UNITED
STATES
 SECURITIES
AND EXCHANGE COMMISSION
 Washington,
D.C. 20549
  FORM
10-K/A
 (Amendment
No. 1)
 (Mark
One
  x
                        ANNUAL
      REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF
      1934For
      the fiscal year ended December 31, 2009o
                        TRANSITION
      REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF
      1934For
      the transition period
      from                 to
                          
                          Commission
      File Number: 001-32587PHARMATHENE,
      INC.(Exact
      name of registrant as specified in its
charter)                Delaware
                            
                            20-2726770(State
      or other jurisdiction of
                              incorporation
      or organization)
                            
                            (I.R.S.
      Employer Identification No.)
  One
      Park Place, Suite 450, Annapolis, MD
                            21401(Address
      of principal executive offices)
                            
                            (Zip
      Code)
  (410)
      269-2600(Registrant’s
      telephone number, including area code)Securities
      registered pursuant to Section 12(b) of the Act:
  Title
      of Each Class:
                            
                            Name
      of Each Exchange on Which Registered:Common
      Stock, par value $0.0001 per share
                            
                            NYSE
      Amex
 Securities
registered pursuant to Section 12(g) of the Act:
 None
  Indicate
by check mark if the registrant is a well-known seasoned issuer, as defined in
Rule 405 of the Securities Act.  Yes
o No
x
  
  Indicate
      by check mark if the registrant is not required to file reports pursuant
      to Section 13 or 15(d) of the Act.
                                    Yes
      o
                                    
                                    No
      xIndicate
      by check mark whether the registrant (1) has filed all reports required to
      be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934
      during the preceding 12 months (or for such shorter period that the
      registrant was required to file such reports), and (2) has been subject to
      such filing requirements for the past 90 days.
                                    Yes
      x
                                    
                                    No
      oIndicate
      by check mark whether the registrant has submitted electronically and
      posted on its corporate Web site, if any, every Interactive Data file
      required to be submitted and posted pursuant to Rule 405 of Regulation S-T
      (§232.405 of this chapter) during the preceding 12 months (or for such
      shorter period that the registrant was required to submit and post such
      files).
                                    Yes
      o
                                    
                                    No
      oIndicate
      by check mark if disclosure of delinquent filers pursuant to Item 405 of
      Regulation S-K is not contained herein, and will not be contained, to the
      best of registrant’s knowledge, in definitive proxy or information
      statements incorporated by reference in Part III of this Form 10-K or any
      amendment to this Form 10-K.
                                    Yes
      x
                                    
                                    No
      oIndicate
      by check mark whether the registrant is a large accelerated filer, an
      accelerated filer, a non-accelerated filer, or a smaller reporting
      company.  See the definitions of “large accelerated filer,”
      “accelerated filer” and “smaller reporting company” in Rule 12b—2 of the
      Exchange Act.  (Check one):o
                                    Large
      Accelerated Filer
                                    o
                                    Accelerated
      Filer
                                    o
                                    Non-Accelerated
      Filer
                                    x
                                    Smaller
      Reporting Company  Indicate
      by check mark whether the registrant is a shell company (as defined in
      Rule 12b-2 of the Act).
                                    Yes
      o
                                    
                                    No
      xThe
      aggregate market value of voting and non-voting common equity held by
      non-affiliates of the registrant was $34,560,632 based upon the closing
      price of the common equity on the NYSE Amex on the last business day of
      the registrant’s most recently completed second fiscal quarter (June 30,
      2009).
                                      
                                      The
      number of shares of the registrant’s Common Stock, par value $0.0001 per
      share, outstanding as of March 15, 2010 was 28,435,598.DOCUMENTS
      INCORPORATED BY REFERENCENone.









EXPLANATORY
NOTE
 
 This Amendment No. 1 on Form 10-K/A
(this “Form 10-K/A”) to the Annual Report on Form 10-K of PharmAthene, Inc. (the
“Company” or “PharmAthene”) for the year ended December 31, 2009, filed with the
Securities and Exchange Commission on March 26, 2010 (the “Original 10-K”) is
being filed for the purposes of:
 
 (i)
                including
      the information required by Part III (Items 10-14) of Form 10-K
      and
 
 (ii)
                including
      disclosure under Item 9.B. of Form 10-K (Other Information) in lieu of
      filing a separate Current Report on Form 8-K containing such disclosure in
      Item 5.02 thereof.
 
 As
a result, Part II, Item 9.B. and Part III, Items 10-14 of the Company’s Original
10-K are hereby amended and restated in their entirety.
 
 As required by Rule 12b-15, in
connection with this Form 10-K/A, the Company’s principal executive officer and
principal financial officer are providing Rule 13a-14(a) certifications dated
April 30, 2010.
 
 Except
as described above, this Form 10-K/A does not modify or update disclosure in, or
exhibits to, the Original 10-K, and such disclosure in, or exhibits to, the
Original 10-K remain unchanged and speak as of the date of the original
filing.  In particular, this Form 10-K/A does not change any
previously reported financial results, nor does it reflect events occurring
after the date of the Original 10-K, except as disclosed in Part II, Item 9.B.
herein.
 
 Unless
the context otherwise requires, all references in this report to the “Company”,
“PharmAthene”, “we”, “us” or “our” refers to the business of the combined
company after the Merger and to the business of former PharmAthene prior to the
Merger, and “HAQ” refers to the business of Healthcare Acquisition Corp. and its
subsidiaries, as a combined entity, prior to the Merger.  Unless the
context otherwise requires, the information contained in this report gives
effect to the consummation of the Merger of August 3, 2007 and the change of our
name from “Healthcare Acquisition Corp.” to “PharmAthene, Inc.”
 
 1
 
 Special
Note Regarding Forward-Looking Statements
  This
Form 10-K/A contains forward-looking statements within the meaning of Section
27A of the Securities Act of 1933, as amended, and Section 21E of the Securities
Exchange Act of 1934, as amended (the “Exchange Act”).  This
information may involve known and unknown risks, uncertainties and other factors
that are difficult to predict and may cause our actual results, performance or
achievements to be materially different from future results, performance or
achievements expressed or implied by any forward-looking
statements.  These risks, uncertainties and other factors include, but
are not limited to, risk associated with the following:
  ·
              the
      reliability of the results of the studies relating to human safety and
      possible adverse effects resulting from the administration of the
      Company’s product candidates,
  ·
              unexpected
      funding delays and/or reductions or elimination of U.S. government funding
      for one or more of our development
programs,
  ·
              the
      award of government contracts to our
  competitors,
  ·
              unforeseen
      safety issues,
  ·
              challenges
      related to the development, technology transfer, scale-up, and/or process
      validation of manufacturing processes for our product
      candidates,
  ·
              unexpected
      determinations that these product candidates prove not to be effective
      and/or capable of being marketed as
products,
  as
well as risks detailed under the caption “Risk Factors” in the Original 10-K
filed on March 26, 2010 and in our other reports filed with the U.S. Securities
and Exchange Commission (the “SEC”) from time to time
hereafter.  Forward-looking statements describe management’s current
expectations regarding our future plans, strategies and objectives and are
generally identifiable by use of the words “may,” “will,” “should,” “expect,”
“anticipate,” “estimate,” “believe,” “intend,”  “project,” “potential” or
“plan” or the negative of these words or other variations on these words or
comparable terminology.  Such statements include, but are not limited
to:
  ·
              statements
      about potential future government contract or grant
  awards,
  ·
              potential
      payments under government contracts or
grants,
  ·
              potential
      regulatory approvals,
  ·
              future
      product advancements,
  ·
              anticipated
      financial or operational results,
and
  ·
              expected
      benefits from our acquisition of the biodefense vaccines business (“Avecia
      Acquisition”) from Avecia Biologics Limited and certain of its affiliates
      (“Avecia”) in April 2008.
  Forward-looking
statements are based on assumptions that may be incorrect, and we cannot assure
you that the projections included in the forward-looking statements will come to
pass.
 
 You are cautioned not to place undue
reliance on these forward-looking statements, which speak only as of the date of
this document.We assume no obligation
to update any such forward-looking statements, other than as required by
law.  Although we undertake no obligation to revise or update any
forward-looking statements, whether as a result of new information, future
events or otherwise, you are advised to consult any additional disclosures that
we may make directly to you or through reports that we, in the future, may file
with the SEC, including Annual Reports on Form 10-K, Quarterly Reports on
Form 10-Q and Current Reports on Form 8-K.
  2
  All
forward-looking statements included herein are expressly qualified in their
entirety by the cautionary statements contained or referred to elsewhere in this
Form 10-K/A or the Original 10-K.  Except as described under
“Explanatory Note” above,  this Form 10-K/A does not modify or update
disclosure in, or exhibits to, the Original 10-K, and such disclosure in, or
exhibits to, the Original 10-K remain unchanged and speak as of the date of the
original filing.  In particular, this Form 10-K/A does not change any
previously reported financial results, nor does it reflect events occurring
after the date of the Original 10-K, except as disclosed in Part II, Item 9.B.
herein.
  PART
II
 
 Item
9.B. Other Information.
 
 On April 26, 2010, the Board of
Directors (the “Board”) of PharmAthene, Inc. (the “Company”) appointed Mitchel
Sayare, Ph.D. to the Board of the Company.  Dr. Sayare accepted the
appointment effective April 27, 2010.
 
 In connection with his appointment to
the Board, Dr. Sayare was granted a stock option to purchase 20,000 shares of
the Company’s common stock at an exercise price of $1.52, the closing price of
the Company’s common stock as reported on the NYSE Amex on April 27,
2010.  The stock option, which was granted under the Company’s Amended
and Restated 2007 Stock Incentive Plan, vested immediately and will expire on
April 27, 2020.
 
 On April 27, 2010, David P. Wright
notified the Company that he was stepping down as Chief Executive Officer of
PharmAthene. The
Compensation Committee of the Board of Directors has nominated Eric I. Richman,
who currently serves as our President and Chief Operating Officer, to assume the
duties of Chief Executive Officer. The Board of Directors will convene a meeting
shortly to ratify the recommendation of the Compensation Committee.
 
 PART
III
 
 Item
10. Directors, Executive Officers and Corporate Governance.
 
 Directors
 
 PharmAthene’s
directors are elected at each Annual Meeting of Stockholders and hold office for
a one-year term or until their successors have been elected and qualified. Our
Amended and Restated Certificate of Incorporation provides that, for so long as
at least 30% of the aggregate principal amount of the Notes remains
outstanding,
 
 ·
              the
      Company shall maintain a Board of Directors consisting of no more than
      nine members, of which two directors (the “Noteholder Directors”) shall be
      elected by the holders (the “Noteholders”) representing a majority of the
      then-outstanding principal amount of our 10% convertible senior notes (the
      “Notes”), voting exclusively and as a separate
  class;
 ·
              each
      of the Compensation Committee and the Governance and Nominating Committee
      of the Board of Directors shall have no more than three
      members;
 ·
              subject
      to applicable law and stock exchange requirements, each Noteholder
      Director will have the right, but not the obligation, to serve as a member
      of each of the Compensation Committee and the Governance and Nominating
      Committee; and
 ·
              our
      Board of Directors shall nominate the Noteholder Directors as designated
      by the designators pursuant to the Note and Warrant Purchase Agreement and
      recommend that the holders of the notes vote to elect such nominees as
      directors.
 
 Consent
is required from holders of at least a majority of the outstanding principal
amount of the Notes to amend or change the above provisions in accordance with
the Notes.  Our Bylaws provide that the number of directors
constituting the entire Board shall be not less than one nor more than nine as
determined by resolution of the Board.
 
 John
Pappajohn, David P. Wright, Joel McCleary, John Gill, Derace L.
Schaffer, M.D., Jeffrey W. Runge, M.D. and Mitchel Sayare, Ph.D. currently
serve as the “Stockholder Directors”, i.e., those of our directors subject to
election by our stockholders.   James H.
Cavanaugh, Ph.D. and Steven St. Peter, M.D. currently serve as
the Noteholder Directors.
 
 Stockholder Directors
 
 Set
forth below is information regarding each Stockholder Director holding office
until our 2010 Annual Meeting.
  3
 
 Name
                Age
                PositionJohn
      Pappajohn
                81
                Chairman
      of the BoardDavid
      P. Wright
                62
                DirectorJoel
      McCleary*
                61
                DirectorJohn
      Gill*
                58
                DirectorDerace
      L. Schaffer, M.D.
                62
                DirectorJeffrey
      W. Runge, M.D.*
                54
                DirectorMichel
      Sayare, Ph.D.
                62
                Director
 
 *Independent
Director.  Since Dr. Sayare only joined the Board effective April 27,
2010, the Board has not yet made an affirmative determination of his
independence pursuant to NYSE AMEX rules.
 
 John
Pappajohn, 81.    Mr. Pappajohn has served as
the Company’s Chairman since April 2005 and was the Company’s secretary from
April 2005 to August 3, 2007. Since 1969, Mr. Pappajohn has been the
President and principal stockholder of Equity Dynamics, Inc., a financial
consulting firm, and the sole owner of Pappajohn Capital Resources, a venture
capital firm. Mr. Pappajohn has been an active private equity investor in
healthcare companies for more than 30 years and has served as a director of
more than 40 public companies. Mr. Pappajohn has been a founder in several
public healthcare companies such as Caremark Rx, Inc., Quantum Health
Resources, and Radiologix, Inc. Mr. Pappajohn received his Bachelor of
Arts degree from the University of Iowa. Mr. Pappajohn also serves as a
director of the following public companies: American CareSource
Holdings, Inc., CNS Response and ConMed Health Management, Inc. He
furthermore serves as a director of CareGuide, Inc.  Mr.
Pappajohn was chosen to serve as a director of the Company because of his
unparalleled experience serving as a director of more than 40 companies and the
substantial insight he has gained into the life sciences and healthcare
industries by actively investing in the industries for more than 40 years, and
by founding and supporting several public healthcare companies.
 
