ISIS PHARMACEUTICALS INC
8-K, 1999-09-02
PHARMACEUTICAL PREPARATIONS
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<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549

                                    FORM 8-K

                                 CURRENT REPORT
                     PURSUANT TO SECTION 13 OR 15(d) OF THE
                         SECURITIES EXCHANGE ACT OF 1934

        Date of Report (Date of earliest event reported): AUGUST 31, 1999

                           ISIS PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)

                                    DELAWARE
                 (State or other jurisdiction of incorporation)

0-19125                                                               33-0336973
(Commission File No.)                          (IRS Employer Identification No.)

                               2292 FARADAY AVENUE
                           CARLSBAD, CALIFORNIA 92008
              (Address of principal executive offices and zip code)

                                 (760) 931-9200
              (Registrant's telephone number, including area code)
<PAGE>   2

ITEM 5.  OTHER EVENTS.

On July 18, 1995, Isis Pharmaceuticals, Inc. ("Isis") and Boehringer Ingelheim
International, GmbH ("BI") formed a collaboration to combine the clinical
development and research programs of both companies in the field of cell
adhesion. Effective August 31, 1999 Isis has reacquired control of the ISIS
2302 drug compound in order to redirect the commercialization of this product.

In connection with the collaboration, Isis and BI entered into a Stock Purchase
Agreement effective July 18, 1995. The Stock Purchase Agreement has been amended
effective August 31, 1999 in accordance with the attached Exhibit 10.2.

ITEM 7.  FINANCIAL STATEMENTS AND EXHIBITS.

        (a)     Financial Statements of Businesses Acquired. Not applicable.

        (b)     Pro Forma Financial Information. Not applicable.

        (c)     Exhibits

                Exhibit 10.1* Agreement dated August 31, 1999 between
                Boehringer Ingelheim International GmbH and Isis
                Pharmaceuticals, Inc.

                Exhibit 10.2 Amendment to the Stock Purchase Agreement dated
                August 31, 1999



*Confidential treatment has been requested with respect to certain portions of
this exhibit. Omitted portions have been filed separately with the Securities
and Exchange Commission.
<PAGE>   3

                                    SIGNATURE

        Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned hereunto duly authorized.

                                            ISIS PHARMACEUTICALS, INC.

Dated:  September 2, 1999                   By: /S/  B. LYNNE PARSHALL
                                               ---------------------------------
                                               B. Lynne Parshall
                                               Executive Vice President


<PAGE>   1

                                                                    EXHIBIT 10.1

*Confidential treatment has been requested with respect to certain portions of
this exhibit. Omitted portions have been filed separately with the Securities
and Exchange Commission.


                                    AGREEMENT

This AGREEMENT, dated as of August 31, 1999 (the "Effective Date"), by and
between BOEHRINGER INGELHEIM INTERNATIONAL GmbH ("BI"), a company organized and
existing under the laws of the Federal Republic of Germany, with its principal
place of business at D-55216 Ingelheim/Rhein, Federal Republic of Germany, and
ISIS PHARMACEUTICALS, INC. ("Isis"), a Delaware corporation with its principal
place of business at 2292 Faraday Drive, Carlsbad, California 92008, U.S.A.,

                              W I T N E S S E T H :

        WHEREAS, pursuant to the Collaborative Agreement, dated as of July 18,
1995, BI and Isis previously entered into collaborative research, development
and commercial relationship in the Field; and

        WHEREAS, BI and Isis have mutually agreed to terminate the Collaborative
Agreement and to set forth in this Agreement, which shall supercede the
Collaborative Agreement as of the Effective Date, their mutual agreement with
respect to collaborative research in the Field

        WHEREAS, BI and Isis have mutually agreed to continue their
collaboration with respect to research under the Research Plan through December
31, 1999, and to discontinue their collaboration with respect to development, in
each case, as provided herein,

        NOW, THEREFORE, in consideration of the foregoing and the mutual
covenants and agreements herein contained, the Parties hereby agree as follows:

                                   ARTICLE 1.

                                   DEFINITIONS

For purposes of this Agreement, the capitalized terms defined in this Agreement
shall have the meanings specified in Appendix A attached hereto.

                                   ARTICLE 2.

                      SCOPE AND STRUCTURE OF COLLABORATION

2.1     Termination of Collaborative Agreement. Pursuant to the Collaborative
        Agreement, BI and Isis established a collaboration for the purpose of
        identifying, developing and commercializing products in the Field. The
        Parties hereby acknowledge and mutually agree that as of the Effective
        Date the Collaborative Agreement shall be terminated. The Parties
        further hereby agree that as of the Effective Date this Agreement shall
        supercede the Collaborative Agreement and no agreement with respect to
        the subject matter hereof shall exist between the Parties other than the
        agreements expressly set forth herein. The Parties further agree that
        they will continue their collaboration with respect to research under
        the Research Plan and discontinue their collaboration with respect to
        development, in each case, as provided herein.

2.2     ISIS 2302.

                (a) The Parties hereby acknowledge and agree that BI has
        abandoned its participation in the further development and
        commercialization of ISIS 2302 in any and all formulations and
        indications of every kind whatsoever. BI acknowledges and agrees that
        Isis has full responsibility and authority to develop and commercialize
        ISIS 2302.



                                      -1-
<PAGE>   2

                (b) As of the Effective Date, Isis shall pay BI a royalty, on a
        country-by-country basis, on Net Sales of any formulation or indication
        of ISIS 2302 occurring on or after the Effective Date as follows:

                        (i) With respect to all sales of any [***] of ISIS 2302
                for [***], such royalty rate shall be [***] of Net Sales;

                        (ii) With respect to all sales of any [***] other than
                for [***], such royalty rate shall be [***] of Net Sales;

                        (iii) With respect to sales of any [***] of ISIS 2302
                for the indications of [***], such royalty rate shall be [***]
                of Net Sales; and

                        (iv) With respect to all sales of ISIS 2302 not
                specified in clause (i), (ii) or (iii) above, such royalty rate
                shall be [***] of Net Sales.

                (c) The obligations to pay royalties under this Section 2.2
        shall continue, on a country-by-country basis, until the later of (i)
        the [***], or (ii) [***] anniversary of the Effective Date.

2.3     Additional Compounds. The Parties further agree that, as of the
        Effective Date, they shall have the respective rights and obligations
        set forth in this Section 2.3 with respect to the Additional Compounds.

