Document:

exv10w1

Exhibit 10.1

	 		
			
	Idenix/PAREXEL
	 	Confidential

MASTER SERVICES AGREEMENT

This
Master Services Agreement (“Agreement”) is effective as of April 1, 2008 (“Effective Date”),
and is by and between Idenix Pharmaceuticals, One Kendall Square, Building 1400, Cambridge, MA
02139, (“Sponsor”) and PAREXEL International, LLC, 200 West Street, Waltham, MA 02451 (“PAREXEL”).

      WHEREAS Sponsor is in the business of discovering and developing pharmaceutical products,
and;

      WHEREAS PAREXEL provides a full range of contract research organization services, including
clinical research, drug development, statistics, data management, regulatory, central laboratory,
and other services associated with the clinical trial management process for companies such as
Sponsor, and;

      WHEREAS Sponsor and PAREXEL wish to enter into this Agreement to provide the terms and
conditions under which Sponsor may engage PAREXEL from time to time to provide services for
Sponsor’s studies or projects.

     
NOW THEREFORE, the parties agree as follows:

1. DEFINITIONS

1.1
“Affiliate” means in relation to either party to this Agreement, any company, partnership or
other entity which directly or indirectly controls, is controlled by, or is under common control
with such party. For purposes of this definition, “control” means the beneficial ownership of more
than fifty (50) per cent of the issued voting shares or the legal power to direct or cause the
direction of the general management of the company, partnership or other entity in question, and
“controlled” shall be construed accordingly. It is understood that Novartis Pharma AG is not
considered an affiliate of Sponsor for purposes of this Agreement.

1.2
“Applicable Law” means any international, national, federal, state, provincial, commonwealth,
or local government law, statute, rule, requirement, code, regulation, or ordinance that applies to
a Study, the Services, or this Agreement, as well as the current good clinical practices
guidelines of the International Conference on Harmonization of Technical Requirements
for Registration of Pharmaceuticals for Human Use Topic E6: Guidelines on Good Clinical
Practice (“ICH/GCP”), and applicable version(s) of the World Medical Association Declaration of
Helsinki, and, where applicable, rules governing good manufacturing practice and good laboratory
practice, and rules governing the collection and storage of human tissue samples and the
performance of DNA testing.

1.3 “Protocol” means a detailed written plan for the conduct of a clinical trial.

1.4 “Regulatory Authority” means any national or local agency, authority,
department, inspectorate, minister, ministry official, parliament or public or statutory person
(whether autonomous or not) of any government of any country having jurisdiction over any of the
activities contemplated by this Agreement, including without limitation the European Commission and
the United States Food and Drug Administration.

1.5 “Study” means a clinical trial of Sponsor described by a Protocol with respect to which PAREXEL
provides Services under this Agreement pursuant to a Work Order (as defined below).

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1.6 “Study Drug” or “Study Device” means all Study medications or Study medical devices provided by
the Sponsor to be utilized by PAREXEL in the execution of a Study, as set forth in the applicable
Protocol.

1.7 “Vendor” means a person or entity other than Sponsor, PAREXEL, or their respective Affiliates,
which PAREXEL selects and with which PAREXEL contracts for the provision of materials or services
related to the Services.

2. SERVICES

2.1 PAREXEL will provide to Sponsor the services (“Services”) set forth in the work order(s)
executed by both parties (“Work Order”), substantially in the form of Attachment A hereto. Each
such Work Order will be executed by the parties and is incorporated into and governed by this
Agreement. If any term in a Work Order conflicts with this Agreement, this Agreement will control
except to the extent that the Work Order expressly states that such conflicting term prevails over
this Agreement.

2.2 Either party may request changes to the Services set forth in a Work Order (“Changes”) by
submitting a written request detailing the proposed changes to the other party. The parties will
negotiate and execute a “Change in Scope” reflecting agreed upon Changes and any related terms. If
PAREXEL performs any Changes in good faith upon Sponsor’s written request before the applicable
Change in Scope is executed by both parties, then Sponsor will pay PAREXEL for the performance of
such Changes and any expenses related thereto. If the parties fail to execute the Change in Scope
within ninety (90) days after PAREXEL started to perform the Changes, PAREXEL reserves the right to
terminate said activities.

2.3 PAREXEL may use its Affiliates to perform any obligations of PAREXEL under this Agreement or
any Work Order. The Affiliates of either party may execute a Work Order pursuant to this Agreement.
Upon execution, the parties to the Work Order will assume the rights and obligations of their
respective Affiliates under this Agreement for the purposes of such Work Order.

