ELAN CORP PLC
SC 13D/A, 1999-09-10
PHARMACEUTICAL PREPARATIONS
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                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                 SCHEDULE 13D/A3
                    Under the Securities Exchange Act of 1934

                       LIGAND PHARMACEUTICALS INCORPORATED
- --------------------------------------------------------------------------------
                                (Name of Issuer)

                         Common Stock, $0.001 par value
- --------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                   53220K 20 7
- --------------------------------------------------------------------------------
                                 (CUSIP Number)

                                William F. Daniel
                              Elan Corporation, plc
                                  Lincoln House
                                  Lincoln Place
                                Dublin 2, Ireland
                                (353) 1-709-4000
- --------------------------------------------------------------------------------

- --------------------------------------------------------------------------------
                                    Copy to:
                            Lisabeth F. Murphy, Esq.
                           Athena Neurosciences, Inc.
                              800 Gateway Boulevard
                      South San Francisco, California 94080
                                 (650) 877-0900
- --------------------------------------------------------------------------------
                            Telecopy: (650) 875-3620
- --------------------------------------------------------------------------------

- --------------------------------------------------------------------------------
            (Name, Address and Telephone Number of Person Authorized
                     to Receive Notices and Communications)

                                 August 31, 1999
- --------------------------------------------------------------------------------
             (Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report
the acquisition which is the subject of this Schedule 13D, and is filing this
schedule because of ss.ss. 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the
following box / /.

NOTE: Schedules filed in paper format shall include a signed original and five
copies of the schedule, including all exhibits. See ss. 240.13d-7(b) for other
parties to whom copies are to be sent.

*The remainder of this cover page shall be filled out for a reporting person's
initial filing on this form with respect to the subject class of securities, and
for any subsequent amendment containing information which would alter
disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 ("Act") or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).



<PAGE>


                                  SCHEDULE 13D

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

CUSIP No. 53220K 20 7

- --------------------------------------------------------------------------------
1         NAME OF REPORTING PERSON
          I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES
             ONLY)
          Elan Corporation, plc
          I.R.S. Employer Identification No.: NA
- --------------------------------------------------------------------------------
2         CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP    (a) / /
                                                              (b) / /
          N/A
- --------------------------------------------------------------------------------
3         SEC USE ONLY

- --------------------------------------------------------------------------------
4         SOURCE OF FUNDS

- --------------------------------------------------------------------------------
          WC
- --------------------------------------------------------------------------------
5         CHECK IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
          PURSUANT TO ITEMS 2(d) or 2(e) N/A

- --------------------------------------------------------------------------------
6         CITIZENSHIP OR PLACE OF ORGANIZATION

          Ireland
- --------------------------------------------------------------------------------
                             7         SOLE VOTING POWER

        NUMBER OF                      10,386,208
           SHARES            ___________________________________________________
       BENEFICIALLY          8         SHARED VOTING POWER
         OWNED BY
           EACH                        None
         REPORTING           ___________________________________________________
       PERSON WITH           9         SOLE DISPOSITIVE POWER

                                       10,386,208
                             ---------------------------------------------------
                             10        SHARED DISPOSITIVE POWER

                                       None
- --------------------------------------------------------------------------------
11        AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

            10,386,208
- --------------------------------------------------------------------------------
12        CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES
          CERTAIN SHARES                                          / /
- --------------------------------------------------------------------------------
13        PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

            18.7% (based upon outstanding common stock as of July 31,
            1999)
- --------------------------------------------------------------------------------
14        TYPE OF REPORTING PERSON

          CO
- --------------------------------------------------------------------------------


<PAGE>



Item 1.  Security and Issuer.

     This Schedule 13D/A3 amends the Schedule 13D filed with the Securities and
Exchange Commission (the "Commission") on January 6, 1999, as amended by the
Schedule 13D/A1 filed with the Commission on July 27, 1999 and the Schedule
13D/A2 filed with the Commission on July 29, 1999 (the "Schedule 13D") with
respect to the Common Stock, $0.001 par value ("Common Stock"), of Ligand
Pharmaceuticals Incorporated (the "Issuer"), a Delaware corporation, whose
principal executive offices are located at 10275 Science Center Drive, San
Diego, California 92121.

Item 3.  Sources and Amount of Funds or Other Consideration.

     Item 3 of the Schedule 13D is restated in its entirety as follows:

     Pursuant to a Stock Purchase Agreement, dated as of September 30, 1998, by
and between the Issuer and Elan International Services, Ltd., a wholly-owned
subsidiary of Elan ("EIS"), EIS acquired 1,278,970 shares of Common Stock (the
"First Shares") on September 30, 1998 for an aggregate cash purchase price of
$14,900,000.50.

     Pursuant to a Securities Purchase Agreement, dated as of November 6, 1998,
by and among the Issuer, EIS and Elan (the "Purchase Agreement"), on November 9,
1998, EIS acquired (i) 437,768 additional shares of Common Stock (the "Second
Shares") for an aggregate cash purchase price of $5,099,997.20 and (ii) zero
coupon convertible senior notes due 2008 of the Issuer with an 8.0% per annum
yield to maturity (the "Notes") at an issue price of $30,000,000 (the "Initial
Notes"). The issue price plus all accrued interest on the Initial Notes is
convertible into Common Stock of the Issuer at any time at the option of EIS at
a conversion price of $14.00 per share.

     Pursuant to a Development, License and Supply Agreement, dated as of
November 6, 1998 (the "License Agreement"), by and between the Issuer and Elan,
on November 9, 1998, Elan acquired (i) 429,185 additional shares of Common Stock
of the Issuer (the "Third Shares") and (ii) additional Notes of the Issuer (the
"Second Notes") with an issue price of $10,000,000, in each case, in lieu of
certain cash license fees payable by the Issuer to Elan pursuant to the License
Agreement. The issue price plus all accrued interest on the Second Notes is
convertible into Common Stock of the Issuer at any time at the option of Elan at
a conversion price of $14.00 per share.

     Pursuant to the Purchase Agreement, on July 14, 1999, EIS acquired
additional Notes of the Issuer (the "Third Notes") with an issue price of
$40,000,000. The issue price plus all accrued interest on the Third Notes is
convertible into Common Stock of the Issuer at any time at the option of EIS at
a conversion price of $14.00 per share.

     On August 13, 1999, EIS, Elan and the Issuer executed an amendment to the
Purchase Agreement (the "Letter Agreement"). Among other things, the Letter
Agreement (i) removed certain limitations on the Company's use of

                                      -1-
<PAGE>

proceeds from the sale of any Additional Notes issued after August 13, 1999;
(ii) revised the formula used to calculate the conversion price of Notes issued
after August 13, 1999; and (iii) extended the period during which the Issuer may
request that EIS purchase additional Notes to December 31, 2000.

     Pursuant to the Purchase Agreement, as amended by the Letter Agreement, on
August 31, 1999 EIS acquired additional Notes of the Issuer (the "Fourth Notes"
and, together with the First Shares, the Second Shares, the Third Shares, the
Initial Notes, the Second Notes and the Third Notes, the "Securities") with an
issue price of $20,000,000. The issue price plus all accrued interest on the
Fourth Notes is convertible into Common Stock of the Issuer at any time at the
option of EIS at a conversion price of $9.15 per share.

     The First Shares, the Second Shares, the Initial Notes, the Third Notes and
the Fourth Notes were purchased by EIS with general corporate funds. None of
such funds were borrowed.

Item 4.  Purpose of Transaction.

     Item 4 of the Schedule 13D is restated in its entirety as follows:

     Elan acquired the Securities for the purpose of making an investment in the
Issuer and in connection with the execution of the License Agreement.

     Each of the Initial Notes, the Second Notes and the Third Notes are
convertible into Common Stock of the Issuer at the option of EIS or Elan, as the
case may be, at a conversion price of $14.00 per share. The number of shares of
Common Stock into which the Initial Notes, the Second Notes and the Third Notes
may be converted is based upon the quotient obtained by dividing the issue price
thereof plus all accrued interest thereon to the conversion date by $14.00.

     The Fourth Notes are convertible into Common Stock of the Issuer at the
option of EIS or Elan, as the case may be, at a conversion price of $9.15 per
share. The number of shares of Common Stock into which the Fourth Notes may be
converted is based upon the quotient obtained by dividing the issue price
thereof plus all accrued interest thereon to the conversion date by $9.15.

