<PAGE>

                                                                    Exhibit 10.2

             AMENDMENT NO. 1 TO THE COMMON STOCK PURCHASE AGREEMENT

                                  July 10, 2006


       This Amendment No. 1 (this "Amendment") to the Common Stock Purchase
Agreement (the "Agreement") dated March 24, 2006, by and between Biotech Shares
Ltd., an entity organized and existing under the laws of the Isle of Man (the
"Investor"), and Idera Pharmaceuticals, Inc., a corporation organized and
existing under the laws of the State of Delaware (the "Company"), is entered
into as of the 10th day of July 2006.

       WHEREAS, under the terms of the Agreement the Company has the right to
sell to the Investor up to $2,500,000 of the Company's Common Stock prior to the
effectiveness of the Pre-Issuance Registration Statement (as such term is
defined in the Agreement);

       WHEREAS, the Company and the Investor have agreed pursuant to an
amendment to the Registration Rights Agreement (as defined in the Agreement)
that the Company shall not be obligated to file the Pre-Issuance Registration
Statement with the United States Securities and Exchange Commission until August
14, 2006; and

       WHEREAS, the Company desires to sell to the Investor in excess of
$2,500,000 of the Company's Common Stock prior to such date;

       WHEREAS, in order to allow the Company to sell the desired number of
shares of its Common Stock prior to such date, the Company and the Investor
agree that certain terms of the Agreement must be amended.

       NOW, THEREFORE, the Company and the Investor agree as follows:

Amendment to $2,500,000 Purchase Amount Limitation.
---------------------------------------------------

1.     The second sentence of Section 3(a) of the Agreement is hereby deleted in
       its entirety and the following is substituted in lieu thereof:

       "(a)   If the Purchase Notice involves a Purchase Amount, which when
       aggregated with the Purchase Amount of Common Stock previously sold to
       the Investor hereunder exceeds $3,500,000, the Company shall confirm in
       such Purchase Notice that a registration statement (the "Pre-Issuance
       Registration Statement") covering the resale of the shares of Common
       Stock to be issued on such closing date has been declared and is
       effective and that the certificates representing such shares shall not
       bear a restricted securities legend."

2.     Section 3(d) of the Agreement is hereby deleted in its entirety and the
       following is substituted in lieu thereof:

       "(d)   Notwithstanding the foregoing, the Investor shall have no
       obligation hereunder to purchase any shares of Common Stock if the
       Purchase Amount of such shares, when aggregated with the Purchase Amount
       of Common Stock previously sold to the Investor under this Agreement,
       exceeds $3,500,000 unless the Pre-Issuance Registration Statement


<PAGE>

       has been declared and is effective and the certificates representing such
       shares will not bear a restricted securities legend."

Reverse Split Purchase Price.
-----------------------------

In order to reflect the reverse stock split effected on June 30, 2006, Section
3(b) of the Agreement is hereby deleted in its entirety and the following is
substituted in lieu thereof:

       "(b)   The number of shares of Common Stock to be issued in connection
       with a Purchase Notice shall be determined by dividing (1) the Purchase
       Amount specified in the Purchase Notice by (ii) the greater of (A) $5.12
       and (B) 80% of the volume-weighted average of the Closing Prices (as
       defined below) of the Common Stock for the five consecutive Trading Days
       (as defined below) immediately preceding the date that the Company sends
       such Purchase Notice to the Investor."

Purchase Notice.
----------------

1.     Attached hereto as Exhibit A is a Purchase Notice providing for the sale
       of $3,500,000 of Common Stock to the Investor at a closing to be held on
       July 24, 2006, pursuant to the terms of the Agreement, as amended by this
       Amendment.

2.     The Investor acknowledges the delivery of the Purchase Notice as of the
       date hereof.

Miscellaneous
-------------

1.     This Amendment may be executed in identical counterparts, each of which
       shall be deemed an original but all of which shall constitute one and the
       same agreement. This Amendment, once executed by a party, may be
       delivered by facsimile transmission of a copy of this Amendment bearing
       the signature of the party so delivering this Amendment.

2.     Except as expressly modified by or pursuant to this Amendment, the Common
       Stock Purchase Agreement shall remain in full force and effect without
       any other change or modification.



<PAGE>


IN WITNESS WHEREOF, the parties have caused this Amendment No. 1 to the
Agreement to be duly executed as of the day and year first above written.



                                            COMPANY:

                                            IDERA PHARMACEUTICALS, INC.


                                            By: /s/ Sudhir Agrawal
                                                --------------------------------
                                                Name: Sudhir Agrawal
                                                Title: Chief Executive Officer



                                            INVESTOR:

                                            BIOTECH SHARES LTD.


                                            By: /s/ Oussama Salam
                                                --------------------------------
                                                Name: Oussama Salam
                                                Title: Director




<PAGE>

                                    Exhibit A
                                    ---------

                           IDERA PHARMACEUTICALS, INC.
                                345 VASSAR STREET
                            CAMBRIDGE, MA 02139-4818


                                                                   July 10, 2006


Biotech Shares Ltd.
St. James's Chambers
64A Athol Street
Isle of Man IM1 1JE

       Re:  Purchase Notice


Gentlemen:

       Pursuant to and in accordance with the terms of that certain Common Stock
Purchase Agreement, dated March 24, 2006 (the "PURCHASE AGREEMENT"), as amended,
by and between Biotech Shares Ltd. (the "INVESTOR") and Idera Pharmaceuticals,
Inc. (the "COMPANY"), the Company hereby provides notice (the "PURCHASE NOTICE")
to the Investor that the Company has duly elected to issue and sell to the
Investor, and the Investor is hereby obligated to purchase from the Company, the
number of shares of common stock of the Company, US$0.001 par value per share
(the "COMMON STOCK"), set forth below, on such date and for such dollar amount
as is set forth below (the "DRAWDOWN"):

1.     The number of shares of Common Stock to be issued to the Investor on the
       Drawdown Date (as defined below) to its account with First National Bank
       S.A.L.: 683,593 the "SHARES").

2.     The dollar amount of the Shares: US$3,499,996.16 (the "PURCHASE AMOUNT"
       or "DRAWDOWN AMOUNT").

3.     The closing date for the Drawdown (and the date on which payment of the
       Purchase Amount shall be made to the Company): July 24, 2006 (the
       "DRAWDOWN DATE").

4.     The price per share of the Common Stock used to calculate the number of
       Shares to be issued on the Drawdown Date: US$5.12 per share of Common
       Stock.

       The Company hereby confirms that the Shares and the Drawdown Amount are
in compliance with all of the terms and conditions of the Purchase Agreement.


                                        IDERA PHARMACEUTICALS, INC.


                                        By: /s/ Sudhir Agrawal
                                            ------------------------------------
                                            Name:
                                            Title: