**Exhibit 31.1**

**CERTIFICATION OFPRINCIPAL 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 on Form 10-Q of PharmacopeiaDrug Discovery, Inc.;

2.             Based on my knowledge, this report does not contain any untrue statementof a material fact or omit to state a material fact necessary to make thestatements made, in light of the circumstances under which such statements weremade, not misleading with respect to the period covered by this report;

3.             Based on my knowledge, the financial statements, and other financialinformation included in this report, fairly present in all material respectsthe financial condition, results of operations and cash flows of the registrantas of, and for, the periods presented in this report;

4.             The registrant’s other certifying officers and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant andhave:

a)             designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant is made known to us by others within the entity, particularly duringthe period in which this quarterly report is being prepared;

b)            evaluated the effectiveness of the registrant’sdisclosure controls and procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, as of theend of the period covered by this report based on such evaluation; and

c)             disclosed in this report any change in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial reporting; and

5.             The registrant’s other certifying officers and I have disclosed, basedon our most recent evaluation of internal control over financial reporting, tothe registrant’s auditors and the audit committee of registrant’s board ofdirectors (or persons performing the equivalent functions):

a)             all significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

b)            any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.
| Date: August 4, 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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