Document:

Exhibit 10.4(d)

 

Amendment No. 4 to Research, License and
Royalty Agreement

 

This Amendment
No. 4 to Research, License and Royalty Agreement (the “Amendment”) is entered
into on July 22, 1998 by and between Pharmacopeia, Inc. (“Pharmacopeia”)
and Berlex Laboratories, Inc. (“Berlex”), effective as of February 15,
1998 (the “Amendment Effective Date”), 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, Amendment No. 2 to Research, License and Royalty
Agreement effective as of June 30, 1997, and Amendment No. 3 to Research
License and Royalty Agreement effective as of November 21, 1997.

 

WHEREAS, under
the terms of the Agreement, as amended, Pharmacopeia and Berlex have conducted
certain research activities under the Research Plan concerning identification
of compounds [*];

 

WHEREAS, under
the terms of the Agreement, as amended, Pharmacopeia has identified a Lead
Compound for [*]; and

 

WHEREAS,
Berlex would like Pharmacopeia to conduct certain activities to optimize the
Lead Compound for [*] and Pharmacopeia is willing to conduct such activities on
the terms and conditions set forth herein;

 

NOW THEREFORE,
the parties hereby amend the Agreement as follows:

 

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

 

2.             The following new
Sections 1.51, 1.52 and 1.53 are added following Section 1.50:

 

1.51        “[*]
Term” means the period commencing on the Effective Date and ending thirty-six
(36) months after the Effective Date.

 

1.52        “[*]
Term” shall mean the period commencing on July 1, 1998 and, unless earlier
terminated, ending February 28, 1999.

 

1.53        “Research
Term” means the [*] Term and the [*] Term.

 

3.             Section 1.47 is
amended to read in its entirety as follows:

 

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

 

 

1.47        “Term
of the Agreement” is defined in Section 14.1.

 

4.             The words “during the
[*] Term” are added to the end of Section 2.2.

 

5.             Section 5.1 is
amended to read in its entirety as follows:

 

5.1          [*] Term.

 

(a)           Subject to Article XIV
and Sections 3.2 and 3.5 (as amended herein), the [*] Term for screening
activities under the Research Plan shall extend until [*].  The [*] Term may be further extended with
the written agreement of the Parties.

 

(b)           Berlex shall, at least
[*] prior to the end of the [*] Term, notify Pharmacopeia in writing whether
Berlex wishes to negotiate an extension of the [*] Term.  Such written notice shall include at least
the following information: (i) whether Berlex wishes to continue conducting
research in the Field or wishes to conduct research with respect to additional
or different targets, (ii) an identification of any such proposed additional or
different targets, (iii) the length of the proposed extended [*] Term, and (iv)
the proposed amount of funding for such extended [*] Term.

 

(c)           (i)  Berlex shall make a payment to Pharmacopeia,
in addition to the payments due under Section 5.2, on or before the last day of
the [*] Term (the “Wind-Down Payment”). 
The amount of the Wind-Down Payment shall be [*].  In the event Berlex fails to provide
Pharmacopeia written notice as provided under Section 5.1(b), then the amount
of the Wind-Down Payment shall be [*]. 
However, to the extent that Pharmacopeia’s activities pursuant to the
Research Plan utilize fewer than an average of [*] full time equivalents
(“FTE’s”) between [*] and [*], any research funding paid by Berlex which is
unexpended as of the end of the [*] Term (based on a value of [*] per year per
FTE actually utilized, prorated over the period between [*] and [*]) may be
credited against (x) the Wind-Down Payment, up to the amount of the Wind-Down
Payment, to reduce or eliminate such Wind-Down Payment, or (y) any research
payments due with respect to an extension of the [*] Term beyond [*].

 

(ii) 
In exchange for the Wind-Down Payment, Pharmacopeia shall provide such
number of FTE’s as the Research Committee reasonably agrees, in order to
complete certain activities previously commenced pursuant to the Research Plan.

 

2

 

6.             Section 5.2(1) is
amended to read in its entirety as follows:

 

(1)           [*] within [*] of
receipt of the final written report on the research done during the [*] Term
pursuant to the Research Plan.

 

7.             The following new
Section 5.3 is added after Section 5.2:

 

5.3          [*]
Funding. The parties understand and agree that Berlex has made all payments
pursuant to Section 5.1 and 5.2 for the [*] Term. With respect to the [*] Term,
on or before [*], Berlex shall pay to Pharmacopeia [*]. On or before [*],
Berlex shall pay to Pharmacopeia an amount equal to: [*] less an unused portion
of the Wind-Down Payment to be calculated by Pharmacopeia and communicated to
Berlex by [*].

 

8.             Section 14.1 is
amended to read in its entirety as follows:

 

14.1        Term
of the Agreement. The Term of the Agreement shall commence on the Effective
Date and, unless terminated earlier as provided in this Section 14, shall
continue in full force and effect on a country-by-country basis and
compound-by-compound basis until Berlex and its Sublicensees have no remaining
royalty obligations in a country, at which time this Agreement shall terminate
in such country.

