Research, License & Royalty Agreement

EXHIBIT 10.9(B)


AMENDMENT NO. 2 TO RESEARCH, LICENSE AND ROYALTY AGREEMENT


This Amendment No. 2 to Research, License and Royalty Agreement (the "Amendment") effective as of June 30, 1997, is entered into by and between Pharmacopeia, Inc. ("Pharmacopeia") and Berlex Laboratories, Inc. ("Berlex"), and amends that certain Research, License and Royalty Agreement entered into by Pharmacopeia and Berlex effective as of February 15, 1995 (the "Agreement"), as amended by Amendment No. 1 to Research, License and Royalty Agreement effective as of November 27, 1996.


1. All capitalized terms not defined in this Agreement shall have the meanings
given to them in the Agreement.


2. Section 1.3 is amended to read in its entirety as follows:


1.3 "Additional Berlex Target" shall mean [***].


3. Section 1.17 is amended to read in its entirety as follows:


1.17 "Field" means the use for the prevention, mitigation, or cure of
diseases of any substance which [***].


4. Section 1.36 is amended to read in its entirety as follows:


1.36 "Other Product" means any drug with activity with respect to the
Initial Berlex Target approved for human or animal use that is not a
Product (i.e., not based on a Development Compound accepted as an Accepted
Development Compound in accordance with Section 6.1(b)) and is within the
scope of a Live Claim. It is understood that a drug meeting the criteria of
the preceding sentence and that also has biological activity outside the
Field (i.e. via a different mechanism of action) shall be an Other Product
only if such drug has an activity (Ki) in the Field of less than [***].


5. Section 1.39 is amended to read in its entirety as follows:


1.39 "Product" means any drug with activity within the Field approved for
human or animal use based on a Development Compound that has received
Acceptance in accordance with Section 6.1(b) and is within the scope of a
Live Claim, or a Derivative thereof. It is understood that a drug meeting
the criteria of the preceding sentence which also has biological activity
outside the Field (i.e., via a different mechanism of action) shall be a
Product.


*Information omitted and filed separately with the Commission under Rule 24b-2.


6. Section 2.2 is amended to read in its entirety as follows:


2.2 Number of Scientists. Berlex is making the payments described in
Section V based on the requirement that Pharmacopeia shall provide an
average of [***] full-time equivalent ("FTE") research positions.


7. In Section 3.5, the phrase "Chief Scientific Officer for Pharmacopeia"
shall be replaced with "Senior Vice President of Drug Discovery for
Pharmacopeia."


8. In Section 3.7, the phrase "Chief Scientific Officer for Pharmacopeia"
shall be replaced with "Senior Vice President, Chemistry, of Pharmacopeia."


9. Section 4.8 is amended to read in its entirety as follows:


4.8 Random Libraries.
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(a) For a period of [***] under the Research Plan with respect to the
Initial Berlex Target, Pharmacopeia shall not knowingly screen
Random Libraries with respect to the Initial Berlex Target, nor
shall Pharmacopeia knowingly (i) design Random LIbraries for the
purpose of identifying compounds with activity for the Initial
Berlex Target, (ii) make such Random Libraries, or (iii) use or
sell such Random Libraries to Third Parties or, (iv) use any
structure-function data learned as a result of the research under
the Research Plan for the purposes of subsections (i)-(iii)
above.


(b) For a period of [*** years from the end of the Term, or in the
event research under the Research Plan with respect to the
Additional Berlex Target does not proceed until [***],
until[***], Pharmacopeia shall not knowingly screen Random
Libraries with respect to the Additional Berlex Target, nor shall
Pharmacopeia knowingly (i) design Random Libraries for the
purpose of identifying compounds with activity for the Additional
Berlex Target, (ii) make such Random Libraries, or (iii) use or
sell such Random Libraries to Third Parties or, (iv) use any
structure-function data learned as a result of the research under
the Research Plan for the purposes of subsections (i)-(iii)
above.


(c) It is understood that at any time Pharmacopeia may otherwise make
and provide Random Libraries to Third Parties who may screen such
Random Libraries against any targets, including without
limitation, the Initial Berlex Target and Additional Berlex
Target without the knowledge of Pharmacopeia.


*Information omitted and filed separately with the Commission under Rule 24b-2.


10. Section 4.14 is amended to read in its entirety as follows:


4.14 Commercialization Status. If Berlex is developing a Product or
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Other Products, for a period from the end of the Term to the First
Commercial Sale of a Product or Other Product, Berlex shall keep
Pharmacopeia informed of its development activities with respect to
Products and Other Products, including without limitation, the
achievement of the milestones set forth in Section 6.1 and 6.2 and
the commercialization of Products and Other Products, by semi-
annually providing Pharmacopeia with a written report stating the
status of development of each such Product and Other Product. If
research under the Research Plan with respect to the Additiona ...