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Exhibit 10.46    
    

EMPLOYMENT AGREEMENT  

        AGREEMENT, made and entered into as of February 11, 2008 by and between Vertex Pharmaceuticals Incorporated, a Massachusetts corporation (together with its
successors and assigns, the "Company"), and Lisa Kelly-Croswell (the "Executive"). 

W IT N E S S E T H  

        WHEREAS, the Company is employing the Executive as the Company's Senior Vice President, Human Resources; 

        WHEREAS,
the Company and the Executive desire to enter into an employment agreement, which shall set forth the terms of such employment (this
"Agreement"); and 

        WHEREAS,
the Executive desires to enter into this Agreement and to continue such employment, subject to the terms and provisions of this Agreement. 

        NOW,
THEREFORE, in consideration of the premises and mutual covenants contained herein and for other good and valuable consideration, the receipt of which mutually is acknowledged, the
Company and the Executive (each individually a "Party", and together the "Parties") agree as follows: 

	1.
	DEFINITIONS.

        "Base Salary" shall mean the Executive's base salary in accordance with Section 4 below. 

        "Board" shall mean the Board of Directors of the Company. 

        "Cause" shall mean (i) the Executive is convicted of a crime involving moral turpitude, (ii) the Executive commits a
material breach of any provision of this Agreement not involving the performance or nonperformance of duties, or (iii) the Executive, in carrying out the Executive's duties, acts or fails to
act in a manner that is determined, in the sole discretion of the Board, after written notice of any such act or failure to act and a reasonable opportunity to cure the deficiency has been provided to
the Executive, to be (A) willful gross neglect or (B) willful gross misconduct resulting, in either case, in material harm to the Company unless such act, or failure to act, was believed
by the Executive, in good faith, to be in the best interests of the Company. 

        "Change of Control" shall have the meaning set forth in the Change of Control Agreement. 

        "Change of Control Agreement" shall mean the Change of Control letter agreement between the Company and the Executive dated
July 12, 2007. 

        "Code" shall mean the Internal Revenue Code of 1986, as amended. 

        "Common Stock" shall mean the common stock of the Company. 

        "Disability" or "Disabled" shall mean a disability as determined under the Company's
long-term disability plan or program in effect at the time the disability first occurs, or if no such plan or program exists at the time of disability, then a "disability" as defined under
Section 22(e)(3) of the Code. 

        "Effective Date" shall mean February 11, 2008. 

        "Good Reason" shall mean that, without the Executive's consent, one or more of the following events occurs, and the Executive, at the
Executive's own initiative provides notice of termination within 30 days after such event: 

	(i)
	the
Executive's Base Salary is decreased unless such reduction is part of an across-the-board proportionate reduction in the salaries of the
Company's senior management team; or

	(ii)
	the
office to which the Executive is assigned is relocated to a place 35 or more miles away and such relocation is not at the Executive's request or with the
Executive's prior agreement (and 

 

other
than, for Executives assigned to the Company's principal executive offices, in connection with a change in location of the Company's principal executive offices). 

        "Severance Payment" shall mean an amount equal to the sum of the Base Salary in effect on the date of termination of Executive's
employment, plus the amount of the Target Bonus for the Executive for the year in which the Executive's employment is terminated; provided, however, that if the Executive terminates the Executive's
employment for Good Reason based on a reduction in Base Salary, then the Base Salary to be used in calculating the Severance Payment shall be the Base Salary in effect immediately prior to such
reduction in Base Salary. 

        "Target Bonus" shall mean the target cash bonus for which the Executive is eligible on an annual basis, at a level consistent with the
Executive's title and responsibilities, under the Company's bonus program then in effect and applicable to the Company's senior executives generally. 

	2.
	TERM
OF EMPLOYMENT. 

        The
Company hereby employs the Executive, and the Executive hereby accepts such employment, continuing until termination in accordance with the terms of this Agreement. The period during
which the Executive is employed hereunder is referred to in this Agreement as the "term of employment." 

