LEASE AGREEMENT

Exhibit 10.329

LEASE AGREEMENT

BY AND BETWEEN:

Eastpark at 8A

“Landlord”

- and -

Pharrnacopeia, Inc.

“Tenant”

PREMISES: 3000 Eastpark Boulevard Cranbury, NJ 08512

DATED: August 20, 2003

TABLE OF CONTENTS

AGREEMENT, made August 20, 2003, between Eastpark at 8A, 1000 Eastpark Blvd., Cranbury, New Jersey 08512, “Landlord”; and Pharmacopeia, Inc., 3000 Eastpark Boulevard, Cranbury, NJ 08512, “Tenant”.

WITNESSETH:

WHEREAS, the Landlord intends to lease to the Tenant the entire property known as 3000 Eastpark Boulevard, Cranbury, NJ 08512, (Block 7, Lot 7.03 on the South Brunswick Township Tax Map) (the “Land”) which constitutes a portion of the office/industrial park known as Eastpark at 8A (“Office Park”) together with a building of 58,852 rentable square feet located thereon (“Building” or “Leased Premises”), (the Land and Building shall be referred to together as the “Property”); and

WHEREAS, the parties hereto wish to mutually define their rights, duties and obligations in connection with the Lease;

NOW THEREFORE, in consideration of the promises set forth herein, the Landlord leases unto the Tenant and the Tenant rents from the Landlord the Property, and the Landlord and Tenant do hereby mutually covenant and agree as follows:

The Leased Premises shall consist of the entire Building of 58,852 rentable square feet of office and laboratory space, plus an area in the basement of approximately 6,297 rentable square feet, as measured from outside of exterior walls to center line of common walls, together with all improvements to be constructed thereon by the Landlord for the use of the Tenant, and all easements, tenements, appurtenances, hereditaments, rights and privileges appurtenant thereto, and any and all fixtures and equipment which are to be installed by the Landlord for the use of the Tenant in its occupancy of the Leased Premises. Tenant shall also have the right to use all common areas of the Office Park in a similar manner as other Office Park tenants.

The term of the Lease shall be 12 years and shall be co-terminus with a lease for Building #1, which is also to be occupied by Tenant. The rent shall commence upon Substantial Completion (as defined hereafter). The 12 year term shall commence on the first day of the month following the date on which Substantial Completion is achieved for both Buildings 1 and 3, and shall expire on the day before the 12th anniversary of the Commencement Date, it being the intent of the parties that the leases for both Buildings shall expire on the same date. The Commencement Date is projected to be January 15, 2004.

3.1 The Leased Premises consists of the entire Building currently leased to Tenant. Tenant is taking the Leased Premises in its “as is” condition subject to modifications as shown on the Plans (as hereafter defined) to be prepared by Tenant (“Tenant Improvements”). The Landlord shall provide all necessary labor and materials and perform all the work required to complete the Tenant Improvements. Tenant’s designated representative for all work pertaining to the Tenant Improvements shall be John Harrison and or such other person as is designated in writing by Tenant (“Representative”). The Landlord shall supervise and direct the work on the Tenant Improvements using Landlord’s best skill and attention, and Landlord shall be solely responsible for all construction means, methods, techniques, sequences and procedures and for coordinating all portions of the work on the Tenant Improvements. Landlord warrants to the Tenant that all materials and equipment incorporated in the Tenant Improvements will be new unless otherwise specified, and that all work on the Tenant Improvements will be of good quality, free from known faults and defects, and in substantial conformity with the Plans.

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(b) Neither the Construction Budget nor the Plans shall be changed or altered in any way except by change order approved in writing by Landlord and Tenant (“Change Order”). All Change Orders shall be valid and binding upon Landlord and Tenant only if authorized by written Change Order signed by Landlord and Tenant’s Representative prior to commencement of the work on the Tenant Improvements reflected thereby. The cost or credit to the Tenant due to any Change Order shall be determined per the terms of such Change Order. In the event the Change Order increases the cost set forth in the Construction Budget, then Landlord shall submit an invoice to Tenant and Tenant shall pay the invoice upon completion of the work or upon the ordering of any equipment, whichever is applicable. The Landlord shall have the right to substitute for the materials and equipment required by the Plans, materials and equipment of equal quality and standard, provided said substitutions conform with applicable building codes and are the subject of a Change Order.

