<PAGE>   1
                                                                        EX-10.10

                                    AGREEMENT

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

         THIS AGREEMENT, made as of December 1, 1998, between Ophidian 
Pharmaceuticals, Inc., a Wisconsin corporation, (the "Employer"), and Dr. F.
Michael Hoffmann, (the "Employee");

                                    RECITALS

         The Employer is engaged in the business of the creation and marketing
of pharmaceutical products, and has developed methods, techniques, concepts and
systems for this business which are unique and distinctive.

         The Employer has employed Employee as its Vice President of Genetics
Technology Programs on a full-time basis and Employee desires to change the
status of his employment to part-time. Employee will continue in the position of
Vice President of Genetics Technology Programs. In the course of his employment,
Employer will continue to give him important information about its business
methods, techniques, concepts and systems, and to have him meet and deal with
customers of the Employer, obtain or have access to information about them, and
develop special relationships with them.

         The Employer and the Employee desire to enter into an Agreement with
respect to the continued employment of the Employee by the Employer pursuant to
the terms and conditions hereinafter set forth.

         NOW, THEREFORE, in consideration of the mutual promises of the parties
hereinafter set forth, the parties agree as follows:

         1.   Employment. The employment agreement between Employer and Employee
dated August 1, 1997 for his full-time employment ("Former Agreement") is
terminated as of the effective date of this Agreement and the provisions of the
Former Agreement are null and void. The Employer agrees to continue to employ
the Employee, and the Employee agrees to continue to serve in the employment of
the Employer, upon the terms and conditions hereinafter set forth. It is
understood by the parties that Employee will be, during the term of this
Agreement, employed as a member of the academic faculty of the University of
Wisconsin-Madison and, as such, subject to restrictions placed on faculty
members regarding their outside activities.

         2.   Duties. The Employee shall serve as Vice President of Genetics 
Technology of the Employer. The Employee will have responsibility for developing
business opportunities for genetics technology, specifically in the area of
TGF-beta (as described in the Host Response Program in the Company's Prospectus
dated May 7, 1998) for the Employer and for various administrative and support
functions such as coordinating contact with consultants, corporate partners, and
financial organizations, and coordinating internal laboratory activities with
program objectives. He will participate in the planning and execution of the
Employer's 




<PAGE>   2

strategic development activities in conjunction with research and development
and operations management, advisors and the Board of Directors. He will interact
with executive management in biotechnology and pharmaceutical companies to
establish strategic partnerships. The Employee will report to the President of
the Employer. The Employee shall devote approximately 20% of his professional
attention and energy to the specified business and affairs of the Employer
effort (subject to the limitations set forth in paragraph 1, above) and shall
use his best efforts to promote the interests of the Employer.

         3.   Term. The term of employment of the Employee hereunder shall 
commence as of the effective date of this Agreement, and shall continue for a
period of one (1) year. The Agreement may be extended for additional time
periods subject to written agreement of the parties hereto.

         4.   Compensation. The Employer shall pay to the Employee, and the 
Employee shall accept in full payment for his services to the Employer, such
base compensation. Additional incentive compensation and bonus compensation may
also be paid by the Employer upon completion of specified performance
objectives: certain performance objectives and related bonus compensation are
described in the Employee's letter to Employee dated of even date herewith
("Letter Agreement"). Notwithstanding the foregoing, the gross amount of such
annual compensation (subject to normal payroll deductions) shall be fifty
thousand dollars ($50,000) paid in equal installments twice a month.

         5.   Vacation, Sick Leave and Other Benefits. The Employee shall not be
entitled to any paid vacation days and sick leave or other benefits except as
stipulated in this Agreement because Employer's benefit policy stipulates that
employees who do not work at least 20 hours per week for an undefined period of
time are not eligible for paid vacation days, sick leave or other benefits.

         6.   Expenses. The Employer shall reimburse the Employee for any out of
pocket expenses reasonably incurred by the Employee in the furtherance of the
business of the Employer, upon submission of a satisfactory accounting by the
Employee to the Employer.

         7.   Intellectual Property, Trade Secrets and Competitive Activities. 
The provisions of the Proprietary Information and Inventions Agreement between
the parties dated December 1, 1998, a copy of which is attached hereto as
Addendum A, are incorporated herein by reference.

