SHAMAN PHARMACEUTICALS INC
S-3/A, 1997-01-14
PHARMACEUTICAL PREPARATIONS
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<PAGE>
    AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON JANUARY 14, 1997
 
                                                      REGISTRATION NO. 333-18815
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
 
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------
                               AMENDMENT NO. 1/A
                                       TO
                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                            ------------------------
                          SHAMAN PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)
 
<TABLE>
<S>                          <C>                        <C>
         DELAWARE                      2834                  94-3095806
      (State or other            (Primary Standard        (I.R.S. Employer
      jurisdiction of        Industrial Classification     Identification
     incorporation or              Code Number)               Number)
       organization)
</TABLE>
 
                             213 EAST GRAND AVENUE
                     SOUTH SAN FRANCISCO, CALIFORNIA 94080
                                 (415) 952-7070
         (Address, including zip code, and telephone number, including
          area code, of the Registrant's principal executive offices)
                            ------------------------
                                 LISA A. CONTE
                     PRESIDENT AND CHIEF EXECUTIVE OFFICER
                          SHAMAN PHARMACEUTICALS, INC.
                             213 EAST GRAND AVENUE
                     SOUTH SAN FRANCISCO, CALIFORNIA 94080
                                 (415) 952-7070
  (Name and address, including zip code, and telephone number, including area
                          code, of agent for service)
                            ------------------------
                                   COPIES TO:
 
<TABLE>
<S>                                 <C>
    J. STEPHAN DOLEZALEK, ESQ.            J. CASEY MCGLYNN, ESQ.
 BROBECK, PHLEGER & HARRISON LLP    WILSON, SONSINI, GOODRICH & ROSATI
      TWO EMBARCADERO PLACE              PROFESSIONAL CORPORATION
          2200 GENG ROAD                    650 PAGE MILL ROAD
   PALO ALTO, CALIFORNIA 94301         PALO ALTO, CALIFORNIA 94304
          (415) 424-0160                      (415) 493-9300
</TABLE>
 
                            ------------------------
        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
  AS SOON AS PRACTICABLE AFTER THIS REGISTRATION STATEMENT BECOMES EFFECTIVE.
    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 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. / /
    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. / /
 
                        CALCULATION OF REGISTRATION FEE
 
<TABLE>
<CAPTION>
                                                                        PROPOSED MAXIMUM    PROPOSED MAXIMUM
             TITLE OF EACH CLASS OF                   AMOUNT TO BE       OFFERING PRICE        AGGREGATE           AMOUNT OF
           SECURITIES TO BE REGISTERED                 REGISTERED        PER SHARE (1)     OFFERING PRICE(1)    REGISTRATION FEE
<S>                                                <C>                 <C>                 <C>                 <C>
Common Stock, $0.001 par value per share.........   2,000,000 shares         $6.125           $12,250,000            $3,713
</TABLE>
 
(1) The price of $6.125 per share, which was the average of the high and low bid
    prices of the Common Stock reported by The Nasdaq Stock Market on December
    18, 1996, is set forth solely for the purpose of calculating the
    registration fee in accordance with Rule 457(c) of the Securities Act of
    1933, as amended.
 
    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 WHICH SPECIFICALLY STATES THAT THE REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(A) OF
THE SECURITIES ACT OF 1933 OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME
EFFECTIVE ON SUCH DATE AS THE COMMISSION ACTING PURSUANT TO SAID SECTION 8(A)
MAY DETERMINE.
 
- --------------------------------------------------------------------------------
- --------------------------------------------------------------------------------
<PAGE>
                                    PART II
 
                     INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 14.  OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION
 
    The following table sets forth the various expenses expected to be incurred
by the Registrant in connection with the sale and distribution of the securities
being registered hereby, other than the Placement Agent fees and expenses. All
amounts are estimated except the Securities and Exchange Commission registration
fee and the National Association of Securities Dealers, Inc. filing fee.
 