2.4 The parties agree that in those cases in which a Clinical Pharmacology Unit of PAREXEL conducts
a clinical pharmacology study, the parties shall negotiate additional terms tailored to such
clinical pharmacology study, and shall agree upon such terms in an addendum hereto or in the
applicable Work Order.

2.5 The parties agree that in those cases in which the Services include the use of software owned
by PAREXEL (or licensed to and sublicensable by PAREXEL), such use shall require and be subject to
the parties’ execution of a separate, software license agreement substantially in the form attached
hereto as Attachment B.

2.6 Sponsor acknowledges and agrees that this Agreement is not intended to cover certain
specialized services (“Specialized Services”) which PAREXEL may provide from time to time,
including without limitation serving as legal representative and/or agent for Sponsor in particular
countries where a Study is conducted, and agrees that any such Specialized Services shall require
and be subject to the parties’ execution of a separate services agreement with respect to such
Specialized Services.

2.7 Sponsor shall provide to PAREXEL, in advance of the execution of a Work Order, all information
reasonably available to Sponsor regarding known or reasonably foreseeable hazards associated with
any of the Study Drugs or Study Devices to which such Work Order relates.

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3. THIRD-PARTY AGREEMENTS

3.1 With prior authorization from Sponsor, CRO may use Vendors to provide materials in connection
with the Services, or to perform part of the Services, under any Work Order, provided that the
Vendor agrees in writing (a “Vendor Agreement”) to be bound by terms regarding maintaining the
confidentiality of proprietary information, and regarding ownership of intellectual property, that
are no less stringent than those contained in this Agreement. Subject to Section 12.2 of this
Agreement, PAREXEL shall only be responsible for the diligent selection, instruction and
supervision of Vendors. PAREXEL shall only be responsible for the failure of a Vendor to perform
properly under the applicable Vendor Agreement to the extent that such failure is caused by
PAREXEL’s failure diligently to select, instruct or supervise such Vendor.

3.2 If Sponsor requests that PAREXEL use a particular provider of materials or services in
connection with the Services and PAREXEL does not wish to contract with that provider based on
commercially reasonable reasons (such as the inability to agree with such provider upon mutually
acceptable terms or a negative assessment of such provider’s performance or abilities), then
Sponsor shall contract directly with such provider (a “Sponsor Designated Vendor”) and PAREXEL will
have no responsibility for the selection, instruction or supervision of such Sponsor Designated
Vendor. In no event will PAREXEL be responsible for the performance of any Sponsor Designated
Vendor, nor for any fraud committed by a Sponsor Designated Vendor.

3.3 If, pursuant to the applicable Work Order, Sponsor delegates to PAREXEL the execution of
clinical trial related agreements with investigators, hospitals and/or research institutions
(“Clinical Trial Agreements”) as part of the Services, then Sponsor hereby authorizes PAREXEL and
PAREXEL Affiliates, if applicable, to execute such Clinical Trial Agreements on behalf and (where
applicable) as agent of Sponsor. Sponsor shall have the right to approve all Clinical Trial
Agreement templates for use and all finalized Clinical Trial Agreements prior to execution.
Provided that PAREXEL has received adequate funds from Sponsor, PAREXEL will administer and
disburse payments to the investigators, hospitals or research institutions as described in the
applicable Work Order. Sponsor will provide adequate funds to PAREXEL in advance for such
payments in accordance with a schedule and budget to be mutually agreed upon in advance between the
parties. In no event will PAREXEL be required to disburse payments to any third parties
(including without limitation investigators, hospitals or research institutions) if Sponsor has not
made sufficient advance funds available to PAREXEL to cover such disbursements. In the event the
funds advanced by Sponsor pursuant to this Section are insufficient to cover such payments, Sponsor
will promptly pay to PAREXEL the additional amounts required consistent with the budget for such
payments, and if Sponsor does not provide funds in time to enable PAREXEL to make timely payments,
Sponsor agrees to be liable for and to reimburse PAREXEL for any interest and other charges, costs,
fees and expenses incurred by PAREXEL because of such late payment.
In no event will an investigator, hospital or institution be construed to be PAREXEL’s employee,
subcontractor, agent, consultant, or representative.