(b) Tenant shall be responsible for providing Landlord with, and bearing the cost of sufficient copies of the Plans, and sufficient copies of any revisions made to the Plans, in order to obtain the permits and efficiently manage the construction of the Leased Premises. In the event any Change Orders are required during construction, Tenant shall be responsible for all costs related to the preparation and reproduction of plans therefor, unless the Change Order was solely initiated by Landlord, in which case Landlord shall be responsible for such costs. After construction is complete, Tenant shall be responsible for all costs related to the reproduction of “as built” Plans. In all instances where Plans are required, Tenant shall provide Landlord with a reproducible set. Landlord will also be provided with a current plot file containing the Plans at no cost to Landlord. Tenant agrees to have its Architect execute Exhibit “A” affirming Landlord’s right to the Plans.

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presumed to be the projected Commencement Date set forth in paragraph 2, or any of Tenant’s obligations hereunder including, without limitation, Tenant’s obligation to pay all Rent. In the event that Tenant fails to pay to Landlord the final sum set forth on Exhibit “B”, such failure shall constitute a default under this Lease; and Tenant shall not be permitted to occupy the Leased Premises; and Tenant shall commence payment of all Rent; and Landlord shall be entitled to all rights and remedies available hereunder, at law or in equity, which rights shall be cumulative. All sums so owing to Landlord shall constitute Additional Rent and shall be subject to the imposition of late charges as provided in this Lease.

(b) Apart from extensions of time for delays and extensions of the date for the payment of rent, no payment or allowance of any kind shall be claimed by Tenant, or made to the Landlord as compensation for damages on account of any delay from any cause in the Initial: Landlord completion of the Tenant Improvements, whether such delay be avoidable or unavoidable, anything in this Agreement inconsistent herewith or to the contrary notwithstanding.

3.5 Tenant shall be responsible for the design and installation of its own phone, data and communication systems which systems shall be installed in a manner not to interfere with Landlord’s construction efforts. During construction of Tenant Improvements, a representative of Tenant shall inspect the site no less frequently than once a week and verify and agree that the work in progress has been completed in a manner acceptable to Tenant.

3.6 The Tenant Improvements shall be commenced upon issuance of the building permit by governmental entities having jurisdiction therefor and, subject to authorized adjustments, completion of the Tenant Improvements is estimated to be achieved on or about January 15, 2004. As used herein the term “Substantial Completion” shall mean that the Leased Premises have been built and completed in substantial conformity with the Plans, and a temporary or permanent certificate of occupancy or a temporary or permanent certificate of acceptance (“CO/CA”) has been issued permitting Tenant to use and occupy the Leased Premises, even though minor details, adjustments or punch list items which shall not materially impair Tenant’s use and enjoyment of the Leased Premises may not have been finally completed, but which work Landlord agrees shall be diligently pursued to final completion. Tenant shall allow Landlord and its contractors to enter the Leased Premises during normal working hours after issuance of the CO/CA to complete remaining minor work or punch list items, provided Landlord gives advance notice and makes reasonable efforts not to interfere with Tenant’s operations. It is agreed that for the purpose of this Lease, wherever and whenever the term Substantial Completion is used, it shall not include items of maintenance, service, punch list, or guarantee.

4.1 Tenant is currently occupying the Building under an existing lease (“Old Lease”) and shall continue to occupy the space during construction of the Tenant Improvements and pay Landlord the Rent set forth in the Old Lease until Substantial Completion. The Old Lease shall be deemed terminated upon commencement of this Lease as set forth in paragraph 2. Tenant shall pay base rent (“Base Rent”) hereunder as follows:

(a) During the first 4 years of the term, an estimated annual base rent per square foot of $20.58 for all above ground space and $4.00 for the basement space (provided it is only used in its “as is” condition), for an aggregate annual base rent of $l,236,362.16 (“Initial Base Rent”), payable monthly in the sum of $l03,030.l8.

(b) During the second 4 years of the term, the Base Rent shall be increased by adding to the Initial Base Rent the increase in the Consumer Price Index (“CPI”) as follows, and such sum shall be the Base Rent for the second 4 years of the term (the “Adjusted Base Rent”):

The “All Items” Index Figures for the New York-Northeastern New Jersey average of the “Consumer Price Index for All Urban Consumers” (revised CPI-U) (1982-1984 equal to 100) published by the Bureau of Labor Statistics of the U.S. Department of Labor (“Index”) for the month 2 months prior to the date of Substantial Completion shall be compared with

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the same index for the month 2 months prior to the beginning month of the second 4 years of the Lease term. If there is an increase in the Index that percentage increase shall be used to determine the rent increase over the original Base Rent, as shown in the following example:

If the Index figure for the month 2 months prior to the date of Substantial Completion is 100 (the denominator) and the Index figure for the month 2 months prior to the beginning of the second 4 years of the lease term is 110, the increase in the Index figures will produce an increase of 10%.