 David
P. Wright, 62.    Mr. Wright has served as a
member of the Board since August 3, 2007, was our Chief Executive Officer
from the time of the merger in August 2007 until April 27, 2010 (also serving as
President until March 25, 2010) and from July 2003 to August 3, 2007 was
President and Chief Executive Officer of Former PharmAthene. Prior to joining
the Company, and during 2003, Mr. Wright served as President and Chief
Operating Officer of GenVec Inc, and previously, from 2001 to 2003, as President
and Chief Business Officer of Guilford Pharmaceuticals, Inc.
Mr. Wright served as Executive Vice President of MedImmune, Inc. from
1990 to 2000. Prior to serving at MedImmune, he held various marketing and sales
positions at pharmaceutical companies including SmithKline and French
Laboratories, G.D. Searle, and Glaxo. Mr. Wright received a Master’s degree
from the University of South Florida. Mr. Wright currently serves as a
director of Achillon, Inc.  Mr. Wright was chosen to serve as a
director of the Company because of his extensive executive experience with
PharmAthene, Guilford Pharmaceuticals, Inc. and MedImmune, Inc.
 
 Joel
McCleary, 61.    Mr. McCleary has served as a
member of the Board since August 3, 2007 and from inception to
August 3, 2007 was Chairman of the Board of Former PharmAthene.
Mr. McCleary is founding member of Four Seasons Ventures LLC founded
in 2005. Prior to 2005, Mr. McCleary has served as a White House Aide,
Treasurer of the Democratic Party, President of the Sawyer-Miller Group
International, and President of the Institute for Asian Democracy. He has served
as a consultant to the Department of State. He is a co-founder and board member
of Raydiance Inc. Mr. McCleary received a Bachelor of Arts degree from
Harvard University.  Mr. McCleary was chosen to serve as a
director of the Company primarily because of his impressive public service
record in a variety of governmental and quasi-governmental organizations,
enabling him to offer valuable guidance to the Board and the Company with
respect to our government strategy.
  4
  John
Gill, 58.    Mr. Gill has served as a member of
the Board since August 3, 2007 and from February 2004 to August 3,
2007 served as a member of the Board of Directors and as Chairman of the Audit
Committee of Former PharmAthene. Mr. Gill is currently the President, Chief
Executive Officer and a Director of TetraLogic Pharmaceuticals Corporation, a
private biopharmaceutical company, and has served in these positions since 2004.
He is also an advisor or director of other private companies and non-profit
community organizations. Mr. Gill has previously held positions at
3-Dimensional Pharmaceuticals and SmithKline Beecham. Mr. Gill received a
Bachelor of Arts degree from Rutgers University.  Mr. Gill was
chosen to serve as a director of the Company because of his executive and board
experience in the pharmaceutical industry and his substantial financial
knowledge and expertise.
 
 Derace
L. Schaffer, M.D., 62.    Dr. Schaffer
previously served as Vice Chairman and Chief Executive Officer of the Company
from April 2005 to August 3, 2007. Dr. Schaffer is the founder and
Chief Executive Officer of The Lan Group, a venture capital firm specializing in
healthcare and high technology investments. He has served as Chairman of several
healthcare companies, including Radiologix, Inc. when it was private, and
he has been an active investor with Mr. Pappajohn for approximately twenty
years on a variety of healthcare companies. Dr. Schaffer served as Chief
Executive Officer and Chairman of the Board of Ide Imaging Group, P.C. from 1980
to 2001. Dr. Schaffer has served as a director on many healthcare boards of
directors, including several health systems and more than ten healthcare
services and technology companies. Dr. Schaffer received his postgraduate
radiology training at Harvard Medical School and Massachusetts
General Hospital, where he served as Chief Resident. Dr. Schaffer
currently is also a Clinical Professor of Radiology at
Weill Cornell Medical College. He also serves as a director of
American CareSource Holdings, Inc. and King Pharmaceuticals, Inc. (each, a
public company), served as a director of Allion Healthcare, Inc. (a public
company) until 2008, and serves as a director of
CareGuide, Inc.  Dr. Schaffer was chosen to serve as a director
of the Company because of his substantial experience as an executive, board
member and investor in the healthcare and technology industries and his
practical experience in the medical field.
 
 Jeffrey
W. Runge, M.D., 54.  Dr. Runge has served as a member of the
Board since December 2009.  Dr. Runge is a Principal at The Chertoff
Group, a firm providing advisory services in business risk management, homeland
security and homeland defense.  He is also the President and founder
of Biologue, Inc., which provides consulting in biodefense, medical preparedness
and injury prevention and control.  From 2001 through August of 2008,
Dr. Runge served in the Bush administration, first as the head of the National
Highway Traffic Safety Administration, and, beginning in September 2005, as the
Department of Homeland Security’s (DHS) first Chief Medical
Officer.  Dr. Runge founded the DHS Office of Health Affairs in 2007
and was confirmed by the Senate as DHS’ first Assistant Secretary for Health
Affairs in December of 2007.  Dr. Runge also served as Acting DHS
Undersecretary for Science and Technology from February through August
2006.  In his role at DHS, Dr. Runge oversaw the operations of the
department’s biodefense activities, medical preparedness and workforce health
protection, including managing DHS’ role in Project BioShield, working with the
various federal departments on medical countermeasure
assurance.  Prior to joining DHS, Dr. Runge was Assistant Chairman of
the Department of Emergency Medicine at the Carolinas Medical Center
in Charlotte, NC, from 1984 through 2001.  Dr. Runge earned his
medical degree from the Medical University of South Carolina and his
undergraduate degree from the University of the South.   Dr.
Runge was chosen to serve as a director of the Company because of his invaluable
background in the public sector, particularly his experience in the Bush
administration as a founder of the DHS Office of Health Affairs, as well as his
practical experience in the medical field.
 
 Mitchel
Sayare, Ph.D., 62.   Dr.
Sayare has been a director since April 2010.  Until 2010, Dr. Sayare
served as the Chairman of the Board of public company ImmunoGen, Inc. (a
position he had held since 1989).  In addition, he served as
ImmunoGen’s Chief Executive Officer from 1986 to December 31, 2008, and as
its President from 1986 to 1992, and from 1994 to July 2008. Prior to joining
ImmunoGen, he served as Vice President of Development of Xenogen from 1982 to
1985. Prior to that he was Assistant Professor of Biophysics and Biochemistry at
the University of Connecticut. Dr. Sayare holds a Ph.D. in Biochemistry
from Temple University School of Medicine. Dr. Sayare is a director of ImmunoGen
and Isabella Products, Inc., a privately-held company.  Dr. Sayare was
primarily chosen to serve as a director because of his substantial experience as
a board member and  executive officer of biotechnology
companies.
 
 5
  Noteholder
Directors
  Set
forth below is information regarding each Noteholder Director holding office
until our 2010 Annual Meeting.
  Name
                Age
                PositionJames
      H. Cavanaugh, Ph.D.*
                73
                DirectorSteven
      St. Peter, M.D.*
                43
                Director
 *Independent
Director.
 
 James
H. Cavanaugh, Ph.D., 73.    Dr. Cavanaugh has served
as a member of the Board since the merger on August 3, 2007 and prior to that he
served as a member of the Board of Directors of PharmAthene when it was a
private company. He has been a Managing Director of Healthcare Ventures LLC
since 1989. Dr. Cavanaugh served as President of SmithKline and French
Laboratories U.S. Inc., from March 1985 to February 1989 and as President of
SmithKline Clinical Laboratories from 1981 to 1985. Prior thereto, Dr. Cavanaugh
was the President of Allergan International, a specialty eye care company. Prior
to his industry experience, Dr. Cavanaugh was Deputy Assistant to the President
for Domestic Affairs and Deputy Chief of the White House Staff. Before his White
House tour, he served as Deputy Assistant Secretary for Health and Scientific
Affairs in the U.S. Department of Health, Education and Welfare, and as Special
Assistant to the Surgeon General of the U.S. Public Health Service. He was a
Founding Director of the Marine National Bank in Santa Ana, California. Dr.
Cavanaugh holds a Doctorate and a Master’s degree from the University of Iowa
and a Bachelor of Science degree from Fairleigh Dickinson University.
In addition to serving on the boards of directors of several privately held
health care and biotechnology companies, he has previously served on the Board
of Directors of publicly-held MiddleBrook Pharmaceuticals, the National Venture
Capital Association, the Pharmaceutical Research and Manufacturers Association,
Unihealth America, the Proprietary Association and the Board of Trustees of the
National Center for Genome Resources. He was non-executive Chairman of
Shire Pharmaceuticals Group plc from 1999 to 2008. Dr. Cavanaugh currently
serves as a member of the Board of Directors of Verenium Corporation
(chairman).  Dr. Cavanaugh was chosen to serve as a director of the
Company because of his impressive background as an executive of several
prestigious healthcare companies, his invaluable experience at the White House
and the executive branch in general, and his background as a director of many
healthcare and biotechnology companies.
 
 Steven
St. Peter, M.D., 43.    Dr. St. Peter
has served as a member of the Board since August 3, 2007 and from October
2004 to August 3, 2007 was a member of the Board of Former PharmAthene.
Dr. Steven St. Peter joined MPM Capital in 2004, and he is a Managing
Director based in the Boston office. His investment scope includes both venture
and buyout transactions across the pharmaceuticals and medical technology
industries. He has previous investment experience from Apax Partners and The
Carlyle Group. Dr. St. Peter was previously an assistant Clinical
Professor of Medicine at Columbia University. He completed his Doctor of
Medicine at Washington University and his residency and fellowship at the
Hospital of the University of Pennsylvania. Prior to his medical training, he
was an investment banker at Merrill Lynch. He also holds an M.B.A. from the
Wharton School of the University of Pennsylvania and a B.A. in Chemistry
from the University of Kansas. He is on the Board of the New England Venture
Capital Association and is also a director of EKR Therapeutics, Inc., MPM
Acquisition Corp., Proteon Therapeutics, Inc., Syndax Pharmaceuticals, Inc. and
Xanodyne Pharmaceuticals, Inc.  Dr. St. Peter was chosen to serve as a
director of the Company because of his diverse background as a venture capital
investor, investment banker, professor of medicine and director of several
healthcare companies, which provides him with a unique perspective in serving on
our Board.
 
 In
the Note and Warrant Purchase Agreement executed in connection with the issuance
of the Notes, each Noteholder agreed to vote all of his or her Notes, and shares
underlying the Notes and warrants in whatever manner necessary to ensure that
the Noteholder Directors are elected to the Board.
  6
  Executive
Officers
 
 The
following table sets forth the names, ages and positions of our executive
officers:
 
 Name
              
              Age
              
              OfficeEric
      I. Richman
              
              
              49
              
              President
      and Chief Operating OfficerFrancesca
      Cook
              
              
              45
              
              Senior
      Vice President, Policy and Government AffairsJoan
      Fusco, Ph.D.
              
              
              54
              
              Senior
      Vice President, OperationsThomas
      R. Fuerst, Ph.D.
              
              
              53
              
              Senior
      Vice President, Chief Scientific OfficerJordan
      P. Karp, Esq.
              
              
              43
              
              Senior
      Vice President and General CounselWayne
      Morges, Ph.D.
              
              
              63
              
              Vice
      President, Regulatory Affairs and QualityCharles A.
      Reinhart III
              
              
              49
              
              Senior
      Vice President, Chief Financial OfficerValerie
      Riddle, M.D.
              
              
              49
              
              Senior
      Vice President, Medical Director
 
 The
following are biographical summaries of our executive officers who are not
directors:
 
 Eric I. Richman,
49.   Mr. Richman has been our President and Chief
Operating Officer since March 25, 2010. As such, he has management oversight of
all day-to-day operations of the Company.  Prior to being appointed to
his current position, Mr. Richman was our Senior Vice President, Business
Development and Strategic Planning since the merger on August 3, 2007, and from
August 2003 through August 3, 2007 held the same position with Former
PharmAthene.  Prior to joining the Company, Mr. Richman held
various commercial and strategic positions of increasing responsibility over a
12 year period at MedImmune, Inc. from its inception and was Director,
International Commercialization at that company. Mr. Richman served as
Director of Lev Pharmaceuticals and currently serves as Director of ADMA
Biologics, Inc. and American Bank. Mr. Richman received a Bachelor of
Science in Biomedical Science from the Sophie Davis School of Biomedical
Education (CUNY Medical School) and a Master of Business
Administration from the American Graduate School of International
Management.
 
 Francesca Cook,
45.    Ms. Cook has been our Senior Vice
President, Policy and Government Affairs since March 2010.  Prior to
that, she served as our Vice President, Policy and Government Affairs since the
merger on August 3, 2007 and from October 2003 through August 3, 2007
held the same position with Former PharmAthene prior to the merger with HAQ.
Prior to that, Ms. Cook served as Vice President, Policy &
Reimbursement Services for Guilford Pharmaceuticals, Inc. from March 2001
through October 2003 and Vice President at Covance Health Economics and Outcomes
Services, a health care consulting firm, from 1996 though 2001. Additionally,
Ms. Cook worked in the U.S. Senate and the U.S. Department of Health and
Human Services from 1988 through 1993. Ms. Cook received a Bachelor of Arts
degree in Biology from Mount Holyoke College and a Master of Public
Health degree from Yale University School of Medicine, Department of Public
Health.
 
