Exhibit 10.1

SECOND AMENDMENT TO LEASE

THIS SECOND AMENDMENT TO LEASE (hereinafter referred to as the “Amendment”) is
dated as of this 20th day of July, 2015 by and between FOREST CITY 88 SIDNEY
STREET, LLC, a Delaware limited liability company (“Landlord”) and
AGIOS PHARMACEUTICALS, INC., a Delaware corporation (“Tenant”). Capitalized
terms used herein and not otherwise defined shall have the meaning ascribed to
such term in the Lease.

W I T NE S S E T H

WHEREAS, Landlord and Tenant entered into that certain Lease dated as of
September 15, 2014 (the “Original Lease”), as amended by that certain First
Amendment to Lease (the “First Amendment”) dated as of November 21, 2014 (the
Original Lease and First Amendment shall be referred to collectively as, the
“Lease”) with respect to certain premises located at 88 Sidney Street,
Cambridge, Massachusetts (the “Premises”); and

WHEREAS, Landlord and Tenant desire to amend the Lease to expand the definition
of Premises to include the fifth floor of the Building (the “Fifth Floor
Expansion Space”), provide for an additional improvement allowance, and for
other purposes, as set forth in this Amendment.

NOW, THEREFORE, in consideration of the promises and mutual covenants
hereinafter contained and other valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, Landlord and Tenant hereby agree
as follows:

 

1. Premises. Effective as of the date hereof, the term “Premises” set forth on
Exhibit A of the Lease is deleted in its entirety and replaced with the
following:

“Premises: The Premises shall be comprised of approximately 146,034 rentable
square feet as follows:

 

Floor 1 Suite 100A:      418 rsf    Floor 1 Suite 100B:      340 rsf    Floor 1
Suite 100:      7,086 rsf    Floor 1 Suite 150:      4,928 rsf    Floor 2 Suite
200:      33,452 rsf    Floor 3 Suite 300:      33,464 rsf    Floor 4 Suite 400:
     33,530 rsf    Floor 5 Suite 500:      32,816 rsf   

All as more particularly shown on the floor plans attached to this Lease as
Exhibit B.”

 

2. Annual Fixed Rent. Effective as of the date hereof, the term “Annual Fixed
Rent for the Term” set forth on Exhibit A of the Lease shall be deleted in its
entirety and replaced with the following:

“Annual Fixed Rent: With respect to Suite 100A, Suite 100, Suite 300 and Suite
400: $57.25 per rsf, as adjusted per the terms of Section 3.1 hereof. With
respect to Suite 100B, Suite 150 and Suite 200: $60.00 per rsf, as adjusted per
the terms of Section 3.1 hereof. With respect to Suite 500: $65.00 per rsf, as
adjusted per the terms of Section 3.1 hereof.”

 

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3. Additional Rent. Tenant shall not be obligated to pay Additional Rent with
respect to the Fifth Floor Expansion Space prior to the Rent Commencement Date
for the Fifth Floor Expansion Space.

 

4. Annual Increases to Annual Fixed Rent. Effective as of the date hereof,
Section 3.1 shall be amended by deleting the second paragraph thereof and
replacing it with the following:

“On the first anniversary of the Rent Commencement Date, and on each anniversary
thereafter, Annual Fixed Rent for Suites 100A, 100, 300 and 400 shall increase
to an amount equal to one hundred two percent (102%) of the Annual Fixed Rent
immediately preceding such anniversary. On the first anniversary of the Rent
Commencement Date, and on each anniversary thereafter, Annual Fixed Rent for
Suites 100B, 150 and 200 shall increase to an amount equal to one hundred three
percent (103%) of the Annual Fixed Rent immediately preceding such anniversary.
On the first anniversary of the Rent Commencement Date for Fifth Floor Expansion
Space, and on each anniversary thereafter, Annual Fixed Rent for Suite 500 shall
increase to an amount equal to one hundred three percent (103%) of the Annual
Fixed Rent immediately preceding such anniversary.”

