of Registrant’s principal executive offices)
David P. Wright
Sonnenschein Nath & Rosenthal
1221 Avenue of the Americas
10281
¨ Title of each class of securities Amount to be Proposed maximum offering Proposed maximum aggregate Amount of registration fee Common Stock, par value $0.0001 per share, to be issued upon conversion of 10% convertible notes 9,112,256 (2) $ 2.541667 (3) $ 23,160,322.14 $ 1,292.35 Common stock, par value $0.0001 per share, to be issued upon exercise of fixed-price warrants 2,572,775 $ 2.50 (3) $ 6,431,937.50 $ 358.90 (1) Pursuant to Rule 416 under the Securities Act of 1933, as amended (the “Securities Act”), the Registrant is also registering hereunder an indeterminate number of additional shares of common stock that shall be issuable to prevent dilution resulting from stock splits, stock dividends or similar transactions. (2) Represents the sum of (i) up to 7,591,780 shares of common stock that are issuable in respect of the aggregate principal amount of the 10% convertible notes and (ii) up to 1,520,476 shares of common stock that are issuable in respect of interest that accrues on the 10% convertible notes, assuming conversion of all of the notes on the date of maturity. (3) Calculated pursuant to Rule 457(g) under the Securities Act based on the fixed conversion or exercise price of the security. the securities offered by us pursuant to this prospectus will not exceed $100,000,000. such offering. our securities unless accompanied by a prospectus supplement or a free writing prospectus. 3 of this prospectus and contained in other documents that are incorporated by reference in this prospectus. · · Valortim®, a fully human monoclonal antibody · applicable prospectus supplement. Many of these factors will depend on circumstances beyond our control. We cannot guarantee that we will achieve sufficient revenues for profitability. Even if we do achieve profitability, we cannot guarantee that we can sustain or increase profitability on a quarterly or annual basis in the future. If revenues grow more slowly than we anticipate, or if operating expenses exceed our expectations or cannot be adjusted accordingly, then our business, results of operations, financial condition and cash flows will be materially and adversely affected. Because our strategy a substitution or replacement thereof. We have received funds from BARDA and other U.S. government agencies under various development agreements between us and BARDA. Any development contract deemed to be a substitute or replacement of RFP-BARDA-08-15 could trigger our obligation to make the $5 million payment. Any delay or adverse clinical event arising during any of our clinical trials could force us to conduct additional clinical trials in order to obtain approval from the FDA and other regulatory bodies. Our development costs will increase substantially if we experience material delays in any clinical trials or if we need to conduct more or larger trials than planned. If we cannot maintain successful licensing arrangements and collaborations, enter into new licensing arrangements and collaborations, or effectively accomplish strategic acquisitions, our ability to develop and commercialize a diverse product portfolio could be limited and our ability to compete may be harmed. injury, or if treated individuals subsequently become infected or suffer adverse effects from our products. Regardless of merit or eventual outcome, product liability claims may result in decreased demand for a product, injury to our reputation, withdrawal of clinical trial volunteers, and loss of revenues. Future funding levels for two of our key government customers, BARDA and DoD, for the advanced development and procurement of medical countermeasures are uncertain, and may be subject to budget cuts as the U.S. Congress and the President look to reduce the nation’s budget deficit. The U.S. government will be able to terminate any of its contracts with us either for its convenience or if we default by failing to perform in accordance with the contract schedule and terms. Termination-for-convenience provisions generally enable us to recover only our costs incurred or committed, settlement expenses, and profit on the work completed prior to termination. Termination-for-default provisions do not permit these recoveries and would make us liable for excess costs incurred by the U.S. government in procuring undelivered items from another source. the modification. In addition, we incurred unexpected general and administrative expenses to intervene in the protest. Among the most significant government contracting regulations that affect our business are: · the Federal Acquisition · the business ethics and public integrity obligations, which govern conflicts of interest and the hiring of former government employees, restrict the granting of gratuities and funding of lobbying activities and incorporate other requirements such as the Anti-Kickback Act, the Procurement Integrity Act, the False Claims Act and Foreign Corrupt Practices Act; export and import control laws and regulations; and laws, regulations and executive orders restricting the use and dissemination of information classified for national security purposes and the exportation of certain products and technical data. the