AMYLIN PHARMACEUTICALS INC
S-3/A, 2000-03-27
PHARMACEUTICAL PREPARATIONS
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     AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MARCH 27, 2000


                                                      REGISTRATION NO. 333-87033
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- --------------------------------------------------------------------------------

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


                                AMENDMENT NO. 3

                                       TO

                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                            ------------------------

                          AMYLIN PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                                 <C>
                     DELAWARE                                           33-0266089
           (STATE OR OTHER JURISDICTION                              (I.R.S. EMPLOYER
         OF INCORPORATION OR ORGANIZATION)                        IDENTIFICATION NUMBER)
</TABLE>

                            9373 TOWNE CENTRE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 552-2200
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

                              JOSEPH C. COOK, JR.
               CHAIRMAN OF THE BOARD AND CHIEF EXECUTIVE OFFICER
                          AMYLIN PHARMACEUTICALS, INC.
                            9373 TOWNE CENTRE DRIVE
                          SAN DIEGO, CALIFORNIA 92121
                                 (858) 552-2200
 (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)

                                   COPIES TO:

                              THOMAS A. COLL, ESQ.
                               COOLEY GODWARD LLP
                        4365 EXECUTIVE DRIVE, SUITE 1100
                              SAN DIEGO, CA 92121
                                 (858) 550-6000

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
   From time to time after the effective date of this Registration Statement.

    If the only securities being registered on this Form are being offered
pursuant to dividend or interest reinvestment plans, please check the following
box.  [ ]

    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box.  [X]

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering.  [ ]

    If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering.  [ ]

    If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box.  [ ]


    THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT THAT SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME EFFECTIVE ON
SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a), MAY
DETERMINE.

- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>   2

          THE INFORMATION IN THIS PROSPECTUS IS NOT COMPLETE AND MAY BE CHANGED.
          WE MAY NOT SELL THESE SECURITIES UNTIL THE REGISTRATION STATEMENT
          FILED WITH THE SECURITIES AND EXCHANGE COMMISSION IS EFFECTIVE. THIS
          PROSPECTUS IS NOT AN OFFER TO SELL THESE SECURITIES AND IT IS NOT
          SOLICITING AN OFFER TO BUY THESE SECURITIES IN ANY STATE WHERE THE
          OFFER OR SALE IS NOT PERMITTED.


                  SUBJECT TO COMPLETION, DATED MARCH 27, 2000


PROSPECTUS

                               16,304,009 SHARES

                          AMYLIN PHARMACEUTICALS, INC.

                                  COMMON STOCK

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


     We are registering our common stock for resale by the security holders
identified in this prospectus.



     For a description of the method of distribution of the resale shares, see
page 17 of this prospectus.



     Our common stock is currently traded on the Nasdaq National Market under
the symbol "AMLN." On March 24, 2000, the last reported sales price for our
common stock was $12.75 per share.


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

         INVESTMENT IN OUR COMMON STOCK INVOLVES A HIGH DEGREE OF RISK.

           SEE "RISK FACTORS" BEGINNING ON PAGE 4 OF THIS PROSPECTUS.


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

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR PASSED UPON THE
ADEQUACY OR ACCURACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.


                 The date of this Prospectus is March   , 2000.

<PAGE>   3


                                  OUR BUSINESS



     The SEC allows us to "incorporate by reference" information that we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
considered to be part of this prospectus, and information that we file later
with the SEC will automatically update and supersede this information. You
should read the following summary together with the more detailed information
regarding our company, our common stock and our financial statements and notes
to those statements appearing elsewhere in this prospectus or incorporated here
by reference.



     We are a research and development pharmaceutical company focused on
metabolic disorders and specializing in the identification and development of
drug candidates.



DRUG DEVELOPMENT PROCESS



     In order to study the safety and effectiveness of our drug candidates we
first evaluate their physical and chemical properties in laboratory tests,
followed by evaluation of their effects in laboratory animals. If these studies
show promise, following procedures established by the FDA, we begin clinical
trials of drug candidates in humans. In Phase 1 clinical trials, a drug
candidate is given to a small number of healthy volunteers or patients. These
Phase 1 studies examine the safety and the size of dose that humans can take
without a high incidence of side effects.



     If the Phase 1 trials do not reveal any major problems, such as
unacceptable toxicity, we can progress to Phase 2 studies. Phase 2 clinical
trials involve giving the drug candidate to patients who have the targeted
condition and typically involve up to several hundred patients. Phase 2 studies
are used to examine safety and the effects of the drug candidate relative to the
disease being treated.



     Phase 3 clinical trials involve larger numbers of patients, typically
several hundred to several thousand patients and typically are of longer
duration than Phase 2 clinical trials. Typically, if the Phase 3 of clinical
trials produce acceptable results, all clinical trial data is examined and
included in a new drug application submitted to FDA. If the FDA approves a new
drug application, the new medicine becomes available for physicians to
prescribe.



OUR DRUG CANDIDATES



     SYMLIN. We are developing SYMLIN(TM)(pramlintide acetate) for the treatment
of people with type 1 diabetes and people with type 2 diabetes who use insulin.
SYMLIN is a synthetic analog of the human hormone amylin. We have also completed
over 30 Phase 1 and Phase 2 studies of SYMLIN involving over 1,400 participants,
including people with either type 1 diabetes or type 2 diabetes who use insulin.
We have also reported the results of six Phase 3 studies of SYMLIN (two in type
1 diabetes in the US, two in type 2 diabetes in the US, one each in type 1 and
type 2 diabetes in Europe/Canada) in which neither the participants nor the
investigators knew who received SYMLIN or placebo, and several studies in which
it was known that all participants received SYMLIN. To date, over 3,500
participants have received SYMLIN in our clinical trials. We plan to submit a
new drug application for SYMLIN in mid-2000.



     AC2993. We are currently evaluating AC2993 (synthetic exendin-4) in Phase 2
clinical trials for the treatment of people with type 2 diabetes. To date, over
100 people have received AC2993 in our Phase 1 and Phase 2 clinical studies.



     AC3056. We are currently evaluating AC3056 in preclinical laboratory and
animal studies for potential utility in the treatment of metabolic disorders
relating to cardiovascular disease in order to support the initiation of
clinical trials in humans. We are planning to submit an investigational new


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drug application to the FDA in the first half of 2000 which, if accepted, would
allow us to begin Phase 1 clinical trials.



CORPORATE INFORMATION


     We were incorporated in Delaware in September 1987. Our executive offices
are currently located at 9373 Towne Centre Drive, San Diego, California 92121,
and our telephone number is (858) 552-2200.

     SYMLIN is our trademark. All other brand names or trademarks appearing in
this prospectus are the property of their respective holders.

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<PAGE>   5

                                  RISK FACTORS

     Except for the historical information contained or incorporated by
reference, this prospectus (and the information incorporated by reference)
contains forward-looking statements that involve risks and uncertainties. Our
actual results could differ materially from those discussed here or incorporated
by reference. Factors that could cause or contribute to differences in our
actual results include those discussed in the following section, as well as
those discussed elsewhere in this prospectus and in any other documents
incorporated by reference into this prospectus.

     Investment in Amylin shares involves a high degree of risk. You should
consider the following discussion of risks as well as other information in this
prospectus before purchasing any Amylin shares. Each of these risk factors could
adversely affect our business, operating results and financial condition, as
well as adversely affect the value of an investment in our common stock.

RESULTS FROM OUR CLINICAL TRIALS MAY NOT BE SUFFICIENT TO OBTAIN REGULATORY
CLEARANCE TO MARKET SYMLIN OR AC2993 IN THE UNITED STATES OR ABROAD ON A TIMELY
BASIS, OR AT ALL.