         8.   Termination

              (a)  Termination by Employer for Cause. The Employer may terminate
this Agreement and the Employee's employment effective immediately upon written
notice to the Employee for any of the following reasons:

                   (i)   Commission by the Employee of any act of intentional 
dishonesty material to the Employer.


                                       2
<PAGE>   3

                   (ii)  Conviction of the Employee of an offense involving 
moral turpitude constituting a felony criminal offense under federal, state or
local laws by the Employee.

                   (iii) Prolonged failure of the Employee to devote his
efforts to performance of his duties, subject to the limitations of time as set
forth above, for the Employer or the incompetent performance of such duties.

         Upon such termination as set forth in the paragraph, the Employer shall
have no further obligations to the Employee except to pay the Employee any
unpaid base compensation, incentive compensation, and bonus compensation payable
hereunder with respect to the period prior to the effective date of termination
and reimbursement of expenses to which the Employee is entitled under Paragraph
6 hereof in respect to periods prior to the termination date. The Employee shall
have no further obligations to the Employer, except as provided in Paragraph 7
hereof.

         (b)  Termination by Employer Because of Death . This Agreement and the
Employee's employment shall be terminated immediately upon the death of the
Employee. Upon termination due to the Employee's death, the personal
representative of the Employee's estate or his legal representative, as
appropriate, shall have no further obligation to the Employer except as provided
in Paragraph 7 hereof, and the Employer shall have no further obligation to the
Employee's estate of the Employee, except to pay the Employee's estate any
unpaid base compensation, incentive compensation, and bonus compensation payable
hereunder with respect to the period prior to the effective date of termination
and reimbursement of expenses to which the Employee is entitled under Paragraph
6 hereof in respect to periods prior to the termination date.

         (c)  Termination Without Cause. It is understood and agreed by the
parties hereto that the Employee is an employee-at-will and may be terminated by
the Employer at any time for any reason or no reason. Upon termination as set
forth in this paragraph, the Employer shall have no further obligations to the
Employee except to pay the Employee any unpaid base compensation, incentive
compensation, and bonus compensation payable hereunder with respect to the
period prior to the effective date of termination and reimbursement of expenses
to which the Employee is entitled under Paragraph 6 hereof in respect to periods
prior to the termination date. In addition, upon such termination, the
Employee's right to exercise any unvested options for the purchase of Employer
Stock under any stock option plans of the Employer, shall be accelerated so as
to enable the Employee to fully exercise the options granted under such
agreements The Employee shall have no further obligations to the Employer,
except as provided in Paragraph 7 hereof.

         (d)  Termination by Employee. The Employee may, upon thirty (30) days
advance written notice to the Employer, terminate this Agreement. If Employee
terminates this Agreement because of a change in control of the Employer (as
defined below) then Employee's right to exercise any unvested stock options for
the purchase of any Employer Stock under any stock option plan of the Employer,
shall be accelerated so as to enable the Employee to fully 




                                       3
<PAGE>   4

exercise the options granted under such agreements. A change of control of the
Employer shall be deemed to occur if: (i) securities of the Employer
representing twenty-five (25%) or more of the combined voting power of the
Employer's then outstanding voting securities are acquired pursuant to a tender
offer or an exchange offer; (ii) the shareholders of the Employer approve a
merger, consolidation, or reorganization of the Employer with any other
corporation as a result of which less than seventy-five (75%) of the outstanding
voting securities of the surviving or resulting entities are owned by the former
shareholders of the Employer other than a shareholder who is an affiliate or
associate of any party to such consolidation or merger; (iii) the shareholders
of the Employer transfer assets to a corporation or other person which is not a
wholly owned subsidiary of the Employer; or (iv) the Employer acquires, whether
through purchase, merger or otherwise, all or substantially all of the operating
assets or capital stock of another entity and in connection with such
acquisition persons are elected or appointed to the Board of Directors of the
Employer who are not directors immediately prior to such acquisition and such
persons constitute a majority of the Board of Directors after such acquisition.