	3.
	POSITION.

        On
the Effective Date, the Executive shall be employed as the Company's Senior Vice President, Human Resources. 

	4.
	BASE
SALARY. 

        The
Executive's annualized Base Salary as of the date of this Agreement is $298,700.00, payable in accordance with the regular payroll practices of the Company. The Base Salary shall be
reviewed no less frequently than annually, and any changes thereto (which shall thereafter be deemed the Executive's Base Salary) shall be solely within the discretion of the Board. 

	5.
	TARGET
BONUS PROGRAM. 

        During
the term of employment, the Executive shall be eligible to participate in the Company's Target Bonus program (and other cash incentive compensation programs) applicable to the
Company's senior executives, as any such programs are established and modified from time to time by the Board in its sole discretion, and in accordance with the terms of such program. 

	6.
	INCENTIVE
COMPENSATION PROGRAMS. 

        During
the term of employment, the Executive shall be eligible to participate in the Company's incentive compensation programs applicable to the Company's senior executives, as such
programs may be established and modified from time to time by the Board in its sole discretion. 

	7.
	EMPLOYEE
BENEFIT PROGRAMS. 

        During
the term of employment, the Executive shall be entitled to participate in all employee welfare and pension benefit plans, programs and/or arrangements offered by the Company to
its senior executives, as such plans, programs and arrangements may be amended from time to time, to the same extent and on the same terms applicable to other senior executives. Nothing in this
section shall preclude the Company from amending or terminating any of its employee benefit plans, programs or arrangements. 

	8.
	VACATION.

        During
the term of employment, the Executive shall be entitled to paid vacation days each calendar year in accordance with the Company's vacation policy then in effect. 

2

 
	9.
	TERMINATION
OF EMPLOYMENT. 

        (a)   Termination in Connection with a Change of Control.  To the extent the Executive is entitled, in connection
with the Executive's termination of employment, to severance or other benefits under the Change of Control Agreement, the Executive shall not be entitled to corresponding benefits under this
Section 9. 

        (b)   Termination by the Company for Cause; or Termination by the Executive without Good Reason.  If the Company
terminates the Executive's employment for Cause, or if the Executive voluntarily terminates the Executive's employment, other than for Good Reason, death or Disability, the term of employment shall
end as of the date specified below, and the Executive shall be entitled to the following: 

	(i)
	Base
Salary earned by Executive but not paid through the date of termination of Executive's employment under this Section 9(b); and

	(ii)
	any
amounts earned, accrued or owing to the Executive but not yet paid under Sections 5, 6, or 7 above. 

        Termination
by Company for Cause shall be effective as of the date noticed by the Company. Voluntary termination by Executive other than for Good Reason, death or Disability shall be
effective upon 90 days' prior written notice to the Company and shall not be deemed a breach of this Agreement. 

        If
the Executive voluntarily terminates his or her employment without Good Reason, the Company may elect to waive the period of notice, or any portion thereof, and, if the Company so
elects, the Company will pay the Executive at the rate of the Executive's Base Salary for the notice period or for any remaining portion thereof. 

        (c)   Termination by the Company Without Cause; or Termination by the Executive for Good Reason.  If the Company
terminates the Executive's employment for Cause, or if the Executive voluntarily terminates the Executive's employment, other than for Good Reason, death or Disability, the term of employment shall
end as of the date specified below, and the Executive shall be entitled to the following (provided that, with respect to (iii) and (v) such amounts shall be subject to and in exchange
for a general release by Executive of all claims against the Company, its subsidiaries, and their officers, directors, agents and representatives): 

	(i)
	Base
Salary earned by Executive but not paid through the date of termination of Executive's employment under this Section 9(c);

	(ii)
	all
incentive compensation awards earned by Executive but not paid prior to the date of termination of Executive's employment under this Section 9(c);

	(iii)
	a
cash payment to the Executive in an amount equal to the Severance Payment, payable within ten days after the execution of a general release and expiration without
revocation of any applicable revocation periods under the general release;