                (a) BI shall have the sole right to develop, commercialize, sell
        and license any of the compounds known as [***] or any compound from out
        of the [***] series that had been synthesized as of the Effective Date.
        If BI commercializes any of the compounds known as [***] or any compound
        from out of the [***] series that had been synthesized as of the
        Effective Date, either by itself or through a Third Party, BI shall pay
        Isis a royalty, on a country-by-country basis, of [***] on any and all
        Net Sales of [***] or any compound from out of the [***] series that had
        been synthesized as of the Effective Date, as the case may be. Isis
        hereby represents that during the term of the Collaborative Agreement it
        did not discover any small-molecule compounds in the Field with the
        exception of Isis's small molecule combinatorial libraries.

                (b) Isis shall have the sole right to develop, commercialize,
        sell and license any of the compounds known as [***]. If Isis
        commercializes the compounds known as [***], either by itself or through
        a Third Party, Isis shall pay BI a royalty, on a country-by-country
        basis, of [***] on any and all Net Sales of [***], as the case may be.
        BI hereby represents that during the term of the Collaborative Agreement
        it did not discover any Antisense Molecules in the Field.

                (c) Each Party shall have the right, in its sole discretion, to
        in- and out-license and establish collaborations with Third Parties
        within the Field without the approval of, and without any obligation to,
        the other Party.



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                        2
<PAGE>   3

                (d) The obligations to pay royalties under Section 2.3(a) and
        Section 2.3(b), respectively, shall continue, on a country-by-country
        basis, until the later of (i) the [***], or (ii) the [***] anniversary
        of the Effective Date.

2.4     Both Parties shall have the right to practice the Joint [***] Patent(s);
        provided, however, that:

                        (i) Isis shall have the sole right to develop,
                        commercialize and sell Antisense Molecules covered by
                        any issued Joint [***] Patent(s), and Isis shall pay BI
                        a royalty, on a country-by-country basis, of [***] of
                        any and all Net Sales of such Antisense Molecules or
                        compounds containing such Antisense Molecules;

                        (ii) BI shall have the sole right to develop,
                        commercialize and sell small-molecule compounds covered
                        by any issued Joint [***] Patent(s), and BI shall pay
                        Isis a royalty, on a country-by-country basis, of [***]
                        of any and all Net Sales of such small-molecule
                        compounds or compounds containing such small-molecule
                        compounds; and

                        (iii) Either Party may develop, commercialize and sell
                        any compound that is not (a) an Antisense Molecule or
                        (b) a small-molecule compound, covered by an issued
                        Joint [***] Patent(s), so long as such Party has the
                        intellectual property right to develop, commercialize or
                        sell such compound, and such Party shall pay the other
                        Party a royalty, on a country-by-country basis, of [***]
                        of any and all Net Sales of such compound.

                (b) The obligations to pay royalties under Section 2.4 shall
        continue, on a country-by-country basis, until the later of (i) the
        [***], or (ii) [***] anniversary of the Effective Date.

2.5     [***].


                (a) As of the Effective Date, BI shall pay Isis a royalty, on a
        country-by-country basis, of [***] on Net Sales of the [***] in the
        indications of [***] occurring on or after the Effective Date.

                (b) As of the Effective Date, BI shall pay Isis a royalty, on a
        country-by-country basis, of [***] on Net Sales of any formulation or
        indication of [***] occurring on or after the Effective Date.

                (c) Isis acknowledges and agrees that BI has full responsibility
        and authority to develop and commercialize [***].



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                        3
<PAGE>   4

                (d) The obligations to pay royalties under this Section 2.5
        shall continue, on a country-by-country basis, until the later of (i)
        the [***], as the case may be, or (ii) [***] anniversary of the
        Effective Date.

2.6     Other Compounds. Any given compound in the Field, including without
        limitation, compounds which have been part of the ongoing screening and
        optimization of (i) Antisense Molecules and small-molecule compounds by
        Isis and (ii) small-molecule compounds by BI, throughout the term of the
        Collaborative Agreement, other than ISIS 2302, [***], the Additional
        Compounds, and Antisense Molecules, small-molecule compounds and other
        compounds covered by an issued Joint [***] Patent may be commercialized
        and/or sold by the Party having the intellectual property right to
        develop, commercialize or sell such compound without any obligation
        whatsoever to the other Party under this Agreement.

                                   ARTICLE 3.

                                  RESEARCH PLAN

3.1     Research Plan. The Parties hereby agree to cooperate in carrying out the
        Research Plan during the Research Period, as described in this Article
        3.

3.2     Research Agreement. During the Research Period, BI and Isis hereby agree
        to work cooperatively to fulfill the Research Plan.

3.3     Research Period. The Research Plan shall be undertaken by the Parties
        during the Research Period.

3.4     Research Management Committee. An RMC composed of four (4)
        representatives from each Party shall be appointed upon signing of this
        Agreement. The RMC shall be responsible for managing day-to-day work
        necessary to perform the Research Plan during the Research Period.

3.5     Research Expenses. BI shall make the payments with respect to the
        funding of the Research Plan in the amounts and at the times described
        in this Section 3.5:

                (a) 1999 research expenses for Isis shall be [***].

                (b) Other research expenses relating to the [***] and other
        expenses approved by the RMC for Isis shall be [***].

                (c) 1999 research expenses for BI shall be [***].

                (d) With respect to the expenses described in paragraphs (a),
        (b) and (c) above, BI shall pay Isis [***] on the 45th day after
        December 31, 1999. Other than the payment expressly set forth in this
        Section 3.5(d), there shall be no other costs or expenses of any kind
        with respect to the Research Plan attributable to or payable by BI. Isis
        shall not be responsible for any research expenses relating to [***]
        that have not already been paid as of the Effective Date.



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                        4
<PAGE>   5

                                   ARTICLE 4.

                               COLLABORATIVE COSTS

4.1     Collaborative Costs for 1998. Notwithstanding the termination of the
        Collaborative Agreement, the Parties hereby acknowledge and agree that
        all costs associated with the Collaborative Agreement incurred for
        calendar year 1998 shall be attributed and paid as provided in this
        Section 4.1.

                (a) Such 1998 collaborative costs in the amount of [***] shall
        be attributed to Isis.

                (b) Such 1998 collaborative costs in the amount of [***] shall
        be attributed to BI.

                (c) With respect to such 1998 collaborative costs, BI hereby
        agrees to make a cash payment to Isis in the amount of [***] by wire
        transfer in immediately available funds within ten (10) business days of
        the Effective Date. Except as expressly provided in this Section 4.1(c),
        there shall be no other research or development costs associated with
        the Collaborative Agreement payable by either Party to the other Party
        for calendar year 1998.

4.2     ISIS 2302 Development Costs in 1999. Notwithstanding the termination of
        the Collaborative Agreement, the Parties hereby acknowledge and agree
        that costs with respect to the development of ISIS 2302 in calendar year
        1999 shall be attributed and paid as provided in this Section 4.2.
        Except as expressly provided in this Section 4.2, there shall be no
        other costs payable by either Party to the other Party for development
        costs related to ISIS 2302 in calendar year 1999. With respect to such
        development costs, BI hereby agrees to make a cash payment to Isis in
        the amount of [***] within ten (10) business days of the Effective Date
        and a cash payment to Isis in the amount of [***] on December 31, 1999,
        in each case, by wire transfer in immediately available funds.

