Document:

EX-10.1 Amendment No. 2 to Employment Agreement

Exhibit
10.1

Amendment No. 2 to Employment Agreement

This Amendment No. 2 to the Employment Agreement (as defined below) (the “Amendment”), is made
this 27th day of October, 2010 between Idenix Pharmaceuticals, Inc., a corporation
incorporated under the laws of the State of Delaware (together with its successors and assigns, the
“Company”) and Dr. Jean-Pierre Sommadossi, a resident of the Commonwealth of Massachusetts, and the
Company’s Chairman, President and Chief Executive Officer (the “Employee”).

WHEREAS, the Company and the Employee are parties to that certain Employment Agreement, dated
May 6, 2003, as amended on December 23, 2008 (the “Employment Agreement”), and

WHEREAS, the Company and the Employee wish to amend the Employment Agreement in accordance
with the guidance under IRS Notice 2010-6.

NOW THEREFORE, in consideration of the mutual covenants and responsibilities contained herein,
the Company and the Employee (individually, a “Party” and, together, the “Parties”) hereto agree as
follows, effective immediately, and to the extent consistent with IRS Notice 2010-6, January 1,
2009:

	1.	 	Section 4.D of the Agreement is rewritten in its entirety to read as follows:
	 
	 	 	Termination Upon Death or Disability. The Employment Period and the Employee’s employment
hereunder shall be terminated by the death of the Employee. The Employment Period and the
Employee’s employment hereunder shall be terminated if the Employee shall be rendered
incapable of engaging in any substantial gainful activity by reason of any medically
determinable physical or mental impairment that can be expected to result in death or can be
expected to last for a continuous period of not less than twelve (12) months (a
“Disability”).

	2.	 	Section 5.B. of the Agreement is amended to delete any provision for payment or benefits on
account of Disability.
	 
	3.	 	The following section shall be inserted immediately after Section 5.E of the Agreement:

	 	 	F. Timing of Payments. All payments and benefits provided by this Section 5 shall be paid
to the Employee on the 60th day following the Employee’s termination or
employment or on such later date determined under Section 18(c); provided that the Employee
has executed and submitted an employee release in the form attached hereto and incorporated
herein by reference (the “Employee Release”) and the statutory period during with the
Employee is entitled to revoke such Employee Release has expired on or before that
60th day.
	 
	4.	 	The following sections shall be inserted immediately after Section 7.D of the Agreement:
	 
	 	 	E. Confidentiality. The Employee shall keep confidential and not disclose any and all
non-public information concerning the Company that the Employee acquires during the course of the Employee’s employment with the Company, including, but not limited to, any
non-public information concerning the Company’s business affairs, business prospects, and
financial condition.

 

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	 	 	F. Nondisparagement. Neither the Employee nor the Company shall make any false,
disparaging or derogatory statements to any person or entity, including, without limitation,
any media outlet, industry group, financial institution or current or former employee,
consultant, client or customer of the Company, regarding, in the case of the Employee, the
Company or any of its directors, officers, employees, agents or representatives or about the
Company’s business affairs or financial condition and regarding, in case of the Company, the
Employee; provided, however, that nothing herein shall be construed as preventing the
Employee or the Company from making truthful disclosures to any governmental entity or in
any litigation or arbitration or as otherwise required by applicable law.
	 
	 	 	G. Co-operation with Litigation and Patent Prosecution. To the extent permitted by law,
the Employee agrees to cooperate with the Company in the defense or prosecution of any
patents, patent filings, claims or actions which already have been brought, are currently
pending or filed, or which may be brought in the future against or on behalf of the Company
and relate to matters which occurred while the Employee was employed by the Company, whether
before a state or federal court, any state or federal government agency, or a mediator or
arbitrator. The Employee’s full cooperation in connection with such patent, patent filings,
claims or actions shall include, but not be limited to, being available to meet with counsel
to prepare its claims or defenses, to prepare for trial or discovery or an administrative
hearing or a mediation or arbitration and to act as a witness when requested by the Company
at reasonable times mutually agreed to by the Employee and the Company. As a condition of
such co-operation, the Company shall reasonably compensate the Employee for his time and
effort. In addition, the Company shall reimburse the Employee for any reasonable
out-of-pocket expenses incurred at the request of the Company. Furthermore, to the extent
that the a claim or action is brought by a third party other than the Company against the
Employee for his compliance with this section, the Company shall indemnify the Employee for
such claim or action; provided, however, that the Employee has acted in good faith and with
reasonable care. The Employee agrees that he will notify the Company promptly in the event
that he is served with a subpoena or in the event that he is asked to provide a third party
with information concerning any actual or potential complaint or claim against the Company.
	 