 Thomas R. Fuerst, Ph.D.,
53.Dr. Fuerst has
been our Senior Vice President, Chief Scientific Officer since April 2010.Prior to joining
PharmAthene, Dr. Fuerst was Director, Vaccines and Biologics (2004-2007), and
Senior Science and Technology Advisor (2007-2010) for the U.S. Department of
Health and Human Services (HHS). In these positions, he led the development and
acquisition of vaccines and biotherapeutic products for biodefense and other
emerging public health threats, including anthrax, smallpox, botulism, and
pandemic flu. During his tenure at HHS, Dr. Fuerst helped establish the
Biomedical Advanced Research and Development Authority (BARDA) and oversaw the
planning, implementation, and monitoring of medical countermeasure development
and acquisition. Dr. Fuerst has also served as Executive Director of Corporate
Development at Sanofi Pasteur, Inc., where, among other things, he oversaw the
scientific and business transactions for vaccines and immunotherapeutic products
for infectious diseases and cancer, and played a key role in establishing the
company's biodefense initiative post 9/11. Prior thereto, Dr. Fuerst was Vice
President, Research and Development, at Genelabs Technologies, Inc., and
Director, Molecular Genetics, at MedImmune, Inc. He also served as a senior
fellow at the National Institutes of Health, NIAID, in Bethesda, MD. Dr. Fuerst
holds a B.A. in Biochemistry from the University of California at Berkeley, a
Ph.D. in Molecular Genetics from Cornell University, and a MBA in Science,
Technology, and Innovation from the George Washington
University.
 Joan Fusco, Ph.D.,
54.    Dr. Fusco has been our Senior Vice
President, Operations since February 2008. Prior to joining PharmAthene, from
October 2004 through January 2008, Dr. Fusco served as Senior Vice
President, Operations for Acambis, Inc. From June 2000 through October
2004, Dr. Fusco served as Vice President, Technical Affairs—Vaccines, and
Vice President, Global Project Management—Vaccines for Baxter Healthcare
Corporation, BioScience Division. Dr. Fusco is a graduate of the University
of Pittsburgh where she received a Ph.D. in Microbiology/Biological
Sciences.
  7
  Jordan
P. Karp, Esq., 43.    Mr. Karp has been our
Senior Vice President and General Counsel since June 2008. In September
2008, he was appointed corporate secretary. Prior to joining the Company,
Mr. Karp was employed by Constellation Energy Group, Inc., a
diversified energy company, from October 2001 to November 2007. Mr. Karp
served as Vice President & General Counsel for one of Constellation
Energy’s operating divisions, Constellation NewEnergy, Inc., a retail
marketer of electricity and natural gas, from October 2002 until November 2007.
From November 2007 until Mr. Karp joined the Company, he worked as an
attorney in private practice. Prior to joining Constellation Energy,
Mr. Karp held in-house legal positions of increasing responsibility at MCI
Communications Corp. (telecommunications), Guilford Pharmaceuticals Inc.
(biopharmaceuticals), and Mentor Technologies Group, Inc. (training and
consulting), where Mr. Karp served as Vice President, General
Counsel & Corporate Secretary from November 1999 through June
2001.  In November 2001, Mentor Technologies had an involuntary
petition in bankruptcy filed against it , which was later converted into a
voluntary petition.  Mr. Karp holds a B.A. in Natural Sciences
from The Johns Hopkins University and a J.D. from
Yale Law School.
 
 Wayne
Morges, Ph.D., 63.    Dr. Morges has been our
Vice President, Regulatory Affairs and Quality since the merger on
August 3, 2007, and from January 2005 through August 3, 2007 held the
same position with Former PharmAthene prior to the merger. Prior to that,
Dr. Morges was the Vice President of Global Regulatory Affairs, Vaccines
for Baxter Healthcare Corporation from June 2000 to November 2004. Previously,
Dr. Morges worked at Merck holding various positions of increasing
responsibility in Merck’s vaccine division, including heading Quality &
Regulatory Affairs for licensed biologicals. Dr. Morges holds a Ph.D. in
Microbiology and Immunology from Hahnemann University and Bachelor of
Science and Master of Science degrees from
Penn State University.
 
 Charles
A. Reinhart, III, 49.    Mr. Reinhart has been
our Senior Vice President, Chief Financial Officer since August 14, 2009.
Mr. Reinhart joined PharmAthene on August 10, 2009 as Senior Vice
President, Finance. Prior to joining PharmAthene, Mr. Reinhart served as
Senior Vice President Finance and Corporate Strategy, and was a member of the
Operating Leadership Team of Millennium Pharmaceuticals, Inc. from October
2007 to June 2008, where he was responsible for all aspects of the company’s
finance and strategic sourcing functions. From November 2000 to October 2007,
Mr. Reinhart was Vice President, Finance at Cephalon, Inc. where he
was responsible for worldwide accounting, financial reporting, Sarbanes Oxley
compliance, tax, treasury and budgeting/forecasting functions. Mr. Reinhart
is a C.P.A. He earned his Masters of Business Administration from The Wharton
School at the University of Pennsylvania and his undergraduate degree in
Business and Economics from Lehigh University.
 
 Valerie
Riddle, M.D., 49.    Dr. Riddle has been our
Senior Vice President, Medical Director since March 2010.  Prior to
that, she served as our Vice President, Medical Director since the merger on
August 3, 2007, and from October 2003 through August 3, 2007 held the
same position with Former PharmAthene prior to the merger. Prior to joining the
Company, Dr. Riddle was with Guilford Pharmaceuticals, Inc. as Vice
President, Medical Affairs and was promoted to Vice President, Clinical and
Medical Affairs in 2002. From 1998 to 1999, Dr. Riddle was with
MedImmune, Inc. first as Director, Medical Sciences and, later, as Senior
Director, Medical Sciences. Prior to 1998, Dr. Riddle spent several years
at Washington Hospital Center in Washington, D.C., most recently as
Director, HIV Service. Dr. Riddle received her Bachelor of Arts in
Chemistry, cum laude, from the University of South Florida in 1984 and her
Doctor of Medicine degree from University of South Florida in 1989 and is Board
certified in Internal Medicine and Infectious Diseases.
 
 Section 16(a)
Beneficial Ownership Reporting Compliance
 
 Section 16(a)
of the Securities Exchange Act of 1934, as amended (the “Exchange Act”) requires
our directors, executive officers, and persons who own more than 10% of our
common stock to file reports of ownership and changes in ownership of our common
stock with the SEC. Based solely on our review of copies of these reports filed
with the SEC, we believe there has been compliance with all Section 16(a)
filing requirements applicable to such directors, executive officers and 10%
beneficial owners for 2009.
  8
 
 Corporate
Governance
 
 Corporate
Governance Guidelines
 
 Pursuant
to the Delaware General Corporation Law and the Company’s Bylaws, the Company’s
business, property and affairs are managed by or under the direction of the
Board of Directors. Members of the Board are kept informed of the Company’s
business through discussions with the Chief Executive Officer and other
officers, by reviewing materials provided to them and by participating in
meetings of the Board and its committees. We currently have seven members on our
Board, all of whom are standing for re-election.
 
 Code
of Ethics and Business Conduct
 
 PharmAthene
has a Code of Ethics and Business Conduct that applies to all directors,
officers and employees, which can be found on our website, www.pharmathene.com,
under the heading “Investor Relations” (see “Corporate Governance Information”—
”Code of Ethics and Business Conduct”) or by writing to PharmAthene, Inc.,
One Park Place, Suite 450, Annapolis, MD 21401, c/o Corporate Secretary.
All of our directors, officers and employees are expected to be familiar with
the Code and to adhere to those principles and procedures set forth in the Code
that apply to them. The Company will post any amendments to the Code of Ethics
and Business Conduct, as well as any waivers that are required to be disclosed
by the rules of either the SEC or the NYSE Amex, on the Company’s web site.
 
 Director
Independence
 
 We
use the definition of “independence” under Section 803A of the NYSE Amex
Company Guide, as applicable and as may be modified or supplemented from time to
time and the interpretations thereunder, to determine if the members of our
Board are independent. In making this determination, our Board considers, among
other things, transactions and relationships between each director and his
immediate family and the Company, including those reported in this Form 10-K/A
under the caption “Certain Relationships and Related Transactions.” The purpose
of this review is to determine whether any such relationships or transactions
are material and, therefore, inconsistent with a determination that the
directors are independent. On the basis of such review and its understanding of
such relationships and transactions, our Board affirmatively determined that our
Board was comprised of a majority of independent directors and will remain
comprised of at least 50% of independent directors.
 
 Board
Leadership Structure
 
 To
assure effective and independent oversight of management, our Board of Directors
operates with the roles of Chief Executive Officer and Chairman of the Board
separated in recognition of the differences between these two roles in the
management of the Company.   The Chairman of the Board is an
independent, non-management role.
 
 Our
Board of Directors believes that this leadership structure provides the most
effective leadership model for our company.  By permitting more
effective monitoring and objective evaluation of the Chief Executive Officer’s
performance, this structure increases the accountability of the Chief Executive
Officer.  A separation of the Chief Executive Officer and Chairman
roles also prevents the former from controlling the Board's agenda and
information flow, thereby reducing the likelihood that the Chief Executive
Officer would abuse his power.
 
 Board
Oversight of Risk Management
 
 Our Board believes that overseeing how
management manages the various risks we face is one of its most important
responsibilities to the Company’s stakeholders. Our Board believes that, in
light of the interrelated nature of the Company’s risks, oversight of risk
management is ultimately the responsibility of the full Board; however,it has
delegated this responsibility to the audit committee with respect to financial
risk.  The audit committee periodically meets with management and the
registered independent public accounting firm to review the Company’s major
financial risk exposures and the steps taken to monitor and control such
exposures.  Our Board meets regularly to discuss the strategic
direction and the issues and opportunities facing our company in light of trends
and developments in the biodefense industry and general business
environment.   Throughout the year, our Board provides guidance
to management regarding our strategy and helps to refine our operating plans to
implement our strategy.  The involvement of the Board in setting our
business strategy is critical to the determination of the types and appropriate
levels of risk undertaken by the Company.
  9
  Board
Meetings
 
 During
the fiscal year ended December 31, 2009, the Board held 20 meetings and the
Board Committees held a total of 21 meetings. Each incumbent director attended
more than 75% of the total number of meetings of the Board and the Board
Committees of which he or she was a member during the period he or she served as
a director in fiscal year 2009. The Board of Directors met in executive session
on six occasions in the fiscal year ended December 31, 2009.
 
 Director
Attendance at Annual Meeting
 
 The
Company has no specific policy regarding director attendance at its Annual
Meeting. Generally, however, Board meetings are held immediately preceding and
following the Annual Meeting, with directors attending the Annual Meeting. Our
Annual Meeting held on October 29, 2009 was attended by all seven of our
directors at that time.
 
 Board Committees
 
 The
Board currently has a separately-designated standing Audit Committee established
in accordance with Section 3(a)(58)(A) of the Securities Exchange Act of
1934, as amended. In addition, the Board has a Governance and Nominating
Committee, Compensation Committee and Government Affairs Committee. Each
Committee, with the exception of the Government Affairs Committee, consists
entirely of independent, non-employee directors (see “Director Independence”
below). The charter of each Board Committee (other than the Governmental Affairs
Committee, which does not currently have a charter) is available free of charge
on our website, www.pharmathene.com, under the heading “Investor Relations” (see
“Corporate Governance—Highlights—Audit Committee Charter,” “—Compensation
Committee Charter” and “—Governance and Nominating Committee Charter”) or by
writing to PharmAthene, Inc., One Park Place, Suite 450, Annapolis, MD
21401, c/o Corporate Secretary.
 
 The
following table below sets forth the Committees, current membership of each
Committee and the number of Committee meetings held in 2009.
 
 Fiscal
Year Ended December 31, 2009
 
 Name
                    Audit
                    Governance
                      And
                      Nominating
                    Compensation
                    Government
                      AffairsJoel
      McCleary
                    
                    
                    
                    
                    
                    
                    X
                    *
                    
                    X
                    *John
      Gill
                    X
                    *
                    
                    
                    
                    
                    XJames
      H. Cavanaugh, Ph.D.
                    X
                    
                    
                    X
                    *
                    
                    
                    
                    
                    XSteven
      St. Peter, M.D.
                    
                    
                    
                    X
                    
                    
                    XDavid
      P. Wright
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    XJeffrey
      W. Runge, M.D.Total
      2009 Meetings
                    4
                    
                    
                    4
                    
                    
                    12
                    
                    
                    1
 
 *Committee
Chairperson
 
 The
primary functions of each of the Board Committees are described
below.
  10
  Audit
Committee.    The primary functions of the Audit
Committee are to: review the professional services and independence of our
independent registered public accounting firm and our accounts, procedures and
internal controls; appoint (subject to stockholder approval) the firm selected
to be our independent registered public accounting firm; review and approve the
scope of the annual audit; review and evaluate with the independent public
accounting firm our annual audit and annual consolidated financial statements;
review with management the status of internal accounting controls; evaluate
problem areas having a potential financial impact on us that may be brought to
the Audit Committee’s attention by management, the independent registered public
accounting firm or the Board of Directors; and evaluate all of our public
financial reporting documents.
 
