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                                                                     EXHIBIT 3.5

                           CERTIFICATE OF DESIGNATION
                                     OF THE
                      SERIES B CONVERTIBLE PREFERRED STOCK
                           (PAR VALUE $.001 PER SHARE)
                                       OF
                                CYTEL CORPORATION

                                ----------------

                         PURSUANT TO SECTION 151 OF THE
                GENERAL CORPORATION LAW OF THE STATE OF DELAWARE

                                ----------------


        CYTEL CORPORATION, a company organized and existing under the General
Corporation Law of the State of Delaware (the "Company"), in accordance with the
provisions of Section 103 thereof, and pursuant to Section 151 thereof, DOES
HEREBY CERTIFY:

        That the Certificate of Incorporation of the Company (the "Certificate
of Incorporation") authorizes the creation of up to 10,000,000 shares of the
Company's preferred stock, par value $.001 per share (such preferred stock,
together with all other preferred stock of the Company the creation of which is
in the future authorized by the Certificate of Incorporation, referred to herein
as the "Preferred Stock"); and

        That pursuant to the authority conferred upon the Board of Directors
(the "Board") by the Certificate of Incorporation of the Company, the Board on
February 20, 1998, approved the creation, issuance and the voting powers of
shares of Preferred Stock to be issued in one Series and adopted the following
resolution creating a series of 659,898 shares of Preferred Stock designated as
set forth below:

        RESOLVED, that pursuant to the authority expressly granted to and vested
in the Board by provisions of the Certificate of Incorporation of the Company
and the General Corporation Law of the State of Delaware, the issuance of a
series of Preferred Stock, which shall consist of 659,898 shares of the
10,000,000 shares of Preferred Stock which the Company now has authority to
issue, be, and the same hereby is, authorized, and the Board hereby fixes the
powers, designations, preferences and relative participating, optional or other
special rights, and the qualifications, limitations or restrictions thereof, of
the shares of such series (in addition to the powers, designations, preferences
and relative participating, optional or other special rights, and the
qualifications, limitations or restrictions thereof, set forth in the
Certificate of Incorporation which may be applicable to the Preferred Stock)
authorized by this resolution as follows:

SECTION 1. DESIGNATION OF SERIES B PREFERRED STOCK. The designation of such
series of Preferred Stock authorized by this resolution shall be Series B
Convertible Preferred Stock (the "Series B Preferred"). The Series B Preferred
is issuable solely in whole shares that shall entitle the holder thereof to
exercise the voting rights, to participate in the distributions and to have the
benefit of all other rights of holders of Series B Preferred, as set forth
herein and in the Certificate of Incorporation.


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SECTION 2. DIVIDEND RIGHTS OF SERIES B PREFERRED. So long as any shares of
Series B Preferred shall be outstanding, no dividend, whether in cash or
property, shall be paid or declared nor shall any other distribution be made, on
any Common Stock (other than any dividend or distribution payable solely in
Common Stock of the Company), unless a dividend is paid with respect to all
outstanding shares of Series B Preferred in an amount per share (on an
as-if-converted to Common Stock basis) equal to the amount paid or set aside for
each share of Common Stock.

SECTION 3.     LIQUIDATION PREFERENCE.

        (a) SERIES B PREFERRED. In the event of any voluntary or involuntary
liquidation, dissolution or winding up of the Company, the holders of Series B
Preferred then outstanding shall be entitled to be paid, pro rata, out of the
assets of the Company available for distribution to its stockholders, whether
from capital, surplus or earnings, before any payment shall be made in respect
of any other class or series of stock ranking junior to the Series B Preferred,
an amount equal to $5.91 per share (the "Series B Original Issue Price") (as
adjusted for any combinations, consolidations, stock distributions, stock
dividends or other recapitalizations with respect to such shares) plus any
declared but unpaid dividends on such shares; provided that the total amounts to
which the holders of Series B Preferred are entitled under this provision shall
not exceed the value of the outstanding securities of Epimmune Inc. ("Epimmune")
then owned by the Company. If, upon liquidation, dissolution or winding up of
the Company, the assets of the Company available for distribution to its
stockholders shall be insufficient to pay the holders of the Series B Preferred
the full amounts to which they shall be entitled as set forth above, then the
entire assets of the Company legally available for distribution shall be
distributed pro rata among the holders of the Series B Preferred in proportion
to the preferential amount each such holder would otherwise be entitled to
receive. After setting apart or paying in full the preferential amounts due the
holders of the Series B Preferred, the holders of the Series B Preferred will
not be entitled to any further participation in any distribution of the assets
of the Company, and the entire remaining assets of the Company legally available
for distribution, if any, shall be distributed among the holders of Common Stock
in proportion to the shares of Common Stock then held by them.

        (b) MERGERS, CONSOLIDATIONS NOT DEEMED LIQUIDATIONS. The merger or
consolidation of the Company into or with another company in which the Company
is not the surviving entity or in which the stockholders of this Company
immediately prior to such event shall own less than a majority of the voting
securities of the surviving company, or the sale, transfer, or lease (but not
including a transfer or lease by pledge or mortgage to a bona fide lender) of
all or substantially all of the assets of the Company, shall not be deemed a
liquidation, dissolution or winding up of the Company as those terms are used in
this Section 3.

SECTION 4.     CONVERSION PRIVILEGES.

        (a) RIGHTS OF CONVERSION. Subject to the other provisions of this
Certificate of Designation, each share of Series B Preferred shall be
convertible, without payment of any additional consideration by the holder
thereof and at the option of such holder, into such number of fully paid and
nonassessable shares of Common Stock as is determined by dividing the Series B
Original Issue Price by the Series B Conversion Price (as defined below) in
effect at the time

                                       2.

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of conversion, at any time and from time to time after February 27, 2001, at the
office of the Company or any transfer agent for such stock; provided that the
average of the closing prices per share of the Common Stock on the Nasdaq
National Market (or any other national securities exchange on which the Common
Stock is then traded) for the 10 consecutive trading days ending on the trading
date immediately preceding the date of conversion is $5.00 or greater. The price
at which shares of Common Stock shall be deliverable upon conversion of Series B
Preferred (the "Series B Conversion Price") shall initially equal $7.50 per
share, subject to adjustment as set forth below.

        (b) MECHANICS OF CONVERSION. Before any holder of Series B Preferred
shall be entitled to convert the same into shares of Common Stock pursuant to
Section 4(a) hereof, such holder shall surrender the certificate or certificates
thereof, duly endorsed, at the office of the Company or of any transfer agent
for such stock, and shall give written notice to the Company at such office that
such holder elects to convert the same and shall state therein the name or names
in which such holder wishes the certificate or certificates for shares of Common
Stock to be issued. The Company shall, as soon as practicable thereafter, issue
and deliver at such office to such holder of Series B Preferred or its nominee
or nominees, a certificate or certificates for the number of shares of Common
Stock to which such holder shall be entitled as aforesaid, together with cash in
lieu of any fractional shares. Such conversion shall be deemed to have been made
immediately prior to the close of business on the date of surrender of the
shares of Series B Preferred to be converted. The person or persons entitled to
receive the shares of Common Stock issuable upon such conversion shall be
treated for all purposes as the record holder or holders of such shares of
Common Stock on such date.

        (c) ADJUSTMENT FOR STOCK SPLITS AND COMBINATIONS. If the Company shall
at any time or from time to time after the date that the first share of Series B
Preferred is issued (the "Original Issue Date") effect a subdivision of the
outstanding Common Stock without a corresponding subdivision of the Preferred
Stock, the Series B Conversion Price in effect immediately before that
subdivision shall be proportionately decreased. Conversely, if the Company shall
at any time or from time to time after the Original Issue Date combine the
outstanding shares of Common Stock into a smaller number of shares without a
corresponding combination of the Preferred Stock, the Series B Conversion Price
in effect immediately before the combination shall be proportionately increased.
Any adjustment under this Section 4(c) shall become effective at the close of
business on the date the subdivision or combination becomes effective.