current wave of consolidations in the pharmaceutical industry. It has, for example, become product candidate in 2010. · are more effective; have fewer or less severe adverse side effects; are more adaptable to various modes of dosing; obtain orphan drug exclusivity that blocks the approval of our application for seven years; are easier to administer; or are less expensive than the products or product candidates that we are, or in the future will be, developing. The patent position of biotechnology firms generally is highly uncertain and involves complex legal and factual questions, and, therefore, validity and enforceability cannot be predicted with certainty. To date, no consistent policy has emerged regarding the breadth of claims allowed in biotechnology patents. We currently hold two U.S. patents, have Legislation limiting or restricting liability for medical products used to fight bioterrorism is new, and we cannot be certain that any such protection will apply to our products or if applied what the scope of any such coverage will be. trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. Even if we are successful in defending against these claims, litigation could result in substantial costs and distract management. INFORMATION Number of Shares Beneficially Shares Beneficially Owned Owned Prior to the Offering(1) Number of Shares Being Offered After the Offering(1) Underlying Underlying Name of Selling Stockholder Number(2) Percentage Notes(3) Warrants(4) Number(2) Percentage Healthcare Ventures VII, L.P.(5) 4,218,938 14.38 % 995,238 280,998 3,369,726 11.83 % MPM Asset Management Investors 2004 BVIII LLC, MPM Bioventures III, L.P., MPM Bioventures III GmbH & Co. Beteiligungs KG, MPM Bioventures III Parallel Fund, L.P. and MPM Bioventures III-QP, L.P.(6) 5,692,905 18.59 % 2,582,359 729,108 3,489,443 12.27 % David Wright(7) 877,581 3.03 % 29,173 8,237 852,688 2.95 % Ronald W. Kaiser 8,841 * 4,501 1,271 5,000 * Ontario Teachers’ Pension Plan Board 1,177,862 4.08 % 480,846 135,763 767,568 2.70 % Jerome Parks 24,893 * 29,173 8,237 0 0 % Joel McCleary(8) 195,914 * 19,948 5,633 178,893 * Eric Richman(9) 274,986 * 7,770 2,194 268,356 * Baker Brothers Investments II, L.P., Baker Brothers Life Sciences, L.P. and 14159, L.P.(10) 3,658,830 11.71 % 3,305,682 933,334 838,175 2.95 % Number of Shares Beneficially Shares Beneficially Owned Owned Prior to the Offering(1) Number of Shares Being Offered After the Offering(1) Underlying Underlying Name of Selling Stockholder Number(2) Percentage Notes(3) Warrants(4) Number(2) Percentage Derace Schaffer(11) 1,144,115 3.96 % 472,240 133,333 741,164 2.60 % James H. Desnick 201,475 * 236,120 66,667 0 0 % Edward F. Heil 201,475 * 236,120 66,667 0 0 % R.J. Vassiliou 315,590 1.11 % 94,448 26,667 235,000 * Ann Vassiliou Children’s Trust 170,885 * 141,672 40,000 50,000 * Mary L. Pappajohn(12) 402,951 * 472,240 133,333 0 0 % Christopher Camut(13) 204,424 * 4,722 1,333 200,394 * TOTAL 18,766,665 9,112,256 2,572,775 10,991,407 · · Act, or contribution with respect to payments that the underwriters or agents may make with respect to such liabilities. York. automatically adds to, updates or supersedes the information listed below. · · our Quarterly · our Current · the description of our common stock contained in our registration statement on Form 8-A filed with the SEC on July 27, 2005, including any amendments or reports filed for the purpose of updating such description, including the description of the Company’s securities set forth in the Definitive Proxy Statement filed with the SEC on July 16, 2007, on page 159 under the caption “Description of Securities.” SEC Registration Fee $ 1,292.35 Accounting Fees and Expenses $ 10,000 Legal Fees and Expenses $ 25,000 Printing Fees and Expenses $ 5,000 Miscellaneous $ 3,707.65 Total: $ 45,000 registration statement: 1933, as amended (the “Securities Act” or “Securities Act of 1933”); in the registration statement; registration statement; registration statement; PHARMATHENE, INC. (Registrant) Eric I. Richman Signature Title /s/ (Principal Executive Officer) /s/ Charles A. Reinhart III Charles A. Reinhart III Chief Financial Officer Chairman of the Board /s/ John John Gill Director /s/ Steven St. Peter, M.D. Steven St. Peter, M.D. /s/ Joel McCleary Joel McCleary Index to Exhibits Exhibit No. Description Form of Warrant 5.1 Opinion of Consent of 23.2 Consent of Ernst & Young LLP, 24.1 Powers of Attorney (included on the signature page of this Registration Statement).o12b-212b–2 of the Exchange Act. (Check one):Large accelerated filer oAccelerated Filer¨ Accelerated filer oFilerNon-accelerated¨o (Do not check if a smaller reportingx Smaller reporting company x Title of Each Class of Securities To Be Registered Amount to be registered (1) Proposed maximum offering price per unit(1) Common Stock, par value $0.0001 per share (3) ─ ─ ─ ─ Preferred Stock, par value $0.0001 per share (3) ─ ─ ─ ─ Warrants (4) ─ ─ ─ ─ Total ─ ─ $ 100,000,000 $ 11,610
to be registered
registered (1)
price per share
offering priceThe selling stockholdersWe may not sell these securities until the Registration Statement filed with the Securities and Exchange Commission is effective. This prospectus is not an offer to sell these securities and it is not soliciting an offer to buy these securities in any state or jurisdiction where the offer or sale is not permitted.August 27, 2009July 7, 2011