 

5. Operating Expenses. Section 3.3 of the Lease is hereby amended by adding the
following thereto:

“Annual Estimates. Landlord shall deliver to Tenant a written estimate of
Operating Expenses for each calendar year during the Term (the “Annual
Estimate”), which may be revised by Landlord no more than twice during such
calendar year to reflect actual known or reasonably anticipated increases in
Operating Expenses for that calendar year. Landlord shall use reasonable efforts
to deliver the Annual Estimate to Tenant by 60 days prior to the end of each
calendar year, and shall take into account any comments by Tenant which are
consistent with the rights and obligations of the parties under this
Lease. Landlord shall use good faith efforts to meet with Tenant from time to
time prior to November 1st of each calendar year during the Term upon Tenant’s
request to discuss the Annual Estimate for the upcoming calendar year and
Landlord’s budget for Operating Expenses for the Property for such year . The
Annual Estimate shall include reasonably detailed line-item costs.”

 

6. Tax Protest. Section 3.2 of the Lease is hereby amended by adding the
following thereto:

“Upon Tenant’s reasonable request, the Landlord shall use reasonable efforts to
contest or seek abatement of any Real Estate Taxes affecting the Premises.
Should the Landlord contest or seek abatement of such taxes, then it shall do so
with diligence and shall keep the Tenant appropriately informed, in the
Landlord’s reasonable discretion, as to such action. Upon Tenant’s request,
Landlord shall provide Tenant with a copy of any notice of the assessed
valuation of the Property and/or the Building received by Landlord, as well as
copies of all tax bills and tax notices received by Landlord, and copies of all
papers filed by Landlord in connection with any such Tax Protest or Tax
Proceeding. Tenant’s rights under this Section may be exercised only in respect
of Tax Years occurring subsequent to the Commencement Date.”

 

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7. Tenant Personnel. Tenant shall have the right to station its own security or
other personnel in the lobby of the Building and upon reasonable advance notice
to utilize its own contractors or personnel for cleaning, maintenance and other
similar services in the Building, excluding, however, HVAC or other systems
which may be shown as Landlord’s responsibility on the Tenant/Landlord
Responsibility Matrix attached as Exhibit H-1. In the event Tenant utilizes its
own personnel or contractors for any such security, cleaning, maintenance or
other similar services, Tenant shall pay all costs directly and the same shall
not be included in Landlord’s costs for purposes calculating Operating Expenses
for the Property.

 

8. Condition of Fifth Floor Expansion Space/Landlord’s Work. Landlord shall be
responsible, at its sole cost and expense, to deliver the base building
mechanical systems (HVAC, electrical, life safety and plumbing), including,
without limitation, the hot water heater, and the Shared Laboratory Systems (as
defined in Section 2.3(c) of the Lease) that service the Fifth Floor Expansion
Space in good operating condition and repair, and shall maintain the same in
accordance with Section 5.1 of the Lease. Except as provided in this Section 7,
the parties hereby acknowledge and agree that all work performed by Tenant or
required to be performed by Tenant under the Lease has been performed to the
satisfaction of Landlord. Landlord shall remain responsible, at its sole cost
and expense, for all work to be performed by Landlord under the Lease (except as
otherwise provided in this Second Amendment), including, without limitation,
final completion of all of Landlord’s Work pursuant to Section 2.1(c) of the
Lease.

 

9. Lease Commencement Date for Fifth Floor Expansion Space. The Lease
Commencement Date for Fifth Floor Expansion Space shall be the date of this
Amendment.

 

10. Rent Commencement Date for Fifth Floor Expansion Space. The following shall
be added as a definition on Exhibit A after the definition of Rent Commencement
Date:

 

“Rent Commencement Date for Fifth Floor Expansion Space: November 1, 2015.”

 

11. Tenant/Landlord Responsibility Matrix for the Building. Exhibit H-1 attached
hereto shall be attached to the Lease as a new Exhibit H-1 and shall be referred
to as the Tenant/Landlord Responsibility Matrix for the Building.

