Exhibit
3.1




AMENDED AND
RESTATED


CERTIFICATE OF
INCORPORATION




GENE
LOGICINC., a corporationorganizedand
existingunder and by virtue of the General Corporation Law of the State
of Delaware, hereby certifiesasfollows:
  1.                      Thenameof thecorporation isGENELOGICINC.
  2.                      The
corporation's original Certificate
of Incorporation was filed with theSecretary of State on September 22,
1994.
  3.           The Amended and Restated Certificate ofIncorporationof
thiscorporation,in the
formattached heretoas
Exhibit A, hasbeendulyadopted bytheBoardof
Directorsand bythe stockholdersof the corporationin accordance
with Sections228, 242
and 245 of the General Corporation Law of the State of
Delaware.
  4.                      The
Amended and Restated Certificateof
Incorporation so adapted reads in foil as set forth in Exhibit A attached hereto
and hereby incorporated by reference.
 INWITNESS WHEREOF,GENELOGIC INC. has caused
this Amended and Restated Certificate of Incorporationto be signed by its President and Chief
Executive Officer andattested to by its Senior Vice President and
Chief Financial Officerthis
26th day of November, 1997.
  /s/ Michael J. Brennan, M.D.,
      Ph.D.MICHAEL
      J. BRENNAN, M.D., Ph.D.President
      and Chief Executive OfficerAttest:/s/ Mark D. GesslerMARK
      D. GESSLERSenior
      Vice President and Chief FinancialOfficer









Exhibit
A
  AMENDED
AND RESTATED
 CERTIFICATE
OF INCORPORATION
 OF
 GENE
LOGIC INC.
  I. 
[SUBSEQUENTLY
AMENDED BY CERTIFICATE OF AMENDMENT FILED
DECEMBER 18, 2007 (ATTACHED HERETO)]
  The name of this
corporation is GENELOGIC INC.
  II.
 The
address of the registered office of the corporationin the State of
Delawareis 1209 Orange Street, City of Wilmington, County of New Castle, and the
name of the registered agent of the corporation in the State of Delaware at such
address is The Corporation Trust Company.
  III.
  The purpose of this
corporation is to engage in any lawful act or activity for which a corporation
may be organized under the General Corporation Law of the State of Delaware.
  IV. 
[SUBSEQUENTLY
AMENDED BY CERTIFICATE OF AMENDMENT
FILED MAY 23, 2008 (ATTACHED HERETO)]
  A.Thiscorporationisauthorizedtoissue
twoclassesof
stock tobedesignated, respectively,
"Common Stock" and "Preferred Stock." The total number of shares which the
corporation is authorized to issue is Seventy Million (70,000,000) shares. SixtyMillion
(60,000,000) shares shallbeCommon Stock, each having a
par value of one cent ($.01),
Ten Million (10,000,000)shares shall bePreferred Stock, each
having a par value of one cent ($.01).
  The
Preferred Stock may be issued from time to time in one or more series. TheBoard of Directors is hereby authorized, by filing a certificate (a
"Preferred Stock Designation") pursuant tothe Delaware toGeneral CorporationLaw, tofix or
alterfrom time to time the
designation, powers, preferences and rights of the shares of each such series andthe qualifications,
limitations or restrictions of any wholly unissued series of PreferredStock, and toestablishfrom
timeto timethenumber
ofsharesconstituting any suchseriesoranyofthem;
andtoincreaseordecreasethe
numberofshares ofanyseriessubsequent 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 shallbe decreased in accordance with the foregoing sentence, the shares
constituting such decrease shall resume the status that they had prior to the adoptionof the resolution originally fixingthe number of sharesof suchseries.
  1




V.




Forthe
management of the business andfor the conduct of
theaffairs 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.
 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 shallconstitute the wholeBoard ofDirectors shall befixed exclusivelyby one or more resolutions adopted by the Board of
Directors.
  2.Subjecttothe
rights of the holdersof
any seriesofPreferredStocktoelect
additional directors under specifiedcircumstances,
the directors shall be divided intothreeclassesdesignatedasClass
I, ClassIIand
Class III,respectively.Directorsshall
be assignedtoeachclass
inaccordance
witharesolutionor
resolutionsadopted
by theBoardof
Directors. At the first annual meeting ofstockholders
following the adoption andfiling
of this Certificate of Incorporation,
the term of office of theClass
I directors shall expire and Class I directors shall be elected for afull
term of three years. At thesecondannual
meeting ofstockholdersfollowing
the adoption andfiling
of this Certificate ofIncorporation,
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 ofstockholders
followingtheadoption
andfiling
of this Certificate of Incorporation, the tem 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 annualmeeting
of stockholders,directors
shallbeelected
for a full term of three years to succeed the directors of the classwhose
terms expire at such annual meeting.
  Notwithstandingtheforegoing
provisionsof
this Article, eachdirector shall serveuntilhissuccessor
isdulyelected and qualifiedor untilhisdeath,resignation or
removal.No decreasein the number ofdirectors constituting the BoardofDirectors shall shorten the term of any incumbent
director.
  3.      Subject to the rights of the
holders of any series of Preferred Stock, no director shall be removed without
cause. Subject to any limitations imposed by law,  the Board of Directors or any individual
director may be removed from office at any timewith cause by the
affirmative vote of the holders of a majority of the voting power of all the
then-outstanding shares of voting stock of the corporation entitled to
vote at anelection of directors (the "Voting
Stock").
  2