4.3     Future Development Costs of ISIS 2302. There shall be no other costs or
        expenses of any kind with respect to the development of ISIS 2302
        attributable to or payable by BI after December 31, 1999.

4.4     Other Costs. Except as expressly set forth in this Agreement, there
        shall be no other costs or expenses of any kind with respect to the
        research or development of any compound or product attributable to or
        payable by either Party.

                                   ARTICLE 5.

                              REPAYMENT OF ADVANCES

5.1     Credit Facility under the Collaborative Agreement. The Parties hereby
        acknowledge and agree that BI has made Advances to Isis pursuant to
        Article 7 of the Collaborative Agreement (each, an "Outstanding
        Obligation"), in the aggregate amount of $22,576,405, as follows:



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       5
<PAGE>   6

<TABLE>
<CAPTION>
                                 AMOUNT OF
                                OUTSTANDING        CREDIT MATURITY          INTEREST
DATE OF ADVANCE                 OBLIGATION              DATE                  RATE
- ---------------                 ----------              ----                  ----
<S>                             <C>               <C>                       <C>
October 15, 1996                $8,300,000        October 15, 2003            8.46%
December 30, 1996               $7,900,000        December 30, 2003           8.36%
  June 30, 1997                 $6,376,405        June 30, 2004               8.45%
</TABLE>

5.2     Repayment of Outstanding Obligations; No Further Advances. Isis shall
        repay the principal amount of each Outstanding Obligation to BI in full
        prior to the respective Credit Maturity Date of each Outstanding
        Obligation. The Parties expressly acknowledge and agree that BI and its
        Affiliates have no obligation whatsoever under the Collaborative
        Agreement or hereunder to make any additional Advances to Isis.

5.3     Interest Rate on Outstanding Obligations. Isis shall pay BI interest on
        the unpaid principal amount of each Outstanding Obligation at the
        respective interest rate specified in the column captioned "Interest
        Rate" in the chart set forth in Section 5.1. Interest shall be due and
        payable by Isis to BI two (2) times in each calendar year, on May 31st
        and November 30th, or the first business day thereafter, if any such
        date shall occur on a non-business day.

5.4     Prepayment of Principal.

                (a) Optional Prepayment. Isis may prepay the outstanding
        principal balance of any Outstanding Obligation, in whole or in part, at
        any time without penalty or premium; provided, however, that the accrued
        interest on such prepaid amounts of Outstanding Obligations shall be
        included in the prepayment of principal on the date of such prepayment.

                (b) Mandatory Prepayment. Notwithstanding anything to the
        contrary set forth in this Agreement, for as long as any Outstanding
        Obligation is outstanding:

                (i) for each fiscal year in which commercial sales of [***] or
                any compound from out of the [***] series that had been
                synthesized as of the Effective Date, or any small-molecule
                compounds covered by the Joint [***] Patent(s) occur, Isis shall
                prepay the outstanding principal amount of the Outstanding
                Obligations in an amount calculated for such year equal to [***]
                of the total royalties received by Isis on such commercial sales
                during such year as determined based upon the audited year-end
                financial statements for such year;

                (ii) prior to January 1, 2002, for each fiscal year in which
                commercial sales of ISIS 2302 occur, Isis shall prepay the
                outstanding principal amount of the Outstanding Obligations in
                an amount calculated for such year equal to [***] of the net
                royalties (total royalties received by Isis less the royalty
                paid by Isis to BI) on such commercial sales during such year as
                determined based upon the audited year-end financial statements
                for such year; and

                (iii) after January 1, 2002, for each fiscal year in which
                commercial sales of ISIS 2302 occur, Isis shall prepay the
                outstanding principal amount of the Outstanding Obligations in
                an amount calculated for such year equal to [***] of the net
                royalties (total royalties received by Isis less the royalty
                paid by Isis to BI) on such commercial sales during such year,
                as determined based upon the audited year-end financial
                statements for such year.



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       6
<PAGE>   7

Each mandatory prepayment under this Section 5.4(b) shall be payable within 30
calendar days after completion of Isis' consolidated annual audited year-end
financial statements for such year.

5.5     Method of Payment.

                (a) All interest on each Outstanding Obligation shall be paid in
        cash and in U.S. dollars on the dates described in Section 5.3.

                (b) All optional prepayments on Outstanding Obligations pursuant
        to Section 5.4(a) shall be paid in cash in U.S. dollars.

                (c) All mandatory prepayments on Outstanding Obligations
        pursuant to Section 5.4(b) shall be made in cash in U.S. dollars.

                (d) All regular repayments of principal on Outstanding
        Obligations shall be made on the applicable Credit Maturity Date in cash
        in U.S. dollars and/or, at the option of Isis, in shares of Isis Common
        Stock, par value U.S.$.001 par share, at a price per share equal to
        [***] of the average Fair Market Value (as such term is defined in the
        Stock Purchase Agreement) over the [***] trading days preceding the
        Credit Maturity Date.

                (e) Bank Wire. All payments made to BI in immediately available
        cash funds hereunder shall be addressed and wired to:

               Boehringer Ingelheim International GmbH
               Corporate Department Pharma Controlling
               Citibank AG, Frankfurt/Main, F.R. Germany
               Bank Account: 120/3497/004

                                   ARTICLE 6.

                    RECORDS, REPORTS AND INFORMATION EXCHANGE

6.1     Record Keeping. Isis and BI shall each maintain records in sufficient
        detail and in good scientific and commercial manner appropriate for
        regulatory, patent, know how, trade secret, other intellectual property
        and commercial purposes, including but not limited to the calculation of
        Net Sales, and as shall properly reflect all work done, results achieved
        and costs expended in the performance of each Party's respective
        obligations hereunder and under the Collaborative Agreement. Isis and BI
        shall each provide the other Party the right to inspect and make copies
        (at such other Party's expense) of all such records to the extent
        reasonably required for the performance of its obligations and the
        exercise of its rights under this Agreement.

6.2     Technology and Information Transfer. The Parties shall exchange all Isis
        Background Intellectual Property, BI Intellectual Property and Program
        Intellectual Property, and shall provide reasonable technical assistance
        and training to the other, as shall be necessary to carry out the
        Research Plan. All information transferred, provided or exchanged under
        this Section 6.2 shall be subject to the confidentiality requirements
        set forth in Article 9 and may be used and disclosed only to carry out
        the Research Plan hereunder.