         9.   Partial Invalidity. The terms and provisions of this Agreement 
shall be deemed severable, and if any term or provision of this Agreement or the
application thereof to any person or circumstances shall to any extent by
invalid or unenforceable, the remainder of this Agreement, or the application of
such term or provision to the persons or circumstances other than those as to
which it is invalid or unenforceable, shall not be affected thereby, and each
term, covenant or condition of this Agreement shall be valid and be enforced to
the fullest extent permitted by law.

         10.  Applicable Law. This Agreement is executed, delivered and intended
to be performed pursuant to the laws of the State of Wisconsin.

         11.  Notices. Any notices required or desired to be given hereunder 
shall be complete if sent by Certified or Registered Mail, Return Receipt
Requested, to his residence in the case of the Employee, and to its principal
office in the case of the Employer, or by personal delivery.

         12.  Entire Agreement. This instrument, the Letter Agreement between 
the parties, and the Proprietary Information and Inventions Agreement dated
December 1, 1998, the provisions of which are incorporated herein by reference,
and any stock option agreements entered into pursuant to any qualified stock
option plans of the Employer, contain the entire agreement of the parties, and
may not be changed orally, but only by an agreement in writing executed by both
parties.

         13.  Successors and Assigns. The Employee shall have no power to 
transfer, assign, anticipate, mortgage, or otherwise encumber in advance any of
the sums payable hereunder, nor shall any of such sums be subject to seizure for
the payment of any debt or judgment or be transferable by operation of law in
the event of bankruptcy or insolvency. This Agreement shall inure to the benefit
of, and shall be binding upon, the successors and assigns of the Employer.


                                       4
<PAGE>   5

         IN WITNESS WHEREOF, the parties hereto have executed this Agreement as
of the date first above written.

EMPLOYER:                                            EMPLOYEE:
OPHIDIAN PHARMACEUTICALS, INC.


By:      /s/ Douglas C. Stafford                     /s/ F. Michael Hoffmann    
         --------------------------                  -----------------------    
         Douglas C. Stafford, Ph.D.                  F. Michael Hoffmann, Ph.D.
         President, Chief Executive Officer          Vice President, Genetic 
                                                       Technology

Attest:  /s/ Susan Maynard          
         --------------------------
         Susan Maynard
         Secretary




                                       5

<PAGE>   6
                                   ADDENDUM A


                             PROPRIETARY INFORMATION
                            AND INVENTIONS AGREEMENT
                                November 1, 1998

         In consideration of my employment relationship with Ophidian 
Pharmaceuticals, Inc. (the "Company"), and the compensation now and hereafter
paid to me, I, F. Michael Hoffmann, Ph.D. ("Employee"), hereby agree as follows:

         1.   Recognition of Company's Rights; Nondisclosure. At all times 
during the term of my employment relationship and for five (5) years thereafter,
I will hold in strictest confidence and will not disclose, use, lecture upon or
publish any of the Company's Inventions (defined below), except as such
disclosure, use or publication may be required in connection with my work for
the Company, or unless an officer of the Company expressly authorizes such in
writing. At all times during the term of my employment relationship and
thereafter, I will hold in strictest confidence and will not disclose, use,
lecture upon or publish any of the Company's Proprietary Information (defined
below), other than Inventions, except as such disclosure, use or publication may
be required in connection with my work for the Company, or unless an officer of
the Company expressly authorizes such in writing. I hereby assign to the Company
any rights I may have or acquire in all Proprietary Information and recognize
that all Proprietary Information shall be the sole property of the Company and
its assigns and the Company and its assigns shall be the sole owner of all
patent rights, copyrights, mask work rights, trade secret rights and all other
rights throughout the world (collectively, "Proprietary Rights") in connection
therewith.

         The term "Proprietary Information" shall mean trade secrets,
confidential knowledge, data or any other proprietary information of the
Company. By way of illustration but not limitation, "Proprietary Information"
includes (a) inventions, compounds, test results, scientific trade secrets,
ideas, processes, formulas, source and object codes, data programs, other works
of authorship, cell lines, know-how, improvements, discoveries, developments,
designs and techniques (hereinafter collectively referred to as "Inventions");
and (b) information regarding plans for research, development, new products,
marketing and selling, business plans, budgets and unpublished financial
statements, licenses, prices and costs, suppliers and customers; and information
regarding the skills and compensation of other employees of the Company. The
term "Proprietary Information" shall not include information that: (i) is or
later becomes available to the public through no breach of this Agreement by the
Employee; (ii) is obtained by the Employee from a third party who had the legal
right to disclose the information to the Employee; (iii) is already in the
possession of the Employee on the date this Agreement becomes effective; or (iv)
is required to be disclosed by law, government regulation, or court order. In


<PAGE>   7

addition, the term "Proprietary Information" shall not include information
generated solely by the Employee unless the information (i) is generated as a
direct result of the performance of employment services under this Agreement and
(ii) is not generated in the course of the Employee's activities as a University
of Wisconsin ("UW") faculty member.

