<PAGE>

                                                                   EXHIBIT 10.21

                     NONEXCLUSIVE PATENT LICENSE AGREEMENT

This Nonexclusive Patent License Agreement is made and effective as of February
11, 2000 (the "Effective Date"), by and between 3-Dimensional Pharmaceuticals,
Inc., a corporation having its principal place of business at Eagleview
Corporate Center, 665 Stockton Drive, Suite 104, Exton, PA 19341 ("3DP"), and
DuPont Pharmaceuticals Company (a wholly-owned subsidiary of E. I. DuPont de
Nemours & Co. ("DuPont")) having its principal place of business at Centre Road,
Chestnut Run Plaza, Building 721, Wilmington DE 19880 ("DPC"). 3DP and DPC may
be referred to herein as a "Party" or, collectively, as the "Parties".

WHEREAS, 3DP has developed and patented certain DirectedDiversity(R) technology
for generating chemical compounds having desired biological, chemical and other
properties;

WHEREAS, DPC is engaged in research and development of biologically active
compounds for the treatment of human disease;

WHEREAS, DPC wishes to license certain patent rights from 3DP on a nonexclusive
basis;

WHEREAS, the parties desire to enter into this Agreement to set forth the
licensing terms for such rights;

NOW, THEREFORE, in consideration of the various promises and undertakings set
forth herein, and intending to be legally bound, the Parties agree as follows:


Article 1  DEFINITIONS

The terms in this Agreement with initial letters capitalized, whether used in
the singular or the plural, shall have the meaning set forth below or, if not
listed below, the meaning designated in places throughout this Agreement.

     1.1  "Affiliate" means any corporation or other business entity which
          controls, is controlled by, or is under common control with 3DP or
          DPC. A corporation or other entity shall be regarded as in control of
          another corporation or entity if it owns or directly or indirectly
          controls at least 50% of the voting stock or other ownership interest
          of the other corporation or entity (or alternatively, if it owns the
          maximum such ownership interest permitted by law), 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 at least 50% of the members of the governing
          body of the corporation or other entity.

     1.2  "Agreement" means the present agreement including its Appendices.
<PAGE>

     1.3  "Confidential Information" means all information that has or could
          have commercial value or other utility in a Party's business, or the
          unauthorized disclosure of which could be detrimental to the Party's
          interests, including confidential information, inventions, know-how,
          data and materials relating to the Licensed Patents, and shall include
          without limitation research, technical, clinical development,
          manufacturing, marketing, financial, personnel and other business
          information and plans, whether in oral, written, graphic or electronic
          form.

     1.4  "DPC" means DuPont Pharmaceuticals Company as identified above.

     1.5  "DPC Site" means a Site which is a DPC Site or a Site of a DPC
          Affiliate which is involved in pharmaceutical (including diagnostic
          imaging) research and development.

     1.6  "DuPont" means E. I. DuPont de Nemours & Co. as identified above.

     1.7  "Effective Date" means the effective date of this Agreement as set
          forth above.

     1.8  "Field" means the research and development of chemical materials for
          use in pharmaceutical and diagnostic products. With respect to the
          Other DuPont Site described in Section 3.3, the Parties shall agree to
          the applicable definition of Field.

     1.9  "Improvements" means any inventions, discoveries, improvements or
          enhancements, whether or not patented or patentable, relating to the
          subject matter claimed in the Licensed Patents.

     1.10 "Licensed Patents" means all U.S. and foreign patent applications or
          issued patents identified in Appendix A, and any U.S. and foreign
                                       ----------
          patent applications or issued patents claiming Improvements made by
          3DP in respect thereof, including any provisionals, divisionals,
          continuations, continuations-in-part, reissues and extensions derived
          therefrom, such as patent term restorations, supplementary protection
          certificates, etc., to the foregoing that may be filed by or granted
          to 3DP during the term of this Agreement.

     1.11 "Other DuPont Site" means a Site which is a DuPont Site or a Site of a
          DuPont Affiliate which is not a DPC Site and is not involved in
          pharmaceutical (including diagnostic imaging) research and
          development.

     1.12 "Site" means a discrete research facility, for example, a building or
          building complex at which DPC or an Affiliate of DPC conducts internal
          research and development activities, in a geographic location distinct
          from other research facilities of DPC or an Affiliate of DPC.

     1.13 "Site License Fee" shall have the meaning set forth in Section 3.2
          below.

                                       2
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     1.14 "Third Party" means an individual, corporation or other entity other
          than the Parties and their Affiliates.

     1.15 "3DP" means 3-Dimensional Pharmaceuticals, Inc. as identified above.

Article 2  GRANT OF LICENSE

     2.1  Nonexclusive Patent License. 3DP hereby grants DPC (and its
          ---------------------------
          Affiliates, but only to the extent specifically permitted herein) a
          nonexclusive license, without any right to sublicense, under the
          Licensed Patents in the Field but only in Direct Support of DPC's (or
          its Affiliate's as permitted herein) internal and collaborative
          research and development activities. As used herein, "Direct Support"
          means that DPC (or its Affiliates as permitted herein) may operate
          under the Licensed Patents to identify compounds with activity against
          targets that have been selected through DPC's (or its Affiliate's as
          permitted herein) internal research and development programs or to
          identify compounds for which DPC (or its Affiliates as permitted
          herein) will pay for a share of the development costs or receives at
          least a 10% royalty (or equivalent revenue share) or has any rights of
          commercialization. In accordance with the foregoing, it is
          acknowledged and understood that DPC and its Affiliates are not
          permitted under the license granted herein to compete with 3DP by
          providing combinatorial chemistry services to third parties on a fee-
          for-service basis.