6.3     Exchange Rate; Records of Net Sales. All payments with respect to
        royalties under this Agreement shall be payable [***]. All royalty
        payments to Isis shall be calculated in U.S. dollars on the last
        business day of each quarter or such pro rata share thereof as is then
        applicable, using the applicable exchange



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       7
<PAGE>   8

        rates for such date published in the Wall Street Journal. All royalty
        payments to BI shall be calculated in Deutsche Mark or Euros, at the
        written request of BI prior to the date of calculation, on the last
        business day of each quarter or such pro rata share thereof as is then
        applicable, using the applicable exchange rates for such date published
        in the Wall Street Journal. Both parties shall keep complete and
        accurate records (including Net Sales information on a
        country-by-country basis) in sufficient detail to enable the amounts
        payable to be determined.

6.4     Right to Audit. Upon written request, each Party shall have the right to
        have an independent audit of Net Sales by the other Party and its
        Affiliates performed once after each calendar year on an aggregated
        country-by-country basis and on a country-by-country basis for Major
        Market Countries. As used in this Agreement, "Major Market Countries"
        shall mean the United States, Germany, France, Italy, Japan and the
        United Kingdom. Internal auditors or independent public accountants
        selected by each Party and acceptable to the other shall conduct such
        verification at the respective Party's expense and during regular
        business hours. With respect to Net Sales by a Party's licensees
        (including sub-licensees), the other Party shall have the right to
        request an audit of the Net Sales by such licensees and/or
        sub-licensees, at such requesting Party's expense, once after each
        calendar year on an aggregated country-by-country basis and on a
        country-by-country basis for Major Market Countries, in which case the
        Party receiving such request to audit shall promptly cause an audit to
        be undertaken of Net Sales made by its licensees and/or sub-licensees
        and promptly deliver the results of such audit to the Party requesting
        same. Any discrepancies of 5% or less shall not be considered material.

                                   ARTICLE 7.

                          INTELLECTUAL PROPERTY RIGHTS

7.1     Ownership of Background Intellectual Property. The rights to BI
        Background Intellectual Property and Isis Background Intellectual
        Property shall remain the property of the respective Party which owned
        such rights at the date of execution of this Agreement. Each Party
        hereby acknowledges and agrees that it shall have no rights to the other
        Party's Background Intellectual Property other than the licensed rights
        specifically granted herein.

7.2     Ownership of Joint Intellectual Property. The rights to all Program
        Intellectual Property that are discovered, made or conceived during and
        as a result of the Research Plan solely by employees of one Party or by
        others acting on behalf of the same Party shall be owned by that Party.
        The rights to all Program Intellectual Property that is discovered, made
        or conceived during and as a result of the Research Plan jointly by
        employees of BI and Isis or others acting on their behalf shall be
        jointly owned by BI and Isis. Each Party shall disclose to the other
        Party the making, conception or reduction to practice of Program
        Intellectual Property by employees or others acting on behalf of such
        Party. Inventorship shall be determined in accordance with common
        international practice.

7.3     Joint [***] Intellectual Property. The Parties acknowledge and agree
        that the only joint intellectual property resulting from the Research
        Program (as such term is defined in the Collaborative Agreement) was the
        Joint [***] Patent(s) (as such term is defined herein). The Parties'
        agreement with respect to royalties relating to the Joint [***]
        Patent(s) are set forth in Section 2.4. The Parties' agreements with
        respect to the filing and prosecution of the Joint [***] Patent(s) and
        other matters are set forth in Article 13.



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       8
<PAGE>   9

                                   ARTICLE 8.

                                GRANT OF LICENSES

8.1     Grant of License by BI to Isis. BI hereby agrees to grant and grants to
        Isis a worldwide, royalty-free license to the BI Background Intellectual
        Property and the Program Intellectual Property, owned or controlled by
        BI solely for the purpose of allowing Isis to carry out the Research
        Plan, as provided herein. Such license shall terminate upon the
        termination of the Research Period.

8.2     Grant of License by Isis to BI. Isis hereby agrees to grant and grants
        to BI a worldwide, royalty-free license to the Isis Background
        Intellectual Property and the Program Intellectual Property, owned or
        controlled by Isis solely for the purpose of allowing BI to carry out
        the Research Plan, as provided herein. Such license shall terminate upon
        the termination of the Research Period.

8.3     Characteristics of Licenses. The licenses granted under Sections 8.1 and
        8.2 shall be exclusive for the purposes for which they are granted,
        except as to the Party granting the license, which shall retain all
        rights necessary to conduct the activities contemplated by this
        Agreement and to use the intellectual property freely. Notwithstanding
        the above, the Parties shall have the right to grant sublicenses to
        Affiliates.

8.4     Non-Use of Intellectual Property. Each of BI and Isis hereby covenants
        and agrees that it shall not, nor shall it cause its Affiliates to, use
        directly or indirectly any Isis Background Intellectual Property (in the
        case of BI) or BI Background Intellectual Property (in the case of Isis)
        or Program Intellectual Property (in both cases) for any purpose other
        than to conduct activities under this Agreement during the Research
        Period.

                                   ARTICLE 9.

                                 CONFIDENTIALITY

9.1     Confidentiality. Each Party hereto shall maintain in confidence all
        Confidential Information disclosed by the other Party hereto. Neither
        Party shall use, disclose or grant use of such Confidential Information
        except as expressly authorized by this Agreement and/or without the
        prior written consent of the other Party. To the extent that disclosure
        is authorized by this Agreement, the disclosing Party shall obtain prior
        agreement from its employees, agents, consultants or clinical
        investigators and designated permitted sublicensees to whom disclosure
        is to be made to hold in confidence and not make use of such
        Confidential Information for any purpose other than those permitted by
        this Agreement. Each Party shall use at least the same standard of care
        as it uses to protect its own trade secrets or proprietary information
        to ensure that such employees, agents, consultants and clinical
        investigators do not disclose or make any unauthorized use of such
        Confidential Information. Each Party shall promptly notify the other
        upon discovery of any unauthorized use or disclosure of the Confidential
        Information.

9.2     Authorized Disclosure. Each Party may disclose the Confidential
        Information to the extent such disclosure is reasonably necessary in
        filing or prosecuting patent applications, prosecuting or defending
        litigation or complying with applicable governmental regulations, or
        achieving the purposes of this Agreement; provided that, if such Party
        is required to make any such disclosure of the Confidential Information,
        it shall to the extent practicable give reasonable advance notice to the
        other Party of such disclosure requirement and, except to the extent
        inappropriate in the case of patent applications, shall use reasonable
        efforts to secure confidential treatment of such Confidential
        Information required to be disclosed.



                                       9
<PAGE>   10

                                   ARTICLE 10.

