**Exhibit 31.1**

**CERTIFICATIONOF PRINCIPAL EXECUTIVE OFFICER**

(Pursuant to Rule 13a-14(a) of theSecurities Exchange Act of 1934, as amended,as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002)

I, Leslie J. Browne, Ph.D., certify that:

1.      I have reviewed this quarterly report onForm 10-Q of Pharmacopeia Drug Discovery, Inc.;

2.      Based on my knowledge, this report does notcontain any untrue statement of a material fact or omit to state a materialfact necessary to make the statements made, in light of the circumstances underwhich such statements were made, not misleading with respect to the periodcovered by this report;

3.      Based on my knowledge, the financialstatements, and other financial information included in this report, fairlypresent in all material respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in thisreport;

4.      The registrant’s other certifying officers andI are responsible for establishing and maintaining disclosure controls andprocedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e))for the registrant and have:

a)        designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant is made known to us by others within theentity, particularly during the period in which this quarterly report is beingprepared;

b)       evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

c)        disclosedin this report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter thathas materially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting; and

5.      The registrant’s other certifying officers andI have disclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofregistrant’s board of directors (or persons performing the equivalentfunctions):

a)        allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial information; and

b)       anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.
| Date: November 2, 2006 |   |                                            |
|------------------------|--------|-------------------------------------------------|
|                   |   |                                            |
|                   |   |                                            |
|                   | By:    | /s/ Leslie J. Browne, Ph.D.                |   |
|                   |   | Leslie J. Browne, Ph.D.                         |
|                   |   | President, Chief Executive Officer and Director |
|                   |   | (Principal Executive Officer)                   |

 

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