 

12. Leasehold Improvement Allowance. The defined term “Leasehold Improvements
Allowance” set forth on Exhibit A shall be amended by deleting “$16,189,047.00”
and replacing it with “$20,126,967.00”. Additionally, the third sentence of
Section 3 of Exhibit E to the Lease is hereby deleted in its entirety and
replaced with the following:

“The Tenant must apply to Landlord for reimbursement from the Leasehold
Improvements Allowance applicable to the Fifth Floor Expansion Space in the
amount of Three Million Nine Hundred Thirty-Seven Thousand Nine Hundred Twenty
and 00/100 Dollars ($3,937,920.00) (the “Fifth Floor Leasehold Improvement
Allowance”) within twenty-four (24) months after the Rent Commencement Date for
the Fifth Floor Expansion Space. Tenant may use a portion of the Fifth Floor
Improvement Allowance towards improvements on any floor in the Building, but
only after Tenant has improved the Fifth Floor Expansion Space as approved by
Landlord.”

 

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13. Parking Privileges. The first sentence of the term “Parking Privileges” set
forth on Exhibit A shall be deleted in its entirety and replaced with the
following:

“During the Term, Tenant shall be entitled to use and shall pay for two hundred
eighteen (218) parking passes in accordance with Section 2.4 of the Lease;
provided, however, that from the Rent Commencement Date until the Rent
Commencement Date for Fifth Floor Expansion Space, Tenant shall have the option
to use and pay for a minimum of one hundred fifty-two (152) parking passes, and
from the Rent Commencement Date for Fifth Floor Expansion Space until the first
anniversary of the Rent Commencement Date, Tenant shall have the option to use
and pay for a minimum of two hundred one (201) parking passes. Commencing with
the first anniversary of the Rent Commencement Date, Tenant shall be obligated
to pay for two hundred eighteen (218) parking passes.”

 

14. Security Deposit. The defined term “Security Deposit” set forth on Exhibit A
shall be amended by deleting “$2,189,270.17” and replacing it with
“$2,900,283.50”. Upon execution of this Amendment, Tenant shall deposit Seven
Hundred Eleven Thousand Thirteen and 33/100 Dollars ($711,013.33) with the
Landlord as an additional Security Deposit, so that the total amount of the
Security Deposit set forth on Exhibit A shall be Two Million Nine Hundred
Thousand Two Hundred eighty three and 50/100 Dollars ($2,900,283.50). At
Tenant’s election, such increase in the Security Deposit shall be effectuated by
a substitution of a single new Letter of Credit.

 

15. Floor Plans Showing Premises. Exhibit B to the Lease shall be deleted and
replaced with a new Exhibit B attached hereto.

 

16. Landlord Entity. The parties acknowledge that the Original Lease and the
First Amendment both stated the name of the Landlord entity incorrectly. The
correct name of the Landlord entity is “Forest City 88 Sidney Street, LLC”.

 

17. Counterparts. This Amendment may be executed in any number of counterparts,
each of which shall be deemed an original and all of which together shall
constitute one and the same instrument.

 

18. Brokers. Landlord and Tenant represent and warrant that they have had no
dealings with any broker or agent in connection with this Amendment other than
Colliers International New England, LLC and CBRE/New England and each party
shall indemnify and hold harmless the other party from claims for any brokerage
commission. Landlord shall pay Colliers International New England, LLC and
CBRE/New England a brokerage commission pursuant to the terms of a separate
agreement.

 

19. Ratification. The Lease, as amended hereby, is in full force and effect, and
is ratified and confirmed, and there are no other amendments or modifications
thereto.

 

20. Governing Law. This Amendment will be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts.

 

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21. Consents. This Amendment shall be subject to the prior written consent of
the Ground Lessor, The Massachusetts Institute of Technology, and Landlord will
use good faith best efforts to obtain such consent.

 

22. Due Authority. Each of Landlord and Tenant, for itself, warrants and
represents that this Amendment is its duly adopted, approved and authorized act
and that the person signing this Amendment has full authority to bind, and to
execute this Amendment on behalf of, the party he or she represents.

 

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IN WITNESS WHEREOF, the parties hereto have executed this Amendment under seal,
as of the day, month and year first above written.