                                TERM; TERMINATION

10.1    Term. This Agreement shall commence as of the Effective Date and, unless
        sooner terminated, as provided hereunder, shall continue in effect until
        such date as no royalties shall be payable to any Party hereunder.

10.2    Termination for Breach. In the event either Party breaches a material
        obligation under this Agreement, and such breach is not cured within 90
        days of written notice thereof, the non-breaching Party shall not have
        the right to terminate this Agreement, but shall have the right only to
        pursue an action for damages, arising as a result of such breach
        pursuant to Article 15, and this Agreement shall continue in full force
        and effect, including all licenses and funding obligations hereunder.

10.3    Accrued Rights, Surviving Obligations. Termination, relinquishment or
        expiration of this Agreement or any part thereof for any reason shall be
        without prejudice to any rights that shall have accrued to the benefit
        of either Party prior to such termination, relinquishment or expiration,
        including damages arising from any breach hereunder. Such termination,
        relinquishment or expiration shall not relieve either Party from
        obligations that are expressly indicated to survive termination or
        expiration of this Agreement.

10.4    Survival. Section 2.2, Section 2.3, Section 2.4, Section 2.5, Section
        3.4, Article 4, Article 5, Section 6.4, Article 7, Article 9, Article
        13, Article 14 and Article 15 shall survive the termination of this
        Agreement.

                                   ARTICLE 11.

                         REPRESENTATIONS AND WARRANTIES

Each Party hereby represents and warrants to the other that:

11.1    Corporate Power. Such Party is duly organized and validly existing under
        the laws of the jurisdiction of its incorporation and has full corporate
        power and authority to enter into this Agreement and to carry out the
        provisions hereof.

11.2    Due Authorization. Such Party is duly authorized to execute and deliver
        this Agreement and to perform its obligations hereunder.

11.3    Binding Agreement. This Agreement is a legal and valid obligation
        binding upon it and enforceable in accordance with its terms. The
        execution, delivery and performance of this Agreement by such Party does
        not conflict with any agreement, instrument or understanding, oral or
        written, to which it is a Party or by which it may be bound, nor violate
        any law or regulation of any court, governmental body or administrative
        or other agency having jurisdiction over it.

11.4    No Conflict. Such Party has not granted any licenses or rights to any
        other person which would restrict or conflict with or prevent such Party
        from granting the rights granted to the other Party pursuant to this
        Agreement.



                                       10
<PAGE>   11

                                   ARTICLE 12.

                                  PUBLICATIONS

12.1    Publications

                (a) During the term of this Agreement, Isis and BI each
        acknowledge the other Party's interest in publishing certain of its
        results to obtain recognition within the scientific community and to
        advance the state of scientific knowledge. Accordingly, each Party shall
        have the right to publish such results pertaining to its own products or
        intellectual property without the prior review or consent of the other
        Party; provided, however, that each Party hereby agrees to exercise good
        scientific practice with respect to any publications involving joint
        authorship and, in the case of joint authorship, to provide the other
        Party with notice and a copy of such proposed publication sixty (60)
        days prior to such publication.

                (b) Notwithstanding paragraph (a) of this Section 12.1, with
        respect to CS-11, an integrated clinical trial report shall be prepared
        in accordance with the study protocol. BI and Isis shall each have the
        right to review the final manuscript at least four (4) weeks prior to
        submission for publication.

                                   ARTICLE 13.

                                     PATENTS

13.1    Filing, Prosecution and Maintenance of the Joint [***] Patent(s). With
        respect to the Joint [***] Patent(s), Isis shall have the right, but not
        the obligation, to file, prosecute and maintain the Joint [***]
        Patent(s) and to pay the costs and expenses related thereto. If,
        however, Isis fails to file, prosecute or maintain the Joint [***]
        Patent(s) within a reasonable amount of time, then BI shall have the
        right, but not the obligation, to file, prosecute and maintain the Joint
        [***] Patent(s) and to pay the costs and expenses related thereto. Each
        of the Parties hereto shall consult with the other Party as to the
        filing, prosecution and maintenance of the Joint [***] Patent(s), shall
        furnish to the other Party copies of documents relevant to any filing,
        prosecution or maintenance sufficiently prior to filing such document or
        making any payment due thereunder to allow for review and comment by the
        other Party, and shall seriously consider all such comments.

13.2    Filings. With respect to any patent applications filed or to be filed
        with respect to any intellectual property conceived, created or
        developed either under the Collaborative Agreement or during and as part
        of the Research Plan, (a) BI shall be responsible for filing and
        prosecuting such application on such intellectual property owned solely
        by BI (each, a "BI Application or Patent") and paying the costs and
        expenses related thereto and (b) Isis shall be responsible for filing
        and prosecuting such application on such intellectual property owned
        solely by Isis (each, an "Isis Application and Patent") and paying the
        costs and expenses related thereto. Except as provided in Section 13.1,
        with respect to any such intellectual property jointly owned by BI and
        Isis (each, a "Joint Application or Patent"), (X) for any Joint
        Application or Patent relating or pertaining to small molecules, BI
        shall be responsible for filing such Joint Application or Patent and
        paying the costs and expenses related thereto; (Y) for any Joint
        Application and Patent relating or pertaining to Antisense Molecules or
        Ibis technology, Isis shall be responsible for filing and prosecuting
        such Joint Application or Patent and paying the costs and expenses
        related thereto; and (Z) for any Joint Application or Patent relating or
        pertaining to both small molecules, on the one hand, and Antisense
        Molecules or Ibis technology, on the other, or to none of small
        molecules,



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       11
<PAGE>   12

        Antisense Molecules or Ibis technology, the Parties shall negotiate on a
        case-by-case basis which Party shall be responsible for filing and
        prosecuting such application and paying the costs and expenses related
        thereto.

13.3    Filing, Prosecution and Maintenance. The Party selected for filing a
        given Joint Application or Patent pursuant to Section 13.2 shall have
        the right, but not the obligation, to file, prosecute and maintain such
        Joint Application or Patent and to pay the costs and expenses related
        thereto. If, however, such Party fails to file, prosecute or maintain a
        given Joint Application or Patent within a reasonable amount of time,
        the other non-filing Party shall have the right, but not the obligation,
        to file, prosecute and maintain such Joint Application or Patent and to
        pay the costs and expenses related thereto. Each of the Parties hereto
        shall consult with the other Party as to the filing, prosecution and
        maintenance of each Joint Application or Patent, shall furnish to the
        other Party copies of documents relevant to any filing, prosecution or
        maintenance sufficiently prior to filing such document or making any
        payment due thereunder to allow for review and comment by the other
        Party, and shall seriously consider all such comments.

                                   ARTICLE 14.