     Our drug candidates are subject to extensive government regulations related
to development, clinical trials, manufacturing and commercialization. The
process of obtaining FDA and other regulatory approvals is costly, time
consuming, uncertain and subject to unanticipated delays. The FDA may refuse to
approve an application for approval of a drug candidate if it believes that
applicable regulatory criteria are not satisfied. The FDA may also require
additional testing for safety and efficacy. Moreover, if the FDA grants
regulatory approval of a product, the approval may be limited to specific
indications or limited with respect to its distribution. Foreign regulatory
authorities may apply similar limitations or may refuse to grant any approval.


     The data collected from our clinical trials may not be sufficient to
support approval of SYMLIN or AC2993 by the FDA or any foreign regulatory
authorities. With respect to SYMLIN, the results of our first four Phase 3
clinical studies were not sufficient, standing alone, to support an application
with the FDA for marketing approval. In some of these first four studies, the
statistical requirements agreed in advance with the FDA were not met. However,
the results of the final two Phase 3 clinical studies for SYMLIN that were
reported in August and November 1999 achieved the statistical requirements that
we agreed with the FDA to meet, which, because of additional information
gathered from our prior studies, were slightly different from the requirements
in the four prior studies. We believe that the results of our entire SYMLIN
clinical trial program, including the two most recently completed Phase 3
clinical studies of SYMLIN, should support regulatory approval of SYMLIN.
However, it is possible that the FDA or other regulatory authorities may deem
our SYMLIN clinical trial results insufficient to meet regulatory requirements
for marketing approval or may limit approval for only selected uses.
Manufacturing facilities operated by the third party manufacturers with whom we
contract to manufacture SYMLIN may not pass an FDA preapproval inspection for
SYMLIN. Any failure or delay in obtaining these approvals could prohibit or
delay us from marketing SYMLIN. Consequently, even if we believe that
preclinical and clinical data are sufficient to support regulatory approval for
SYMLIN, the FDA and foreign regulatory authorities may not ultimately approve
SYMLIN for commercial sale in any jurisdiction. If SYMLIN does not meet
applicable regulatory requirements for approval, we may not have the financial
resources to continue research and development of SYMLIN or any of our other
product candidates and we may not be able to generate revenues from the
commercial sale of any of our products.


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<PAGE>   6

DELAYS IN THE CONDUCT OR COMPLETION OF OUR CLINICAL TRIALS OR THE ANALYSIS OF
THE DATA FROM OUR CLINICAL TRIALS MAY RESULT IN DELAYS IN OUR PLANNED FILINGS
FOR REGULATORY APPROVALS, OR ADVERSELY AFFECT OUR ABILITY TO ENTER INTO NEW
COLLABORATIVE ARRANGEMENTS.


     We cannot predict whether we will encounter problems with any of our
completed or ongoing clinical studies that will cause us or regulatory
authorities to delay or suspend our ongoing clinical studies or delay the
analysis of data from our completed or ongoing clinical studies. If the results
of our ongoing and planned clinical studies for AC2993 are not available when we
expect or if we encounter any delay in the analysis of our clinical studies for
SYMLIN or AC2993:



     - we may delay the submission of our applications for regulatory approval
       of SYMLIN with regulatory authorities in North America and Europe;


     - we may not have the financial resources to continue research and
       development of any of our product candidates; and

     - we may not be able to enter into collaborative arrangements relating to
       any product subject to delay in regulatory filing.

     Any of the following reasons could delay the completion of our ongoing and
future clinical studies:

     - delays in enrolling volunteers;

     - lower than anticipated retention rate of volunteers in a trial; or


     - serious side effects experienced by study participants relating to the
       product candidate.


EVEN IF WE OBTAIN INITIAL REGULATORY APPROVAL FOR OUR PRODUCTS, IF WE FAIL TO
COMPLY WITH EXTENSIVE CONTINUING REGULATIONS ENFORCED BY DOMESTIC AND FOREIGN
REGULATORY AUTHORITIES, IT COULD HARM OUR ABILITY TO GENERATE REVENUES AND THE
MARKET PRICE OF OUR STOCK COULD FALL.


     Even if we are able to obtain United States regulatory approval for SYMLIN,
the approval will be subject to continual review, and newly discovered or
developed safety issues may result in revocation of the marketing approval.
Moreover, if and when we obtain marketing approval for SYMLIN, the marketing of
the product will be subject to extensive regulatory requirements administered by
the FDA and other regulatory bodies, including adverse event reporting
requirements and the FDA's general prohibition against promoting products for
unapproved uses. The SYMLIN manufacturing facilities are also subject to
continual review and periodic inspection and approval of manufacturing
modifications. Domestic manufacturing facilities are subject to biennial
inspections by the FDA and must comply with the FDA's Good Manufacturing
Practices regulations. In complying with these regulations, manufacturers must
spend funds, time and effort in the areas of production, record keeping,
personnel and quality control to ensure full technical compliance. The FDA
stringently applies regulatory standards for manufacturing. Failure to comply
with any of these postapproval requirements can, among other things, result in
warning letters, product seizures, recalls, fines, injunctions, suspensions or
revocations of marketing licenses, operating restrictions and criminal
prosecutions. Any of these enforcement actions or any unanticipated changes in
existing regulatory requirements or the adoption of new requirements could
adversely affect our ability to market products and generate revenues and thus
adversely affect our ability to continue as a going concern and cause our stock
price to fall.



     The manufacturers of SYMLIN also are subject to numerous federal, state and
local laws relating to such matters as safe working conditions, manufacturing
practices, environmental protection, fire hazard control and hazardous substance
disposal. In the future, our manufacturers may incur significant costs to comply
with those laws and regulations which could increase our manufacturing costs and
reduce our ability to operate profitably.


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<PAGE>   7

EXISTING PRICING REGULATIONS AND REIMBURSEMENT LIMITATIONS MAY REDUCE OUR
POTENTIAL PROFITS FROM THE SALE OF OUR PRODUCTS.

     The requirements governing product licensing, pricing and reimbursement
vary widely from country to country. Some countries require approval of the sale
price of a drug before it can be marketed. In many countries, the pricing review
period begins after product licensing approval is granted. As a result, we or
our partners may obtain regulatory approval for a product in a particular
country, but then be subject to price regulations that reduce our profits from
the sale of the product. Also, in some foreign markets pricing of prescription
pharmaceuticals is subject to continuing government control even after initial
marketing approval.

     Our ability to commercialize our products successfully also will depend in
part on the extent to which reimbursement for the cost of our products and
related treatments will be available from government health administration
authorities, private health insurers and other organizations. Third-party payors
are increasingly challenging the prices charged for medical products and
services. If we succeed in bringing SYMLIN and/or AC2993 to the market, we
cannot assure you that either product will be considered cost effective and that
reimbursement will be available or will be sufficient to allow us to sell SYMLIN
and/or AC2993 on a competitive basis.

WE WILL REQUIRE FUTURE CAPITAL AND ARE UNCERTAIN OF THE AVAILABILITY OR TERMS OF
ADDITIONAL FUNDING. IF FUNDING BECOMES UNAVAILABLE, IS INADEQUATE, OR IS NOT
AVAILABLE ON ACCEPTABLE TERMS, IT MAY ADVERSELY AFFECT THE VALUE OF YOUR SHARES.

     We must continue to find sources of capital in order to complete the
development and commercialization of SYMLIN and AC2993. Our future capital
requirements will depend on many factors, including:


     - the time and costs involved in obtaining regulatory approvals;


     - the costs of manufacturing SYMLIN and AC2993;


     - our ability to establish one or more marketing, distribution or other
       commercialization arrangements for SYMLIN and AC2993;



     - progress with our preclinical studies and clinical studies;


     - scientific progress in our other research programs and the magnitude of
       these programs;

     - the costs involved in preparing, filing, prosecuting, maintaining, and
       enforcing patents or defending ourselves against competing technological
       and market developments; and

     - the potential need to repay outstanding indebtedness.


