School of Medicine.
 
    Dr. Kluge has served as Vice President of Chemistry since October 1995. 
From 1973 to 1995, Dr. Kluge served in various positions at Syntex 
Corporation (which later became Roche

                                       16
<PAGE>

Bioscience following the acquisition of Syntex by Hoffmann-La Roche Inc.), 
including Vice President and Director, Institute of Organic Chemistry, where 
he invented two currently marketed pharmaceutical products: laidlomycin 
propionate and ketorolac. Dr. Kluge received his B.A. in Chemistry from Park 
College, his M.S. and Ph.D. in Chemistry from the University of Massachusetts 
and his M.B.A. from the University of Santa Clara.

    Mr. Shea has served as Treasurer and Chief Accounting Officer since June 
1996 and has served as Director of Finance and Administration since September 
1993. From 1987 to 1993, he served as Manager of Accounting/MIS and Budget 
and Financial Analyst at ImmuLogic Pharmaceutical Corporation, a 
biotechnology company. Mr. Shea received his B.S. in Accounting/Law from 
Babson College.

RISK FACTORS

    Stockholders and prospective purchasers of the Company's Common Stock 
should carefully consider the following risk factors, in addition to the 
other information appearing in this Annual Report on Form 10-K.

    Early Stage of Product Development; No Assurance of Successful 
Commercialization. Since inception, the Company has generated no revenue from 
product sales. The Company's research and development programs are at an 
early stage, and the Company does not expect that any drugs resulting from 
its research and development efforts, or from the joint efforts of the 
Company and its collaborative partners, will be commercially available for a 
significant number of years, if at all. The Company is currently in the 
process of optimizing lead candidates to select drug candidates for 
pre-clinical development; however, to date, the Company has not, 
independently or with its collaborative partners, completed the optimization 
of any lead candidates or selected any drug candidates. Any future drug 
candidates developed by the Company will require signification additional 
research and development efforts, including extensive pre-clinical (animal 
and in vitro data) and clinical testing and regulatory approval, prior to 
commercial sale. None of the Company's potential drug candidates have 
advanced to any phase of pre-clinical or clinical trials. There can be no 
assurance that the Company's approach to drug discovery, acting independently 
or with the efforts of any collaborative partner of the Company, will be 
effective or will result in the development of any drug. The Company's 
potential drug candidates will be subject to the risks of failure inherent in 
the development of pharmaceutical products based on new technologies. These 
risks include the possibilities that any or all of the Company's drug 
candidates will be found to be unsafe, ineffective or toxic or otherwise fail 
to meet applicable regulatory standards or receive necessary regulatory 
clearances; that these drug candidates, if safe and effective, will be 
difficult to develop into commercially viable drugs or to manufacture on a 
large scale or will be uneconomical to market; that proprietary rights of 
third parties will preclude the Company from marketing such drugs; or that 
third parties will market superior or equivalent drugs. The failure to 
develop safe, commercially viable drugs would have a material adverse effect 
on the Company's business, operating results and financial condition.

    UNCERTAINTY DUE TO UNPROVEN TECHNOLOGY.  While the Company has demonstrated
that certain compounds have the ability to inhibit the activity of certain
aminoacyl-tRNA synthetases,

                                       17
<PAGE>

the Company has not proven that this activity can be utilized clinically as a 
therapeutic. There can be no assurance that the Company's drug discovery 
approach will lead to the discovery or development of any drugs or drug 
candidates or that there will be any clinical benefits associated with any 
drugs or drug candidates discovered and developed by the Company.

    Dependence on Collaborative Partners and Others. 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 with 
Bristol-Myers Squibb, Merck and Pfizer (collectively, the "Collaborative 
Agreements"). The Company's receipt of revenues (whether in the form of 
continued research funding, technology licensing fees, drug development 
milestones or royalties on sales) under the Collaborative Agreements is 
dependent upon the decisions made by and the manufacturing and marketing 
resources of its collaborative partners. The Company's collaborative partners 
are not obligated to develop or commercialize any drug candidates resulting 
from the Collaborative Agreements. The amount and timing of resources 
dedicated by the Company's collaborative partners to their respective 
collaborations with the Company is not within the Company's control. 
Moreover, certain drug candidates discovered by the Company may be viewed by 
the Company's collaborative partners as competitive with such partners' drugs 
or drug candidates. Accordingly, there can be no assurance that the Company's 
collaborative partners will elect to proceed with the development of drug 
candidates which the Company believes to be promising or that they will not 
pursue their existing or alternative technologies in preference to such drug 
candidates. There can be no assurance that the interests of the Company will 
continue to coincide with those of its collaborative partners, that some of 
the Company's collaborative partners will not develop independently or with 
third parties drugs that could compete with drugs of the types contemplated 
by the Collaborative Agreements, or that disagreements over rights or 
technology or other proprietary interests will not occur.

    If any of the Company's collaborative partners breaches or terminates its 
agreement with the Company, or otherwise fails to conduct its collaborative 
activities in a timely manner, the development or commercialization of any 
drug candidate or research program under these Collaborative Agreement may be 
delayed, the Company may be required to undertake unforeseen additional 
responsibilities or to devote unforeseen additional resources to such 
development or commercialization, or such development or commercialization 
could be terminated. Any such event could materially adversely affect the 
Company's financial condition, intellectual property position and operations.

    Additional Financing Requirements; Uncertainty of Available Funding. The 
Company will require substantial additional funds for its drug discovery and 
development programs, for operating expenses, for pursuing regulatory 
clearances, for the development of manufacturing, marketing and sales 
capabilities and for prosecuting and defending its intellectual property 
rights before it can expect to realize significant revenues from commercial 
sales. The Company intends to seek such additional funding through public or 
private financing or collaborative or other arrangements with corporate 
partners. If additional funds are raised by issuing equity securities, 
further dilution to existing stockholders may result and future investors may 
be granted rights superior to those of existing stockholders. There can be no 
assurance, however, that additional

                                       18
<PAGE>

financing will be available from any of these sources or, if available, will 
be available on acceptable or affordable terms.

    HISTORY OF LOSSES AND EXPECTATION OF FUTURE LOSSES.  The Company has
incurred a cumulative operating loss of approximately $15.7 million through
December 31, 1996. 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.

    UNCERTAINTY OF PATENTS AND PROPRIETARY RIGHTS.  The Company's success 
will depend in part on its ability to obtain U.S. and foreign patent 
protection for its drug candidates and processes, preserve its trade secrets 
and operate without infringing the proprietary rights of third parties. There 
can be no assurance that any additional patents will issue from any of the 
patent applications owned by, or licensed to, the Company. Further, there can 
be no assurance that any rights the Company may have under issued patents 
will provide the Company with significant protection against competitive 
products or otherwise be commercially viable. Legal standards relating to the 
validity of patents covering pharmaceutical and biotechnological inventions 
and the scope of claims made under such patents are still developing. There 
is no consistent policy regarding the breadth of claims allowed in 
biotechnology patents. The patent position of a biotechnology firm is highly 
uncertain and involves complex legal and factual questions. There can be no 
assurance that any existing or future patents issued to, or licensed by, the 
Company will not subsequently be challenged, infringed upon, invalidated or 
circumvented by others. In addition patents may have been granted, or may be 
granted, covering products or processes that are necessary or useful to the 
development of the Company's drug candidates. If the Company's drug 
candidates or processes are found to infringe upon the patents, or otherwise 
impermissibly utilize the intellectual property, of others, the Company's 
development, manufacture and sale of such drug candidates could be severely 
restricted or prohibited. In such event, the Company may be required to 
obtain licenses from third parties to utilize the patents or proprietary 
rights of others. There can be no assurance that the Company will be able to 
obtain such licenses on acceptable terms, or at all. There has been 
significant litigation in the industry regarding patents and other 
proprietary rights. If the Company becomes involved in litigation regarding 
its intellectual property rights or the intellectual property rights of 
others, the potential costs of such litigation and the potential damages that 
the Company could be required to pay could be substantial.

    In addition to patent protection, the Company relies on trade secrets, 
proprietary know-how and technological advances which it seeks to protect, in 
part, by confidentiality agreements with its collaborative partners, 
employees and consultants. There can be no assurance that these 
confidentiality agreements will not be breached, that the Company would have 
adequate remedies for any such breach, or that the Company's trade secrets, 
proprietary know-how and technological advances will not otherwise become 
known or be independently discovered by others.

    IMPACT OF EXTENSIVE GOVERNMENT REGULATION.  The FDA and comparable 
agencies in foreign countries impose substantial requirements upon the 
introduction of pharmaceutical products


                                       19
<PAGE>

through lengthy and detailed pre-clinical, laboratory and clinical testing 
procedures, sampling activities and other costly and time-consuming 
procedures to establish their safety and efficacy. All of the Company's drug 
candidates will require governmental approvals for commercialization, none of 
which have been obtained. Pre-clinical and clinical trials and manufacturing 
of the Company's drug candidates will be subject to the rigorous testing and 
approval processes of the FDA and corresponding foreign regulatory 
authorities. Satisfaction of these requirements typically takes a significant 
number of years and can vary substantially based on the type, complexity and 
novelty of the product. There can be no assurance as to when Cubist, 
independently or with its collaborative partners, might first submit an IND 
for FDA or other regulatory review.

    The effect of government regulation may be to delay marketing of the 
Company's potential drugs for a considerable or indefinite period of time, 
impose costly procedural requirements upon the Company's activities and 
furnish a competitive advantage to larger companies or companies more 
experienced in regulatory affairs. Delays in obtaining governmental 
regulatory approval could adversely affect the Company's marketing as well as 
the Company's ability to generate significant revenues from commercial sales. 
There can be no assurance that FDA or other regulatory approvals for any drug 
candidates developed by the Company will be granted on a timely basis or at 
all. Moreover, if regulatory approval of a drug candidate is granted, such 
approval may impose limitations on the indicated use for which such drug may 
be marketed. Even if initial regulatory approvals for the Company's drug 
candidates are obtained, the Company, its drugs and its manufacturing 
facilities would be subject to continual review and periodic inspection, and 
later discovery of previously problems with a drug, manufacturer or facility 
may result in restrictions on such drug or manufacturer, including withdrawal 
of the drug from the market. The regulatory standards are applied stringently 
by the FDA and other regulatory authorities and failure to comply can, among 
other things, result in fines, denial or withdrawal of regulatory approvals, 
product recalls or seizures, operating restrictions and criminal prosecutions.

    As with many biotechnology and pharmaceutical companies, the Company is 
subject to numerous environmental and safety laws and regulations. Any 
violation of, and the cost of compliance with, these regulations could 
materially adversely affect the Company's business, operating results and 
financial condition.

ITEM 2. DESCRIPTION OF PROPERTY

    The Company's headquarters and research and development facilities are 
located in a 24,000 square foot facility leased by the Company in Cambridge, 
Massachusetts at 24 Emily Street. The Company believes that this space will 
be adequate for its research and drug development activities for at least the 
next two years.

ITEM 3. LEGAL PROCEEDINGS

    The Company is not a party to any material legal proceedings.

                                       20
<PAGE>

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

    No matters were submitted to a vote of security holders during the last 
quarter of the fiscal year ended December 31, 1996.

                                    PART II

ITEM 5. MARKET FOR REGISTRANTS' COMMON EQUITY AND RELATED STOCKHOLDER MATTERS

MARKET INFORMATION

    Since October 25, 1996, the effective date of the Company's initial 
public offering, the Company's common stock has traded on the Nasdaq National 
Market under the symbol "CBST". Prior to such date, no established public 
trading market existed for the Company's common stock. The following table 
sets forth, for the period indicated, the high and low sale prices per share 
of the Company's common stock as reported by the Nasdaq National Market.

<TABLE>
<CAPTION>
                                                                                 HIGH        LOW
                                                                               ---------  ---------
<S>                                                                            <C>        <C>
Fourth Quarter (commencing on October 25, 1996)..............................  $    7.00  $    5.50
</TABLE>

HOLDERS

    As of March 14, 1997, the Company had approximately 114 stockholders of 
record. This does not reflect persons or entitles who hold their stock in 
nominee or "street" name through various brokerage firms.

DIVIDENDS

    THE COMPANY HAS NOT PAID DIVIDENDS ON ITS COMMON STOCK.

    The Company anticipates it will continue to reinvest earnings to finance 
future growth, and therefore does not intend to pay dividends in the 
foreseeable future.

RECENT SALES OF UNREGISTERED SECURITIES

    Described below is information regarding all securities of the Company 
sold by the Company during the fiscal year ended December 31, 1996, which 
were not registered under the Securities Act of 1933, as amended (the 
"Securities Act"). The share and per share amounts set forth below have been 
adjusted to reflect the Company's one for seven reverse stock split of its 
common stock effected on October 17, 1996.

                                       21
<PAGE>

    In February 1996, the Company issued a warrant to Comdisco, Inc. for up 
to 33,333 shares of Series C Convertible Preferred Stock at an exercise price 
of $0.90 per share. The issuance of such warrant was made in reliance upon 
Section 4(2) of the Securities Act. Upon the closing of the Company's initial 
public offering of its common stock, the warrant became exercisable for up to 
4,761 shares of Common Stock at an exercise price of $6.30.

    In June 1996, the Company issued and sold 2,816,902 shares of Series D 
Convertible Preferred Stock to Bristol-Myers Squibb Company at a purchase 
price of $1.42 per share. The issuance and sale of such shares was made in 
reliance upon Section 4(2) of the Securities Act. Upon the closing of the 
Company's initial public offering of its common stock, such shares of Series 
D Convertible Preferred Stock converted into 402,414 shares of Common Stock. 
The effective purchase price paid by Bristol-Myers Squibb Company for such 
402,414 shares of Common Stock was $9.94 per share. In addition, the Company 
issued 264,262 shares of Common Stock to Bristol-Myers Squibb Company 
promptly after the closing of the Company's initial public offering pursuant 
to certain antidilution rights of Bristol-Myers Squibb.

    In December 1996, the Company granted stock options to certain employees 
and officers of the Company exercisable for approximately 28,959 shares of 
Common Stock. The grants were made under the Company's Amended and Restated 
1993 Stock Option Plan. The exercise prices of the stock options ranged from 
$1.96 per share to $6.00 per share. These grants were made in reliance upon 
Rule 701 under the Securities Act.

