Exhibit 10.1

CONSULTING AGREEMENT

This CONSULTING AGREEMENT (this “Agreement”) is made as of this 9th day of
April, 2007 by and between John A. Skolas, 12 Lenape Drive, New Hope, PA 18938
(“Consultant”), and Genaera Corporation (“GENAERA”), located at 5110 Campus
Drive, Plymouth Meeting, PA 19462.

WHEREAS, Consultant is desirous of providing consulting services to GENAERA and
GENAERA is desirous of retaining Consultant to perform such services;

NOW THEREFORE, in consideration of the mutual promises hereinafter set forth,
and intending to be legally bound hereby, GENAERA and Consultant agree as
follows:

 

1. Subject to the terms and conditions set forth in this Agreement, GENAERA
hereby engages Consultant as an independent contractor to perform services in
the area of legal and transactional matters. This Agreement shall not obligate
GENAERA to use Consultant’s services and it shall not obligate Consultant to
provide services for GENAERA. This Agreement shall govern services requested in
writing by GENAERA which Consultant is willing and able to perform.

 

2. The initial term of this Agreement shall commence on May 1, 2007 and end on
December 31, 2007. The parties may agree to extend the term for successive
periods thereafter.

 

3. GENAERA shall compensate Consultant for the services rendered by Consultant
under this Agreement as set forth in this Paragraph 3.

 

  a. GENAERA shall pay Consultant $250.00 per hour payable within 30 days of
GENAERA’s receipt of Consultant’s invoice, reflecting hours and services
performed.

 

  b. GENAERA shall reimburse Consultant for (i) out-of-pocket expenses
reasonably incurred by Consultant in performing his obligations hereunder,
including postage, overnight courier and duplicating expenses, and
(ii) out-of-pocket travel, hotel and meal expenses reasonably incurred by
Consultant, provided that the expense was requested or approved in advance by
GENAERA.

 

4. This Agreement will be effective for the term stated above unless earlier
terminated by GENAERA upon thirty (30) days written notice to Consultant. Any
such termination shall not affect the rights or obligations of either party
accruing prior thereto.

 

5. Consultant will return to GENAERA any property of GENAERA that has come into
his possession, upon the request of GENAERA, and, in any event, upon termination
of this Agreement.

 

6.

Consultant shall not disclose any information relating to the business or
technology of

 

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GENAERA to any third party, or use any such information for any purpose, except
to perform the services as indicated in this Agreement. Additionally, Consultant
shall not use any material, compounds, chemicals, biologicals, or derivatives
thereof which may be provided by GENAERA (“Materials”), except as necessary to
perform the services an indicated in this Agreement. Nothing contained herein
shall be deemed to be a license to Consultant to any GENAERA technology or
Materials. No copies are to be made of any proprietary or confidential
information of GENAERA that is provided to Consultant in tangible form, and all
such tangible information shall remain GENAERA property. If Consultant is
requested or required (by oral questions, interrogatories, request for
information or documents, subpoena, civil investigation demand or similar
process) to disclose any proprietary or confidential information of GENAERA,
Consultant shall provide prompt written notice to GENAERA. The provisions of
this Section 6 shall survive the expiration or sooner termination of this
Agreement.

 

7. Consultant acknowledges that any and all inventions and discoveries, whether
or not patentable, that he or she conceives and/or makes, which are a direct or
indirect result of his performance under this Agreement and/or relate to
information received from GENAERA or Materials, shall be the sole property of
GENAERA, and shall be promptly disclosed to GENAERA. GENAERA shall have the sole
right to use, sell, license, publish or otherwise disseminate or transfer rights
in any such invention or discovery. Consultant shall execute all applications,
assignments or other instruments which GENAERA shall deem necessary or useful in
order to apply for and obtain copyrights and Letters Patent in the United States
and any foreign countries, or other protections for any such invention and
discovery. Consultant shall assign, grant and convey to GENAERA all of his or
rights, title and interest, now existing or that may exist in the future, in and
to any such inventions, discoveries and copyrights. The provisions of this
Section 7 shall survive the expiration or sooner termination of the term of this
Agreement.

 

8. The options granted under the Non-Qualified Stock Option Grants to
Consultant, dated October 20, 2003, July 23, 2004, December 8, 2004, July 27,
2005, December 8, 2005 and July 18, 2006 and the award under the Restricted
Stock Grant to Consultant, dated as of May 10, 2004, shall continue to vest
during the term of this Agreement.

 

9. Consultant represents that he is not a party to any existing agreement which
would prevent his fulfilling their obligations under this Agreement, and that
the terms and obligations are not inconsistent with any obligation he may have.
Consultant is responsible for ensuring that any consulting agreement he enters
into is not in conflict with other commitments to any other person or entity.

 

10. Consultant is an independent contractor under this Agreement. Consultant is
not an employee of GENAERA and will not be entitled to participate in or receive
any benefit or right under any GENAERA employee benefit and welfare plans,
including, without limitation, insurance, pension, savings and security plans.

 

11. This Agreement constitutes the sole agreement between Consultant and GENAERA
with respect to the services to be performed by Consultant hereunder and shall
supersede all prior agreements and understandings with respect thereto. No
change, modification, alteration or addition to any provision of this Agreement
shall be binding unless in writing and signed by both Consultant and a duly
authorized representative of GENAERA.

 

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12. This Agreement shall become binding when any one or more counterparts
hereof, individually or taken together, shall bear the signatures of Consultant
and GENAERA. This Agreement may be executed in two or more counterparts, each of
which shall be deemed to be an original as against any party whose signature
appears therein, but all of which together shall constitute one in the same
instrument.

 

13. This Agreement shall be construed, interpreted and applied in accordance
with laws in the Commonwealth of Pennsylvania.

 

14. Consultant certifies that his Social Security Number or Employer
Identification Number is                         . Consultant acknowledges that
GENAERA will rely upon the foregoing certification in filing certain documents
and instruments required by law in connection with this Agreement including,
without limitation, Form 1099 under the Internal Revenue Code of 1986, as
amended (or any successor form).

 

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

 

GENAERA CORPORATION By:  

/s/ John L. Armstrong, Jr.

  John L. Armstrong, Jr.   President and Chief Executive Officer CONSULTANT By:
 

/s/ John A. Skolas

  John A. Skolas

 

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