ALEXION PHARMACEUTICALS INC
424B3, 2000-12-06
PHARMACEUTICAL PREPARATIONS
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<PAGE>
                                                    FILED PURSUANT TO RULE 424B3
                                                      REGISTRATION NO. 333-36738

PROSPECTUS SUPPLEMENT
(To prospectus dated August 23, 2000)

                                     [LOGO]

           $120,00,000 5 3/4% CONVERTIBLE SUBORDINATED NOTES DUE 2007
   AND 1,127,555 SHARES OF COMMON STOCK ISSUABLE UPON CONVERSION OF THE NOTES

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

    This document supplements the prospectus dated August 23, 2000 relating to
the sale of $120,000,000 5 3/4% Convertible Subordinated Notes due 2007 and
1,127,555 shares of our common stock issuable upon conversion of the notes. We
are not selling any shares; the securityholders named in the prospectus are
offering their shares. This prospectus supplement is incorporated by reference
into the prospectus.

                OUR NASDAQ NATIONAL MARKET TRADING SYMBOL--ALXN

                   CLOSING PRICE (DECEMBER 5, 2000): $83.125

    This supplement replaces section entitled "Selling Securityholders" on page
16 with the information described on the following page.

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

    THE SECURITIES AND EXCHANGE COMMISSION AND STATE SECURITIES REGULATORS HAVE
NOT APPROVED OR DISAPPROVED THESE SECURITIES, OR DETERMINED IF THIS PROSPECTUS
IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL
OFFENSE.

             INVESTING IN THESE NOTES OR OUR COMMON STOCK INVOLVES
                             A HIGH DEGREE OF RISK.
                    SEE "RISK FACTORS" BEGINNING ON PAGE 5.

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

          THE DATE OF THIS PROSPECTUS SUPPLEMENT IS DECEMBER 6, 2000.
<PAGE>
                            SELLING SECURITYHOLDERS

    We originally sold the notes to the initial purchasers on March 3, 2000. The
initial purchasers have advised us that they resold the notes in transactions
exempt from the registration requirements of the Securities Act of 1933 to
"qualified institutional buyers" (as defined in Rule 144A of the Securities
Act). These subsequent purchasers, or their transferees, pledgees, donees or
successors, may from time to time offer and sell any of the notes and/or shares
of our common stock issuable upon conversion of the notes pursuant to this
prospectus.

    We are registering these notes and shares of common stock pursuant to a
registration rights agreement, dated March 3, 2000, between us and the initial
purchasers. Under the agreement, we filed the registration statement of which
this prospectus is part. We must also keep the registration statement effective
until March 8, 2002 or the earlier of (a) the sale pursuant to the registration
statement of all the securities registered, (b) the date on which all the
securities (x) held by the persons who are not our affiliates may sell such
securities under Rule 144(k) or (y) cease to be outstanding or (c) a subsequent
shelf registration statement covering all of these securities has been declared
effective under the Securities Act.

                                       2
<PAGE>
    Except as otherwise indicated, the following table contains information as
of July 25, 2000 with respect to the selling securityholders and the principal
amount of notes and the underlying common stock beneficially owned by each
selling securityholder that may be offered using this prospectus.

