<PAGE>   1
                                                                     EXHIBIT 4.7


THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED (THE "SECURITIES ACT"), OR ANY STATE
SECURITIES LAWS. THESE SECURITIES HAVE BEEN ACQUIRED FOR INVESTMENT AND MAY NOT
BE SOLD OR OTHERWISE TRANSFERRED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION
STATEMENT FOR THESE SECURITIES UNDER THE SECURITIES ACT AND APPLICABLE STATE
SECURITIES LAWS, OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT
REGISTRATION IS NOT REQUIRED AND THAT AN APPLICABLE EXEMPTION IS AVAILABLE.


                               WARRANT TO PURCHASE
                        50,000 SHARES OF COMMON STOCK OF
                          AMYLIN PHARMACEUTICALS, INC.
                           (VOID AFTER MARCH 2, 2008)

        This certifies that Alkermes Controlled Therapeutics Inc. II, a
Pennsylvania corporation, or its permitted assigns (the "Holder"), for value
received, is entitled to purchase from AMYLIN PHARMACEUTICALS, INC., a Delaware
corporation (the "Company"), having a place of business at 9373 Towne Centre
Drive, San Diego, California 92121, Fifty Thousand (50,000) fully paid and
nonassessable shares of the Company's Common Stock ("Stock") for cash at a price
of $10.01 per share (the "Stock Purchase Price") at any time or from time to
time on or after March 2, 2001 and up to and including 5:00 p.m. (Pacific time)
on March 2, 2008, such day being referred to herein as the "Expiration Date,"
upon surrender to the Company at its principal office (or at such other location
as the Company may advise the Holder in writing) of this Warrant properly
endorsed with the Form of Subscription attached hereto as Addendum A duly filled
in and signed and upon payment in cash or by check of the aggregate Stock
Purchase Price for the number of shares for which this Warrant is being
exercised determined in accordance with the provisions hereof. The Stock
Purchase Price and the number of shares purchasable hereunder are subject to
adjustment as provided in Section 3 of this Warrant.

        This Warrant is subject to the following terms and conditions:

        1.     EXERCISE; ISSUANCE OF CERTIFICATES; PAYMENT FOR SHARES.

               1.1    GENERAL. This Warrant is exercisable at the option of the
holder of record hereof at any time or from time to time on or after March 2,
2001 and up to and including the Expiration Date for all or any part of the
shares of Stock (but not for a fraction of a share) which may be purchased
hereunder. The Company agrees that the shares of Stock purchased under this
Warrant shall be and are deemed to be issued to the Holder hereof as the record
owner of such shares as of the close of business on the date on which this
Warrant shall have been surrendered, properly endorsed, the completed, executed
Form of Subscription delivered and payment made for such shares. Certificates
for the shares of Stock so purchased, together with any other securities or
property to which the Holder hereof is entitled upon such exercise, shall be
delivered to the Holder hereof by the Company at the Company's expense within a
reasonable time after the rights represented by this Warrant have been so
exercised. In case of a purchase of less than all the shares which may be
purchased under this Warrant, the Company shall cancel this Warrant and execute
and deliver a new Warrant or Warrants of like tenor for the balance of


                                       1
<PAGE>   2

the shares purchasable under the Warrant surrendered upon such purchase to the
Holder hereof within a reasonable time. Each stock certificate so delivered
shall be in such denominations of Stock as may be requested by the Holder hereof
and shall be registered in the name of such Holder.

        Notwithstanding anything to the contrary contained in this Section 1,
the Holder shall either (i) exercise this Warrant in full by paying to the
Company, by cash or check, an amount equal to the aggregate Stock Purchase Price
of the shares being purchased, or (ii) convert this Warrant into shares equal to
the value (as determined below) of this Warrant by surrender of this Warrant a
the principal office of the Company together with the Form of Subscription in
which event the Company shall issue to the Holder a number of shares of Common
Stock computed using the following formula:

               X = Y (A-B)
                   -------
                      A

Where:         X = the number of shares of Common Stock to be issued to the
                   Holder
               Y = the number of shares of Common Stock under this Warrant
               A = the fair market value of one share of Common Stock (at the
                   date of such surrender)
               B = the Stock Purchase Price (as adjusted to the date of such
                   surrender)

        As used herein, current fair market value of Common Stock shall mean
with respect to each share of Common Stock the closing price of the Company's
Common Stock as quoted on the Nasdaq Stock Market, or, if on any day the Common
Stock is not so listed, the average of the highest bid and the lowest asked
price on such day in the domestic over-the-counter market as reported by the
National Quotation Bureau, Incorporated, or any similar successor organization,
in each case averaged over a period of 15 trading days consisting of the day as
of which the current fair market value of Common Stock is being determined and
the 14 consecutive trading days prior to such day. If at any time the Common
Stock is not listed on any securities exchange or quoted in the over-the-counter
market, the current fair market value of Common Stock shall be used for the
calculation of A above, and shall be determined in good faith by the Board of
Directors of the Company.