 

LANDLORD:

Forest City 88 Sidney Street, LLC,

a Delaware limited liability company

By: FC HCN 88 Holding, LLC, a Delaware limited liability company, Its sole
member By: FC HCN University Park, LLC, a Delaware limited liability company,
Its sole member By: Forest City University Park, LLC, a Delaware limited
liability company Its managing member By: /s/ Michael Farley Name: Michael
Farley Its: Vice President

 

TENANT:

AGIOS PHARMACEUTICALS, INC.,

a Delaware corporation

By: /s/ Glenn Goddard Name: Glenn Goddard Title: SVP, Finance

 

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EXHIBIT B

Floor Plans Showing the Premises

SEE ATTACHED

 

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Exhibit H-1

Tenant / Landlord Responsibility Matrix for the Fifth Floor Expansion Space

Agios

88 Sidney Street

Cambridge, MA

Tenant / Landlord Responsibility Matrix

June 11, 2015

 

Description

  

Landlord

  

Tenant

SITEWORK       Domestic sanitary sewer connection to street    X    Lab waste
sewer connection to individual tenant pH neutralization system    X    Roof
storm drainage    X    Nstar primary and secondary electrical service    X   
Nstar gas service    X    Domestic water service to Building    X    Fire
protection water service to Building    X    STRUCTURE       Structural
enhancements for specific Tenant load requirements       X Structural framing
dunnage above roof for Base Building equipment    X    Structural framing
dunnage above roof for Tenant equipment (subject to Landlord review and
approval).       X Framed openings for Base Building utility risers    X   
Framed openings for Tenant utility risers in addition       X Miscellaneous
metals items and/or concrete pads for Base Building equipment    X   
Miscellaneous metals items and/or concrete pads for Tenant equipment       X
ROOFING       Single ply EPDM roofing system with rigid insulation    X   
Roofing penetrations for Base Building equipment/systems    X    Roofing
penetrations for Tenant equipment/systems by LL’s roofer to LL Spec       X
Walkway pads to Base Building equipment    X    Walkway pads to Tenant equipment
      X Roofing alterations due to Tenant changes       X EXTERIOR      
Building exterior consisting of precast concrete and windows    X    Main
Building entrances    X    Loading dock with loading dock elevator and stairwell
      X Acoustic screening of Base Building rooftop equipment    X    Acoustic
screening of Tenant rooftop equipment (space available within base building
screening       X

 

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ELEVATORS       Three (2) passenger elevators, one (1) service with a capacity
of 4,000 lbs.    X    WINDOW TREATMENT       Furnish and install Building
standard blinds for all windows       X TENANT AREAS       Finishes at inside
face of exterior walls       X Finishes at inside face at Tenant side of core
partitions       X Toilet rooms within Tenant Premises in addition to those
provided by base building       X Electrical closets within Tenant Premises   
   X Tel/data rooms for interconnection with Tenant tel/data       X Tenant
kitchen areas       X Modifications to core areas to accommodate Tenant
requirements       X Partitions, ceilings, flooring, painting, finishes, doors,
frames, hardware, millwork, casework, equipment, and build out.       X Fixed or
movable casework.       X Laboratory Equipment including but not limited to
biosafety cabinets, autoclaves, glass washers.       X Chemical Fume Hoods,
bench fume hood       X Shaft enclosures for Base Building systems’ risers    X
   Shaft enclosures for Tenant risers (in addition to risers put in place for
tenant use)       X FIRE PROTECTION       Fire service entrance including fire
department connection, alarm valve, and flow protection    X    Core area
distribution piping and sprinkler heads    X    Stair distribution piping and
sprinkler heads    X    All run outs, drop heads, and related equipment within
Tenant premises       X Modification of sprinkler piping and head locations to
suit Tenant layout and hazard index       X Specialized extinguishing systems or
containment for tenant program areas       X Preaction dry-pipe systems       X
Fire extinguisher cabinets at core common areas    X    Fire extinguisher
cabinets in Tenant Premises       X PLUMBING       Domestic water service with
backflow prevention and Base Building risers    X    Domestic water distribution
within Tenant Premises       X Tenant restroom plumbing fixtures compliant with
accessibility requirements (in addition to those provided by the Base Building)
      X Wall hydrants in common core areas (where required by code)    X   
Tenant metering and sub-metering at Tenant connection       X Storm drainage
system    X    Sanitary waste and vent service    X    Two stage active pH
neutralization system (individual tenant system)       X Lab waste and vent pipe
distribution       X