        (d) ADJUSTMENT FOR COMMON STOCK DIVIDENDS AND DISTRIBUTIONS. If the
Company at any time or from time to time after the Original Issue Date makes, or
fixes a record date for the determination of holders of Common Stock entitled to
receive, a dividend or other distribution payable in additional shares of Common
Stock, in each such event the Series B Conversion Price that is then in effect
shall be decreased as of the time of such issuance or, in the event such record
date is fixed, as of the close of business on such record date, by multiplying
the Series B Conversion Price then in effect by a fraction (i) the numerator of
which is the total number of shares of Common Stock issued and outstanding
immediately prior to the time of such issuance or the close of business on such
record date, and (ii) the denominator of which is the total number of shares of
Common Stock issued and outstanding immediately prior to the time of such
issuance or the close of business on such record date plus the number of shares
of Common

                                       3.

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Stock issuable in payment of such dividend or distribution; provided, however,
that if such record date is fixed and such dividend is not fully paid or if such
distribution is not fully made on the date fixed therefor, the Series B
Conversion Price shall be recomputed accordingly as of the close of business on
such record date and thereafter the Series B Conversion Price shall be adjusted
pursuant to this Section 4(d) to reflect the actual payment of such dividend or
distribution.

        (e) ADJUSTMENTS FOR OTHER DIVIDENDS AND DISTRIBUTIONS. If the Company at
any time or from time to time after the Original Issue Date makes, or fixes a
record date for the determination of holders of Common Stock entitled to
receive, a dividend or other distribution payable in securities of the Company
other than shares of Common Stock, in each such event provision shall be made so
that the holders of the Series B Preferred shall receive upon conversion
thereof, in addition to the number of shares of Common Stock receivable
thereupon, the amount of other securities of the Company which they would have
received had their Series B Preferred been converted into Common Stock on the
date of such event and had they thereafter, during the period from the date of
such event to and including the conversion date, retained such securities
receivable by them as aforesaid during such period, subject to all other
adjustments called for during such period under this Section 4 with respect to
the rights of the holders of the Series B Preferred or with respect to such
other securities by their terms.

        (f) ADJUSTMENT FOR RECLASSIFICATION, EXCHANGE AND SUBSTITUTION. If at
any time or from time to time after the Original Issue Date, the Common Stock
issuable upon the conversion of the Series B Preferred is changed into the same
or a different number of shares of any class or classes of stock, whether by
recapitalization, reclassification or otherwise (other than a subdivision or
combination of shares or stock dividend or a reorganization, merger,
consolidation or sale of assets provided for elsewhere in Section 2 or this
Section 4), in any such event each holder of Series B Preferred shall have the
right thereafter to convert such stock into the kind and amount of stock and
other securities and property receivable upon such recapitalization,
reclassification or other change by holders of the maximum number of shares of
Common Stock into which such shares of Series B Preferred could have been
converted immediately prior to such recapitalization, reclassification or
change, all subject to further adjustment as provided herein or with respect to
such other securities or property by the terms thereof.

        (g) REORGANIZATIONS, MERGERS, CONSOLIDATIONS OR SALES OF ASSETS. If at
any time or from time to time after the Original Issue Date, there is a capital
reorganization of the Common Stock (other than a subdivision or combination of
shares or stock dividend or a reorganization, merger, consolidation or sale of
assets provided for elsewhere in Section 2 or this Section 4), as a part of such
capital reorganization, provision shall be made so that the holders of the
Series B Preferred shall thereafter be entitled to receive upon conversion of
the Series B Preferred the number of shares of stock or other securities or
property of the Company to which a holder of the number of shares of Common
Stock deliverable upon conversion would have been entitled on such capital
reorganization, subject to adjustment in respect of such stock or securities by
the terms thereof. In any such case, appropriate adjustment shall be made in the
application of the provisions of this Section 4 with respect to the rights of
the holders of Series B Preferred after the capital reorganization to the end
that the provisions of this Section 4 (including adjustment of the Series B
Conversion Price then in effect and the number of shares issuable upon
conversion

                                       4.

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of the Series B Preferred) shall be applicable after that event and be as nearly
equivalent as practicable.