          The rights granted hereunder may be extended by DPC to one (1) Other
          DuPont Site, provided that in such event DuPont or its Affiliate shall
          be bound in the same way as DPC with respect to all the terms and
          conditions of this Agreement. In such event DuPont (or its Affiliate
          as permitted herein) shall have a nonexclusive license, without any
          right to sublicense, under the Licensed Patents in the Field but only
          in Direct Support of DuPont's (or its Affiliate's as permitted herein)
          internal and collaborative research and development activities. As
          used in this paragraph, "Direct Support" means that DuPont (or its
          Affiliate as permitted herein) may operate under the Licensed Patents
          to identify compounds with activity against targets that have been
          selected through DuPont's (or its Affiliate's as permitted herein)
          internal research and development programs or to identify compounds
          for which DuPont (or its Affiliate as permitted herein) will pay for a
          share of the development costs or receives at least a 10% royalty (or
          equivalent revenue share) or has any rights of commercialization.

     2.2  Limitations on License Grant. Except as permitted under Section 2.1,
          ----------------------------
          DPC (and any of its Affiliates, to the extent permitted below) may not
          operate under the Licensed Patents on behalf of any Third Parties such
          as, for example, in connection with providing research or development
          services to any Third Party on a contractual basis. The foregoing
          license

                                       3
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          grant is further limited to on-site activities at one or more actual
          DPC Sites, and does not include or permit off-site or remote access
          through the internet or otherwise. In addition, the foregoing license
          does not permit activities by DPC or DuPont or their Affiliates under
          this Agreement that are covered by that certain Collaborative Research
          and License Agreement, effective on October 12, 1998, between 3DP and
          E. I. DuPont de Nemours & Co.

     2.3  Term and Renewal. The initial term of this Agreement shall expire on
          ----------------
          April 1, 2000. However, this Agreement may be renewed by DPC on an
          annual basis by payment of the Site License Fees as set forth in
          Section 3.2.

     2.4  Non-Assertion. During the term of this Agreement and so long as DPC
          -------------
          has not committed any material breach with respect to any obligation
          hereunder, 3DP will not assert any patent or patent application
          against DPC to prevent DPC from practicing the rights granted to DPC
          under Article 2 hereof.

Article 3  FINANCIAL TERMS

     3.1  License Fee. In consideration of the grant of rights under Article 2
          -----------
          of this Agreement, DPC agrees to pay an initial nonrefundable license
          fee of [**] within thirty (30) days of the Effective Date of this
          Agreement. This initial license fee shall be creditable against the
          first annual Site License Fee payable in accordance with Section 3.2.

     3.2  Individual Site License Fees. [**]

     3.3  Location of DPC Sites. The location(s) of the DPC Site(s) may include
          ---------------------
          the Wilmington Experimental Station, to the extent that DPC conducts
          research and development activities there, and other DPC Sites to be
          determined at DPC's sole discretion. Notwithstanding the foregoing,
          DPC may permit one (1) Other DuPont Site to operate under the Licensed
          Patents subject to the approval of 3DP, such approval not to be
          unreasonably withheld. Once approved, DPC may not transfer the license
          to another Other DuPont Site without the approval of 3DP, such
          approval not to be unreasonably withheld. Any such Other DuPont Site
          shall be considered to be a DPC Site for the purpose of determining
          License Fees, and operations under the Licensed Patents at any such
          Site shall be subject to all of the other terms and conditions of this
          Agreement.

     3.4  Mode of Payment. All license payments to 3DP hereunder shall be made
          ---------------
          by wire transfer of United States Dollars in the requisite amount to
          such bank account as 3DP may designate by notice to DPC. Payments
          shall be free and clear of any taxes, fees or charges, to the extent
          applicable.



**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                       4
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     3.5  Most Favored Licensee Provision.  [**]

          Upon the written request of DPC and not more than once in each
          calendar year, 3DP shall permit an independent certified public
          accounting firm of nationally recognized standing selected by DPC and
          acceptable to 3DP (which acceptance by 3DP shall not be unreasonably
          withheld), at DPC's expense, to have access during normal business
          hours to such records of 3DP as may be reasonably necessary to verify
          3DP's compliance with the provisions of this Section 3.5. The
          accounting firm shall enter into an acceptable and customary
          confidentiality agreement with 3DP obligating the accounting firm to
          retain in confidence all information of 3DP which it obtains in
          performing such audits hereunder, and such audit shall be subject to
          3DP's third party confidentiality obligations. Such accounting firm
          shall report to DPC and 3DP whether or not 3DP is in compliance with
          this Section 3.5. If 3DP is not in compliance with this Section 3.5,
          such accounting firm shall disclose the financial terms of the Third
          Party license which contains more favorable financial terms than those
          applicable to DPC hereunder. In no event shall such accounting firm
          disclose the identity of the Third Party with whom 3DP has entered
          into a license.

     3.6  [**]

**Certain portions of this Exhibit have been ommitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                       5
<PAGE>

          [**]

Article 4  OBLIGATIONS OF DPC

     4.1  Annual Reports. DPC shall provide 3DP with written annual reports
          --------------
          within sixty (60) days after the end of each calendar year during the
          term of this Agreement to identify the DPC (or Affiliate's) Sites that
          are operating under the Licensed Patents.

Article 5  CONFIDENTIALITY

     5.1  Confidentiality Obligations. The Parties agree that, for the term of
          ---------------------------
          this Agreement and for ten (10) years thereafter, either Party that
          receives Confidential Information (a "Receiving Party") from the other
          Party (a "Disclosing Party") shall keep completely confidential and
          shall not publish or otherwise disclose and shall not use for any
          purpose (except as expressly permitted hereunder) any Confidential
          Information furnished to it by the "Disclosing Party" pursuant to this
          Agreement (including without limitation, know-how), except to the
          extent that it can be established by the Receiving Party that such
          Confidential Information:

          (a)  was already known to the Receiving Party, other than under an
               obligation of confidentiality from the Disclosing Party;

          (b)  was generally available to the public or otherwise part of the
               public domain at the time of its disclosure to the Receiving
               Party;

          (c)  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)  was subsequently lawfully disclosed to the Receiving Party by a
               Third Party;

          (e)  can be shown by written records to have been independently
               developed by the Receiving Party without reference to the
               Confidential Information received from the Disclosing Party and
               without breach of any of the provisions of this Agreement; or


**Certain portions of this Exhibit have been omitted based upon a request for
confidential treatment that has been filed with the Commission. The omitted
portions have been filed separately with the Commission.

