Document:

<PAGE>
                                                                   Exhibit 10.13

                            SECOND AMENDMENT TO LEASE

      This SECOND AMENDMENT TO LEASE (this "Second Amendment")of September 16,
2003 is executed by and between KS Parcel A, LLC as successor to Kendall Square,
LLC ("Landlord") and Vertex Pharmaceuticals Incorporated ("Tenant").

      Reference is made to that certain lease dated January 18, 2001, as amended
by First Amendment to Lease dated as of May 9, 2002 and Confirmation of
Commencement Date and Rentable Square Footage dated January 30, 2003 ("Lease"),
by and between Landlord and Tenant with respect to a portion of the Building on
the Lot (as such terms are defined in the Lease) located in Cambridge,
Massachusetts.

      WHEREAS, Landlord and Tenant desire further to amend the terms of the
Lease, to ratify and confirm the terms of the Lease as amended, and to confirm
certain other matters, all as more particularly set forth below.

      NOW, THEREFORE, in consideration of the mutual promises and other matters
herein contained, and other good and valuable consideration, the receipt and
legal sufficiency of which is hereby acknowledged, Landlord and Tenant agree as
follows:

      1.    Each capitalized term which is used but not defined herein shall
have the respective meaning ascribed thereto in the Lease.

      2.    The last sentence of the next to last paragraph of Section 3.2.1 of
the Lease is deleted and the following is substituted in place thereof: "Subject
to Sections 7.1 (h) and 10.6 hereof, Tenant shall, in any event, (a) commence on
or before August 15, 2003 and substantially complete on or before April 30, 2004
all Tenant's Work required for the initial occupancy of floors one, two and
three as shown on the Tenant Work Plans ("Phase I Work"), (b) commence on or
before October 1, 2004 and substantially complete Tenant's Work as to an
additional twenty five percent (25%) of the Premises within twenty-four (24)
months after the Commencement Date ("Phase II Work"), and (c) commence on or
before October 1, 2005 and substantially complete Tenant's Work as to the
remainder of the Premises within thirty-six (36) months after the Commencement
Date ("Phase III Work"), such improvements as remain to be completed under
clauses (b) and (c) to be performed in accordance with Construction Documents to
be timely prepared by Tenant and approved by Landlord as provided in Section
3.2.1 and otherwise in the Lease, and to have a cost of approximately $18
million in the case of the Phase I Work and approximately $17 million in the
case of the Phase II and Phase III Work.

      3.    Clause (a) of Section 7.1 of the Lease is amended by deleting the
remainder of said clause following the parenthesis (concluding with the words
"...twelve (12) consecutive calendar months)" and the following is substituted
in place thereof: "or if within thirty (30) days after notice from Landlord to
Tenant specifying any default other than a default listed in clause (h) below
Tenant has not commenced diligently to correct the default or defaults so
specified or

                                       -1-
<PAGE>

has not thereafter diligently pursued such correction to completion,"

      4.    Clause (h) of Section 7.1 of the Lease is deleted (up to but not
including the parenthesis beginning with the words, "the foregoing events
described in clauses (a) through (h)...") and the following is substituted in
place thereof: "(h) due to any cause other than a Force Majeure Event, if Tenant
fails to commence or substantially complete the Phase I Work by the dates set
forth in the next to last paragraph of Section 3.2.1 hereof or shall suspend or
otherwise fail to diligently pursue the construction of any Tenant's Work or if
Tenant shall fail to provide the Letters of Credit in the amounts, at the times
and in the form required under a certain Agreement of Surety Indemnity between
Tenant and The Lyme Timber Company, the surety furnishing the bond with respect
to the Phase I, II and III Work, and any such default shall continue for ten
(10) days after written notice from Landlord to Tenant, or if Tenant fails to
commence or to substantially complete the Phase II Work or the Phase III Work in
the amounts and percentages of the Premises specified in the next to last
paragraph of Section 3.2.1 hereof by the respective dates determined pursuant to
such next to last paragraph of Section 3.2.1 and any such commencement failure
shall continue for nine (9) months or completion failure shall continue for six
(6) months, in each case after written notice from Landlord to Tenant," Further,
add at the end of Section 7.1 the following: As used in clause (h) above,
"substantially complete" Tenant's Work shall mean (1) that Tenant has received a
temporary or final certificate of occupancy for such Work from the City of
Cambridge, and (2) only incidental items of work remain to be completed,
provided that Tenant obtains a final certificate of occupancy within a
reasonable period of time thereafter, not to exceed 90 days.

      5.    As used herein, "Tenant Work Plans" means those plans and
specifications described in Attachment A hereto with respect to the Phase I
Work, with such modifications thereto, if any, as are included in Attachment A,
which Tenant Work Plans are hereby approved by Landlord subject to and as
provided in the Lease. The parties acknowledged that the Phase I Work shown on
the Tenant Work has a cost of approximately $18 million.

      6.    Landlord hereby approves William A. Berry and Sons, Inc. as Tenant's
Contractor for Tenant's Work.

      7.    Tenant has this day provided a performance bond pursuant to Sections
5.1.5 and 3.2.1 from a surety acceptable to Landlord. Tenant has also submitted
insurance certificates evidencing the insurance coverages required under the
Lease, which submissions have been approved by Landlord. Landlord hereby waives
the requirement in Section 3.2.1 that Tenant provide a statutory lien bond with
respect to Tenant's Work.

      8.    The submission of a form of this Second Amendment or any summary of
its terms shall not constitute an offer by Landlord to Tenant; but the Lease
shall only be amended and the parties bound when this Second Amendment is
executed and delivered by both Landlord and Tenant, each acting in their sole
discretion, and approved by the holder of any mortgagee of the Premises having
the right of approval. The Lease, as amended hereby, is ratified and confirmed
in all respects.