<TABLE>
<S>                                                                 <C>
SEC registration fee..............................................  $   3,713
NNM listing fees..................................................     17,500
NASD filing fee...................................................      *
Blue Sky fees and expenses........................................      *
Accounting fees and expenses......................................     70,000
Legal fees and expenses...........................................    100,000
Printing and engraving expenses...................................      2,500
Miscellaneous fees and expenses...................................     86,287
                                                                    ---------
    Total.........................................................  $ 280,000
                                                                    ---------
                                                                    ---------
</TABLE>
 
- ------------------------
 
*   To be filed by amendment
 
ITEM 15.  INDEMNIFICATION OF DIRECTORS AND OFFICERS
 
    Section 145 of the Delaware General Corporation Law, as amended (the
"DGCL"), provides that a corporation may indemnify any person who was or is a
party or is threatened to be made a party to any threatened, pending or
completed action, suit or proceeding, whether civil, criminal or investigative
(other than an action by or in the right of the corporation) by reason of the
fact that he is or was a director, officer, employee or agent of the
corporation, or is or was serving at the request of the corporation as a
director, officer, employee or agent of another corporation, partnership, joint
venture, trust or other enterprise, against expenses (including attorneys'
fees), judgments, fines and amounts paid in settlement actually and reasonably
incurred by him in connection with such action, suit or proceeding, if he acted
in good faith and in a manner he reasonably believed to be in or not opposed to
the best interests of the corporation, and, with respect to any criminal action
or proceeding, had no reasonable cause to believe his conduct was unlawful.
Section 145 further provides that a corporation similarly may indemnify any such
person serving in any such capacity who was or is a party or is threatened to be
made a party to any threatened, pending or completed action or suit by or in the
right of the corporation to procure a judgment in its favor, against expenses
actually and reasonably incurred in connection with the defense or settlement of
such action or suit if he acted in good faith and in a manner he reasonably
believed to be in or not opposed to the best interests of the corporation and
except that no indemnification shall be made in respect of any claim, issue or
matter as to which such person shall have been adjudged to be liable to the
corporation unless and only to the extent that the Delaware Court of Chancery or
such other court in which such action or suit was brought shall determine upon
application that, despite the adjudication of liability but in view of all the
circumstances of the case, such person is fairly and reasonably entitled to
indemnity for such expenses which the Court of Chancery or such other court
shall deem proper.
 
    Section 102(b)(7) of the DGCL permits a corporation to include in its
certificate of incorporation a provision eliminating or limiting the personal
liability of a director to the corporation or its stockholders for monetary
damages for breach of fiduciary duty as a director, provided that such provision
shall not eliminate or limit the liability of a director (i) for any breach of
the director's duty of loyalty to the corporation or its stockholders, (ii) for
acts or omissions not in good faith or which involve intentional misconduct or a
knowing violation of law, (iii) under Section 174 of the DGCL (relating to
unlawful payment of dividends and unlawful stock purchase and redemption) or
(iv) for any transaction from which the director derived an improper personal
benefit.
 
                                      II-1
<PAGE>
    The Registrant's Restated Certificate of Incorporation provides that the
Registrant's directors shall not be liable to the Registrant or its stockholders
for monetary damages for breach of fiduciary duty as a director, except to the
extent that exculpation from liabilities is not permitted under the DGCL as in
effect at the time such liability is determined. The Registrant has entered into
indemnification agreements with all of its officers and directors, as permitted
by the DGCL.
 
ITEM 16.  EXHIBITS AND FINANCIAL STATEMENT SCHEDULES.
 
    The exhibits listed in the Exhibit Index as filed as part of this
Registration Statement.
 
    (a)  Exhibits
 
<TABLE>
<CAPTION>
  EXHIBIT
   NUMBER      DESCRIPTION
- ------------   --------------------------------------------------
<S>            <C>
 1.1**         Form of Placement Agency Agreement.
 
 1.2**         Form of Escrow Agreement.
 
 1.3**         Form of Stock Purchase Agreement.
 
 3.1(5)        Restated Certificate of Incorporation, as filed
                 with the Delaware Secretary of State on October
                 1, 1993.
 
 3.2(8)        Amended and Restated By-Laws, as amended May 23,
                 1996.
 
 4.1(8)        Certificate of Designation of Preferences of
                 Series A Preferred Stock of the Registrant, as
                 filed with the Delaware Secretary of State on
                 July 27, 1996.
 
 5.1**         Opinion of Brobeck, Phleger & Harrison LLP.
 
10.1(1)(12)    1990 Stock Option Plan, as amended.
 
10.2(1)(12)    1992 Stock Option Plan.
 
10.3(1)(12)    401(k) Plan.
 