                                 INDEMNIFICATION

14.1    Indemnification for Products. Unless otherwise provided herein, each
        Party agrees to indemnify and hold the other Party harmless, from and
        against all Third Party claims, demands, liabilities, damages and
        expenses (including attorney's fee) arising out of such Party's, its
        Affiliates or agents, research, development, manufacture, use, handling,
        storage, commercialization or sale of ISIS 2302 or any Additional
        Compound, but only to the extent such claims, demands and the like
        result from the negligence of the indemnifying Party, its Affiliates or
        agents and not to result from the negligence of the Party seeking to be
        indemnified. The Party providing the indemnity shall have the right to
        conduct the defense. Notwithstanding the foregoing, neither Party shall
        be responsible for any Third Party claims, demands, liabilities, damages
        and expenses (including attorney's fees) which may arise out of the use
        by the other Party of any information and data received by the other
        Party from it, its Affiliates and/or its licensees or sublicensees. In
        the event either Party receives notice of a claim with respect to ISIS
        2302 or any Additional Compound, such Party shall inform the other as
        soon as reasonably practicable and the Parties shall confer in good
        faith as to how best to handle the claim in an efficient and equitable
        manner.

                                   ARTICLE 15.

                        DISPUTE RESOLUTION; GOVERNING LAW

15.1    Dispute Resolution. In case of any possible disputes arising out of or
        relating or pertaining to the Collaborative Agreement and/or this
        Agreement, the Parties shall use their reasonable best efforts to try to
        settle those disputes amicably and, if unsuccessful, shall submit the
        matter for review under the Rules of Conciliation and Arbitration of the
        International Chamber of Commerce by one or more arbitrators appointed
        in accordance with said Rules. If resolution of such disputes
        satisfactory to both Parties cannot be reached in this manner, then
        either Party shall have the right to bring an action to resolve such
        dispute before a court of jurisdiction where the Party being sued
        maintains its principal executive offices.

15.2    Governing Law. This Agreement shall be governed and construed in
        accordance with the laws of the State of New York.



                                       12
<PAGE>   13

                                   ARTICLE 16.

                                  MISCELLANEOUS

16.1    Taxes. In the event a Party paying a royalty hereunder is required to
        withhold taxes imposed upon the Party receiving a royalty by virtue of
        the statutes, laws, codes or governmental regulations of a given country
        in which products subject to such royalties are sold, then such payments
        shall be made by the royalty-paying Party on behalf of the other Party
        by deducting them from the royalty payment due such other Party and
        remitting such taxes to the proper authorities on a timely basis; and
        the royalty payments provided for under this Agreement shall be adjusted
        appropriately, provided that the royalty-paying Party supplies the other
        Party with official documentation and/or tax receipts on such
        withholdings supporting such taxes and such payments as may be required
        by such other Party for its tax records.

16.2    Export. In order to comply with the United States Export Administration
        Act of 1979, as amended from time to time (the "Export Act"), each Party
        hereby certifies that no technology or information licensed from the
        other, and no product thereof, shall be made available or re-exported,
        directly or indirectly, to any areas outside the United States except in
        compliance with all applicable laws and regulations of the Bureau of
        Export Administration in accordance with the Export Act. BI shall give
        Isis such written assurance against re-export as required by the Export
        Act.

16.3    Force Majeure. Neither Party shall be held liable or responsible to the
        other Party nor be deemed to have defaulted under or breached this
        Agreement for failure or delay in fulfilling or performing any term of
        this Agreement when such failure or delay is caused by or results from
        causes beyond the reasonable control of the affected Party, including
        but not limited to fire, floods, embargoes, war, act of war (whether war
        be declared or not), insurrections, riots, civil commotions, strikes,
        lockouts or other labor disturbances, acts of God or acts, omissions or
        delays in acting by any governmental authority or the other Party;
        provided, however, it is understood that this Section 16.3 is intended
        only to suspend and not discharge a Party's obligations under this
        Agreement and that when the causes of the failure or delay are removed
        or alleviated, the affected Party shall resume performance of its
        obligations hereunder.

16.4    Assignment. This Agreement may not be assigned or otherwise transferred
        nor, except as expressly provided hereunder, may any right or
        obligations hereunder be assigned or transferred, by either Party
        without the written consent of the other Party; provided, however, that
        either Isis or BI may, without such consent, assign this Agreement and
        its rights and obligations thereunder to a wholly-owned subsidiary. Isis
        and BI may elect to assign this Agreement (a) in connection with the
        transfer or sale of all or substantially all of its business to which
        this Research Plan is related, if such assets include substantially all
        of the assets relating to its performance of its respective obligations
        hereunder, or (b) in the event of its merger or consolidation with
        another company at any time during the term of this Agreement. Each
        Party shall promptly inform the other of the identity and location of
        any permitted assignee. Any purported assignment in violation of the
        preceding sentence shall be void. Any permitted assignee shall assume
        all obligations of its assignor under this Agreement.

16.5    Severability. In case any provision contained in this Agreement shall be
        held to be invalid, illegal or unenforceable in any respect, the
        validity, legality and enforceability of the remaining provisions
        contained herein shall not in any way be affected or impaired thereby.



                                       13
<PAGE>   14

16.6    Notices. All notices, requests, consents and other communications
        hereunder shall be in writing, shall be delivered personally, by
        facsimile transmission or mailed by first-class registered or certified
        airmail or by internationally recognized overnight express courier,
        postage prepaid, and shall be deemed given upon personal delivery, upon
        confirmation of receipt of such facsimile transmission or on the 10th
        day following such mailing and shall be addressed as follows:

                      if to Isis, to:

                      Isis Pharmaceuticals, Inc.
                      2292 Faraday Drive
                      Carlsbad, California 92008
                      Attn.: Ms. B. Lynne Parshall
                             Executive Vice President

                or to such other person at such other address as Isis shall
                designate to BI in writing; and

                      if to BI, to:

                      Boehringer Ingelheim International GmbH
                      Postbox 200
                      D 55216 Ingelheim/Rhein
                      Federal Republic of Germany
                      Attn.: Corporate Division Pharma Business Development
                      Telephone: 49 61 32 77 2430
                      Telecopy: 49 61 32 77 3926

        with copy to

                      Boehringer Ingelheim International GmbH
                      Postbox 200
                      D 55216 Ingelheim/Rhein
                      Federal Republic of Germany
                      Attn.: Head of Corporate Legal Department
                      Telephone: 49 61 32 77 2106
                      Telecopy: 49 61 32 77 4080

        or to such other person(s) at such other address(es) as BI shall
        designate to Isis in writing.

16.7    Entire Agreement. This Agreement constitutes the full and entire
        understanding and agreement among the Parties with regard to the
        subjects hereof and no Party shall be liable or bound to any other Party
        in any manner by any representations, warranties, covenants, or
        agreements except as specifically set forth herein or therein. Nothing
        in this Agreement, expressed or implied, is intended to confer upon any
        Party, other than the Parties hereto and their respective successors and
        assigns, any rights, remedies, obligations, or liabilities under or by
        reason of this Agreement, except as expressly provided herein.

16.8    Amendment and Waiver. Any term of this Agreement may be waived or
        amended in a writing agreed to by Isis and BI.

16.9    Headings. The headings of the various sections of this Agreement have
        been inserted for convenience of reference only and shall not be deemed
        to be part of this Agreement.



                                       14
<PAGE>   15

16.10   Independent Contractors. It is expressly agreed that Isis and BI shall
        be independent contractors and that the relationship between the two
        Parties shall not constitute a partnership or agency of any kind.
        Neither Isis nor BI shall have the authority to make any statements,
        representations or commitments of any kind, or to take any action, which
        shall be binding on the other, without the prior written authorization
        of the Party to do so.

16.11   Waiver. This waiver by either Party hereto of any right hereunder or the
        failure to perform or of a breach by the other Party shall not be deemed
        a waiver of any other right hereunder or of any other breach or failure
        by said other Party whether of a similar nature or otherwise.

16.12   English language. The official text of this Agreement or any notices
        given or accounts or statements required shall be in English.

16.13   Public Announcements. Isis and BI shall consult with each other before
        issuing any press release or otherwise making any public statements or
        disclosures with respect to the transactions contemplated by this
        Agreement or by that certain Amendment to the Stock Purchase Agreement,
        dated as of August 31, 1999, by and between Isis and BI, and shall not
        issue any such press release or make any such public statement or
        disclosure prior to such consultation, except as may be required by
        applicable law.



                                       15
<PAGE>   16

        IN WITNESS WHEREOF, the Parties have executed this Agreement as of the
date first set forth above.

                ISIS PHARMACEUTICALS, INC.

                By: _____________________________________________
                Name:
                Title:

                BOEHRINGER INGELHEIM INTERNATIONAL GmbH

                By: _____________________________________________
                Name:
                Title:

                By: _____________________________________________
                Name:
                Title:



                                       16
<PAGE>   17

                                   APPENDIX A

                                   DEFINITIONS

- -       "Additional Compounds" shall mean, collectively, the compounds known as
        [***] and any compound from out of the [***] series that had been
        synthesized as of the Effective Date, the compounds known as [***].

- -       "Advance" shall have the meaning set forth in Article 7 of the
        Collaborative Agreement.

- -       "Affiliate" shall mean any corporation or other entity which controls,
        is controlled by, or is under common control with a Party to this
        Agreement. A corporation or other entity shall be regarded as in control
        of another corporation or entity if it owns or directly or indirectly
        controls more than fifty percent (50%) of the voting stock or other
        ownership interest of the other corporation or entity, or if it
        possesses, directly or indirectly, the power to direct or cause the
        direction of the management and policies of the corporation or other
        entity or the power to elect or appoint fifty percent (50%) or more of
        the members of the governing body of the corporation or other entity.

- -       "Agreement" shall mean this Agreement, dated as of August 31, 1999, by
        and between BI and Isis, including all appendices, exhibits and
        schedules attached hereto.

- -       "Antisense Molecule" shall mean [***]. An "oligonucleotide" may include
        [***].

- -       "Bankruptcy" shall have the meaning set forth in the Stock Purchase
        Agreement.

- -       "BI Background Intellectual Property" shall mean all issued patents and
        patent applications owned or controlled by BI or any of its Affiliates,
        together with any reissues, reexamination certificates, divisions,
        continuations or continuations-in-part and extensions (patent term
        restoration, supplementary protection certificate, etc.) thereof and
        know-how necessary or useful to carry out the Research Plan.

- -       "Change in Control" shall have the meaning set forth in the Stock
        Purchase Agreement.

- -       "Collaborative Agreement" shall mean that certain Collaborative
        Agreement, dated as of July 18, 1995, between Boehringer Ingelheim
        International GmbH and its Affiliates and Isis and the appendices,
        exhibits and schedules thereto, as amended.

- -       "Confidential Information" means any confidential information, trade
        secrets, know how and any other information relating to any research
        project, work in process, future development, scientific engineering,
        manufacturing, marketing, business plan, financial or personnel matter
        relating to either Party, whether under the Collaborative Agreement or
        this Agreement, such Party's present or future products, sales
        suppliers, customers, employees, investors or business, whether in oral,
        written, graphic or electronic form. Confidential Information shall not
        include:



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       17
<PAGE>   18

        (a) information already known to the receiving Party, other than under
        an obligation of confidentiality, at the time of disclosure by the other
        Party;

        (b) information generally available to the public or otherwise part of
        the public domain at the time of its disclosure to the other Party,

        (c) information that became generally available to the public or
        otherwise part of the public domain after its disclosure and other than
        through any act or omission of the receiving Party in breach of this
        Agreement;

        (d) information disclosed to the receiving Party, other than under in
        obligation of confidentiality, by a Third Party who had no obligation to
        the other Party not to disclose such information to others.

        The Parties agree that the material financial terms of this Agreement
        shall also be considered Confidential Information of both Parties. The
        ownership and control of all Confidential Information relating or
        pertaining to Antisense Molecules shall be deemed to have been
        transferred to Isis hereunder and the ownership and control of all
        Confidential Information relating or pertaining to small molecules shall
        be deemed to have been transferred to BI hereunder in a manner
        consistent with the treatment of Additional Compounds pursuant to
        Section 2.3.

- -       "Credit Maturity Date" means, as to each Advance, the date seven (7)
        years after the date upon which such Advance was made pursuant to the
        Collaborative Agreement.

- -       "Field" shall mean the identification, optimization and development of
        molecules which interfere with the normal process of leucocyte adhesion
        to cellular and extracellular substrates to be used in the treatment of
        immune and non-immune based inflammatory diseases. Specifically included
        within the Field are (a) Antisense Molecules which directly inhibit the
        expression of ICAMs, VCAM-1, PECAM-1, selectins and(beta)2 integrins,
        (b) compounds which modulate the interaction of leucocyte integrins,
        with their respective binding ligands and the interaction of selectins
        with their binding structures, (c) non-antisense compounds which
        modulate the expression of ICAMs, VCAM-1, PECAM-1, selectins and
        leucocyte integrins by interfering with in intracellular process, and
        (d) compounds which inhibit the shedding of selectins, ICAMs, VCAM-1,
        and PECAM-1 from the cell surface.

- -       "Isis Background Intellectual Property" shall mean all issued patents
        and patent applications owned or controlled by Isis or any of its
        Affiliates, together with any reissues, reexamination certificates,
        divisions, continuations or continuations-in-part and extensions (patent
        term restoration, supplementary protection certificate, etc.) thereof
        and know-how necessary or useful to carry out the Research Plan.