 The
current members of our Audit Committee each meet the independence criteria for
directors set forth under the rules of the NYSE Amex and the additional
independence criteria for members of audit committees specified in
Section 803B of the NYSE Amex Company Guide and Rule 10A-3 under the
Securities Exchange Act of 1934, as amended. Each member of our Audit Committee
is financially literate under the current listing standards of the NYSE Amex.
Our Board has determined that John Gill, the chairman of the Audit Committee,
qualifies as an “audit committee financial expert,” as such term is defined by
SEC rules. See page 15 of this Form 10-K/A for the Audit Committee
Report.
 
 Governance
and Nominating Committee.    The current members of
our Governance and Nominating Committee are “independent” as required by
Section 804 of the NYSE Amex Company Guide.
 
 The
primary functions of the Governance and Nominating Committee are to: review and
make recommendations on the range of skills and expertise which should be
represented on the Board, and the eligibility criteria for individual Board and
Committee membership; review and recommend to the Board the appropriate
structure of the Board; identify individuals qualified to become Board members
and recommend to the Board the nominees for election to the Board at the next
Annual Meeting of Stockholders; implement a policy and procedures with regard to
consideration of any director candidate recommended by Stockholders; retain and
terminate any search firm to be used to identify director candidates, and to
approve the search firm, fees and other retention terms; and review and
recommend to the Board the appropriate structure of Board Committees, Committee
assignments and the Board Committee chairman.
 
 Among
the factors the Governance and Nominating Committee considers when determining
persons to be nominated include whether such individuals are actively engaged in
business endeavors, have an understanding of financial statements, corporate
budgeting and capital structure, are familiar with the requirements of a
publicly traded company, are familiar with industries relevant to our business
endeavors, are willing to devote significant time to the oversight duties of the
Board of Directors of a public company, and are able to promote a diversity of
views based on the person’s education, experience and professional employment.
The Governance and Nominating Committee evaluates each individual in the context
of the board as a whole, with the objective of recommending a group of persons
that can best implement our business plan, perpetuate our business and represent
stockholder interests. The Governance and Nominating Committee may require
certain skills or attributes, such as financial or accounting experience, to
meet specific board needs that arise from time to time.
 
 The
Company is of the view that the continuing service of qualified incumbents
promotes stability and continuity in the board room, contributing to the ability
of the Board of Directors to work as a collective body, while giving the Company
the benefit of the familiarity and insight into the Company’s affairs that its
directors have accumulated during their tenure. Accordingly, the process of the
Governance and Nominating Committee for identifying nominees reflects the
Company’s practice of re-nominating incumbent directors who continue to satisfy
the Governance and Nominating Committee’s criteria for membership on the Board
of Directors, whom the Governance and Nominating Committee believes continue to
make important contributions to the Board of Directors and who consent to
continue their service on the Board of Directors. The Governance and Nominating
Committee will identify and/or solicit recommendations for new candidates when
there is no qualified and available incumbent.
 
 The
Governance and Nominating Committee will consider nominees recommended by
security holders. There are no differences in the manner in which the committee
evaluates nominees for director based on whether the nominee is recommended by a
security holder, subject to the requirements under our Amended and Restated
Certificate of Incorporation with respect to the appointment of two directors by
the holders of the Notes for as long as at least 30% of the aggregate principal
amount of the Notes remains outstanding. Stockholders who would like to have our
Governance and Nominating Committee consider their recommendations for
nominees for the position of director, should submit their recommendations, in
accordance with the procedures set forth below, in writing to: Corporate
Secretary, PharmAthene, Inc., One Park Place, Suite 450, Annapolis,
MD 21401. In order to be considered for inclusion in the proxy statement
and form of proxy for the annual meeting of stockholders to be held in 2011, the
stockholder’s notice must be received by us not less than 120 days before
the first anniversary of the date of this proxy statement, i.e., January 1,
2011. If we change the date of our 2011 Annual Meeting by more than
30 days from the date of the2010 Annual Meeting, then the deadline is a reasonable time before we begin
to print and send our proxy materials.
  11
  For
nominations, a stockholder’s notice must include: (i) as to each person
whom the stockholder proposes to nominate for election as a director,
(A) the name, age, business address and residential address of such person,
(B) the principal occupation or employment of such person, (C) the
class and number of shares of stock of PharmAthene that are beneficially owned
by such person, (D) any other information relating to such person that is
required to be disclosed in solicitations of proxies for election of directors
or is otherwise required by the rules and regulations of the SEC promulgated
under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and
(E) the written consent of the nominee to be named in the proxy statement
as a nominee and to serve as a director if elected and (ii) as to the
stockholder giving the notice, (A) the name, business address, and
residential address, as they appear on our stock transfer books, of the
nominating stockholder, (B) a representation that the nominating
stockholder is a stockholder of record and intends to appear in person or by
proxy at the meeting to nominate the person or persons specified in the notice,
(C) the class and number of shares of stock of our Company beneficially
owned by the nominating stockholder and (D) a description of all
arrangements or understandings between the nominating stockholder and each
nominee and any other person or persons (naming such person or persons) pursuant
to which the nomination or nominations are to be made by the nominating
stockholder.
 
 Compensation
Committee.    The current members of our Compensation
Committee are “independent” as required by Section 805 of the NYSE Amex
Company Guide.
 
 The
Company’s executive compensation program is administered by the Compensation
Committee. Each member of the Committee qualifies as an outside director within
the meaning of Section 162(m) of the Internal Revenue Code of 1986, as
amended (the “Internal Revenue Code”). The primary functions of the Compensation
Committee are to: consider, recommend, oversee and implement executive
compensation plans, policies and programs; review the performance and determine
the compensation of our executive officers and directors, including the
negotiation of any employment agreements with such persons, oversight and
administration of the 2007 Long-Term Incentive Compensation Plan, as amended
(the “2007 Plan”) and the grant of options and awards under the 2007 Plan.
Pursuant to Section 805 of the NYSE Amex Company Guide, compensation of our
Chief Executive Officer is determined, or recommended to the Board for
determination, by the Compensation Committee comprised solely of independent
directors. The Chief Executive Officer is not present during voting or
deliberations. Compensation for all other officers is determined, or recommended
to the Board for determination, by the Compensation Committee comprised solely
of independent directors.
 
 Under
the Compensation Committee Charter, our CEO and our Chairman of the Board may
recommend to the Compensation Committee individual compensation awards for our
officers. The Compensation Committee would then have to review the
recommendation and make its own recommendation to the Board.
 
 Government
Affairs Committee.    The primary functions of the
Government Affairs Committee are to: oversee and review the status of government
initiatives relating to funding and appropriations for the purchase of
therapeutics and prophylactics for biological and chemical weapons and other
threats to the population and to advise the Board on other governmental
considerations in the Board’s deliberations and decision-making
processes.
 
 Noteholder
Directors.    Pursuant to our Amended and Restated
Certificate of Incorporation, the two directors appointed by the Noteholders
have the right to serve as members of each of the Compensation and the
Governance and Nominating Committee of our Board for as long as at least 30% of
the original principal amount of the Notes remains outstanding.
  12
  Process
for Communicating with Board Members
 
 Interested
parties may communicate with any and all members our Board of Directors by
transmitting correspondence addressed to one or more directors by name at the
following address: PharmAthene, Inc., One Park Place, Suite 450,
Annapolis, MD 21401, c/o Corporate Secretary. Communications from our
stockholders to one or more directors will be collected and organized by our
Corporate Secretary and will be forwarded to the Chairman of the Board of
Directors or to the identified director(s) as soon as practicable. If multiple
communications are received on a similar topic, the Corporate Secretary may, in
his or her discretion, forward only representative correspondence.
 
 The
Chairman of the Board of Directors will determine whether any communication
addressed to the entire Board of Directors should be properly addressed by the
entire Board of Directors or a committee thereof. If a communication is sent to
the Board of Directors or a Committee, the Chairman of the Board of Directors or
the Chairman of that committee, as the case may be, will determine whether a
response to the communication is warranted.
  13
  Audit
Committee Report1
 
 The
Audit Committee has reviewed and discussed the audited financial statements for
the fiscal year ended December 31, 2009 with management of the Company and
has furnished the following report for inclusion in this Form
10-K/A.
 
 The
Audit Committee consists of two (2) directors named below. Each member of
the Audit Committee is an independent director as defined by applicable SEC
rules and NYSE Amex listing standards. In addition, the Board has determined
that John Gill is the “audit committee financial expert” as defined by
applicable SEC rules and that James H. Cavanaugh, Ph.D. satisfies the “financial
sophistication” criteria under the applicable rules of the NYSE Amex. The Audit
Committee operates under a written charter adopted by the Board, which is
available free of charge on our website under the heading “Investor Relations”
(see “Corporate Governance—Audit Committee Charter”), or by writing to
PharmAthene, Inc., One Park Place, Suite 450, Annapolis, MD 21401, c/o
Corporate Secretary.
 
 Management
is responsible for the Company’s internal controls and preparing the Company’s
consolidated financial statements. The Company’s independent accountants are
responsible for performing an independent audit of the consolidated financial
statements in accordance with generally accepted auditing standards and issuing
a report thereon. The Committee is responsible for overseeing the conduct of
these activities and appointing the Company’s independent accountants. As stated
above and in the Committee’s charter, the Committee’s responsibility is one of
oversight. The Committee does not provide any expert or special assurance as to
the Company’s financial statements concerning compliance with laws, regulations
or generally accepted accounting principles. In performing its oversight
function, the Committee relies, without independent verification, on the
information provided to it and on representations made by management and the
independent accountants.
 
 The
Audit Committee reviewed and discussed the Company’s consolidated financial
statements for the year ended December 31, 2009 with management and the
independent accountants. Management represented to the Audit Committee that the
Company’s consolidated financial statements were prepared in accordance with
generally accepted accounting principles. The Audit Committee discussed with the
independent accountants matters required to be discussed by Statement on
Auditing Standard No. 61, as amended, Communication with Audit Committees,
as adopted by the Public Company Accounting Oversight Board. The Committee also
reviewed, and discussed with management, management’s report on internal control
over financial reporting in accordance with Section 404 of the
Sarbanes-Oxley Act.
 
 The
Company’s independent accountants provided to the Audit Committee the written
disclosures and the letter required by Independence Standards Board Standard
No. 1, Independence Discussions with Audit Committees, and the Committee
discussed with the independent accountants their independence. The Audit
Committee concluded that Ernst & Young’s provision of non-audit
services, as described in this Form 10-K/A, to the Company and its affiliates is
compatible with Ernst & Young’s independence.
 
 Based
on the Audit Committee’s discussion with management and the independent
accountants and the Audit Committee’s review of the representations of
management, the written disclosures and the letter from the independent
accountants and the report of the independent accountants, the Committee
recommended that the Board include the audited consolidated financial statements
in the Form 10-K for the year ended December 31, 2009 for filing with
the SEC.
 
 SUBMITTED
BY THE AUDIT COMMITTEE OF THE BOARD OF DIRECTORS
 
 John
Gill, Chairman
 James
H. Cavanaugh, Ph.D.
  1  The
material in this report is not “soliciting material” and is not deemed “filed”
with the SEC and is not to be incorporated by reference in any of our filings
under the Securities Act of 1933 or the Securities Exchange Act of 1934, in each
case, as amended, whether made before or after the date hereof and irrespective
of any general incorporation language in any such filing.
  14
  Item
11. Executive Compensation
 
 Summary
Compensation Table
 
 The
following Summary Compensation Table sets forth, for the fiscal years ended
December 31, 2009 and 2008, all compensation awarded to, earned by, or paid
to our former Chief Executive Officer in 2009 and the two most highly
compensated executive officers (other than our CEO) who received annual
compensation in excess of $100,000. There were no nonqualified deferred
compensation earnings paid to any executive in 2009.
 
 
 Name
      and Principal Position
              
              Year
              
              Salary
                ($)
              
              Bonus
                ($)
              
              Stock
                Awards
                ($)(1)
              
              Option
                Awards
                ($)(1)
              
              Nonequity
                Incentive
                Plan
                Compensation
                ($)(2)
              
              All
      Other
                Compen-sation
                ($)
              
              Totals
                ($)David
      P. Wright
              
              2009
              
              426,433
              
              —
              
              91,475
              
              67,543
              
              —
              
              15,320
              
              600,771Chief
      Executive Officer, Director(3)
              
              2008
              
              407,680
              
              —
              
              —
              
              —
              
              37,917
              
              13,188
              
              458,785
 
 Eric
      I. Richman
              
              2009
              
              287,782
              
              —
              
              75,210
              
              55,533
              
              —
              
              8,520
              
              427,045Presidentand
      Chief Operating Officer(4)
              
              2008
              
              275,126
              
              —
              
              —
              
              —
              
              31,175
              
              8,020
              
              314,321
 
 Wayne
      Morges, Ph.D.
                  
                  2009
                  
                  260,247
                  
                  —
                  
                  62,954
                  
                  163,451
                  
                  —
                  
                  9,778
                  
                  496,430Vice
      President,
                    Regulatory
      Affairs and Quality
                  
                  2008
                  
                  249,757
                  
                  —
                  
                  —
                  
                  —
                  
                  26,095
                  
                  9,820
                  
                  285,672
 
 
 
 (1)Dollar amounts shown
reflect the aggregate grant date fair value of stock/options computed in
accordance with FASB ASC Topic 718 (formerly FAS 123R). The fair value was
estimated using the assumptions detailed in Note 16 to the Company’s
Consolidated Financial Statements included in our Annual Reports on
Form 10-K for the fiscal years ended December 31, 2009 and 2008,
respectively.
 
 (2)Dollar amounts
shown reflect the cash portion of the bonus granted by our Board in January 2009
for the 2008 fiscal year under our 2008 Bonus Program.
 