4. PAYMENTS

4.1 Sponsor will pay to PAREXEL the fees specified in the applicable Work Order. In addition to
the payment of Service fees, Sponsor will reimburse PAREXEL for all reasonable out-of-pocket
expenses, including without limitation, printing, shipping, wire transfer fees, telephone, travel
and lodging, incurred by PAREXEL in providing the Services, and payments made on behalf of Sponsor
to third parties, if applicable (“Pass-Through Expenses”).

4.2 Unless otherwise expressly provided in a Work Order, no schedule of charges set forth therein
will be construed as a commitment to perform the Services within a fixed period of time or at a
fixed

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price. Should the parties agree to a Change in Scope, the Service fees and any related Pass-Through Expenses will be adjusted as mutually agreed in writing signed by both parties.

4.3 All invoices are due net thirty (30) days from the date of PAREXEL’s invoice. Sponsor will pay interest on any unpaid invoice at the rate of one percent (1%) per month until such invoice(s) is paid in full. Payments will be made to PAREXEL in accordance with the following table:

	 	 	 
	U.S. Check Remittance Address

	 	For Wires/Electronic Funds Transfers, (within US
use ABA; for International use SWIFT):
	 
	 	 
	PAREXEL International, LLC

	 	Beneficiary Bank:            LaSalle National Bank
	5239 Paysphere Circle

	 	                                         135 South LaSalle Street
	Chicago, IL 60674

	 	                                        Chicago, IL 60674
	 
	 	 
	 

	 	ABA: 071-000-505
	 

	 	SWIFT: LASLUS44
	 

	 	Beneficiary Name: PAREXEL International, LLC
	 

	 	Beneficiary Account: 5800-333-022

     PAREXEL
Federal Tax ID No.: 04-3517643

4.4 PAREXEL will be responsible for taxes based on its net income. All other taxes will be the
responsibility of Sponsor and such taxes are not included in PAREXEL’s Service fees.

4.5 If PAREXEL incurs costs, fees or expenses in a currency other than the currency set forth in the
applicable Work Order, then the amounts to be paid by Sponsor to PAREXEL will be increased to reflect
any increase in cost to PAREXEL as a result of changes in currency exchange rates. The amount of any
increase will be determined by reference to the difference between the spot currency exchange rates for
the Work Order budget currency and the currency in which the applicable fee, cost or expense is
incurred, as published in the www.oanda.com on the last business day of the month in which the project
budget is executed and the month in which the applicable fee, cost or expense is incurred by PAREXEL.

5. TERM AND TERMINATION

5.1 This Agreement will commence on the Effective Date and will terminate on the fifth anniversary
of the Effective Date, unless earlier terminated in accordance with this Agreement. Unless otherwise
mutually agreed to in writing, any Work Order, the duration of which extends beyond the expiration or
termination of this Agreement, will continue to be performed for the term of such Work Order, and will
continue to be governed by the terms of this Agreement.

5.2 Either party may terminate this Agreement and/or any individual Work Order(s) for a material
breach of this Agreement or the applicable Work Order(s); provided that, the breaching party fails to cure
such material breach within ninety (90) days after receipt of written notice specifying such material
breach.

5.3 Either party may terminate this Agreement or any Work Order without cause upon ninety (90)
days prior written notice to the other party.

5.4 Upon the expiration or any termination of this Agreement and/or any Work Order(s): (i)
PAREXEL will discontinue providing the applicable Services, except to the extent reasonably required to
safely close out a study (“Closeout Services”), and will terminate existing third party obligations to the
extent practicable and cancelable; and (ii) Sponsor will pay PAREXEL for all Services performed,
including without limitation, Closeout Services, non-cancelable costs and all Pass-Through Expenses
incurred by PAREXEL up to and including the completion of Closeout Services. Sponsor agrees that,

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upon any termination, it will no longer be entitled to the project rates set forth in the
applicable Work Order that were conditioned upon completion of the terminated project, and
furthermore agrees that it will pay PAREXEL for all Services performed in accordance with this
Agreement (including, but not limited to, works-in-progress and Closeout Work) at PAREXEL’s
then-current time and materials billing rate. Any final payment still owed to PAREXEL, or any
refund due Sponsor, pursuant to this Section, will be made by Sponsor or PAREXEL, as applicable,
within thirty (30) days of the final reconciliation invoice(s) from PAREXEL.

5.5 Either party may terminate this Agreement or any Work Order immediately upon written notice to
the other party upon the happening of any of the following events: (i) if the Services involve
participation of human subjects in a Study and risk to such subjects associated with the
continuation of the Services becomes unacceptable, or (ii) if any certificate, authorization,
approval or exemption from a Regulatory Authority required for the conduct of the Services is
revoked, suspended, or expires without renewal, or (iii) if such party is of the reasonable opinion
that the continuation of the Services would be in violation of Applicable Law.