ITEM. 6. SELECTED FINANCIAL DATA

<TABLE>
<CAPTION>
                                                                                                             PERIOD FROM    
                                                                                                              INCEPTION     
                                                                      YEARS ENDED DECEMBER 31,               (MAY 1, 1992)  
                                                             ------------------------------------------    TO DECEMBER 31,  
                                                               1996       1995       1994       1993            1992        
                                                             ---------  ---------  ---------  ---------  -------------------
<S>                                                          <C>        <C>        <C>        <C>        <C>                
                                                                          (IN THOUSANDS, EXCEPT PER SHARE DATA)             
Statement of Operations Data:
Total revenues.............................................  $   4,985  $   1,271  $      --  $      --       $      --     
Research and development expenses..........................      6,871      4,965      3,309      1,169              32     
General and administrative expenses........................      1,989      1,708      1,449        547               6     
Net loss...................................................     (3,799)    (5,396)    (4,813)    (1,688)            (35)    
Net loss per share.........................................  $   (1.39) $   (3.99  $   (4.82) $   (1.99)                    
Weighted average number of common shares outstanding.......      2,737      1,352        999        848                     
</TABLE>

<TABLE>
<CAPTION>
                                                                                     YEARS ENDED DECEMBER 31,               
                                                                            ------------------------------------------      
                                                                              1996       1995       1994       1993         
                                                                            ---------  ---------  ---------  ---------      
                                                                                          (IN THOUSANDS)                    
<S>                                                                         <C>        <C>        <C>        <C>            
Balance Sheet Data:
Cash and cash equivalents and short and long-term investments.............  $  19,329  $   3,056  $   1,221  $   4,457      
Total assets..............................................................     23,452      7,048      4,250      7,241      
Long-term obligations.....................................................      1,053      1,257      2,032      1,164      
Stockholder's equity......................................................     20,299      4,895        823      5,488      
</TABLE>

ITEM. 7 MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
        RESULTS OF OPERATIONS

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

                                       22
<PAGE>

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. Through December 31, 1996, the 
Company's collaborative partners have provided the Company with $5.6 million 
of funding in the form of research support payments, a technology licensing 
fees and a milestone payment and with a $4.0 equity investment. Under the 
collaborative agreements, the Company is entitled to receive additional 
research support payments, additional 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

Years ended December 31, 1996 and 1995

    REVENUES.  Total revenues in the year ended December 31, 1996 were 
$4,985,000 compared to $1,271,000 in the year ended December 31, 1995, an 
increase of $3,714,000 or 292.2%. The revenue recognized in the year ended 
December 31, 1996 primarily consisted of $1,500,000 in technology licensing 
fees from the Merck collaboration; $2,116,000 in research support funding 
from the Bristol-Myers Squibb, Merck and Pfizer collaborations; $1,000,000 in 
milestone payments from the Bristol-Myers Squibb collaboration; and $369,000 
in SBIR grants. In the year ended December 31, 1995, revenues consisted of 
$500,000 in technology licensing fees and $488,000 in research support 
funding from the Pfizer collaboration and $283,000 from SBIR Phase I grant 
funding.

    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development 
expenses in the year ended December 31, 1996 were $6,871,000 compared to 
$4,965,000 in the year ended December 31, 1995, an increase of $1,906,000 or 
38.4%. The increase was largely due to increased costs related to additional 
personnel, purchases of compounds to expand the Company's compound collection 
and purchases of laboratory research supplies that are utilized by such 
additional personnel.

    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses 
in the year ended December 31, 1996 were $1,989,000 compared to $1,709,000 in 
the year ended December 31, 1995, an increase of $280,000 or 16.4%. The 
increase was primarily due to costs relating to additional personnel and 
recruiting, relocation, and legal expenses.

                                       23
<PAGE>

    INTEREST INCOME AND EXPENSE.  Interest income in the year ended December 
31, 1996 was $306,000 compared to $239,000 in the year ended December 31, 
1995, a increase of $67,000 or 28%. The increase in interest income was due 
to an increase in the average cash, cash equivalent and investment balance 
during the year ended December 31, 1996 as compared to the year ended 
December 31, 1995. Interest expense was $229,000 in the year ended December 
31, 1996 as compared to $233,000 during the year ended December 31, 1995.

    NET LOSS.  The net loss during the year ended December 31, 1996 was 
$3,799,000 compared to $5,396,000 during the year ended December 31, 1995, a 
decrease of $1,597,000 or 29.6%. The decrease was primarily due to the 
increased revenues associated with the Bristol-Myers Squibb, Merck and Pfizer 
collaborations, which were offset only in part by additional expenses 
incurred to support the advancement of the Company's internal research 
programs.

Years ended December 31, 1995 and 1994

    REVENUES.  Total revenues in 1995 were $1,271,000. No revenues were 
received in 1994. The Company recognized $283,000 relating to three SBIR 
Phase I grants awarded during 1995. In addition, sponsored research revenues 
were recognized upon the signing of the Pfizer Agreement in December 1995. 
Revenues included $500,000 in license fees and $488,000 in research funding.

    RESEARCH AND DEVELOPMENT EXPENSES.  Total research and development 
expenses were $4,965,000 in 1995 compared to $3,309,000 in 1994, an increase 
of $1,656,000 or 50.0%. The increase was largely due to increased costs 
related to additional personnel, increased facility-related expenses 
reflecting the construction of 6,500 square feet of additional laboratory 
space and increased license and collaboration expenses.

    GENERAL AND ADMINISTRATIVE EXPENSES.  General and administrative expenses 
were $1,709,000 in 1995 compared to $1,449,000 in 1994, an increase of 
$260,000 or 17.9%. The increase is primarily due to increased compensation 
expenses reflecting a full year of executive compensation and increased 
patent application expenses offset by decreased relocation expenses.

    INTEREST INCOME AND EXPENSE.  Interest income was $239,000 in 1995 
compared to $113,000 in 1994, an increase of $126,000 or 110.9% This increase 
was due to an increase in the average cash balance from two equity financings 
during 1995 raising approximately $9,000,000. Interest expense was $233,000 
in 1995 compared to $168,000 in 1994, an increase of $65,000 or 38.7%. This 
increase was due to additional capital lease obligations entered into during 
1995.

    NET LOSS.  The net loss was $5,396,000 during 1995 and $4,813,000 during 
1994, an increase of $583,000 or 12.1%. The increase was primarily due to 
additional expenses incurred to support the advancement of the Company's 
internal research programs. Offsetting these additional expenses were 
revenues associated with the Pfizer Agreement and SBIR Phase I grants.

LIQUIDITY AND CAPITAL RESOURCES

                                       24
<PAGE>

    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 December 31, 1996 was 
$19,329,000 compared to $3,056,000 at December 31, 1995. For the year ended 
December 31, 1996, the Company raised $15,200,000 in an initial public 
offering, $4,000,000 in private equity financings, and received $2,116,000 in 
sponsored research payments, $1,500,000 in technology license fees, 
$1,000,000 in milestone payments and $369,000 in SBIR grants.

    Net cash used in operations in the year ended December 31, 1996 was 
$1,772,000 compared to $6,514,000 in the year ended December 31, 1995. The 
cash used in operations was primarily to fund research and development and 
for general and administrative expenses.

    In October 1996, the Company sold 2,500,000 shares of its common stock at 
$6.00 per share in connection with the Company's initial public offering of 
common stock (the "IPO"). In addition, in November 1996, the underwriters of 
the shares offered by the Company in the IPO exercised their over-allotment 
option and the Company sold an additional 375,000 shares of its common stock 
at a price of $6.00 per share. The total number of shares of common stock 
sold by the Company in connection with the IPO was 2,875,000 shares and the 
total net proceeds received by the Company in connection with the sale of all 
of such shares were $15,200,000.

    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. Through December 
31, 1996, the Company's collaborative partners have provided the Company with 
$2.6 million of research support payments, $2.0 million in technology 
licensing fees, $1.0 million in milestones 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.

    From inception through December 31, 1996, the Company had invested an 
aggregate of $4,899,000 (of which $1,064,000 was invested during the fiscal 
year ended December 31, 1996) in property and equipment, primarily in 
facility renovations and laboratory equipment under capital leases. The 
obligations under capital leases at December 31, 1996 were $1,321,000. 
Minimum annual principal payments due under capital leases total $703,000 in 
1997. Principal payments decline each year thereafter until expiration in 
2000. The Company made principal payments under its capital lease obligations 
of $469,000 in the year ended on December 31, 1996.

    The Company believes that its existing cash, cash equivalents, other 
capital resources, interest income and future revenues 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. However, the Company's actual cash 
requirements may vary materially from those now planned and will depend on 
numerous factors. There can be no assurance that the Company's existing 
capital resources, interest income and revenues from the Collaborative 
Agreements

                                       25
<PAGE>

will be sufficient to fund the Company's operating expenses and capital 
requirements during such period.

    The Company will need to raise substantial additional capital to fund its 
operations after mid-1998. The Company intends to seek such additional 
funding through public or private financing or collaborative or other 
arrangements with corporate partners. See "Risk Factors--Additional Financing 
Requirements; Uncertainty of Available Funding."


                                       26
<PAGE>

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

                          CUBIST PHARMACEUTICALS, INC.

                         INDEX TO FINANCIAL STATEMENTS

<TABLE>
<CAPTION>
                                                                                                                    PAGE  
                                                                                                                  ------- 
<S>                                                                                                               <C>     
Report of Independent Accountants................................................................................    30   
Balance Sheets as of December 31, 1996 and 1995..................................................................    31   
Statements of Operations for the years ended December 31, 1996, 1995 and 1994....................................    32   
Statements of Cash Flows for the years ended December 31, 1996, 1995 and 1994....................................    33   
Statements of Changes in Stockholders' Equity for the years ended December 31, 1996, 1995 and 1994...............    34   
Notes to Financial Statements....................................................................................    37   
</TABLE>

                                       27
<PAGE>

                       REPORT OF INDEPENDENT ACCOUNTANTS

To the Board of Directors and Stockholders of
Cubist Pharmaceuticals, Inc.:

    We have audited the accompanying balance sheets of Cubist 
Pharmaceuticals, Inc. as of December 31, 1996 and 1995, and the related 
statements of operations, changes in stockholders' equity, and cash flows for 
each of the three years in the period ended December 31, 1996. These 
financial statements are the responsibility of the Company's management. Our 
responsibility is to express an opinion on these financial statements based 
on our audits.

    We conducted our audits in accordance with generally accepted auditing 
standards. Those standards require that we plan and perform the audit to 
obtain reasonable assurance about whether the financial statements are free 
of material misstatement. An audit includes examining, on a test basis, 
evidence supporting the amounts and disclosures in the financial statements. 
An audit also includes assessing the accounting principles used and 
significant estimates made by management, as well as evaluating the overall 
financial statement presentation. We believe that our audits provide a 
reasonable basis for our opinion.

    In our opinion, the financial statements referred to above present 
fairly, in all material respects, the financial position of Cubist 
Pharmaceuticals, Inc. as of December 31, 1996 and 1995, and the results of 
its operations and cash flows for each of the three years in the period ended 
December 31, 1996 in conformity with generally accepted accounting principles.

Boston, Massachusetts                                   Coopers & Lybrand L.L.P.
February 12, 1997

                                       28
<PAGE>

                          CUBIST PHARMACEUTICALS, INC.

                                 BALANCE SHEETS

<TABLE>
<CAPTION>
                                                                                 DECEMBER 31,                
                                                                         ------------------------------      
                                                                             1996             1995           
                                                                         --------------  --------------      
<S>                                                                      <C>             <C>                 
ASSETS
Current Assets:
  Cash and cash equivalents............................................  $  19,329,353     $  2,049,555      
  Short-term investments...............................................             --        1,006,569      
  Accounts receivable..................................................        505,267          988,000      
  Prepaid expenses and other current assets............................        286,642           66,996      
                                                                         --------------   -------------      
  Total current assets.................................................     20,121,262        4,111,120      
Property and equipment.................................................      4,898,538        3,834,953      
  Less: Accumulated depreciation and amortization......................     (1,741,152)      (1,056,802)     
                                                                         --------------   -------------      
  Property and equipment, net..........................................      3,157,386        2,778,151      
Other assets...........................................................        173,799          158,571      
                                                                         --------------   -------------      
    Total assets.......................................................  $  23,452,447     $  7,047,842      
                                                                         --------------   -------------      
                                                                         --------------   -------------      
LIABILITIES AND STOCKHOLDERS' EQUITY
Current Liabilities:
  Accounts payable.....................................................  $     741,409     $    124,856      
  Accrued expenses.....................................................        484,732          189,663      
  Deferred revenue.....................................................        126,900               --      
  Current portion of long-term debt....................................        188,062          168,565      
  Current portion of capital lease obligations.........................        559,767          413,223      
                                                                         --------------   -------------      
    Total current liabilities..........................................      2,100,870          896,307      
Long-term debt, net of current portion.................................        291,683          479,745      
Long-term capital lease obligation, net of current portion.............        761,284          777,017      
                                                                         --------------   -------------      
     Total liabilities.................................................  $   3,153,837     $  2,153,069      
                                                                         --------------   -------------      
Commitments (Note I)

Stockholders' Equity:
Preferred Stock non-cumulative; convertible, $.001
  par value; authorized 5,000,000 shares, 1996, and
  43,000,000 shares, 1995; issued 1996 no shares;
  issued 1995 34,751,183 shares........................................             --           34,751      

Common Stock, $.001 par value; authorized
  25,000,000 shares, 1996, and 52,000,000 shares, 1995;
  issued 1996 9,544,373 shares; issued 1995 1,016,662 shares..........           9,544           1,017      
Additional paid-in capital.............................................      36,019,608      16,790,878      
Accumulated deficit....................................................     (15,730,542)    (11,931,873)     
                                                                         --------------   -------------      
    Total stockholders' equity.........................................      20,298,610       4,894,773      
                                                                         --------------   -------------      
    Total liabilities and stockholders' equity.........................  $   23,452,447    $  7,047,842      
                                                                         --------------   -------------      
                                                                         --------------   -------------      

</TABLE>

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

                                       29
<PAGE>

                          CUBIST PHARMACEUTICALS, INC.

                            STATEMENTS OF OPERATIONS

<TABLE>
<CAPTION>
                                                         FOR THE YEARS ENDED DECEMBER 31,
                                                 ------------------------------------------------ 
                                                      1996              1995            1994
                                                 -------------     -------------    -------------  

<S>                                             <C>                <C>              <C>                     

Sponsored research revenues..................    $   4,985,052     $   1,271,333    $          --  
Operating expenses:
  Research and development...................        6,871,149         4,964,876        3,309,161  
  General and administrative.................        1,989,284         1,708,513        1,448,928  
                                                 -------------     -------------    -------------  
    Total operating expenses.................        8,860,433         6,673,389        4,758,089  
Interest income..............................          306,017           239,030          113,338  
Interest expense.............................         (229,305)         (232,980)        (168,284) 
                                                 -------------     -------------    -------------  
  Net loss...................................    $  (3,798,669)    $  (5,396,006)   $  (4,813,035) 
                                                 -------------     -------------    -------------  
                                                 -------------     -------------    -------------  

Net loss per common share....................    $       (1.39)    $       (3.99)   $       (4.82) 
                                                 -------------     -------------    -------------  
Weighted average number of common shares.....        2,737,121         1,352,499          998,766  
                                                 -------------     -------------    -------------  
                                                 -------------     -------------    -------------  
</TABLE>

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

                                       30

<PAGE>

                         CUBIST PHARMACEUTICALS, INC.