Applying the formula, 10% of $1,236,362.16 is equal to $123,636.22. Adding that amount to the original Base Rent produces an annual rent for the second 4 years of $1,359,998.38 payable in equal monthly installments of $l13,333.20.

However, in no event shall the increase in rent be more than 12%.

(1) In the event that the Index figure is discontinued the parties shall agree on an equivalent and substituted Cost of Living Index to be applied in the same manner. In the event the parties cannot mutually agree as to a substituted Index, then the issue shall be submitted for arbitration to the American Arbitration Association to take place in South Brunswick or any of its contiguous municipalities, with the cost thereof divided between the parties.

(2) If the base year (1982-84 equal to 100) herein above referred to with respect to the “Index” shall be changed after the execution of the Lease, appropriate adjustments based on such new Index shall be made so as to have a proper application of the Cost of Living formula.

(c) During the third 4 years of the term, the Base Rent shall increase according to the same CPI formula set forth above using the Adjusted Base Rent, but not more than 12 % over the Adjusted Base Rent for the second 4 years.

4.2 In addition to the Base Rent, Tenant shall pay as additional rent (“Additional Rent”) all real estate taxes for the Property, plus its proportionate share of the repairs, maintenance, insurance and any other charges allocated amongst tenants, as more specifically described in paragraph 8 (“Common Area Expenses”), based on the relationship between the rentable square footage leased to Tenant and the rentable square footage of building construction completed and occupied in the Office Park. Tenant’s Common Area Expenses shall be adjusted as of each January 1st during the term based on the increase in Common Area Expenses set forth in paragraph 8.

4.3 The Base Rent and Additional Rent shall be referred to hereafter as “Rent”.

4.4 Tenant covenants to pay the Rent in lawful money of the United States which shall be legal tender for the payment of all debts, public and private, at the time of payment. Such Rent shall be paid to Landlord at its office address hereinabove set forth, or at such other place as Landlord may, from time to time, designate by notice to Tenant.

4.5 Rental payments shall be payable in advance in equal monthly installments on the first day of each calendar month. The Rent shall be payable by Tenant without any set-off or deduction of any kind or nature whatsoever and without notice or demand. The sum of all increases required to be paid as Additional Rent or Base Rent in accordance with this Lease, shall be paid to Landlord within 10 days following the giving of notice hereof by Landlord of such increases.

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5.1 The Tenant shall have the right to the exclusive use of all parking spaces serving the Property. The Landlord and Tenant mutually agree that they will not block, hinder or otherwise obstruct the access driveways and parking areas so as to impede the free flow of vehicular traffic in the Office Park. In connection with the use of the loading platforms, if any, Tenant agrees that it will not use the same so as to unreasonably interfere with the use of the access driveways and parking areas. Tenant shall not store trailers or other vehicles on any portion of the access driveways or does parking areas, and may not utilize any portion often Property for any other purpose unless consented to in advance by Landlord.

The Tenant covenants and agrees to use and occupy the Leased Premises only as an office, pilot scale manufacturing facility and laboratory, which use is expressly subject to all applicable zoning ordinances, rules and regulations of any governmental instrumentalities, boards or bureaus having jurisdiction thereof. Tenant’s use of the Leased Premises shall not interfere with the peaceable and quiet use and enjoyment by other tenants at their respective leased premises located in the Office Park, nor shall Tenant’s activities cause Landlord to be in default under its leases with such other tenants.

7.1 Tenant shall generally maintain and repair the Leased Premises, in a good and workmanlike manner, and shall, at the expiration of the term, deliver the Leased Premises in good order and condition, damages by fire or casualty, the elements and ordinary wear and tear excepted. Tenant covenants and agrees that it shall not cause or permit any waste, damage or disfigurement to the Leased Premises, or any overloading of the floors. Tenant shall maintain and make all repairs to the floor surface, plumbing and electrical systems including all ballasts and fluorescent fixtures located within the Leased Premises, and the entire HVAC system. Landlord shall be responsible for repairs necessary to the roof, exterior and load-bearing walls, and electric and plumbing systems to the point where they enter the Leased Premises, unless repair is necessitated by any act of Tenant, or its agents, employees or contractors.

7.2 The Tenant shall, at its own cost and expense, pay all utility meter and service charges, including gas, water and electric servicing the Leased Premises. The Tenant agrees to maintain all leased areas at a minimum temperature of 45 degrees, excluding cold rooms on other rooms specifically designed for a lower temperature, to prevent the freezing of domestic water and sprinkler pipes. Tenant shall not store any items outside the Leased Premises, and shall deliver its garbage and recyclables to the central receiving area on the Property. Tenant shall dispose of all hazardous/medical waste with an approved hauler at its own cost.

