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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
 
                           ---------------------------

                                   FORM 10-Q
 
[x] Quarterly report pursuant to Section 13 pr 15(d) of the Securities and
    Exchange Act of 1934 For the quarterly period ended March 31, 1997
 
                                       OR
 
[ ] Transition report pursuant to Section 13 or 15(d) of the Securities and
    Exchange Act of 1934 For the transition period from ________ to ________

 
                         Commission File Number 0-19319
 
                       Vertex Pharmaceuticals Incorporated
               (Exact name of registrant as specified in its charter)

         Massachusetts                                        04-3039129
(State or other jurisdiction of                            (I.R.S. Employer
 incorporation or organization)                           Identification No.)

           130 Waverly Street, Cambridge, Massachusetts 02139-4242 
          (Address of principal executive offices, including zip code)

                                   (617) 577-6000
               (Registrant's telephone number, including area code)
 
     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 the number of shares outstanding of each of the issuer's 
classes of common stock, as of the latest practicable date.
 
Common Stock, par value $.01 per share                        24,721,133
                Class                                Outstanding at May 6, 1997
 
                                       -1-

                        VERTEX PHARMACEUTICALS INCORPORATED
 
                                     INDEX
 
                                                                          PAGE
 
Part I. - Financial Information
 
     Item 1. Condensed Consolidated Financial Statements
 
             Report of Independent Accountants                             3
 
             Condensed Consolidated Balance Sheets -
 
                  March 31, 1997 and December 31, 1996                     4
 
             Condensed Consolidated Statements of Operations -
 
                  Three Months Ended March 31, 1997 and 1996               5
 
             Condensed Consolidated Statements of Cash Flows -
 
                  Three Months Ended March 31, 1997 and 1996               6
 
             Notes to Condensed Financial Statements                       7
 
     Item 2. Management's Discussion and Analysis of Financial
             Condition and Results of Operations                           8
 

Part II. - Other Information                                              10
 
Signatures                                                                11

                                       -2-

 
                       REPORT OF INDEPENDENT ACCOUNTANTS
 
To the Board of Directors and Stockholders of Vertex Pharmaceuticals 
Incorporated:
 
We have reviewed the accompanying condensed balance sheet of Vertex 
Pharmaceuticals Incorporated as of March 31, 1997, and the related condensed 
consolidated statements of operations and cash flows for the three-month 
period then ended. These financial statements are the responsibility of the 
company's management.
 
We conducted our review in accordance with standards established by the 
American Institute of Certified Public Accountants. A review of interim 
financial information consists principally of applying analytical procedures 
to financial data and making inquiries of persons responsible for financial 
and accounting matters. It is substantially less in scope than an audit 
conducted in accordance with generally accepted auditing standards, the 
objective of which is the expression of an opinion regarding the financial 
statements taken as a whole. Accordingly, we do not express such an opinion.
 
Based on our review, we are not aware of any material modifications that 
should be made to the accompanying financial statements for them to be in 
conformity with generally accepted accounting principles.

                                       /s/ Coopers & Lybrand L.L.P.
                                       COOPERS & LYBRAND L.L.P.
 
Boston, Massachusetts 
April 22, 1997
 
                                       -3-





                      VERTEX PHARMACEUTICALS INCORPORATED
 
                     CONDENSED CONSOLIDATED BALANCE SHEETS
                                   (Unaudited)
                                 (In thousands)

                                                                   MARCH 31,       DECEMBER 31,
                                                                     1997             1996
                                                                  ------------     ------------
                                                                                
     
                                          ASSETS

Current assets:
     Cash and cash equivalents...................................  $ 84,927       $   34,851
     Short-term investments......................................   190,157           95,508
     Prepaid expenses and other current assets...................     1,687            1,791
                                                                  ----------       ----------
 
          Total current assets...................................   276,771          132,150
 
Restricted cash..................................................     2,316            2,316
Property and equipment, net......................................    10,109            8,663
Other assets.....................................................       445              370
                                                                  ----------       ----------
          Total assets...........................................  $289,641       $  143,499
                                                                  ----------       ----------
                                                                  ----------       ----------
 
        
                              LIABILITIES AND STOCKHOLDERS' EQUITY
 
Current liabilities:
     Obligations under capital lease.............................  $  2,839       $    2,910
     Accounts payable and accrued expenses.......................     6,262            4,146
                                                                  ----------       ----------
          Total current liabilities..............................     9,101            7,056
                                                                  ----------       ----------
Obligations under capital leases, excluding current
     portion.....................................................     5,333             5,617
                                                                  ----------       ----------
          Total liabilities......................................    14,434            12,673
                                                                  ----------       ----------
Stockholders' equity:
     Common stock................................................       247               211
     Additional paid-in capital..................................   377,976           227,510
     Equity adjustments..........................................      (306)               49
     Accumulated deficit.........................................  (102,710)          (96,944)
                                                                  ----------       ----------
          Total stockholders' equity.............................   275,207           130,826
                                                                  ----------       ----------
          Total liabilities and stockholders' equity.............  $289,641        $  143,499
                                                                  ----------       ----------
                                                                  ----------       ----------

 
                             The accompanying notes are an integral part of 
                            these condensed consolidated financial statements.