                            STATEMENTS OF CASH FLOWS
 
<TABLE>
<CAPTION>
                                                                    FOR THE YEARS ENDED DECEMBER 31,
                                                              --------------------------------------------
<S>                                                           <C>            <C>             <C>
                                                                   1996            1995           1994
                                                              -------------  --------------  -------------
Cash flows from operating activities:
  Net loss..............................................       $(3,798,669)   $(5,396,006)    $(4,813,035)
  Adjustments to reconcile net loss to net cash used in
    operating activities:
    Depreciation and amortization.......................           740,408        570,556        355,977
    Changes in assets and liabilities:
       Accounts receivable..............................           482,733       (988,000)            --
       Prepaid expenses and other current assets........          (219,646)        15,713        (12,688)
       Other assets.....................................           (15,228)        (8,390)        (5,001)
       Accounts payable and accrued expenses............           911,622       (708,104)       716,018
       Deferred revenue.................................           126,900             --             --
                                                              ------------   ------------   ------------
          Total adjustments.............................         2,026,789     (1,118,225)     1,054,306
                                                              ------------   ------------   ------------
Net cash used in operating activities...................        (1,771,880)    (6,514,231)    (3,758,729)

Cash flows from investing activities:
  Purchase of equipment.................................          (640,329)            --       (150,726)
  Leasehold improvements................................          (423,256)       (99,325)      (688,329)
  Purchase of short-term investments....................                --     (3,942,610)            --
  Redemption of short-term investments..................         1,006,569      2,936,041      2,612,158
  Redemption of long-term investments...................                --             --        511,934
                                                              ------------   ------------   ------------
Net cash provided by/(used in) investing activities.....           (57,016)    (1,105,894)     2,285,037

Cash flows from financing activities:
  Issuance of stock.....................................        19,146,448       8,467,928        148,314
  Proceeds from venture capital bridge loan.............                --              --      1,000,000
  Proceeds from long-term debt..........................                --         345,500             --
  Repayments of long-term debt..........................          (168,565)       (141,130)       (86,080)
  Proceeds from capital lease financing.................           599,593          94,671             --
  Principal payments of capital lease obligations.......          (468,782)       (318,272)      (212,428)
                                                              ------------    ------------   ------------
Net cash provided by financing activities...............        19,108,694       8,448,697        849,806

Net increase (decrease) in cash and cash equivalents....        17,279,798         828,572       (623,886)
Cash and cash equivalents at beginning of year..........         2,049,555       1,220,983      1,844,869
                                                              ------------    ------------   ------------
Cash and cash equivalents at end of year................      $ 19,329,353     $ 2,049,555    $ 1,220,983
                                                              ------------    ------------   ------------
                                                              ------------    ------------   ------------
Supplemental disclosures of cash flow information: 
  Cash paid during the year for interest................      $    229,305     $   232,980    $   168,284
</TABLE>
 
    The accompanying notes are an integral part of the financial statements.
  
                                       31


<PAGE>

                             CUBIST PHARMACEUTICALS, INC.
                    STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY
 
                For the Years Ended December 31, 1996, 1995 and 1994

<TABLE>
<CAPTION>

                                     # OF          # OF          # OF         # OF  
                                    SHARES        SHARES        SHARES       SHARES      # OF SHARES        $           $  
                                  PREFERRED A   PREFERRED B   PREFERRED C  PREFERRED D      COMMON     PREFERRED     COMMON 
                                 -------------  -----------  ------------  ------------  -----------  ----------  ----------
<S>                              <C>            <C>          <C>           <C>           <C>          <C>         <C>   
12/31/93 Balance..............    5,000,000    14,270,000        --            --         546,862      $19,270        $547 

Series B Preferred Stock par 
  $.001 at $.50 share.........                     463,370                                                  463 
Common Stock par $.007
  at $.07 and $.35 share......                                                              60,714                       61   
Exercise of Common Stock 
  Options.....................                                                             302,451                      302 
Notes Receivable Preferred
  Series B....................
Notes Receivable Common
  Stock.......................
Issuance of Stock Options.....
Amortization of Deferred
 Compensation.................
Net Loss......................
                                   ---------    ----------                                 -------      -------        ----
12/31/94 Balance                   5,000,000    14,733,370       --            --          910,027      $19,733        $910
                                   ---------    ----------                                 -------      -------        ----
                                   ---------    ----------                                 -------      -------        ----

</TABLE>

<TABLE>
<CAPTION>
                                                         $
                                               ADDITIONAL PAID-IN CAPITAL
                                       -------------------------------------------          $               $
                                       ISSUANCE OF         NOTES        DEFERRED       ACCUMULATED     STOCKHOLDERS'
                                         SHARES         RECEIVABLE    COMPENSATION       DEFICIT          EQUITY
                                       -----------     -------------  -------------  ----------------  ------------
<S>                                    <C>              <C>            <C>                <C>          <C>


12/31/93 Balance                       $7,625,587       $(435,000)         --          $(1,722,832)      $5,487,572

Series B Preferred Stock par
  $.001 at $.50 share.........            231,221                                                           231,684

Common Stock par $.007 
  at $.07 and $.35 share......             21,189                                                            21,250

Exercise of Common Stock
  Options.....................             86,485                                                            86,787
Notes Receivable Preferred
  Series B....................                           (131,685)                                         (131,685)
Notes Receivable Common
  Stock.......................                            (65,842)                                          (65,842)
Issuance of Stock Options                  17,150                      $(17,150)
Amortization of Deferred 
 Compensation.................                                            6,120                               6,120
Net Loss......................                                                          (4,813,035)      (4,813,035)
                                       ----------       ---------      --------         ----------       ----------
12/31/94 Balance                       $7,981,632       $(632,527)     $(11,030)        $(6,535,867)     $  822,851
                                       ----------       ----------     ---------        ------------     ----------
                                       ----------       ----------     ---------        ------------     ----------
</TABLE>

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

                                       32

<PAGE>
                             CUBIST PHARMACEUTICALS, INC.
                 STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (Continued)

                    For the Years Ended December 31, 1996, 1995 and 1994
<TABLE>
<CAPTION>
                                     # OF          # OF          # OF         # OF  
                                    SHARES        SHARES        SHARES       SHARES     # OF SHARES     $           $  
                                  PREFERRED A   PREFERRED B   PREFERRED C  PREFERRED D     COMMON    PREFERRED    COMMON 
                                 -------------  -----------  ------------  ------------ -----------  ----------  ----------
<S>                              <C>            <C>          <C>           <C>           <C>         <C>         <C>      
Series C Preferred Stock 
  par $.001 at $.60 share.....                                 15,017,813                             $15,018
Series C Preferred Stock
  Offering Expenses...........
Common Stock par $.007 
  at $35 and $.42 share.......                                                             114,082                    114
Exercise of Common Stock
  Options.....................                                                                 785                      1
Repurchase of Common
  Stock.......................                                                              (8,232)                    (8)
Repayment of Notes
  Receivable Preferred
  Series B....................
Notes Receivable Common
  Stock.......................
Forgiveness of Promissory
  Notes.......................
Issuance of Stock 
  Options.....................
Amortization of Deferred
 Compensation.................
Net Loss......................
                                   ---------    ----------     ----------                ----------     -------    ------
12/31/95 Balance                   5,000,000    14,733,370     15,017,813     --         $1,016,662     $34,751
                                   ---------    ----------     ----------                ----------     -------    ------
                                   ---------    ----------     ----------                ----------     -------    ------
</TABLE>
<TABLE>
<CAPTION>
                                                         $
                                               ADDITIONAL PAID-IN CAPITAL
                                       -------------------------------------------          $                $
                                       ISSUANCE OF         NOTES        DEFERRED       ACCUMULATED     STOCKHOLDERS'
                                         SHARES         RECEIVABLE    COMPENSATION       DEFICIT          EQUITY
                                       -----------     -------------  -------------  ----------------  ------------
<S>                                    <C>              <C>            <C>                <C>          <C>
Series C Preferred Stock par 
  $.001 at $.60 share.........           8,995,670                                                       9,010,688
Series C Preferred Stock
  Offering Expenses...........             (45,787)                                                        (45,787)
Common Stock par $.007
  at $35 and $.42 share.......              47,274                                                          47,388
Exercise of Common Stock
  Options.....................                 274                                                             275
Repurchase of Common
  Stock.......................              (2,873)                                                         (2,881)
Repayment of Notes
  Receivable Preferred.......
  Series B...................                             435,000                                          435,000
Notes Receivable Common
  Stock.......................                             (4,989)                                          (4,989)
Forgiveness of Promissory
  Notes.......................                             23,615                                           23,615
Issuance of Stock
  Options.....................              28,020                     (28,020)
Amortization of Deferred 
  Compensation................                                           4,619                               4,619
Net Loss                                                                                (5,396,006)     (5,396,006)
                                       -----------      ----------    --------        ------------      ----------
12/31/95 Balance                       $17,004,210      $(178,901)    $(34,431)       $(11,931,873)     $4,894,773
                                       -----------      ----------    --------        ------------      ----------
                                       -----------      ----------    --------        ------------      ----------
</TABLE>
    The accompanying notes are an integral part of the financial statements.

                                   33
<PAGE>
                             CUBIST PHARMACEUTICALS, INC.
                 STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (Continued)

                    For the Years Ended December 31, 1996, 1995 and 1994
<TABLE>
<CAPTION>
                                     # OF          # OF          # OF         # OF  
                                    SHARES        SHARES        SHARES       SHARES     # OF SHARES     $           $  
                                  PREFERRED A   PREFERRED B   PREFERRED C  PREFERRED D     COMMON    PREFERRED    COMMON 
                                 -------------  -----------  ------------  ------------ -----------  ----------  ----------
<S>                              <C>            <C>          <C>           <C>           <C>         <C>         <C>     

Series D Preferred Stock par
  $.001 at 1.42 share.........                                               2,816,902                  2,817
Conversion of Preferred Stock
  to Common Stock par $.001...    (5,000,000)   (14,733,370)  (15,017,813)  (2,816,902)  5,366,849    (37,568)      5,367
Exercise of Stock Options.....                                                              58,244                     58
Repurchase of Common
  Stock.......................                                                             (36,634)                   (37)
Initial Public Offering, net
  of expenses.................                                                           3,139,252                 3,139
Forgiveness of Promissory
  Notes.......................
Issuance of Common Stock 
  Options and Warrants........
Amortization of Deferred
 Compensation.................
Net Loss......................
                                  ----------     ---------     ---------   ---------     ---------     --------     ------
12/31/96 Balance                      --            --            --           --        9,544,373        --         9,544
                                                                                          --------      -------     ------
                                                                                          --------      -------     ------

</TABLE>


<TABLE>
<CAPTION>
                                                          $
                                               ADDITIONAL PAID-IN CAPITAL                   $              $
                                       -------------------------------------------
                                       ISSUANCE OF         NOTES        DEFERRED       ACCUMULATED     STOCKHOLDERS'
                                         SHARES         RECEIVABLE    COMPENSATION       DEFICIT          EQUITY
                                       -----------     -------------  -------------  ----------------  ------------
<S>                                    <C>             <C>            <C>            <C>               <C>

Series D Preferred Stock par
  $.001 at 1.42 share.........           3,941,727                                                        3,944,544
Conversion of Preferred Stock 
  to Common Stock par $.001...              32,201                                                                0
Exercise of Stock Options.....              35,232                                                           35,290
Repurchase of Common
  Stock.......................             (12,273)                                                         (12,310)
Initial Public Offering, net 
  of expenses.................          15,151,343                                                       15,151,482
Forgiveness of Promissory
  Notes.......................                             24,442                                            24,442
Issuance of Common Stock 
  Options and Warrants........             101,378                       (101,378)                                0
Amortization of Deferred 
  Compensation................                                             56,058                            56,058
Net Loss......................                                                           (3,798,669)     (3,798,669)
                                       -----------      ---------        --------       ------------    -----------
12/31/96 Balance..............         $36,253,818      $(154,459)       $(79,751)      $(15,730,542)   $20,298,610
                                       -----------      ---------        --------       ------------    -----------
                                       -----------      ----------       --------       ------------    -----------

</TABLE>

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


<PAGE>
                          CUBIST PHARMACEUTICALS, INC. 
                         NOTES TO FINANCIAL STATEMENTS--(CONTINUED)
 
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.
 
B. INITIAL PUBLIC OFFERING
 
    On October 25, 1996, Cubist Pharmaceuticals, Inc. completed its initial
public offering raising $13,062,000, net of expenses. On that date, the holders
of the Company's outstanding Preferred Stock converted all of their shares of
Preferred Stock into Common Stock.
 
    On November 5, 1996, the Company's underwriters exercised their option to
purchase additional shares raising an additional $2,092,000, net of expenses.
 
    On October 17, 1996, the Company effected a 1-for-7 reverse stock split of
the Common Stock. Accordingly, all share and per share amounts have been
adjusted to reflect the stock split as though it had occurred at the beginning
of the initial period presented.
 
C. ACCOUNTING POLICIES
 
    Basis of Presentation 

    The accompanying financial statements are stated on an accrual basis. 
Certain amounts in the 1995 and 1994 financial statements have been 
reclassified to conform to the current year presentation.
 
    Use of Estimates 

    The preparation of financial statements in conformity with generally 
accepted accounting principles requires management to make certain estimates 
and assumptions that affect the reported amounts of assets and liabilities, 
and disclosure of contingent assets and liabilities at the date of the 
financial statements and the reported amounts of revenues and expenses during 
the reported period. Actual results could differ from those estimates.
 
    Risks and Uncertainties 
    
    The Company is subject to risks common to companies in the biotechnology 
industry including, but not limited to, development by its competitors of new 
technological innovations, dependence on key personnel, protection of 
proprietary technology, and compliance with FDA government regulations.
 
    Cash Equivalents 

    Cash equivalents consist of short-term interest-bearing instruments (U.S. 
Government treasuries and money market accounts) with original maturities of 
three months or less. These investments are carried at cost which 
approximates market value.
 