        (h) CERTIFICATES AS TO ADJUSTMENTS. Upon the occurrence of each
adjustment or readjustment of the number of shares of Common Stock issuable upon
conversion of a share of Series B Preferred pursuant to this Section 4, the
Company at its expense shall promptly compute such adjustment or readjustment in
accordance with the terms hereof and prepare and furnish to each holder of
Series B Preferred a certificate setting forth such adjustment or readjustment
and showing in detail the facts upon which such adjustment or readjustment is
based. The Company shall, upon the written request at any time of any holder of
Series B Preferred, furnish or cause to be furnished to such holder a like
certificate prepared by the Company setting forth (i) such adjustments and
readjustments, (ii) the Series B Conversion Price at the time in effect, and
(iii) the number of shares of Common Stock and the amount, if any, of other
property which at the time would be received upon the conversion of the Series B
Preferred.

        (i) NOTICES OF RECORD DATE. In the event of any taking by the Company of
a record of the holders of any class of securities for the purpose of
determining the holders thereof who are entitled to receive any dividend (other
than a cash dividend) or other distribution, any security or right convertible
into or entitling the holder thereof to receive additional shares of Common
Stock, or any right to subscribe for, purchase or otherwise acquire any shares
of stock of any class or any other securities or property, or to receive any
other right, the Company shall mail to each holder of Series B Preferred at
least 10 days prior to the date specified therein, a notice specifying the date
on which any such record is to be taken for the purpose of such dividend,
distribution, security or right, and the amount and character of such dividend,
distribution, security or right.

        (j) ISSUE TAXES. The holders of Series B Preferred shall pay any and all
issue, transfer and other taxes that may be payable in respect of any issue or
delivery of shares of Common Stock on conversion of shares of Series B Preferred
pursuant hereto.

        (k) RESERVATION OF STOCK ISSUABLE UPON CONVERSION. The Company shall at
all times reserve and keep available out of its authorized but unissued shares
of Common Stock, solely for the purpose of effecting the conversion of the
shares of the Series B Preferred, such number of its shares of Common Stock as
shall from time to time be sufficient to effect the conversion of all
outstanding shares of the Series B Preferred; and if at any time the number of
authorized but unissued shares of Common Stock shall not be sufficient to effect
the conversion of all then outstanding shares of the Series B Preferred, the
Company will take such corporate action as may, in the opinion of its counsel,
be necessary to increase its authorized but unissued shares of Common Stock to
such number of shares as shall be sufficient for such purpose, including,
without limitation, engaging in best efforts to obtain the requisite stockholder
approval of any necessary amendment to the Certificate of Incorporation. All
shares of Common Stock which are issuable upon such conversion shall, when
issued, be duly and legally issued, fully paid and nonassessable and free of all
taxes, liens and charges.

        (l) FRACTIONAL SHARES. No fractional share shall be issued upon the
conversion of any share or shares of Series B Preferred. All shares of Common
Stock (including fractions thereof) issuable upon conversion of more than one
share of Series B Preferred by a holder

                                       5.

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thereof shall be aggregated for purposes of determining whether the conversion
would result in the issuance of any fractional share. If, after the
aforementioned aggregation, the conversion would result in the issuance of a
fraction of a share of Common Stock, the Company shall, in lieu of issuing any
fractional share, pay the holder otherwise entitled to such fraction a sum in
cash equal to the fair market value of such fraction on the date of conversion
(as determined in good faith by the Board).

        (m) NOTICES. Any notice required by the provisions of this Section 4
shall be in writing and shall be deemed effectively given: (i) upon personal
delivery to the party to be notified, (ii) when sent by confirmed telex or
facsimile if sent during normal business hours of the recipient; if not, then on
the next business day, (iii) five days after having been sent by registered or
certified mail, return receipt requested, postage prepaid, or (iv) one day after
deposit with a nationally recognized overnight courier, specifying next day
delivery, with written verification of receipt. All notices shall be addressed
to each holder of record at the address of such holder appearing on the books of
the Company.

SECTION 5.     VOTING RIGHTS.