10.4(1)(12)    Form of Stock Purchase Agreement.
 
10.5(1)(12)    Form of Stock Option Agreement.
 
10.6(1)        Form of Confidentiality Agreement-Employees &
                 Consultants.
 
10.7(1)        Form of Confidentiality Agreement-Strategic
                 Planning.
 
10.8(1)        Form of Indemnification Agreement.
 
10.9(1)(12)    Form of Employment Agreement.
 
10.10(1)       Form of Agreement with Scientific Strategy Team
                 Members.
 
10.11(1)       Form of Proprietary Information and Inventions
                 Agreement-Employees.
 
10.12(1)       Form of Proprietary Information and Inventions
                 Agreement-Consultants.
 
10.13(1)       Letter Agreements dated December 8, 1989, May 30,
                 1990, June 21, 1990, August 24, 1990 and July
                 22, 1991, between Shaman and National Institute
                 of Allergy and Infectious Diseases.
 
10.14(1)(10)   License Agreement dated February 8, 1990, between
                 Shaman and Dr. Michael Tempesta.
 
10.15(1)(12)   Stock Purchase Agreement dated June 15, 1990,
                 between Shaman and Lisa A. Conte.
 
10.16(1)       Master Equipment Lease Agreement dated September
                 28, 1990, between Shaman and MMC/GATX
                 Partnership No. I, with related schedules.
 
10.17(1)       Series B Preferred Stock Warrants dated September
                 28, 1990 and June 28, 1991, issued to MMC/GATX
                 Partnership No. I.
</TABLE>
 
                                      II-2
<PAGE>
<TABLE>
<CAPTION>
  EXHIBIT
   NUMBER      DESCRIPTION
- ------------   --------------------------------------------------
<S>            <C>
10.18(1)(10)   License Agreement dated December 5, 1990, as
                 amended January 19, 1992, between Shaman and the
                 University of British Columbia.
 
10.19(1)       Master Equipment Lease Agreement dated December
                 26, 1990, between Shaman and Lease Management
                 Services, Inc.
 
10.20(1)       Master Equipment Lease Agreement dated April 22,
                 1991, between Shaman and Industrial Way I
                 Limited Partnership.
 
10.21(1)(10)   Contract Services Agreement dated May 23, 1991,
                 February 1, 1992, February 4, 1992, September
                 23, 1992 and October 30, 1992, between Shaman
                 and New Drug Services, Inc.
 
10.22(1)(10)   License Agreement dated September 25, 1991,
                 between Shaman and Inverni della Beffa SpA.
 
10.23(1)(10)   Manufacturing Agreement dated September 25, 1991
                 between Shaman and Indena SpA.
 
10.24(1)(10)   Master Clinical Trial Agreement dated September
                 30, 1991 between Shaman and International Drug
                 Registration, Inc.
 
10.25(1)       Series D Preferred Stock Warrant dated February 3,
                 1992, issued to MMC/GATX Partnership No. I.
 
10.26(1)(10)   Supply Agreement dated June 1, 1992.
 
10.27(1)(10)   Supply Agreement dated June 1, 1992.
 
10.28(2)       Screening Agreement dated August 31, 1992, as
                 amended June 2, 1993, between Shaman and Merck
                 Research Laboratories.
 
10.29(1)(10)   Agreement dated October 16, 1992, between Shaman
                 and International Medical Technical Consultants,
                 Inc.
 
10.30(4)(10)   Research Agreement dated October 21, 1992, as
                 amended April 27, 1994, between Shaman and Eli
                 Lilly and Company.
 
10.31(1)       Registration Rights Agreement dated October 22,
                 1992, as amended December 14, 1992, between
                 Shaman and certain holders of preferred stock of
                 Shaman.
 
10.32(1)       Industrial Lease Agreement dated January 1, 1993,
                 between Shaman and Grand/Roebling Investment
                 Company.
 
10.33(1)       Three Party Agreement dated as of January 1, 1993,
                 by and among Berlex Laboratories, Inc., Shaman
                 and Grand/Roebling Investment Company.
 
10.34(2)(10)   Letter Agreement dated March 1, 1993, between
                 Shaman and Lederle-Praxis Biologicals, Division
                 of American Cynamide Corporation.
 
10.35(3)       Contract Service Agreements dated May 10, 1993,
                 between Shaman and
                 R.C. Benson & Sons, Inc.
 
