CERTIFICATE OF INCORPORATION
 
                                       OF
 
                          ANADYS PHARMACEUTICALS, INC.
 
     ANADYS PHARMACEUTICALS, INC., a corporation organized and existing under
and by virtue of the General Corporation Law of the State of Delaware (the
"CORPORATION"), hereby certifies that:
 
     ONE:      The name of the Corporation is Anadys Pharmaceuticals, Inc. The
corporation originally was incorporated under the name ScripTech
Pharmaceuticals, Inc. and the original Certificate of Incorporation of the
Corporation was filed with the Secretary of State of the State of Delaware on
September 17, 1992.
 
     TWO:      Pursuant to Sections 242 and 245 of the General Corporation Law
of the State of Delaware, this Amended and Restated Certificate of Incorporation
restates and integrates and further amends the provisions of the Certificate of
Incorporation of the Corporation as heretofore supplemented or amended.
 
     THREE.    The text of the Amended and Restated Certificate of Incorporation
as heretofore amended or supplemented is hereby restated and further amended to
read in its entirety as follows:
 
                                   ARTICLE I.
 
     The name of this corporation is Anadys Pharmaceuticals, Inc.
 
                                   ARTICLE II.
 
     The address of the registered office of the Corporation in the State of
Delaware shall be 1209 Orange Street, Wilmington, County of New Castle, Delaware
19801 and the name of the registered agent of this Corporation in the State of
Delaware at such address shall be The Corporation Trust Company.
 
                                  ARTICLE III.
 
     The purpose of this corporation is to engage in any lawful act or activity
for which a corporation may be organized under the Delaware General Corporation
Law ("DGCL").
 
                                   ARTICLE IV.
 
     A.        This corporation is authorized to issue two classes of stock to
be designated, respectively, "Common Stock" and "Preferred Stock." The total
number of shares which the corporation is authorized to issue is one hundred
million (100,000,000) shares. Ninety million (90,000,000) shares shall be Common
Stock, each having a par value of one-tenth of one
 
<PAGE>
 
cent ($.001). Ten million (10,000,000) shares shall be Preferred Stock, each
having a par value of one-tenth of one cent ($.001).
 
     B.        The Preferred Stock may be issued from time to time in one or
more series. The Board of Directors is hereby expressly authorized to provide
for the issue of all of any of the shares of the Preferred Stock in one or more
series, and to fix the number of shares and to determine or alter for each such
series, such voting powers, full or limited, or no voting powers, and such
designation, preferences, and relative, participating, optional, or other rights
and such qualifications, limitations, or restrictions thereof, as shall be
stated and expressed in the resolution or resolutions adopted by the Board of
Directors providing for the issuance of such shares and as may be permitted by
the DGCL. The Board of Directors is also expressly authorized to increase or
decrease the number of shares of any series subsequent to the issuance of shares
of that series, but not below the number of shares of such series then
outstanding. In case the number of shares of any series shall be decreased in
accordance with the foregoing sentence, the shares constituting such decrease
shall resume the status that they had prior to the adoption of the resolution
originally fixing the number of shares of such series. The number of authorized
shares of Preferred Stock may be increased or decreased (but not below the
number of shares thereof then outstanding) by the affirmative vote of the
holders of a majority of the Common Stock, without a vote of the holders of the
Preferred Stock, or of any series thereof, unless a vote of any such holders is
required pursuant to the terms of any certificate of designation filed with
respect to any series of Preferred Stock
 
     C.        Each outstanding share of Common Stock shall entitle the holder
thereof to one vote on each matter properly submitted to the stockholders of the
Corporation for their vote; provided, however, that, except as otherwise
required by law, holders of Common Stock shall not be entitled to vote on any
amendment to this Certificate of Incorporation (including any certificate of
designation filed with respect to any series of Preferred Stock) that relates
solely to the terms of one or more outstanding series of Preferred Stock if the
holders of such affected series are entitled, either separately or together as a
class with the holders of one or more other such series, to vote thereon by law
or pursuant to this Certificate of Incorporation (including any certificate of
designation filed with respect to any series of Preferred Stock).
 
                                   ARTICLE V.
 
     For the management of the business and for the conduct of the affairs of
the corporation, and in further definition, limitation and regulation of the
powers of the corporation, of its directors and of its stockholders or any class
thereof, as the case may be, it is further provided that:
 
     A.        BOARD OF DIRECTORS
 
     1. The management of the business and the conduct of the affairs of the
corporation shall be vested in its Board of Directors. The number of directors
which shall constitute the Board of Directors shall be fixed exclusively by
resolutions adopted by a majority of the authorized number of directors
constituting the Board of Directors.
 