5.6 Termination of this Agreement or of a Work Order for any reason shall not affect the rights of
the parties which have accrued on or before termination.

6. CONFIDENTIALITY AND PRIVACY COMPLIANCE

6.1 “Confidential Information” means the confidential and/or proprietary information of a party
that either is marked as “Confidential,” “Proprietary” or the substantial equivalent at the time of
disclosure or that a reasonable person would believe to be confidential and/or proprietary based on
the circumstances of its disclosure. The terms of this Agreement and any Work Order, including
without limitation, pricing, constitute the Confidential Information of both parties and may not be
disclosed by either party except in accordance with this Section or the other party’s prior
written consent. Confidential Information will not include information that (i) is or becomes part
of the public domain through no fault of the recipient; (ii) was in the recipient’s rightful
possession prior to disclosure by discloser; (iii) is rightfully disclosed to the recipient by a
third party with the right to disclose the information; or (iv) is independently developed by
the recipient without use of the discloser’s Confidential Information.

6.2 In the event the receiving party receives a subpoena or other validly issued administrative or
judicial process requesting Confidential Information of the disclosing party, the receiving party
will, to the extent permitted by the requesting government agency, notify the disclosing party of
such request.

6.3 Sponsor hereby agrees that PAREXEL may disclose Confidential Information to IRBs, ECs and any
competent government authority to protect the health and well being of study subjects and the
integrity of the study, provided that PAREXEL has first issued a notice pursuant to Section 18.1 of
this Agreement giving the Sponsor itself reasonable time to directly inform such third parties of
any such issue and further provided Sponsor failed to do so. PAREXEL agrees that Sponsor may
disclose Confidential Information to Novartis Pharma AG or any affiliate thereof.

6.4 Each party may use the other party’s Confidential Information only in connection with its
rights and obligations under this Agreement. Each party will maintain in confidence and will not
disclose the other party’s Confidential Information, using the same degree of care, but no less
than reasonable care, as it uses to protect its own confidential information of a similar nature.
The receiving party may disclose the disclosing party’s Confidential Information only to the
receiving party’s Affiliates and its and their respective employees and independent contractors and
outside consultants (including its legal counsel, its insurance carriers and agents, and its
financial and accounting advisers) who (i) have a need to know such Confidential Information, (ii)
are made aware of the Confidential Information’s confidential and/or proprietary nature and (iii)
are under an obligation to protect confidential and/or proprietary information.

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6.5 To the extent applicable, PAREXEL and Sponsor will comply with all applicable national and
international laws, regulations and guidelines relating to protection of the personal information
of study subjects, including the European Commission Directive 95/46 (the “Directive”) as it
relates to the protection of the personal information of EU study subjects, and the Standards for
Privacy of Individually Identifiable Health Information (Privacy Rule) under the Health Insurance
Portability and Accountability Act of 1996 (HIPAA). With respect to the study subjects’ personal
data, Sponsor and/or its Affiliates will be the data controller as such term is defined in the
Directive.

7. OWNERSHIP

7.1 Sponsor will retain and have full ownership rights in all information, reports and other
proprietary or protectable property that relate exclusively to its products and their applications
or that are based on Sponsor’s Confidential Information.

7.2 Notwithstanding anything to the contrary contained in this Agreement or any Work Order, PAREXEL
reserves all rights, title and interest in and to all intellectual property (including without
limitation, designs, utilities, tools, models, methodologies, programs, systems, analysis
frameworks, leading practices and specifications) that is owned, developed, or licensed by, or on
behalf of, PAREXEL prior to, or independent of, PAREXEL’s performance under this Agreement or any
Work Order, even if utilized to provide the Services, including without limitation, all
modifications or enhancements to such intellectual property developed in the course of performing
the Services.

7.3 Sponsor will be responsible for archiving of Study documents according to ICH/GCP.
PAREXEL will return all documents required by the respective ICH guidelines / local laws relating
to the Services performed (according to the drug laws of the participating countries) upon
completion of the Services under any Work Order, or at any earlier point in time when requested to
do so by Sponsor, to Sponsor for archiving. PAREXEL may retain one copy of Confidential Information
to satisfy regulatory and audit requirements as well as for feasibility purposes solely related to
the general design and management of clinical studies without reference to or disclosure of
Sponsor’s Confidential Information.