     The Issuer has granted to Elan and EIS certain registration rights for the
First Shares, the Second Shares and the Third Shares and the shares of Common
Stock issuable upon conversion of the Initial Notes, the Second Notes, the Third
Notes and the Fourth Notes.

     Pursuant to and subject to the conditions set forth in the Purchase
Agreement, as amended by the Letter Agreement, at the Issuer's request, EIS
will, in its sole discretion, purchase additional Notes with an issue price of
up to $10,000,000 on or before December 31, 2000. Such Notes will be convertible
into Common Stock of the Issuer at the option of EIS at a

                                      -2-
<PAGE>

conversion price equal to the average of the closing prices of the Common Stock
for the 20 consecutive trading days immediately preceding the issue date of such
Notes, plus a premium. In addition, pursuant to the License Agreement, Elan may,
at the option of the Issuer, acquire additional shares of Common Stock in lieu
of certain cash fees which may become payable by the Issuer to Elan pursuant
thereto upon the achievement of certain milestones.

     Other than as set forth above, neither Elan nor EIS has any present plans
or intentions which would result in or relate to any of the transactions
described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

     The foregoing descriptions of the Purchase Agreement, the License Agreement
and the Letter Agreement do not purport to be complete and are qualified in
their entirety by reference to the full text thereof (copies of the Purchase
Agreement and the Letter Agreement were filed as Exhibits 1 and 2 to the
Schedule 13D). A copy of the Letter Agreement is filed herewith as Exhibit 3.
The Purchase Agreement, the License Agreement and the Letter Agreement are
incorporated herein by reference.

Item 5.  Interest in Securities of the Issuer.

     Item 5 (a) of the Schedule 13D is restated in its entirety as follows:

     (a) Elan is the beneficial owner of 10,386,208 shares of Common Stock, or
approximately 18.7%, of the outstanding shares of Common Stock (based upon the
outstanding shares of Common Stock as of July 31, 1999 and the shares of Common
Stock issuable upon conversion of the Initial Notes, the Second Notes, the Third
Notes and the Fourth Notes). To the best knowledge of Elan, no other person
named in Item 2 above beneficially owns any shares of Common Stock of the
Issuer.

Item 7.  Items to be Filed as Exhibits.

Exhibit 1* Securities Purchase Agreement, dated as of November 6, 1998, by
           and among Elan Corporation, plc ("Elan"), Elan International
           Services, Ltd. and the Issuer.

Exhibit 2* Development, License and Supply Agreement, dated as of November 9,
           1998, by and between Elan and the Issuer.

Exhibit 3  Letter Agreement, dated as of August 13, 1999, between Elan, EIS
           and the Issuer.


- ----------

*        Previously filed.

                                      -3-
<PAGE>



                                    Signature


     The undersigned certifies that, after reasonable inquiry and to the best of
its knowledge and belief, the information set forth in this statement is true,
complete and correct.

September 10, 1999

                             ELAN CORPORATION, PLC


                             By: /s/ William F. Daniel
                                 -------------------------------
                                 Name: William F. Daniel
                                 Title: Group Financial Controller




<PAGE>



                                  Exhibit Index

Exhibit No.                          Exhibit

1*         Securities Purchase Agreement, dated as of November 6, 1998, by and
           among Elan Corporation, plc, Elan International Services, Ltd. and
           Ligand Pharmaceuticals Incorporated.

2*         Development, License and Supply Agreement, dated as of November 9,
           1998, by and between Elan Corporation, plc and Ligand Pharmaceuticals
           Incorporated.

3          Letter Agreement, dated as of August 13, 1999, between Elan
           Corporation, plc, Elan International Services, Ltd. and Ligand
           Pharmaceuticals Incorporated





- ----------

*        Previously filed.






