Exhibit 10.1

SURRENDER AND TERMINATION AGREEMENT

THIS SURRENDER AND TERMINATION AGREEMENT (this “Agreement”) is made as of
December 18, 2009 by and between WE GEORGE STREET, L.L.C., a Delaware limited
liability company with an address of c/o Winstanley Enterprises LLC, 150 Baker
Avenue Extension, Suite 303, Concord, Massachusetts 01742 (“Landlord”) and
ACHILLION PHARMACEUTICALS, INC., a Delaware corporation with an address of 300
George Street, New Haven, Connecticut 06511 (“Tenant”).

BACKGROUND:

A. Landlord leases to Tenant, and Tenant leases from Landlord, approximately
5,263 rentable square feet of space known as Suite 803 (the “Premises”) in the
building located at 300 George Street, New Haven, Connecticut (the “Property”),
pursuant to that certain Lease dated as of March 30, 2001 (the “Lease”) between
Landlord and Yale University (“Yale”), as assigned to Tenant by Assignment and
Assumption of Leases dated as of March 30, 2001 (as amended, the “Assignment”),
which Assignment was amended by First Amendment to Assignment and Assumption of
Lease dated as of December 1, 2005.

B. Tenant desires to surrender the Lease and the Premises to Landlord, and
Landlord is willing to accept said surrender, all upon the terms and conditions
hereinafter set forth.

NOW THEREFORE, for good and valuable consideration, the receipt and sufficiency
of which are hereby acknowledged, Landlord and Tenant agree as follows:

1. Terms used but not defined herein shall have the meaning ascribed to each in
the Lease.

2. Subject to the provisions of this Agreement and notwithstanding anything to
the contrary in the Lease, Tenant shall relinquish its right to possession of
the Premises and all of its rights, interests, obligations and benefits relating
to Tenant’s right to occupy the Premises on or before March 15, 2010 (the
“Surrender Date”). The Surrender Date shall be deemed to have occurred on the
date Tenant shall deliver vacant possession of the Premises to Landlord, free of
all tenancies and rights of others to occupancy, with all of Tenant’s personal
property removed and any laboratory areas decontaminated in accordance with the
Laboratory Decommissioning Standard ANSI/AIHA Z9.11 latest edition, and in the
condition otherwise required by the Lease, all as determined by Landlord in its
reasonable discretion. Surrender of the Premises shall include surrender of the
generator associated with the Premises and all improvements performed by or for
the benefit of Tenant. As of the Surrender Date, the Lease shall be deemed
expired and Tenant shall be relieved of all its obligations under the Lease,
except for those provisions of the Lease that specifically survive such
expiration.

3. Tenant’s obligation to pay rent to Landlord under the Lease shall expire as
of the Surrender Date; provided that notwithstanding the foregoing, Tenant’s
obligation to pay to Landlord rent pursuant to the Lease shall be reinstated in
the event Tenant does not surrender possession of the Premises as provided in
Section 2 above.

--------------------------------------------------------------------------------

4. In connection with the surrender of the Premises, Landlord shall provide
Tenant with a moving allowance of $50,000.00 (the “Allowance”). Such Allowance
shall be used solely for out-of-pocket costs incurred by Tenant for moving its
personal property out of the Premises and for performing any fit-up and/or
reconfiguration work at Tenant’s other premises at the Property necessary to
consolidate Tenant’s operations into said premises.

5. Tenant represents, warrants and covenants to Landlord that, as of the date
hereof, and on the Surrender Date, (a) the Lease has not been assigned,
transferred or encumbered, whether as security or otherwise, (b) Tenant is the
sole holder of tenant’s entire interest under the Lease, (c) there are no
subleases or other occupancy agreements affecting any portion of the Premises,
and (d) no consents or approvals, other than from Connecticut Innovations,
Incorporated, are required for Tenant to enter into this Agreement.

6. Tenant and Landlord represent and warrant to the other that each has not
dealt with any broker, finder or like agent in connection with this Agreement,
and each does hereby agree to indemnify and hold the other and its members,
partners, officers, directors, shareholders, representatives, agents and
employees, harmless of and from any claim of, or liability to, any broker,
finder or like agent claiming a commission or fee in connection with the
negotiation, execution or delivery of this Agreement, together with all expenses
related thereto, including, without limitation, reasonable attorneys’ fees and
disbursements.

7. The provisions of this Agreement shall inure to the benefit of, and be
binding upon, the parties hereto and their respective heirs, legal
representative, successors and assigns.

8. This Agreement contains the entire agreement between Landlord and Tenant and
supersedes all prior agreements and understandings, if any, relating to the
subject matter hereof. This Agreement may be amended or supplemented only by an
instrument in writing executed by both parties.

9. This Agreement shall not be binding upon or enforceable against either party
unless and until both parties shall have executed and unconditionally delivered
this Agreement to the other party.

10. Time is of the essence with respect to the Tenant’s obligation to surrender
the Premises and make the payment required by this Agreement.

11. This Agreement may be executed in any number of counterparts, each of which
shall be deemed to be an original, and all of such counterparts shall constitute
one Agreement.

(Signatures on following page)

 

2

--------------------------------------------------------------------------------

IN WITNESS WHEREOF, Landlord and Tenant have duly executed this Surrender and
Termination Agreement as of the day and year first above written.

 

WE GEORGE STREET, L.L.C. By:   WE George Street Holdings LLC   Its Manager   By:
  WE George Street Manager Corp.     Its Sole Member     By:  

/s/ Carter Winstanley

      Carter J. Winstanley       Its President ACHILLION PHARMACEUTICALS, INC.
By:  

/s/ Mary Kay Fenton

Name:   Mary Kay Fenton Title:   CFO

Consented to by Tenant’s Lender:

CONNECTICUT INNOVATIONS, INCORPORATED By:  

/s/ Peter Longo

Name:   Peter Longo Title:   President and Executive Director

 

3