                                      -2-
 
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     2. Subject to the rights of the holders of any series of Preferred Stock to
elect additional directors under specified circumstances, the directors shall be
divided into three classes designated as Class I, Class II and Class III,
respectively. At the first annual meeting of stockholders following the initial
classification of the Board of Directors, the term of office of the Class I
directors shall expire and Class I directors shall be elected for a full term of
three years. At the second annual meeting of stockholders following such initial
classification, the term of office of the Class II directors shall expire and
Class II directors shall be elected for a full term of three years. At the third
annual meeting of stockholders following such initial classification, the term
of office of the Class III directors shall expire and Class III directors shall
be elected for a full term of three years. At each succeeding annual meeting of
stockholders, directors shall be elected for a full term of three years to
succeed the directors of the class whose terms expire at such annual meeting.
 
     Notwithstanding the foregoing provisions of this section, each director
shall serve until his successor is duly elected and qualified or until his
death, resignation or removal. No decrease in the number of directors
constituting the Board of Directors shall shorten the term of any incumbent
director.
 
     3. Subject to the rights of the holders of any series of Preferred Stock,
any vacancies on the Board of Directors resulting from death, resignation,
disqualification, removal or other causes and any newly created directorships
resulting from any increase in the number of directors, shall, unless the Board
of Directors determines by resolution that any such vacancies or newly created
directorships shall be filled by the stockholders, except as otherwise provided
by law, be filled only by the affirmative vote of a majority of the directors
then in office, even though less than a quorum of the Board of Directors, and
not by the stockholders. Any director elected in accordance with the preceding
sentence shall hold office for the remainder of the full term of the director
for which the vacancy was created or occurred and until such director's
successor shall have been elected and qualified.
 
     B.
 
     1. BYLAW AMENDMENTS The Board of Directors is expressly empowered to adopt,
amend or repeal the Bylaws of the corporation. The stockholders shall also have
power to adopt, amend or repeal the Bylaws of the corporation; provided,
however, that, in addition to any vote of the holders of any class or series of
stock of the corporation required by law or by this Certificate of
Incorporation, the affirmative vote of the holders of at least sixty-six and
two-thirds percent (66 2/3%) of the voting power of all of the then-outstanding
shares of the capital stock of the corporation entitled to vote generally in the
election of directors, voting together as a single class, shall be required to
adopt, amend or repeal any provision of the Bylaws of the corporation.
 
     2. The directors of the corporation need not be elected by written ballot
unless the Bylaws so provide.
 
                                      -3-
 
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     3. No action shall be taken by the stockholders of the corporation except
at an annual or special meeting of stockholders called in accordance with the
Bylaws. No action shall be taken by the stockholders by written consent or
electronic transmission.
 
     4. Advance notice of stockholder nominations for the election of directors
and of business to be brought by stockholders before any meeting of the
stockholders of the corporation shall be given in the manner provided in the
Bylaws of the corporation.
 
                                   ARTICLE VI.
 
     A.        The liability of the directors for monetary damages shall be
eliminated to the fullest extent under applicable law. If the DGCL is amended to
authorize corporate action further eliminating or limiting the personal
liability of directors, then the liability of a director of the corporation
shall be eliminated to the fullest extent permitted by the DGCL, as so amended.
 
     B.        Any repeal or modification of this Article VI shall be
prospective and shall not affect the rights under this Article VI in effect at
the time of the alleged occurrence of any act or omission to act giving rise to
liability or indemnification.
 
                                  ARTICLE VII.
 
     A.        The corporation reserves the right to amend, alter, change or
repeal any provision contained in this Certificate of Incorporation, in the
manner now or hereafter prescribed by statute, except as provided in paragraph
B. of this Article VII, and all rights conferred upon the stockholders herein
are granted subject to this reservation.
 
     B.        Notwithstanding any other provisions of this Certificate of
Incorporation or any provision of law which might otherwise permit a lesser vote
or no vote, but in addition to any affirmative vote of the holders of any
particular class or series of the corporation required by law or by this
Certificate of Incorporation or any certificate of designation filed with
respect to a series of Preferred Stock, the affirmative vote of the holders of
at least sixty-six and two-thirds percent (66-2/3%) of the voting power of all
of the then-outstanding shares of capital stock of the corporation entitled to
vote generally in the election of directors, voting together as a single class,
shall be required to alter, amend or repeal Articles V, VI, and VII.
 
     FOUR:     This Amended and Restated Certificate of Incorporation has been
duly approved by the Board of the Company.
 
     FIVE:     This Amended and Restated Certificate of Incorporation was
approved by the holders of the requisite number of shares of said corporation in
accordance with Section 228 of the General Corporation Law. This Amended and
Restated Certificate of Incorporation has been duly adopted in accordance with
the provisions of Sections 242 and 245 of the DGCL by the stockholders of the
Company.
 
                                      -4-
 
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     IN WITNESS WHEREOF, this Certificate has been subscribed this 30th day of
March, 2004 by the undersigned who affirms that the statements made herein are
true and correct.
 
                                      /s/ Kleanthis G. Xanthopoulos, Ph.D.
                                      ------------------------------------------
                                      Kleanthis G. Xanthopoulos, Ph.D.
                                      President and Chief Executive Officer
 
                                      -5-