Filed Pursuant to Rule 424(b)(3) REGISTRATION NO. 333-37794 PROSPECTUS SUPPLEMENT NO. 2 DATED SEPTEMBER 14, 2000 TO THE PROSPECTUS DATED AUGUST 1, 2000 OF VERTEX PHARMACEUTICALS INCORPORATED This Prospectus Supplement No. 2 amends the information in the table under the caption "Selling Holders" in the Prospectus dated August 1, 2000 by deleting the information contained in the table regarding the Selling Security Holders with respect to the principal amount of notes and common stock of Vertex Pharmaceuticals Incorporated and substituting therefor the following table: NUMBER OF SHARES OF COMMON STOCK ISSUABLE PRINCIPAL AMOUNT OF NOTES UPON CONVERSION OF THE BENEFICIALLY OWNED NOTES THAT MAY BE NAME OF SECURITY HOLDER AND OFFERED(1) OFFERED(2) ----------------------- ------------------------- ---------------------- AIG SoundShore Holdings Ltd. $1,670,000 41,418 AIG SoundShore Opportunity Holding Fund Ltd. $2,400,000 59,523 AIG SoundShore Strategic Holding Fund Ltd. $1,400,000 34,722 Alta Partners Holdings, Inc. (3) $5,000,000 124,007 American Masters Fund "AG Absolute Return Series" Limited $1,000,000 24,801 Angelo, Gordon & Co., L.P. $500,000 12,400 Argent Classic Convertible Arbitrage Fund (Bermuda) L.P. $5,000,000 124,007 Bear, Stearns & Co. Inc.(4) $500,000 12,400 BNP Arbitrage SNC $6,500,000 161,210 BP Amoco PLC Master Trust $2,200,000 54,563 CIBC World Markets $3,250,000 80,605 Credit Suisse First Boston Corporation $3,800,000 94,246 The Common Fund F/A/O Absolute Return Fund $300,000 7,440 -1-
NUMBER OF SHARES OF COMMON STOCK ISSUABLE PRINCIPAL AMOUNT OF NOTES UPON CONVERSION OF THE BENEFICIALLY OWNED NOTES THAT MAY BE NAME OF SECURITY HOLDER AND OFFERED(1) OFFERED(2) ----------------------- ------------------------- ---------------------- Deutsche Bank Securities $4,900,000 121,527 Donaldson, Lufkin & Jenrette Securities Corp. $500,000 12,400 Estate of James Campbell $950,000 23,561 First Albany Corporation $111,000 2,752 Grace Brothers, Ltd. $1,500,000 37,202 Helix Convertible Opportunities Fund Ltd $910,000 22,569 Helix Convertible Opportunities, L.P. $1,790,000 44,394 Highbridge International LLC $9,250,000 229,414 ITG, Inc. $200,000 4,960 Jefferies & Company $200,000 4,960 J.P. Morgan Securities, Inc. $4,375,000 108,506 KBC Financial Products $5,000,000 124,007 Key Asset Management Inc. $200,000 4,960 Lazard Freres & Cie Paris (5) $1,500,000 37,202 LDG Limited $200,000 4,960 McMahan Securities Co., L.P. $1,600,000 39,682 Merrill Lynch, Pierce, Fenner and Smith Inc. (4) $3,690,000 91,517 MichaelAngelo, L.P. $1,750,000 43,402 Morgan Stanley & Co. $10,000,000 248,015 -2-
NUMBER OF SHARES OF COMMON STOCK ISSUABLE PRINCIPAL AMOUNT OF NOTES UPON CONVERSION OF THE BENEFICIALLY OWNED NOTES THAT MAY BE NAME OF SECURITY HOLDER AND OFFERED(1) OFFERED(2) ----------------------- ------------------------- ---------------------- New York Life Insurance and Annuity Corporation $1,100,000 27,281 New York Life Insurance Company $6,500,000 161,210 Quattro Fund Ltd $500,000 12,400 R2 Investments, LDC $27,600,000 684,523 Raphael II, Ltd. $1,000,000 24,801 RCG Multi-Strategy Account, L.P. $750,000 18,601 Robertson Stephens (3) $12,500,000 310,019 Salomon Brothers Asset Management, Inc. $36,930,000 915,922 SG Cowen Securities (3) $10,000,000 248,015 TQA Master Fund, LTD $2,700,000 66,964 TQA Master Plus Fund, LTD $1,000,000 24,801 Tribeca Investments LLC $8,500,000 210,813 UBS Warburg LLC $5,500,000 136,408 White River Securities LLC $500,000 12,400 Zurich HFR Master Fund $100,000 2,480 (1) The number of securities beneficially owned is determined under the rules of the SEC and the information is not necessarily indicative of beneficial ownership for any other purpose. Under those rules, beneficial ownership includes any securities as to which the individual has sole or shared voting power or investment power and also any securities which the individual has the right to acquire within 60 days through the exercise of any stock option or other right. The inclusion in the table of securities, however, does not constitute an admission that the selling holders are direct or indirect beneficial owners of those securities. The selling holders have sole voting power and investment power with respect to all securities or capital stock listed as owned by the selling holders. -3-
(2) Adjusted to reflect the two-for-one stock split of our common stock effected by way of a stock dividend distributed on August 31, 2000, and the resulting adjustment in the conversion price of the notes from $80.64 to $40.32 per share. (3) As of September 11, 2000, Alta Partners Holdings, Inc. beneficially owned 117,700 shares of our Common Stock. These shares are not part of this offering. (4) Acted as one of the initial purchasers of the notes. (5) As of May 22, 2000, Lazard Freres & Cie Paris owned 7,360 shares of our common stock. These shares are not part of this offering. This Prospectus Supplement No. 2 should be read in conjunction with the Prospectus dated August 1, 2000