 

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Hot water generation for core restrooms    X    Non-potable Hot water generation
for Tenant use       X Central lab air compressor and piping risers    X   
Compressed air pipe distribution in Tenant Premises for specific points of use
      X Central lab vacuum system and pipe risers       X Lab vacuum pipe
distribution in Tenant Premises for specific points of use       X Tepid water
generator and pipe risers       X Tepid water pipe distribution in Tenant
Premises       X RO/DI water generator and pipe risers       X RO/DI water pipe
distribution in Tenant Premises for specific points of use       X Manifolds,
piping, and other requirements including cylinders, not specifically mentioned
above       X NATURAL GAS       Natural gas service to Building and piping to
Base Building boilers and Base Building generator    X    Natural gas service,
pressure regulator and meter for Tenant equipment       X Natural gas piping
from Tenant meter to Tenant Premises or Tenant equipment area.       X Natural
gas pipe distribution within Tenant Premises       X Natural gas pressure
regulator vent pipe riser from valve location through roof       X HEATING,
VENTILATION, AIR CONDITIONING       Once-through supply air handling units with
30% prefilters, 85% final filters, with corresponding heating and cooling. Units
are sized for approximately 1.5 cfm per square foot of lab space. 65%/35%
lab/office ratio.    X    Boiler capacity for hot water reheats at lab/office
space    X    Hot water reheat distribution to reheat coils       X Vertical
supply air duct distribution       X Tenant Space Supply air duct distribution,
VAV terminals, equipment connections, insulation, air terminals, dampers,
hangers,       X Roof mounted laboratory exhaust fans       X Vertical exhaust
air duct risers for general lab exhaust       X Roof mounted laboratory exhaust
fans for specialty exhaust systems.       X Exhaust air duct distribution,
exhaust air valves, equipment connections, insulation, air terminals, dampers,
hangers, etc. within Tenant Premises.       X Exhaust air duct distribution,
exhaust air valves, equipment connections, insulation, air terminals, dampers,
hangers, etc.       X General Exhaust for Tenant Spaces from Risers       X
Restroom exhaust for core area restrooms    X    Restroom exhaust for restrooms
within Tenant Premises       X Electric room ventilation system for electrical
closets within Tenant premises       X Sound attenuation for Tenant equipment to
comply with Cambridge Noise Ordinance       X Additional/ dedicated cooling for
Tenant requirements.       X

 

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ELECTRICAL       Electrical utility service to switchgear in main electrical
vault    X    Provide the tenant with a proportionate share of the available
power based on a sqft allocation    X    Standby power distribution within
Tenant Premises 100% of existing service       X Lighting and power distribution
for core areas    X    Lighting and power distribution for Tenant Premises      
X Tenant Check Meter (s) for Tenant Connected Loads       X Common area life
safety emergency lighting/signage    X    Tenant Premises life safety emergency
lighting/signage       X Tenant panels, transformers, etc. in addition to Base
Building       X Tenant UPS system, battery backup, and associated
equipment/distribution       X FIRE ALARM       Base Building fire alarm system
with devices in core areas    X    Fire alarm sub panels and devices for Tenant
Premises with integration into Base Building system       X Alteration to fire
alarm system to facilitate Tenant program       X TELEPHONE/DATA       Tel Data
Riser Conduit from demark to each floor       X Tenant tel/data rooms       X
Pathways from demarcation room directly into Tenant tel/data rooms       X
Tel/Data cabling from demarcation room Tenant tel/data room.       X Fiber optic
service for Tenant use       X Tel/data infrastructure including but not limited
to servers, computers, phone systems, switches, routers, MUX panels, equipment
racks, ladder racks, etc.       X Provisioning of circuits and service from
service providers       X Audio visual systems and support       X Station
cabling from Tenant tel/data room to all Tenant locations, within the suite and
exterior to the suite, if needed       X SECURITY       Card access at Building
entries       X Card access into or within Tenant Premises on separate Tenant
installed and managed system       X

 

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