	(iv)
	any
amounts earned, accrued or owing to the Executive but not yet paid under Sections 5, 6 or 7 above;

	(v)
	if
COBRA coverage is elected by the Executive, the Company shall pay the cost of COBRA continuation premiums on the Executive's behalf to continue standard medical,
dental and life insurance coverage for the Executive (or the cash equivalent of same in the event the Executive is ineligible for continued coverage) until the earlier of:

	(A)
	the
date 12 months after the date the Executive's employment is terminated; or 

3

 

	(B)
	the
date, or dates, on which the Executive receives equivalent coverage and benefits under the plans, programs and/or arrangements of a subsequent employer (such coverage and benefits
to be determined on a coverage-by-coverage or benefit-by-benefit basis). 

        If
Executive is a "specified employee" under Section 409A(a)(2)(B)(i) of the Code, any payment of "nonqualified deferred compensation" (as defined under Section 409A of the
Code and related guidance) attributable to a "separation from service" (as defined under Section 409A of the Code and related guidance) shall not commence until the first full business day that
is more than 6 months after the applicable separation from service ("Deferred Payment Date"). Any payments that would otherwise have been made
between the separation from service and the Deferred Payment Date, but for this paragraph, shall be made in a lump sum on the Deferred Payment Date. Payments that, in any case, are scheduled to be
made after the Deferred Payment Date shall continue according to the applicable payment schedule. To the extent that the termination of the Executive's employment does not constitute a separation of
service under Section 409A(a)(2)(A)(i) of the Code (as the result of further services that reasonably are anticipated to be provided by the Executive to the Company at the time the Executive's
employment is terminated), the payment of any nonqualified deferred compensation will be further delayed until the date that is the first full business day that is more than 6 months after the
date of a subsequent event constituting a separation of service under Section 409A(a)(2)(A)(i) of the Code. 

	10.
	ASSIGNABILITY;
BINDING NATURE. 

        This
Agreement shall be binding upon and inure to the benefit of the Parties and their respective successors, heirs (in the case of the Executive) and assigns. No rights or obligations
of the Company
under this Agreement may be assigned or transferred by the Company except that such rights or obligations may be assigned or transferred pursuant to a merger or consolidation in which the Company is
not the continuing entity, or the sale or liquidation of all or substantially all of the assets of the Company; provided,  however, that the assignee or
transferee is the successor to all or substantially all of the assets of the Company and such assignee or transferee
assumes the liabilities, obligations and duties of the Company, as contained in this Agreement, either contractually or as a matter of law. 

	11.
	REPRESENTATIONS.

        The
Company represents and warrants that it is fully authorized and empowered to enter into this Agreement, and that the performance of its obligations under this Agreement will not
violate any agreement between it and any other person, firm or organization. The Executive represents and warrants that no agreement exists between him and any other person, firm or organization that
would be violated by the performance of the Executive's obligations under this Agreement. 

	12.
	INDEMNIFICATION;
INSURANCE. 

        The
Executive shall at all times be indemnified and eligible for advancement of expenses on the same basis as is provided for the Company's other executive officers and in accordance
with the provisions of the Company's charter and by-laws then in effect. The Executive shall also be covered under all of the Company's policies of liability insurance maintained for the
benefit of its directors and officers on the same basis as is provided for its other executive officers. 

	13.
	ENTIRE
AGREEMENT; TERMINATION. 

        This
Agreement, the agreements referenced herein, and the Employee Non-Disclosure, Non-Competition & Inventions Agreement between the Executive and the
Company, contain the entire understanding and agreement between the Parties concerning the subject matter hereof and supersedes all prior agreements, understandings, discussions, negotiations and
undertakings, whether written or oral, between the Parties with respect thereto. Subject to the terms of this Agreement, the Company shall be entitled to terminate the Executive's employment at any
time, and the Executive may terminate 

4

 

the
Executive's employment by the Company, at any time, in each case by written notice provided in accordance with Section 20 of this Agreement. 