 

9.             Section 1.6, 1.40,
3.2(a), 3.8, 4.9, 4.14, 5.2, 6.2, and 7.3 are amended by replacing each
instance of the word “Term” with the words “[*] Term.” Section 3.2(e) is
amended by replacing the words “Term of the Agreement” with the words “[*]
Term.”

 

10.           Sections 1.5, 1.12,
1.19, 1.37, 3.3, 3.9, 4.5(c), 4.6, 4.8(b), 4.13(d), 10.1(b), 13.1, 13.2,
14.2(e) and 14.3(d) are amended by replacing each instance of the word “Term”
with the words “Research Term.” Sections 4.6 and 13.6 are amended by replacing
the words “Term of this Agreement” with the words “Research Term.”

 

11.           Section 8.1 is amended by replacing each
instance of the word “Term” with the words “Term of this Agreement.”

 

12.           Except as specifically modified or amended
hereby, the Agreement shall remain in full force and effect and, as modified or
amended, is hereby ratified, confirmed and approved.  No

 

3

 

provision of
this Amendment may be modified or amended except expressly in a writing signed
by both parties nor shall any terms be waived except expressly in a writing
signed by the party charged therewith. 
This Amendment shall be governed in accordance with the laws of the
State of Delaware, without regard to principles of conflicts of laws.

 

IN WITNESS
WHEREOF, each of the parties has executed this Amendment as of the date
indicated on this Amendment.

 

	
  BERLEX LABORATORIES, INC.

  	
   

  	
  PHARMACOPEIA, INC.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By:

  	
  /s/ Dale Stringfellow

  	
   

  	
  By:

  	
  /s/ Joseph A. Mollica

  
	
  Name:

  	
  Dale Stringfellow

  	
   

  	
  Name:

  	
  Joseph A. Mollica, Ph.D.

  
	
  Title:

  	
  President

  	
   

  	
  Title:

  	
  Chairman and CEO

  
	
  Date: 

  	
  July 21, '98

  	
   

  	
  Date:

  	
  July 20, 1998

  

 

4Exhibit 10.4(e)

 

This Amendment No. 5 to the Research, License and Royalty Agreement
(the “Amendment”) is entered into by and between Pharmacopeia, Inc.
(“Pharmacopeia”) and Berlex Laboratories, Inc. (“Berlex”), and amends the
Research, License and Royalty Agreement between Berlex and Pharmacopeia dated
February 15, 1995 (“the 1995 Agreement”), as previously amended in Amendment
Nos. 1 through 4.

 

1.             [*]

 

2.                                      Subject
to paragraph 5 of this Amendment, the milestone and royalty payments specified
in Section VI and VII of the 1995 Agreement shall be replaced by the following
paragraphs 2 and 3:

 

2.1           Within
[*] of receipt by Berlex of [*].

 

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

 

 

2.2           Within [*] of receipt by Berlex of [*]

 

2.3                                  2.3         Subject to paragraph 4 of this
Amendment, Berlex shall also make the following payments [*]:

 

2.3.1 Filing of an IND: [*]

 

2.3.2 Start of a Phase III Study: [*]

 

2.3.3 Filing of an NDA: [*]; and

 

2.3.4 First Commercial Sale: [*]

 

For the avoidance
of doubt, with respect to any compounds [*], the foregoing milestone payments
will be paid only once irrespective of the number of products containing [*],
or the number of [*], that achieve the milestone.

 

3.             With respect to any
compounds [*], subject to paragraph 4 of this Amendment, Berlex shall pay to
Pharmacopeia [*].

 

4.             The milestone and
royalty payments set forth in paragraphs 2.3.2, 2.3.3, 2.3.4 and 3 hereof will
be payable to Pharmacopeia [*]

 

5.             [*]

 

2

 

 

 

6.                   Berlex has the
right to [*].

 

7.                   To the extent
reasonably necessary for Pharmacopeia to comply with SEC reporting requirements
Berlex agrees to issue joint press releases with Pharmacopeia within thirty
(30) days of each of the following events: (a) the effective date [*]; and (b)
Pharmacopeia’s receipt of milestone payments as described in this Amendment.

 

Except as expressly stated in this Amendment, all other terms and
conditions of the 1995 Agreement, including the meanings of all capitalized
terms, shall remain in full force and effect. 
In the event of any inconsistency between the terms of this Amendment
and the Agreement, the terms of this Amendment will prevail.

 

IN WITNESS WHEREOF, each of the Parties has executed this Amendment as
of the dates indicated below.

 

	
  Berlex Laboratories, Inc.

  	
  Pharmacopeia, Inc.

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ Lutz Lingnau

  	
   

  	
  /s/ Michael G. Lenahan

  	
   

  
	
  Signature

  	
   

  	
  Signature

  	
   

  
	
   

  	
   

  	
   

  	
   

  
	
  1-24-03

  	
   

  	
  1-20-03

  	
   

  
	
  Date

  	
   

  	
  Date

  	
   

  
	
   

  	
   

  

 

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