	 	 	The Employee hereby agree that at the request of and without charge to the Company, but at
the Company’s expense, he will execute a written assignment to the Company of any idea,
discovery, invention, improvement, writing or other material or design conceived by the
Employee during the term of his employment with the Company and will assign to the Company
any application for letters patent or for trademark registration made thereon, and to any
common-law or statutory copyright therein; and that he will do whatever may be necessary or
desirable to enable the Company to secure any patent, trademark, copyright, or other
property right therein in the United States and in any foreign country, and any division,
renewal, continuation, or continuation in part thereof, or for any reissue of any patent issued thereon.

 

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	 	 	In the event the Company is unable, after reasonable effort, and in any event after ten
(10) business days, to secure the Employee’s signature on a written assignment to the
Company of any application for letters patent or to any common-law or statutory copyright or
other property right therein, whether because of the Employee’s physical or mental
incapacity or for any other reason whatsoever, the Employee irrevocably designate and
appoint the General Counsel of the Company as the Employee’s attorney-in-fact to act on the
Employee’s behalf to execute and file any such application and to do all other lawfully
permitted acts to further the prosecution and issuance of such letters patent, copyright or
trademark.

	5.	 	The existing Section 7.E of the Agreement is rewritten to reference Section 7.H.
	 
	6.	 	Section 8 is amended to refer to the Employee Release referred to in Section 5.F. of the
Agreement.
	 
	7.	 	All other terms and conditions of the Agreement remain in full force and effect.

IN WITNESS WHEREOF, the Parties have executed this Amendment as of the date first written
above and this Amendment shall be effective and binding on the Parties from such date.

	 	 	 	 	 
	 	IDENIX PHARMACEUTICALS, INC.

 	 
	 	/s/Maria Stahl
 	 
	 	Maria Stahl 	 
	 	Senior Vice President and General Counsel 	 
	 
	 	EMPLOYEE

 	 
	 	/s/ Jean-Pierre Sommadossi
 	 
	 	Jean-Pierre Sommadossi 	 
	 	Chairman and Chief Executive Officer 	 

 

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Form of General Release Agreement

The undersigned (“You”) hereby acknowledges and agrees that by signing this Release Agreement
and accepting the severance benefits provided for in your Employment Agreement, dated May 6, 2003,
as amended as of the date hereof, You are releasing the Company its officers, directors,
stockholders, corporate affiliates, subsidiaries, parent companies, successors and assigns, agents
and employees (each in their individual and corporate capacities) (the “Related Parties”) from any
and all claims, charges and complaints (“Claims”) of any kind whatsoever from the beginning of time
through and including                     (the “Separation Date”) . Your waiver and release bars you from
recovering against the Company any form of relief including, without limitation, equitable relief
(whether declaratory, injunctive or otherwise), the recovery of any damages or any other form of
monetary recovery whatsoever (including, without limitation, back pay, front pay, compensatory
damages, emotional distress damages, punitive damages, attorneys’ fees and any other costs) against
the Company up through and including the Separation Date. You understand that there could be
unknown or unanticipated Claims resulting from your employment with the Company and the termination
thereof and agree that such Claims are intended to be, and are, included in this waiver and
release.

Without limiting the foregoing general waiver and release, You specifically waive and release
the Company from any Claims arising from or related to your employment relationship with the
Company or the termination thereof, including without limitation: (i) Claims under any state
(including, without limitation, Massachusetts or any other state where You worked for the Company,
specifically including the Massachusetts Fair Employment Practices Act, Mass. Gen. Laws ch. 151B,
§1 et seq.) or federal discrimination (including but not limited to the Age Discrimination in
Employment Act 29 U.S.C. §621 et seq., the Americans with Disabilities Act of 1990, 42 U.S.C.
§12101 et seq. and Title VII of the Civil Rights Act of 1964 42 U.S.C. §20000e et seq.), fair
employment practices or other employment related statute, regulation or executive order (as they
may have been amended through the date on which You sign this Agreement); (ii) Claims under any
other state (including, without limitation, Massachusetts or any other state where You worked for
the Company) or federal employment related statute, regulation or executive order (as they may have
been amended through the date on which You sign this Agreement) relating to wages, hours or any
other terms and conditions of employment; (iii) Claims under any state (including, without
limitation Massachusetts or any other state where You worked for the Company) or federal common law
theory, including but not limited to any claims arising under the Employment Agreement; and (iv)
any other Claim arising under other state or federal law.

You acknowledge and agree that, but for providing this waiver and release, You would not be
receiving the severance benefits provided for in this Agreement.

 

4EX-10.2 Subsidiaries of the Company

Exhibit 10.2

Subsidiaries of the Company

	 	 	 
	 	 	State or Other Jurisdiction of
	Name of Subsidiary	 	Incorporation or Organization
	Idenix (Massachusetts) Inc.
	 	Massachusetts
	Idenix Pharmaceuticals S.r.l.*
	 	Italy
	Idenix (Cayman) Limited
	 	Cayman Islands
	Idenix SARL**
	 	France

	 	 	 
	*	 	Wholly-owned by Idenix SARL
	 
	**	 	Wholly-owned by Idenix (Cayman) Limited

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