- -       "Joint [***] Patent(s)" shall mean all joint issued patents and joint
        patent applications, together with any reissues, reexamination
        certificates, divisions, continuations or continuations-in-part and
        extensions (patent term restoration, supplementary protection
        certificate, etc.) thereof relating to antagonism of [***] activity
        covered by the Collaborative Agreement.

- -       "Net Sales" shall mean the gross invoiced price charged by BI or Isis
        (as appropriate) or its respective Affiliates or licensees (including
        sub-licensees), as the case may be, for a given product to an
        independent Third Party less the following customary deductions:



                                               *CONFIDENTIAL TREATMENT REQUESTED
                                       18
<PAGE>   19


        (i)     trade and quantity discounts actually granted;
        (ii)    credits for returns or allowances;
        (iii)   the amount of any sales tax or other taxes assessed directly on
                the sale of such product which is not refunded;
        (iv)    charge back payments or rebates granted to managed health care
                organizations or federal, state and local governments, their
                agencies, purchasers and reimbursers.

        In the case of sales of a given product by a Party's licensee or
        sub-licensee under an agreement in the ordinary course of a Party's
        business containing terms customary for the pharmaceuticals industry, if
        net sales are calculated under such agreement differently than Net Sales
        are calculated hereunder, "Net Sales" hereunder shall be deemed to be
        calculated in the manner calculated under the applicable agreement,
        provided that such calculation of net sales shall be reasonably
        consistent with this definition of "Net Sales." Each Party shall be
        obligated to notify the other Party on a timely basis of the method of
        calculation of net sales under all such agreements with licensees or
        sub-licensees.

- -       "Party" shall mean BI or Isis and "Parties" shall mean BI and Isis
        collectively.

- -       "Program Intellectual Property" shall mean all patents and patent
        applications together with any reissues, reexamination certificates,
        divisions, continuations or continuations-in-part and extensions (patent
        term restoration, supplementary protection certificate, etc.) thereof
        and know-how conceived, created or developed by either Party, solely or
        jointly, during and as part of the Research Plan.

- -       "Research Management Committee" (RMC) shall mean the joint committee
        composed of an equal number of representatives of BI and Isis
        responsible for overseeing the Research Plan as described in Section 3.4
        of this Agreement.

- -       "Research Period" shall mean the time period commencing on the Effective
        Date and ending on December 31, 1999.

- -       "Research Plan" shall mean a description of the activities as defined by
        the RMC to be performed by BI and Isis during the Research Period of the
        Research Plan, consisting of the design and performance of experiments
        for the purpose of evaluating the Ibis technology and functional
        genomics using antisense technology.

- -       "Stock Purchase Agreement" shall mean that certain Stock Purchase
        Agreement, dated July 18, 1995, between Isis and BI.

- -       "Third Party" shall mean any entity other than Isis and BI and their
        respective Affiliates and licensees (which shall include sub-licensees).




                                       19

<PAGE>   1

                                                                    EXHIBIT 10.2

                    AMENDMENT TO THE STOCK PURCHASE AGREEMENT

                This AMENDMENT TO THE STOCK PURCHASE AGREEMENT (this
"Amendment"), made this 31st day of August, 1999, by and between Isis
Pharmaceuticals, Inc., a Delaware corporation ("Isis"), and Boehringer Ingelheim
International GmbH, a German corporation ("Boehringer"),

                              W I T N E S S E T H :

        WHEREAS, Isis and BI entered into that certain stock purchase agreement,
dated as of July 18, 1995 (the "Stock Purchase Agreement");

        WHEREAS, Paragraph 11.5 of the Stock Purchase Agreement provides that
any term thereof may be amended in a writing agreed to by Isis and Boehringer;
and

        WHEREAS, Isis and Boehringer have agreed to amend the Stock Purchase
Agreement as provided herein,

        NOW, THEREFORE, in consideration of the mutual agreements and covenants
set forth herein, and for other good and valuable consideration, the parties
hereby agree that the Stock Purchase Agreement shall be amended as of the date
hereof as follows:

        Section 1. Sub-paragraphs (b), (c) and (d) of Paragraph 3.1 and the
final paragraph of Paragraph 3.1 of the Stock Purchase Agreement (Agreement to
Sell and Purchase the Additional Shares) shall be deleted in their entirety.

        Section 2. Paragraph 3.2 of the Stock Purchase Agreement (Delivery of
Additional Shares at a Subsequent Closing; Purchase price) shall be deleted in
its entirety.

        Section 3. The first sentence of Paragraph 10 of the Stock Purchase
Agreement (Termination) shall be amended to read in its entirety as follows:

                This Agreement shall terminate upon (i) any Change in Control of
                Isis, (ii) the Bankruptcy of Isis or (iii) the termination of
                the New Agreement pursuant to Article 10 thereof.

        Section 4. Sub-paragraph (e) of Paragraph 8.1 (Board Representation) is
amended in its entirety to read as follows:

                (e)     Paragraph 8.1 shall terminate upon the earliest to occur
                        of:
                        (i)     May 1, 2000;
                        (ii)    The effectiveness of any Change in Control; or
                        (iii)   Boehringer ceases to hold at least 2,000,000
                                shares of

                Common Stock (appropriately adjusted for stock splits, stock
                dividends, recapitalization and the like). If Paragraph 8.1
                terminates, the BI Designate shall resign from the Board.

        Section 5. In Exhibit A, the definition of "Additional Shares shall be
amended to read in its entirety as follows:


<PAGE>   2

                "ADDITIONAL SHARES" shall mean the shares issued to Boehringer
                Ingelheim under Paragraph 3.1 of the Agreement prior to the
                effective date of the Amendment.

        Section 6. Exhibit A shall be amended by the addition of the following
definitions:

                "AMENDMENT" shall mean that certain Amendment to the Stock
                Purchase Agreement, dated August 31, 1999, by and between Isis
                and Boehringer.

                "NEW AGREEMENT" shall mean that certain Agreement, dated as of
                August 31, 1999, by and between Boehringer and Isis.

        Section 7. This Amendment shall be governed by and construed in
accordance with the laws of the State of Delaware and the federal law of the
United States of America.



                                       2
<PAGE>   3

        IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be
executed by their duly authorized representatives as of the day and year first
above written.

                     ISIS PHARMACEUTICALS, INC.

                     By: __________________________________
                     Name:
                     Title:

                     BOEHRINGER INGELHEIM INTERNATIONAL GMBH

                     By: __________________________________
                     Name:
                     Title:

                     By: __________________________________
                     Name:
                     Title:



                                       3


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