    Short-term Investments 

    Short-term investments, with an original maturity of more than three 
months and less than one year when purchased, consisted entirely of U.S. 
Government agency securities at December 31, 1995. Short-term investments, 
all of which are held to maturity, are stated at amortized cost, which 
approximates market value.
 
                                       35

<PAGE>

    Property and Equipment 

    Property and equipment are recorded at cost. Depreciation is provided 
using the straight-line method over the estimated useful lives of the related 
assets, generally three years for computer equipment and five years for 
laboratory equipment, furniture and fixtures. Leasehold improvements are 
stated at cost and are amortized over the lesser of the life of the lease or 
their estimated useful lives. The leasehold improvements are also utilized as 
collateral up to a value of $479,745, which relates to the balance of 
long-term debt. Maintenance and repairs are charged to expense as incurred, 
while major betterment's are capitalized. When assets are retired or 
otherwise disposed of, the assets and related allowances for depreciation and 
amortization are eliminated from the accounts and any resulting gain or loss 
is reflected in income.
 
    Research and Development 


    All research and development costs are expensed as incurred.
 
    Income Taxes 

    Research and experimentation and other tax credits, when utilized, will 
be recorded using the flow-through method of accounting as a reduction of the 
current provision for federal and state income taxes.
 
    Earnings Per 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.
 
D. PROPERTY AND EQUIPMENT
 
    At December 31, property and equipment consisted of:
 
<TABLE>
<CAPTION>
                                                      1996          1995
                                                  ------------  ------------
<S>                                               <C>           <C>
Leasehold improvements...........................  $  2,489,736  $  2,066,480
Laboratory equipment.............................     1,799,587     1,319,606
Furniture and fixtures...........................       251,427       226,891
Computer equipment...............................       357,788       221,976
                                                   ------------  ------------
                                                      4,898,538     3,834,953
Less accumulated depreciation and amortization...    (1,741,152)   (1,056,802)
                                                   ------------  ------------
Property and equipment, net......................  $  3,157,386  $  2,778,151
                                                   ------------  ------------
                                                   ------------  ------------
</TABLE>

E. ACCRUED EXPENSES
 
    At December 31, accrued expenses consisted of:
 
<TABLE>
<CAPTION>
                                                        1996        1995
                                                    ----------  ------------
<S>                                                 <C>         <C>
Payroll and benefits.............................  $  125,087  $   57,723
Vacation.........................................      60,019      40,255
Construction.....................................      46,250          --
Legal, audit and patent..........................      68,275      80,185
Database.........................................      42,200          --
Annual report....................................      60,000          --
Utilities........................................      76,339      11,500
Miscellaneous....................................       6,562          --
                                                    ----------  ------------
Total accrued expenses...........................  $  484,732  $  189,663
                                                    ----------  ------------
                                                    ----------  ------------
</TABLE>
 
F. COLLABORATIVE RESEARCH AGREEMENTS
 
    On December 15, 1995, the Company entered into a collaborative research
agreement with Pfizer. Under the terms of the agreement, Pfizer paid the Company
a technology licensing fee upon execution and research support 

                                       36

<PAGE>

payments. These payments are recognized as income earned under the terms of 
the agreement. In addition, Pfizer will reimburse the Company for expenses 
related to the screening of Pfizer compounds against the Company's targets 
and certain milestone payments. These payments are recognized as revenue when 
the related expenses are incurred. The Company included in sponsored research 
revenues $587,000 and $988,000 in 1996 and 1995, respectively, in accordance 
with the agreement. Pfizer also has an option to initiate a drug discovery 
program using compounds from the drug screening program. Upon initiation of a 
drug discovery program, Pfizer is obligated to purchase $5,000,000 of the 
Company's Common Stock.
 
    In June 1996, the Company entered into a collaborative research agreement
with Bristol-Myers Squibb. Under the terms of the agreement, Bristol-Myers
Squibb purchased from the Company $4,000,000 of the Company's Preferred Stock
upon execution of the agreement, and has agreed to make payments to the Company
upon the achievement of certain milestones. These milestone payments are
recognized as income as earned under the terms of the agreement. In addition,
Bristol-Myers Squibb will reimburse the Company for research and development
expenses relating to the production of certain targets and also for expenses
relating to the screening of Bristol-Myers Squibb compounds against the
Company's targets over three years, with an option to fund a fourth year. These
payments are recognized as revenue when the related expenses are incurred.
During 1996, the Company included in sponsored research revenues $1,516,668 for
certain research and development revenues in accordance with the agreement.
 
    In June 1996, the Company entered into a collaborative research agreement
with Merck & Co., Inc. ("Merck"). Under the terms of the agreement, Merck paid
the Company a technology licensing fee upon execution and will pay certain
milestone payments. These payments are recognized as income as earned under the
terms of the agreement. In addition, Merck will reimburse the Company for
research and development expenses relating to the production of certain targets;
for expenses relating to the screening of Merck compounds against the Company's
targets; and for expenses relating to compound optimization. These payments are
recognized as revenue when the related expenses are incurred. During 1996, the
Company included in sponsored research revenues $1,500,000 for the technology
licensing fee and $1,012,300 for certain research and development revenues in
accordance with the agreement.
 
G. STOCKHOLDERS' EQUITY
 
    Common Stock 

    As of December 31, 1996, 998,745 shares of Common Stock were issued to 
employees, scientific founders and consultants of the Company. Certain of 
these shares issued are subject to repurchase, at the Company's option, at 
the original issuance price in accordance with vesting provisions upon 
termination of the relationship. At December 31, 1996, 179,896 shares remain 
subject to repurchase.
 
    Warrants 

    During 1996, the Company granted warrants to purchase 33,333 shares of 
Series C Convertible Preferred Stock at a purchase price of $0.90 per share. 
These warrants converted to Common Stock warrants at the Initial Public 
Offering and expire on October 25, 2001.
 
    On October 23, 1996, the Company amended the warrants issued to Drs. Rebek
and Schimmel in May 1995 to extend the expiration date of such warrants from the
effective date of the Company's initial public offering to May 15, 2005, and to
provide that the warrants will vest in four equal annual installments commencing
upon the first anniversary of their grant date. As a result of this amendment,
the Company recorded deferred compensation in the amount of $62,000 to be
amortized to the income statement over the remaining vesting period from October
1996 to May 1999.
 
    Notes Receivable from Related Parties 

    The Company has accepted promissory notes from the Chief Executive 
Officer in consideration for the Preferred Stock and Common Stock options 
issued to him. The aggregate principal amount of these notes at December 31, 
1996 is $154,459 and is reflected in stockholders' equity as a reduction to 
paid-in capital. These notes have an annual interest rate of 4% and fall due 
between July 21, 1997 and November 28, 1997. During 1996, 

                                       37

<PAGE>

$24,442 of principal and accrued interest under the promissory notes was 
forgiven and it is expected that additional amounts will be forgiven in 1997.
 
H. STOCK OPTIONS
 
    The Company has a stock option plan, which is described below. In October
1995, the FASB issued SFAS 123, Accounting for Stock-Based Compensation. SFAS
123 is effective for periods beginning after December 15, 1995. SFAS 123
requires that companies either recognize compensation expense for grants of
stock, stock options, and other equity instruments based on fair value, or
provide pro forma disclosure of net income and earnings per share in the notes
to the financial statements. The Company adopted the disclosure provisions of
SFAS 123 in 1996 and has applied APB Opinion 25 and related Interpretations in
accounting for its plans. Had compensation costs for the Company's stock-based
compensation plan been determined based on the fair value at the grant dates as
calculated in accordance with SFAS 123, the Company's net loss and loss per
share for the years ended December 31, 1996 and 1995 would have been increased
to the pro forma amounts indicated below:
 

<TABLE>
<CAPTION>
                                 1996                            1995
                 ------------------------------  ------------------------------
                 NET LOSS     LOSS PER SHARE     NET LOSS     LOSS PER SHARE
                ------------  ---------------  -------------  ---------------
<S>             <C>            <C>              <C>            <C>
As Reported....  $(3,798,669)    $(1.39)        $(5,396,006)    $(3.99)
Pro forma......  $(4,053,670)    $(1.48)        $(5,408,006)    $(4.00)
</TABLE>

    The fair value of each stock option was estimated on the date of grant 
using Black-Scholes option-pricing model with the following weighted-average 
assumptions: an expected life of four (4) years, expected volatility of 86%, 
a dividend yield of 0% and a risk-free interest rate of 6.09%.
 
    The Company has a stock option plan under which options to purchase
1,500,000 shares of its Common Stock may be granted to employees, directors,
officers or consultants. The options are granted at fair market value on the
date of the grant as determined by the Board of Directors, vest ratably over a
four-year period and expire ten years from the date of grant. In addition, the
Company has issued to certain consultants and directors non-qualified stock
options to purchase 126,993 shares of its Common Stock. During 1995 and 1994,
the Company has allowed employees and consultants to exercise their full grants
to take advantage of certain favorable tax benefits. The Company has reserved
the right to repurchase any unearned shares at the original purchase price if
the employee or consultant does not fulfill their vesting requirement.


                                       38

<PAGE>

    A summary of the status of the Company's stock option plan as of December
31, 1996, 1995, 1994, and changes during each of the years then ended, is
presented below:
 
<TABLE>
<CAPTION>
                                                 1996                    1995                   1994
                                         ----------------------  ------------------------  -----------  ---------
                                                      WAEP*                  WAEP*                       WAEP*
                                         NUMBER     PER SHARE    NUMBER      PER SHARE     NUMBER       PER SHARE
                                        ---------  -----------  -----------  -----------  -----------   ---------
<S>                                      <C>        <C>          <C>        <C>          <C>            <C>

Balance at January 1.................    159,057   $     .40      42,214   $     .24      124,571    $     .17
Granted..............................    414,103        2.52     121,442         .42      227,335          .35
Exercised............................     21,610         .61         785         .35      302,451          .30
Canceled.............................     50,790         .97       3,814         .35        7,241          .35
                                       ---------       -----   ---------         ---   -----------      ---------
Balance at December 31...............    500,760   $    1.93     159,057   $     .40       42,214    $     .24
Options exercisable at December 31...     86,560   $    1.19      25,617   $     .26       32,303    $     .24

Weighted average grant-date fair value
 of options granted during the year..         $2.52                    $.42                        $.35

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

* Weighted-Average Exercise Price

</TABLE>
 
 
    The following table summarizes information about stock options outstanding
at December 31, 1996:

<TABLE>
<CAPTION>
                                          OPTIONS OUTSTANDING           
                ---------------------------------------------------------------------
   RANGE OF
   EXERCISE                          REMAINING CONTRACTUAL  WEIGHTED-AVERAGE EXERCISE
    PRICES      NUMBER OUTSTANDING           LIFE                     PRICE            
- --------------  -------------------  ---------------------  -------------------------  
<C>             <C>                  <S>                    <C>                        

$.007--$1.96...        440,067              9.0 years               $    1.18          
$5.95--$7.00...         60,693              9.7 years                    6.45          
                       -------               --------                   -----          
 ..............         500,760              9.1 years               $    1.82          
                       -------               --------                   -----          
                       -------               --------                   -----          
</TABLE>

<TABLE>
<CAPTION>
                              OPTIONS EXERCISABLE  
   RANGE OF     -----------------------------------------------  
   EXERCISE                           WEIGHTED-AVERAGE EXERCISE
    PRICES      NUMBER EXERCISABLE             PRICE
- --------------  -------------------  -------------------------
<S>             <C>                  <C>
                                     
$.007--$1.96..          83,023              $     .96
$5.95--$7.00..           3,537                   6.47
                        ------                  -----
 ..............          86,560              $    1.19
                        ------                  -----
                        ------                  -----
                
                
                
</TABLE>
 
36,634 and 8,232 shares of previously exercised options were repurchased in 
1996 and 1995, respectively, because vesting schedules were not fulfilled.
 
I. LEASE COMMITMENTS
 
    The Company leases its facilities under an operating lease agreement 
which expires on September 15, 2003 and is renewable at the Company's option 
for one additional five-year period. Under the terms of the lease, the 
Company is obligated to pay its prorated share of common operating expenses 
and real estate taxes as well as base rents. In addition, the Company entered 
into an amendment to the agreement with the landlord under which the landlord 
provided financing to the Company for a portion of the buildout cost 
($543,393) at an interest rate of 12% per year payable in equal monthly 
installments of $12,087 over five years through October 1998. At December 31, 
1996, the outstanding principal balance was $237,771. The Company also 
provided a security deposit of $100,000 upon execution of the lease. The 
security deposit bears interest in a segregated account, and is partially 
refundable ($79,000 plus interest) upon the fifth anniversary, and fully 
refundable plus interest within thirty days after the expiration of the 
lease, provided no event of default has occurred. The Company also financed 
an additional $345,500 during the first quarter of 1995 relating to a 6,510 
square foot facility expansion completed during the first week of January 
1995. This additional debt is payable in equal monthly installments of $7,685 
over five years with an annual interest rate of 12% through February 2000. No 
additional security deposit was required. At December 31, 1996, the 
outstanding principal balance was $241,974.

    The Company leases certain equipment under long-term capital leases. The 
cost of this equipment included in fixed assets was $2,320,201 at the end of 
1996 and $1,720,940 at the end of 1995, with associated accumulated 
depreciation of $1,042,297 at December 31, 1996 and $627,366 at December 31, 
1995. The Company has an option to purchase all of the leased 

                                       39

<PAGE>

equipment at a price to be negotiated at lease end. Future lease payments for 
non-cancelable leases for the respective years ended December 31 are as 
follows:
 
<TABLE>
<CAPTION>
                                    OPERATING LEASES           CAPITAL LEASES
                                  ---------------------      ------------------
<S>                               <C>                       <C>            
1997............................  $  171,365                  $  702,878
1998............................     171,365                     403,790
1999............................     192,364                     283,670
2000............................     207,679                     126,970
2001 and thereafter.............     579,771                         --
                                  --------------              -------------
Total minimum lease   
   payments.....................  $1,322,544                 $ 1,517,308
                                  --------------             ---------------
Less amount representing 
 interest payments..............                                (196,257)
                                                             ---------------
Present value of minimum lease 
 payments.......................                               1,321,051
Less current portion............                                (559,767)
                                                            ----------------
Long-term obligation............                             $   761,284
                                                            ----------------
                                                            ----------------
</TABLE>
 
    Lease payments under operating leases were $248,784 in fiscal year 1996,
$207,898 in fiscal year 1995 and $269,991 in fiscal year 1994.
 
