Exhibit 10.1

AMENDMENT TO AGREEMENT AND PLAN OF MERGER

THIS AMENDMENT TO AGREEMENT AND PLAN OF MERGER (this “Amendment”) is made and
entered into as of September 18, 2009, by and among LIGAND PHARMACEUTICALS
INCORPORATED, a Delaware corporation (“Parent”); NEON SIGNAL, LLC, a Delaware
limited liability company and a wholly-owned Subsidiary of Parent (“Merger
Sub”); and NEUROGEN CORPORATION, a Delaware corporation (the “Company”). This
Amendment is made with regard to the Agreement and Plan of Merger dated
August 23, 2009, by and among Parent, Merger Sub and the Company (the
“Agreement”).

1. The Agreement is hereby amended by changing the definition of “Target Net
Cash Amount” in Article I of the Agreement to read in full as follows:

“Target Net Cash Amount” shall mean $7,900,000 if the Determination Date occurs
on any date during the month of September 2009, with a $5,000 decrease for each
calendar day thereafter if the Determination Date occurs on any date thereafter.

2. Except as expressly set forth herein, the Agreement remains unchanged and in
full force and effect.

3. This Amendment may be executed in counterparts, each of which shall be deemed
to be an original, and all of which taken together shall be deemed to constitute
one and the same instrument. The parties agree that delivery of an executed
counterpart of a signature page of this Amendment electronically or by facsimile
shall be effective as delivery of a manually executed counterpart of this
Amendment.

[Remainder of page left intentionally blank. Signature page follows.]

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IN WITNESS WHEREOF, Parent, Merger Sub and the Company have caused this
Amendment to be executed as of the date first written above.

 

LIGAND PHARMACEUTICALS INCORPORATED By:  

/s/ John Sharp

Name:  

John Sharp

Title:  

CFO

NEON SIGNAL, LLC By:  

Ligand Pharmaceuticals Incorporated,

its Member-Manager

  By:  

/s/ John Sharp

  Name:  

John Sharp

  Title:  

CFO

NEUROGEN CORPORATION By:  

/s/ Steve Davis

Name:  

Steve Davis

Title:  

President & CEO

(Signature Page to Amendment to Merger Agreement)

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ACKNOWLEDGED AND AGREED:

 

WARBURG PINCUS PRIVATE EQUITY VIII, L.P.     STEPHEN R. DAVIS By:  

Warburg Pincus Partners, LLC,

its General Partner

   

/s/ Stephen R. Davis

By:  

Warburg Pincus & Co.,

its Managing Member

    JULIAN BAKER

By:

 

/s/ Jonathan Leff

   

/s/ Julian Baker

Name:  

Jonathan Leff

    Title:  

Partner

    Date:  

9/10/09

   

 

FBB ASSOCIATES

/s/ Julian Baker

JULIAN BAKER, A GENERAL PARTNER

   

BAKER BROTHERS LIFE SCIENCES, L.P.

BY: BAKER BROTHERS LIFE SCIENCES

CAPITAL, L.P., (GENERAL PARTNER)

BY: BAKER BROTHERS LIFE SCIENCES

CAPITAL (GP), LLC, (GENERAL PARTNER)

BY: JULIAN BAKER, MANAGING MEMBER

   

/s/ Julian Baker

BAKER/TISCH INVESTMENTS, L.P.

BY: BAKER/TISCH CAPITAL, L.P.,

(GENERAL PARTNER)

BY: BAKER/TISCH CAPITAL (GP), LLC, (GENERAL PARTNER)

BY: JULIAN BAKER, MANAGING MEMBER

   

BAKER BROS. INVESTMENTS, L.P.

BY: BAKER BROS. CAPITAL, L.P., (GENERAL PARTNER)

BY: BAKER BROS. CAPITAL (GP), LLC,

(GENERAL PARTNER)

BY: JULIAN BAKER, MANAGING MEMBER

/s/ Julian Baker

   

/s/ Julian Baker

BAKER BROS. INVESTMENTS II, L.P.

BY: BAKER BROS. CAPITAL, L.P.,

(GENERAL PARTNER)

BY: BAKER BROS. CAPITAL (GP), LLC,

(GENERAL PARTNER)

BY: JULIAN BAKER, MANAGING MEMBER

   

BAKER BIOTECH FUND I, L.P.

BY: BAKER BIOTECH CAPITAL, L.P.,

(GENERAL PARTNER)

BY: BAKER BIOTECH CAPITAL (GP), LLC,

(GENERAL PARTNER)

BY: JULIAN BAKER, MANAGING MEMBER

/s/ Julian Baker

   

/s/ Julian Baker

(Signature Page to Amendment to Merger Agreement)