 (3)On April 27,
2010, David P. Wright notified the Company that he was stepping down as Chief
Executive Officer of PharmAthene.  Mr. Wright serves on our Board
of Directors but to date has not received any compensation for his service in
this capacity.
 
 (4)  Mr.
Richman was appointed our President and Chief Operating Officer on March 25,
2010.  At December 31, 2009 he was our Senior Vice President, Business
Development and Strategic Planning.
 
 15
 
 Outstanding
Equity Awards at Fiscal Year-End
 
 The
following table sets forth information concerning the outstanding equity awards
of each of the named executive officers in the Summary Compensation Table as of
December 31, 2009.
 As
of December 31, 2009
 Option
      Awards(1)
                                                      
                                                      Stock
      Awards(2)Name
                                                      
                                                      Number
      of
                                                        Securities
                                                        Underlying
                                                        Unexercised
                                                        Options(#)
                                                        Exercisable
                                                      
                                                      Number
      of
                                                        Securities
                                                        Underlying
                                                        Unexercised
                                                        Options(#)
                                                        Unexercisable
                                                      
                                                      Option
                                                        Exercise
                                                        Price
      ($)
                                                      
                                                      Option
                                                        Expiration
                                                        Date
                                                      
                                                      Number
      of
                                                        Shares
      or
                                                        Units
      of
                                                        Stock
      That
                                                        Have
      Not
                                                        Vested
      (#)
                                                      
                                                      Market
      Value
                                                        of
      Shares or
                                                        Units
      of
                                                        Stock
      That
                                                        Have
      Not
                                                        Vested
      ($)(3)David
      P. Wright,
                                                      
                                                      
                                                      51,695
                                                      
                                                      —
                                                      
                                                      
                                                      2.96
                                                      
                                                      7/15/13
                                                      (4)
                                                      56,250
                                                      (10)
                                                      $
                                                      110,250Chief
      Executive Officer,
                                                      
                                                      
                                                      46,807
                                                      
                                                      —
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/18/15
                                                      (5)
                                                      37,185
                                                      (11)
                                                      
                                                      72,883Director(16)
                                                      
                                                      
                                                      11,071
                                                      
                                                      0
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/01/16
                                                      (6)16.096
                                                      
                                                      460
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/04/17
                                                      (7)390,000
                                                      
                                                      390,000
                                                      
                                                      
                                                      5.36
                                                      
                                                      8/30/17
                                                      (8)—
                                                      
                                                      37,185
                                                      
                                                      
                                                      2.46
                                                      
                                                      1/21/19
                                                      (9)Eric
      I. Richman
                                                      
                                                      
                                                      28,638
                                                      
                                                      —
                                                      
                                                      
                                                      2.96
                                                      
                                                      11/15/13
                                                      (12)
                                                      10,000
                                                      (14)
                                                      $
                                                      19,600President
      and
                                                      
                                                      
                                                      11,043
                                                      
                                                      —
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/18/15
                                                      (5)
                                                      30,573
                                                      (11)
                                                      
                                                      59,923Chief
      Operating Officer(17)
                                                      
                                                      
                                                      8,052
                                                      
                                                      230
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/04/17
                                                      (7)4,510
                                                      
                                                      —
                                                      
                                                      
                                                      3.80
                                                      
                                                      2/22/16
                                                      (6)164,667
                                                      
                                                      95,333
                                                      
                                                      
                                                      5.20
                                                      
                                                      10/02/17
                                                      (13)—
                                                      
                                                      30,573
                                                      
                                                      
                                                      2.46
                                                      
                                                      1/21/19
                                                      (9)Wayne
      Morges, Ph.D.
                                                      
                                                      
                                                      15,184
                                                      
                                                      —
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/31/15
                                                      (15)
                                                      4,167
                                                      (14)
                                                      $
                                                      8,167Vice
      President,
                                                      
                                                      
                                                      4,107
                                                      
                                                      —
                                                      
                                                      
                                                      3.80
                                                      
                                                      2/22/16
                                                      (6)
                                                      25,591
                                                      (11)
                                                      
                                                      50,158Regulatory
      Affairs and Quality
                                                      
                                                      
                                                      4,026
                                                      
                                                      115
                                                      
                                                      
                                                      3.80
                                                      
                                                      1/04/17
                                                      (7)72,833
                                                      
                                                      42,167
                                                      
                                                      
                                                      5.20
                                                      
                                                      10/02/17
                                                      (13)—
                                                      
                                                      89,986
                                                      
                                                      
                                                      2.46
                                                      
                                                      1/21/19
                                                      (9)
 
 (1)
Reflects options granted under our 2007 Plan as well as options initially
granted under the 2002 Long-Term Incentive Plan and assumed by us in the merger
and now outstanding under the 2007 Plan.
 
 (2)
Reflects restricted common stock awards granted under our 2007 Plan on
August 30, 2007 and October 2, 2007. Unless otherwise indicated in the
footnotes below, all shares of restricted stock vest in three equal annual
installments of 33.3% of the grant beginning on the first anniversary of the
date of grant.
 
 (3)
Reflects a closing price of our common stock on December 31, 2009 of $1.96
per share. The closing price of our common stock on April 29, 2010 was
$1.44.
 
 (4)
Reflects options granted on July 15, 2003 which vested in equal annual
installments over four years on the anniversary of the date of
grant.
 
 (5)
Reflects options granted on January 18, 2005 pursuant to which 25% vested
immediately and the remainder vested in equal monthly installments over
36 months beginning in the second month following the date of
grant.
 
 (6)
Reflects options granted on February 22, 2006, pursuant to which 25% vested
immediately and the remainder vest in equal monthly installments over
36 months beginning in the second month following the date of
grant.
 
 (7)
Reflects options granted on January 4, 2007 which vest in equal monthly
installments over 36 months beginning on the month following the date of
grant.
  16
 
 (8) Reflects options granted on August 30, 2007
pursuant to which 25% vest on the first anniversary of the date of grant and the
remainder vest in equal monthly installments over 48 months beginning on
the month following the first anniversary.
 
 (9)
Reflects options granted on January 21, 2009 pursuant to which 25% vest on the
first, second, third and fourth anniversaries of the grant date.
 
 (10)  Reflects
a restricted stock award of 100,000 shares granted on August 30, 2007
pursuant to which 25% vested on the first anniversary of the date of grant, an
additional 6.25% of the award vested between September and December 2008, and
the remainder vests on an annual basis over the succeeding four (4) years
following the first anniversary date as follows: 12.5% of the award on the
second anniversary of the date of grant and 18.75% of the award on each of the
succeeding three anniversaries so that 100% of the award vests over
5 years. See “Employment Agreements—David P. Wright.”
 
 (11)
Reflects restricted stock granted on January 21, 2009 pursuant to which 33.3%
vests on each anniversary of the date of grant.
 
 (12)
Reflects options granted on October 14, 2003 which vested in equal annual
installments over four years on the anniversary of the date of
grant.
 
 (13)
Reflects options granted on October 2, 2007 pursuant to which 20% vested
immediately, 20% vested on the first anniversary of the date of grant and the
remainder vests in equal monthly installments over 36 months beginning on
the first month following the first anniversary.
 
 (14)
Reflects a restricted stock award granted on October 2, 2007 pursuant to
which 33.3% vests on each anniversary of the date of grant.
 
 (15)
Reflects options granted on January 1, 2005, which vested in equal annual
installments over four years on the anniversary of the date of
grant.
 
 (16)On April 27, 2010,
David P. Wright notified the Company that he was stepping down as Chief
Executive Officer of PharmAthene.
 
 (17)  Mr.
Richman was appointed our President and Chief Operating Officer on March 25,
2010. At December 31, 2009 he was our Senior Vice President, Business
Development and Strategic Planning.
 
 Employment
Agreements
 
 David
P. Wright
 
 On
April 27, 2010, David P. Wright notified the Company that he was stepping down
as Chief Executive Officer of PharmAthene.   In connection with
the merger, the Company had entered into an employment agreement with David P.
Wright regarding his employment as Chief Executive Officer of the Company. The
agreement was subsequently amended effective as of January 21, 2009. Under
the agreement, Mr. Wright received a base salary of $392,000 per year
subject to increase (which was consistent with the salary he previously received
as Former PharmAthene’s Chief Executive Officer) and was eligible to receive
annual bonus compensation of up to 30% of his base salary plus additional
bonuses at the option and discretion of the Compensation
Committee.  Mr. Wright’s salary effective January 1, 2009
was $426,433. On August 30, 2007, the Compensation Committee granted to
Mr. Wright a stock option to purchase 780,000 shares of the Company’s
common stock pursuant to the 2007 Plan at an exercise price of $5.36, which was
equal to the fair market value of a share of the Company’s common stock on the
date of the grant as determined in accordance with applicable law and
regulations as the closing price of the Company’s common stock on
August 30, 2007, and a restricted stock award of 100,000 shares of the
Company’s common stock. The option has a term of ten (10) years and,
subject to possible acceleration of vesting, vests over a five (5) year
period with 25% having vested on August 30, 2008, the first anniversary of
the grant date, and the remainder vesting monthly on a pro-rata basis over the
succeeding 48 months following the first anniversary date. The restricted
stock award initially had the same vesting schedule as the option award, but the
employment agreement with Mr. Wright was amended effective as of
January 21, 2009, to change the schedule such that, after the initial 25%
of the award vested on August 30, 2008, the first anniversary of the grant
date, and an additional 6.25% of the award vested between September and December
2008, the remainder would vest on an annual basis over the succeeding four
(4) years following that anniversary date as follows: 12.5% of the award on
the second anniversary date and 18.75% of the award on each of the succeeding
three anniversaries so that 100% of the award vests over
5 years.
  17
  As
Chief Executive Officer, Mr. Wright was eligible to receive additional
grants of stock options and restricted stock at the discretion of the
Compensation Committee and participated in PharmAthene’s standard employee
benefits package (including group medical, dental and vision insurance coverage,
paid holiday, vacation and sick leave, and 401(k) plan participation) and an
automobile allowance in an amount not to exceed $1,000 per month. Also pursuant
to the terms of his employment agreement, Mr. Wright was reimbursed for all
reasonable, documented business expenses incurred in the course of performing
his duties andfor legal expenses, up to $10,000,
incurred in connection with the review and negotiation of his employment
agreement. The agreement requires that, until the expiration of a period of
12 months following termination of his employment, Mr. Wright shall
not directly or indirectly engage in the development, production, marketing or
sale of products that compete with the products of PharmAthene or assist others
in a competing business or induce other employees of PharmAthene to terminate
their employment with PharmAthene or engage in a competing business. The
employment agreement also requires Mr. Wright to refrain from directly or
indirectly disclosing any confidential information obtained while having worked
at PharmAthene.
 
 The
employment agreement states that if employment is terminated without cause or
Mr. Wright resigns for good reason, in each case as defined below,
Mr. Wright is entitled to severance payments in the form of a continuation
of his base salary immediately prior to such termination for a period of
12 months following the effective date of the termination and, in addition,
an amount of shares equal to up to 25% of the total aggregate amount of options
and restricted stock granted on August 30, 2007 would become vested with
the remaining balance of unvested options and restricted stock being forfeited.
The employment agreement further provided that, in the event of a change in
control of PharmAthene, as defined under the employment agreement, and the
termination of Mr. Wright’s employment either in connection with the change
in control, by the Company without cause or by Mr. Wright with good reason
within 12 months following the change in control, in addition to the
severance payments to which Mr. Wright would be entitled, all stock options
and shares of restricted stock held by Mr. Wright that are not then vested
would become immediately and fully vested.
 
 Under
Mr. Wright’s employment agreement, as under our standard executive
employment agreement, a termination “for cause” is a termination for
(1) willful and substantial misconduct that materially injures us and is
not corrected; (2) repeated neglect of duties or failure to act, which can
reasonably be expected to materially and adversely affect our business or
affairs, after written notice from us; (3) material breach of the
confidentiality and related provisions of the employment agreement or of our
policies; (4) commission of material fraud with respect to our business and
affairs; (5) conviction of, or nolo contendere plea to, a felony;
(6) demonstrable gross negligence or (7) habitual insobriety or use of
illegal drugs adversely affecting the executive’s duties. Termination “for good
reason” means a termination for (a) any material breach by the Company of
our obligations under the employment agreement; (b) any material reduction
in the executive’s duties, authority or responsibilities without the executive’s
consent; (c) any assignment to the executive of duties or responsibilities
materially inconsistent with the executive’s position and duties under the
employment agreement without consent; (d) a relocation of the Company’s
principal executive offices or our determination to require the executive to be
based more than 25 miles away; (e) depriving the executive of any material
benefit plan and (f) failing to have a successor or assignee of the Company
or someone acquiring substantially all of our assets specifically assume the
employment agreement. The detriment must in each case persist for at least
20 days after the Company receives written notice from the executive before
it constitutes termination for good reason.
 
 Eric
I. Richman and Wayne Morges, Ph.D.
 