10.36(3)(10)   Clinical Trial Agreement dated July 21, 1993,
                 between Shaman and the University of Rochester.
 
10.37(3)(10)   Letter Agreement dated August 24, 1993, between
                 Shaman and University of Michigan.
 
10.38(3)(10)   Laboratory Services Agreement dated September 1,
                 1993, between Shaman and Hazelton Washington,
                 Inc.
 
10.39(3)       Loan and Security Agreement dated September 27,
                 1993, between Shaman and Household Commercial of
                 California.
 
10.40(3)       Master Equipment Lease Agreement dated September
                 30, 1993, between Shaman and MMC/GATX
                 Partnership No. I, with related schedules.
</TABLE>
 
                                      II-3
<PAGE>
<TABLE>
<CAPTION>
  EXHIBIT
   NUMBER      DESCRIPTION
- ------------   --------------------------------------------------
<S>            <C>
10.41(3)       Common Stock Warrant dated September 30, 1993,
                 issued to MMC/GATX Partnership No. I.
 
10.42(3)       Common Stock Warrant dated October 5, 1993, issued
                 to Meier Mitchell & Co.
 
10.43(5)(10)   Joint Research and Product Development Agreement,
                 dated May 24, 1995, by and between Ono
                 Pharmaceutical Co., Ltd. and Registrant.
 
10.43(a)(9)    Amendment Agreement, dated December 4, 1996, to
                 the Joint Research and Product Development
                 Agreement by and between Ono Pharmaceutical Co.,
                 Ltd. and Registrant.
 
10.44(5)(10)   License Agreement, dated June 8, 1995, by and
                 between Bayer AG and Registrant.
 
10.45(6)(11)   Development Agreement, dated January 11, 1996, by
                 and between Abbott Laboratories and Registrant.
 
10.46(6)       Loan Agreement, dated October 20, 1995, by and
                 between The Daiwa Bank, Limited and Registrant.
 
10.47(6)       Assignment and Assumption, dated February 2, 1996,
                 between The Daiwa Bank, Limited and The Sumitomo
                 Bank, Limited.
 
10.48(7)       Letter dated March 29, 1996 from The Sumitomo
                 Bank, Limited to the Registrant amending the
                 Loan Agreement dated October 20, 1995.
 
10.49(8)(11)   Subscription Agreement dated July 25, 1996 by and
                 between the Registrant and Fletcher
                 International Limited.
 
10.50(9)(11)   Joint Research and Product Development and
                 Commercialization Agreement dated September 23,
                 1996, by and between Lipha, Lyonnaise
                 Industrielle Pharmaceutique s.a. and the
                 Registrant.
 
10.51(9)(11)   Stock Purchase Agreement dated September 23, 1996,
                 by and between Lipha, Lyonnaise Industrielle
                 Pharmaceutique s.a. and the Registrant.
 
23.1*          Consent of Ernst & Young LLP, Independent
                 Auditors.
 
23.2**         Consent of Brobeck, Phleger & Harrison LLP
                 (included in the opinion filed as
                 Exhibit 5.1).
 
24.1**         Power of Attorney (included in Part II of this
                 Registration Statement under the caption
                 "Signatures").
</TABLE>
 
- ------------------------
 
*   Filed herewith.
 
**  Previously filed.
 
(1) Incorporated by reference to exhibits filed with the Registrant's
    Registration Statement on Form S-1, File No. 33-55892 which was declared
    effective January 26, 1993.
 
(2) Incorporated by reference to exhibits filed with the Registrant's Quarterly
    Report on Form 10-Q for the quarter ended March 31, 1993.
 
(3) Incorporated by reference to exhibits filed on November 10, 1993 with
    Registrant's Registration Statement on Form S-1, File No. 33-71506.
 
(4) Incorporated by reference to exhibits filed with Registrant's Quarterly
    Report on Form 10-Q for the quarter ended March 31, 1994.
 
(5) Incorporated by reference to exhibits filed with Registrant's Quarterly
    Report on Form 10-Q for the quarter ended June 30, 1995, as amended.
 
                                      II-4
<PAGE>
(6) Incorporated by reference to exhibits filed with Registrant's Annual Report
    on Form 10-K for the year ended December 31, 1995.
 
