<PAGE>

                                                                     EXHIBIT 3.1

                          CERTIFICATE OF INCORPORATION

                                       OF

                          MEDICHEM LIFE SCIENCES, INC.

                Pursuant to Sections 242 and 245 of the General
                    Corporation Law of the State of Delaware

                                   ARTICLE 1
                                      Name

          The name of the corporation is MediChem Life Sciences, Inc. (the
"Corporation").


                                   ARTICLE 2
                     Registered Office and Registered Agent

          The address of the Corporation's registered office in the State of
Delaware is 1209 Orange Street, Wilmington, DE 1980l, in the County of New
Castle. The name of its registered agent at such address is The Corporation
Trust Company.


                                   ARTICLE 3
                                    Purpose

          The purpose of the Corporation is to engage in any lawful act or
activity for which corporations may be organized under the Delaware General
Corporation Law ("DGCL").


                                   ARTICLE 4
                                 Capital Stock

          4.1  Amount.  The Corporation has the authority to issue One Hundred
and Ten Million (110,000,000) shares of capital stock ("Stock").

          4.2  Preferred Stock.  The Corporation has the authority to issue up
to Ten Million (10,000,000) of the initial One Hundred and Ten Million
(110,000,000) shares as a separate and single class of shares known as
"Preferred Stock," which may be issued in one or more series.

          4.3  Common Stock.  Of the One Hundred and Ten Million (110,000,000)
shares the Corporation has authority to issue,  One Hundred Million
(100,000,000) shares will constitute a separate class of shares known as "Common
Stock," which shall have $0.01 par value per share.
<PAGE>

          4.4  The following is a description of the relative powers,
preferences and participating, optional or other special rights, and the
qualifications, limitations or restrictions of the Common Stock.

               (a) Voting. At every meeting of the stockholders of the
Corporation in connection with the election of directors and all other matters
submitted to a vote of stockholders, every holder of Common Stock is entitled to
one vote in person or by proxy for each share of Common Stock registered in the
name of the holder on the transfer books of the Corporation. Except as otherwise
required by law, the holders of Common Stock shall vote together as a single
class, subject to any right that may be conferred upon holders of Preferred
Stock to vote together with holders of Common Stock on all matters submitted to
a vote of stockholders of the Corporation.

               (b) Dividends and Other Distributions. Subject to the rights of
the holders of Preferred Stock, holders of Common Stock are entitled to receive
such dividends and other distributions in cash, stock of any corporation (other
than Common Stock) or property of the Corporation as may be declared thereon by
the Board of Directors from time to time out of assets or funds of the
Corporation legally available therefor, and shall share equally on a per share
basis in all such dividends and other distributions.

               (c) Liquidation, Dissolution and Winding Up.  In the event of any
liquidation, dissolution or winding up of the affairs of the Corporation,
whether voluntary or involuntary, after payment in full of the amounts required
to be paid to the holders of Preferred Stock, the remaining assets and funds of
the Corporation are distributed pro rata to the holders of shares of Common
Stock. For purposes of this subsection (c), the voluntary sale, conveyance,
lease, exchange or transfer (for cash, shares of stock, securities or other
consideration) of all or substantially all of the assets of the Corporation or a
consolidation or merger of the Corporation with one or more other corporations
(whether or not the Corporation is the corporation surviving the consolidation
or merger) shall not be deemed to be a liquidation, dissolution or winding up,
voluntary or involuntary.

               (d) Reorganizations and Consolidations. In case of any
reorganization or any consolidation of the Corporation with one or more other
corporations or a merger of the Corporation with another corporation, each
holder of a share of Common Stock is entitled to receive with respect to that
share the same kind and amount of shares of stock and other securities and
property (including cash) receivable upon the reorganization, consolidation or
merger by any other holder of Common Stock.

          4.5  The number of authorized shares of 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 votes entitled to be cast
by the holders of the Common Stock, irrespective of the provisions of Section
242(b)(2) of DGCL or any corresponding provision hereinafter enacted.

                                      -2-
<PAGE>

          4.6  To the full extent permitted by the DGCL, as the same exists or
may hereafter be amended, the Board of Directors is authorized by resolution to
divide and issue the shares of Preferred Stock in classes or series and to fix
the voting powers and any designations, preferences, and relative,
participating, optional or other special rights of any such class or series of
Preferred Stock and any qualifications, limitations or restrictions thereof as
are stated and expressed in the resolution or resolutions providing for the
issue of such stock adopted by the Board of Directors.

          4.7  No holder of Stock of the Corporation has any preemptive or
preferential right of subscription to any shares of any class of Stock of the
Corporation whether now or hereafter authorized, or to any obligation
convertible into stock of the Corporation, or any right of subscription
therefor, other than such rights, if any, as the Board of Directors in its
discretion from time to time determines.


                                   ARTICLE 5
                               Board of Directors

          5.1  The business and affairs of the Corporation are managed by or
under the direction of a Board of Directors. The number of directors of the
Corporation constituting the whole board are fixed in the manner provided in the
by-laws.  The election of directors need not be by ballot.

