UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  SCHEDULE 13G

                    UNDER THE SECURITIES EXCHANGE ACT OF 1934

                               (AMENDMENT NO. 2)*


                           IDERA PHARMACEUTICALS, INC.
--------------------------------------------------------------------------------
                                (Name of Issuer)


                                  COMMON STOCK
--------------------------------------------------------------------------------
                         (Title of Class of Securities)


                                    44860M801
--------------------------------------------------------------------------------
                                 (CUSIP Number)


                                DECEMBER 31, 2005
--------------------------------------------------------------------------------
             (Date of Event which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

[ ]       Rule 13d-1(b)

[X]       Rule 13d-1(c)

[ ]       Rule 13d-1(d)


------------------
*The  remainder of this cover page shall be filled out for a reporting  person's
initial filing on this form with respect to the subject class of securities, and
for any  subsequent  amendment  containing  information  which  would  alter the
disclosures provided in a prior cover page.

The information required in the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the  Securities  Exchange  Act of
1934 ("Act") or otherwise  subject to the liabilities of that section of the Act
but  shall be  subject  to all other  provisions  of the Act  (however,  see the
Notes).



                                       1

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CUSIP No.                                13G                 Page 2 of 12 Pages
----------------                                             -------------------


    1.      NAMES OF REPORTING PERSONS

            Great Point Partners, LLC

    2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
            (a)     [ ]

            (b)     [ ]

--------------------------------------------------------------------------------
    3.      SEC USE ONLY

--------------------------------------------------------------------------------
    4.      CITIZENSHIP OR PLACE OF ORGANIZATION

            USA

                        5.    SOLE VOTING POWER
  NUMBER OF SHARES

    BENEFICIALLY        6.    SHARED VOTING POWER
                                                                 5,962,394
   OWNED BY EACH
                        7.    SOLE DISPOSITIVE POWER
  REPORTING PERSON

        WITH            8.    SHARED DISPOSITIVE POWER
                                                                 5,962,394

    9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

                     5,962,394

    10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
            SHARES (See Instructions)                                        [ ]


    11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

                     5.29%

    12.     TYPE OF REPORTING PERSON (See Instructions)

                     OO



----------------                                             -------------------
CUSIP No.                                13G                 Page 3 of 12 Pages
----------------                                             -------------------


    1.      NAMES OF REPORTING PERSONS

            Biomedical Value Fund, L.P.

    2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
            (a)     [ ]

            (b)     [ ]

--------------------------------------------------------------------------------
    3.      SEC USE ONLY

--------------------------------------------------------------------------------
    4.      CITIZENSHIP OR PLACE OF ORGANIZATION

            Delaware, USA

                        5.    SOLE VOTING POWER
  NUMBER OF SHARES

    BENEFICIALLY        6.    SHARED VOTING POWER
                                                                 3,082,211
   OWNED BY EACH
                        7.    SOLE DISPOSITIVE POWER
  REPORTING PERSON

        WITH            8.    SHARED DISPOSITIVE POWER
                                                                 3,082,211

    9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

                     3,082,211

    10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
            SHARES (See  Instructions)                                       [ ]


    11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

                     2.75%

    12.     TYPE OF REPORTING PERSON (See Instructions)

                     PN



----------------                                             -------------------
CUSIP No.                                13G                 Page 4 of 12 Pages
----------------                                             -------------------


    1.      NAMES OF REPORTING PERSONS

            Great Point GP, LLC

    2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
            (a)     [ ]

            (b)     [ ]

--------------------------------------------------------------------------------
    3.      SEC USE ONLY

--------------------------------------------------------------------------------
    4.      CITIZENSHIP OR PLACE OF ORGANIZATION

            Delaware, USA

                        5.    SOLE VOTING POWER
  NUMBER OF SHARES

    BENEFICIALLY        6.    SHARED VOTING POWER
                                                                 3,082,211
   OWNED BY EACH
                        7.    SOLE DISPOSITIVE POWER
  REPORTING PERSON

        WITH            8.    SHARED DISPOSITIVE POWER
                                                                 3,082,211

    9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

                     3,082,211

    10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
            SHARES (See Instructions)                                        [ ]


    11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

                     2.75%

    12.     TYPE OF REPORTING PERSON (See Instructions)

                     OO



----------------                                             -------------------
CUSIP No.                                13G                 Page 5 of 12 Pages
----------------                                             -------------------



    1.      NAMES OF REPORTING PERSONS

            Biomedical Offshore Value Fund, Ltd.