         2.   Third Party Information. I understand, in addition, that the 
Company has received and in the future will receive from third parties
confidential or proprietary information ("Third Party Information") subject to a
duty on the Company's part to maintain the confidentiality of such information
and to use it only for certain limited purposes. During the term of my
employment and thereafter, I will hold Third Party Information in the strictest
confidence and will not disclose (to anyone other than Company personnel who
need to know such information in connection with their work for the Company) or
use, except in connection with my work for the Company, Third Party Information
unless expressly authorized by an officer of the Company in writing. The term
"Third Party Information" shall not include information that: (i) is or later
becomes available to the public through no breach of this Agreement by the
Employee; (ii) is obtained by the Employee directly from a third party who had
the legal right to disclose the information to the Employee; (iii)is already in
the possession of the Employee on the date this Agreement becomes effective; or
(iv) is required to be disclosed by law, government regulation, or court order.

         3.   Employee's Information. The Employee may disclose to the Company
any information that the Employee would normally freely disclose to other
members of the scientific community at large, whether by publication, by
presentation at seminars, or in informal scientific discussions. However, the
Employee shall not disclose to the Company information that is proprietary to UW
and is not generally available to the public other than through formal
technology transfer procedures.

         4.   Assignment of Inventions.

              4.1  Assignment. Subject to paragraph 4.4 below, I hereby assign 
to the Company all my rights, title and interest in and to any and all
Inventions (and all Proprietary Rights with respect thereto) whether or not
patentable or registrable under copyright or similar statutes, made or conceived
or reduced to practice or learned by me, either alone or jointly by others, in
the course of my employment with the Company and not in the course of my
activities as a UW faculty member. Subject to paragraph 4.4 below, I hereby also
assign to the Company all my rights, title and interest in and to any and all
Inventions (and all Proprietary Rights with respect thereto) whether or not
patentable or registrable under copyright or similar statutes, made or conceived
or reduced to practice or learned by me, either alone or jointly with others
following my employment with the Company where such Inventions are based on
Proprietary Information or Third Party Information. Inventions assigned to or as
directed by the Company by this paragraph are 



<PAGE>   8

hereinafter referred to as "Company Inventions." I recognize that this Agreement
does not require assignment of any invention which as developed without using
the Company's equipment, supplies, facilities, or trade secret information
except for those inventions that directly result from any work performed by the
Employee for the Company in accordance with the preceding sentences of this
Paragraph 4.1

              4.2 Government. I also assign to the United States all my rights,
title and interest in and to any and all Inventions, full title to which is
required to be in the United States by a contract between the Company and the
United States or any of its agencies.

              4.3  Works for Hire. I acknowledge that all original works of
authorship which are made by me (solely or jointly with others) within the scope
of the employment relationship and which are protectable by copyright are "works
made for hire," as that term is defined in the United States Copyright Act (17
U.S.C., Section 101).

              4.4  UW Intellectual Property. The Company shall have no rights by
reason of this Agreement in any publication, invention, discovery, improvement
or other intellectual property whatsoever, whether or not publishable,
patentable, or copyrightable, which is developed as a result of a UW program of
research financed, in whole or in part, by funds provided by or under the
control of the federal or state governments. The Company also acknowledges and
agrees that it will enjoy no priority or advantage as a result of this Agreement
is gaining access, whether by license or otherwise, to any proprietary
information or intellectual property that arises from any research undertaken by
the Employee in his capacity as a member of the faculty of UW.