                                                  -4-

 
                                   VERTEX PHARMACEUTICALS INCORPORATED
 
                             CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                               (Unaudited)
                                  (In thousands, except per share data)
 


                                                                      Three Months Ended March 31,
                                                                      ----------------------------
                                                                             1997       1996
                                                                           ---------  ---------
                                                                                
 
Revenues:
     Collaborative and other research and development............          $   4,660  $   2,473
     Interest income.............................................              2,258      1,278
                                                                          ----------  ----------
          Total revenues.........................................              6,918      3,751
                                                                          ----------  ----------
Costs and expenses:
     Research and development....................................             10,314      9,337
     General and administrative..................................              2,218      1,763
     Interest....................................................                152        119
                                                                           ----------  ----------
          Total costs and expenses...............................             12,684     11,219
                                                                           ----------  ----------
Net loss.........................................................          $  (5,766) $  (7,468)
                                                                          ----------  ----------
                                                                          ----------  ----------

Net loss per common share........................................          $   (0.26) $   (0.43)
                                                                          ----------  ----------
                                                                          ----------  ----------

Weighted average number of common shares outstanding.............             21,975     17,332
                                                                          ----------  ----------
                                                                          ----------  ----------


 
                              The accompanying notes are an integral part of
                             these condensed consolidated financial statements.
 
                                                    -5-


                                    VERTEX PHARMACEUTICALS INCORPORATED
 
                              CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                                 (Unaudited)
                                                (In thousands)



                                                                      Three Months Ended March 31,
                                                                      -----------------------------
 
                                                                     1997                       1996
                                                                  ----------                  ----------
                                                                                           
 
Cash flows from operating activities:
     Net loss..........................................            $(5,766)                  $  (7,468)
     Adjustment to reconcile net loss to net cash
       used by operating activities:
         Depreciation and amortization.................                814                         828
     Changes in assets and liabilities:
         Prepaid expenses and other current assets.....                104                        (371)
         Accounts payable and accrued expenses.........              2,116                      (2,315)
         Deferred revenue..............................                --                        1,000
                                                                 ---------                    ----------
           Net cash provided (used) by operating
             activities................................             (2,732)                     (8,326)
                                                                 ---------                    ----------

Cash flows from investing activities:
     Short-term investments............................            (94,997)                      1,267
     Expenditures for property and equipment...........             (2,260)                       (579)
     Other assets......................................                (75)                       (939)
                                                                 ---------                    ----------
          Net cash provided (used) by investing 
            activities.................................            (97,332)                       (251)
                                                                 ---------                    ----------

Cash flows from financing activities:
     Proceeds from public offering of common stock.....            148,810                        ----
     Other issuances of common stock...................              1,692                         870
     Proceeds from equipment sale/leaseback............                343                        ----
     Repayment of capital lease obligations............               (698)                       (504)
                                                                 ---------                    ----------
          Net cash provided (used) by financing      
            activities.................................            150,147                         366
                                                                 ---------                    ----------
Effect of exchange rate changes on cash................                 (7)                         (1)
                                                                 ---------                    ----------
Decrease in cash and cash equivalents..................             50,076                      (8,212)
Cash and cash equivalents at beginning of period.......             34,851                      28,390
                                                                 ---------                    ----------
Cash and cash equivalents at end of period.............            $84,927                   $  20,178
                                                                 ---------                    ----------
                                                                 ---------                    ----------

 
                            The accompanying notes are an integral part of
                          these condensed consolidated financial statements.
 
                                                         -6-


                                           VERTEX PHARMACEUTICALS INCORPORATED
 
                                         NOTES TO CONDENSED FINANCIAL STATEMENTS
 
1.  BASIS OF PRESENTATION
 
    The accompanying condensed consolidated financial statements are 
unaudited and have been prepared by the Company in accordance with generally 
accepted accounting principles.
 
    Certain information and footnote disclosures normally included in the 
Company's annual financial statements have been condensed or omitted. The 
interim financial statements, in the opinion of management, reflect all 
adjustments (including normal recurring accruals) necessary for a fair 
statement of the results for the interim periods ended March 31, 1997 and 
1996.
 
    The results of operations for the interim periods are not necessarily 
indicative of the results of operations to be expected for the fiscal year, 
although the Company expects to incur a substantial loss for the year ended 
December 31, 1997. These interim financial statements should be read in 
conjunction with the audited financial statements for the year ended December 
31, 1996, which are contained in the Company's 1996 Annual Report to its 
shareholders and in its Form 10-K filed with the Securities and Exchange 
Commission.
 