 Messrs. Richman
and Morges are signatories to our standard executive employment agreement. Under
this agreement, executives are paid an annual base salary, payable in equal
periodic installments. The base salary is subject to review annually by the
Compensation Committee and is subject to increase at the option and sole
discretion of the Compensation Committee. Messrs. Richman and Morges are
also eligible to receive, at the sole discretion of the Compensation Committee,
an annual cash bonus of up to an additional 30%, initially, of their base
salary. In addition, the executives are eligible for additional bonuses at the
option and sole discretion of the Compensation Committee based on the
achievement of certain pre-determined performance milestones and are eligible to
receive such stock, option and other awards under our 2007 Plan as may be
granted by the Compensation Committee or its designee in its sole discretion.
The executives are also entitled to participate in our standard employee
benefits package (including group medical, dental and vision insurance coverage,
life insurance and death benefit and 401(k) plan
participation).  Under their agreements, the executives are
furthermore entitled an automobile allowance in an amount not to exceed $1,000
per month.
  18
  The
agreements require that during his employment and for a period of 12 months
following termination of the employment, the executive shall not directly or
indirectly engage in the development, production, marketing or sale of products
that compete with our products or assist others in a competing business or
induce other employees of PharmAthene to terminate their employment with us or
engage in a competing business. The executive is furthermore required to refrain
from directly or indirectly disclosing any confidential information obtained
while working at PharmAthene.
 
 If
the executive voluntarily resigns employment or is terminated for cause (as
defined under “—David P. Wright” above), he will have no further rights or
claims against us except for the right to receive (i) the unpaid portion of
his or her base salary on a pro-rata basis; (ii) payment of the executive’s
accrued but unpaid amounts and extension of applicable benefits in accordance
with the terms of any incentive compensation, retirement, employee welfare or
other employee benefit plans or programs of PharmAthene in which the executive
is then participating in accordance with the terms of such plans or programs and
(iii) reimbursement for any reasonable and necessary business and travel
expenses.
 
 If
the executive is terminated other than for cause or he resigns for good reason
(as defined under “—David P. Wright” above), the executive is entitled to
receive the payments in (i) through (iii) above as well as severance
payments in the form of a continuation of his or her base salary in effect
immediately prior to such termination for a period of between 6 and
12 months following the effective date of the termination, payable in
consideration for and only after he executes a general release containing terms
reasonably satisfactory to us.
 
 Mr. Richman’s
original employment agreement provides for a base salary of $195,000 per year
starting in 2003, subject to adjustments and eligibility to receive annual bonus
compensation at the option and discretion of the Compensation Committee.
Mr. Richman’s current salary, which was increased effective March 25, 2010
in connection with his appointment as President and Chief Operating Officer, is
$330,950. Mr. Morges’ employment agreement provides for a base salary of
$249,757 per year, subject to adjustments and eligibility to receive annual
bonus compensation at the option and discretion of the Compensation Committee.
Mr. Morges current salary effective April 4, 2010 is $270,657.
 
 Equity Compensation Plan Information
 
 The
following table provides information regarding the number of securities to be
issued under our 2007 Plan, the weighted-average exercise price of options
issued under the 2007 Plan and the number of securities remaining available for
future issuance under the 2007 Plan, in each case as of December 31,
2009:
  19
 
 Plan
      category
              
              Number
      of securities
                to
      be issued upon
                exercise
      of outstanding
                options,
      warrants and
                rights
              
              Weighted-average
                exercise
      price of
                outstanding
      options,
                warrants
      and rights
              
              Number
      of securities
                remaining
      available
                for
      future issuance
                under
      equity
                compensation
      plansEquity
      compensation plans approved by security holders
              
              
              4,913,366
              (1)
              $
              3.88
              
              
              4,752,244
              (2)Equity
      compensation plans not approved by security holders
              
              
              —
              
              
              —
              
              
              —Total
              
              
              4,913,366
              
              $
              3.88
              
              
              4,752,244
 
 (1)
Does not include 489,338 shares of restricted stock granted under the 2007 Plan
as of December 31, 2009.
 
 (2)
This amount includes shares underlying unexercised options already granted and
reported in the first column.  Under our 2007 Plan, such shares are
not treated as issued and are not counted as used against the plan limits until
the options are exercised.  If we were to exclude shares underlying
unexercised options already granted, this amount would be (161,122), a negative
amount, as of December 31, 2009.   Under our 2007 Plan, the
number of shares available for issuance under such plan is automatically
increased as of the first day of our fiscal year, beginning in 2009 and
occurring each year thereafter through 2015, by a number that is equal to the
least of (i) 1,100,000 shares, (ii) 2.5% of the outstanding shares of
common stock as of the end of our immediately preceding fiscal year, and
(iii) any lesser number of shares determined by the Board; provided,
however, that the aggregate number of shares available for issuance pursuant to
such increases may not exceed a total of 5,700,000 shares.
 
 Further
information regarding our 2007 Plan is contained in Note 13 to our consolidated
financial statements for the fiscal year ended December 31, 2009 contained
in our Annual Report on Form 10-Kfor that year.
 
 Bonus
Program
 
 The
Compensation Committee of the Board of Directors of the Company has adopted a
bonus program (the “Bonus Program”) for our executive officers and other
employees to be identified from time to time by the Chief Executive Officer. The
Bonus Program was established to provide for the payment to members of
management and identified employees of a bonus that is linked to achievement of
key corporate performance objectives and, in the case of executives, also to the
achievement of key personal objectives which are approved by the Compensation
Committee. The goal of the Bonus Program is to reward personnel by providing
further compensation to members of management and identified employees based on
the achievement of specified annual goals that the Compensation Committee and
the Board of Directors believe correlate closely with the growth of long-term
stockholder value. We believe that the Bonus Program will also promote greater
communication and foster the appropriate feedback for enhanced productivity and
effectiveness.
 
 The
Bonus Program is intended to be applicable to the following members of
management: the Chief Executive Officer, the President and Chief Operating
Officer, the Senior Vice President and Chief Financial Officer, the Senior Vice
President-Operations, the Senior Vice President & General Counsel, the
Senior Vice President-Medical Director, the Vice President-Regulatory Affairs
and Quality, the Senior Vice President, Policy and Government Affairs and the
Senior Vice President-Chief Scientific Officer. Annually and based upon the
recommendations of the Chief Executive Officer and the Compensation Committee,
the Board of Directors will approve (i) a target bonus pool amount;
(ii) a target bonus payout for each executive in the Bonus Program,
(iii) the financial achievement percentages and bonus modifiers that will
be used to determine the component of the bonus based upon a comparison of the
Company’s financial and operational performance for the fiscal year against the
Board approved financial and operating plan for the fiscal year, (iv) the
executives’ personal objectives for the fiscal year, and (v) the weight or
importance of the corporate financial performance objectives and the personal
objectives. After the end of each fiscal year, the Compensation Committee will
measure the Company’s actual financial performance and consider each executive’s
personal performance to determine the appropriate adjustment to the executive’s
target bonus.
 
 Determining
the annual target bonus pool.    In each fiscal year,
the Board of Directors will determine a target bonus pool for that fiscal year
and determine how much of that pool should be allocated to executive officers
and how much should be allocated to all other personnel. This pool will be a
target which may be revised by the Board at their discretion.
  20
 
 For
fiscal year 2010, the target bonus pool is equal to the approximate sum of 30%
of the aggregate base salary of the executive officers and certain other key
employees and 10% of the aggregate base salary of all other employees of the
Company.
 
 The
pool is to be divided among the relevant executives with reference to the
achievement of specific personal and corporate targets. The Compensation
Committee shall have the discretion to award more or less than the initial pool
amount; and any particular executive or key employee may be awarded a bonus that
is greater or less than 30% of their base salary and any non-executive employee
may be awarded a bonus that is greater or less than 10% of their base salary.
Finally, the pool may be increased to the extent new executive officers and
other employees may be hired during the year.
 
 Determining
the annual target bonus.    During each fiscal year,
the Compensation Committee shall determine the target bonus for each executive
in the Bonus Program taking into account any terms regarding bonuses which may
be contained in each executive’s employment agreement. Under his employment
agreement, Mr. Wright was eligible to receive a bonus equal to up 30% of
his base salary. The Board will consider all factors that it deems relevant to
such determination, including, but not limited to, the recommendations of our
Chief Executive Officer (except with respect to his own bonus), competitive
market conditions, and the Board’s assessment of the level of growth reflected
in the Company’s financial performance objectives. The executives are not
subject to a maximum bonus payout. All bonuses will be paid in
cash.
 
 For
fiscal year 2010, the target bonus payout for executive officers and certain
other key employees is 30% of the 2010 base salary of the relevant executive
officer and such other key employees. The target bonus payout for non-executive
employees has been set at 10% of the 2010 base salary of the relevant
non-executive employee. These annual target bonus levels may be modified based
upon the terms of employment agreements with our executives, which have been
approved by the Chief Executive Officer and Board of Directors, as applicable,
changes in market conditions or performance of the Company in each case in the
sole discretion of the Board of Directors.
 
 Determining
the financial achievement percentages, bonus modifiers and corporate financial
plan.    In each fiscal year, the Compensation
Committee will review with the executive team and establishcorporate performance objectives for the fiscal
year that will apply to all executive officers, including the chief executive
officer and achievement percentages and bonus modifiers that will be used to
evaluate the portion of the bonus applicable to each executive based upon the
Company’s financial performance. The Board will review and consider senior
management’s recommendations for financial achievement percentages, bonus
modifiers and the fiscal year financial plan and discuss such recommendations
with senior management before making final determinations.
 
 The
Compensation Committee has established with management specific strategic goals
for 2010 as follows, with percentage weighting reflecting the approximate
percentage value to be placed upon the achievement of each target:
 ·
                  Secure
      additional significant advanced development funding  for SparVaxTM.(20%)
  ·
              Secure
      an advanced development contract with significant funding for Valortim®
      (20%)
  ·
              Secure
      additional significant funding for Protexia®
  (20%)
  ·
                      Financial
      performance in line with budgets and forecasts presented to the Board of
      Directors subject to later modifications presented to and approved by the
      Board (10%)·
                      Achieve
      positive stock price performance and communications with the markets
      (30%)
 Determining
personal objectives.    Also in each fiscal year, the
Compensation Committee, will consider and approve each executive’s personal
objectives for the fiscal year. Each executive’s personal objectives will be
agreed upon by the executive and approved by our Chief Executive Officer (except
with respect to his own personal objectives). The personal objectives of our
Chief Executive Officer will be the corporate objectives for all executive
officers.
  21
  Determining
relative weight of corporate performance objectives and personal
objectives.    The Compensation Committee will also
evaluate the weight or importance that will be placed on achievement of the
corporate performance objectives and the personal objectives.
 
 Measuring
performance.    After the end of the fiscal year, the
Compensation Committee will measure the Company’s actual performance (using the
predetermined corporate achievement percentages) and assess each executive’s
personal performance against his or her personal objectives to determine the
appropriate bonus allocable to each executive officer from the target bonus
pool. The Committee will consider the executive’s overall contribution to the
Company’s success and, in the case of executives other than the Chief Executive
Officer, the recommendation of the Chief Executive Officer. In determining the
appropriate bonuses, the Compensation Committee will also consider other
performance considerations related to unforeseen events occurring during the
fiscal year. In appropriate circumstances, the Committee has discretion to award
a bonus that is less than the amount determined by the procedures outlined
above, including to award no bonus at all or greater than the amounts that might
be determined by the procedures outlined above.
 
 DolmatConnell &
Associates, our compensation consultant, reviewed the structure of our Bonus
Program in 2007 and at that time made recommendations which have been
incorporated into the Bonus Program and have not been materially changed since
then. DolmatConnell was engaged in 2007 to review and make recommendations with
respect to compensation of directors, executive officers and other employees,
the Compensation Committee charter and to advise the Compensation Committee as
to best practices in committee rules and procedures.
 
 22
 
 Director
Compensation
 
 The
following table sets forth the cash and non-cash compensation of our directors
(other than our former Chief Executive Officer, who was not separately
compensated for his service on the Board) for the fiscal year ended
December 31, 2009. In the paragraph following the table and in the
footnotes, we describe our standard compensation arrangement for service on the
Board of Directors and Board Committees.
 
 For
the Fiscal Year Ended December 31, 2009
 
 Name(1)
                  
                  Fees
                    Earned
      or
                    Paid
      in
                    Cash($)(2)
                  
                  Option
                    Awards
                    ($)(3)
                  
                  Total
                    ($)John
      Pappajohn
                  
                  
                  28,750
                  
                  50,283
                  
                  79,033Joel
      McCleary
                  
                  
                  34,500
                  
                  50,283
                  
                  84,783John
      Gill(4)
                  
                  
                  40,500
                  
                  131,011
                  
                  171,511James
      H. Cavanaugh, Ph.D.
                  
                  
                  37,500
                  
                  50,283
                  
                  87,783Steven
      St. Peter, M.D.
                  
                  
                  28,000
                  
                  50,283
                  
                  78,283Derace
      L. Schaffer, M.D.
                  
                  
                  22,500
                  
                  50,283
                  
                  72,783Jeffrey
      W. Runge, M.D.
                  
                  
                  —
                  
                  18,476
                  
                  18,476
 
 
 (1)See the
Summary Compensation Table for disclosure related to compensation paid to David
P. Wright, our former Chief Executive Officer. To date, Mr. Wright has not
received any additional compensation for his services as a member of our Board
of Directors.
 
 (2)Fees earned are based on
membership on the Board of Director, committee membership and leadership
positions. Please refer to our general policy on compensation of the members of
our Board of Directors below in the section entitled “General Policy Regarding
Compensation of Directors.” In addition to the other compensation received,
members of the Board of Directors are reimbursed for the reasonable
out-of-pocket costs incurred by them in connection with travel to and from Board
and committee meetings. None of such reimbursements amounted to $10,000 or
more.
 
 (3)The amounts in this
column represent the aggregate grant date fair value computed in accordance with
FAS ASC Topic 718.  As of December 31, 2009, the aggregate number
of option awards outstanding (vested and unvested) for each of
Mr. Pappajohn and Dr. Schaffer was 50,000, for Dr. Cavanaugh was 52,759,
for Mr. Gill was 92,759, for Mr. McCleary was 102,759, for
Dr. St. Peter was 51,104 and for Dr. Runge was
20,000.
 