                                       6
<PAGE>

          (f)  the disclosing party has specifically agreed in writing that the
               receiving party may disclose.

          The obligations of confidentiality and non-use set forth in this
          Section 6.1 shall also apply to biological material and chemical
          compounds and associated information (including without limitation
          know-how) disclosed by one Party to the other prior to or during the
          term of this Agreement; provided however, that such obligation of
          confidentiality and non-use shall not apply with respect to compounds
          which are assigned to DPC or exclusively licensed to DPC by 3DP.

     5.2  Written Assurances and Permitted Uses of Confidential Information.

          (a)  The Receiving Party may disclose Confidential Information to the
               extent the Receiving Party is compelled to disclose such
               information by a court or other tribunal of competent
               jurisdiction, provided however, that in such case the Receiving
               Party shall immediately give notice to the Disclosing Party so
               that the Disclosing Party may seek a protective order or other
               remedy from said court or tribunal. In any event, the Receiving
               Party shall disclose only that portion of the Confidential
               Information that, in the opinion of its legal counsel, is legally
               required to be disclosed and will exercise reasonable efforts to
               ensure that any such information so disclosed will be accorded
               confidential treatment by said court or tribunal.

          (b)  To the extent it is reasonably necessary or appropriate to
               fulfill its obligations and exercising its rights under this
               Agreement, the Parties may disclose Confidential Information to
               their Affiliates on a need-to-know basis on condition that such
               Affiliates agree to keep the Confidential Information
               confidential for the same time periods and to the same "extent as
               the Party is required to keep the Confidential Information
               confidential under this Agreement.

          (c)  The existence and the terms and conditions of this Agreement
               which the Parties have not specifically agreed to disclose
               pursuant to this Section 5.2 shall be treated by each Party as
               Confidential Information of the other Party.

          (d)  If a Party is required to make any disclosure of the other
               Party's Confidential Information, it will give at least thirty
               (30) days written, advance notice to the latter Party of such
               disclosure requirement. If a Party is required to disclose
               Confidential Information to comply with applicable laws or
               governmental regulations, including but not limited to submitting
               information to tax authorities or to comply with any discovery or
               similar request for production of documents in litigation or
               similar alternative

                                       7
<PAGE>

               dispute resolution proceedings, such party may make such
               disclosure provided it gives prompt notice to the other Party,
               and provided it makes all reasonable efforts to comply with all
               administrative or other procedures or to establish a reasonable
               protective or similar order under which the confidential nature
               of the information will be maintained.

     5.3  Permitted Disclosures for Business Development Purposes.
          -------------------------------------------------------
          Notwithstanding the foregoing, or any other provision in this
          Agreement to the contrary, 3DP may describe the financial terms of
          this Agreement in confidence, in connection with capital raising or
          financing activities, provided however, that any such recipient of
          such disclosure shall agree in writing to keep such terms confidential
          for the same time periods and to the same extent as 3DP is required to
          keep Confidential Information confidential under this Agreement.
          Furthermore, DPC acknowledges that 3DP may be obligated to disclose
          terms of this Agreement and make public a copy of this Agreement in
          the event it becomes a public company as required by applicable U.S.
          law; provided however, that the terms and copy of this Agreement shall
          be redacted such that the extent of any such disclosure shall be
          limited to that which in the opinion of 3DP's legal counsel is legally
          required to be disclosed.

Article 6  PATENTS AND INFRINGEMENT

     6.1  Licensed Patents. 3DP shall prepare, file, prosecute and maintain the
          ----------------
          Licensed Patents at 3DP's expense and in a manner deemed appropriate
          in 3DP's sole judgment.  3DP agrees to keep DPC fully advised of the
          status of all Licensed Patents, upon reasonable written request from
          DPC.

     6.2  Infringement of the Licensed Patents by Third Parties. In the event
          -----------------------------------------------------
          that DPC becomes aware of any infringement by Third Parties of any of
          the Licensed Patents, subject to any confidentiality obligations DPC
          may have, DPC shall promptly notify 3DP. 3DP shall respond to any such
          infringement by Third Parties in a manner deemed appropriate by 3DP in
          its sole judgment.

     6.3  Third Party Patent Rights.  If any warning letter or other notice of
          -------------------------
          infringement is received by a Party, or action, suit or proceeding is
          brought against a Party alleging infringement of a patent of any Third
          Party with respect to operations under the Licensed Patents, the
          Parties shall promptly discuss and decide the best way to respond.

Article 7  REPRESENTATIONS AND WARRANTIES

     7.1  Authority. Each Party represents and warrants that it has the full
          ---------
          right, power and authority to execute, deliver and perform its
          obligations pursuant to this Agreement.

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     7.2  No Conflicts.  Each Party represents and warrants that the execution,
          ------------
          delivery and performance of this Agreement does not conflict with, or
          constitute a breach or default under any of its charter or
          organizational documents, any law, order, judgment or governmental
          rule or regulation applicable to it, or any material agreement,
          contract, commitment or instrument to which it is a party.

     7.3  No Existing Third Party Rights. The Parties represent and warrant that
          ------------------------------
          their obligations under this Agreement are not encumbered by any
          rights granted by either Party to any Third Parties, which are or may
          be inconsistent with the rights and licenses granted in this
          Agreement.

     7.4  No Unauthorized Operations Under Licensed Patents.  DPC represents and
          -------------------------------------------------
          warrants that it will not operate under the Licensed Patents at any
          Site not identified to 3DP pursuant to Article 3 of this Agreement.