                        ELAN INTERNATIONAL SERVICES, LTD.
                               102 St. James Court
                              Flatts, Smiths Parish
                                  Bermuda FL 04


                              ELAN CORPORATION, PLC
                                  Lincoln House
                                  Lincoln Place
                                    Dublin 2
                                     Ireland


                                                                 August 13, 1999


Ligand Pharmaceuticals Incorporated
10275 Science Center Drive
San Diego, California 92121

Attention:  Paul V. Maier


Ladies and Gentlemen:

     Reference is made to the Securities Purchase Agreement, dated as of
November 6, 1998 (the "Purchase Agreement"), by and among Ligand Pharmaceuticals
Incorporated (the "Company"), Elan International Services, Ltd. (the
"Purchaser"), and Elan Corporation, plc ("Elan"). Capitalized terms used in this
letter agreement and not otherwise defined herein have the meanings assigned to
such terms in the Purchase Agreement.

     By their signatures below, the Company, the Purchaser and Elan hereby agree
as follows:

     (1) Effective as of the date of this letter agreement, in connection with
the issuance and sale of any Additional Notes by the Company from and after the
date of this letter agreement, the Purchase Agreement is hereby amended as
follows:

          (a) Section 1(b) of the Purchase Agreement is hereby amended such that
     the gross proceeds received by the Company as a result of the issuance and
     sale of Additional Notes after the date of this letter agreement may be
     used by the Company for general corporate purposes.


<PAGE>
                                      -2-


          (b) Section 12(c)(ii)(y) of the Purchase Agreement is hereby amended
     by replacing "0.025" with "0.10".

          (c) Section 12(c) of the Purchase Agreement is hereby amended by
     deleting in its entirety the proviso at the end of the first sentence
     thereof and the second sentence thereof.

          (d) Section 1(b) of the Purchase Agreement is hereby amended by
     replacing "December 31, 1999" with "December 31, 2000".

     (2) On the basis of the representations, warranties, agreements and
covenants contained in the Purchase Agreement and subject to the terms and
conditions set forth therein, the Purchaser agrees to purchase from the Company
on August 31, 1999, Additional Notes having an Additional Note Issuance Price of
$20,000,000; provided, however, that the obligation of the Purchaser to purchase
such Additional Notes shall be subject to the approval of the Board of Directors
of the Purchaser. In addition, the Purchaser waives the delivery by the Company
of a Purchase Request with respect to the issuance and sale of such Additional
Notes.

     The amendments to the Purchase Agreement set forth in this letter agreement
shall apply only to Additional Notes issued and sold by the Company on or after
the date hereof. The Initial Notes and Additional Notes issued and sold by the
Company prior to the date of this letter agreement shall remain unchanged and in
full force and effect.

     Except as specifically amended hereby, all of the terms, conditions, and
provisions of the Purchase Agreement shall remain unchanged and in full force
and effect. No reference to this letter agreement need be made in any Additional
Notes issued and sold by the Company on or after the date hereof or in any other
instrument or document relating to such Additional Notes, a reference to the
Purchase Agreement in any of such to be deemed to be a reference to the Purchase
Agreement as amended by this letter agreement.

     The execution, delivery and effectiveness of this letter agreement shall
not, except as expressly provided herein, operate as a waiver of any right,
power or remedy of the Purchaser, any Affiliate of the Purchaser or Elan under
the Purchase Agreement or any of the Initial Notes or the Additional Notes, nor
constitute a waiver of any provision of the Purchase Agreement, the Initial
Notes or the Additional Notes.


<PAGE>
                                      -3-


     This letter agreement shall be governed by and construed in accordance with
the laws of the State of New York.

     This letter agreement may be executed in any number of counterparts, each
of which when so executed and delivered shall be deemed to be an original
without the production of other counterparts and all of which taken together
shall constitute one and the same instrument.

                          Sincerely,

                          ELAN INTERNATIONAL SERVICES, LTD.


                          By: /s/ Thomas G. Lynch
                              -----------------------------------
                              Name:  Thomas G. Lynch
                              Title: Chairman



                          ELAN CORPORATION, PLC


                          By: /s/ Thomas G. Lynch
                              -----------------------------------
                              Name:  Thomas G. Lynch
                              Title: Executive Vice President and
                                     Chief Financial Officer


Accepted and agreed as of the date first written above:

LIGAND PHARMACEUTICALS INCORPORATED


By: /s/ Paul V. Maier
    -------------------------------------
    Name:  Paul V. Maier
    Title: Senior Vice President
           and Chief Financial Officer





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