        (a) Except as provided in this Section 5 or as otherwise from time to
time required by law, the Series B Preferred shall vote together with the Common
Stock as a single class. The holder of each share of Series B Preferred shall be
entitled to that number of votes equal to the number of shares of Common Stock
into which such share would then be converted upon the application of Section
4(a) above and shall be entitled to notice of all stockholders' meetings in
accordance with the By-laws of the Company. The foregoing voting provisions
shall not apply if, at or prior to the time when the act with respect to which
such vote would otherwise be required shall be effected, all outstanding shares
of Series B Preferred shall have been converted into Common Stock.

        (b) Notwithstanding anything contained in Section 5(a) to the contrary,
if any shares of Series B Preferred held by G.D. Searle & Co. (the "Shares")
when aggregated with all other shares of voting capital stock of the Company or
its subsidiary Epimmune Inc. ("Epimmune") held by G.D. Searle & Co. would (if
not for this Section 5(b)) entitle G.D. Searle & Co. to vote more than 19.4% of
the outstanding common stock of Epimmune (assuming the conversion of all such
shares of such capital stock into common stock of Epimmune pursuant to the
respective terms thereof), then any such Shares in excess of 19.4% shall be
entitled to no vote.

        In facilitation of the foregoing voting restriction, the following
formula shall be applied to determine the number of shares of Series B Preferred
held by Searle which shall be entitled to a vote:

        X = PC + (((CE*SC-.194*TC*TE+SE*TC)/(.194*TE-SE-CE)) x R)

where:

        TE =   total number of shares of Epimmune common stock (on an
               as-converted basis) outstanding

                                       6.

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        CE =   number of shares of Epimmune common stock (on an as-converted
               basis) owned by Cytel

        SE =   number of shares of Epimmune common stock (on an as-converted
               basis) owned by Searle

        TC =   total number of shares of Cytel Common Stock (on an as-converted
               basis) outstanding

        SC =   total number of shares of Cytel Common Stock (on an as-converted
               basis) owned by Searle

        PC =   total number of shares of Cytel Series B Preferred owned by
               Searle

        X  =   number of shares of Cytel Series B Preferred Stock owned by
               Searle that will have voting rights, where 0<X<PC

        R =    Series B Conversion Price divided by the Series B Original Issue
               Price


                                       7.


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        IN WITNESS WHEREOF, Cytel Corporation has caused this Certificate to be
signed by its President and Chief Executive Officer, and attested by its
Secretary, this 26th day of February, 1998.

                                            CYTEL CORPORATION



                                            By: /s/ VIRGIL THOMPSON
                                               ---------------------------------
                                               Virgil Thompson,
                                               President and Chief Executive
                                               Officer


Attest:


/s/ DEBORAH SCHUEREN
------------------------------
Deborah Schueren,
Secretary


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                            CERTIFICATE OF CORRECTION
                                       OF
                        CERTIFICATE OF DESIGNATION OF THE
                      SERIES B CONVERTIBLE PREFERRED STOCK
                                       OF
                                CYTEL CORPORATION

It is hereby certified that:

     1.   The name of the corporation is Cytel Corporation (the "Corporation").

     2.   The Certificate of Designation of the Series B Convertible Preferred
          Stock, which was filed with the Secretary of State of the State of
          Delaware on February 26, 1998 (the "Certificate"), is hereby
          corrected.

     3.   The inaccuracy or defect of said Certificate of Incorporation to be
          corrected is as follows:

          The stated par value per share of the Series B Convertible Preferred
          Stock indicated in the title of the Certificate as $.001 per share
          should be corrected and restated to read $.01 per share. The stated
          par value per share of the Corporation's preferred stock indicated in
          the second paragraph of the Certificate as $.001 per share should be
          corrected and restated to read $.01 per share.

          IN WITNESS WHEREOF, Cytel Corporation has caused this Certificate to
be signed by Edward C. Hall, Chief Financial Officer and Secretary.


                                        CYTEL CORPORATION


                                        By:  /s/Edward C. Hall
                                           --------------------------------
                                           Edward C. Hall
                                           Chief Financial Officer and
                                           Secretary