        2.     SHARES TO BE FULLY PAID; RESERVATION OF SHARES. The Company
covenants and agrees that all shares of Stock which may be issued upon the
exercise of the rights represented by this Warrant will, upon issuance, be duly
authorized, validly issued, fully paid and nonassessable and free from all
preemptive rights of any shareholder and free of all taxes, liens and charges
with respect to the issue thereof. The Company further covenants and agrees that
during the period within which the rights represented by this Warrant may be
exercised, the Company will at all times have authorized and reserved, for the
purpose of issue or transfer upon exercise of the subscription rights evidenced
by this Warrant, a sufficient number of shares of authorized but unissued Stock,
or other securities and property, when and as required to provide for the
exercise of the rights represented by this Warrant. The Company will take all
such action as may be necessary to assure that such shares of Stock may be
issued as provided herein without violation of any applicable law or regulation,
or of any requirements of any domestic securities exchange upon which the Stock
may be listed; provided, however, that the Company shall not be required to
effect a registration under Federal or State securities laws with respect to
such exercise. The


                                       2
<PAGE>   3

Company will not take any action which would result in any adjustment of the
Stock Purchase Price (as defined in Section 3 hereof) if the total number of
shares of Stock issuable after such action upon exercise of all outstanding
warrants, together with all shares of Stock then issuable upon exercise of all
options and upon the conversion of all convertible securities then outstanding,
would exceed the total number of shares of Stock then authorized by the
Company's Certificate of Incorporation.

        3.     ADJUSTMENT OF STOCK PURCHASE PRICE AND NUMBER OF SHARES. The
Stock Purchase Price and the number of shares purchasable upon the exercise of
this Warrant shall be subject to adjustment from time to time upon the
occurrence of certain events described in this Section 3. Upon each adjustment
of the Stock Purchase Price, the Holder of this Warrant shall thereafter be
entitled to purchase, at the Stock Purchase Price resulting from such
adjustment, the number of shares obtained by multiplying the Stock Purchase
Price in effect immediately prior to such adjustment by the number of shares
purchasable pursuant hereto immediately prior to such adjustment, and dividing
the product thereof by the Stock Purchase Price resulting from such adjustment.

               3.1    SUBDIVISION OR COMBINATION OF STOCK. In case the Company
shall at any time subdivide its outstanding shares of Stock into a greater
number of shares, the Stock Purchase Price in effect immediately prior to such
subdivision shall be proportionately reduced, and conversely, in case the
outstanding shares of Stock of the Company shall be combined into a smaller
number of shares, the Stock Purchase Price in effect immediately prior to such
combination shall be proportionately increased.

               3.2    DIVIDENDS IN STOCK, OTHER STOCK, PROPERTY,
RECLASSIFICATION. If at any time or from time to time all holders of shares of
the Company's Common Stock (or any shares of stock or other securities at the
time receivable upon the exercise of this Warrant) shall have received or become
entitled to receive, without payment therefor:

                      (A)    Stock or any shares of stock or other securities
which are at any time directly or indirectly convertible into or exchangeable
for Stock, or any rights or options to subscribe for, purchase or otherwise
acquire any of the foregoing by way of dividend or other distribution, or

                      (B)    Stock or additional stock or other securities or
property (including cash) by way of spin-off, split-up, reclassification,
combination of shares or similar corporate rearrangement, (other than shares of
Stock issued as a stock-split, adjustments in respect of which shall be covered
by the terms of Section 3.1 above), then and in each such case, the Holder
hereof shall, upon the exercise of this Warrant, be entitled to receive, in
addition to the number of shares of Stock receivable thereupon, and without
payment of any additional consideration therefor, the amount of stock and other
securities and property which such Holder would hold on the date of such
exercise had he been the holder of record of such Stock as of the date on which
holders of Stock received or became entitled to receive such shares or all other
additional stock and other securities and property.

               3.3    REORGANIZATION, RECLASSIFICATION, CONSOLIDATION, MERGER OR
Sale. If any capital reorganization of the capital stock of the Company, or any
consolidation or merger of the Company with another corporation, or the sale of
all or substantially all of its assets to


                                       3
<PAGE>   4

another corporation shall be effected in such a way that holders of Stock shall
be entitled to receive stock, securities, or other assets or property, then, as
a condition of such reorganization, reclassification, consolidation, merger or
sale, lawful and adequate provisions shall be made whereby the Holder hereof
shall thereafter have the right to purchase and receive (in lieu of the shares
of the Stock of the Company immediately theretofore purchasable and receivable
upon the exercise of the rights represented hereby) such shares of stock,
securities or other assets or property as may be issued or payable with respect
to or in exchange for a number of outstanding shares of such Stock equal to the
number of shares of such stock immediately theretofore purchasable and
receivable upon the exercise of the rights represented hereby. In any
reorganization described above, appropriate provision shall be made with respect
to the rights and interests of the Holder of this Warrant to the end that the
provisions hereof (including, without limitation, provisions for adjustments of
the Stock Purchase Price and of the number of shares purchasable and receivable
upon the exercise of this Warrant) shall thereafter be applicable, as nearly as
may be, in relation to any shares of stock, securities or assets thereafter
deliverable upon the exercise hereof.

               3.4    NOTICE OF ADJUSTMENT. Upon any adjustment of the Stock
Purchase Price or any increase or decrease in the number of shares purchasable
upon the exercise of this Warrant, the Company shall give written notice
thereof, by first class mail, postage prepaid, addressed to the registered
Holder of this Warrant at the address of such Holder as shown on the books of
the Company. The notice shall be signed by the Company's chief financial officer
and shall state the Stock Purchase Price resulting from such adjustment and the
increase or decrease, if any, in the number of shares purchasable at such price
upon the exercise of this Warrant, setting forth in reasonable detail the method
of calculation and the facts upon which such calculation is based.

               3.5    OTHER NOTICES. If at any time:

                      (A)    the Company shall declare any cash dividend upon
its Common Stock;

                      (B)    the Company shall declare any dividend upon its
Common Stock payable in stock or make any special dividend or other distribution
to the holders of its Common Stock;

                      (C)    the Company shall offer for subscription pro rata
to the holders of its Common Stock any additional shares of stock of any class
or other rights;

                      (D)    there shall be any capital reorganization or
reclassification of the capital stock of the Company; or consolidation or merger
of the Company with, or sale of all or substantially all of its assets to,
another corporation; or

                      (E)    there shall be a voluntary or involuntary
dissolution, liquidation or winding-up of the Company;

then, in any one or more of said cases, the Company shall give, by first class
mail, postage prepaid, addressed to the Holder of this Warrant at the address of
such Holder as shown on the books of the Company, (a) at least 20 days' prior
written notice of the date on which the books of


                                       4
<PAGE>   5

the Company shall close or a record shall be taken for such dividend,
distribution or subscription rights or for determining rights to vote in respect
of any such reorganization, reclassification, consolidation, merger, sale,
dissolution, liquidation or winding-up, and (b) in the case of any such
reorganization, reclassification, consolidation, merger, sale, dissolution,
liquidation, winding-up or pro-rata subscription, at least 20 days' prior
written notice of the date when the same shall take place; provided, however,
that the Holder shall make a best efforts attempt to respond to such notice as
early as possible after the receipt thereof. Any notice given in accordance with
the foregoing clause (a) shall also specify, in the case of any such dividend,
distribution or subscription rights, the date on which the holders of Common
Stock shall be entitled thereto. Any notice given in accordance with the
foregoing clause (b) shall also specify the date on which the holders of Stock
shall be entitled to exchange their Stock for securities or other property
deliverable upon such reorganization, reclassification, consolidation, merger,
sale, dissolution, liquidation, winding-up, or conversion, as the case may be.

        4.     ISSUE TAX. The issuance of certificates for shares of Stock upon
the exercise of the Warrant shall be made without charge to the Holder of the
Warrant for any issue tax (other than any applicable income taxes) in respect
thereof; provided, however, that the Company shall not be required to pay any
tax which may be payable in respect of any transfer involved in the issuance and
delivery of any certificate in a name other than that of the then Holder of the
Warrant being exercised.