     7.5  Continuing Representations. The representations and warranties of each
          --------------------------
          Party contained in this Article 7 shall survive the execution and
          delivery of this Agreement and shall remain true and correct at all
          times during the term of this Agreement with the same effect as if
          made on and as of such later date.

     7.6  Disclaimer of Warranties.  3DP MAKES NO REPRESENTATIONS AND EXTENDS NO
          ------------------------
          WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED, WITH
          RESPECT TO THE LICENSED PATENTS INCLUDING, BUT NOT LIMITED TO,
          WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

     7.7  3DP represents and warrants that Appendix A is accurate and complete
                                           ----------
          and identifies all patent rights owned by 3DP as of the Effective Date
          which are necessary for the use of the methods and technology claimed
          in the Licensed Patents in accordance with the license granted
          hereunder.

     7.8  DPC represents and warrants that as of the Effective Date, DPC is not
          operating under a valid, enforceable claim within the Licensed
          Patents. DPC further represents and warrants that it will not operate
          under a valid, enforceable claim within the Licensed Patents at any
          Site unless and until DPC activates a Site License pursuant to Section
          3.2 for that Site.

Article 8  TERM AND TERMINATION

     8.1  Term. This Agreement shall commence upon the Effective Date and
          ----
          terminate on April 1, 2000 unless extended pursuant to the provisions
          of Sections 2.3 and 3.2 of this Agreement.

     8.2  Termination for Breach. The failure by a Party to comply with any of
          ----------------------
          the material obligations contained in this Agreement shall entitle the
          other

                                       9
<PAGE>

          Party to give notice to have the default cured. If such default is not
          cured within sixty (60) days after the receipt of such notice, or
          diligent steps are not taken to cure if by its nature such default
          could not be cured within sixty (60) days, the notifying Party shall
          be entitled, without prejudice to any of its other rights conferred on
          it by this Agreement, and in addition to any other remedies that may
          be available to it, to terminate this Agreement, provided, however,
          that such right to terminate shall be stayed in the event that, during
          such sixty (60) day period, the Party alleged to have been in default
          shall have: (a) initiated arbitration in accordance with Section 9.1,
          below, with respect to the alleged default, and (b) diligently and in
          good faith cooperated in the prompt resolution of such arbitration
          proceedings.

     8.3  No Waiver. The right of a Party to terminate this Agreement, as
          ---------
          provided in Section 8.2, shall not be affected in any way by its
          waiver or failure to take action with respect to any prior default.

     8.4  Insolvency or Bankruptcy.

          (a)  Either Party may, in addition to any other remedies available by
               law or in equity, terminate this Agreement by written notice to
               the other Party in the event the latter Party shall have become
               insolvent or bankrupt, or shall have an assignment for the
               benefit of its creditors, or there shall have been appointed a
               trustee or receiver of the other Party or for all or a
               substantial part of its property or any case or proceeding shall
               have been commenced or other action taken by or against the other
               Party in bankruptcy or seeking reorganization, liquidation,
               dissolution, winding-up, arrangement or readjustment of its debts
               or any other relief under any bankruptcy, insolvency,
               reorganization or other similar act or law of any jurisdiction
               now or hereafter in effect, or there shall have been issued a
               warrant of attachment, execution, distraint or similar process
               against any substantial part of the property of the other Party,
               and any such event shall have continued for 90 days undismissed,
               unbonded and undischarged.

          (b)  All rights and licenses granted under or pursuant to this
               Agreement by DPC or 3DP are, and shall otherwise be deemed to be,
               for purposes of Section 365(n) of the U.S. Bankruptcy Code,
               licenses of right to "Intellectual property" as defined under
               Section 101 of the U.S. Bankruptcy Code. The Parties agree that
               the Parties as licensees of such rights under this Agreement,
               shall retain and may fully exercise all of their rights and
               elections under the U.S. Bankruptcy Code. The Parties further
               agree that, in the event of the commencement of a bankruptcy
               proceeding by or against either

                                       10
<PAGE>

               Parties under the U.S. Bankruptcy Code, the Parties hereto which
               is not a party to such proceeding shall be entitled to a complete
               duplicate of (or complete access to, as appropriate) any such
               intellectual property and all embodiments of such intellectual
               property, and same, if not already in their possession, shall be
               promptly delivered to them (i) upon any such commencement of a
               bankruptcy proceeding upon their written request therefor, unless
               the Party subject to such proceedings elects to continue to
               perform all of their obligations under this Agreement or (ii) if
               not delivered under (i) above, upon the rejection of this
               Agreement by or on behalf of the Party subject to such proceeding
               upon written request therefor by a nonsubject Party.

     8.5  Termination by DPC. Subject to Section 8.6, DPC shall have the right
          ------------------
          to terminate the license granted hereunder upon written notice to 3DP
          or by failure to pay at least 1 annual Site License Fee in accordance
          with Sections 2.3 and 3.2.

     8.6  Survival of Obligations.  The termination or expiration of this
          -----------------------
          Agreement shall not relieve the Parties of any obligations accruing
          prior to such termination, and any such termination shall be without
          prejudice to the rights of either Party against the other. The
          provisions of Sections 3.4 and 6.4 and Articles 4, 5, 9, 10 and 11
          shall survive any termination of this Agreement.

Article 9 DISPUTE RESOLUTION

     9.1  Dispute Resolution.  Any dispute concerning or arising out of this
          ------------------
          Agreement or concerning the existence or validity hereof, shall be
          determined by the following procedure.

          (a)  Both Parties understand and appreciate that their long term
               mutual interest will be best served by affecting a rapid and fair
               resolution of any claims or disputes which may arise out of
               services performed under this contract or from any dispute
               concerning the terms of this Agreement. Therefore, both Parties
               agree to use their best efforts to resolve all such disputes as
               rapidly as possible on a fair and equitable basis. Toward this
               end, both Parties agree to develop and follow a process for
               presenting, rapidly assessing, and settling claims on a fair and
               equitable basis which takes into account the precise subject and
               nature of the dispute.