    2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
            (a)     [ ]

            (b)     [ ]

--------------------------------------------------------------------------------
    3.      SEC USE ONLY

--------------------------------------------------------------------------------
    4.      CITIZENSHIP OR PLACE OF ORGANIZATION

            Cayman Islands

                        5.    SOLE VOTING POWER
  NUMBER OF SHARES

    BENEFICIALLY        6.    SHARED VOTING POWER
                                                                 2,880,183
   OWNED BY EACH
                        7.    SOLE DISPOSITIVE POWER
  REPORTING PERSON

        WITH            8.    SHARED DISPOSITIVE POWER
                                                                 2,880,183

    9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

                     2,880,183

    10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
            SHARES (See Instructions)                                        [ ]


    11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

                     2.58%

    12.     TYPE OF REPORTING PERSON (See Instructions)

                     CO



----------------                                             -------------------
CUSIP No.                                13G                 Page 6 of 12 Pages
----------------                                             -------------------


    1.      NAMES OF REPORTING PERSONS

            Dr. Jeffrey R. Jay, M.D.

    2.      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP
            (a)     [ ]

            (b)     [ ]


    3.      SEC USE ONLY

    4.      CITIZENSHIP OR PLACE OF ORGANIZATION

            Delaware, USA

                        5.    SOLE VOTING POWER
  NUMBER OF SHARES                                               349,200

    BENEFICIALLY        6.    SHARED VOTING POWER
                                                                 5,962,394
   OWNED BY EACH
                        7.    SOLE DISPOSITIVE POWER
  REPORTING PERSON

        WITH            8.    SHARED DISPOSITIVE POWER
                                                                 5,962,394

    9.      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

                     6,311,594

    10.     CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN
            SHARES (See Instructions)                                        [ ]


    11.     PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)

                     5.6%

    12.     TYPE OF REPORTING PERSON (See Instructions)

                     IN



----------------                                             -------------------
CUSIP No.                                13G                 Page 7 of 12 Pages
----------------                                             -------------------


     ITEM 1.        NAMES OF REPORTING PERSONS

                    (a)      Idera Pharmaceuticals, Inc..

                    (b)      345 Vassar Street
                             Cambridge, MA 02139
                             U.S.A.


     ITEM 2.

                    (a)      Name of Person Filing
                                      Great Point Partners, LLC
                                      Biomedical Value Fund, L.P.
                                      Great Point GP, LLC
                                      Biomedical Offshore Value Fund, Ltd.
                                      Dr. Jeffrey R. Jay, M.D.

                    (b)      Address of Principal Business Office, or
                             if none, Residence
                                      2 Pickwick Plaza
                                      Suite 450
                                      Greenwich, CT 06830

                    (c)      Citizenship

                    Great Point Partners, LLC is a limited liability company
                    organized under the laws of the State of Delaware.
                    Biomedical Value Fund, L.P. is a limited partnership
                    organized under the laws of the State of Delaware. Great
                    Point GP, LLC is a limited liability company organized under
                    the laws of the State of Delaware. Biomedical Offshore Value
                    Fund, Ltd. is a limited liability corporation organized
                    under the laws of the Cayman Islands. Dr. Jeffrey R. Jay,
                    M.D. is a citizen of the United States.

                    (d)      Title of Class of Securities

                             Common Stock

                    (e)      CUSIP Number

                             44860M801

     ITEM           3. IF THIS STATEMENT IS FILED PURSUANT TO SS.240.13D-1(b) OR
                    240.13D.2(b) OR (c), CHECK WHETHER THE PERSON FILING IS A:

                             Not Applicable.

                    (a)   [ ]   Broker or dealer registered under Section 15 of
                                the Act (15 U.S.C. 78o)

                    (b)   [ ]   Bank as defined in Section 3(a)(6) of the Act
                                (15 U.S.C. 78c).

                    (c)   [ ]   Insurance company as defined in Section 3(a)(19)
                                of the Act (15. U.S.C. 78c).

                    (d)   [ ]   Investment Company registered under Section 8 of
                                 the Investment Company Act of 1940
                                (15 U.S.C. 80a-8).

                    (e)   [ ]   An investment adviser in accordance with
                                ss.240.13d-1(b)(1)(ii)(E).

                    (f)   [ ]   An employee benefit plan or endowment fund in
                                accordance with ss.240.13d-1(b)(1)(ii)(F).


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CUSIP No.                                13G                 Page 8 of 12 Pages
----------------                                             -------------------


                    (g)   [ ]   A parent holding company or control person in
                                accordance with ss.240.13d-1(b)(1)(ii)(G).

                    (h)   [ ]   A savings associations as defined in Section
                                3(b) of the Federal Deposit Insurance Act (12
                                U.S.C. 1813).

                    (i)   [ ]   A church plan that is excluded from the
                                definition of an investment company under
                                Section 3(c)(14) of the Investment Company Act
                                of 1940 (15 U.S.C. 80a-3).

                    (j)   [ ]   Group, in accordance with
                                ss.240.13d-1(b)(1)(ii)(J).



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CUSIP No.                                13G                 Page 9 of 12 Pages
----------------                                             -------------------


     ITEM 4.        OWNERSHIP

                    Biomedical Value Fund, L.P. ("BVF") is the direct beneficial
                    owner of 3,082,211 shares (the "BVF Shares"), consisting of
                    2,205,740 shares of Common Stock and warrants to purchase
                    876,471 shares of Common Stock. Great Point GP, LLC, is the
                    general partner of BVF, and by virtue of such status may be
                    deemed to be the beneficial owner of the BVF Shares. Great
                    Point Partners, LLC is the investment manager of BVF, and by
                    virtue of such status may be deemed to be the beneficial
                    owner of the BVF Shares. Dr. Jeffrey R. Jay, M.D. has voting
                    and investment power with respect to the BVF Shares, and
                    therefore may be deemed to be the beneficial owner of the
                    BVF Shares.