     You should be aware that in the future:



     - we may not obtain additional financial resources when necessary or on
       terms favorable to us, if at all;


     - any available additional financing may not be adequate; and


     - we may be required to use financing to repay existing indebtedness to our
       current or future creditors, including Johnson & Johnson.



     As of December 31, 1999, the total principal and interest due to Johnson &
Johnson was approximately $50.6 million, which is secured by our issued patents
and patent applications relating to amylin, including several that relate to
SYMLIN. In the event we require additional capital and we are unable to obtain
additional financing on acceptable terms, we would not have the financial
resources to continue research and development of SYMLIN, AC2993 or any of our
other product


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<PAGE>   8

candidates and we would curtail or cease our operations, which would adversely
affect the value of your shares.

WE HAVE A HISTORY OF OPERATING LOSSES, ANTICIPATE FUTURE LOSSES, MAY NOT
GENERATE REVENUES FROM PRODUCT SALES AND MAY NEVER BECOME PROFITABLE.


     We have experienced significant operating losses since our inception in
1987. As of December 31, 1999, we had an accumulated deficit of approximately
$292 million. We expect to incur significant additional operating losses over
the next several years. We have derived substantially all of our revenues to
date from development funding, fees and milestone payments under collaborative
agreements and from interest income. To date, we have not received any revenues
from product sales. To achieve profitable operations, we, alone or with others,
must successfully develop, manufacture, obtain required regulatory approvals and
market our products. We may not ever become profitable. If we become profitable,
we may not remain profitable.



WE HAVE NOT PREVIOUSLY SOLD, MARKETED OR DISTRIBUTED A PRODUCT, AND OUR ABILITY
TO ENTER INTO THIRD PARTY RELATIONSHIPS IS IMPORTANT TO OUR SUCCESSFUL
DEVELOPMENT AND COMMERCIALIZATION OF PRODUCTS AND POTENTIAL PROFITABILITY.



     We have not previously sold, marketed or distributed a product. To market
any of our products, we must obtain access to marketing and sales forces with
technical expertise and with supporting distribution capability. We believe that
we may need to enter into marketing and distribution arrangements for SYMLIN
and/or AC2993 or find a corporate partner who can provide support for
commercialization of SYMLIN and/or AC2993. We may not be able to enter into
marketing and distribution arrangements for SYMLIN or AC2993 or find a corporate
partner for these drug candidates. If we do not, or are not able to, enter into
a marketing or distribution arrangement or find a corporate partner who can
provide support for commercialization of SYMLIN and/or AC2993, we may perform
some marketing and distribution activities for these potential drug products. We
may not be able to successfully perform these marketing or distribution
activities. Moreover, any new marketer or distributor or corporate partner for
SYMLIN or AC2993 may not establish adequate sales and distribution capabilities
or gain market acceptance for products, if any.


OUR COMMERCIALIZATION PLANS FOR SYMLIN AND AC2993 ARE DEPENDENT ON THE
PERFORMANCE OF, AND OUR RELATIONSHIPS WITH, THIRD PARTIES THAT PROVIDE US WITH
PRODUCT DEVELOPMENT, CLINICAL AND REGULATORY SUPPLIES AND SERVICES.


     We depend to a significant degree on third parties to perform the majority
of product development, clinical and regulatory functions for our product
candidates. In particular, we rely to a significant degree on third parties for
the preparation of our planned regulatory submission for SYMLIN. While we
believe that business relations between us and our third-party suppliers and
service providers have been good, we cannot predict whether third-party
suppliers and service providers will continue to cooperate with us in the
performance of our most important services or functions. Any difficulties or
interruptions of service with our third-party product development, clinical and
regulatory suppliers and service providers could disrupt the development of our
product candidates, the completion of our clinical trials, the manufacture of
our products and delay our filing for regulatory approval of SYMLIN.


WE DO NOT MANUFACTURE OUR OWN PRODUCTS AND MAY NOT BE ABLE TO OBTAIN ADEQUATE
SUPPLIES, WHICH COULD CAUSE DELAYS OR REDUCE PROFIT MARGINS.

     The manufacturing of sufficient quantities of new drugs is a time consuming
and complex process. We currently have no facilities for the manufacture of
clinical study or commercial supplies of SYMLIN or AC2993. We currently rely on
third parties to manufacture SYMLIN and AC2993.

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<PAGE>   9


We work with three contract suppliers who have the capabilities for the
commercial manufacture of SYMLIN. We, alone or together with a new corporate
partner, may not be able to make the transition to commercial production. While
we believe that our business relations between us and our contract manufacturers
are good, we cannot predict whether these manufacturers will meet our
requirements for quality, quantity or timeliness for the manufacture of SYMLIN
or AC2993. Therefore, we may not be able to obtain supplies of products on
acceptable terms or in sufficient quantities, if at all. Our dependence on third
parties for the manufacture of products may also reduce our profit margins and
ability to develop and deliver products with sufficient speed.


     If any of our existing manufacturers cease to manufacture SYMLIN, we may
need to locate and engage another manufacturer. The cost and time to establish
manufacturing facilities to produce SYMLIN would be substantial. As a result,
using a new manufacturer could delay bringing SYMLIN to market, disrupt our
ability to supply SYMLIN or reduce our profit margins. Any delay or disruption
in the manufacturing of SYMLIN could require us to raise additional funds.


OUR OTHER RESEARCH AND DEVELOPMENT PROGRAMS MAY NOT RESULT IN ADDITIONAL DRUG
CANDIDATES, WHICH COULD REQUIRE THAT WE RAISE ADDITIONAL FUNDS.



     Any additional product candidates will require significant research,
development, preclinical and clinical testing, regulatory approval and
commitments of resources before commercialization. We cannot predict whether our
research will lead to the discovery of any additional product candidates that
could generate revenues for us. If we do not develop additional drug candidates,
or if our discovery efforts are delayed, we may have to raise additional funds
to continue our business.



IF WE ARE UNABLE TO OBTAIN NEW PATENTS BASED ON CURRENT PATENT APPLICATIONS OR
FOR FUTURE INVENTIONS, WE MAY NOT BE ABLE TO PREVENT OTHERS FROM USING OUR
INTELLECTUAL PROPERTY.



     We own or hold exclusive rights to 28 issued United States patents and
approximately 30 pending United States patent applications. Of these issued
patents and patent applications, we have a total of 11 issued U.S. patents and
nine pending applications that we believe are relevant to the development and
commercialization of SYMLIN and one issued US patent and 12 pending applications
that we believe are relevant to the development and commercialization of AC2993.
We also own or hold exclusive rights to various foreign patent applications that
correspond to issued United States patents or pending United States patent
applications.



     Our success will depend in part on our ability to obtain patent protection
for our products and technologies both in the United States and other countries.
We cannot guarantee that any patents will issue from any pending or future
patent applications owned by or licensed to us. Our rights under any issued
patents may not provide us with sufficient protection against competitive
products or otherwise cover commercially valuable products or processes. For
instance, a third party may successfully circumvent our patents. In addition,
because patent applications in the United States are maintained in secrecy until
patents issue and publication of discoveries in the scientific or patent
literature often lag behind actual discoveries, we cannot be sure that the
inventors of subject matter covered by our patents and patent applications were
the first to invent or the first to file patent applications for these
inventions. In the event that a third party has also filed a patent for any of
its inventions, we may have to participate in interference proceedings declared
by the US Patent and Trademark Office to determine priority of invention, which
could result in substantial cost to us, even if the eventual outcome is
favorable to us. Furthermore, we may not have identified all United States and
foreign patents that pose a risk of infringement.


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LITIGATION REGARDING PATENTS AND OTHER PROPRIETARY RIGHTS MAY BE EXPENSIVE,
CAUSE DELAYS IN BRINGING PRODUCTS TO MARKET AND HARM OUR ABILITY TO OPERATE.



     Our success will depend in part on our ability to operate without
infringing the proprietary rights of third parties. Legal standards relating to
the validity of patents covering pharmaceutical and biotechnological inventions
and the scope of claims made under these patents are still developing. As a
result, the enforceability of patents is uncertain and involves complex legal
and factual questions. Third parties may challenge or infringe upon existing or
future patents. In the event that a third party challenges a patent, a court may
invalidate the patent or determine that the patent is not enforceable.
Proceedings involving our patents or patent applications or those of others
could result in adverse decisions about:



     - the patentability of our inventions and products relating to our drug
       candidates; and/or



     - the enforceability, validity or scope of protection offered by our
       patents relating to our drug candidates.



     The manufacture, use or sale of our drug candidates may infringe on the
patent rights of others. If we are unable to avoid infringement of the patent
rights of others, we may be required to seek a license, defend an infringement
action or challenge the validity of the patents in court. Patent litigation is
costly and time consuming. We may not have sufficient resources to bring these
actions to a successful conclusion. In addition, if we do not obtain a license,
develop or obtain non-infringing technology, and fail successfully to defend an
infringement action or to have infringing patents declared invalid, we may:


     - incur substantial money damages;


     - encounter significant delays in bringing our drug candidates to market;
       and/or



     - be precluded from participating in the manufacture, use or sale of our
       drug candidates or methods of treatment requiring licenses.


CONFIDENTIALITY AGREEMENTS WITH EMPLOYEES AND OTHERS MAY NOT ADEQUATELY PREVENT
DISCLOSURE OF TRADE SECRETS AND OTHER PROPRIETARY INFORMATION.

     In order to protect our proprietary technology and processes, we also rely
in part on confidentiality agreements with our corporate partners, employees,
consultants, outside scientific collaborators and sponsored researchers and
other advisors. These agreements may not effectively prevent disclosure of
confidential information and may not provide an adequate remedy in the event of
unauthorized disclosure of confidential information. In addition, others may
independently discover trade secrets and proprietary information. Costly and
time-consuming litigation could be necessary to enforce and determine the scope
of our proprietary rights, and failure to obtain or maintain trade secret
protection could adversely affect our competitive business position.

COMPETITION IN THE BIOTECHNOLOGY AND PHARMACEUTICAL INDUSTRIES MAY RESULT IN
COMPETING PRODUCTS, SUPERIOR MARKETING OF OTHER PRODUCTS AND LOWER REVENUES OR
PROFITS FOR US.

     We believe that competition may be intense for all of our product
candidates. Our competitors include multinational pharmaceutical and chemical
companies, specialized biotechnology firms and universities and other research
institutions. A number of our competitors are pursuing the development of novel
pharmaceuticals which target the same diseases that we are targeting, and we
expect that the number of companies seeking to develop products and therapies
for the treatment of diabetes and other metabolic disorders will increase. Many
of our competitors have substantially greater financial, technical and human
resources than we do. In addition, many of these competitors have significantly
greater experience than we do in undertaking preclinical testing and human
clinical studies of new pharmaceutical products and in obtaining regulatory
approvals of human therapeutic

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<PAGE>   11


products. Accordingly, our competitors may succeed in obtaining FDA approval for
products more rapidly than we do and provide those competitors with an advantage
for the marketing of products with similar potential uses. Furthermore, if we
are permitted to commence commercial sales of products, we may also be competing
with respect to manufacturing efficiency and marketing capabilities, areas in
which we have limited or no experience.


     Our target patient population for SYMLIN is people with diabetes whose
therapy includes multiple insulin injections daily. AC2993 is currently being
studied for the treatment of type 2 diabetes. Other products are currently in
development or exist in the market that may compete directly with the products
that we are seeking to develop and market. Various products are available to
treat type 2 diabetes, including:


<TABLE>
  <S>                           <C>
  - sulfonylureas               - meglitinides
  - metformin                   - alpha-glucosidase inhibitors
  - insulin                     - thiozolidinediones
</TABLE>


     In addition, several companies are developing various approaches to improve
treatments for type 1 and type 2 diabetes. We cannot predict whether our
products, even if successfully tested and developed, will have sufficient
advantages over existing products to cause health care professionals to adopt
them over other products or that our products will offer an economically
feasible alternative to existing products.


WE MAY NOT BE ABLE TO KEEP UP WITH THE RAPID TECHNOLOGICAL CHANGE IN THE
BIOTECHNOLOGY AND PHARMACEUTICAL INDUSTRIES, WHICH COULD MAKE OUR PRODUCTS
OBSOLETE AND REDUCE OUR REVENUES.



     Biotechnology and related pharmaceutical technologies have undergone and
continue to be subject to rapid and significant change. Our future will depend
in large part on our ability to maintain a competitive position with respect to
these technologies. Any compounds, products or processes that we develop may
become obsolete before we recover expenses incurred in developing those products
which may require that we raise additional funds to continue our operations.


OUR FUTURE SUCCESS DEPENDS ON OUR ABILITY TO RETAIN OUR CHIEF EXECUTIVE OFFICER
AND OUR SENIOR VICE PRESIDENT OF CLINICAL AFFAIRS AND TO ATTRACT, RETAIN AND
MOTIVATE QUALIFIED PERSONNEL.

     We are highly dependent on Joseph C. Cook, Jr., our Chief Executive
Officer, and Orville G. Kolterman, M.D., our Senior Vice President of Clinical
Affairs, and the other principal members of our scientific and management staff,
the loss of whose services might impede the achievement of our research and
development objectives. Recruiting and retaining qualified scientific personnel
to perform research and development work in the future will also be critical to
our success. Although we believe we will be successful in attracting and
retaining skilled and experienced scientific personnel, we may not be able to
attract and retain these personnel on acceptable terms given the competition
between numerous pharmaceutical and biotechnology companies, universities and
other research institutions for experienced scientists and management personnel.
We do not maintain "key person" insurance on any of our employees. In addition,
we rely on consultants and advisors, including scientific and clinical advisors,
to assist us in formulating research and development strategy. Our consultants
and advisors may be employed by employers other than us and may have commitments
to or consulting or advisory contracts with other entities that may limit their
availability to us.

OUR BUSINESS HAS A SUBSTANTIAL RISK OF PRODUCT LIABILITY CLAIMS, AND INSURANCE
MAY BE EXPENSIVE OR UNAVAILABLE.

     Our business exposes us to potential product liability risks that are
inherent in the testing, manufacturing and marketing of human therapeutic
products. Product liability claims could result in a recall of products or a
change in the indications for which they may be used. Although we currently

                                       10
<PAGE>   12

have product liability insurance, we cannot assure you that insurance will
provide adequate coverage against potential liabilities. Furthermore, product
liability insurance is becoming increasingly expensive. As a result, we may not
be able to maintain current amounts of insurance coverage, obtain additional
insurance or obtain insurance at a reasonable cost or in sufficient amounts to
protect against losses that could have a material adverse effect on us.

OUR ACTIVITIES INVOLVE THE USE OF HAZARDOUS MATERIALS, WHICH SUBJECT US TO
REGULATION, RELATED COSTS AND DELAYS AND POTENTIAL LIABILITIES.

     Our research and development involves the controlled use of hazardous
materials, chemicals and various radioactive compounds. Although we believe that
our safety procedures for handling and disposing of those materials comply with
the standards prescribed by state and federal regulations, the risk of
accidental contamination or injury from these materials cannot be eliminated. If
an accident occurs, we could be held liable for resulting damages, which could
be substantial. We are also subject to numerous environmental, health and
workplace safety laws and regulations, including those governing laboratory
procedures, exposure to blood-borne pathogens and the handling of biohazardous
materials. Additional federal, state and local laws and regulations affecting
our operations may be adopted in the future. We may incur substantial costs to
comply with and substantial fines or penalties if we violate any of these laws
or regulations.

PROVISIONS IN AMYLIN'S CORPORATE CHARTER AND BYLAWS MAY DISCOURAGE TAKE-OVER
ATTEMPTS AND THUS DEPRESS THE MARKET PRICE OF OUR STOCK.

     Provisions in Amylin's certificate of incorporation, as amended, may have
the effect of delaying or preventing a change of control or changes in its
management. These provisions include:

     - the right of the board of directors to elect a director to fill a vacancy
       created by the expansion of the board of directors; and

     - the ability of the board of directors to issue, without stockholder
       approval, up to 7,375,000 shares of preferred stock with terms set by the
       board of directors.

     Each of these provisions could discourage potential take-over attempts and
could adversely affect the market price of our common stock.

SUBSTANTIAL FUTURE SALES OF OUR COMMON STOCK BY EXISTING STOCKHOLDERS OR BY US
COULD CAUSE OUR STOCK PRICE TO FALL.


     Sales by existing stockholders of a large number of shares of our common
stock in the public market after this offering or the perception that additional
sales could occur could cause the market price of our common stock to drop. As
of March 1, 2000, we had approximately 62.5 million shares of common stock
outstanding, of which approximately 37.9 million are freely tradeable,
approximately 12.6 million may be sold in accordance with Rule 144 and
approximately 12.0 million are currently restricted but may be sold in the
future in accordance with registration statements covering these shares.
Likewise, additional equity financings or other share issuances by us, including
shares issued in connection with strategic alliances, could adversely affect the
market price of our common stock.


SIGNIFICANT VOLATILITY IN THE MARKET PRICE FOR OUR COMMON STOCK COULD EXPOSE US
TO LITIGATION RISK.

     The market prices for securities of biopharmaceutical and biotechnology
companies, including our common stock, have historically been highly volatile,
and the market from time to time has experienced significant price and volume
fluctuations that are unrelated to the operating performance of these
biopharmaceutical and biotechnology companies. Given the uncertainty of our
future funding and our planned filing for regulatory approval of SYMLIN, we
expect that we may continue to

                                       11
<PAGE>   13

experience volatility of our stock price throughout 2000. In addition, the
following factors may have a significant effect on the market price of our
common stock:

     - announcements of additional clinical study results;


     - announcements of determinations by regulatory authorities with respect to
       our drug candidates;



     - developments in our relationships with current or future collaborative
       partners;


     - fluctuations in our operating results;

     - public concern as to the safety of drugs developed by us;

     - technological innovations or new commercial therapeutic products by us or
       our competitors;

     - developments in patent or other proprietary rights;

     - governmental policy or regulation; and

     - general market conditions.

     Broad market and industry factors may materially adversely affect the
market price of our common stock, regardless of our actual operating
performance. In the past, following periods of volatility in the market price of
a company's securities, securities class-action litigation has often been
instituted against those companies. This type of litigation, if instituted,
could result in substantial costs and a diversion of management's attention and
resources, which would materially adversely affect our business, financial
condition and results of operations.

                                       12
<PAGE>   14


                      WHERE YOU CAN FIND MORE INFORMATION



     THIS PROSPECTUS IS PART OF A REGISTRATION STATEMENT WE FILED WITH THE
SECURITIES AND EXCHANGE COMMISSION. YOU SHOULD RELY ONLY ON THE INFORMATION
CONTAINED IN OR INCORPORATED BY REFERENCE IN THIS PROSPECTUS. WE HAVE NOT
AUTHORIZED ANYONE ELSE TO PROVIDE YOU WITH DIFFERENT INFORMATION. WE ARE NOT
MAKING AN OFFER OF THESE SECURITIES IN ANY STATE WHERE THE OFFER IS NOT
PERMITTED. YOU SHOULD NOT ASSUME THAT THE INFORMATION IN THIS PROSPECTUS IS
ACCURATE AS OF ANY DATE OTHER THAN THE DATE PROVIDED ON THE FRONT PAGE OF THIS
PROSPECTUS, REGARDLESS OF THE TIME OF DELIVERY OF THIS PROSPECTUS OR ANY SALE OF
COMMON STOCK.


     We file annual, quarterly and special reports, proxy statements and other
information with the SEC. You may read and copy the documents we file at the
SEC's public reference rooms in Washington, D.C., New York, New York and
Chicago, Illinois. You can request copies of these documents by writing to the
SEC and paying a fee for the copying cost. Please call the SEC at 1-800-SEC-0330
for further information on the public reference rooms. Our SEC filings are also
available to the public at no cost from the SEC's website at http://www.sec.gov.

     We incorporate by reference the documents listed below, except as
superseded or modified by this registration statement, and any future filings we
will make with the SEC under Sections 13(a), 13(c), 14 or 15(d) of the
Securities and Exchange Act of 1934:


     1. Annual report on Form 10-K for the fiscal year ended December 31, 1999;
and



     2. Notice of Annual Meeting and Proxy Statement for annual meeting of
stockholders held on May 24, 1999.


     You may request a copy of these filings at no cost, by writing or
telephoning us at the following address:

       Investor Relations
        Amylin Pharmaceuticals, Inc.
        9373 Towne Centre Drive
        San Diego, California 92121
        Telephone: (858) 552-2200

                                       13
<PAGE>   15

                DISCLOSURE REGARDING FORWARD-LOOKING STATEMENTS

     This prospectus, including the documents that we incorporate by reference,
contains forward-looking statements within the meaning of Section 27A of the
Securities Act and Section 21E of the Exchange Act. Any statements about our
expectations, beliefs, plans, objectives, assumptions or future events or
performance are not historical facts and may be forward-looking. These
statements are often, but not always, made through the use of words or phrases
like "anticipate," "estimate," "plans," "projects," "continuing," "ongoing,"
"expects," "management believes," "the Company believes," "the Company intends,"
"we believe," "we intend" and similar words or phrases. Accordingly, these
statements involve estimates, assumptions and uncertainties which could cause
actual results to differ materially from those expressed in them. Any
forward-looking statements are qualified in their entirety by reference to the
factors discussed throughout this prospectus. Among the key factors that could
cause actual results to differ materially from the forward-looking statements:

     - scientific and technological uncertainties regarding our product
       candidates;

     - risks and uncertainties regarding the adequacy of our clinical trial
       processes and whether the results of those clinical trials will be
       adequate to support regulatory filings and/or approvals;


     - risks associated with timing of filing for regulatory approval of SYMLIN,
       and if regulatory approval is received, time to market thereafter;



     - our ability to raise additional needed capital or consummate strategic or
       corporate partner transactions on favorable terms or at all; and


     - dependence on third party service providers and manufacturers of our
       products.


     Because the risk factors referred to above, as well as the risk factors
beginning on page 4 of this prospectus, could cause actual results or outcomes
to differ materially from those expressed in any forward-looking statements made
by us or on our behalf, you should not place undue reliance on any of those
forward-looking statements. Further, any forward-looking statement speaks only
as of the date on which it is made, and we undertake no obligation to update any
forward-looking statement to reflect events or circumstances after the date on
which the statement is made or to reflect the occurrence of unanticipated
events. New factors emerge from time to time, and it is not possible for us to
predict which factors will arise. In addition, we cannot assess the impact of
each factor on our business or the extent to which any factor, or combination of
factors, may cause actual results to differ materially from those contained in
any forward-looking statements.


                                       14
<PAGE>   16

                                SECURITY HOLDERS

     We are registering for resale certain shares of Amylin common stock held by
the security holders identified below. The following table sets forth:

     - the name of the security holders,

     - the number and percent of shares of Amylin common stock that the security
       holders beneficially owned prior to the offering for resale of any of the
       shares of Amylin common stock being registered by this registration
       statement,

     - the number of shares of Amylin common stock that may be offered for
       resale for the account of the security holders pursuant to this
       prospectus, and

     - the number and percent of shares of Amylin common stock to be held by the
       security holders after the offering of the resale shares (assuming all of
       the resale shares are sold by the security holders).


     Messrs. Bryson, Cook, Greene and Rumsfeld and Ms. Graham are members of our
board of directors and Mr. Cook is also our Chief Executive Officer.


     This table is prepared based on information supplied to us by the listed
security holders, schedules 13G and Forms 3 and 4, and other public documents
filed with the SEC, and assumes the sale of all of the resale shares. The
applicable percentages of ownership are based on an aggregate of 53,913,246
shares of Amylin common stock issued and outstanding on December 20, 1999,
adjusted as required by rules promulgated by the SEC.


<TABLE>
<CAPTION>
                                         SHARES BENEFICIALLY                  SHARES BENEFICIALLY
                                                OWNED             NUMBER             OWNED
                                          PRIOR TO OFFERING      OF SHARES       AFTER OFFERING
                                        ----------------------     BEING     ----------------------
           SECURITY HOLDERS              NUMBER      PERCENT      OFFERED     NUMBER      PERCENT
           ----------------             ---------   ----------   ---------   ---------   ----------
<S>                                     <C>         <C>          <C>         <C>         <C>
Allen Andersson(1)....................  9,320,459      17.3%     7,605,559   1,714,900      3.2%
Susan Riecken(2)......................  9,320,459      17.3%     7,605,559   1,714,900      3.2%
Funds Managed by Domain Associates,
  LLC(3)..............................  5,910,207      11.0%     5,237,605     672,602      1.3%
Charles A. Dunn Jr. and Sharon G.
  Dunn, Co-Trustees UTD 5/5/81........    209,866         *        209,866           0        *
Vaughn D. Bryson(4)...................     52,013         *         42,013      10,000        *
Donald H. Rumsfeld(5).................    116,277         *        104,027      12,250        *
Rumsfeld Family Trust.................    103,926         *        108,926           0        *
VMN Associates........................    103,926         *        108,926           0        *
Funds Managed by Kingsbury Associates,
  L.P.(6).............................  1,459,401       2.7%     1,459,401           0        *
The Greene Family Trust(7)............  2,164,843       4.0%       415,806   1,749,037      3.2%
Joseph C. Cook, Jr.(8)................  1,514,925       2.8%       311,880   1,203,045      2.2%
Ginger L. Graham(9)...................     88,755         *         40,000      48,755        *
Funds Managed by Deerfield
  Partners(10)........................  1,600,000       3.0%       600,000   1,000,000      1.9%
Jeffrey R. Swarz(11)..................     21,750         *          5,000      16,750        *
Terry C. Vance(12)....................     36,750         *         15,000      21,750        *
Ronald M. Nordmann....................     20,000         *         20,000           0        *
Peter M. Hecht........................     20,000         *         20,000           0        *
1149336 Ontario, Inc.(13).............     15,000         *         10,000       5,000        *
</TABLE>


                                       15
<PAGE>   17

- -------------------------
  *  less than 1%

 (1) This amount includes 2,602,729 shares held by Susan Riecken, Mr.
     Andersson's spouse.

 (2) This amount includes 6,717,730 shares held by Allen Andersson, Ms.
     Riecken's spouse.

 (3) Includes 5,115,046 shares held by Domain Partners IV, L.P., 122,559 shares
     held by DP IV Associates, L.P., 653,847 shares held by Domain Partners II,
     L.P., and 18,755 shares which Mr. James C. Blair has the right to acquire
     within 60 days after the date of this table pursuant to outstanding
     options. Mr. Blair is a member of the Board of Directors of Amylin and also
     is a general partner of One Palmer Square Associates II, L.P., and a
     managing member of One Palmer Square Associates IV, LLC. One Palmer Square
     Associates II, L.P. is the general partner of Domain Partners II, L.P. One
     Palmer Square Associates IV, LLC is the general partner of Domain Partners
     IV, L.P. and DP IV Associates, L.P.


 (4) Includes 10,000 shares held by the Vaughn D. Bryson Irrevocable Trust, U-A
     1/14/99. Mr. Bryson is a director of Amylin.



 (5) Includes 6,250 shares which Mr. Rumsfeld has the right to acquire within 60
     days after the date of this table pursuant to outstanding options. Also
     includes 5,000 shares held by a partnership of which Mr. Rumsfeld is a
     general partner. Mr. Rumsfeld disclaims beneficial ownership of those
     shares except to the extent of his pecuniary interest in the partnership.



 (6) Includes 1,369,401 shares held of record by Kingsbury Capital Partners,
     L.P. III, 70,000 shares held of record by Kingsbury Capital Partners, L.P.
     II and 10,000 shares held of record by the Timothy J. and Cynthia K.
     Wollaeger Trust. Mr. Timothy J. Wollaeger is a general partner of Kingsbury
     Associates, L.P., the general partner of Kingsbury Capital Partners, L.P.
     III and Kingsbury Capital Partners, L.P. II. Mr. Wollaeger is also a
     trustee of the Timothy J. and Cynthia K. Wollaeger Trust.



 (7) This amount includes 75,769 shares held by The Greene Children's Trust, of
     which Howard E. Greene, Jr. is trustee, and 8,755 shares which Mr. Greene
     has the right to acquire within 60 days after the date of this table
     pursuant to outstanding options. Mr. Greene is the trustee of The Greene
     Family Trust.



 (8) Includes 130,752 shares held of record by Farview Management Co., L.P. and
     181,128 shares held of record by Judith E. and Joseph C. Cook, Jr. Also
     includes 40,000 and 749,246 shares which Farview Management Co., L.P. and
     Mr. Cook, respectively, have the right to acquire within 60 days after the
     date of this table pursuant to outstanding options. Mr. Cook is a partner
     of Farview Management, Co., L.P.



(9) Includes 48,755 shares which Ms. Graham has the right to acquire within 60
    days after the date of this table pursuant to outstanding options.



(10) Includes 1,184,000 shares held of record by Deerfield Partners, L.P. and
     416,000 shares held of record by Deerfield International Limited.



(11) Includes 16,750 shares which Mr. Swarz has the right to acquire within 60
     days after the date of this table pursuant to outstanding options.



(12) Includes 16,750 shares which Mr. Vance has the right to acquire within 60
     days after the date of this table pursuant to outstanding options.



(13) Includes 5,000 shares which an executive officer of 1149336 Ontario, Inc.
     has the right to acquire within 60 days after the date of this table
     pursuant to outstanding options. All of the 10,000 shares being offered for
     resale are issuable upon the exercise of an outstanding warrant to purchase
     10,000 shares of common stock.


                                       16
<PAGE>   18

                              PLAN OF DISTRIBUTION

     The resale shares may be sold from time to time by the security holders in
one or more transactions at:

     - fixed prices,

     - market prices at the time of sale,

     - varying prices determined at the time of sale, or

     - negotiated prices.

The security holders may offer their resale shares in one or more of the
following transactions:


     - on any national securities exchange or quotation service on which the
       Amylin common stock may be listed or quoted at the time of sale,
       including the Nasdaq National Market;


     - in the over-the-counter market;

     - in private transactions;

     - through options;

     - by pledge to secure debts or other obligations; or

     - a combination of any of the above transactions.