          (b)  If any dispute or claim arising under this Agreement cannot be
               readily resolved by the Parties pursuant to the process described
               above, then the Parties agree to refer the matter to a panel
               consisting of the Chief Executive Officer ("CEO") of each Party
               or their designees for review and a non-binding resolution. A
               copy of

                                       11
<PAGE>

               the terms of this Agreement, agreed upon facts (and areas of
               disagreement), and concise summary of the basis for each side's
               contentions will be provided to both such CEOs who shall review
               the same, confer, and attempt to reach a mutual resolution of the
               issue.

          (c)  If the matter has not been resolved utilizing the foregoing
               process, and the Parties are unwilling to accept the non-binding
               decision of the indicated panel, either or both Parties may elect
               to pursue definitive resolution through binding arbitration,
               which the Parties agree to accept in lieu of litigation or other
               legally available remedies (with the exception of injunctive
               relief where such relief is necessary to protect a Party from
               irreparable harm pending the outcome of any such arbitration
               proceeding). Binding arbitration shall be settled in accordance
               with the Rules of Conciliation and Arbitration of the
               International Chamber of Commerce by a panel of three arbitrators
               chosen in accordance with these Rules. This Agreement shall be
               governed by and construed in accordance with the substantive laws
               of the State of Delaware without regard to the conflicts of laws
               provisions of Delaware. The arbitration will be held in
               Wilmington, Delaware. Judgment upon the award rendered may be
               entered in any court having jurisdiction and the Parties hereby
               consent to the said jurisdiction and venue, and further
               irrevocably waive any objection which either Party may have now
               or hereafter to the laying of venue of any proceedings in said
               courts and to any claim that such proceedings have been brought
               in an inconvenient forum, and further irrevocably agree that a
               judgment or order in any such proceeding shall be conclusive and
               binding upon the Parties and may be enforced in the courts of any
               other jurisdiction.

Article 10  INDEMNIFICATION

          (a)  Indemnification of 3DP. DPC shall indemnify and defend 3DP and
               its Affiliates and the directors, officers, employees, agents and
               counsel of 3DP and such Affiliates and the successors and assigns
               of any of the foregoing (the "3DP Indemnitees"), and hold the 3DP
               Indemnitees harmless from and against any and all losses
               resulting from any claim, suit or proceeding brought by a Third
               Party against a 3DP Indemnitee, arising from or occurring as a
               result of the operations by DPC under the Licensed Patents; or
               the manufacture, import, use, offer for sale or sale of products
               developed in whole or in part through the operations by DPC under
               the Licensed Patents; except to the extent any such claim, suit
               or proceeding results from the breach of any of the provisions of
               this Agreement, negligence or willful misconduct of 3DP.

                                       12
<PAGE>

     10.2      Procedure. Any of the 3DP Indemnitees that intends to claim
               ---------
               indemnification under this Article 10 shall promptly notify DPC
               (the "Indemnitor") in writing of any loss in respect of which the
               3DP Indemnitee intends to claim such indemnification, and the
               Indemnitor shall have the right to participate in, and, to the
               extent the Indemnitor so desires, to assume the defense thereof
               with counsel mutually satisfactory to the Parties; provided,
               however, that a 3DP Indemnitee shall have the right to retain its
               own counsel, with the fees and expenses to be paid by the
               Indemnitee, if representation of such Indemnitee by the counsel
               retained by the Indemnitor would be inappropriate due to actual
               or potential differing interests between such 3DP Indemnitee and
               the Indemnitor in such proceeding. The Indemnitor shall control
               the defense and/or settlement of any such loss, and the indemnity
               agreement in this Article 10 shall not apply to amounts paid in
               connection with any loss if such payments are made without the
               consent of the Indemnitor, which consent shall not be withheld
               unreasonably. The failure to deliver written notice to the
               Indemnitor within a reasonable time after the commencement of any
               such action, if prejudicial to its ability to defend such action,
               shall relieve such Indemnitor of any liability to the 3DP
               Indemnitee under this Article 10. At the Indemnitor's request,
               the 3DP Indemnitee under this Article 10, and its employees and
               agents, shall cooperate fully with the Indemnitor and its legal
               representatives in the investigation of any loss covered by this
               indemnification and provide true, correct and complete
               information with respect thereto.

Article 11  MISCELLANEOUS

     11.1      Entire Agreement.  This Agreement and its Appendices constitute
               ----------------
               and contain the entire understanding and agreement of the Parties
               respecting the subject matter of this Agreement and cancels and
               supersedes any all prior negotiations, correspondence,
               understandings and agreements between the Parties, whether oral
               or written, regarding such subject matter.

     11.2      Further Actions.  Each Party agrees to execute, acknowledge and
               ---------------
               deliver such further instruments and to do all such other acts as
               may be necessary or appropriate in order to carry out the
               purposes and intent of this Agreement.

     11.3      Binding Effect.  This Agreement and the rights granted herein
               --------------
               shall be binding upon and shall inure to the benefit of 3DP, DPC
               and their successors and permitted assigns .

     11.4      Assignment.  This Agreement may be assigned by either Party in
               ----------
               connection with the sale or transfer of substantially all of its
               assets that relate to this Agreement, or in the event of its
               merger or consolidation or

                                       13
<PAGE>

               change of control or similar transaction. Any permitted assignee
               shall assume all obligations of its assignor under this
               Agreement.

     11.5      No Implied Licenses.  No rights to any other patents, know-how or
               -------------------
               technical information, or other intellectual property rights,
               other than as explicitly identified herein, are granted or deemed
               granted by this Agreement. No right, expressed or implied, is
               granted by this Agreement to a Party to use in any manner the
               name or any other trade name or trademark of the other Party in
               connection with the performance of this Agreement.