          5.2  The directors are divided into three classes, Class I, Class II
and Class III.  The initial term of office of the Class I, Class II and Class
III directors shall expire at the annual meeting of stockholders in 2001, 2002,
and 2003, respectively.  The number of directors are apportioned among the
classes by the Board of Directors so as to maintain the number of directors in
each class as nearly equal as reasonably possible, and any additional director
of any class elected to fill a vacancy resulting from an increase in such class
shall hold office for a term that shall coincide with the remaining term of that
class.  Beginning in 2001, at each annual meeting of stockholders, successors to
the class of directors whose term expires at that annual meeting are elected for
a three-year term.  In no case will a decrease in the number of directors
shorten the term of any incumbent director even though such decrease may result
in an inequality of the classes until the expiration of such term.  A director
shall hold office until the annual meeting of the year in which his or her term
expires and until his or her successor are elected and shall qualify, subject,
however, to prior death, resignation, retirement or removal from office.  Except
as required by law or the provisions of this Certificate of Incorporation, all
vacancies on the Board of Directors and newly created directorships are filled
by the Board of Directors.  Any director elected to fill a vacancy not resulting
from an increase in the number of directors shall have the same remaining term
as that of his or her predecessor. Notwithstanding anything to the contrary
contained in this Certificate of Incorporation, the affirmative vote of the
holders of a majority of the voting power of the shares entitled to vote
generally in the election of directors are required to amend, alter or repeal,
or to adopt any provision inconsistent with, this Article 5.

          5.3  Notwithstanding the foregoing, whenever the holders of any one or
more classes or series of Preferred Stock issued by the Corporation have the
right, voting separately by class or series to elect directors at an annual or
special meeting of stockholders, the election, term of office, filling of
vacancies and other features of such directorship are governed by the terms of
this Certificate of Incorporation and any resolutions of the Board of Directors
applicable thereto, and such directors so elected shall not be divided into
classes pursuant to this Article 5.

                                      -3-
<PAGE>


          5.4  Subject to the rights of the holders of any classes or series of
Preferred Stock, any director, or the entire Board of Directors, may be removed
from office at any time, but only for cause and only by the affirmative vote of
the holders of a majority of the voting power of all the shares of the
Corporation entitled to vote for the election of directors.


                                   ARTICLE 6
                              Amendment of By-laws

          In furtherance and not in limitation of the powers conferred by the
laws of the State of Delaware, the Board of Directors expressly is authorized to
make, alter, amend and repeal the by-laws of the Corporation, in any manner not
inconsistent with the laws of the State of Delaware or this Certificate of
Incorporation, subject to the power of the stockholders of the Corporation to
amend, alter or repeal any by-laws made by the Board of Directors.
Notwithstanding the foregoing, the affirmative vote of the holders of a majority
of the voting power of all the shares of the Corporation entitled to vote for
the election of directors shall be required for the amendment of Articles 1 and
2 and Section 5.10 of the by-laws of the Corporation.


                                   ARTICLE 7
                              Stockholder Meetings

          Subject to the rights of the holders of Preferred Stock, any action
required or permitted to be taken by the stockholders of the Corporation must be
effected at a duly called annual or special meeting of such holders and may not
be effected by any consent in writing by such holders.  Subject to the rights of
the holders of Preferred Stock, special meetings of stockholders of the
Corporation may be called only by the Chairman of the Board or by the Board of
Directors pursuant to a resolution.  Business transacted at any special meeting
of stockholders are confined to the purpose or purposes of the meeting as stated
in the notice of the meeting.  Notwithstanding anything contained in this
Certificate of Incorporation to the contrary, any amendment to or deletion of
this Article 7 shall require the affirmative vote of the holders of a majority
of the voting power of all outstanding shares of capital stock of the
Corporation entitled to vote generally in the election of directors.


                                   ARTICLE 8
                            Limitation of Liability

          A director of the Corporation shall not be personally liable to the
Corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except for liability (a) for any breach of the director's
duty of loyalty to the Corporation or its stockholders, (b) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (c) under Section 174 of the DGCL or (d) for any transaction
from which the director derived an improper personal benefit.If DGCL is amended
after approval of this Article by the stockholders to authorize the further
elimination or limitation of the liability of directors, then the liability of
directors are eliminated or limited to the full extent authorized by the DGCL,
as so amended.


                                      -4-
<PAGE>

                                   ARTICLE 9
                            Amendment of Certificate

          Subject to the provisions of this Certificate of Incorporation, 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, and all rights conferred upon stockholders in this
Certificate of Incorporation are granted subject to this reservation.

                                      -5-
<PAGE>

          IN WITNESS WHEREOF, the undersigned has executed this certificate as
of the 31st day of May, 2000.


                                                        /s/ Michael T. Flavin
                                                     ---------------------------
                                                          Michael T. Flavin

                                      -6-