8. INSURANCE

8.1 Both parties shall carry, at their sole expense, with financially sound and reputable insurers
with an AM Best rating of not less than “A” or an S&P rating of not less than “A-,” insurance
coverage (including workers’ compensation, errors and omissions, automobile liability and
commercial general liability) with respect to the conduct of its business in such amounts as are
customary for well-insured companies engaged in similar business. At minimum, each party will
maintain in force during the term of this Agreement and any Work Order insurance coverage at the
minimum levels required by law or regulation in each country in which the Services will be
provided or as specified below, whichever is greater. The amounts stated below in USD can be
converted to the appropriate local currency but, as converted, shall not be less than minimums
referenced below. Certifications evidencing such insurance will be made available to the other
party upon written request.

	 	(a)	 	Employer’s Liability. $1,000,000
	 
	 	(b)	 	Workers’ Compensation. Statutory minimums required.
	 
	 	(c)	 	Automobile. $1,000,000 per accident.
	 
	 	(d)	 	Commercial General Liability. $1,000,000 per occurrence and $2,000,000 in
the aggregate

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	 	(e)	 	Umbrella Liability. $5,000,000 per occurrence and in the aggregate

	 
	 	(f)	 	Errors and Omissions. $5,000,000 per claim and in the aggregate
	 
	 	(g)	 	Products Liability. $10,000,000 per occurrence (Sponsor only, with PAREXEL
to be listed as an additional insured)

8.2 In addition, if required under Applicable Law, Sponsor will maintain in full force and effect
during the term of this Agreement and any Work Order, insurance coverage for all subjects who have
been enrolled into any Study and in whom Study-related procedures are undertaken as specified in
the applicable Protocol. If such insurance is required under Applicable Law, Sponsor will certify
that any such insurance is in place and meets such requirements. Certificates of insurance
evidencing such coverage, and showing the expiration date of such policy, will be made available
to PAREXEL promptly upon written request.

9. AUDIT

9.1 Subject to Section 9.2 below, during the term of this Agreement, at times mutually agreed upon
by the parties during PAREXEL’s normal business hours, Sponsor may, without disruption to PAREXEL’s
normal business operations, audit PAREXEL’s facilities used to perform the Services, Study
documentation and financial records that relate exclusively to the Services (except for any
financial terms contained in Vendor agreements) for the purpose of determining PAREXEL’s compliance
with this Agreement and the applicable Work Order(s). Any such audit will be subject to the
confidentiality obligations set forth in this Agreement. Within ten (10) days from the completion
of the audit, Sponsor will provide a report detailing the results of such audit to PAREXEL.

9.2 Notwithstanding anything to the contrary contained in this Agreement, (a) no third party
auditor used by Sponsor to conduct an audit under this Agreement (“Third Party Auditor”) will be
(i) a competitor of PAREXEL or any of its Affiliates, or (ii) permitted to access or to examine any
information, materials or sites, until such Third Party Auditor has entered into a non-disclosure
agreement with PAREXEL and (b) Sponsor (and its Third Party Auditors) will only have the right to
access information, materials and sites that relate exclusively to PAREXEL’s performance of
obligations to Sponsor under this Agreement, and only if such access would not compromise PAREXEL’s
confidentiality obligations to another party and/or its internal QA programs.

9.3 PAREXEL Service fees and Pass-Through Expenses associated with audits performed by Sponsor or
on behalf of Sponsor or by Regulatory Authorities at PAREXEL’s facilities, at investigative sites
and in connection with Services under this Agreement are considered outside the scope of Services,
unless specifically defined otherwise in a Work Order.

10. DEBARMENT

PAREXEL represents that, consistent with Section 306(a) and Section 306(b) of the Federal Food,
Drug and Cosmetic Act (21 U.S.C. § 335a(a) and 335a(b)), none of its employees is debarred and
PAREXEL will not knowingly hire any debarred individual to perform Services under this Agreement.