     11.6      No Waiver.  No waiver, modification or amendment of any provision
               ---------
               of this Agreement shall be valid or effective unless made in
               writing and signed by a duly authorized officer of each Party. No
               waiver, modification or amendment of any provision of this
               Agreement shall be valid or effective unless made in writing and
               signed by a duly authorized officer of each Party. The failure of
               either Party to assert a right hereunder or to insist upon
               compliance with any term or condition of this Agreement shall not
               constitute a waiver of that right or excuse a similar subsequent
               failure to perform any such term or condition.

     11.7      Force Majeure.  The failure of a Party to perform any obligation
               -------------
               under this Agreement by reason of acts of God, acts of
               governments, riots, wars, strikes, accidents or deficiencies in
               materials or transportation or other causes of a similar
               magnitude beyond its control shall not be deemed to be a breach
               of this Agreement.

     11.8      Independent Contractors.  Both Parties are independent
               -----------------------
               contractors under this Agreement. Nothing contained in this
               Agreement is intended nor is to be construed so as to constitute
               3DP or DPC as partners or joint venturers with respect to this
               Agreement. Neither Party shall have any express or implied right
               or authority to assume or create any obligations on behalf of or
               in the name of the other Party or to bind the other Party to any
               other contract, agreement, or undertaking with any Third Party.

     11.9      Notices and Deliveries.  Any formal notices, request, delivery,
               ----------------------
               approval or consent required or permitted to be given under this
               Agreement shall be in writing and shall be deemed to have been
               sufficiently given when it is received, whether delivered in
               person, transmitted by facsimile with contemporaneous
               confirmation, or delivery by registered letter (or its
               equivalent) or delivery by certified overnight courier service,
               to the Party to which it is directed at its address shown below
               or such other address as such Party shall have last given by
               notice to the other Parties.

                                       14
<PAGE>

               If to DPC:

               Vice President, Product Planning and Acquisitions
               DuPont Pharmaceuticals Company
               974 Centre Road, Chestnut Run Plaza
               Wilmington, DE 19805
               Fax: 302-992-3040

               with a copy to:

               Associate General Counsel
               Legal Division
               DuPont Pharmaceuticals Company
               974 Centre Road, Chestnut Run Plaza, WR1028
               Wilmington, DE 19805
               Fax: 302-992-3999


               If to 3DP:

               3-Dimensional Pharmaceuticals, Inc.
               Eagleview Corporate Center
               665 Stockton Drive, Suite 104
               Exton, PA 10341

               ATTN:  Chief Executive Officer

               with a copy to:

               Morgan, Lewis & Bockius LLP
               1701 Market Street
               Philadelphia, PA 19103

               ATTN: David R. King, Esq.

     11.10     Public Announcements. The Parties shall consult with each other
               --------------------
               and reach mutual written agreement before making any public
               announcement concerning this Agreement or its subject matter. A
               joint press release to announce the signing of this Agreement is
               attached as Appendix B to this Agreement, and the Parties agrees
                           ----------
               to coordinate the dissemination of this press release.
               Notwithstanding the foregoing, the Parties may disclose the
               existence and general nature of this Agreement and may make
               disclosures for purposes of satisfying legal and regulatory
               requirements in accordance with Article 5; however, neither Party
               shall use the name of the other Party for promotional purposes.

                                       15
<PAGE>

     11.11     Headings. The captions to the sections and articles in this
               --------
               Agreement are not a part of this Agreement, and are included
               merely for convenience of reference only and shall not affect its
               meaning or interpretation.

     11.12     Severability. If any provision of this Agreement becomes or is
               ------------
               declared by a court of competent jurisdiction to be illegal,
               unenforceable or void, this Agreement shall continue in full
               force and effect without said provision, so long as the
               Agreement, taking into account said voided provision(s),
               continues to provide the Parties with the same practical economic
               benefits as the Agreement containing said voided provision(s) did
               on the date of this Agreement. If, after taking into account said
               voided provision(s), the Parties are unable to realize the
               practical economic benefit contemplated on the date of this
               Agreement, the Parties shall negotiate in good faith to amend
               this Agreement to reestablish the practical economic benefit
               provided the Parties on the date of this Agreement.

     11.13     No Consequential Damages.  IN NO EVENT SHALL EITHER PARTY OR ANY
               ------------------------
               OF ITS RESPECTIVE AFFILIATES BE LIABLE TO THE OTHER PARTY OR ANY
               OF ITS AFFILIATES FOR SPECIAL, INDIRECT, INCIDENTAL OR
               CONSEQUENTIAL DAMAGES, WHETHER IN CONTRACT, WARRANTY, TORT,
               NEGLIGENCE, STRICT LIABILITY OR OTHER WISE, INCLUDING, BUT NOT
               LIMITED TO, LOSS OF PROFITS OR REVENUE, OR CLAIMS OF CUSTOMERS OF
               ANY OF THEM OR OTHER THIRD PARTIES FOR SUCH OR OTHER DAMAGES.

     11.14     Applicable Law.  This Agreement shall be governed by and
               --------------
               interpreted in accordance with the laws of the State of Delaware
               without reference to its conflicts of laws provisions.

     11.15     Advice of Counsel.  DPC and 3DP have each consulted with counsel
               -----------------
               of their choice regarding this Agreement, and each acknowledges
               and agrees that this Agreement shall not be deemed to have been
               drafted by one party or another and will be construed
               accordingly.

     11.16     Counterparts.  This Agreement may be executed in counterparts, or
               ------------
               facsimile versions, each of which shall be deemed to be an
               original, and both of which together shall be deemed to be one
               and the same agreement.

                                       16
<PAGE>

In WITNESS WHEREOF, the Parties have caused this Agreement to be executed by
their respective duly authorized officers as of the day and year first above
written, each copy of which shall for all purposes be deemed to be an original.


