Exhibit 10.14

ARCA BIOPHARMA, INC.

FIRST AMENDMENT TO NOTE AND WARRANT PURCHASE AGREEMENT

THIS FIRST AMENDMENT TO NOTE AND WARRANT PURCHASE AGREEMENT (this “Amendment”)
is made and entered into as of October 10, 2008 by and between ARCA biopharma,
Inc., a Delaware corporation (the “Company”), the undersigned Purchasers
(individually, a “Purchaser” and collectively, the “Purchasers”) and Parent.

RECITALS

A. The Company has authorized the sale of its 6% convertible promissory notes
due March 31, 2009 and warrants to purchase shares of the Company’s capital
stock.

B. The Company and the Purchasers have entered into that certain Note and
Warrant Purchase Agreement, dated September 24, 2008 (the “Purchase Agreement”)
pursuant to which the Purchasers agreed to purchase the Notes at the Closing.
Capitalized terms used, but not defined herein, shall have the meanings assigned
to them in the Purchase Agreement.

C. Section 5.7 of the Purchase Agreement allows the Company, a majority of the
Principal Series Preferred Stockholders (as such term is defined in the Restated
Charter) and, for so long as the Merger Agreement remains in full force and
effect, Parent, to amend the Purchase Agreement.

D. The Company, the undersigned Purchasers, who represent at least a majority of
the Principal Series Preferred Stockholders (as such term is defined in the
Restated Charter), and Parent, desire to amend the Purchase Agreement as
provided below.

AMENDMENT

NOW, THEREFORE, in consideration of the above recitals and the mutual covenants
contained herein, the parties hereby agree as follows:

1. Section 1.2 of the Purchase Agreement is hereby deleted in its entirety and
replaced with the following language:

1.2 Issuance of Warrants. Subject to the terms of this Agreement, and for the
additional consideration (the “Warrant Consideration”) set forth opposite such
Purchaser’s name on the Schedule of Purchasers under the heading “Warrant
Consideration,” the Company shall issue to each Purchaser a warrant to purchase
shares of Common Stock of the Company. Subject to certain adjustments provided
in the warrant, each warrant issuable pursuant to this Section 1.2 shall entitle
the Purchaser to acquire the number of shares equal to the quotient of
(a) one-fifth ( 1/5th) of such Purchaser’s total purchase price (“Total Purchase
Price”) set forth opposite such

 

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Purchaser’s name on the Schedule of Purchasers under the heading “Total Purchase
Price”) divided by (b) the exercise price of each warrant, rounded up to the
nearest share. The warrants shall be in substantially the form attached hereto
as Exhibit B (each, a “Warrant” and collectively, the “Warrants”).

2. Section 1.4 of the Purchase Agreement is hereby deleted in its entirety and
replaced with the following language:

1.4 Delivery. At the Closing: (a) each Purchaser will deliver to the Company a
check or wire transfer funds in the total amount of such Purchaser’s Total
Purchase Price, (b) the Company shall issue and deliver to each Purchaser a Note
in favor of such Purchaser payable in the principal amount of such Purchaser’s
Loan Amount and a Warrant, and (c) the Company shall execute and deliver such
other documents as the Purchasers shall reasonably require in order to
consummate the transactions contemplated herein. In connection with the Closing,
the Company shall have filed with the Delaware Secretary of State the
Certificate of Amendment to the Restated Charter (as defined below) in
substantially the form attached hereto as Exhibit C (the “Charter Amendment”).

3. The Schedule of Purchasers attached to the Purchase Agreement is hereby
replaced in its entirety with the Schedule of Purchasers attached hereto as
Exhibit A.

4. Except as expressly amended by this Amendment, the Purchase Agreement shall
remain in full force and effect without change.

5. This Amendment may be executed in any number of counterparts, each of which
when executed and delivered shall be an original, but all of which together
shall constitute one and the same instrument.

[signature pages follow]

 

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IN WITNESS WHEREOF, the parties have executed this AMENDMENT as of the date
first written above.