PROSPECTUS
9,112,256 SharesCommon Stock Underlying 10% Convertible Notes2,572,775 Sharesthose securities, either individually or in units, in one or more offerings. The aggregate public offering price of Common Stock Underlying Fixed-Price Warrantsrelatesprovides you with a general description of the securities that we may offer. Each time we offer securities, we will provide a supplement to this prospectus that will contain more specific information about the resaleterms of that offering, including the prices at which those securities will be sold. We may also add, update or change in the prospectus supplement any of the information contained in this prospectus.by the selling stockholdersthrough a combination of PharmAthene, Inc. (described in the section entitled “Selling Stockholders” on page 15 of this prospectus) of up to 11,685,031 shares of our common stock, par value $0.0001 per share, including (i) up to 9,112,256 shares of common stock issuable upon conversion of the 10% Convertible Notes issued to investors pursuant to the Note and Warrant Purchase Agreement, dated as of July 24, 2009, as amended (which we refer to as the “Note and Warrant Purchase Agreement”), between PharmAthene, Inc. and the investors named therein, and (ii) up to 2,572,775shares of our common stock issuable upon exercise of warrants with a fixed exercise price of $2.50 per share issued pursuant to the Note and Warrant Purchase Agreement (which we refer to as the “warrants”).The selling stockholders may offer and sell, from time to time, in the open marketthese methods or in privately negotiated transactions and at market prices, fixed prices or negotiated prices, all or any portion of such shares in amounts and on terms to be determined atother manner as described under the time of sale. For additional information on the possible methods of sale that may be used by the selling stockholders, you should refer to the section entitledheading “Plan of Distribution” on page 18 of this prospectus. Weand in the corresponding section in the applicable prospectus supplement. Each time we offer securities, the relevant prospectus supplement will not receive anyprovide the specific terms of the plan of distribution for such offering and the net proceeds that we expect to receive from the resale of shares of our common stock by the selling stockholders.On August 25, 2009,Each prospectus supplement will indicate if the last reported sale price per sharesecurities offered pursuant to that supplement will be listed on any securities exchange.common stock on that exchange was $3.06.common stocksecurities involves certain risks. You should carefully read the entireboth this prospectus and any accompanyingthe applicable prospectus supplement, carefullyas well as any documents incorporated by reference in this prospectus and/or the applicable prospectus supplement, before you make your investment decision. See “Risk Factors” beginning on page 3.2009.2011.ABOUT THIS PROSPECTUS 1 SUMMARY 2 RISK FACTORS 3 SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS 16 USE OF PROCEEDS 17 DESCRIPTION OF COMMON STOCK 17 DESCRIPTION OF PREFERRED STOCK 17 DESCRIPTION OF WARRANTS 20 PLAN OF DISTRIBUTION 22 LEGAL MATTERS 24 EXPERTS 24 WHERE YOU CAN FIND MORE INFORMATION 24 INCORPORATION BY REFERENCE 24 Neither the Company nor the selling stockholdersWe have not authorized any other person to provide you with different information. If anyone provides you with different or inconsistent information, you should not rely on it. The Company is not making any offer to sell these securities and the selling stockholdersWe are not making an offer to sell these securities in any jurisdiction where the offer or sale is not permitted. You should assume that the information appearing in this prospectus is accurate only as of the date appearing on the front cover pageof this prospectus only and that information contained in any prospectus supplement or document incorporated by reference in this prospectus is only accurate as of the date of the document incorporated by reference.such prospectus supplement or document. Our business, financial condition, results of operations and prospects may have subsequently changed.On August 3, 2007, Healthcare Acquisition Corp. (“HAQ”consummated a merger (the “Merger”)and/or the applicable prospectus supplement, before you make your investment decision. The information incorporated by reference includes important business and financial information about us that is not included nor delivered with this document. This information is available without charge on the SEC’s website at www.sec.gov or upon written or oral request to PharmAthene, Inc., One Park Place, Suite 450, Annapolis, MD 21401, (410) 269-2600. If any statement in this prospectus, the applicable prospectus supplement or any document incorporated by reference one of these documents is inconsistent with a Delaware corporation which atstatement in another of those document having a later date, the time was known as “PharmAthene, Inc.” (“Former PharmAthene”), whereby Former PharmAthene became a wholly-owned subsidiary of HAQ, HAQ changed its namestatement