                    Biomedical Offshore Value Fund, Ltd. ("BOVF") is the direct
                    beneficial owner of 2,880,183 shares (the "BOVF Shares"),
                    consisting of 2,205,660 shares of Common Stock and warrants
                    to purchase 674,523 shares of Common Stock. Great Point
                    Partners, LLC is the investment manager of BOVF, and by
                    virtue of such status may be deemed to be the beneficial
                    owner of the BOVF Shares. Dr. Jeffrey R. Jay, M.D. has
                    voting and investment power with respect to the BOVF Shares,
                    and therefore may be deemed to be the beneficial owner of
                    the BOVF Shares.

                    Notwithstanding the above, Great Point Partners, LLC and Dr.
                    Jay disclaim beneficial ownership of the BVF Shares and the
                    BOVF Shares and Great Point GP, LLC disclaims beneficial
                    ownership of the BVF Shares, except to the extent of their
                    respective pecuniary interests.



                    The Information in Items 1 and 5 through 11 on the cover
                    pages of this Amendment No. 1 to Schedule 13G is hereby
                    incorporated by reference.

                    Provide the following information regarding the aggregate
                    number and percentage of the class of securities of the
                    issuer identified in Item 1.

                    (a)   Amount beneficially owned: _______________.

                    (b)   Percent of class: _____________.

                    (c)   Number of shares as to which the person has:

                          (i)   Sole power to vote or to direct the vote ______.

                          (ii)  Shared power to vote or to direct
                                the vote _________.

                          (iii) Sole power to dispose or to direct the
                                disposition of __________.

                          (iv)  Shared power to dispose or to direct the
                                disposition of _____________.

ITEM 5.             OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS

                    Not Applicable.

ITEM 6.             OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER
                    PERSON:

                    Not Applicable.



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CUSIP No.                                13G                 Page 10 of 12 Pages
----------------                                             -------------------


ITEM 7.             IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
                    ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT
                    HOLDING COMPANY

                    Not Applicable.

ITEM 8.             IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP

                    Not Applicable.

ITEM 9.             NOTICE OF DISSOLUTION OF GROUP

                    Not Applicable.

ITEM 10.            CERTIFICATION

By signing below I certify  that,  to the best of my knowledge  and belief,  the
securities  referred to above were not acquired and are not held for the purpose
of or with the effect of  changing or  influencing  the control of the issuer of
the securities  and were not acquired and are not held in connection  with or as
participant in any transaction having that purpose or effect.





----------------                                             -------------------
CUSIP No.                                13G                 Page 11 of 12 Pages
----------------                                             -------------------


                                    SIGNATURE

         After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this statement is true, complete and
correct.

Date:  February 13, 2006

                          BIOMEDICAL VALUE FUND, L.P.


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Great Point GP, LLC,
                                             as general partner,
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          GREAT POINT GP, LLC


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Dr. Jeffrey R. Jay, M.D.
                                              as senior managing member

                          BIOMEDICAL OFFSHORE VALUE FUND, LTD.


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Great Point Partners, LLC,
                                             as investment manager,
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          GREAT POINT PARTNERS, LLC


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          DR. JEFFREY R. JAY, M.D.

                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------



                                                                       EXHIBIT A


              AGREEMENT REGARDING THE JOINT FILING OF SCHEDULE 13G


The undersigned hereby agree as follows:

         (i)      Each of them is individually  eligible to use the Schedule 13G
to which this Exhibit is attached,  and such  Schedule 13G is filed on behalf of
each of them; and

         (ii)     Each of them is  responsible  for the  timely  filing  of such
Schedule 13G and any amendments  thereto,  and for the completeness and accuracy
of the information concerning such person contained therein; but none of them is
responsible for the  completeness or accuracy of the information  concerning the
other  persons  making the filing,  unless  such  person  knows or has reason to
believe that such information is inaccurate.

Date:  February 13, 2006

                          BIOMEDICAL VALUE FUND, L.P.


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Great Point GP, LLC,
                                             as general partner,
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          GREAT POINT GP, LLC


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Dr. Jeffrey R. Jay, M.D.
                                              as senior managing member

                          BIOMEDICAL OFFSHORE VALUE FUND, LTD.


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Great Point Partners, LLC,
                                             as investment manager,
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          GREAT POINT PARTNERS, LLC


                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------
                                            By Dr. Jeffrey R. Jay, M.D.,
                                             as senior managing member

                          DR. JEFFREY R. JAY, M.D.

                          Signature:        /s/ Dr. Jeffrey R. Jay, M.D.
                                            ------------------------------------