     The security holders may effect these transactions by selling to or through
one or more broker-dealers, and broker-dealers involved in these transactions
may receive compensation in the form of underwriting discounts, concessions or
commissions from the security holders. The security holders and any
broker-dealers that participate in the distribution may, under certain
circumstances, be deemed to be "underwriters" within the meaning of the
Securities Act, and any commissions received by those broker-dealers and any
profits realized on any resale of the resale shares by them might be deemed to
be underwriting discounts and commissions under the Securities Act.

     Under applicable rules and regulations under the Exchange Act, any person
engaged in the distribution of the resale shares may not simultaneously engage
in market making activities with respect to Amylin's common stock for a period
of two business days prior to the commencement of the distribution. In addition
and without limiting the foregoing, the security holders and any other person
participating in a distribution will be subject to applicable provisions of the
Exchange Act and the rules and regulations thereunder, including without
limitation, Regulation M under the Exchange Act, which may limit the timing of
purchases and sales of shares of Amylin common stock by the security holders or
any other person.

     We will make copies of this prospectus available to the security holders
and have informed the security holders of the need for delivery of a copy of
this prospectus to each purchaser of the resale shares prior to or at the time
of any sale of the resale shares.

     The security holders will pay all underwriting discounts, commissions,
transfer taxes and other expenses associated with the sale of the resale shares
by them. We will pay all costs and expenses associated with the registration of
the resale shares. We estimate that our expenses in connection with this
offering will be approximately $113,485.

                                       17
<PAGE>   19

                                USE OF PROCEEDS

     We will not receive any of the proceeds from the sale of any of the resale
shares by the security holders. All proceeds from the sale of the resale shares
will be for the accounts of the security holders.

                                 LEGAL MATTERS

     Cooley Godward LLP, San Diego, California will pass upon the validity of
the issuance of the common stock offered by this prospectus.

                                    EXPERTS


     The consolidated financial statements of Amylin Pharmaceuticals, Inc. at
December 31, 1999 and 1998, and for each of the three years in the period ended
December 31, 1999, incorporated by reference in this prospectus and registration
statement have been audited by Ernst & Young LLP, independent auditors, as set
forth in their report incorporated by reference here in, and are incorporated by
reference in reliance upon that report given on the authority of Ernst & Young
LLP as experts in accounting and auditing.


                                       18
<PAGE>   20

                                    PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

     The following table sets forth all expenses payable by the Registrant in
connection with the sale of the common stock being registered. All the amounts
shown are estimates except for the registration fee.

<TABLE>
<S>                                                           <C>
SEC Registration Fee........................................  $ 23,485
Legal fees and expenses.....................................  $ 75,000
Transfer Agent's Fees.......................................  $  5,000
Accounting fees and expenses................................  $ 10,000
                                                              --------
  Total.....................................................  $113,485
                                                              ========
</TABLE>

ITEM 15. INDEMNIFICATION OF OFFICERS AND DIRECTORS.

     Under Section 145 of the Delaware General Corporation Law, the Registrant
has broad powers to indemnify its directors and officers against liabilities
they may incur in such capacities, including liabilities under the Securities
Act of 1933, as amended (the "Securities Act").

     The Registrants Certificate of Incorporation and By-laws include provisions
to (i) eliminate the personal liability of its directors for monetary damages
resulting from breaches of their fiduciary duty to the extent permitted by
Section 102(b)(7) of the General Corporation Law of Delaware (the "Delaware
Law") and (ii) require the Registrant to indemnify its Directors and officers to
the fullest extent permitted by Section 145 of the Delaware Law, including
circumstances in which indemnification is otherwise discretionary. Pursuant to
Section 145 of the Delaware Law, a corporation generally has the power to
indemnify its present and former directors, officers, employees and agents
against expenses incurred by them in connection with any suit to which they are
or are threatened to be made, a party by reason of their serving in such
positions so long as they acted in good faith and in a manner they reasonably
believed to be in or not opposed to, the best interests of the corporation and
with respect to any criminal action, they had no reasonable cause to believe
their conduct was unlawful. The Registrant believes that these provisions are
necessary to attract and retain qualified persons as directors and officers.
These provisions do not eliminate the directors' duty of care, and, in
appropriate circumstances, equitable remedies such as injunctive or other forms
of non-monetary relief will remain available under Delaware Law. In addition,
each director will continue to be subject to liability for breach of the
director's duty of loyalty to the Registrant, for acts or omissions not in good
faith or involving intentional misconduct, for knowing violations of law, for
acts or omissions that the director believes to be contrary to the best
interests of the Registrant or its stockholders, for any transaction from which
the director derived an improper personal benefit, for acts or omissions
involving a reckless disregard for the director's duty to the Registrant or its
stockholders when the director was aware or should have been aware of a risk of
serious injury to the Registrant or its stockholders, for acts or omissions that
constitute an unexcused pattern of inattention that amounts to an abdication of
the director's duty to the Registrant or its stockholders, for improper
transactions between the director and the Registrant and for improper
distributions to stockholders and loans to directors and officers. The provision
also does not affect a director's responsibilities under any other law, such as
the federal securities law or state or federal environmental laws.

     The Registrant has entered into indemnity agreements with each of its
directors and executive officers that require the Registrant to indemnify such
persons against expenses, judgments, fines, settlements and other amounts
incurred (including expenses of a derivative action) in connection with any
proceeding, whether actual or threatened, to which any such person may be made a
party by

                                      II-1
<PAGE>   21

reason of the fact that such person is or was a director or an executive officer
of the Registrant or any of its affiliated enterprises, such person acted in
good faith and in a manner such person reasonably believed to be in or not
opposed to the best interests of the Registrant and, with respect to any
criminal proceeding, had no reasonable cause to believe his conduct was
unlawful. The indemnification agreements also set forth certain procedures that
will apply in the event of a claim for indemnification thereunder.

     At present, there is no pending litigation or proceeding involving a
director or officer of the Registrant as to which indemnification is being
sought nor is the Registrant aware of any threatened litigation that may result
in claims for indemnification by any officer or director.

     The Registrant has an insurance policy covering the officers and directors
of the Registrant with respect to certain liabilities, including liabilities
arising under the Securities Act or otherwise.

ITEM 16. EXHIBITS

(a) Exhibits.


<TABLE>
<CAPTION>
    EXHIBIT
    NUMBER                       DESCRIPTION OF DOCUMENT
    -------                      -----------------------
    <C>        <S>
       3.1     Registrant's Amended and Restated Certificate of
               Incorporation.(1)
       3.2     Registrant's Amended and Restated Bylaws.(1)
       3.3     Registrant's Certificate of Amendment of Amended and
               Restated Certificate of Incorporation.(2)
       3.4     Certificate of Designation of the 5% Series A Convertible
               Preferred Stock of the Registrant.(3)
       3.5     Amendment to Registrant's Amended and Restated Bylaws.(4)
       4.1     Reference is made to Exhibits 3.1-3.5.
       4.2     Form of Stock Purchase Agreement dated March 22, 1999
               between the Registrant and purchasers of the Registrant's 5%
               Series A Convertible Preferred Stock.(3)
       4.3*    Form of Stock Purchase Agreement dated October 6, 1999
               between the Registrant and purchasers of the Registrant's
               Common Stock.
       4.4*    Warrant Agreement dated December 8, 1999 issued by the
               Registrant to 1149336 Ontario, Inc.
       5.1*    Opinion of Cooley Godward LLP.
      23.1     Consent of Ernst & Young LLP, Independent Auditors.
      23.3     Consent of Cooley Godward LLP. Reference is made to Exhibit
               5.1.
</TABLE>


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

 *  Previously filed.