J. EMPLOYEE BENEFITS
 
    The Company instituted a 401(k) savings plan in 1993, in which 
substantially all of its permanent employees are eligible to participate. 
Participants may contribute up to 15% of their annual compensation to the 
plan, subject to certain limitations. The Company contributes a matching 
amount of up to 1.5% of a participant's total compensation or $500 annually, 
whichever is less. The Company contributed $16,025, $14,072, and $9,524 
during 1996, 1995, and 1994, respectively.
 
K. INCOME TAXES
 
    The Company follows the liability method of accounting for income taxes in
accordance with the provisions of Statement of Financial Accounting Standards
(SFAS) No. 109, "Accounting for Income Taxes," whereby a deferred tax liability
is measured by the enacted tax rates which will be in effect when any
differences between the financial statements and tax basis of assets reverse.
The deferred tax liability can be reduced by net operating losses being carried
forward for tax purposes.
 
    The tax effects of temporary differences that give rise to significant
portions of the deferred tax assets and liabilities are presented below:
 
<TABLE>
<CAPTION>
                                                         1996           1995
                                                     -------------  -------------
<S>                                                  <C>            <C>
Net operating loss carryforwards                     $   4,376,000  $   4,671,000
Capitalized research and development                     1,700,000       --
Research and experimentation credits                       765,000        325,000
Other, net                                                 306,000       --
                                                      ------------     -----------
Total Deferred Tax Assets                            $   7,147,000  $   4,996,000
                                                       -----------     -----------
Valuation reserve                                    $  (7,147,000) $  (4,996,000)
                                                      ------------     -----------
                                                      ------------     -----------
</TABLE>
 
    The federal and state net operating loss and tax credit carryforwards begin
to expire in the years 2007 and 1997, respectively. Research and experimentation
tax credits of approximately $325,000 begin to expire in 2008. The net operating
loss carryforwards may be subject to an annual limitation as a result of the
change in ownership due the initial public offering. The Company has established
a valuation reserve against the deferred tax benefit arising from these
carryforwards due to the uncertainty of earning sufficient taxable income to
receive the benefit and accordingly has not given recognition to these tax
benefits in these financial statements. These carryforwards are also subject to
review by the Internal Revenue Service.
 
                                       40
<PAGE>

ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON 
        ACCOUNTING AND FINANCIAL DISCLOSURE
 
    None.
 
                                    PART III
 
ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT
 
    Information with respect to Directors and compliance with Section 16(a) of
the Securities Exchange Act may be found in the sections captioned "Proposal No.
1--Election of Directors", "Executive Compensation" and "Section 16(a)
Beneficial Ownership Reporting Compliance" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 19, 1997. Such information is incorporated
herein by reference. Information with respect to Executive Officers may be found
under the section captioned "Executive Officers of the Registrant" in Part I of
this Annual Report on Form 10-K.
 
ITEM 11. EXECUTIVE COMPENSATION
 
    The information required with respect to this item may be found in the
sections captioned "Executive Compensation" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 19, 1997. Such information is incorporated
herein by reference.
 
ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT
 
    The information required with respect to this item may be found in the
section captioned "Principal Stockholders" and "Proposal No. 1--Election of
Directors" appearing in the definitive Proxy Statement to be delivered to
Stockholders in connection with the Annual Meeting of Stockholders to be held on
May 19, 1997. Such information is incorporated herein by reference.
 
ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS
 
    The Information required with respect to this item may be found in the
section captioned "Certain Transactions" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 19, 1997. Such information is incorporated
herein by reference.
 
                                    PART IV

                                        41

<PAGE>


ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K
 
    (a) Documents Filed as part of Form 10-K
 
    1. Financial Statements.
 
    The following financial statements and supplementary data are included in
Part II Item 8 filed as part of this report:
 
      - Balance Sheets as of December 31, 1995 and 1996
 
      - Statements of Operations for the years ended December 31, 1994, 1995 and
        1996
 
      - Statements of Stockholders' Equity for the years ended December 31,
        1994, 1995 and 1996
 
      - Statements of Cash Flows for the years ended December 31, 1994, 1995 and
        1996
 
      - Notes to Financial Statements
 
      - Report of Independent Auditors
 
    2. Financial Statement Schedule.
 
    None.
 
    Schedules not listed above have been omitted because they are not
applicable, not required or the information required is shown in the financial
statements or the notes thereto.
 
    3. List of Exhibits.
 
 EXHIBITS
- -----------
   *3.3      Restated Certificate of Incorporation of the Registrant.
   *3.4      Amended and Restated By-Laws of the Registrant, as amended to 
             date.
   *4.1      Specimen certificate for shares of Common Stock.
  *10.1      Patent License Agreement between the Registrant and the 
             Massachusetts Institute of Technology, dated March 10, 1994.
  *10.2      License Agreement between the Registrant and the Board of 
             Trustees of Leland Stanford Junior University, dated April 1, 
             1994.
  *10.3      Employment Agreement between the Registrant and Scott M. 
             Rocklage, dated June 20, 1994.
  *10.4      Consulting Agreement between the Registrant and Paul R. 
             Schimmel, dated May 1, 1992.
  *10.5      Consulting Agreement between the Registrant and Julius Rebek, 
             Jr., dated May 1, 1992.
  *10.6      Amended and Restated 1993 Stock Option Plan.
  *10.7      Collaborative Research Agreement between the Registrant and 
             Pfizer Inc., dated December 15, 1995.
  *10.8      Collaborative Research and License Agreement between the 
             Registrant and Merck & Co., Inc., dated June 13, 1996.

                                        42

<PAGE>

  *10.9      Collaborative Research and License Agreement between the 
             Registrant and Bristol-Myers Squibb Company and the Registrant, 
             dated June 25, 1996.
  *10.10     Supply and Services Agreement, dated as of November 1, 1995, by 
             and between Terrapin Technologies, Inc. and the Registrant.
  *10.11     Screening Agreement, dated November 28, 1995, between the 
             Registrant and Monsanto Company.
  *10.12     Letter Agreement, dated January 18, 1996, between Pharm-Eco 
             Laboratories, Inc. and the Registrant.
  *10.13     Agreement with ArQule, Inc., dated June 4, 1996.
  *10.14     Lease Agreement between Registrant and Stimpson Family Trust 
             dated April 30, 1993, regarding 24 Emily Street, Cambridge, MA., 
             as amended by the First Amendment to Lease, dated September 19, 
             1994.
  *10.15     Form of Employee Confidentiality and Nondisclosure Agreement.
  *10.16     Master Lease Agreement between the Registrant and Comdisco, 
             Inc., dated as of August 30, 1993, as amended February 7, 1995, 
             and as further amended on February 26, 1996.
  *10.17     Series B Convertible Preferred Stock Purchase Warrant between 
             the Registrant and Comdisco, Inc., dated August 30, 1993.
  *10.18     Series C Convertible Preferred Stock Purchase Warrants between 
             the Registrant and Comdisco, Inc., dated February 28, 1995 and 
             February 26, 1996.
  *10.19     Series C Convertible Preferred Stock Purchase Options issued to 
             Dr. Paul Schimmel and Dr. Julius Rebek in May 1995, as amended 
             by certain Letter Agreements, dated October 23, 1995, between 
             the Registrant and each of Dr. Schimmel and Dr. Rebek.
  *10.20     Amended and Restated Stockholders Rights Agreement by and among 
             the Registrant and the parties signatory thereto.
   10.21     Secured Promissory Note, dated as of July 21, 1994, by Scott M. 
             Rocklage to the Registrant.
   10.22     Amendment to Promissory Note, dated as of July 21, 1996, by and 
             between the Registrant and Scott M. Rocklage.
   10.23     Promissory Note, dated as of October 18, 1995, by and between 
             the Registrant and Scott M. Rocklage.
  +10.24     Compound Library Screening Agreement between the Registrant and 
             Genzyme Corporation, dated February 24, 1997.
  +10.25     Library Sample Evaluation Agreement between the Registrant and 
             Pharmacopeia, Inc., dated as of September 11, 1996.
   11.1      Computation of Income Per Share.
   23.2      Consent of Coopers & Lybrand L.L.P.

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

*   Incorporated by reference from the Company's Registration Statement on 
    Form S-1 (Registration No. 333-6795).

+   Confidential Treatment requested as to certain portions.

                                       43

<PAGE>


                                   SIGNATURES
 
    Pursuant to the requirements of Section 13 or 15(d) 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.

                                /s/ SCOTT M. ROCKLAGE
                                ----------------------------------
                                SCOTT M. ROCKLAGE
                                PRESIDENT AND CHIEF EXECUTIVE OFFICER


    Pursuant to the requirements of the  Securities Exchange Act of 1934, 
this report has been signed below by the following persons on its behalf of 
the registration and in the  capacities on the dates indicated.


          SIGNATURE                      TITLE                      DATE
- ------------------------------  -------------------------------  ------------
                                President, Chief Executive
    /s/ SCOTT M. ROCKLAGE               and Director
- ------------------------------    (Principal Executive
      Scott M. Rocklage           Officer)
      /s/ THOMAS A. SHEA        Treasurer       (Principal
- ------------------------------    Financial and Accounting
        Thomas A. Shea            Officer)
      /s/ JOHN K.CLARKE         Chairman of the Board of
- ------------------------------    Directors
        John K.clarke
       /s/ BARRY BLOOM          Director
- ------------------------------
         Barry Bloom
     /s/ GEORGE CONRADES        Director
- ------------------------------
       George Conrades
      /s/ ELLEN M.FEENEY        Director
- ------------------------------
        Ellen M.feeney
   /s/ TERRANCE G. MCGUIRE      Director
- ------------------------------
     Terrance G. Mcguire
    /s/ JULIUS REBEK, JR.       Director
- ------------------------------
      Julius Rebek, Jr.
     /s/ PAUL R. SCHIMMEL       Director
- ------------------------------
       Paul R. Schimmel
 
                                      -44-



<PAGE>

                                                                 EXHIBIT A
 
                            SECURED PROMISSORY NOTE
 
    $131,685                                         Boston, Massachusetts
                                                         July       , 1994
                           
    FOR VALUE RECEIVED, the undersigned, Scott M. Rocklage (the "Maker"), 
by this Secured Promissory Note (this "Note"), absolutely and 
unconditionally promises to pay to the order of CUBIST PHARMACEUTICALS, 
INC., a Delaware corporation (the "Payee"), the aggregate principal amount 
of One Hundred Thirty-One Thousand Six Hundred Eighty-Five Dollars 
($131,685) on July       , 1996 (the "Maturity Date"), and to pay interest 
on the principal amount outstanding from time to time hereunder, from the 
date hereof through and including the date on which such principal amount 
is paid in full, at a rate of       percent (      %) per annum simple 
interest. Interest hereunder shall be due and payable on the first 
anniversary hereof and on the Maturity Date or any accelerated maturity 
hereof.
 
    The Maker shall have the right to prepay the unpaid principal amount of 
this Note in full at any time, or in part from time to time, without 
premium or prepayment penalty, provided that there is paid with each such 
principal prepayment all accrued and unpaid interest to the date of 
prepayment (calculated on the basis of a 365-day year for the actual number 
of days for which the same is due).
 
    All payments of interest and principal hereunder shall be made at the 
principal residence or business address of the holder hereof. All payments 
hereunder shall be applied first to any unpaid accrued interest, second to 
payment of all, if any, other amounts except principal due under or in 
respect of this Note, and third to repayment of principal.
 
    This Note is made and delivered by the Maker to the Payee pursuant to 
that certain Subscription Agreement, dated as of July       , 1994, among 
the Payee and the Maker, and is secured pursuant to the provisions of a 
certain Stock Pledge Agreement, dated of even date herewith, between the 
Maker and the Payee.

    Anything implied herein to the contrary notwithstanding, in the event 
that (1) the Maker shall fail to pay when due all or any portion of the 
principal of or interest on this Note, (2) the Maker shall make an 
assignment of the whole or a substantial part of his assets for the benefit 
of creditors, or (3) there shall be commenced by or against the Maker any 
proceeding under any bankruptcy, insolvency, readjustment of debt or 
similar law of any jurisdiction, (each event referred to in clauses (1) 
through (3) above being hereinafter referred to herein as an "Event of 
Default") then without notice to or demand upon the Maker the entire unpaid 
principal of this Note, and all interest accrued thereon, shall (if not 
already due and payable) immediately become and be due and payable to the 
order of the holder hereof.


<PAGE>

    The Maker hereby, to the fullest extent permitted by applicable law: 
(a) waives presentment, demand, notice, protest, and all other demands and 
notices in connection with delivery, acceptance, performance, default, 
acceleration or enforcement of or under this Note; (b) assents to any 
extension or postponement of the time of payment or any other indulgence, 
and to any substitution, exchange or release of collateral; and (c) agrees 
to pay to the holder, on demand, all costs and expenses of collection, 
including, without limitation, reasonable attorneys' fees and legal 
expenses, incurred by the holder in enforcing this Note, whether or not 
litigation is commenced.
 
    No failure by the holder to exercise, or delay by the holder in 
exercising, any right or remedy hereunder shall operate as a waiver 
thereof, or of any other right or remedy, and no single or partial exercise 
of any right or remedy shall preclude any other or further exercise thereof 
or of any other right or remedy. Acceptance by the holder of any payment 
after the maturity of this Note has been accelerated shall not constitute a 
waiver of such acceleration.
 
    This Note shall take effect as an instrument under seal and shall be
governed by and construed in accordance with the law of The Commonwealth of
Massachusetts.


                                                       --------------------
                                       2

<PAGE>
                          AMENDMENT TO PROMISSORY NOTE
 
    This Amendment to Promissory Note (this "Amendment") is entered into as 
of this 21st day of July, 1996 by and between Cubist Pharmaceuticals, Inc., 
a Delaware Corporation, (the "Payee") and Scott M. Rocklage (the "Maker").
 
    This Amendment is attached to and made a part of that certain Secured 
Promissory Note, dated as of July 21, 1994 (the "Promissory Note"), in the 
principal amount of One Hundred Thirty-One Thousand Six Hundred Eighty-Five 
Dollars ($131,685.00) made payable by the Maker to the Payee.
 
    WHEREAS, the Maker and the Payee wish to amend the Promissory Note.
 
    NOW, THEREFORE, for the sum of ten and 00/100 Dollars ($10.00) and 
other good and valuable consideration the receipt and sufficiency of which 
are hereby acknowledged, Maker and Payee hereby amend the Promissory Note 
as follows:
 
    The date "July 21, 1996" appearing in the fifth line of the first 
paragraph immediately prior to the words "(the "Maturity Date")" is hereby 
deleted and replaced with the date "July 21, 1997".
 
    EXCEPT AS SPECIFICALLY AMENDED BY THIS AMENDMENT, THE PROMISSORY NOTE 
REMAINS UNMODIFIED AND IN FULL FORCE AND EFFECT ACCORDING TO ITS TERMS.
 