	14.
	AMENDMENT
OR WAIVER. 

        No
provision in this Agreement may be amended unless such amendment is agreed to in writing and signed by the Executive and an authorized officer of the Company. No waiver by either
Party of any breach by the other Party of any condition or provision contained in this Agreement to be performed by such other Party shall be deemed a waiver of a similar or dissimilar condition or
provision at the same or any prior or subsequent time. Any waiver must be in writing and signed by the Executive or an authorized officer of the Company, as the case may be. 

	15.
	SEVERABILITY.

        If
any provision or portion of this Agreement shall be determined to be invalid or unenforceable for any reason, in whole or in part, the remaining provisions of this Agreement shall be
unaffected thereby and shall remain in full force and effect to the fullest extent permitted by law. 

	16.
	SURVIVORSHIP.

        The
respective rights and obligations of the Parties hereunder shall survive any termination of the Executive's employment to the extent necessary to the intended preservation of such
rights and obligations. 

	17.
	BENEFICIARIES/REFERENCES.

        The
Executive shall be entitled, to the extent permitted under any applicable law, to select and change a beneficiary or beneficiaries to receive any compensation or benefit payable
hereunder following the Executive's death by giving the Company written notice thereof. In the event of the Executive's death or a judicial determination of the Executive's incompetence, reference in
this Agreement to the Executive shall be deemed, where appropriate, to refer to the Executive's beneficiary, estate or other legal representative. 

	18.
	GOVERNING
LAW/JURISDICTION. 

        This
Agreement shall be governed by and construed and interpreted in accordance with the laws of The Commonwealth of Massachusetts without reference to principles of conflict of laws. 

	19.
	RESOLUTION
OF DISPUTES. 

        Any
disputes arising under or in connection with this Agreement may, at the election of the Executive or the Company, be resolved by binding arbitration, to be held in Massachusetts in
accordance with the Rules and Procedures of the American Arbitration Association. If arbitration is elected, the Executive and the Company shall mutually select the arbitrator. If the Executive and
the Company cannot agree on the selection of an arbitrator, each Party shall select an arbitrator and the two arbitrators shall select a third arbitrator, and the three arbitrators shall form an
arbitration panel that shall resolve the dispute by majority vote. Judgment upon the award rendered by the arbitrator or arbitrators may be entered in any court having jurisdiction thereof. Costs of
the arbitrator or arbitrators and other similar costs in connection with an arbitration shall be shared equally by the Parties; all other costs, such as attorneys' fees incurred by each Party, shall
be borne by the Party incurring such costs. 

	20.
	NOTICES.

        All
notices that are required or permitted hereunder shall be in writing and sufficient if delivered personally, sent by facsimile (and promptly confirmed by personal delivery,
registered or certified mail 

5

 

or
overnight courier), sent by nationally-recognized overnight courier or sent by registered or certified mail, postage prepaid, addressed as follows: 

	If to the Company:	 	Vertex Pharmaceuticals Incorporated

130 Waverly Street

Cambridge, MA 02139-4242

Attn: Chief Executive Officer

with copies to:

the General Counsel
	

If to the Executive:	
 	

at the Executive's home address listed in the Company records.

        Any
such notice shall be deemed to have been given: (a) when delivered if personally delivered or sent by facsimile on a business day; (b) on the business day after
dispatch if sent by nationally-recognized overnight courier; and/or (c) on the fifth business day following the date of mailing if sent by mail. 

	21.
	HEADINGS.

        The
headings of the sections contained in this Agreement are for convenience only and shall not be deemed to control or affect the meaning or construction of any provision of this
Agreement. 

	22.
	COUNTERPARTS. 

        This
Agreement may be executed in two or more counterparts. 