11. INDEMNIFICATION

11.1 PAREXEL will defend, indemnify and hold harmless Sponsor, its Affiliates and their respective
directors, officers, employees, and independent contractors
(“Sponsor Indemnitees”) from and
against all damages, liabilities, judgments, settlements, penalties, and costs and expenses
(including without

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limitation, reasonable fees and disbursements of counsel and costs and expenses associated with
document production and testimony) as incurred by Sponsor Indemnitees, arising out of or in
connection with any third party (including without limitation, government agencies) claims, suits,
actions, proceedings, investigations and demands (“Third Party Claims”) arising out of or in
connection with (a) the breach of this Agreement or any individual Work Order(s) by PAREXEL and/or
(b) any bad faith, negligence or willful misconduct on the part of PAREXEL; provided, however,
that PAREXEL shall have no obligation of indemnity hereunder with respect to any Third Party Claim
to the extent Sponsor is required to indemnify any PAREXEL Indemnitee for such Third Party Claim
as set forth in Section 11.2 below.

11.2 Sponsor will defend, indemnify and hold harmless PAREXEL, its Affiliates, and their
respective directors, officers, employees and independent contractors (“PAREXEL Indemnitees”) from
and against all damages, liabilities, judgments, settlements, penalties, and costs and expenses
(including without limitation, reasonable fees and disbursements of counsel and costs and expenses
associated with document production and testimony) as incurred by PAREXEL Indemnitees, arising out
of or in connection with any Third Party Claims arising out of or in connection with this
Agreement, including without limitation, a Protocol, any product used in a Study and Sponsor’s bad
faith, negligence and/or willful misconduct. Sponsor will have no obligation to indemnify PAREXEL
Indemnitees, and PAREXEL will defend, indemnify and hold harmless Sponsor, to the extent that any
Third Party Claim is attributable to PAREXEL’s negligence or willful misconduct, or breach of this
Agreement.

11.3 The party seeking indemnification for any Third Party Claim covered by this Section (“Covered
Claim”) will promptly notify the indemnifying party. The indemnifying party will have sole control
of the defense, settlement or compromise of the Covered Claim and the indemnified party will
cooperate with the indemnifying party, at the indemnifying party’s expense, in the defense,
settlement or compromise of the Covered Claim. Neither party will settle any Covered Claim without
the other party’s prior written consent, which consent will not be unreasonably withheld or
delayed. Notwithstanding anything to the contrary contained herein, the failure of the indemnified
party to promptly notify the indemnifying party of any Covered Claim will not relieve the
indemnifying party of its indemnification obligations unless the indemnifying party is materially
prejudiced by such failure to provide notice.

11.4 Notwithstanding anything to the contrary contained in this Agreement, if a conflict of
interest exists between the parties with respect to the Third Party Claim, or if the assumption and
conduct of the defense by the indemnifying party would adversely affect the indemnified party in
any manner or prejudice its ability to conduct a successful defense, then the indemnified party
will have the right to undertake the defense, compromise and settlement of such claim for the
account and at the expense of the indemnifying party.

12. DISCLAIMER AND LIMITATION OF LIABILITY

12.1
Except as expressly set forth in this Agreement, PAREXEL does not make, and hereby disclaims,
all representations and warranties, whether express, implied or statutory, written or oral,
including without limitation, the warranties of merchantability, fitness for a particular purpose,
title and non-infringement. Without in any way limiting the generality of the immediately
preceding sentence, PAREXEL makes no representations or warranties with respect to the development
or approval by the U.S. Food and Drug Administration or other regulatory body of any product of
Sponsor.

12.2 The aggregate liability of each party and its Affiliates to the other party, regardless of the
theory of liability, for any claim, breach or default under this Agreement, will be limited to
proven direct damages incurred. In no event will either party or its Affiliates be liable for
special, indirect, incidental,

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punitive or consequential damages, including without limitation, lost profits, regardless of
whether a party has been advised of the possibility of such damages.

13. DELAYS

13.1 PAREXEL’s performance under this Agreement or any Work Order may be contingent upon the
performance of obligations by another party, including, but not limited to, Sponsor itself and
third parties. To the extent that PAREXEL is delayed or unable to perform its obligations under
this Agreement or any Work Order as a result of another party’s failure to perform in a timely
manner, such delay or failure to perform by PAREXEL will not be deemed a breach by PAREXEL.

13.2 Neither party will be responsible for any default under this Agreement by reason of strikes,
riots, wars, acts of terrorism, fire, acts of God, acts in compliance with any law, or any other
cause beyond its reasonable control, provided that the affected party shall immediately give notice
thereof to the other party, and shall take all reasonable steps to overcome the effects of such
event as soon as possible, and such party’s delay in performance shall be excused only for the
period of delay caused by such event.