(1) Filed as an exhibit to Registrant's Registration Statement on Form S-1 (No.
    333-44195) or amendments thereto and incorporated herein by reference.

(2) Filed as an exhibit to Registrant's Registration Statement on Form S-3 (No.
    333-58831) or amendments thereto, and incorporated herein by reference.

(3) Filed as an exhibit to Registrant's Annual Report on form 10-K for the
    fiscal year ended December 31, 1998.

(4) Filed as an exhibit to Registrant's Quarterly Report on Form 10-Q for the
    quarter ended September 30, 1999.

ITEM 17. UNDERTAKINGS.

     Insofar as indemnification for liabilities arising under the Securities Act
of 1933 may be permitted to directors, officers, and controlling persons of the
Registrant pursuant to the provisions

                                      II-2
<PAGE>   22

described in Item 15 or otherwise, the Registrant has been advised that in the
opinion of the SEC, such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
Registrant of expenses incurred or paid by a director, officer, or controlling
person of the Registrant in the successful defense of any action, suit, or
proceeding) is asserted by such director, officer, or controlling person in
connection with the securities being registered, the Registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Act and will
be governed by the final adjudication of such issue.

     The undersigned Registrant hereby undertakes:

          (1) to file, during any period in which offers or sales are being
     made, a post-effective amendment to this registration statement:

             (i) to include any prospectus required by section 10(a)(3) of the
        Securities Act of 1933;

             (ii) to reflect in the prospectus any facts or events arising after
        the effective date of the registration statement (or the most recent
        post-effective amendment thereof) which, individually or in the
        aggregate, represent a fundamental change in the information set forth
        in the registration statement;

             (iii) to include any material information with respect to the plan
        of distribution not previously disclosed in the registration statement
        or any material change to such information in the registration
        statement;

     provided, however, that clauses (i) and (ii) do not apply if the
     information required to be included in a post-effective amendment by these
     clauses is contained in periodic reports filed by the Registrant pursuant
     to section 13 or section 15(d) of the Securities Exchange Act of 1934 that
     are incorporated by reference in the registration statement;

          (2) that, for the purpose of determining any liability under the
     Securities Act, each such post-effective amendment that contains a form of
     prospectus shall be deemed to be a new registration statement relating to
     the securities offered therein, and the offering of such securities at that
     time shall be deemed to be the initial bona fide offering thereof;

          (3) to remove from registration by means of a post-effective amendment
     any of the securities being registered which remain unsold at the
     termination of the offering; and

          (4) that, for purposes of determining any liability under the
     Securities Act of 1933, each filing of the Registrant's annual report
     pursuant to section 13(a) or section 15(d) of the Securities Exchange Act
     of 1934 (and, where applicable, each filing of an employee benefit plan's
     annual report pursuant to Section 15(d) of the Securities Exchange Act of
     1934) that is incorporated by reference in the registration statement shall
     be deemed to be a new registration statement relating to the securities
     offered therein, and the offering of such securities at that time shall be
     deemed to be the initial bona fide offering thereof.

                                      II-3
<PAGE>   23

                                   SIGNATURES


     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on the 27th day of
March 2000.


                                          AMYLIN PHARMACEUTICALS, INC.

                                          By:      /s/ JOSEPH C. COOK
                                            ------------------------------------
                                                    Joseph C. Cook, Jr.
                                              Chairman of the Board and Chief
                                                     Executive Officer

     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.


<TABLE>
<CAPTION>
                      SIGNATURE                                    TITLE                   DATE
                      ---------                                    -----                   ----
<C>                                                    <S>                            <C>
                 /s/ JOSEPH C. COOK                    Chairman of the Board and      March 27, 2000
- -----------------------------------------------------  Chief Executive Officer
                 Joseph C. Cook, Jr.

                 /s/ JAMES C. BLAIR*                   Director                       March 27, 2000
- -----------------------------------------------------
                   James C. Blair

                                                       Director                       March   , 2000
- -----------------------------------------------------
                  Vaughn D. Bryson

                /s/ JAMES C. GAITHER*                  Director                       March 27, 2000
- -----------------------------------------------------
                  James C. Gaither

                /s/ GINGER L. GRAHAM*                  Director                       March 27, 2000
- -----------------------------------------------------
                  Ginger L. Graham

             /s/ HOWARD E. GREENE, JR.*                Director                       March 27, 2000
- -----------------------------------------------------
                Howard E. Greene, Jr.

               /s/ VAUGHN M. KAILIAN*                  Director                       March 27, 2000
- -----------------------------------------------------
                  Vaughn M. Kailian

                                                       Director                       March   , 2000
- -----------------------------------------------------
                 Donald H. Rumsfeld

                                                       Director                       March   , 2000
- -----------------------------------------------------
                 Jay S. Skyler, M.D.

                /s/ MARTIN R. BROWN*                   Senior Vice President of       March 27, 2000
- -----------------------------------------------------  Operations (Principal
                   Martin R. Brown                     Accounting Officer)

*By: /s/ JOSEPH C. COOK, JR.
- -----------------------------------------------------
     Joseph C. Cook, Jr.
     Attorney-in-Fact
</TABLE>


                                      II-4
<PAGE>   24

                               INDEX TO EXHIBITS


<TABLE>
<CAPTION>
EXHIBIT
NUMBER                       DESCRIPTION OF DOCUMENT
- -------                      -----------------------
<C>        <S>
 3.1       Registrant's Amended and Restated Certificate of
           Incorporation.(1)
 3.2       Registrant's Amended and Restated Bylaws.(1)
 3.3       Registrant's Certificate of Amendment of Amended and
           Restated Certificate of Incorporation.(2)
 3.4       Certificate of Designation of the 5% Series A Convertible
           Preferred Stock of the Registrant.(3)
 3.5       Amendment to Registrant's Amended and Restated Bylaws.(4)
 4.1       Reference is made to Exhibits 3.1-3.5.
 4.2       Form of Stock Purchase Agreement dated March 23, 1999
           between the Registrant and purchasers of the Registrant's 5%
           Series A Convertible Preferred Stock.(3)
 4.3*      Form of Stock Purchase Agreement dated October 6, 1999
           between the Registrant and purchasers of the Registrant's
           Common Stock.
 4.4*      Warrant Agreement dated December 8, 1999 issued by the
           Registrant to 1149336 Ontario, Inc.
 5.1*      Opinion of Cooley Godward LLP.
23.1       Consent of Ernst & Young LLP, Independent Auditors.
23.3       Consent of Cooley Godward LLP. Reference is made to Exhibit
           5.1.
</TABLE>


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

 *  Previously filed.


(1) Filed as an exhibit to Registrant's Registration Statement on Form S-1 (No.
    333-44195) or amendments thereto, and incorporated herein by reference.

(2) Filed as an exhibit to Registrant's Registration Statement on Form S-3 (No.
    333-58831) or amendments thereto, and incorporated herein by reference.

(3) Filed as an exhibit to Registrant's Annual Report on Form 10-K for the
    fiscal year ended December 31, 1998.

(4) Filed as an exhibit to Registrant's Quarterly Report on Form 10-Q for the
    quarter ended September 30, 1999.

<PAGE>   1

                                                                    EXHIBIT 23.1

               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS

We consent to the reference to our firm under the caption "Experts" in the
registration Statement (Form S-3 No. 333-87033) and related Prospectus for
Amylin Pharmaceuticals, Inc. for the registration of 16,304,009 shares of its
common stock and to the incorporation by reference therein of our report dated
February 22, 2000, with respect to the consolidated financial statements and
schedules of Amylin Pharmaceuticals, Inc. included in its Annual Report (Form
10-K) for the year ended December 31, 1999, filed with the Securities and
Exchange Commission.

                                                               Ernst & Young LLP

San Diego, California
March 24, 2000


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