 

COMPANY:     PURCHASERS: ARCA BIOPHARMA, INC.     SKYLINE VENTURE PARTNERS
QUALIFIED PURCHASER FUND IV, L.P. Signature:  

/s/ Christopher D. Ozeroff

    By:   Skyline Venture Management IV, LLC Print Name:   Christopher D.
Ozeroff       Its General Partner Title:   Executive Vice President Business
Development and General Counsel     By:  

/s/ John G. Freund

        John G Freund, Managing Director       INTERWEST PARTNERS IX, LP      
By:   InterWest Management Partners IX, LLC       By:  

/s/ Linda Grais

        Linda Grais, Venture Member       ATLAS VENTURE FUND VII, L.P.       By:
  Atlas Venture Associates VII, L.P.         its General Partner       By:  
Atlas Venture Associates VII, Inc.         its General Partner       Signature:
 

/s/ Kristen Laguerre

      Print Name:  

Kristen Laguerre

      Title:  

Vice President

FIRST AMENDMENT TO NOTE AND WARRANT PURCHASE AGREEMENT

SIGNATURE PAGE

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      BOULDER VENTURES IV, L.P.       By:   BV Partners IV, L.L.C., its General
Partner       Signature:  

/s/ Kyle Lefkoff

      Print Name:  

Kyle Lefkoff

      Title:  

Managing Member

      BOULDER VENTURES IV (ANNEX), L.P.       By:   BV Partners IV, L.L.C., its
General Partner       Signature:  

/s/ Kyle Lefkoff

      Print Name:  

Kyle Lefkoff

      Title:  

Managing Member

      THE PEIERLS FOUNDATION, INC.       Signature:  

/s/ E. Jeffrey Peierls

      Print Name:  

E. Jeffrey Peierls

      Title:  

President

      NUVELO, INC.       Signature:  

/s/ Lee Bendekgey

      Print Name:  

Lee Bendekgey

      Title:  

Sr. VP, CFO and General Counsel

FIRST AMENDMENT TO NOTE AND WARRANT PURCHASE AGREEMENT

SIGNATURE PAGE

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SCHEDULE OF PURCHASERS

 

NAME AND ADDRESS

   LOAN AMOUNT    WARRANT
CONSIDERATION    TOTAL PURCHASE
PRICE

SKYLINE VENTURE PARTNERS QUALIFIED

PURCHASER FUND IV, L.P.

   $ 1,742,362    $ 83,334    $ 1,825,696

525 University Ave

Suite 520

Palo Alto, CA 94301

Attention: Kerry Kenny

Facsimile: (650) 329-1090

         INTERWEST PARTNERS IX, LP    $ 1,395,144    $ 66,728    $ 1,461,872

2710 Sand Hill Road

Second Floor

Menlo Park, CA 94025

Attention: Linda Grais

Facsimile: (650) 854-4706

         ATLAS VENTURE FUND VII, L.P.    $ 3,506,900    $ 167,730    $ 3,674,630

890 Winter Street, Suite 320

Waltham, MA 02451

Attention: General Counsel

Facsimile: (781) 622-1701

         BOULDER VENTURES IV, L.P.    $ 88,176    $ 4,217    $ 92,393

1900 Ninth Street, Suite 200

Boulder, CO 80302

Attention: Kyle Lefkoff

Facsimile: (303) 444-0267

        

BOULDER VENTURES IV

(ANNEX), L.P.

   $ 1,331,715    $ 63,694    $ 1,395,409

1900 Ninth Street, Suite 200

Boulder, CO 80302

Attention: Kyle Lefkoff

Facsimile: (303) 444-0267

         THE PEIERLS FOUNDATION, INC.    $ 286,306    $ 13,694    $ 300,000

c/o U.S. Trust Company of N.Y.

114 West 47th Street

New York, NY 10036

Attention: Mr. John Kennedy

         TOTAL    $ 8,350,603.00    $ 399,397.00    $ 8,750,000.00