 (4)On August 14, 2009, in
recognition of his services as chair of the Audit Committee of the Board, the
Company granted to John Gill an option to purchase 40,000 shares of our common
stock at an exercise price of $2.92 per share based on the closing price of our
common stock on the grant dated as reported on the American Stock Exchange (now
NYSE Amex) on that day.  Fifty percent of such options vested
immediately and fifty percent will vest on the first anniversary of the grant
date. The fair value of the options was $2.02 per share, determined using the
Black-Scholes option valuation method.
 
 General
Policy Regarding Compensation of Directors
 
 On
June 8, 2009, the Board approved the following annual compensation for
non-employee members of our Board:
 
 •$30,000 cash retainer for
membership on the Board,
 
 •$25,000 additional cash
retainer for the chairman of the Board,
 
 •$1,500 cash payment per
regular Board meeting attended in excess of four per year (including telephonic
meetings),
  23
  •$15,000 cash retainer for
the Audit Committee chair,
 
 •$5,000 cash retainer for
membership on the Audit Committee (other than Audit Committee
chair);
 
 •$12,000 cash retainer for
the Compensation Committee chair,
 
 •$3,000 cash retainer for membership on the Compensation Committee (other
than Compensation Committee chair),
 
 •$10,000 cash retainer for
the Governance and Nominating Committee chair,
 
 •$2,500 cash retainer for
membership on the Governance and Nominating Committee (other than Governance and
Nominating Committee chair), and
 
 •$750 cash payment per
committee meeting attended in excess of six per year.
 
 In
addition, every non-employee member of our Board is entitled annually to receive
an option to purchase 20,000 shares of our common stock on the date of our
annual meeting of stockholders, at an exercise price per share based on the
closing price of our common stock on the grant date as reported on the NYSE
Amex, and immediately vesting on the grant date. For fiscal years 2008 and 2009,
these option grants were made in March 2009 (at which time the award was still
10,000 options) and August 2009, respectively.  In August 2009, in
recognition of the services he provides as chair of the Audit Committee,
Mr. Gill was granted an option to purchase 40,000 shares of common stock at
an exercise price of $2.92 per share based on the closing price of the
common stock on the grant date as reported on the NYSE Amex.
 
 In
addition to the above compensation, upon initially joining the Board, a member
is entitled to receive options to purchase 20,000 shares of common stock.
 
 Compensation
Committee Interlocks and Insider Participation
 
 During
the fiscal year ended December 31, 2009, the members of our Compensation
Committee were Joel McCleary, John Gill and Steven St. Peter, M.D. All of
these members, who continue to serve on the Compensation Committee, are
independent directors, and no member is or has been an employee or former
employee of PharmAthene. In addition, no Committee member had any relationship
requiring disclosure under “Item 13.  Certain Relationships and
Related Transactions” in this Form 10-K/A.
  24
 
 During
the fiscal year ended December 31, 2009, none of our executive officers
served on the Compensation Committee (or its equivalent) or on the Board of
Directors of another entity, one of whose executive officers served on our
Compensation Committee or our Board of Directors.
 
 Item
12. Security Ownership of Certain Beneficial Owners and Management and
RelatedStockholder Matters
  The
following table sets forth information, as it was available to the Company on
April 30, 2010, based on information furnished by the persons named below,
obtained from our transfer agent and/or obtained from certain beneficial
ownership filings made by the persons named below with the SEC, with respect to
the beneficial ownership of shares of the Company’s common stock by
(i) each person known by us to be the owner of more than 5% of our
outstanding shares of the Company’s common stock (inclusion in this table shall
not be deemed an admission of affiliate status), (ii) each director,
nominee for director and named executive officer and (iii) all directors
and executive officers as a group. Except as indicated in the footnotes to the
table, the persons named in the table have sole voting and investment power with
respect to all shares of common stock shown as beneficially owned by
them.
 
 Name
      of Beneficial Owner(1)
                  
                  Number
      of Shares
                    Beneficially
      Owned
                  
                  Percentage
      of
                    Outstanding
      Shares(2)Funds
      Affiliated with MPM Bioventures III, L.P.(3)
                  
                  
                  6,570,822
                  
                  19.8
                  %HealthCare
      Ventures VII, L.P.(4)
                  
                  
                  4,557,562
                  
                  14.6
                  %AmTrust
      Capital Management, Inc. (and affiliate)(5)
                  
                  
                  1,972,874
                  
                  6.6
                  %Kelisia
      Holdings Limited (and affiliate)(6)
                  
                  
                  3,733,334
                  
                  12.4
                  %Baker
      Brothers Investments II, L.P., Baker Brothers Life
      Sciences, L.P. and 14159, L.P(7)
                  
                  
                  4,032,306
                  
                  9.9
                  %(7)John
      Pappajohn(8)**
                  
                  
                  861,164
                  
                  2.9
                  %David
      P. Wright(9)**
                  
                  
                  1,020,676
                  
                  3.3
                  %James
      H. Cavanaugh, Ph.D.(10)**
                  
                  
                  4,557,562
                  
                  14.6
                  %Steven
      St. Peter, M.D.(11)**
                  
                  
                  51,104
                  
                  *John
      Gill(12)**
                  
                  
                  72,759
                  
                  *Joel
      McCleary(13)**
                  
                  
                  227,973
                  
                  *Derace
      L. Schaffer, M.D.(14)**
                  
                  
                  1,354,661
                  
                  4.4
                  %Eric
      I. Richman(15)**
                  
                  
                  320,628
                  
                  1.1
                  %Jeffrey
      W. Runge(16)**
                  
                  
                  20,000
                  
                  *Michel
      Sayare, Ph.D.**(17)
                  
                  
                  20,000
                  
                  *Wayne
      Morges, Ph.D. (18)
                  
                  
                  168,353
                  
                  *All
      directors and executive officers as a group (17 persons)
                  
                  
                  9,303,100
                  
                  27.6
                  %
 
 
 *Less than 1.0%
 
 **Director
 
 (1)Unless otherwise
indicated in other footnotes, the address for each beneficial owner is c/o
PharmAthene, Inc., One Park Place, Suite 450, Annapolis,
MD 21401.
 
 (2)Based on 30,086,019
shares of common stock outstanding as of April 30, 2010. Beneficial ownership is
determined in accordance with the rules and regulations of the SEC. In computing
the number of shares beneficially owned by a person and the percentage ownership
of that person, shares of common stock underlying warrants, Notes or subject to
options held by that person that are currently exercisable or exercisable within
60 days are deemed outstanding. Such shares, however, are not deemed
outstanding for the purposes of computing the percentage ownership of any other
person. Except as indicated in the following footnotes or pursuant to applicable
community property laws, each stockholder named in the table has sole voting and
investment power with respect to the shares set forth opposite such
stockholder’s name.
 
 (3)Includes 2,352,271 shares
issuable upon conversion of the 10% Convertible Notes (including shares
underlying interest that will accrue within 60 days of April 30, 2010) and
729,108 shares issuable upon exercise of the related warrants. MPM
BioVentures III GP, L.P. and MPM BioVentures III LLC
are the direct and indirect general partners of MPM
BioVentures III-QP, L.P., MPM
BioVentures III GmbH & Co. Beteiligungs KG, MPM
BioVentures III, L.P. and MPM BioVentures III Parallel
Fund, L.P. The Series A members of MPM BioVentures III LLC
and managers of MPM Asset Management Investors 2004 BVIII LLC are Luke
Evnin, Ansbert Gadicke, Nicholas Galakatos, Dennis Henner,
Nicholas Simon III, Michael Steinmetz and Kurt Wheeler, who
disclaim beneficial ownership of these shares except to the extent of their
proportionate pecuniary interest therein. Dr. StevenSt. Peter, a member of our Board of Directors,
is affiliated with the MPM Funds, but is not a member of the general partners
and thus is not deemed to have beneficial ownership of the shares owned by the
MPM Funds. The address for the MPM Funds is The John Hancock Tower,
200 Clarendon Street, 54th floor, Boston, MA, 02116.
  25
 
 (4)Includes 906,562 shares
issuable upon conversion of the 10% Convertible Notes (including shares
underlying interest that will accrue within 60 days of April 30, 2010),
280,998 shares issuable upon exercise of the related warrants and the shares
underlying the options mentioned below. Dr. James Cavanaugh, a member of
our Board of Directors, is a general partner of HealthCare Partners
VII, L.P., which is the general partner of HealthCare Ventures
VII, L.P. In such capacity he may be deemed to share voting and investment
power with respect to these shares. Dr. Cavanaugh disclaims beneficial
ownership of these shares except to the extent of his proportionate pecuniary
interest therein. Dr. Cavanaugh owns options to purchase 52,759 shares of
common stock which were exercisable as of April 30, 2010 or will be exercisable
within 60 days thereof and are therefore included in this number (out of a
total of 52,759 options held by Dr. Cavanaugh). The remaining general
partners of HealthCare Partners VII, L.P. are Dr. Christopher
Mirabelli, Mr. Harold Werner, Mr. Augustine Lawlor and Mr. John
Littlechild. The address for HealthCare Ventures VII, L.P. is 44 Nassau
Street, Princeton, New Jersey 08542.
 
 (5)Includes shares issuable
upon the exercise of 10,000 immediately vested options granted to Leap Tide
Capital Management, Inc. (formerly known as AmTrust Capital
Management, Inc.), a Delaware corporation (“AmTrust”) effective
March 10, 2009 in connection with a consulting agreement. All other
information regarding AmTrust and its affiliate is based on information
disclosed in a Statement on Schedule 13G (the “AmTrust 13G”) filed with the
SEC on October 27, 2008. According to the AmTrust 13G, each of AmTrust and
Jan Loeb, its President and member of its board of directors, and a citizen of
the United States, may be deemed to beneficially own the 1,962,874 shares of
common stock (not including the 10,000 above). The address for AmTrust and Jan
Loeb is 10451 Mill Run Circle, Owings Mills, Maryland, 21117.
 
 (6) Based on information
disclosed in a Statement on Schedule 13D filed with the SEC on
October 10, 2008: Kelisia is an indirect, wholly-owned subsidiary of
Panacea Biotech Limited, a public limited company established under the laws of
India (“Panacea Biotec”), and as such, Panacea Biotec may be deemed to have
indirect beneficial ownership of the 6,478,432 shares of common stock. The
address for Kelisia is 29 Theklas Lyssioti Street, Cassandra Centre
2nd Floor, 3731 Limassol, Cyprus. The address for Panacea Biotec is B-1
Extn./A-27, Mohan Co-op. Industrial Estate, Mathura Road, New Delhi -110044,
India.
 
 (7)Includes 3,011,147 shares
issuable upon conversion of the 10% Convertible Notes (including shares
underlying interest that will accrue within 60 days of April 30, 2010) and
933,333 shares issuable upon exercise of the related warrants. The Notes and
warrants are only convertible to the extent that the holders thereof and their
affiliates would beneficially own, for purposes of Section 13(d) of the
Securities Exchange Act of 1934, as amended, no more than 9.999% of the
outstanding shares of common stock of PharmAthene after conversion. As a result
of this restriction, the number of shares that may be issued on conversion of
the Notes by the holder may change depending upon changes in the outstanding
shares. The number of shares issuable upon conversion of the Notes and warrants
held by any particular Baker Bros. affiliate will also depend upon the extent to
which the Notes and warrants held by other Baker Bros. affiliates have
previously been converted.
 
 (8)Includes options to
purchase 50,000 shares of common stock. Mr. Pappajohn is the Chairman of
our Board of Directors. In addition, Mr. Pappajohn’s spouse was the
beneficial owner of 563,497 (or 1.87%) of our shares of common stock as of April
30, 2010.
 
 (9)Includes
137,185 restricted shares (included herein irrespective of the vesting date),
options to purchase 586,364 shares of common stock (representing the portion of
unexercised options to purchase a total of  999,388 shares of common
stock that was exercisable as of April 30, 2010 or will become exercisable
within 60 days thereof), 26,575 shares issuable upon conversion of the 10%
Convertible Notes (including shares underlying interest that will accrue within
60 days of April 30, 2010) and 8,237 shares issuable upon exercise of the
related warrants. On April 27, 2010, David P. Wright notified the Company that
he was stepping down as Chief Executive Officer of PharmAthene.
  26
 
 (10)Dr. Cavanaugh
is a general partner of HealthCare Partners VII, L.P., which is the general
partner of HealthCare Ventures VII, L.P. In such capacity, he may be deemed
to share voting and investment power with respect to the shares of our common
stock held by HealthCare Ventures VII, L.P. and issuable to HealthCare
Ventures VII, L.P. upon the conversion of Notes. Dr. Cavanaugh
disclaims beneficial ownership of these shares except to the extent of his
proportionate pecuniary interest therein. Dr. Cavanaugh’s beneficially
owned shares also include options to purchase 52,759 shares of our common stock
that were exercisable as of April 30, 2010 or will become exercisable within
60 days thereof, 906,562 shares issuable upon conversion of the 10%
Convertible Notes (including shares underlying interest that will accrue within
60 days of April 30, 2010) and 280,998 shares issuable upon exercise of the
related warrants. Dr. Cavanaugh’s address is c/o HealthCare Ventures
VII, L.P., 44 Nassau Street, Princeton, New Jersey 08542.
Dr. Cavanaugh is a member of our Board of Directors.
 