in the document having the later date modifies or supersedes the earlier statement. Inc.” “the Company,” “we,” “us,” “our,” and Former PharmAthene changed its namesimilar terms refer to “PharmAthene US Corporation.” Effective February 27, 2009 PharmAthene US Corporation was merged with and into PharmAthene, Inc., with PharmAthene, Inc. being the surviving corporation. Unless specifically noted otherwise, as used throughout this prospectus, “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.its subsidiaries on a consolidated basis. The phrase “this prospectus” refers to this prospectus and any applicable prospectus supplement, unless the context otherwise requires. Whenever we refer to “you” or “yours”, we mean the persons to whom offers are made under this prospectus.We currently have fiveOur current lead product candidates in various stages of development:are:·SparVax™ -, a second generation recombinant protective antigen (“rPA”) anthrax vaccine, (an identical population of highly specific antibodies produced from a single clone) for the prevention and treatment of anthrax infection,Protexia®rBChE (recombinant butyrylcholinesterase), which mimics a natural bioscavenger- countermeasures for the treatment or prevention of nerve agent poisoning by organophosphateorganophosphorous compounds, including nerve gases and pesticides,·RypVax™ - a recombinant dual antigen vaccine for pneumonic and bubonic plague (“rYP”), and·a third generation rPA anthrax vaccine.described below relating tobefore making an investment in our common stock.decision. The risks and uncertainties described below are not the only ones we face. Additional risks and uncertainties not presently known to us or that we currently consider immaterial may also impair our business operations. If any of the following risks actually occur, our business and financial condition and/or results of operations could be materially adversely affected,harmed. In that case, the trading price of our common stock could decline and you could lose all of your investment.Risk Relateddecline. You should also refer to Request for Proposal RFP-BARDA-08-15If we do not receive the award byinformation included in our other filings with the U.S. Department of Health and Human Services (the “DHHS”) for an rPA anthrax vaccine, we likely will need to curtailSEC, including our operations significantly and wemost recent annual report on Form 10-K or quarterly report on Form 10-Q, as the case may be, placed at a competitive disadvantageand in the biodefense industry.On February 29, 2008, the DHHS issued a formal Request for Proposal (RFP-BARDA-08-15) for an “Anthrax Recombinant Protective Antigen (rPA) Vaccine for the Strategic National Stockpile,” which includes a requisition for 25 million doses of an rPA anthrax vaccine. We submitted a response to this solicitation on July 31, 2008. While the original solicitation indicated that an award would be made by September 26, 2008, which was later extended to December 31, 2008, DHHS subsequently delayed the award date further because, among other things, of a protest filed by a bidder that had been eliminated from further consideration under the solicitation. The U.S. General Accounting Office (the “GAO”) subsequently denied that protest. On April 15, 2009, DHHS issued an amendment to the RFP requiring that each bidder submit by April 30, 2009 a comprehensive plan to the FDA outlining the bidder’s regulatory strategy for the rPA anthrax vaccine to be developed under a contract should one be awarded under the solicitation. Pursuant to an amendment dated April 22, 2009, DHHS further extended the submission deadline to June 15, 2009. On July 9, 2009, the Company announced that the FDA completed its review of the Company’s proposed development plan for SparVax ™ , and the Company has shared the FDA’s feedback with BARDA as required by these two amendments. Timing for an award under this solicitation remains uncertain. There can be no assurance that DHHS will not again extend the timeline for issuing an award, add other requirements, or that the Company will be awarded a contract under that solicitation.We are currently aware of at least one other bidder for the award with substantially greater financial and other resources, manufacturing capabilities and commercialization capabilities than we have. Because the U.S. government is currently the only customer for our product candidates, if we fail to receive the award for the rPA anthrax vaccine, we could be forced to abandon or severely curtail our efforts with respect to our lead product candidate, SparVax™, which, in turn, could place us at a competitive disadvantage. We have been engaged in discussions with DHHS with respect to our ability to satisfy the requirements of the RFP. DHHS has requested additional information that, if not determined by them to be satisfactory, could result in our elimination from consideration for procurement. No assurances can be given that DHHS will make an award to us or that if made, it will not include substantial conditions, that we can satisfy all of these conditions or that we can begin to receive any proceeds from any such award within any specific period of time. In any event, we still have not completed development of SparVax™ and our ability to recognize any meaningful proceeds from the sale of SparVax™ will still depend upon our completing the development and testing of such product.threeyears ended December 31, 2010, 2009 and six months ended June 30, 2009,2008 we incurred operatingnet losses of approximately $6.8$34.8 million, $32.3 million, and $12.4$36.4 million, respectively, and had an accumulated deficit of approximately $136.7$189.9 million at June 30, 2009.December 31, 2010. As of such date, we had working capital of approximately $17.4 million and equity of $12.2 million. Our losses to date have resulted principally from research and development costs related to the development of our product candidates, general and administrative costs related to operations, and costs related to the Avecia Acquisition.