	23.
	SECTION 409A
COMPLIANCE. 

        It
is the intention of the Company and the Executive that this Agreement and the payments provided for herein meet the requirements of Section 409A of the Code, to the extent
applicable to this Agreement and such payments. The Company and the Executive agree to cooperate in good faith in preparing and executing, at such time as sufficient guidance is available under
Section 409A and from time to time thereafter, such amendments to this Agreement, if any, as the Executive may reasonably request solely for the purpose of assuring that this Agreement and the
payments provided hereunder meet the requirements of Section 409A. Nothing in this Section 23 shall require the Company to increase the Executive's compensation or make the Executive
whole for any requested changes. 

	24.
	TAX
WITHHOLDING; NO GUARANTEE OF ANY TAX CONSEQUENCES. 

        All
payments hereunder shall be subject to all applicable withholding for any federal, state or local income taxes including any excise taxes under the Code. Notwithstanding any other
provision of this Agreement to the contrary or other representation, the Company does not in any way guarantee the tax consequences of any payment or compensation under this Agreement including,
without limitation, under Section 409A of the Code. 

6

 

        IN
WITNESS WHEREOF, the undersigned have executed this Agreement as of the date first written above. 

	 	Vertex Pharmaceuticals Incorporated
	
 	

 
	 	/s/  JOSHUA S. BOGER      
 Joshua S. Boger

President & Chief Executive Officer
	

 	
Executive
	
 	

/s/  LISA KELLY-CROSWELL      
 Lisa Kelly-Croswell

7

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Exhibit 10.48    
    

	

	 	 
	 	 	VERTEX PHARMACEUTICALS INCORPORATED

130 WAVERLY STREET • CAMBRIDGE, MA 02139-4242

TEL. 617.444.6100 • FAX 617.444-6483

http://www.vrtx.com
	

 	
 	
February 11, 2008

Lisa
Kelly-Croswell

40 Wyman Road

Lexington, MA 02420 

Re:    Amendment to Change of Control Agreement

Dear
Lisa: 

        The
Change of Control Agreement dated as of July 12, 2007 between you and Vertex Pharmaceuticals Incorporated (the "Agreement")
hereby is amended, effective on the date hereof, as follows:

	A.
	 Delete Section I.7 in its entirety.

 
	B.
	 Delete Section II in its entirety and substitute the following therefor:

	II.
	Severance Benefits upon Change of Control.    If:

	(A)
	your
employment is terminated by the Company (except for termination for Cause or due to a Disability) and the Termination Date is within 90 days prior to a Change of Control
or within 12 months after a Change of Control; or

	(B)
	you,
of your own initiative, (i) terminate your employment for Good Reason and (ii) provide notice of termination within 30 days after the event that constitutes
Good Reason and the event giving rise to the notice occurs within 90 days prior to a Change of Control or within 12 months after a Change of Control;

	

	then,
in exchange for a general release by you of all claims against the Company, its subsidiaries, and its and their officers, directors and
representatives, in a form satisfactory to the Company, you shall receive the following benefits:

	1.
	Severance Payment.    The Company shall make a cash payment (the "Severance
Payment") to you in an amount equal to:

	(a)
	your
annual base salary (provided, however, that if you terminate your employment for Good Reason based on a reduction in your annual base salary, then the annual base salary to be
used in calculating the Severance Payment shall be your annual base salary in effect immediately prior to such reduction in annual base salary) plus your target bonus under any bonus program
applicable to you for the year in which the Termination Date occurs; plus

	(b)
	a
pro rata portion of your target bonus for the portion of the year in which the Termination Date occurs under any bonus program applicable to you; plus

	(c)
	all
cash incentive compensation awards earned by you but not paid prior to the Termination Date; provided that, if a fiscal year has been completed and the 

 

incentive
award for such fiscal year has not been determined, the incentive compensation for such completed fiscal year shall equal the target bonus for such fiscal year. 

