Exhibit 10.1

AMENDMENT NO. 3 TO LEASE

THIS AMENDMENT NO. 3 TO LEASE (this “Amendment”) is made and entered into as of
the 20th day of August, 2015 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, MA 01742 TENANT:    Achillion
Pharmaceuticals, Inc.    300 George Street    New Haven, CT 06510 BUILDING:   
300 George Street    New Haven, CT 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 whereunder the parties 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 NMRl
(“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 whereunder the parties added 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 executed an Amendment No. 2 to Lease dated as of
March 31, 2010 whereunder the parties (i) terminated the Suite 800 Lease and
revised the Premises to include all of the space leased by Tenant in the
Building consisting of Suite 202, Suite 800, Suite

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CS02, and Suite NMR1, comprising the Premises to be 31,800 square feet in the
aggregate, and (ii) extended the Term of the Lease through March 31, 2017, and
(iii) made certain other modifications and corrections to the Lease; and

WHEREAS, Tenant desires to lease an additional area of approximately 6,832
rentable square feet on the ground floor of the Building, on the terms and
conditions set forth below.

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. This Amendment shall be effective as of January 1, 2016,
notwithstanding the date of execution.

2. Commencing on January 1, 2016 (the “Expansion Commencement Date”) Landlord
hereby leases to Tenant, and Tenant hereby leases from Landlord, additional
space on the ground floor of the Building consisting of approximately 6,832
rentable square feet of floor area located as shown on the floor plan attached
hereto as Exhibit A (the “Ground Floor Expansion Premises”). From and after the
Expansion Commencement Date, the definition of “Premises” as contained in the
Lease shall be modified and deemed to include the Ground Floor Expansion
Premises and shall consist of approximately 38,632 rentable square feet in the
aggregate, subject to the right of remeasurement as set forth in the Lease.

3. Tenant shall, upon the Expansion Commencement Date, take the Ground Floor
Expansion Premises in ‘as-is” condition. The taking of possession of the Ground
Floor Expansion Space by Tenant shall be conclusive evidence of Tenant’s
acceptance, and that the Ground Floor Expansion Space was in good and
satisfactory condition, at the time possession was taken by Tenant, subject to
the Landlord’s ongoing compliance with laws and repair and maintenance
obligations under the Lease.

4. The Base Rent pursuant to the provisions set forth in Section 1.(d) of the
Lease is hereby modified to provide that from and after the Expansion
Commencement Date, Base Rent for the Term (as extended below) shall be payable
in the following amounts:

 

Period

   Rentable Square
Feet (RSF)      Base Rent
per RSF      Annual
Base Rent      Monthly
Installments  

Expansion Commencement Date – 03/31/2016

     31,800       $ 20.07       $ 638,226.00       $ 53,185.50   

04/01/2016 – 03/31/2020

     38,632       $ 21.07       $ 813,976.24       $ 67,831.35   

5. Section 1.(f) is revised such that Tenant’s Pro Rata Share is 7.44%.

6. Section 1.(g) is revised such that Term shall end on March 31, 2020.

7. Section 1.(j) is revised such that Termination Date is March 31, 2020.

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8. Section 13 of the Amendment No. 2 to Lease is hereby deleted.

9. Section 14 of the Amendment No. 2 to Lease is hereby deleted.

10. Landlord hereby grants Tenant an allowance of $100,000.00 (the “Allowance”)
for Alterations to the Ground Floor Expansion 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.

11. 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.

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

13. 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.

14. 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.

15. 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. 3 to
Lease as of the day and year first above written.

 

LANDLORD:

WE GEORGE STREET, L.L.C.,

a Delaware limited liability company

By:   WE George Street Holding LLC,   a Delaware limited liability company,  
Its Sole Member   By:   BMR-George Member LLC,     a Delaware limited liability
company,     Its Managing Member     By:  

/s/ Carter Winstanley

    Name:   Carter J. Winstanley     Title:   Authorized Representative TENANT:
ACHILLION PHARMACEUTICALS, INC.   By:  

/s/ Mary Kay Fenton

  Name:   Mary Kay Fenton   Title:   Chief Financial Officer

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EXHIBIT A

PREMISES

 

LOGO [g27663layout.jpg]

LEGEND
VERTICAL PENETRATIONS
BUILDING COMMON AREA
FLOOR COMMON AREA
TENANT SPACE
AVAILABLE SPACE
TENANT BORDER
TENANT MECHANICAL
TENANT GA BOMA 6,964 SF
ARCHITECTS
SVIGALS
+PARTNERS
84 Orange Street New Haven Connecticut 06510
203-786-5110
DRAWING TITLE
GROUND FLOOR-TENANT GA
FILE NO:
JOB NO:
300 GEORGE STREET BOMA
SCALE: 1/8"=1'-0"
DATE: 6/01/15
JOB NO: 0640.00
DRAWING
PAGE NO

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EXHIBIT B

PAYMENT OF ALLOWANCE

A. Landlord agrees to contribute the sum up to $100,000 (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 Ground Floor Expansion 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 Ground Floor Expansion 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 Ground Floor Expansion Premises.

(e) All plumbing fixtures, pipes and accessories to be installed within the
Ground Floor Expansion 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
Ground Floor Expansion Premises that are required to be separately metered.

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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).

(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”. Tenant shall be responsible to pay any 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.