    [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
 

                                     

<PAGE>

    IN WITNESS WHEREOF, the undersigned have executed this Amendment as a 
sealed instrument as of the date first above written.


                                         MAKER: 


WITNESS: -----------------------         ----------------------------
                                         Scott M. Rocklage 


                                         PAYEE: 

                                         Cubist Pharmaceuticals, Inc. 

WITNESS:------------------------         By: -------------------------
                                         Name: -----------------------
                                         Title:-----------------------



                                       2

<PAGE>
                                PROMISSORY NOTE
 
 $4,989.06                                             Boston, Massachusetts 
                                                             October 18, 1995
 
    FOR VALUE RECEIVED, the undersigned, Scott M. Rocklage (the "Maker"), 
by this Promissory Note (this "Note"), absolutely and unconditionally 
promises to pay to the order of CUBIST PHARMACEUTICALS, INC., a Delaware 
corporation (the "Payee"), the aggregate principal amount of Four Thousand 
Nine Hundred Eighty Nine Dollars and Six Cents ($5,989.06) on November 28, 
1997 (the "Maturity Date"), and to pay interest on the principal amount 
outstanding from time to time hereunder, from the date hereof through and 
including the date on which such principal amount is paid in full, at a 
rate of four percent (4%) per annum simple interest. Interest hereunder 
shall be due and payable on the first anniversary hereof, the second 
anniversary hereof and on the Maturity Date or any accelerated maturity 
hereof.
 
    The Maker shall have the right to prepay the unpaid principal amount of 
this Note in full at any time, or in part from time to time, without 
premium or prepayment penalty, provided that there is paid with each such 
principal prepayment all accrued and unpaid interest to the date of 
prepayment (calculated on the basis of a 365-day year for the actual number 
of days for which the same is due).
 
    All payments of interest and principal hereunder shall be made at the 
principal residence or business address of the holder hereof. All payments 
hereunder shall be applied first to any unpaid accrued interest, second to 
payment of all, if any, other amounts except principal due under or in 
respect of this Note, and third to repayment of principal.
 
    This Note is made and delivered by the Maker to the Payee pursuant to 
that certain letter agreement, dated October 18, 1995, between the Payee 
and the Maker.
 
    Anything implied herein to the contrary notwithstanding, in the event 
that (1) the Maker shall fail to pay when due all or any portion of the 
principal of or interest on this Note, (2) the Maker shall make an 
assignment of the whole or a substantial part of his assets for the benefit 
of creditors, or (3) there shall be commenced by or against the Maker any 
proceeding under any bankruptcy, insolvency, readjustment of debt or 
similar law of any jurisdiction, (each event referred to in clauses (1) 
through (3) above being hereinafter referred to herein as an "Event of 
Default") then without notice to or demand upon the Maker the entire unpaid 
principal of this Note, and all interest accrued thereon, shall (if not 
already due and payable) immediately become and be due and payable to the 
order of the holder hereof.


                             
<PAGE>

    The Maker hereby, to the fullest extent permitted by applicable law: 
(a) waives presentment, demand, notice, protest and all other demands and 
notices in connection with deliver, acceptance, performance, default, 
acceleration or enforcement of or under this Note; (b) assents to any 
extension or postponement of the item of payment or any other indulgence, 
and to any substitution, exchange or release of collateral; and (c) agrees 
to pay to the holder, on demand, all costs and expenses of collection, 
including, without limitation, reasonable attorneys' fee and legal 
expenses, incurred by the holder in enforcing this Note, whether or not 
litigation is commenced.
 
    No failure by the holder to exercise, or delay by the holder in 
exercising, any right or remedy hereunder shall operate as a waiver 
thereof, or of any other right or remedy, and no single or partial exercise 
of any right or remedy shall preclude any other or further exercise thereof 
or of any other right or remedy. Acceptance by the holder of any payment 
after the maturity of this Note has been accelerated shall not constitute a 
waiver of such acceleration.
 
    This Note shall take effect as an instrument under seal and shall be 
governed by and construed in accordance with the law of the Commonwealth of 
Massachusetts.
 

- ---------------------------
    Scott M. Rocklage
 
                                       2

<PAGE>

                             Confidential Treatment 
                     COMPOUND LIBRARY SCREENING AGREEMENT
 
    This Agreement, effective as of the date last written below, is between 
Genzyme Corporation ("Genzyme") and Cubist Pharmaceuticals, Inc. ("Cubist").
 
    1. Information Exchange.
 
    (a) Within thirty (30) days after receiving an executed original of 
this Agreement, each party shall provide the other with such information as 
the Receiving Party (as defined in Paragraph 6) may reasonably request for 
the purpose of evaluating the therapeutic potential of any products that 
may arise from a collaboration between the parties. Such information shall 
include ****************************************************************
***********************************************************************
************************************************************************* 
************************************************************************* 
************************************************.  Genzyme shall confirm to 
Cubist that each biological target disclosed by Cubist is not the subject 
of any research program currently conducted by Genzyme internally or with 
any third party collaborator.
 
    (b) The Receiving Party shall determine in its sole discretion whether 
to proceed with the screening activities described in Paragraph 2 and shall 
notify the other party of such determination. If either party determines 
not to proceed with such screening activities, this Agreement shall 
terminate upon receipt of notice to the other party of such determination. 
If both parties elect to proceed with the screening activities, Genzyme 
will provide Cubist with Compounds as described in Paragraph 2 within 
thirty (30) days after receipt of Cubist's notice to proceed.
 
    2. Screening of Compound Libraries and Deconvolution Services.
 
    (a) Subject to the provisions of Paragraph 1, Genzyme will make 
available to Cubist all compounds within Genzyme's libraries as of the 
effective date this Agreement ("Compounds"). Compounds added to Genzyme's 
libraries after such date will be made available to Cubist on a semiannual 
basis during the term of this Agreement. Compounds will be 

  * Confidential treatment requested: material has been omitted and filed 
    separately with the Commission.

                                  

<PAGE>



delivered in quantities of **************************************
************************ (a "Mixture"). Genzyme grants Cubist a 
non-exclusive, worldwide right to use the Compounds to screen against 
biological targets identified by Cubist to evaluate the biological activity 
of the Compounds. Such right may not be sublicensed and does not include 
the right to sell or otherwise transfer the Compounds to third parties. 
Cubist will use commercially reasonable efforts to screen all Compounds 
provided by Genzyme against each of the targets identified by Cubist 
pursuant to Paragraph 1 (a).
 
    (b) Subject to a Mixture satisfying criteria agreed upon by Cubist and 
Genzyme for biological activity (e.g., potency and dose-responsiveness) 
against a target screened by Cubist, Genzyme will provide the following 
services: **************************************************************
************************************************************************
************************************************************************
************************************************************************
******************************************************.
 
    3. Availability of License.
 
    (a) Cubist shall notify Genzyme of all Active Compounds identified by 
Cubist. "Active Compound" shall mean a Compound that has exhibited 
biological activity against a target warranting, in Cubist's reasonable 
business judgment, further development.
 
    (b) If any Active Compound previously has been committed to a third 
party or to an internal Genzyme program, Cubist shall have no rights in or 
to such Active Compound. In all other cases, Genzyme shall disclose to 
Cubist the chemical composition and structure of the Active Compound and 
Cubist shall have a right of first negotiation to obtain a license (the 
"Negotiation Right"), in accordance with the procedures set forth in 
Paragraph 3(c).
 
    (c) Cubist may exercise the Negotiation Right upon written notice to 
Genzyme which is received by Genzyme at any time during the term of this 
Agreement, whereupon the parties will engage in good faith negotiations to 
establish the terms and conditions of a mutually acceptable research 
collaboration agreement. Such research collaboration agreement will 
provide, among other matters, for the following: (i) establishments of 
committees to manage the collaboration; (ii) licenses under intellectual 
property rights of each party to conduct medicinal chemistry and 
preclinical development of the Active Compound; (ii) 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                    2

<PAGE>


responsibilities of the parties for specific preclinical development 
activities; (iv) commercialization strategy for the Active Compound following 
preclinical development; and (v) sharing of commercialization revenues after 
recovery by each party of its preclinical development costs.
 
    (d) If the parties are unable to negotiate and execute a mutually acceptable
collaboration agreement within ************* after the date upon which Cubist
exercised the Negotiation Right, Genzyme shall have the right to license the
Active Compound to any third party, subject to non-disclosure restrictions set
forth in Paragraph 6.
 
    4. Use and Transfer Restrictions. Cubist acknowledges and agrees that the
Compounds (including without limitation all Active Compounds) are proprietary to
and owned by Genzyme and or may be covered by claims of U.S. and international
patents or parent applications of Genzyme. Cubist agrees to use the Compounds
only for the purposes set forth in this Agreement. Cubist agrees (i) not
transfer such Compounds to any third party without the prior written consent of
Genzyme, (ii) to permit access to the Compounds only to its employees and
consultants requiring such access, (iii) to inform such employees and
consultants of the proprietary nature of the Compounds, and (iv) to take
reasonable precautions, at least as stringent as those observed by Cubist to
protect its own proprietary material, to ensure that such employees and
consultants observe the obligations of Cubist pursuant to this Paragraph. Upon
the expiration or termination of this Agreement, Cubist shall, at the
instruction of Genzyme, either destroy or return any unused Compounds.
 
    5. Compliance with Law. Cubist agrees to comply with all federal, state and
local laws and regulations applicable to the use, storage, disposal, and
transfer of all the Compounds, including without limitation the Toxic Substances
Control Act (15 USC 2601 et. seq.) and implementing regulations (in particular,
40 CFR 720.36 [Research and Development Exemption]), the Food, Drug, and
Cosmetic Act (21 USC 301 et. seq.) and implementing regulations, and all Export
Administration Regulations of the Department of Commerce. Cubist assumes sole
responsibility for any violation of such laws or regulations by Cubist or any of
its affiliates.
 
    6. Confidential Information.
 
    (a) As used in this Agreement, the term "Confidential Information" means any
technical or business information furnished by one party ("Disclosing Party") to
the other party ("Receiving Party") in connection with this Agreement and
specifically designated as confidential 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                     3

<PAGE>


including, without limitation, any information disclosed by the parties 
pursuant to Paragraphs 1, 2 and 3 of this Agreement. Such Confidential 
Information may also include, without limitation, trade secrets, know-how, 
inventions, formulations, compositions, technical data or specifications, 
testing methods, business or financial information, research and 
development activities, product and marketing plans, customer and supplier 
information. Confidential Information that is disclosed in writing shall be 
marked with the legend "confidential". Confidential Information that is 
disclosed orally or visually shall be documented in a written notice 
prepared by the Disclosing Party and delivered to the Receiving Party 
within thirty (30) days of the date of disclosure. Such notice shall 
summarize the Confidential Information disclosed to the Receiving Party and 
reference the time and place of disclosure.
 
    (b) The Receiving Party shall and shall cause its employees engaged in the
research to: (i) maintain all Confidential Information in strict confidence,
except that the Receiving Party may disclose or permit the disclosure of any
Confidential Information to its directors, officers, employees, consultants, and
advisors who are obligated to maintain the confidential nature of such
Confidential Information and who need to know such Confidential Information for
the purposes set forth in this Agreement; (ii) use all Confidential Information
solely for purposes set forth in this Agreement; and (iii) reproduce the
Confidential Information only to the extent necessary to effect the purpose set
forth in this Agreement, with all such reproductions being considered
Confidential Information.
 
    (c) The obligations of the Receiving Party under Paragraph 6(b) shall 
not apply to the extent that the Receiving Party can demonstrate by written 
documentation that certain Confidential Information: (i) was in the public 
domain prior to the time of its disclosure under this Agreement; (ii) 
entered the public domain after the time of its disclosure under this 
Agreement through means other than an unauthorized disclosure resulting 
from any act or omission by the Receiving Party; (iii) was independently 
developed or discovered by the Receiving party prior to the time of its 
disclosure under this Agreement; (iv) is or was disclosed to the Receiving 
Party at any time, whether prior to or after the time of its disclosure 
under this Agreement, by a third party having no fiduciary relationship 
with the Disclosing Party and having no obligations of confidentiality with 
respect to such Confidential Information; or (v) is required to be 
disclosed to comply with applicable laws or regulations, or with a court or 
administrative order, provided that the Disclosing Party receives prior 
written notice of such disclosure and 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                       4

<PAGE>

that the Receiving party takes all reasonable and lawful actions to obtain 
confidential treatment for such disclosure and, if possible, to minimize 
the extent of such disclosure.
 
    (d) The Receiving Party agrees that the Disclosing Party (or any third party
entrusting its own confidential information to the Disclosing Party) is and
shall remain the exclusive owner of the Confidential Information disclosed by
the Disclosing Party and all patent, copyright, trademark, trade secret, and
other intellectual property rights in, or arising from such Confidential
Information. No option, license, or conveyance of such rights to the Receiving
Party is granted or implied under this Agreement. If any such rights are to be
granted to the Receiving Party, such grant shall be expressly set forth in a
separate written instrument.
 
    (e) Upon the termination by either party of this Agreement, the Receiving
Party shall return to the Disclosing Party all originals, copies, and summaries
of documents, materials, and other tangible manifestations of Confidential
Information in the possession or control of the Receiving Party. The obligations
set forth in this Agreement shall remain in effect for a period of five (5)
years after such termination by either party.
 
    (f) The Receiving Party agrees that any breach of its obligations under this
Paragraph 6 will cause irreparable harm to the Disclosing Party; therefore, the
Disclosing Party shall have, in addition to any remedies available at law, the
right to obtain requitable relief to enforce this Agreement.
 
    7. No Warranties. Any Compounds delivered pursuant to this Agreement 
are understood to be experimental in nature and may have hazardous 
Properties. GENZYME MAKES NO REPRESENTATIONS, AND EXTENDS NO WARRANTIES OF 
ANY KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO THE COMPOUNDS, THERE 
ARE NO EXPRESS OR IMPLIED WARRANTIES OR MERCHANTABILITY OR FITNESS FOR A 
PARTICULAR PURPOSE, OR THAT THE USE OF THE COMPOUNDS WILL NOT INFRINGE ANY 
PATENT OR OTHER INTELLECTUAL PROPERTY RIGHTS OF A THIRD PARTY.
 