	

	Except
with respect to any portion of the Severance Payment that is delayed as set forth in this paragraph, the Severance Payment shall be made in cash
within ten days after the execution by you of the general release referred to above and expiration without revocation of any applicable revocation periods under such general release (or, if the Change
of Control resulting in your becoming entitled to such benefits occurs after such execution and expiration, within ten days after the Change of Control). The Severance Payment shall be divided into
two portions, consisting of a portion that does not constitute "nonqualified deferred compensation" within the meaning of Section 409A of the Code and a portion, if any, that does constitute
nonqualified deferred compensation. If you are a "specified employee" as defined in Section 409A(a)(2)(B)(i) of the Code, the commencement of the delivery of any such payments that constitute
nonqualified deferred compensation payable upon a "separation from service" under Section 409A(a)(2)(A)(i) of the Code will be delayed until the first business day that is more than six months
after your Termination Date. The determination of whether, and the extent to which, any of the payments to be made to you hereunder are nonqualified deferred compensation shall be made after the
application of all applicable exclusions, including those set forth under Treasury Reg. § 1.409A-1(b)(9). Any payments that are intended to qualify for the
exclusion for separation pay due to involuntary separation from service set forth in Reg. §1.409A-1(b)(9)(iii) must be paid no later than the last day of the second
taxable year following the taxable year in which the Termination Date occurs. To the extent that the termination of your employment does not constitute a separation of service under
Section 409A(a)(2)(A)(i) of the Code (as the result of further services that are reasonably anticipated to be provided by you to the Company at the time your employment is terminated), the
payment of any non-qualified deferred compensation will be further delayed until the first business day that is more than six months after the date of a subsequent event constituting a
separation of service under Section 409A(a)(2)(A)(i) of the Code.

	2.
	Accelerated Vesting.

	(a)
	Stock
options for the purchase of the Company's securities held by you as of the Termination Date and not then exercisable shall immediately become exercisable in full. The options to
which this accelerated vesting applies shall remain exercisable until the earlier of (a) the end of the 90-day period immediately following the later of (i) the Termination
Date or (ii) the date of the Change of Control and (b) the date the stock option(s) would otherwise expire; and

	(b)
	the
Company's lapsing repurchase right with respect to shares of restricted stock held by you shall lapse in full (subject to your making satisfactory arrangements with the Company
providing for the payment to the Company of all required withholding taxes).

	

	Notwithstanding
anything to the contrary in this Agreement, the terms of any option agreement or restricted stock agreement shall govern the acceleration,
if any, of vesting or lapsing of the Company's repurchase rights and period of exercisability of such awards, as applicable, except to the extent that the terms of this agreement are more favorable to
you. 

2

 

	3.
	Continued Insurance Coverage.    If COBRA coverage is elected by you, the Company shall pay the cost of COBRA continuation
premiums on your behalf to continue standard medical, dental and life insurance coverage for you (or the cash equivalent of same if you are ineligible for continued coverage) for a period of
18 months from the Termination Date.

	4.
	No Mitigation.    You shall not be required to mitigate the amount of the Severance Payment or any other benefit provided
under this Agreement by seeking other employment or otherwise, nor shall the amount of any payment or benefit provided for in this Agreement be reduced by any compensation earned by you as the result
of other employment, by retirement benefits, or be offset against any amount claimed to be owed by you to the Company or otherwise (except for any required withholding taxes); provided, that if the
Company makes any other severance payments to you under any other program or agreement, such amounts shall be offset against the payments the Company is obligated to make pursuant to this Agreement. 

As
so amended, the Agreement shall remain in full force and effect. If you agree to the foregoing amendment, please so indicate by signing and returning the enclosed copy of this letter. 

	 	 	VERTEX PHARMACEUTICALS INCORPORATED
	

 	
 	

By:	
 	

 
	 	 	 	 	/s/  JOSHUA S. BOGER      
 Joshua S. Boger

President and Chief Executive Officer
	

Accepted and Agreed:	
 	

 	
 	

 
	

/s/  LISA KELLY-CROSWELL      
 Lisa Kelly-Croswell	
 	

 	
 	

 

3

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Exhibit 10.48

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