Exhibit 10.1

AMENDMENT NO. 2 TO LEASE

THIS AMENDMENT NO. 2 TO LEASE (this “Amendment”) is made and entered into as of
the 31st day of March, 2010 between Landlord and Tenant named below:

 

  LANDLORD:   

WE George Street, L.L.C.

c/o Winstanley Enterprises LLC

150 Baker Avenue Extension, Suite 303

Concord, Massachusetts 01742

     TENANT:   

Achillion Pharmaceuticals, Inc.

300 George Street

New Haven, Connecticut 06510

     BUILDING:   

300 George Street

New Haven, Connecticut 06510

  

WHEREAS, Landlord and Tenant executed a lease dated as of May 5, 2000 (as
amended, the “Suite 800 Lease”) by which Tenant leases approximately 20,148
rentable square feet on the 8th floor of the Building known as Suite 800 (“Suite
800”); and

WHEREAS, Landlord and Tenant executed letters dated May 5, 2000, July 21,
2000, August 7, 2000 and December 22, 2000 regarding the initial alterations,
the amount of the security deposit and provision of a letter of credit in lieu
of a cash security deposit under the Suite 800 Lease; and

WHEREAS, Landlord and Tenant executed an Amendment No. 1 to Lease dated as of
February 1, 2001 that amended the Suite 800 Lease to add approximately 200
rentable square feet of space on the first floor of the Building known as Suite
CS02 (“Suite CS02”) and approximately 446 rentable square feet of space in the
basement of the Building known as Suite NMR1 (“NMR1”); and

WHEREAS, Landlord and Tenant executed a lease dated as of March 6, 2002 (as
amended, the “Lease”) by which Tenant leases approximately 8,768 rentable square
feet on the second floor of the Building (“Initial Suite 202”); and

WHEREAS, Landlord and Tenant executed an Amendment No. 1 to Lease dated as of
September 10, 2002 that amended the Lease to add approximately 2,293 rentable
square feet of space on the second floor of the Building to Initial Suite 202
such that Tenant leases a total of approximately 11,061 rentable square feet of
space on the second floor, and all of which is known as Suite 202 (“Suite 202”);
and

WHEREAS, Landlord and Tenant desire to terminate the Suite 800 Lease and amend
the Lease to (i) include all of the space leased by Tenant in the Building,
(ii) extend the term of the Lease, and (iii) make certain other modifications
and corrections to the Lease, all as more particularly set forth below.

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

1. Capitalized terms used but not defined herein shall have the meaning ascribed
to each in the Lease, as previously amended. Notwithstanding anything herein to
the contrary, the provisions of this Amendment shall be effective as of April 1,
2010.

2. The Suite 800 Lease is hereby terminated, provided that Tenant shall continue
to lease Suite 800, Suite CS02 and Suite NMR1 without interruption pursuant to
the Lease, as amended herein.

3. Section 1.(c) is revised to provide that the Premises shall mean Suite 202,
consisting of approximately 11,542 rentable square feet, Suite 800 consisting of
approximately 19,540 rentable square feet (which includes a non-contiguous
mechanical room of 333 rentable square feet), Suite CS02 consisting of
approximately 223 rentable square feet, and Suite NMR1 consisting of
approximately 495 rentable square feet. Tenant acknowledges and agrees that the
rentable square footage of all of the suites comprising the Premises have been
revised based on recent remeasurements. Section 1.(c) is also revised to provide
that the “Rentable Square Footage of the Premises” is deemed to be 31,800 square
feet in the aggregate, subject to the right of remeasurement as set forth in
Section 2(c). Exhibit A of the Lease is hereby deleted and replaced with Exhibit
A attached hereto, which includes all four suites that constitute the Premises.

4. Section 1.(d) is hereby revised to provide that the Base Rent for the Term
(as extended below) shall be as follows:

 

Period

   Rent Per RSF    Annual Base Rent    Monthly Installments

04/01/10 – 03/31/12

   $ 18.07    $ 574,626.00    $ 47,885.50

04/01/12 – 03/31/14

   $ 19.07    $ 606,426.00    $ 50,535.50

04/01/14 – 03/31/16

   $ 20.07    $ 638,226.00    $ 53,185.50

04/01/16 – 03/31/17

   $ 21.07    $ 670,026.00    $ 55,835.50

5. Section 1.(e) is revised such that Lease Year 8 shall be deemed to end on
March 31, 2010, and each subsequent Lease Year shall mean the 12 month period
thereafter.