· developing our existing products and developing and testing new product candidates;· carrying out our intellectual property strategy;· establishing our competitive position;· pursuing third-party collaborations;3· developing our existing products and developing and testing new product candidates; · continuing to receive government funding and identifying new government funding opportunities; · receiving regulatory approvals; · carrying out our intellectual property strategy; · establishing our competitive position; · · acquiring or in-licensing products; and · manufacturing and marketing products. · acquiring or in-licensing products;· receiving regulatory approvals;· manufacturing and marketing products; and· continuing to receive government funding and identifying new government funding opportunities.might includeincludes potential acquisitions of other businesses, acquisition expenses and any cash used to make these acquisitions will reduce our available cash. Whilebelieve that funds received from the recent convertible debt financing we completed in July 2009 along with existing cash resources will be sufficientare required to enable us to fund our existing research and development programs, pay our debt service costs and support our currently anticipated general and administrative activities through the endAvecia (now a subsidiary of 2010, there can be no assurance that unexpected financial obligations or other activities that increase our use of cash will not result in our depleting our cash resources quicker than presently anticipated. Furthermore, if we receive the award from DHHS for advanced development and procurement of SparVax™Merck & Co., we would be obligated to make $10Inc.) $5 million in milestone payments to Avecia within 90 days of entering into a multi-year funded development contract that was to be issued by BARDA under solicitation number RFP-BARDA-08-15 (or any substitution or replacement thereof) for the further development of SparVax TM. RFP-BARDA-08-15 was cancelled by BARDA in December 2009. Accordingly, our obligation to pay Avecia the $5 million payment would mature only upon our receipt of such award.currentcontinuing turmoil affecting the banking system and financial markets and the possibility that financial institutions may consolidate or cease operations has resulted in a tightening in the credit markets, a low level of liquidity in many financial markets and extreme volatility in fixed income, credit, currency and equity markets. In addition, the note and warrant purchase agreement entered into in connection with the issuance of the 10% Convertible Notes and warrants limits us and our subsidiaries from incurring senior indebtedness (other than customary trade payables) in excess of $10 million without the prior written approval of no less than a majority of the aggregate principal amount of the 10% Convertible Notes then outstanding. As a result, of both the market turmoil and the limits on issuance of senior indebtedness, there can be no assurances that we will be successful in obtaining sufficient financing on commercially reasonable terms or at all. Our requirements for additional capital may be substantial and will be dependent on many factors, including the success of our research and development efforts, our ability to commercialize and market products, our ability to successfully pursue our licensing and collaboration strategy, the receipt of continued government funding, competing technological and marketing developments, costs associated with the protection of our intellectual property and any future change in our business strategy.wouldwill not fail to meet safety standards in human testing, even if those product candidates wereare found to be effective in animal studies. To develop and commercialize biodefense treatment and prophylactic product candidates, we must provide the U.S. Food and Drug Administration (the “FDA”)FDA and foreign regulatory authorities with human clinical and non-clinical animal data that demonstrate adequate safety and effectiveness. To generate these data, we will have to subject our product candidates to significant additional research and development efforts, including extensive non-clinical studies and clinical testing. We cannot be sure that our approach to drug discovery will be effective or will result in the development of any drug. Even if our product candidates are successful when tested in animals, such success would not be a guarantee of the safety or effectiveness of such product candidates in humans.