 (11)Consists of
options to purchase 51,104 shares of our common stock which were exercisable as
of April 30, 2010 or will become exercisable within 60 days thereof.
Dr. St. Peter is a member of our Board of
Directors.  Dr. St. Peter is affiliated with the MPM Funds
discussed in footnote (3) above, but is not a member of the general partners and
thus is not deemed to have beneficial ownership of the shares owned by the MPM
Funds.
 
 (12)Consists of
options to purchase 72,759 shares of common stock which were exercisable as of
April 30, 2010 or will be exercisable within 60 days thereof and are
therefore included in this number (out of a total of 92,759 options held by
Mr. Gill). Mr. Gill is a member of our Board of
Directors.
 
 (13)Includes options to
purchase 102,759 shares of common stock that were exercisable as of April 30,
2010 or will become exercisable within 60 days thereof) and 18,171 shares
issuable upon conversion of the 10% Convertible Notes (including shares
underlying interest that will accrue within 60 days of April 30, 2010) and
5,633 shares issuable upon exercise of the related warrants. Mr. McCleary
is a member of our Board of Directors.
 
 (14)Includes options to
purchase 50,000 shares of common stock, 430,164 shares issuable upon conversion
of the 10% Convertible Notes (including shares underlying interest that will
accrue within 60 days of April 30, 2010) and 133,333 shares issuable upon
exercise of the related warrants. Dr. Schaffer is a member of our Board of
Directors. Of the 430,164 shares issuable upon conversion of the 10% Convertible
Notes, 40% are issuable in respect of Notes held directly by Dr. Schaffer
and 60% are issuable in respect to Notes held in Dr. Schaffer’s
IRA.
 
 (15)Includes 60,573
restricted shares (included herein irrespective of vesting date), options to
purchase a total of 250,783 shares of common stock (representing the portion of
options to purchase a total of 443,046 shares of common stock that was
exercisable as of April 30, 2010 or will become exercisable within 60 days
thereof), 7,078 shares issuable upon conversion of the 10% Convertible Notes
(including shares underlying interest that will accrue within 60 days of
April 30, 2010) and 2,194 shares issuable upon exercise of the related
warrants.  On March 25, 2010, Mr. Richman was appointed our President
and Chief Operating Officer.
 
 (16)Includes options to
purchase a total of 20,000 shares of common stock  that were
exercisable as of April 30, 2010 or will become exercisable within 60 days
thereof. Dr. Runge is a member of our Board of Directors.
 
 (17)Includes options to
purchase a total of 20,000 shares of common stock that were exercisable as of
April 30, 2010 or will become exercisable within 60 days thereof). Dr.
Sayare is a member of our Board of Directors.
 
 (18)  Includes
38,091 restricted shares (included herein irrespective of vesting date), options
to purchase a total of 130,262 shares of common stock (representing the portion
of options to purchase a total of 228,418 shares of common stock that was
exercisable as of April 30, 2010 or will become exercisable within 60 days
thereof.
  27
 
 Item
13. Certain Relationships and Related Transactions, and Director
Independence
 
 There
are no familial relationships among our directors, nominees and/or executive
officers.
 
 In
connection with the August 3, 2007 merger, PharmAthene, its principal
Stockholders and its advisors had been contacted by third party investors
(collectively, the “New Investors”) indicating an interest in making an
investment in PharmAthene through the purchase of a significant number of shares
of common stock in privately negotiated transactions with our existing
Stockholders but required that, in connection with the purchases, they receive
additional shares of our common stock from our founders and from certain
Stockholders of Former PharmAthene, receiving shares of our common stock as a
result of the merger.
 
 As
a result, our principal stockholders and management team entered into agreements
to provide the New Investors with these additional shares contingent upon the
approval and consummation of the merger and advised the New Investors that they
were required to obtain the right to vote the shares to be purchased and vote
any shares so purchased in favor of the proposals before the Special Meeting of
Stockholders or obtain from the sellers of such shares a vote in favor of the
proposals. The New Investors purchased, in the aggregate, 2,429,360 shares of
our common stock. The purchase option agreements entered into by John Pappajohn,
Derace Schaffer, M.D., Edward Berger, Wayne Schellhammer and Matthew Kinley, our
founders and executive officers and directors prior to the merger (collectively,
the “HAQ Insiders”), and the New Investors granted the New Investors options to
acquire up to 1,266,752 shares of our common stock in the aggregate (which
amount was subject to reduction pro rata to the extent that less than 2,800,000
shares of our common stock was purchased by the New Investors); since only
2,429,360 shares of common stock were purchased by the New Investors in the
aggregate, 1,099,070 shares became subject to the options. The options were
purchased for an aggregate purchase price of $100 and the exercise price per
share was $.0001 per share. The options became exercisable in August 2008 and
were exercised in full in 2008 and 2009.
 
 The HAQ
Insiders were entitled to certain registration rights for their IPO Shares, as
described in our IPO prospectus and in the definitive proxy statement filed with
the SEC on July 16, 2007. These rights provided that the holders of the
majority of these pre-IPO shares would be entitled to require us, on up to two
occasions, to register these shares. The holders of the majority of these shares
were able to elect to exercise these registration rights at any time. In
addition, the HAQ Insiders had certain “piggy-back” registration rights on
registration statements. The New Investors, as assignees of the HAQ Insiders of
the pre-IPO shares, also became entitled to these registration rights. We filed
a registration statement on Form S-3 covering the resale of these shares
(to the extent such shares could not already be sold without restrictions),
which was declared effective by the SEC on February 10,
2009.
 
 On
August 3, 2007, holders of existing bridge notes of Former PharmAthene
received 8% convertible notes in exchange for such bridge notes in
connection with the HAQ merger. Between August 3, 2007 and August 3,
2009 (the maturity date of the 8% convertible notes), funds affiliated with
Bear Stearns Health Innoventures Management, LLC held 8% convertible
notes in the aggregate principal amount of $2,541,079.  Elizabeth
Czerepak, a member of our Board until July 2008, was also a member of Bear
Stearns Health Innoventures Management, LLC. Between August 3, 2007
and July 28,2009, HealthCare
Ventures VII, L.P. and MPM Bioventures III, L.P. and
affiliated funds held 8% convertible notes in the aggregate principal amount of
$1,815,057 and $4,709,554, respectively.
 
 As
of July 28, 2009, we cancelled a portion of our then outstanding 8%
convertible notes and issued 10% convertible notes (the “Notes”) and related
stock purchase warrants to holders of the cancelled 8% convertible notes as well
as to certain new investors in a private placement. This private placement
resulted in:
 
 •the exchange of
a portion of our 8% convertible notes in the aggregate principal amount plus
accrued interest totaling $8.8 million for new Notes, convertible into
shares of common stock at a conversion price of approximately $2.54 per
share;
 
 •the issuance of additional
Notes in the aggregate principal amount of $10.5 million to new investors;
and
  28
  •the issuance to the
recipients of the Notes of stock purchase warrants to purchase up to
2.6 million shares of common stock at $2.50 per share, which warrants are
exercisable from January 28, 2010 through January 28,
2015.
 
 HealthCare
Ventures VII, L.P. and MPM Bioventures III, L.P. and its
affiliated funds were among those holders of 8% convertible notes who
chose, in lieu of receiving a cash payment representing principal and accrued
interest, to receive Notes and related stock purchase warrants. In particular,
HealthCare Ventures VII, L.P. received Notes in the aggregate
principal amount of $2,107,483 and warrants to purchase up to 280,998 shares of
common stock. MPM Bioventures III, L.P. and affiliated funds
received Notes in the aggregate principal amount of $5,468,315 and warrants to
purchase up to 729,109 shares of common stock. Our director Dr. James
Cavanaugh is a general partner of HealthCare Partners VII, L.P., which
is the general partner of HealthCare Ventures VII, L.P. Our director
Dr. Steven St. Peter, while affiliated with the MPM Funds, is not
a member of the general partners and thus is not deemed to have beneficial
ownership of the shares owned by the MPM Funds. In addition, our CEO and
director David Wright, our director Joel McCleary and our executive officer Eric
Richman exchanged their 8% convertible notes for Notes in the principal amount
of $61,777, $31,046 and $9,454, respectively, as well as warrants to purchase
8,237, 4,140 and 1,261 shares of common stock, respectively. Of the
$10.5 million in aggregate principal amount of Notes sold to new investors,
$1,000,000 was purchased by the spouse of the Chairman of our Board, John
Pappajohn, and $1,000,000 was purchased by our director Derace Schaffer, each of
whom also received warrants to purchase 133,333 shares of common stock. An
additional $28,196 in aggregate principal amount of Notes was purchased by our
director Joel McCleary and our executive officers Christopher Camut and Eric
Richman, who also received warrants to purchase an aggregate of 3,759 shares of
common stock.
 
 The
information required by Item 407(a) of Regulation S-K on Director Independence
is incorporated herein by reference to “Item 10.  Directors, Executive
Officers and Corporate Governance - Directors” in this Form
10-K/A.
 
 
 Item
14.  Principal Accounting Fees and Services.
 
 Audit
Fees, Audit Related Fees, Tax Fees and Other Fees
 
 The
following table sets forth the aggregate fees billed to the Company during
the fiscal years ended December 31, 2009 and 2008 by E&Y:
 Fiscal
                      2009
                    
                    Fiscal
                      2008Audit
      Fees(1)
                    
                    $
                    736,261
                    
                    
                    $
                    579,000Audit
      Related Fees(2)
                    
                    $
                    142,360
                    
                    
                    $
                    188,026Tax
      Fees(3)
                    
                    $
                    0
                    
                    
                    $
                    12,180All
      Other Fees
                    
                    $
                    —
                    
                    
                    $
                    —Total
      Fees
                    
                    $
                    878,621
                    
                    
                    $
                    779,206
 
 (1)Audit Fees consist of
fees billed for professional services rendered for the audit of the Company’s
consolidated annual financial statements included in our Annual Report on
Form 10-K and review of the interim consolidated financial statements
included in our Quarterly Reports on Form 10-Q and services that are
normally provided by our independent registered public accountants in connection
with statutory and regulatory filings or engagements. For the fiscal year ended
December 31, 2009 and 2008, fees for professional services billed by
E&Y were $736,261 and $579,000, respectively.
 
 (2)Audit-Related Fees
consist of fees billed for assurance and related services that are reasonably
related to the performance of the audit or review of the Company’s consolidated
financial statements and are not reported under “Audit Fees.” This category
includes fees related to Sarbanes-Oxley compliance.  For the fiscal
years ended December 31, 2009 and 2008, fees for professional
services billed by E&Y were $142,360 and $188,026,
respectively.
  29
  (3)Tax Fees were billed
for services including assistance with tax compliance and the preparation of tax
returns, tax consultation services, assistance in connection with tax audits and
tax advice related to mergers, acquisitions and dispositions. For the fiscal
years ended December 31, 2009 and 2008, fees for professional services
billed by E&Y were $0 and $12,180, respectively.
 
 Pre-Approval
of Audit and Permissible Non-Audit Services
 
 Our
Audit Committee has considered whether the provisions of services described in
the table above are compatible with maintaining auditor independence. Our Audit
Committee requires pre-approval of all audit and non-audit services in one of
two methods, and each of the permitted non-auditing services described above has
been pre-approved by the Audit Committee. Under the first method, the engagement
to render the services would be entered into pursuant to pre-approval policies
and procedures established by the Audit Committee, provided (i) the
policies and procedures are detailed as to the services to be performed,
(ii) the Audit Committee is informed of each service, and (iii) such
policies and procedures do not include delegation of the Audit Committee’s
responsibilities under the Exchange Act to the Company’s management. Under the
second method, the engagement to render the services would be presented to and
pre-approved by the Audit Committee (subject to the de minimis exceptions for
non-audit services described in Section 10A(i)(1)(B) of the Exchange Act
that are approved by the Audit Committee prior to the completion of the audit).
The Chairman of the Audit Committee has the authority to grant pre-approvals of
audit and permissible non-audit services by the registered independent public
accounting firm, provided that all pre-approvals by the Chairman must be
presented to the full Audit Committee at its next scheduled
meeting.
 
 
 PART IV
  Item 15. Exhibits and Financial
Statement Schedules.
  (b)Exhibit Index
  The
following is a list of exhibits filed with this report.
  Exhibit No.
              
              Description31.1
              
              Certification
      of Principal Executive Officer and Principal Financial Officer Pursuant to
      SEC Rule 13a-14(a)/15d-14(a).  As a result of the notice of
      resignation of our former Chief Executive Officer received on April 27,
      2010, the individual providing this certification is performing the
      functions of a principal executive officer.31.2
              
              Certification
      of Principal Executive Officer and Principal Financial Officer Pursuant to
      SEC Rule 13a-14(a)/15d-14(a).
  30
 
 SIGNATURES
  Pursuant
to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the Registrant has duly caused this report to be signed on its
behalf by the undersigned thereunto duly authorized, in the city of Annapolis,
State of Maryland, on the 30th day of April, 2010.
  PHARMATHENE,
      INC.By:
              /s/Eric
      I. RichmanEric
      I. RichmanPresident
      and Chief Operating Officer
  31
 
  INDEX
TO EXHIBITS
  No.
              
              Description31.1
              
              Certification
      of Principal Executive Officer and Principal Financial Officer Pursuant to
      SEC
                Rule 13a-14(a)/15d-14(a).  As
      a result of the notice of resignation of our former Chief Executive
      Officer received on April 27, 2010, the individual providing this
      certification is performing the functions of a principal executive
      officer.31.2
              
              Certification
      of Principal Executive Officer and Principal Financial Officer Pursuant to
      SEC Rule 13a-14(a)/15d-14(a).
   32