<TABLE>
<CAPTION>
                                           PRINCIPAL
                                           AMOUNT OF
                                             NOTES       PERCENTAGE OF      NUMBER OF       PERCENTAGE TO
                                          BENEFICIALLY       NOTES       SHARES THAT MAY    COMMON STOCK
NAME OF SELLING SECURITYHOLDER               OWNED        OUTSTANDING      BE SOLD (1)     OUTSTANDING (2)
------------------------------            ------------   -------------   ---------------   ---------------
<S>                                       <C>            <C>             <C>               <C>
Argent Classic Convertible
  Arbitrage Fund (Bermuda) L.P. ........  $ 8,300,000         6.9%            77,989           *
BNP Arbitrage SNC.......................  $ 7,500,000         6.3%            70,472           *
BNP Cooper Neff Convertible
  Strategies Fund, L.P. ................  $   500,000           *              4,698           *
Calamos Market Neutral Fund
  Calamos Investment Trust..............  $ 1,280,000         1.1%            12,027           *
CIBC World Markets......................  $ 1,500,000         1.3%            14,094           *
Consulting Group Capital Market Funds...  $   340,000           *              3,194           *
Credit Suisse First Boston
  Corporation...........................  $14,500,000        12.1%           136,246           *
D. E. Shaw Investments, L.P. ...........  $   800,000           *              7,517           *
D. E. Shaw Valence L.P. ................  $ 1,200,000         1.0%            11,275           *
Deutsche Bank Securities Inc. ..........  $ 9,950,000         8.3             93,493           *
Elf Aquitaine...........................  $   250,000           *              2,349           *
Fir Tree Institutional Value Fund,
  L.P. .................................  $ 4,569,025         3.8%            42,931           *
Fir Tree Value Fund, L.P. ..............  $12,212,025        10.2%           114,747           *
Fir Tree Value Partners, LDC............  $ 1,243,950         1.0%            11,688           *
Highbridge International LLC (5)........  $ 6,000,000         5.0%            56,377           *
JMG Capital Partners, LP................  $ 2,937,000         2.4%            27,596           *
JMG Triton Offshore Fund, Ltd. .........  $ 2,938,000         2.4%            27,606           *
J.P. Morgan Securities, Inc. ...........  $   280,000           *              2,630           *
Lord Abbette Bond Debenture Fund........  $ 3,750,000         3.1%            35,236           *
Museum of Fine Arts, Boston (6).........  $    27,000           *                253           *
Oxford Lord Abbette & Co. ..............  $ 1,000,000           *              9,396           *
Parker-Hannifin Corporation (6).........  $    47,000           *                441           *
ProMutual (6)...........................  $   100,000           *                939           *
Robertson Stephens......................  $ 5,000,000         4.2%            46,981           *
R2 Investments, LCD.....................  $18,600,000        15.5%           174,770           *
University of Rochester (6).............  $    26,000           *                244           *
Tribeca Investments, LLC................  $ 5,000,000         4.2%            46,981           *
ZCM/HFR Index Management, L.L.C. .......  $   120,000           *              1,127           *
Any other holder of Notes or future
  transferee, pledgee, donee or
  successor of any holder (3)(4)........  $10,230,000         8.4%            94,244           *
</TABLE>

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

*   Less than 1%.

(1) Assumes conversion of all of the holder's notes at a conversion price of
    $106.425 per share of common stock. However, this conversion price will be
    subject to adjustment as described under "Description of Notes--Conversion
    of Notes." As a result, the amount of common stock issuable upon conversion
    of the notes may increase or decrease in the future.

(2) Calculated based on Rule 13d-3(d)(1)(i) of the Exchange Act using 18,016,311
    shares of common stock outstanding as of December 1, 2000. In calculating
    this amount, we treated as outstanding the number of shares of common stock
    issuable upon conversion of all of that particular holder's notes. However,
    we did not assume the conversion of any other holder's notes.

(3) Information about other selling securityholders will be set forth in
    prospectus supplements, if required.

                                       3
<PAGE>
(4) Assumes that any other holders of notes, or any future transferees,
    pledgees, donees or successors of or from any such other holders of notes,
    do not beneficially own any common stock other than the common stock
    issuable upon conversion of the notes at the initial conversion rate.

(5) Information as of November 14, 2000.

(6) Information as of November 8, 2000.

    We prepared this table based on the information supplied to us by the
selling securityholders named in the table.

    The selling securityholders listed in the above table may have sold or
transferred, in transactions exempt from the registration requirements of the
Securities Act, some or all of their notes since the date on which the
information in the above table is presented. Information about the selling
securityholders may change over time. Any changed information will be set forth
in prospectus supplements.

    Because the selling securityholders may offer all or some of the notes and
shares of common stock issued upon conversion of the notes, and because there
are currently no agreements, arrangements or understandings with respect to the
sale of any of the notes or shares of common stock that will be held by the
selling securityholders after completion of this offering, no estimate can be
given as to the principal amount of notes or shares of common stock that will be
held by the selling securityholders after completion of this offering. See "Plan
of Distribution."

                                       4
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