7.3 Landlord does not warrant that any services Landlord or any public utilities supply will not be interrupted. Services may be interrupted because of accidents, repairs, alterations, improvements or any other reason beyond the reasonable control of Landlord, not including the gross negligence of Landlord or its agents.

8.1 The Tenant shall pay to the Landlord, monthly, as Additional Rent its proportionate share of the following items all of which shall be known as Common Area Expenses:

(a) The costs incurred by the Landlord for the operation, maintenance or repair of the following items in the Office Park, (“Operating Costs”):

(1) lawns and landscaping;

(2) standard water usage and standby sprinkler charges;

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(3) exterior lighting;

(4) exterior sewer lines;

(5) exterior utility lines;

(6) repair and maintenance of any signs serving the Office Park;

(7) snow removal;

(8) standard garbage disposal and recycling;

(9) general ground maintenance;

(10) parking lot, driveways and walkways;

(11) maintenance contracts for the roof;

(12) pest control;

(13) central station monitoring for fire sprinkler system; and

(14) other ordinary maintenance expenses normally incurred by Landlord relating to the Building and common areas of the Office Park.

Notwithstanding the above, the following items shall be excluded from Common Area Expenses:

(a) Cost of decorating, redecorating, cleaning or other services not provided on a regular basis to the tenants of the Office Park;

(b) Wages, salaries, fees and fringe benefits paid to administrative or executive personnel or officers or partners of Landlord, unless employed at competitive rates as independent contractors at the building or Office Park;

(c) All cost relating to activities for the solicitation, negotiation and execution of leases of space in the Office Park;

(d) Cost of any repair made by Landlord because of the total or partial destruction of the building or the condemnation of a portion of the building;

(e) Any insurance premium for which Landlord is to be reimbursed by Tenant, pursuant to this Lease, or by any other tenant of the Office Park;

(f) Depreciation, interest or rents paid or incurred by Landlord;

(g) Any charge to Landlord for income taxes, franchise taxes or similar taxes:

(h) Collection costs for bad debt expenses not related to Tenant;

(i) Cost of tenant improvements;

(j) Legal, accounting, bank or other fees incurred in connection with any equity or debt financing or sale of the building or Office Park;

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(k) Costs of specialized services provided to other tenants but not provided to tenants generally;

(l) Capital expenditures;

(m) Cost to comply with ADA related to the interior of the individual buildings, but not exterior doors or the Office Park;

(n) Costs to cure violations of law or ordinances;

(o) Electric for non-public areas.

(b) The cost of the annual insurance premiums charged to the Landlord for insurance coverage which insure the buildings in the Office Park. The insurance shall be for the full replacement value of all insurable improvements with any customary extensions of coverage including, but not limited to, vandalism, malicious mischief, sprinkler damage and comprehensive liability, and insurance for one year’s rent. The Landlord shall maintain said insurance in effect at all times hereunder. Any increase in the insurance premiums due to a change in rating of the Building which is solely attributable to Tenant’s use, or due to special Tenant equipment, shall be paid entirely by the Tenant. Tenant expressly acknowledges that Landlord shall not maintain insurance on Tenant’s furniture, fixtures, machinery, inventory, equipment or other personal property; and

(c) A management fee of 3% of the Tenant’s Base Rent.

8.2 Within 90 days of the expiration of the first calendar year of the Term, the Landlord shall furnish to Tenant a detailed breakdown of the actual Common Area Expenses. Tenant shall have the right, within 30 days of receipt of the breakdown, and during normal business hours, to examine Landlords books and records with respect to the Common Area Expenses. In the event Tenant’s Proportionate Share shall be greater than the aggregate paid by the Tenant during the prior period, Tenant shall pay any difference, in one lump sum within 30 days after demand. In the event Tenant shall have overpaid its Proportionate Share, any such overage shall be applied to the Base Rent and Additional Rent prospectively due under the Lease. This procedure shall be followed during each year of the lease term, and at the expiration of the Lease, any overage or underage shall be credited or paid after computation by the Landlord, which obligation of Landlord and Tenant shall survive the expiration of the lease term.

8.3 In addition to the payments set forth in Paragraph 8.1, from and after Commencement Date and during the term, Tenant shall pay all real estate taxes and assessments levied by the municipality on the Leased Premises and the Tenant Improvements. Landlord shall immediately forward to Tenant all tax