4.     
Subject to the rightsof the
holders of any series of Preferred Stock,any
vacancies ontheBoard of
Directorsresulting
from death, resignation,disqualification, removal or other causes and
any newlycreateddirectorships resulting from any increase in the number ofdirectors, shall, unless the Board
of Directors determines by resolution that any such vacancies or newly created
directorships shall befilled 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 havebeen elected and qualified.
  B.
  1.Subject to
paragraph(h) of Section 43 of theBy-laws, the By-laws may be altered or
amended or new By-laws adopted by the affirmative vote of at leastsixty-six and two-thirdspercent(66-2/3%) of the voting powerofall ofthe then-outstanding shares of the
Voting Stock. TheBoard of
Directors shall also have the
powertoadopt,
amend or repeal By-laws.
  2.      The
directors of the corporation need
not be elected by written ballotunless the By-laws so
provide.
  3.      No action
shall be taken by the stockholders of the corporation exceptat an annual or special meeting of stockholders called in accordance with
the By-laws, and
no action shall betaken by the stockholders by written
consent.
  4.      Advance
notice of stockholder nominationsfor the electionof directors and of business to be
brought by stockholdersbefore any meeting of the stockholdersofthe corporationshall hegiven in
themannerprovided
in the By-laws ofthe
corporation.
  VI.
  A.     
A director of the corporation shall not be personally liable to the corporation
or its stockholders for monetary damages for any breach of fiduciary duty as a
director, except for liability (i) for any breach of the director’s
duty of loyalty to the corporation
or its stockholders, (ii) for acts or omissions not in good faith or whichinvolve intentional
misconduct or a knowing violation of law, (iii) under Section 174 ofthe
Delaware General Corporation Law, or (iv) for any transaction from which the
director derived an improper personal benefit. If the Delaware General CorporationLaw is amended after approval by the stockholdersof this Article to authorize corporate action further eliminating or
limiting the personal liability of directors, then the liability of a director
shall be eliminated or limited to the
fullestextent permitted by the Delaware GeneralCorporationLaw, as
soamended.
  3




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.
  VII.
  A.      The corporationreserves 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 providedin paragraphB
of this Article VII, and all rights conferred upon the stockholdersherein are
granted subject to this reservation.
  B.      Notwithstandingany
otherprovisions ofthis
Certificateof Incorporationorany
provision oflaw which might
otherwise permit a lesservoteornovote,but
inaddition to any
affirmative vote of the holders of any particular class or series of the Voting
Stook required by law, this Certificate of Incorporation orany Preferred StockDesignation, the
affirmative vote of the holders of at least sixty-six and two-thirds
percent(66-2/3%)
ofthevotingpower
ofallofthethen-outstanding
shares of the Voting Stock,voting
togetherasasingleclass,
shallberequiredto
alter,amendorrepeal
ArticlesV, VIand
VII.
  4




CERTIFICATE
OF AMENDMENT
 OF
 AMENDED
AND RESTATED CERTIFICATE OF INCORPORATION
 OF
 GENE
LOGIC INC.
  Gene Logic
Inc. (the "Corporation"), a corporation duly organized and existing under the
General Corporation Law of the State of Delaware (the " DGCL"), does, by its
Treasurer, hereby certify that:
  1.        The
name of the Corporation is Gene Logic Inc.
  2.        The
Amended and Restated Certificate of Incorporation of the Corporation (the
"Certificate of Incorporation") was filed on November 26, 1997 under the name
Gene Logic Inc.
  3.        Pursuant
to Section 242 of the DGCL, at a meeting duly convened and held on October 23,
2007, the Board of Directors of the Corporation found that the following
proposed amendment of the Certificate of Incorporation was advisable and
directed that such proposed amendment be submitted for consideration and action
thereon by the stockholders of the Corporation at a special meeting of
stockholders.
  Article 1
of the Certificate of Incorporation is amended in its entirety to read as
follows:
 "I
 The name
of this Corporation is Ore Pharmaceuticals Inc."
  4.        Pursuant
to Section 242 of the DGCL, the holders of a majority of the issued and
outstanding shares of capital stock of the Corporation entitled to vote on the
matter, including the holders of a majority of the issued and outstanding shares
of each class entitled to vote on the matter, voted in favor of, approved and
adopted the foregoing proposed amendment of the Certificate of Incorporation at
a special meeting of the Corporation convened and held on December 10,
2007.
  5.        The
foregoing amendment of the Certificate of Incorporation, was duly adopted in
accordance with the provisions of Section 242 of the DGCL.
  6.        This
Certificate of Amendment shall become effective at 5:00 PM Eastern Time on
December 14, 2007 for accounting purposes.
  The
Corporation has caused this Certificate of Amendment to be signed and executed
in its corporate name by its Treasurer and attested to by its Secretary, who
declare, affirm, acknowledge and certify, under the penalties of perjury, that
this is their free act and deed and that the facts stated herein are true as of
the 18th day of December, 2007.
  ATTEST
                      GENE
      LOGIC INC.,A
      Delaware corporationBy:
      /s/ F. Dudley
      Staples
                      By:
      /s/ Philip L.
      Rohrer, Jr.F.
      Dudley Staples, Corporate Secretary
                      Philip
      L. Rohrer, Jr.,
Treasurer