2.  CASH AND CASH EQUIVALENTS
 
    For purposes of the statement of cash flows, the Company considers all 
highly liquid investments with maturities of three months or less at the date 
of purchase to be cash equivalents. Changes in cash and cash equivalents may 
be affected by shifts in investment portfolio maturities as well as by actual 
net cash receipts or disbursements.
 
3.  NET LOSS PER COMMON SHARE
 
    The net loss per common share is computed based upon the weighted average 
number of common shares outstanding. Common equivalent shares are not 
included in the per-share calculations where the effect of their inclusion 
would be anti-dilutive.
 
    The Financial Accounting Standards Board has issued Statement of 
Financial Accounting Standards No. 128 ("SFAS 128"), "Earnings Per Share" 
which modifies the way in which earnings per share ("EPS") is calculated and 
disclosed. SFAS 128 is effective for financial statements for periods ending 
after December 15, 1997. The adoption of SFAS 128 is not expected to have a 
material impact on the Company's EPS calculation.
 
4.  PUBLIC OFFERING OF COMMON STOCK
 
    On March 12, 1997, the Company completed a public offering of 3,450,000 
shares of its common stock. The Company anticipates using the net proceeds of 
$148,810,000 primarily to fund research and product development programs, 
including clinical trials, and for general corporate purposes.


                                       -7-

 
                        VERTEX PHARMACEUTICALS INCORPORATED
 
               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS
 
    The Company is engaged in the discovery, development and 
commercialization of novel, small molecule pharmaceuticals for the treatment 
of major diseases for which there are currently limited or no effective 
treatments. The Company is a leader in the use of structure-based drug 
design, an approach to drug discovery that integrates advanced biology, 
biophysics and chemistry. The Company is conducting nine significant 
pharmaceutical research and development programs to develop pharmaceuticals 
for the treatment of viral diseases, multidrug resistance in cancer, 
hemoglobin disorders, autoimmune diseases, inflammatory diseases and 
neurodegenerative disorders. Three of these programs are in the development 
phase, and the other six are in the research phase. During the first quarter 
of 1997, Vertex's partner, Glaxo Wellcome plc ("Glaxo Wellcome"), initiated 
Phase III clinical trials of VX-478 (141W94), the lead compound in the 
Company's HIV program. Kissei Pharmaceutical Co., Ltd. ("Kissei") is also 
developing VX-478 as Vertex's partner for the HIV program in the Far East. 
Vertex recently expanded Phase II clinical trials of VX-710, the Company's 
lead compound in its cancer multidrug resistance program. Vertex initiated a 
Phase II study of the administration of VX-710 in combination with paclitaxel 
in patients with breast cancer. In addition, BioChem Therapeutic Inc 
("BioChem"),Vertex's partner for development and marketing of VX-710 in 
Canada initiated a Phase II study of VX-710 and doxorubicin in patients with 
soft tissue sarcoma. The Company, together with its partners Alpha 
Therapeutic ("Alpha") and Ravizza Farmaceutici Sp.A. ("Ravizza"), also 
continued development of VX-366 in its hemoglobin disorders program.
 
    To date, the Company has not received any revenues from the sale of 
pharmaceutical products and does not expect to receive such revenues in the 
near future, if ever. The Company has incurred since its inception, and 
expects to incur over the next several years, significant operating losses as 
a result of expenditures for its research and development programs. The 
Company expects that losses will fluctuate from quarter to quarter and that 
such fluctuations may be substantial.
 
RESULTS OF OPERATIONS
 
    Three Months Ended March 31, 1997 Compared with Three Months Ended March 
31, 1996. 

    For the first quarter of 1997, the Company's total revenues were 
$6,918,000 as compared to $3,751,000 during the same period in 1996. From 
quarter to quarter, the Company s revenues fluctuate as a result of changes 
in the timing and amount of partner research support payments, partner 
reimbursements of Vertex drug development costs, and payments for the 
achievement of various research and development milestones. Revenues for the 
first quarter in 1997 included a $2,000,000 payment from Kissei. This payment 
from Kissei was associated with an ongoing Phase II clinical trial of 
Vertex's HIV protease inhibitor, VX-478, as single-drug therapy for HIV 
infection. The other factor contributing to the increase in quarterly revenue 
for the three months ended March 31, 1997 compared to the three months ended 
March 31, 1996 was higher investment income from increased cash and 
short-term investments, including the proceeds of public offerings of the 
Company's stock in August 1996 and March 1997. In the first quarter of 1997, 
the Company received $4,237,000 in revenue from its collaborative agreements, 
$2,258,000 in interest received on invested funds and $423,000 from 
government grants and other revenue. In the first quarter of 1996, the 
Company received $2,281,000 in revenue from its collaborative agreements, 
$1,278,000 in interest received on invested funds and $192,000 from 
government grants and other revenue.