                                     - 2 -
<PAGE>

      9.    With respect to additional security for performance of Tenant's
Work, The Lyme Timber Company ("Lyme") has of even date with this Second
Amendment issued a Performance Bond in favor of the Landlord ("Performance
Bond"), which Performance Bond is secured by an Agreement of Surety Indemnity
("Indemnity") by Tenant in favor of Lyme and secured by a Letter of Credit
("Letter of Credit") in favor of Lyme, each of even date herewith. In the event
of an Event of Default by Tenant pursuant to Section 7.1 of the Lease, if Lyme
has drawn on the Letter of Credit but such drawn funds have not been applied to
construction of Tenant's Work, Landlord shall deduct from any calculation of
sums mat Tenant may owe Landlord due to such Event of Default any sums
attributable to a failure to complete any of Tenant's Work that would be covered
by the sums drawn by Lyme on the Letter of Credit, whether or not Landlord has
received such sums.

      Executed as of the date first written above.

LANDLORD:                                   TENANT:

KS PARCEL A, LLC                            VERTEX PHARMACEUTICALS INCORPORATED
By: Kendall Square, LLC, its Manager
    By: Lyme Properties, LLC, its Manager

By: /s/ David M. Roby                       By: /s/ Jan F. Smith
    ---------------------------------           --------------------------------
    David M. Roby                               Name:  Jan F. Smith
    Manager                                     Title: Chief Financial Officer

                                       -3-<PAGE>
                                                                   Exhibit 10.14

                            THIRD AMENDMENT TO LEASE

      This THIRD AMENDMENT TO LEASE (this "Third Amendment") as of December 22,
2003 is executed by and between KS Parcel A, LLC as successor to Kendall Square,
LLC ("Landlord") and Vertex Pharmaceuticals Incorporated ("Tenant").

      Reference is made to that certain lease dated January 18, 2001, as amended
by First Amendment to Lease dated as of May 9, 2002 and Confirmation of
Commencement Date and Rentable Square Footage dated January 30, 2003 and Second
Amendment to Lease dated as of September 16, 2003 ("Lease"), by and between
Landlord and Tenant with respect to a portion of the Building on the Lot (as
such terms are defined in the Lease) located in Cambridge, Massachusetts.

      Landlord and Tenant desire further to amend the terms of the Lease, to
ratify and confirm the terms of the Lease as amended, and to confirm certain
other matters, all as more particularly set forth below.

      NOW, THEREFORE, in consideration of the mutual promises and other matters
herein contained, and other good and valuable consideration, the receipt and
legal sufficiency of which is hereby acknowledged, Landlord and Tenant agree as
follows:

      1.    Each capitalized term which is used but not defined herein shall
have the respective meaning ascribed thereto in the Lease.

      2.    The date "April 30, 2004" as contained in the last sentence of the
next to last paragraph of Section 3.2.1 of the Lease is deleted and the
following is substituted in place thereof: "April 30, 2004 as such date is
extended by the Phase I Work Holiday Period". Further, said next to last
paragraph of Section 3.2.1 of the Lease is also amended by adding the following
sentences as the final sentences to such next to last paragraph: "The 'Phase I
Work Holiday Period' shall be the number of calendar days commencing with the
date of this Third Lease Amendment and ending on the earlier of (a) February 28,
2004 or (b) the date Landlord notifies Tenant that it no longer believes it will
be possible for Tenant to enter into a sublease transaction with the
Massachusetts Institute of Technology that is acceptable to Landlord as provided
for in the Lease. Tenant acknowledges that Landlord is cooperating in Tenant's
attempt to negotiate such a sublease, but that Landlord retains all rights to
subsequently agree or not agree to such sublease upon being presented with a
written sublease setting forth all of the terms and conditions, such agreement
by Landlord to be then evidenced only by its written consent thereto."

      3.    Landlord and Tenant agree that Tenant may suspend and need not
diligently prosecute the Phase I Work during the Phase I Work Holiday Period,
and that Tenant's suspension of or failure so to prosecute such Work during such
Period shall not give rise to a default by Tenant under the Lease.

<PAGE>

      4.    As hereby amended, the Lease is ratified, confirmed and continued in
effect.

      5.    The surety which has issued a bond pursuant to a certain Agreement
of Surety Indemnity dated as of September 16, 2003 has consented to this Third
Amendment, it being understood and agreed with said surety that except with
respect to the underlying Lease obligations expressly modified by this Third
Amendment, all other obligations with respect to said Agreement of Surety
Indemnity, including without limitation the obligations to provide letters of
credit in the amounts and at the times therein provided, are ratified, confirmed
and continued in effect.

      Executed as of the date first written above.

LANDLORD:                                   TENANT:

KS PARCEL A, LLC                            VERTEX PHARMACEUTICALS INCORPORATED

By: Kendall Square, LLC, its Manager
    By: Lyme Properties, LLC, its Manager

      By: /s/ David E. Clem                  By: /s/ Ian F. Smith
          -------------------------------        -------------------------------
          Its Manager                            Name:  Ian F. Smith
                                                 Title: SVP & CFO

The undersigned surety under an Agreement of Surety Indemnity dated as of
September 16, 2003 hereby consents to the foregoing Third Amendment to Lease.

The Lyme Timber Company, a New Hampshire limited partnership

By:   Woodland Management Associates, LLC, a
      New Hampshire limited liability company, its
      general partner

      By: /s/ David M. Roby
          --------------------------------
          David M. Roby, Manager

                                        2

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00085-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00085-of-00352.parquet"}]]