CERTIFICATE
OF AMENDMENT
  OF
  AMENDED
AND RESTATED CERTIFICATE OF INCORPORATION
  OF
  ORE
PHARMACEUTICALS INC.
  Ore
Pharmaceuticals Inc. (the "Corporation"), a corporation duly organized and
existing under the General Corporation Law of the State of Delaware (the
"DGCL"), does hereby certify that:
  1.                      The
name of the Corporation is Ore Pharmaceuticals Inc.
  2.                      The
Amended and Restated Certificate of Incorporation was filed with the Secretary
of State of the State of Delaware (the "Secretary") on November 26, 1997 under
the name Gene Logic Inc. A Certificate of Ownership and Merger was filed with
the Secretary on October 31, 2001 and a Certificate of Amendment was so filed on
December 18, 2007.
  3.                      Pursuant
to Section 242 of the DGCL, at a meeting duly convened and held on March 21,
2008, the Board of Directors of the Corporation found that the following
proposed amendment of the Amended and Restated Certificate of Incorporation of
the Corporation, as amended, was advisable and directed that such proposed
amendment be submitted for consideration and action thereon by the stockholders
of the Corporation at the 2008 annual meeting of stockholders called pursuant to
notice given in accordance with Section 222 of the DGCL:
  The first
paragraph of Article IV, Section A of the Amended and Restated Certificate of
Incorporation of the Corporation, as amended, shall be deleted in its entirety
and the following two paragraphs shall be substituted therefor:
  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 Seventy Million (70,000,000)
shares. Sixty Million (60,000,000) shares shall be common stock, each having a
par value of one cent ($.01). Ten Million (10,000,000) shares shall be Preferred
Stock, each having par value of one cent ($.01).
  At the
time that this Certificate of Amendment becomes effective pursuant to the DGCL
(the "Effective Time"), each five (5) shares of the Corporation's Common Stock
then issued and outstanding (the "Old Common Stock") shall, automatically and
without any action on the part of the respective holders thereof, be combined,
converted and changed into one (1) share of Common Stock of the Corporation;
provided, however, that the Corporation shall issue no fractional shares as a
result of the actions set forth herein but shall instead round up to the nearest
whole share such that holders who would otherwise be entitled to receive a
fractional share of Common Stock as a result of the Reverse Stock Split will
receive an additional fractional share of Common Stock in order to bring the
number of shares held by the stockholder to a whole number of shares and,
provided further, that neither the number of shares of Common Stock authorized
pursuant to the first sentence of this Article Fourth nor the par value of such
shares shall be altered. Each stock certificate that, immediately prior to the
Effective Time, represented shares of Old Common Stock then outstanding shall,
from and after the Effective Time, automatically and without the necessity of
presenting the same for exchange, represent that number of whole shares of
Common Stock outstanding after the Effective Time into which the shares of Old
Common Stock represented by such certificate shall have been reclassified;
provided, however, that each holder of record of a certificate that represented shares of
Old Common Stock shall receive, upon surrender of such certificate, a new
certificate representing the number of whole shares of Common Stock into which the
shares of Old Common Stock represented by such certificate shall have been
reclassified.
  4.                     Pursuant
to Section 242 of the DGCL, the holders of a majority of the issued and
outstanding shares of capital stock of the Corporation entitled to vote on the
matter voted in favor of, approved
and adopted, the foregoing proposed amendment of the Amended and Restated
Certificate of Incorporation
of the Corporation, as amended, at the 2008 annual meeting of stockholders duly
convened and held on May 23, 2008.
  5.                     The
foregoing amendment of the Amended and Restated Certificate of Incorporation of
the Corporation, as amended, was duly adopted in accordance with the provisions
of Sections 141 and 242 of the General Corporation Law of the State of
Delaware.
  6.                     This
Certificate of Amendment shall become effective at 5:00 p.m. Eastern Time on May
23, 2008.
  The
Corporation has caused this Certificate of Amendment to be signed and executed
in its corporate name by its Treasurer and attested to by its Secretary, who
declare, affirm, acknowledge and certify,
under the penalties of perjury, that this is their free act and deed and that
the facts stated herein are true as of the 23rd day of May, 2008.
  ATTEST
              ORE
      PHARMACEUTICALS INC,a Delaware
      corporationBy:
      /s/ F. Dudley
      Staples
              By:
      /s/ Philip L.
      Rohrer, Jr.F.
      Dudley Staples, Corporate Secretary
              Philip
      L. Rohrer, Jr., Treasurer