    8. Indemnification. Cubist assumes all liability for, and agrees to
indemnify, defend, and hold harmless Genzyme and its directors, officers,
representatives, employees, and agents against, all losses, expenses (including
without limitation any reasonable legal expenses), claims, demands, damages,
judgments, suits, or other actions arising form 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                     5


<PAGE>


the use, storage, or disposal of the Compounds by Cubist and its affiliates 
and sublicenses, or form any breach of its obligations under Paragraph 5 of 
this Agreement. Genzyme assumes all liability for, and agrees to indemnify, 
defend, and hold harmless Cubist and its directors, officers, 
representatives, employees, and agents against, all losses, expenses 
(including without limitation any reasonable legal expenses), claims, 
demands, damages, judgements, suits, or other actions arising from the use, 
storage, or disposal of the Compounds by Genzyme and its affiliates.
 
    9. Termination. Subject to early termination pursuant to Paragraph 
1(b), this Agreement shall commence on the date last written below and 
continue for a period of *************************************************
**************************************************************************
*************************************************************************
******************************************. Sections 3 (paragraph (d) only),
4, 5, 6, 7 and 8, shall survive termination of this Agreement.
 
    10. Miscellaneous. This Agreement shall not be assigned or otherwise 
transferred by either party without the prior written consent of the other 
party to this Agreement. This Agreement shall be governed by the laws of 
the Commonwealth of Massachusetts. This Agreement constitutes the entire 
understanding of the parties and supersedes all prior agreements, written 
or oral, with respect to the subject matter hereof. Any notice required or 
permitted under this Agreement shall be in writing delivered personally or 
by facsimile (and promptly confirmed by personal delivery or courier) or 
courier, postage prepaid (where applicable), addressed to the other party 
at its address indicated below, or to such other address as the addressee 
shall have last furnished in writing to the addressor and shall be 
effective upon receipt by the addressee. Each party shall obtain prior 
written permission from the other before using the name, symbol and/or 
marks of the other in any form of publicity.

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                  6


<PAGE>
 


 ACCEPTED AND AGREED: 

GENYZME CORPORATION                       CUBIST PHARMACEUTICALS, INC. 


By: /s/ James R. Rasmussen                By:/s/ Scott M. Rocklage 

Name: James R. Rasmussen                  Name: Scott M. Rocklage 

Title: Senior VP, Research                Title: President and CEO 

Date: February 24, 1997                   Date: February 24, 1997 

Address:                                  Address: 
Genzyme Corporation                       Cubist Pharmaceuticals, Inc.
One Kendall Square                        24 Emily Street
Cambridge, Massachusetts 02319            Cambridge, Massachusetts 02139 
Tel: (617) 252-7500                       Tel: (617) 576-1999 
Fax: (617) 252-7600                       Fax: (617) 576-0232


 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                    7



<PAGE>
                          Confidential Treatment
                      LIBRARY SAMPLE EVALUATION AGREEMENT
 
    This Library Sample Evaluation Agreement (the "Agreement"), effective 
as of September 11, 1996 (the "Effective Date"), is made by and between 
Pharmacopeia, Inc., a Delaware corporation having a principal place of 
business at 101 College Road East, Princeton, New Jersey 08540 
("Pharmacopeia"), and Cubist Pharmaceuticals, Inc., a Delaware corporation 
having a principal place of business at 24 Emily Street, Cambridge, 
Massachusetts 02139 ("Cubist").
 
                                   BACKGROUND
 
    A. Pharmacopeia has developed novel proprietary methods for the 
generation of encoded compound libraries. Pharmacopeia believes that its 
proprietary technology, by rapidly producing diverse and targeted compound 
libraries, will accelerate the drug discovery process and increase 
productivity of drug discovery programs.
 
    B. Cubist wishes to obtain from Pharmacopeia samples of combinatorial 
libraries to be screened by Cubist against certain agreed targets, and 
Pharmacopeia is willing to provide such samples to Cubist for such purpose, 
on the terms and conditions set forth herein.
 
    NOW THEREFORE, it is agreed by and between the parties as follows:
 
 1. DEFINITIONS
 
    1.1 "Columbia License" means that certain License Agreement effective 
as of July 16, 1993, as amended and restated as of October 6, 1995, entered 
by and between Pharmacopeia, Inc., the Trustees of Columbia University in 
the City of New York and the Cold Spring Harbor Laboratory. 

    1.2 "Confidential Information" means (i) any proprietary or 
confidential information or material in tangible form disclosed hereunder 
that is marked as "Confidential" at the time it is delivered to the 
receiving party, or (ii) proprietary or confidential information disclosed 
orally hereunder which is identified as confidential or proprietary when 
disclosed and such disclosure of confidential information is confirmed in 
writing within thirty (30) days by the disclosing party.

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

<PAGE>
 

    1.3 "Library Compound" means any compound contained in a Library 
Sample. 

    1.4 "Library Sample" means a sample of compounds selected from a 
Pharmacopeia compound library and transferred to Cubist pursuant to this 
Agreement. 

    1.5 "Licensed Patents" means any patent applications that claim any 
compound in the library from which the Library Sample is derived; any 
substitutions, divisions, continuations, and continuations-in-part of the 
preceding patent applications; any foreign counterparts of the preceding 
applications; and any patents issuing on the preceding applications, 
including registrations, revalidations, reissues, reexaminations, 
extensions or other governmental actions which extend claims or durations 
of such patents; in each case, which is owned or controlled, in whole or 
part, by license, assignment or otherwise by Pharmacopeia during the term 
of this Agreement, and subject to any limitations and prohibitions of such 
license or sublicense. It is understood that the Licensed Patents shall not 
include any intellectual property owned or licensed by Pharmacopeia 
relating to creation or use of combinatorial libraries, tag and/or marker 
compound engineering and encoding, and/or high throughput screening assays 
(hereinafter the "Excluded Technology"). 

    1.6 "Screening Period" means the ************* period following the 
date of shipment by Pharmacopeia of each Library Sample to Cubist or such 
longer period as may be established under Section 2.3.2 below. 

    1.7 "Target" means any molecular target set for on Exhibit B hereto, 
and any other molecular targets agreed in writing by Cubist and 
Pharmacopeia.
 
 2. LIBRARY SAMPLE
 
    2.1  LIBRARY SAMPLE.  Subject to the terms and conditions of this 
Agreement, Pharmacopeia shall provide four copies of the Library Sample to 
Cubist for screening by Cubist against the Targets as set forth in more 
detail on Exhibit A. The Library Sample shall be available delivery to 
Cubist as soon as practicable following Cubist's payment of the Library 
Sample Access Fee pursuant to Section 5.1.
 
    2.2  LIMITED USE.  The Library Sample shall be used by Cubist
 *************************************************************************

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                  -2-

<PAGE>

****************************************************************************
*************************************************************************
**************************************************************************
***********************.

    2.3  SCREENING BY CUBIST.  

         2.3.1 Target Exclusivity. To provide Cubist a period of 
exclusivity for screening of the Library Sample against the Targets, 
Pharmacopeia agrees that until the termination of the Screening Period, as 
such period may be extended, Pharmacopeia shall not knowingly deliver to 
any third party any compound from the Library Sample for screening against 
any of the Targets; provided, Pharmacopeia may itself screen or provide to 
third parties compounds from such Library Sample, or the library from which 
it was derived, for screening against any molecular target which is not a 
Target hereunder at such time. 

        2.3.2 Extentions of Screening Period. Cubist may request that 
Pharmacopeia extend the Screening Period for an additional period (after the 
initial ************************** Screening Period) by notifying 
Pharmacopeia no later than thirty (30) days prior to the date on which such 
Screening Period will expire. It is understood and agreed that if 
Pharmacopeia, in its sole discretion, does not so extend the Screening 
Period, Cubist shall have no further rights to screen the Library Sample. The 
length of any such additional period will be as agreed by the parties.
 
    2.4  REARRAYS.  After joint review of the screening data and upon 
mutual agreement, Pharmacopeia shall rearray (at one compound per well) 
those wells identified by the parties as containing compounds with activity 
against any of the Targets.
 
    2.5  ADDITIONAL LIBRARY SAMPLE.  If Cubist screens the initial Library 
Sample but does not identify any Library Compound with respect to which it 
wishes to negotiate with Pharmacopeia for a further agreement pursuant to 
Section 4.1, Cubist may request up to four copies of a further Library 
Sample with notice to Pharmacopeia during the Screening Period. 
Pharmacopeia then shall provide to Cubist a further Library Sample drawn 
from a different Pharmacopeia library, and Cubist may screen such further 
Library Sample, subject to the terms and conditions herein. Pursuant to 
this Section 2.5, Cubist may receive 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                               -3-

<PAGE>


Library Samples from ************** additional Pharmacopeia compound 
libraries. Upon shipment of such further Library Sample, Cubist's right to 
negotiate a further agreement with respect to any Library Compound in a 
previous Library Sample shall terminate.
 
    2.6  ADDITIONAL TARGETS.  At any time during the Screening Period, 
Cubist may provide Pharmacopeia notice that Cubist wishes to drop a Target 
from this Agreement and designate an additional target as a Target for all 
purposes of this Agreement. Within fifteen (15) days of receipt of such 
notice, Pharmacopeia shall, at its sole discretion, accept or deny the 
designation of each such proposed target as a Target by notice to Cubist. 
Upon Pharmacopeia's notice of such acceptance, if any, Cubist's right to 
negotiate a further agreement with respect to such dropped Target shall 
terminate.
 
    2.7  OWNERSHIP OF LIBRARY SAMPLES.  Pharmacopeia, shall retain all 
right, title and interest in and to the Library Sample and Library 
Compounds, and all Pharmacopeia intellectual property rights related 
thereto.
 
 3. LICENSE
 
    3.1  SCREENING LICENSE.  Subject to the terms and conditions of this 
Agreement, Pharmacopeia grants to Cubist a non-exclusive, non-transferable 
license, under the applicable Licensed Patents solely to screen the Library 
Sample to identify Library Compounds with activity against one or more of 
the Targets.
 
    3.2  COLUMBIA SUBLICENSE.  Subject to the terms and conditions of this 
Agreement and Columbia License, if necessary, Pharmacopeia will grant to 
Cubist a non-exclusive, non-transferable sublicense under the Columbia 
License solely to screen the Library Sample to identify Library Compounds 
with activity against one or more of the Targets.
 
    3.3  RETAINED RIGHTS.  No right or license in or to intellectual 
property rights of Pharmacopeia relating to the Library Sample or Library 
Compounds (or otherwise) is granted nor implied hereunder, except for the 
sole purpose of conducting the screening. Pharmacopeia retains rights not 
expressly granted to Cubist in Section 3.1 above, including without 
limitation, the right make, have made and use Library Compounds in the 
Library Sample for its own research purposes. It is understood and agreed 
that the license granted to Cubist in Section 3.1 above does not include 
the right to create, make or have made combinatorial libraries, 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                       -4-

<PAGE>

tags, markers or other encoding compositions, or use methods or processes 
relating to the preceding.
 
 4. FURTHER AGREEMENTS
 
    4.1  NEGOTIATION OF FURTHER AGREEMENT.  If Cubist determines that one 
or more Library Compounds have biological activity with respect to a Target 
and wishes to negotiate with Pharmacopeia a further agreement relating to 
such Library Compounds, Cubist may notify Pharmacopeia thereof during the 
Screening Period. In such event, the parties shall negotiate in good faith 
the terms of a further agreement for a period of ************************* 
from Pharmacopeia's receipt of such notice, or such longer period as the 
parties may agree (the "Negotiation Period"). The nature of such further 
agreement may be a license, collaboration or any other form as may be 
agreed by the parties. If the parties fail to enter into a further written 
agreement with respect to a particular Library Compounded during the 
Negotiation Period, Cubist shall acquire no right to such Library Compound.
 
    4.2  NO DECODES.  Until the parties reach definitive agreement pursuant 
to Section 4.1, or unless otherwise agreed in writing by the parties, 
Pharmacopeia shall not knowingly decode any Library Compound identified by 
Cubist to Pharmacopeia as having activity with respect to any Target.
 
    4.3  SCREENING BY PHARMACOPEIA.  If Cubist notifies Pharmacopeia as 
provided in Section 4.1, but the parties fail to enter into a further 
agreement, following the first anniversary of the end of the Screening 
Period, Pharmacopeia may screen and allow others to screen the Library 
Sample and the library from which it was derived against any Target; 
provided, Pharmacopeia may disclose to third parties that the Library 
Sample has been screen against such a Target, but shall not disclose to 
third parties that Cubist screened the Library Sample or the results of 
such screening.
 
    4.4  NO NOTICE OF LIBRARY COMPOUND ACTIVITY.  If Cubist fails to 
provide Pharmacopeia notice pursuant to Section 4.1 that it wishes to 
negotiate a further agreement with respect to any Library Compound in a 
particular Library Sample during the Screening Period, following the end of 
such Screening Period Pharmacopeia may screen and allow third parties to 
screen, such Library Sample and the library from which it was derived for 
activity against any Target, without further obligation to

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                    -5-

<PAGE>


 Cubist, and may commercialize any Library Compound therein itself or with 
third parties.
 
    4.5  THIRD PARTY RIGHTS.  It is understood that Pharmacopeia is in the
business of providing combinatorial libraries to third parties, and that
Pharmacopeia may grant such third parties rights to acquire licenses for
compounds in or derived from compounds in such libraries prior to the execution
of any further agreement between the parties hereto. Accordingly, any rights
granted to Cubist in a further agreement between the parties hereto shall be
limited to the extent that (i) a third party (either alone or jointly with
Pharmacopeia) has filed a patent application with respect to such a compound
prior to the filing by Cubist (either alone or jointly with Pharmacopeia) of a
patent application with respect to such a compound, (ii) Pharmacopeia has
previously granted a third party a license or other rights with respect to such
a compound, or (iii) as shown by contemporaneous documentation, Pharmacopeia has
previously decided to develop a particular compound on its own behalf. It is
further understood that compounds provided to third parties in the course of
Pharmacopeia's other business activities may result in third party patent
applications and patents, including patent applications and patents owned by
such third parties, or owned jointly by Pharmacopeia and such third parties,
which could affect the rights Cubist may wish to acquire from Pharmacopeia with
respect to any Library Compound.
 
 5. PAYMENTS
 
    5.1  LIBRARY SAMPLE ACCESS FEE.  Within thirty (30) days of the 
Effective Date, Cubist shall pay to Pharmacopeia a fee of ******************.
 
    5.2  PAYMENT METHOD.  All payments due under this Agreement shall be 
made to an account designated by Pharmacopeia. All payments hereunder shall 
be made in U.S. dollars. Any payments that are not paid on the date such 
payments area due under this Agreement shall bear interest to the extent 
permitted by applicable law at the prime rate as reported by the Chase 
Manhattan Bank, New York, New York, on the date such payment is due, plus 
an additional two percent (2%), calculated on the number of days such 
payment is delinquent.
 