(7) Incorporated by reference to exhibits filed with Registrant's Quarterly
    Report on Form 10-Q for the quarter ended March 31, 1996.
 
(8) Incorporated by reference to exhibits filed with Registrant's Quarterly
    Report on Form 10-Q for the quarter ended June 30, 1996, as amended.
 
(9) Incorporated by reference to exhibits filed with Registrant's Quarterly
    Report on Form 10-Q for the quarter ended September 30, 1996, as amended.
 
(10) Confidential treatment has been granted with respect to certain portions of
    these agreements.
 
(11) Confidential treatment pursuant to Rule 24b-2 under the Securities Exchange
    Act of 1934, as amended, has been requested for certain portions of this
    document.
 
(12) Management contract or compensation plan.
 
    (b) Financial Statement Schedules
 
ITEM 17.  UNDERTAKINGS.
 
    Insofar as indemnification for liabilities arising under the Securities Act
may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the foregoing provisions, or otherwise, the Registrant
has been advised that in the opinion of the Securities and Exchange Commission
such indem-nification is against public policy as expressed in the Securities
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 Securities
Act and will be governed by the final adjudication of such issue.
 
    The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Exchange Act (and, where applicable, each filing of an employee benefit plan's
annual report pursuant to Section 15(d) of the Exchange Act) 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.
 
    The undersigned Registrant hereby undertakes that:
 
        (1) For purposes of determining any liability under the Securities Act,
    the information omitted from the form of prospectus filed as part of this
    Registration Statement in reliance upon Rule 430A and contained in a form of
    prospectus filed by the Registrant pursuant to Rule 424(b)(1) or (4) or
    497(h) under the Securities Act shall be deemed to be part of this
    Registration Statement as of the time it was declared effective.
 
        (2) For purposes of determining any liability under the Securities Act,
    each 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.
 
                                      II-5
<PAGE>
                                   SIGNATURE
 
    Pursuant to the requirements of the Securities Act of 1933, the Company
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 Amendment No. 1/A
to Registration Statement to be signed on its behalf by the undersigned,
thereunto duly authorized, in the City of South San Francisco, State of
California, on the 13th day of January, 1997.
 
                                          SHAMAN PHARMACEUTICALS, INC.
                                          By /s/ LISA A. CONTE
                                            ------------------------------------
                                            Lisa A. Conte
                                            PRESIDENT AND CHIEF EXECUTIVE
                                          OFFICER
 
    Pursuant to the requirements of the Securities Act of 1933, this Amendment
No. 1/A to Registration Statement has been signed below by the persons whose
signatures appear below, which persons have signed such Registration Statement
in the capacities and on the dates indicated:
 
             NAME                         TITLE                    DATE
- ------------------------------  --------------------------  -------------------
 
                                Director, President and
      /s/ LISA A. CONTE           Chief Executive Officer
- ------------------------------    (Principal Executive       January 13, 1997
        Lisa A. Conte             Officer)
 
                                Vice President and Chief
              *                   Financial Officer
- ------------------------------    (Principal Financial       January 13, 1997
     Barbara J. Goodrich          Officer)
 
              *
- ------------------------------  Chairman of the Board        January 13, 1997
         G. Kirk Raab
 
              *
- ------------------------------  Director                     January 13, 1997
    Herbert H. McDade, Jr.
 
              *
- ------------------------------  Director                     January 13, 1997
        M. David Titus
 
              *
- ------------------------------  Director                     January 13, 1997
        John A. Young
 
*By       /s/ LISA A. CONTE
      -------------------------
           (Lisa A. Conte)
          ATTORNEY-IN-FACT
 
                                      II-6

<PAGE>
                                                                    EXHIBIT 23.1
 
               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS
 
We consent to the reference to our firm under the captions "Selected Financial
Data" and "Experts" in Amendment No. 1 to the Registration Statement (Form S-3
No. 333-18815) and related prospectus of Shaman Pharmaceuticals, Inc. for the
registration of 2,000,000 shares of its common stock and to the incorporation by
reference therein of our report dated January 5, 1996, with respect to the
financial statements of Shaman Pharmaceuticals, Inc. included in its Annual
Report (Form 10-K) for the year ended December 31, 1995, filed with the
Securities and Exchange Commission.
 
                                                               Ernst & Young LLP
 
January 3, 1997
Palo Alto, California


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