         5.   Enforcement of Proprietary Rights. I will assist the Company in 
every proper way to obtain and from time to time enforce United States and
foreign Proprietary Rights relating to Company Inventions in any and all
countries. To that end I will execute, verify and deliver such documents and
perform such other acts (including appearances as a witness) as the Company may
reasonably request for use in applying for, obtaining, perfecting, evidencing,
sustaining and enforcing such Proprietary Rights and the assignment thereof. In
addition, I will execute, verify and deliver assignments of such Proprietary
Rights to the Company or its designee. My obligation to assist the Company with
respect to Proprietary Rights relating to such Company Inventions in any and all
countries shall continue beyond the termination of my employment, but the
Company shall compensate me at a reasonable rate after my termination for the
time actually spent by me at the Company's request on such assistance.

         In the event the Company is unable for any reason, after reasonable
effort, to secure my signature on any document needed in connection with the
actions specified in the preceding paragraph, I hereby irrevocably designate and
appoint 



<PAGE>   9

the Company and its duly authorized officers and agents as my agent and attorney
in fact, to act for and in my behalf to execute, verity and file any such
documents and to do all other lawfully permitted acts to further the purposes of
the preceding paragraph thereon with the same legal force and effect as if
executed by me. I hereby waive and quitclaim to the Company any and all claims,
of any nature whatsoever, which I now or may hereafter have for infringement of
any Proprietary Rights assigned hereunder to the Company.

         6.   Obligation to Keep Company Informed. During the period of my 
employment with the Company and thereafter, I will promptly disclose to the
Company fully and in writing and will hold in trust for the sole right and
benefit of the Company any and all Company Inventions.

         7.   Prior Inventions. Inventions, if any, patented or unpatented, 
which I made prior to the commencement of my employment with the Company, as can
be shown by written documentation, are excluded from the scope of this
Agreement.

         8.   Services as an employee. Confidentiality obligations defined 
herein are made in connection with an employment agreement between the employee
and the Company.

         9.   No Improper Use of Materials. During my employment with the 
Company, I will not improperly use or disclose any confidential information or
trade secrets, if any, of any former or current employer or any other person to
whom I have an obligation of confidentiality, and I will not bring onto the
premises of the Company any unpublished documents or any property belonging to
any former or current employer or any other person to whom I have an obligation
of confidentiality unless consented to in writing by that former employer or
person.

         10.  No Conflicting Obligation. I represent that my performance of all
the terms of this Agreement and as a Employee of the Company does not and will
not breach any agreement to keep in confidence information acquired by me in
confidence or in trust prior to my employment with the Company. I have not
entered into, and I agree I will not enter into, any agreement either written or
oral in conflict herewith.

         11.  Return of Company Documents. When my employment is terminated with
the Company, I will deliver to the Company any and all drawings, notes,
memoranda, specifications, devices, formulas, molecules, cells and documents,
together with all copies thereof, and any other material containing or
disclosing any Company Inventions, Third Party Information, or Proprietary
Information of the Company, except one complete record of each document may be
retained for archival purposes to assure compliance with this Agreement.
<PAGE>   10

         12.  Legal and Equitable Remedies. Because my services are personal and
unique and because I may have access to and become acquainted with the
Proprietary Information of the Company, the Company shall have the right to
enforce this Agreement and any of its provisions by injunction, specific
performance or other equitable relief, without bond, without prejudice to any
other rights and remedies that the Company may have for a breach of this
Agreement.

         13.  Notices. Any notices required or permitted hereunder shall be 
given to the appropriate party at the address specified below or at such other
address as the party shall specify in writing. Such notice shall be deemed given
upon personal delivery to the appropriate address or if sent by certified or
registered mail, three days after the date of mailing.

         14   General Provisions.

              14.1 Governing Law. This Agreement will be governed by and
construed according to the laws of the State of Wisconsin.

              14.2 Entire Agreement. This Agreement is the final, complete and 
exclusive agreement of the parties with respect to the confidentiality and
ownership of intellectual property as of the date shown above. No modification
of or amendment to this Agreement, nor any waiver of any rights under this
Agreement, will be effective unless in writing signed by the party to be
changed. Any subsequent change or changes in my duties, salary or compensation
will not affect the validity or scope of this Agreement.

              14.3 Severability. If one or more of the provisions in this 
Agreement affecting the rights or property of UW are adjudicated unenforceable
by law, this Agreement shall terminate as of the date such adjudication is
effective. If one or more other provisions in this Agreement are deemed
unenforceable by law, then the remaining provisions will continue in full force
and effect.