    5.3  TAX MATTERS.  Any sales taxes, use taxes, transfer taxes or 
similar governmental charges required to be paid in connection with the 
transfer of the Library Sample shall be the sole responsibility of Cubist. 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                  -6-

<PAGE>


In the event that Pharmacopeia is required to pay any such amounts, Cubist 
shall promptly remit payment to Pharmacopeia of such amounts.
 
 6. CONFIDENTIALITY
 
    6.1  CONFIDENTIAL INFORMATION.  Except as expressly provided herein, 
the parties agree that, for the term of this Agreement and for five (5) 
years thereafter, the receiving party shall not disclose and except as 
expressly provided in this Article 6, shall not use for any purpose other 
than the performance of this Agreement, any Confidential Information 
furnished to it by the disclosing party hereto pursuant to this Agreement 
except to the extent that it can be established by the receiving party by 
competent proof that such information:
 
    (a) was already known to the receiving party, other than under an 
obligation of confidentiality, at the time of disclosure;
 
    (b) was generally available to the public or otherwise part of the 
public domain the time of its disclosure to the receiving party;
 
    (c) became generally available to the public or otherwise part of the 
public domain after its disclosure and other than through any act or 
omission of the receiving party breach of this Agreement;
 
    (d) was independently developed by the receiving party as demonstrated 
by documented evidenced prepared contemporaneously with such independent 
development; or
 
    (e) was subsequently lawfully disclosed to the receiving party by a 
person other than a party.
 
    6.2  PERMITTED USE AND DISCLOSURES.  Each party hereto may use or 
disclose Confidential Information disclosed to it by the other party to the 
extent such use or disclosure is reasonably necessary and permitted in the 
exercise of the rights granted hereunder, prosecuting or defending 
litigation, or complying with applicable governmental regulations or court 
orders or otherwise submitting information to tax or other governmental 
authorities, provided that if a party is required make any such disclosure 
of another party's Confidential Information, other than pursuant to a 
confidentiality agreement, it will give reasonable advance notice to the 
other party of such disclosure and, save to the extent inappropriate in the 
case of patent applications, will use its reasonable efforts to secure 
confidential treatment of such Confidential Information in consultation 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                    -7-

<PAGE>


with the other prior to its disclosure (whether through protective orders 
or otherwise) and disclose only the minimum necessary to comply with such 
requirements.
 
    6.3  NONDISCLOSURE OF TERMS.  Each of the parties hereto agrees not to 
disclose to any third party the terms of this Agreements without the prior 
written consent of the other party hereto, except to such party's 
attorneys, advisors, investors and other on a need to know basis under 
circumstances that reasonably ensure the confidentiality thereof, or to the 
extent required by law.
 
 7. INDEMNIFICATION
 
    7.1  CUBIST.  Cubist agrees to indemnify, defend and hold Pharmacopeia 
and its directors, officers, employees and agents (the "Pharmacopeia 
Indemnitees") harmless from and against any losses, costs, claims, damages, 
liabilities or expense (including reasonable attorneys' and professional 
fees and court and other expenses of litigation) arising out of or in 
connection with third party claims relating to the use of the Library 
Sample under this Agreement, except to the extent due to the negligence or 
intentional misconduct of Pharmacopeia.
 
    7.2  PHARMACOPEIA.  Pharmacopeia agrees to indemnify, defend and hold 
Cubist and its Affiliates and their respective directors, officers, 
employees and agents (the "Cubist Indemnitees") harmless from and against 
any losses, costs, claims, damages, liabilities or expense (including 
reasonable attorneys' fees and court and other expenses of litigation) 
arising out of or in connection with third party claims relating to the 
preparation and delivery of the Library Sample, except to the extent due to 
the negligence or intentional misconduct of Cubist.
 
 8. TERM AND TERMINATION
 
    8.1  TERM.  The term of this Agreement shall begin as of the Effective 
Date and, unless terminated earlier as provided in this Article 8, continue 
in full force and effect until*********************************************
***************************************************************************
*******************************.
 
    8.2  TERMINATION FOR CAUSE.  Either party may terminate this Agreement 
in the event the other party shall have materially breached or defaulted in 
the performance of any of its obligations hereunder, and such 

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                       -8-

<PAGE>


default shall have continued for ************* after written notice thereof 
was provided to the breaching party by the nonbreaching party. Any 
termination shall become effective at the end of such *********************** 
period unless the breaching party (or any other party on its behalf) has 
cured any such breach or default prior to the expiration of the 
*************** period or has commenced the cure within such ********** 
period and thereafter uses its best efforts to complete the cure as soon as 
practicable; provided, in the case of a failure to pay any amount due 
hereunder, such default may be the basis of a termination ************ 
following the date that notice of such default was provided to the breaching 
party.
 
    8.3  TERMINATION UPON BANKRUPTCY OR INSOLVENCY.  If voluntary or 
involuntary proceedings by or against a party are instituted in bankruptcy 
under any insolvency law, or a receiver or custodian is appointed for such 
party, or proceedings are instituted by or against such party for corporate 
reorganization or the dissolution of such party, which proceedings, if 
involuntary, shall not have been dismissed within sixty (60) days 
thereafter, the other party may immediately terminate this Agreement 
effective upon notice of such termination.
 
    8.4  TERMINATION BY CUBIST.  Cubist shall have the right to terminate 
this Agreement on sixty (60) days prior written notice to Pharmacopeia.
 
    8.5  EFFECT OF BREACH OR TERMINATION. 

         8.5.1 Accrued Obligations. Termination of this Agreement for any 
reason shall not release any party hereto from any liability which, at the 
time of such termination, has already accrued to the other party or which 
is attributable to a period prior to such termination nor preclude either 
party from pursuing all rights and remedies it may have hereunder or at law 
or in equity with respect to any breach of this Agreement. 

         8.5.2 Return of Materials. Upon any termination of this Agreement, 
Cubist and Pharmacopeia shall promptly return to the other party all 
Confidential Information of the other (except for one (1) copy which may be 
retained solely for archival purposes), and Cubist shall return to 
Pharmacopeia or destroy any remaining Library Compounds. 

         8.5.3. Survival. Sections 2.7. 4.2, 4.3, 5.3, 8.5 and 8.6, and 
Articles 6, 7 and 9 of this Agreement shall survive the expiration or 
termination of this Agreement for any reason.


 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                       -9-

<PAGE>


 9. MISCELLANEOUS
 
    9.1  GOVERNING LAW.  This Agreement and any dispute arising from the 
performance breach hereof shall be governed by and construed and enforced 
in accordance with, the laws of state of New Jersey without reference to 
conflicts of laws principles.
 
    9.2  NO IMPLIED LICENSES.  Only the licenses granted pursuant to the 
express terms of the Agreement shall be of any legal force or effect. No 
license rights shall be created by implication, estoppel or otherwise.
 
    9.3  WAIVER.  It is agreed that no waiver by any party hereto of any 
breach or default of any of the covenants or agreements herein set forth 
shall be deemed a waiver as to any subsequent and/or similar breach or 
default.
 
    9.4  ASSIGNMENT.  This Agreement shall not be assignable by either 
party to any third party hereto without the written consent of the other 
party, except either party may assign this Agreement, without such consent, 
to an entity that acquires all or substantially all of the business or 
assets of such party to which this Agreement pertains, whether by merger, 
reorganization, acquisition, sale, or otherwise. This Agreement shall be 
binding upon and accrue to the benefit of the parties hereto and their 
successors and any permitted assigns.
 
    9.5  INDEPENDENT CONTRACTORS.  The relationship of the parties hereto 
is that of independent contractors. The parties hereto are not deemed to be 
agents, partners or joint venturers of the others for any purpose as a 
result of this Agreement or the transactions contemplated thereby.
 
    9.6  DISCLAIMER OF WARRANTIES.  THE LIBRARY SAMPLE PROVIDED HEREUNDER 
IS PROVIDED AS-IS. PHARMACOPEIA MAKES NO REPRESENTATIONS AND EXTENDS NO 
WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO THE 
LICENSED PATENTS, LIBRARY SAMPLE, THE LIBRARY COMPOUNDS, OR ANY 
CONFIDENTIAL INFORMATION DISCLOSED PURSUANT TO ARTICLE 6, INCLUDING, BUT 
NOT LIMITED TO, ANY WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR 
PURPOSE, VALIDITY OF THE LICENSED PATENTS, OR NONFRINGEMENT BY THE 
PRECEDING OF ANY INTELLECTUAL PROPERTY RIGHTS OR THIRD PARTIES.


 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                  -10-

<PAGE>


    9.7  NOTICES.  All notices, requests and other communications hereunder 
shall be in writing and shall be personally delivered or by registered or 
certified mail, return receipt requested, postage prepaid, in each case to 
the respective address specified below, or such other address as may be 
specified in writing to the other parties hereto and shall be deemed to 
have been given upon receipt: 

             Pharmacopeia:          Pharmacopeia, Inc.
                                    101 College Road East
                                    Princeton, New Jersey 08540
                                    Attn: Chief Executive Officer

             Cubist:                Cubist Pharmaceuticals, Inc.
                                    24 Emily Street 
                                    Cambridge, Massachusetts 02139 
                                    Attn: Chief Executive Officer
 
    9.8  SEVERABILITY.  In the event that any provision of this Agreement 
becomes or is declared by a court of competent jurisdiction to be illegal, 
unenforceable or void, this Agreement shall continue in full force and 
effect without said provision.
 
    9.9  NO CONSEQUENTIAL DAMAGES.  IN NO EVENT SHALL ANY PARTY TO THIS 
AGREEMENT HAVE ANY LIABILITY TO THE OTHER FOR ANY SPECIAL, INDIRECT, 
CONSEQUENTIAL OR INCIDENTAL DAMAGES ARISING UNDER THIS AGREEMENT UNDER ANY 
THEORY OF LIABILITY.
 
    9.10  COMPLETE AGREEMENT.  This Agreement with its Exhibits, 
constitutes the entire agreement between the parties with respect to the 
subject matter hereof, and all prior agreements respecting the subject 
matter hereof, either written or oral, express or implied, shall be 
abrogated, canceled, and are null and void and of no effect. No amendment 
or change hereof or addition hereto shall be effective or binding on either 
of the parties hereto unless reduced to writing and executed by the 
respective duly authorized representatives of Pharmacopeia and Cubist.
 
    9.11  DISPUTE RESOLUTION.  Any dispute under this Agreement which is 
not settled by mutual consent shall be finally settled by binding 
arbitration, conducted in accordance with the Commercial Arbitration Rules 
of the American Arbitration Association by one (1) arbitrator appointed in 
accordance with said rules. The arbitration shall be held in New York, New 
York. The costs of the arbitration, including

 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                  -11-

<PAGE>


 administrative and arbitrators' fees, shall be shared equally by the 
parties, and each party shall bear its own costs and attorneys' and 
witness' fees. The decision of the arbitrator shall be written, final and 
non-appealable and may be enforced in any court of competent jurisdiction.
 
    9.12  COUNTERPARTS.  This Agreement may be executed in counterparts, 
each of which shall be deemed to be an original and all of which together 
shall be deemed to be one and the same agreement.
 
    IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be 
duly executed by their authorized representatives and delivered as of the 
Effective Date.


 CUBIST PHARMACEUTICALS, INC.             PHARMACOPEIA, INC. 


By: /s/ Neal Farber                       By: /s/ Joseph A. Mollica
    --------------------                      --------------------------

Name: Neal Farber, Ph.D.                  Name: Joseph A. Mollica, Ph.D.

Title: UP Corporate Development           Title: Chairman and Chief 
                                                 Executive Officer
 
 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                     -12-

<PAGE>


                              EXHIBIT A

   ************************************************************************
 **************************************************************************
 **************************************************************************
 **************************************************************************
 *************************************************************************
 ***********************************





 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.


                                     -13-

<PAGE>


                                   EXHIBIT B

    *********************************************************************
 ************************************************************************
 ************************************************************************
 ************************************************************************
 ************************************************************************
 *************************************************************************
 



 * Confidential treatment requested: material has been omitted and filed 
   separately with the Commission.

                                    -14-




<PAGE>



                               EXHIBIT 11.1

                       CUBIST PHARMACEUTICALS, INC.
                     Computation of Net Income Per Share

<TABLE>
<CAPTION>

                                                                     Twelve Months Ended              
                                                                        December 31,                  
                                                     ------------------------------------------------ 
                                                          1996             1995           1994        
                                                     -------------   --------------   -------------   
<S>                                                  <C>              <C>             <C>             

Beginning Balance January 1........................      1,016,662          910,027        546,862    

Issuance of Common Stock...........................      1,537,337           76,228         85,661    
Issuance of Cheap Stock............................        183,122          366,244        366,244    

Weighted Average Shares at December 31.............      2,737,121        1,352,499        998,766    
Net Loss...........................................    ($3,798,670)     ($5,396,006)   ($4,813,035)   
Net Loss per Share.................................         ($1.39)          ($3.99)        ($4.82)   
                                                     -------------   --------------   -------------   
                                                     -------------   --------------   -------------   

</TABLE>



<TABLE> <S> <C>

<PAGE>
<ARTICLE> 5
<CIK> 0000912183
<NAME> CUBIST PHARMACEUTICALS INC.
<MULTIPLIER> 1,000
<CURRENCY> U.S. DOLLARS
       
<S>                             <C>
<PERIOD-TYPE>                   YEAR
<FISCAL-YEAR-END>                          DEC-31-1996
<PERIOD-START>                             JAN-01-1996
<PERIOD-END>                               DEC-31-1996
<EXCHANGE-RATE>                                      1
<CASH>                                          19,329
<SECURITIES>                                         0
<RECEIVABLES>                                      505
<ALLOWANCES>                                         0
<INVENTORY>                                          0
<CURRENT-ASSETS>                                20,121
<PP&E>                                           4,899
<DEPRECIATION>                                 (1,741)
<TOTAL-ASSETS>                                  23,452
<CURRENT-LIABILITIES>                            2,101
<BONDS>                                          1,053
                                0
                                          0
<COMMON>                                            10
<OTHER-SE>                                      20,289
<TOTAL-LIABILITY-AND-EQUITY>                    23,452
<SALES>                                              0
<TOTAL-REVENUES>                                 4,985
<CGS>                                                0
<TOTAL-COSTS>                                    8,860
<OTHER-EXPENSES>                                     0
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                 229
<INCOME-PRETAX>                                (3,799)
<INCOME-TAX>                                         0
<INCOME-CONTINUING>                                  0
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                   (3,799)
<EPS-PRIMARY>                                   (1.39)
<EPS-DILUTED>                                   (1.39)
        

</TABLE>


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