        5.     CLOSING OF BOOKS. The Company will at no time close its transfer
books against the transfer of any warrant or of any shares of Stock issued or
issuable upon the exercise of any warrant in any manner which interferes with
the timely exercise of this Warrant.

        6.     NO VOTING OR DIVIDEND RIGHTS; LIMITATION OF LIABILITY. Nothing
contained in this Warrant shall be construed as conferring upon the Holder
hereof the right to vote or to consent or to receive notice as a shareholder of
the Company or any other matters or any rights whatsoever as a shareholder of
the Company. No dividends or interest shall be payable or accrued in respect of
this Warrant or the interest represented hereby or the shares purchasable
hereunder until, and only to the extent that, this Warrant shall have been
exercised. No provisions hereof, in the absence of affirmative action by the
Holder to purchase shares of Stock, and no mere enumeration herein of the rights
or privileges of the Holder hereof, shall give rise to any liability of such
Holder for the Stock Purchase Price or as a shareholder of the Company, whether
such liability is asserted by the Company or by its creditors.

        7.     WARRANTS TRANSFERABLE. Subject to compliance with applicable
federal and state securities laws, this Warrant and all rights hereunder are
transferable, in whole, without charge to the Holder hereof (except for transfer
taxes), upon surrender of this Warrant properly endorsed. Each taker and holder
of this Warrant, by taking or holding the same, consents and agrees that this
Warrant, when endorsed in blank, shall be deemed negotiable, and that the Holder
hereof, when this Warrant shall have been so endorsed, may be treated by the
Company, at the Company's option, and all other persons dealing with this
Warrant as the absolute owner hereof for any purpose and as the person entitled
to exercise the rights represented by this Warrant, or to the transfer hereof on
the books of the Company any notice to the contrary notwithstanding; but until
such transfer on such books, the Company may treat the registered owner hereof
as the owner for all purposes.


                                       5
<PAGE>   6

        8.     MODIFICATION AND WAIVER. This Warrant and any provision hereof
may be changed, waived, discharged or terminated only by an instrument in
writing signed by the Company and the Holder.

        9.     NOTICES. Any notice, request or other document required or
permitted to be given or delivered to the Holder hereof or the Company shall be
delivered or shall be sent by certified mail, postage prepaid, to each such
holder at its address as shown on the books of the Company or to the Company at
the address indicated therefor in the first paragraph of this Warrant or such
other address as either may from time to time provide to the other.

        10.    BINDING EFFECT ON SUCCESSORS. This Warrant shall be binding upon
any corporation succeeding the Company by merger, consolidation or acquisition
of all or substantially all of the Company's assets. All of the obligations of
the Company relating to the Stock issuable upon the exercise of this Warrant
shall survive the exercise and termination of this Warrant. All of the covenants
and agreements of the Company shall inure to the benefit of the successors and
assigns of the Holder hereof.

        11.    DESCRIPTIVE HEADINGS AND GOVERNING LAW. The description headings
of the several sections and paragraphs of this Warrant are inserted for
convenience only and do not constitute a part of this Warrant. This Warrant
shall be construed and enforced in accordance with, and the rights of the
parties shall be governed by, the laws of the State of Delaware without regard
to conflict of laws principles.

        12.    LOST WARRANTS. The Company represents and warrants to the Holder
hereof that upon receipt of evidence reasonably satisfactory to the Company of
the loss, theft, destruction, or mutilation of this Warrant and, in the case of
any such loss, theft or destruction, upon receipt of an indemnity reasonably
satisfactory to the Company, or in the case of any such mutilation upon
surrender and cancellation of such Warrant, the Company, at its expense, will
make and deliver a new Warrant, of like tenor, in lieu of the lost, stolen,
destroyed or mutilated Warrant.

        13.    FRACTIONAL SHARES. No fractional shares shall be issued upon
exercise of this Warrant. The Company shall, in lieu of issuing any fractional
share, pay the holder entitled to such fraction a sum in cash equal to such
fraction multiplied by the then effective Stock Purchase Price.

        IN WITNESS WHEREOF, the Company has caused this Warrant to be duly
executed by its officers, thereunto duly authorized as of the 2nd day of March,
2001.

                                        AMYLIN PHARMACEUTICALS, INC.,
                                        a Delaware corporation


                                        By: ___________________________________
                                            Joseph C. Cook, Jr.
                                            Chief Executive Officer and
                                            Chairman of the Board of Directors



                                       6