3 DIMENSTIONAL                         DUPONT PHARMACEUTIALS
PHARMACEUTICALS, INC.                  COMPANY


By:  /s/ David C. U'Prichard           By: /s/ Paul A. Friedman
   ----------------------------           ------------------------

Name:  David C. U'Prichard, Ph.D.      Name:  Paul A. Friedman, M.D.

Title:  Chief Executive Officer        Title:  President, DuPont Pharmaceuticals
                                               Research Laboratories

                                       17
<PAGE>

                      Appendix A:  Licensed Patent Rights


<TABLE>
<CAPTION>
-------------------------------------------------------------------------------------------------------------------------
    3DP                Application Number         Filing Date                             Title
    ---                -----------------          -----------                             -----
 Reference             or Patent Number           or Issue Date
 ---------             ----------------           -------------
-------------------------------------------------------------------------------------------------------------------------
<S>                    <C>                    <C>                        <C>
1503.0010000           Patent No. 5,463,564   Issued October 31, 1995    System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.0010001           Patent No. 5,574,656   Issued November 12, 1996   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.0010002           Patent No. 5,684,711   Issued November 4, 1997    System, Method, and Computer Program Product
                                                                         for at Least Partially Automatically Generating
                                                                         Chemical Compounds Having Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.0010003           Patent No. 5,901,069   Issued May 4, 1999         System, Method, and Computer Program Product
                                                                         for at LEAST PARTIALLY AUTOMATICALLY GENERATING
                                                                         Chemical Compounds Having Desired Properties From
                                                                         a List of Potential Chemical Compounds to
                                                                         Synthesize
-------------------------------------------------------------------------------------------------------------------------
1503.0010004           Appl. No. 09/213,156   Filed December 17, 1998    Method of Generating Chemical Compounds
                                                                         Having Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001AU00           Patent No. 688598      Issued September 17, 1998  System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503001AU10            Appl. No. 71886/98     Filed June 12, 1998        System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001CA00           Appl. No. 2,199,264    Filed September 11, 1995   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001EP00           Appl. No. 95933748.6   Filed September 11, 1995   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001HU00           Appl. No. P9801578     Filed September 11, 1995   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001IL00           Patent No. 115292      Issued October 28, 1999    System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001IL10           Patent No. 125017      Issued October 28, 1999    Computer Based System and Method of
                                                                         Automatically Generating Chemical Compounds
-------------------------------------------------------------------------------------------------------------------------
1503.001IN00           Appl. No. 1068CAL95    Filed September 7, 1995    System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001JP00           Appl. No. 510247/1996  Filed September 11, 1995   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001PC00           Appl. No.              Filed September 11, 1995   System and Method of Automatically Generating
                       PCT/US95/11365                                    Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
1503.001TW00           Appl. No. 84109873     Filed September 26, 1995   System and Method of Automatically Generating
                                                                         Chemical Compounds with Desired Properties
-------------------------------------------------------------------------------------------------------------------------
</TABLE>

                                       18
<PAGE>

<TABLE>
<CAPTION>
-------------------------------------------------------------------------------------------------------------------------------
    3DP                Application Number         Filing Date                                Title
    ---                ------------------         -----------                                -----
 Reference              Or Patent Number         or Issue Date
 ---------              ----------------         -------------
-------------------------------------------------------------------------------------------------------------------------------
<S>                    <C>                       <C>                       <C>
1503.0200001           Appl. No. 08/963,870      Filed November 4, 1997    System, and Method, and Computer Program Product
                                                                           for Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.0200002           Appl. No. 08/963,872      Filed November 4, 1997    System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.0200003           Appl. No. 09/073,845      Filed May 7, 1998         System, Method, and Computer Program Product for
                                                                           Representing Proximity Data in a Multi-Dimensional
                                                                           Space
-------------------------------------------------------------------------------------------------------------------------------
[**]
-------------------------------------------------------------------------------------------------------------------------------
1503.020AU01           Appl. No. 54407/98        Filed November 4, 1997    System, Method, and Computer Program Product for
                                                                           Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.020AU02           Appl. No. 51800/98        Filed November 4, 1997    System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.020CA01           Appl. No. 2,269,669       Filed November 4, 1997    System, Method, and Computer Program Product for
                                                                           Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.020CA02           Appl. No. 2,270,527       Filed November 4, 1997    System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.020EP01           Appl. No. 97948320.3      Filed November 4, 1997    System, Method, and Computer Program Product for
                                                                           Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.020EP02           Appl. No. 97946679.4      Filed November 4, 1997    System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.020IL01           Appl. No. 129498          Filed November 4, 1997    System, Method, and Computer Program Product for
                                                                           Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.020IL02           Appl. No. 129728          Filed May 4, 1997         System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.020JP01           Appl. No. 521902/1998     Filed November 4, 1997    System, Method, and Computer Program Product for
                                                                           Identifying Chemical Compounds Having Desired
                                                                           Properties
-------------------------------------------------------------------------------------------------------------------------------
1503.020JP02           Appl. No. 521903/1998     Filed November 4, 1997    System, Method, and Computer Program Product for the
                                                                           Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
-------------------------------------------------------------------------------------------------------------------------------
1503.020PC01           Appl. No.                 Filed November 4, 1997    System, Method, and Computer Program Product for the
                       PCT/US97/20918                                      Visualization and Interactive Processing and
                                                                           Analysis of Chemical Data
 -------------------------------------------------------------------------------------------------------------------------------
1503.020PC02           Appl. No.                 Filed November 4, 1997    System, Method, and Computer Program Product for
                       PCT/US97/20919                                      Identifying Chemical Compounds Having Desired
                                                                           Properties.
 -------------------------------------------------------------------------------------------------------------------------------
[**]
-------------------------------------------------------------------------------------------------------------------------------
</TABLE>

     ** Certain portions of this Exhibit have been omitted based upon a request
     for confidential treatment that has been filed with the Commission. The
     omitted portions have been filed separately with the Commission.