6. Section 1.(f) is revised such that Tenant’s Pro Rata Share is 6.13%.

7. Section 1.(g) is revised such that the Term shall end on March 31, 2017.

8. Section 1.(j) is revised such that the Termination Date is March 31, 2017.

 

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9. Section 1.(l) is revised such that the Security Deposit is $152,500.00. The
provisions of Section 6(b) are hereby deleted.

10. Section 1.(o) is revised such that the Permitted Use shall include the right
of Tenant to use Suite NMR1 as a nuclear magnetic resonance facility. Isotopes
that have been approved by Landlord for use in Suite NMR1 are 32P, 33P, 14C, 3H,
35S and 125I. Tenant agrees that included in the Closure Obligation under
Section 32(b) is the obligation to decommission and close all areas of the
Premises (i) so as to render the Premises suitable for “Unrestricted Use” as
defined in and within the meaning of Subpart E of 10 CFR 20 and all other
applicable Laws, and (ii) in accordance with the Laboratory Decommissioning
Standard ANSI/AIHA Z9.11 latest edition (“Z9.11”), assuming that the next use of
the laboratory space shall be for general office or other unrestricted
commercial purposes. Tenant shall provide to Landlord a termination letter from
the Nuclear Regulatory Commission or delegated state evidencing release of the
Premises and the Building for Unrestricted Use, and an investigation report or
an investigation/decontamination report that contains a written statement of
“acceptable level of risk” (as such term is used in Z9.11) prepared by a
Certified Industrial Hygienist that demonstrates compliance with Z9.11, in
addition to the documentation required to demonstrate proper closure of all
hazardous waste storage areas at the Premises.

11. Section 1.(p) is revised such that the Rent shall be payable to the order of
WE George Street, L.L.C. at c/o Winstanley Enterprises LLC, 150 Baker Avenue
Extension, Suite 303, Concord, Massachusetts 01742.

12. Tenant acknowledges and agrees that the Grandfathered cfm Level and the
Grandfathered wsf Level shall only apply to Initial Suite 202.

13. Landlord, at its expense, at any time during the Term, may relocate Tenant
from Suite NMR1 and/or Suite CS02 to reasonably comparable space (“Relocation
Space”) within the Building without Tenant’s consent but with not less than 60
days’ prior written notice to Tenant. In order for any Relocation Space to be
deemed “reasonably comparable space” it must have a reasonably comparable
layout, have substantially the same utility to Tenant (given Tenant’s particular
use of the particular suite) and have no material effect on Tenant’s ability to
conduct its activities in that suite. Landlord shall, at its cost, build out the
Relocation Space so that its build out is substantially the same as the original
suite. Such build out shall be completed prior to Tenant having to move to the
Relocation Space. From and after the date of the relocation, the “Premises”
shall include the Relocation Space into which Tenant has been moved and shall
not include the space from which Tenant has been moved, and the Base Rent and
Tenant’s Pro Rata Share shall be adjusted based on the rentable square footage
of the Relocation Space. Landlord shall pay Tenant’s reasonable costs for moving
to the Relocation Space, including without limitation the cost of moving
Tenant’s furniture and equipment.

14. Landlord hereby grants Tenant an allowance of $100,000.00 (the “Allowance”)
for Alterations to the Premises to be performed by Tenant pursuant to the
provisions of Section 9(c) and other applicable provisions of the Lease. Payment
of the Allowance for the Alterations shall be made in accordance with the
provisions set forth in Exhibit B attached hereto and made a part hereof.

 

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15. Landlord may in the future enter into one or more environmental use
restrictions (the “ELUR”) as defined and described in Section 22a-133k and
Sections 22a-133n through 22a-133s inclusive of the Connecticut General Statutes
and their associated regulations (as such statutes and/or regulations may be
amended or replaced from time to time) in connection with the investigation
and/or remediation of the environmental condition of the Property which ELUR
shall restrict the use of the Property to commercial/industrial use and which
shall prohibit demolition of the Building. Tenant agrees that the Lease and
Tenant’s leasehold estate therein shall be automatically and irrevocably subject
to and subordinate to the ELUR at such time as the ELUR (or any modification) is
recorded on the New Haven Land Records. Landlord shall, on request of Tenant,
make a copy of the ELUR available to Tenant. Notwithstanding the foregoing,
Tenant agrees at the request of Landlord to execute and deliver, at no cost to
Landlord, an instrument in recordable form confirming the foregoing
subordination. Failure of Tenant to execute and deliver such subordination
within 10 days after Landlord’s request shall constitute a default under the
Lease.

16. Landlord and Tenant represent and warrant to the other that each has full
authority to enter into this Amendment and further agree to hold harmless,
defend, and indemnify the other from any loss, costs (including reasonable
attorneys’ fees), damages, or claim arising from any lack of such authority.

17. As modified herein, the Lease is hereby ratified and confirmed and shall
remain in full force and effect.

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

19. This Amendment constitutes the entire agreement by and between the parties
hereto and supersedes any and all previous agreements, written or oral, between
the parties. No modification or amendment of this Amendment shall be effective
unless the same shall be in writing and signed by the parties hereto. The
provisions of this Amendment shall inure to the benefit of, and be binding upon,
the parties hereto and their respective legal representatives, successors and
assigns.

20. This Amendment 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. This Amendment shall become effective when duly executed and
delivered by all parties hereto.

(Signatures on following page)

 

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IN WITNESS WHEREOF, Landlord and Tenant have signed this Amendment No. 2 to
Lease 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 Managing Member

    By:   /s/ Carter Winstanley      

Carter J. Winstanley

Its President

ACHILLION PHARMACEUTICALS, INC. By:   /s/ Mary Kay Fenton  

Mary Kay Fenton

Chief Financial Officer

 

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EXHIBIT A

PREMISES

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EXHIBIT B

PAYMENT OF ALLOWANCE

A. Landlord agrees to contribute the Allowance to be applied toward the cost of
the Alterations. The Allowance shall be used only for:

(1) Soft costs, including, without limitation, payment of the cost of preparing
any initial space plan and the final working drawings and specifications,
including mechanical, electrical, plumbing and structural drawings and of all
other aspects of Tenant’s plans.

(2) The payment of plan check, permit and license fees relating to construction
of the Alterations.

(3) Construction of Alterations, including, without limitation, the following:

(a) Installation within the Premises of all partitioning, doors, floor
coverings, ceilings, wall coverings and painting, millwork and similar items.

(b) All electrical wiring, lighting fixtures, outlets and switches, and other
electrical work to be installed within the Premises.

(c) All additional Tenant requirements including, but not limited to, heating,
ventilation and air conditioning, plumbing systems and other systems.

(d) All fire and life protection systems such as fire walls, alarms and
accessories, safety control systems, sprinklers and fire piping, and wiring
installed within the Premises.

(e) All plumbing fixtures, pipes and accessories to be installed within the
Premises.

(f) Testing and inspection costs.

(g) Contractor’s fees, including, but not limited to, any fees based on general
conditions.

(h) Architectural, engineering and energy management services.

(i) Installation of check meters or submeters for all utilities serving the
Premises that are required to be separately metered.

B. Upon completion of each third of the Alterations that will be reimbursed
using the Allowance, Tenant shall submit to Landlord an application for payment
(less the amount of the standard retainage), which shall be signed by Tenant’s
general contractor and the architect, for the portion of the work completed,
together with the following information:

(1) A copy of a receipted invoice or other evidence reasonably satisfactory to
Landlord of the payment by Tenant to Tenant’s contractor(s) for the work
performed in connection with the prior application for payment (not applicable
to the first application for payment).

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(2) Lien waivers from all parties supplying labor or material in connection with
the Alterations, in form reasonably acceptable to Landlord, which waiver may be
conditioned only upon payment of work covered by the application for payment.

(3) A copy of the final Certificate of Occupancy or other final communication or
approval issued by the building department or other appropriate governmental
authority having jurisdiction regarding the Alterations (not applicable except
for the last application for payment).

C. The approved cost of the performance of the Alterations shall be charged
against the Allowance. Landlord and Tenant acknowledge that the cost of
installing the Alterations may exceed the Allowance. The amount by which the
cost of the Alterations exceeds the Allowance is referred to as the “Excess
Cost”.

D. In no event shall the Allowance be used for the purchase of equipment,
furniture or other items of personal property of Tenant. In the event the entire
Allowance is not utilized or disbursed, any unused amount shall accrue to the
sole benefit of Landlord, it being understood that Tenant shall not be entitled
to any credit, abatement or other concession in connection therewith. Tenant
shall be responsible for all applicable state sales or use taxes, if any,
payable in connection with the Alterations, Allowance and/or Excess Cost.