              14.4 Successors and Assigns. This Agreement will be binding upon
my heirs, executors, administrators and other legal representatives and will be
for the benefit of the Company, its successors, and its assigns.

              14.5 Survival. The provisions of this Agreement shall survive the
termination of my employment and the assignment of this Agreement by the Company
to any successor in interest or other assignee.

              14.6 Waiver. No waiver by either party of any breach of this
Agreement shall be a waiver of any preceding or succeeding breach. No waiver by
either party of any right under this Agreement shall be construed as a waiver of
any other right. The Company shall not be required to give notice to enforce
strict adherence to all terms of this Agreement.
<PAGE>   11

              14.7 Defense and Indemnification. The Company agrees, at its sole
expense, to defend the Employee and UW against, and to indemnify and hold the
Employee and UW harmless from, any claims or suits by a third party, against the
Employee and UW, or any liabilities or judgments based thereon, either arising
from this Agreement, the Employee's performance of services for the Company
under this Agreement, or any Company products which results from the Employee's
performance of services under this Agreement.

         I UNDERSTAND THAT THIS AGREEMENT AFFECTS MY RIGHTS TO INVENTIONS I MAKE
DURING MY EMPLOYMENT, AND RESTRICTS MY RIGHT TO DISCLOSE OR USE THE COMPANY'S
CONFIDENTIAL INFORMATION DURING OR SUBSEQUENT TO MY EMPLOYMENT RELATIONSHIP WITH
THE COMPANY.

         I HAVE READ THIS AGREEMENT CAREFULLY AND UNDERSTAND ITS TERMS.

Dated: November 23, 1998              /s/ F. Michael Hoffman    
                                      ------------------------- 
                                      F. Michael Hoffman, Ph.D.

                           Address:   3905 Council Crest Road
                                      Madison, WI  53711


ACCEPTED AND AGREED TO:

OPHIDIAN Pharmaceuticals, Inc.



By:      /s/ Douglas C. Stafford    
         -------------------------- 
         Douglas C. Stafford
         President & CEO

Dated:   December 1, 1998

<PAGE>   12
                                                 INFORMATION REDACTED FOR WHICH
                                                 CONFIDENTIAL TREATMENT HAS BEEN
                                                 REQUESTED



December 1, 1998

F. Michael Hoffmann, Ph.D.
3905 Council Crest Road
Madison, WI  53711

Dear Michael:

This letter is intended to set forth the understanding between Ophidian and you
concerning business development activities surrounding the TGF-beta program as
described as the Host Response Program in the Company's Prospectus dated May 7,
1998. Ophidian recognizes your central role in the future development of this
program that may lead to commercial partnerships or some form of capitalization
from a third party. In recognition of your ongoing and active role in
establishing these business opportunities, Ophidian is willing to provide the
following incentives to you.

Both parties acknowledge that the funding from third parties to continue the
research and business objectives of the TGF-beta program can be structured in a
variety of ways which cannot all be specified at this time. The funding may take
the form of a partnership or a joint venture with Ophidian, the sale of all or a
portion of the assets of the TGF-beta program to a third party, or other
variations of the above. Ophidian will pay you a bonus based on the amount of
the payment it receives if (i) Ophidian and a third party enter into an
agreement for third party funding within three years from the date of this
letter agreement, (ii) you have made material contributions to the TGF-beta
program prior to the signing of the third party agreement and (iii) Ophidian
receives payment from the third party for the licensing or transfer of Ophdian's
ownership rights in the TFG-beta program within one year of the effective date
of the third party funding agreement.

<TABLE>
<CAPTION>
Payment to Ophidian                  Bonus to Hoffman
-------------------                  ----------------
<S>                                    <C>
         *                              $50,000
         *                              $100,000
</TABLE>

If Ophidian enters into more than one agreement for third party funding, it will
pay you a bonus for each funding agreement that meets the criteria stated above.

Sincerely,

/s/ Douglas C. Stafford


Douglas C. Stafford, Ph.D.
President, Ophidian Pharmaceuticals, Inc.


*Information redacted for which confidential treatment has been requested.