                                       19
<PAGE>

                       Appendix B:  Joint Press Release



FOR IMMEDIATE RELEASE
For 3DP, Contact:                             For DuPont Contact:
-------------------------------------------------------------------------------
Business
Michael J. Wassil                              Thomas R. Barry
Chief Financial Officer                          302-992-5020
(610) 458-6073

Media
Jerry Parrot
Jerry Parrot & Associates
703-757-0950

                   DuPont and 3-Dimensional Pharmaceuticals
                     Announce Drug Discovery Collaboration

  -  DuPont also Licenses 3DP's DirectedDiversity(R) Drug Discovery Patents-

Exton, PA and Wilmington, DE - February XX, 2000 - DuPont Pharmaceuticals
Company, a wholly-owned independent subsidiary of DuPont (NYSE: DD), and 3-
Dimensional Pharmaceuticals, Inc. (3DP) today announced a strategic
collaboration in which 3DP will use its proprietary DirectedDiversity technology
to assist DuPont Pharmaceuticals in the discovery of innovative new drugs for
specific biological targets.

3DP will apply its iterative drug discovery process to generate custom
combinatorial chemistry libraries based on molecules and information provided by
DuPont Pharmaceuticals and will optimize those molecules into preclinical drug
candidates. DuPont Pharmaceuticals will be responsible for preclinical and
clinical development, marketing and sales of the resulting products.

                                       20
<PAGE>

For the initial target, 3DP will receive payments of up to $9 million, including
an up-front technology access fee, research and development funding and
milestone payments. 3DP will also receive royalties on sales of resulting
products and will be eligible to receive additional payments if more than one
target is selected to be included in the collaboration.

The parties also announced an additional agreement in which DuPont
Pharmaceuticals will obtain a non-exclusive license to 3DP's proprietary
DirectedDiversity(R) drug discovery patents.  Under the license agreement,
DuPont Pharmaceuticals will receive a non-exclusive license to 3DP's
DirectedDiversity(R) patents in support of DuPont Pharmaceuticals internal
research Programs, and will pay an annual Site License fee for each DuPont
Pharmaceuticals facility using the technology.

DuPont Pharmaceuticals is committed to aggressive exploration and use of
leading-edge discovery technologies to speed the process of research and
development and to improve the quality of new drugs entering clinical trials,"
said Paul Friedman, M.D., President of DuPont Pharmaceuticals Research
Laboratories.

David C. U'Prichard, Ph.D., Chief Executive Officer of 3-Dimensional
Pharmaceuticals, noted that 3DP's technology platform allows the company to
discover and refine drugs against a wide range of molecular targets more quickly
than conventional approaches.  "DuPont is one of the great pioneering research-
based companies, and we are particularly pleased with this important recognition
of 3DP's proprietary DirectedDiversity(R) drug discovery process.  Our
scientists look forward with great anticipation to working with their colleagues
at DuPont Pharmaceuticals," he said.  "We are confident that the collaboration
we are announcing today will prove productive for both parties".

                                       21
<PAGE>

DirectedDiversity(R) Chemi-Informatic Technology uses proprietary computer
algorithms to design, select and iteratively refine combinatorial libraries of
novel, small-molecule drugs based on screening "hits" obtained from 3DP or other
screening libraries, target-protein 3D structures, or pharmacophore models
derived from lead compounds.

To prime the discovery process, 3DP has synthesized DirectedDiversity(R)
Screening Libraries totaling more than 200,000 individually synthesized drug-
like compounds.  These compounds represent proven pharmacophore classes and
constitute an optimally diverse sampling of the DirectedDiversity(R) Accessible
Compound Libraries, which now total more than 1.5 billion compounds, each of
which is available for on-demand synthesis using parallel synthesis technology.

DirectedDiversity(R) is a major component of 3DP's DiscoverWorks, which
provides a uniquely integrated platform for the high-throughput synthesis,
screening, and optimization of chemical compounds.  DiscoverWorks can be
applied flexibly to a wide range of molecular targets identified through genome
sequencing efforts - even in situations where the target's biological function
is ambiguous or unknown.  DiscoverWorks enhances the efficiency of conventional
drug discovery, making the process more rapid and reliable.

Earlier this year, 3DP received the fourth in a series of patents covering its
DirectedDiversity(R) process.  DirectedDiversity(R) controls and manages the
overall information flow for combinatorial drug discovery and provides the
computational tools needed to optimize drug properties rapidly using parallel
automated chemical synthesis. 3DP has a flexible licensing program available to
those companies interested in obtaining licenses to its DirectedDiversity(R)
patent portfolio.

                                       22
<PAGE>

Based in Wilmington, Delaware, DuPont Pharmaceuticals is a worldwide business
that focuses on research, development and delivery of pharmaceuticals to treat
unmet medical needs in the fight against HIV, cardiovascular disease, central
nervous system disorders, cancer and inflammatory diseases.  The company also is
a leader in medical imaging.

DuPont is a science company, delivering science-based solutions that make a
difference in people's lives in food and nutrition, health care, apparel, home
and construction, electronics, and transportation.  Founded in 1802, the company
operates in 65 countries and has 97,000 employees.

3-Dimensional Pharmaceuticals, Inc. (http://www.3dp.com) is a leading innovator
in drug discovery.  The company has developed a proprietary technology platform
known as DiscoverWorks, which uniquely integrates structure-based drug design,
combinatorial chemistry and high-throughput screening.  DiscoverWorks reduces
discovery costs, increases the rate of success and enhances the ultimate
commercial value of a drug development pipeline. 3DP is using its proprietary
technology both in collaboration with other companies and in its own research
programs, which currently target orally active small-molecule pharmaceuticals to
treat cardiovascular disease and cancer.

                                       23