                                       -8-

 
    The Company's total costs and expenses increased to $12,684,000 in the 
first quarter of 1997, from $11,219,000 during the same period in 1996. 
Research and development expenses were $10,314,000 in the first quarter of 
1997 as compared to $9,337,000 during the same period in 1996. The Company 
experienced higher research costs associated with an increase in the number 
of research employees as well as certain project specific activities. General 
and administrative expenses increased during the first quarter of 1997 to 
$2,218,000 from $1,763,000 in the first quarter of 1996 due primarily to an 
increase in costs associated with patent protection for the Company's 
intellectual property as well as an increase in marketing efforts by the 
Company's subsidiary, Altus Biologics Inc. Interest expense increased to 
$152,000 in the first quarter of 1997 as compared to $119,000 during the same 
period in 1996 due to higher levels of equipment financing.
 
    The Company incurred a net loss of $5,766,000 or $.26 per share in the 
first quarter of 1997 as compared to a net loss of $7,468,000 or $.43 per 
share in the first quarter of 1996.

LIQUIDITY AND CAPITAL RESOURCES
 
    The Company's operations have been funded principally through strategic 
collaborative agreements, public offerings and private placements of the 
Company's equity securities, equipment lease financing, government grants and 
interest income. The Company expects to incur increased research and 
development and related supporting expenses and, consequently, continued 
losses on a quarterly and annual basis as it continues to develop existing 
and future compounds and to conduct clinical trials of potential drugs. The 
Company also expects to incur substantial administrative and 
commercialization expenditures in the future and additional expenses related 
to the filing, prosecution, defense and enforcement of patent and other 
intellectual property rights.
 
    The Company expects to finance these substantial cash needs with its 
existing cash and investments at March 31, 1997 of approximately $275 
million, together with interest earned thereon, future payments under its 
existing collaborative agreements, and facilities and equipment financing. To 
the extent that funds from these sources are not sufficient to fund the 
Company's activities, it will be necessary to raise additional funds through 
public offerings or private placements of securities or other methods of 
financing. There can be no assurance that such financing will be available on 
acceptable terms, if at all.
 
    In March 1997, the Company completed a public offering of 3,450,000 
shares of its common stock, which included an over-allotment option exercised 
by the underwriters for 450,000 shares, at a price to the public of $45.50 
per share, with net proceeds to the Company of approximately $148,810,000. 
The Company plans to use these proceeds primarily to fund research and 
product development programs, including clinical trials, and for general 
corporate purposes.
 
    The Company's aggregate cash and investments increased by $144,725,000 
during the three months ended March 31, 1997 to $275,084,000, principally due 
to the public offering completed in March 1997. Cash used by operations, 
principally to fund research and development activities, was $2,732,000 
during the same period. The Company also expended $2,260,000 during this 
period to acquire property and equipment, principally for research equipment 
and facilities. During the first quarter of 1997 the Company entered into 
equipment lease financing in the aggregate amount of $343,000 and repaid 
$698,000 of its lease obligations.
 
                                      -9-


                                    PART II.
 
                               OTHER INFORMATION
 
Item 1.  Legal Proceedings:
 
         None
 
Item 2.  Changes in Securities:
 
         None
 
Item 3.  Defaults Upon Senior Securities:
 
         None
 
Item 4.  Submission of Matters to a Vote of Security Holders:
 
         None
 
Item 5.  Other Information:
 
         None
 
Item 6.  Exhibits:
 
         27   Financial Data Schedule. (Exhibit 27 is submitted as an exhibit 
              only in the electronic format of this Quarterly Report on 
              Form 10-Q submitted to the Securities and Exchange Commission.)
 
         99   Letter of Independent Accountants
 
         Reports on Form 8-K:
 
         On February 25, 1997 the Company filed its Financial Statements for 
         the year ended December 31, 1996 with the Securities and Exchange 
         Commission in a Current Report on Form 8-K.

                                       -10-
 
     
                                    SIGNATURES
 
    Pursuant to the requirements of the Securities Exchange Act of 1934, the 
registrant has duly caused this report to be signed on its behalf by the 
undersigned thereunto duly authorized.
 
                                     VERTEX PHARMACEUTICALS INCORPORATED 




Date: May 12, 1997                   /s/ Thomas G. Auchincloss, Jr 
                                     -----------------------------------------
                                     Thomas G. Auchincloss, Jr.
                                     Vice President of Finance and Treasurer
                                     (Principal Financial Officer)




Date: May 12, 1997                    /s/ Hans D. van Houte 
                                     -----------------------------------------
                                     Hans D. van Houte
                                     Controller
                                     (Principal Accounting Officer)
 
                                     -11-