13.3 If Sponsor delays or suspends the Services to be provided pursuant to a Work Order for a
period of one (1) month or longer, the parties may agree in writing that certain PAREXEL staff will
continue to be assigned to perform such Services. In such event, during the period of delay or
suspension, Sponsor will pay a monthly maintenance fee in an amount to be mutually agreed by the
parties. If such delay or suspension lasts six (6) months, then PAREXEL will have the right to
terminate or amend the respective Work Order.

14. PUBLICITY

The parties agree that they will obtain the other party’s prior written approval before using each
other’s name, symbols and/or marks in any form of publicity.

15. INDEPENDENT CONTRACTOR

The relationship of the parties to each other under this Agreement will be that of independent
contractors, and nothing contained herein will be construed to constitute, create, or in any way
be interpreted as, a joint venture, partnership, or business organization of any kind. Except as
expressly provided for in this Agreement, under no circumstances will the employees or agents of
one party be considered employees or agents of the other party.

16. NON-SOLICITATION

During the Term of this Agreement and for a period of twelve (12) months following any termination
or expiration of this Agreement, each party agrees, on behalf of itself, and its Affiliates, not to
directly or indirectly solicit for employment, employ or otherwise retain any employee or
consultant of the other party or its Affiliates providing (or who has provided) or is involved in
(or who has been involved in) Services under this Agreement; provided that it will not be a
violation of this Section if an employee or consultant of such party responds to an indirect
solicitation (e.g., advertisements in media of general circulation). In the event either party
breaches this provision, the breaching party shall pay to the other party one (1) year of the
employee’s or consultant’s salary, to be calculated as such person’s base salary at the time of his
or her departure from the non-breaching party, together with any bonuses and incentives paid by the
non-breaching party to such person within the prior twelve-month period.

17. ASSIGNMENT

Either party may assign this Agreement to an Affiliate or a successor in interest by reason of
merger,

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acquisition, partnership, license agreement or otherwise; provided that no assignment to a direct
competitor of the other party will be valid. Except as expressly provided in this Section, neither
party will have the right to assign this Agreement or any of its rights or obligations hereunder
without the prior written consent of the other party, which consent will not be unreasonably
withheld or delayed.

18. GENERAL

18.1 Notice. Any notice or communication required or permitted hereunder, will be in writing and
sent by first class mail, or postage prepaid, to the parties at the following addresses:

	 	 	 
	To PAREXEL:	 	To Sponsor:
	PAREXEL International, LLC

	 	Idenix Pharmaceuticals
	200 West Street

	 	One Kendall Square, Building 1400
	Waltham, MA 02451

	 	Cambridge, MA 02139
	ATTN: General Counsel

	 	ATTN: John Sullivan-Bolyai

18.2 Entire Agreement. This Agreement, including any Work Order(s), constitutes the entire
understanding of the parties hereto with respect to the subject matter hereof and supersedes and
replaces all prior contracts, agreements, and understandings relating to the same subject matter,
whether written or oral. No waiver, consent, change or modification to this Agreement will be
binding, unless in writing and signed by duly authorized representatives of PAREXEL and Sponsor.

18.3 Severability. If any term of this Agreement is declared unenforceable, then the
unenforceability thereof will not affect the remaining terms of this Agreement.

18.4 Governing Law; Compliance with Law. This Agreement will be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts, U.S.A. without regard to its
conflict of laws provisions. PAREXEL and Sponsor will comply with all Applicable Law relating to
the Studies and Services.

18.5 Survival. The Sections of this Agreement that by their nature would survive the expiation or
termination of this Agreement shall survive the expiration or termination of this Agreement.

IN WITNESS WHEREOF, the parties hereto have executed this Agreement through their duly authorized
representatives effective as of the Effective Date.

	 	 	 	 	 	 	 	 	 	 	 
	PAREXEL International, LLC	 	 	 	Idenix Pharmaceuticals	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ James F. Winschel Jr.
 

Name James F. Winschel Jr.
	 	 
	 	By
	 	/s/ Douglas L. Mayers, MD.
 

Name: Douglas L. Mayers, MD
	 	 
	 

	 	Title: Treasurer
	 	 	 	 	 	Title:   Exec VP + CMO	 	 
	 

	 	Date: 4-30-08
	 	 	 	 	 	Date:   2 May 2008	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 		 	 	 	 	 	 	 	 

Page 10 of 11

 

			
	 	 	 
	Idenix/PAREXEL
	 	April 1, 2008

ATTACHMENT A

FORM OF WORK ORDER

This Work
Order is entered into pursuant to the Master Services Agreement
(“Agreement”), dated
[INSERT EFFECTIVE DATE OF APPLICABLE AGREEMENT], between
PAREXEL International LLC,. (“PAREXEL”)
and Idenix Pharmaceuticals (“Sponsor”). Capitalized terms in this Work Order and not defined herein
are used with the meanings ascribed to them in the Agreement.

Scope and Objectives:

Services to be provided by PAREXEL:

Assumptions:

Acceptance Criteria:

Deliverables:

Schedule:

Acceptance Procedures:

Timeline and Milestones:

Staffing Requirements:

Fees and Expenses:

Payment Method:

	 	 	 	 	 	 	 	 	 
	PAREXEL International, LLC	 	 	 	Idenix Pharmaceuticals
	 
	 	 	 	 	 	 	 	 
	By:

	 	 	 	 	 	By:	 	 
	 

	 	 

Print Name:
	 	 	 	 	 	 

Print Name:
	 

	 	Title:
	 	 	 	 	 	Title:
	 

	 	Date:
	 	 	 	 	 	Date:

Page 11 of 11exv10w01

Exhibit 10.01

AMENDMENT NO. 2008-1

TO

BROOKS AUTOMATION, INC.

DEFERRED COMPENSATION PLAN

WHEREAS, Brooks Automation, Inc., a Delaware corporation (the “Company”), maintains the Brooks
Automation Inc. Deferred Compensation Plan (the “Plan”), effective as of June 20, 2006; and

WHEREAS, all capitalized terms used herein have the meanings set forth in the Plan unless otherwise
indicated in this amendment; and

WHEREAS, the Company desires to amend the Plan to allow participation by members of its Board of
Directors; and

WHEREAS, the Company is empowered to amend the Plan pursuant to Section Article 10.2 of the Plan.

Amendment.
The Company may, at any time, amend or modify the Plan in whole or in part;
provided, that no amendment or modification shall be effective if it would cause a
Participant’s Account Balance, determined immediately after the amendment takes effect, to be
lower than it was immediately before the amendment took effect.

NOW, THEREFORE, the Company hereby amends the Plan, effective as of July 1, 2008 (the “Effective
Date”), as follows:

	1.	 	Section 2.1 shall be replaced in its entirety with the following language:
	 
	 	 	Selection by Administrator. Eligibility for the Plan shall be limited to Directors and
to a select group of management or highly compensated Employees who are selected by the
Administrator in its sole discretion. The Administrator shall separately select those
management or highly compensated Employees, if any, who are eligible for the SERP Feature.

	2.	 	Section 3.2 shall be replaced in its entirety with the following language:
	 
	 	 	Elective Deferrals: Maximum Requirements. For any Plan Year, a Participant’s Elective
Deferrals, if any, shall be subject to the following percentage maxima:

	 	 	 	 	 
	Deferral	 	Maximum Percentage
	Base Salary
	 	 	90	%
	Bonus
	 	 	100	%
	Commissions
	 	 	100	%
	Director Fees
	 	 	100	%

 

 

	 	 	If a Participant first becomes eligible to make Elective Deferrals during a Plan Year, the
foregoing maximum percentages shall be applied to the future compensation affected by the
Participant’s mid-year election. For compensation that is earned based upon a specified
performance period, “future compensation” shall be deemed for this purpose not to exceed
the total amount of such compensation earned for the performance period, multiplied by a
fraction, the numerator of which is the number of days remaining in the service period
after the Participant’s deferral election take effect, and the denominator of which is the
total number of days in the performance period.
	 
	3.	 	Section 8 shall be replaced in its entirety with the following language:
	 
	 	 	Distribution of Small Accounts. If, at the time an Account becomes payable under
Article 4, 5, 6 or 7 thereof, the vested balance of such Account is $15,000 or less, payment
shall be made in a single lump sum payment (or, if payable under Article 7 to more than one
Beneficiaries, in lump sum payments) notwithstanding any election to have payment made under
the Annual Installment Method.
	 
	4.	 	Except as specifically provided in this amendment, the remaining provisions of the Plan shall
remain in full force and effect.

IN WITNESS WHEREOF, the Company has signed this amendment as of May 6, 2008.

	 	 	 	 	 
	 	Brooks Automation, Inc. 

a Delaware corporation

 	 
	 	By:  	/s/ Thomas S. Grilk
 	 
	 	 	Title: Senior Vice President, General Counsel & Secretary 	 
	 	 	 	 
	 

2

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