“ Risk Factors—“—Necessary Reliance on the Animal Rule in Conducting Trials is Time-Consuming and Expensive ..Expensive.” For example, we have not finished generating and presented to the FDA comparability data for bulk drug substance produced at Avecia and bulk drug substance produced at Fujifilm RTP to establish substantial product equivalence. If once these data are presented to the FDA, the agency does not believe they confirm substantial product equivalence, the Company could be required to conduct additional non-clinical studies, human clinical studies, manufacturing or other work, which would extend dramatically the development timeline for the SparVax TM4Necessary Reliance on the Animal Rule in Conducting Trials is Time-Consuming and Expensive.To obtain FDA approval for our biological warfare defense products under current FDA regulations, we are required to utilize animal model studies for efficacy and provide animal and human safety data under the “Animal Rule.” For many of the biological and chemical threats, animal models are not yet available, and as such we are developing, or will have to develop, appropriate animal models, which is a time-consuming and expensive research effort. Further, we may not be able to sufficiently demonstrate the animal correlation to the satisfaction of the FDA, as these corollaries are difficult to establish and are often unclear. The FDA may decide that our data are insufficient for approval and require additional preclinical, clinical or other studies, refuse to approve our products, or place restrictions on our ability to commercialize those products. Further, other countries do not, at this time, have established criteria for review and approval of these types of products outside their normal review process; i.e., there is no “Animal Rule” equivalent, and consequently there can be no assurance that we will be able to make a submission for marketing approval in foreign countries based on such animal data.Additionally, few facilities in the U.S. and internationally have the capability to test animals with anthrax, plague, nerve agents, or other lethal biotoxins or chemical agents or otherwise assist us in qualifying the requisite animal models. We have to compete with other biodefense companies for access to this limited pool of highly specialized resources. We therefore may not be able to secure contracts to conduct the testing in a predictable timeframe or at all.Even if we succeed in commercializing our product candidates, they may not become profitable and manufacturing problems or side effects discovered at later stages can further increase costs of commercialization.We cannot assure you that any drugs resulting from our research and development efforts will become commercially available. Even if we succeed in developing and commercializing our product candidates, we may never generate sufficient or sustainable revenues to enable us to be profitable. Even if effective, a product that reaches market may be subject to additional clinical trials, changes to or re-approvals of our manufacturing facilities or a change in labeling if we or others identify side effects or manufacturing problems after a product is on the market. This could harm sales of the affected products and could increase the cost and expenses of commercializing and marketing them. It could also lead to the suspension or revocation of regulatory approval for the products.We and our contract manufacturers (“CMO”s) will also be required to comply with the applicable FDA current Good Manufacturing Practice (“cGMP”) regulations. These regulations include requirements relating to quality control and quality assurance as well as the corresponding maintenance of records and documentation. Manufacturing facilities are subject to inspection by the FDA. These facilities must be approved to supply licensed products to the commercial marketplace. We and our contract manufacturers may not be able to comply with the applicable cGMP requirements and other FDA regulatory requirements. Should we or our contract manufacturers fail to comply, we could be subject to fines or other sanctions or could be precluded from marketing our products.In particular, as part of the transfer of our existing contract with NIAID for the development of SparVax™ to BARDA on April 1, 2009, the terms of that contract were modified to provide for the transfer of the manufacturing process for the bulk drug substance for SparVax™ from Avecia Biologics in the U.K. to a U.S.-based contract manufacturing organization. We believe that if we are awarded a contract under RFP-BARDA-08-15 for the advanced development and procurement of 25 million doses of SparVax™, the U.S. government will require that such new CMO manufacture the bulk drug substance for SparVax™. This contract manufacturer has not manufactured that bulk drug substance before, and there can be no assurance we will be successful in our technology transfer efforts or that this new contract manufacturer will ever be able to manufacture sufficient amounts of cGMP quality bulk drug substance necessary for us to meet our obligations under any such advanced development and procurement contract.5We may fail to fully realize the potential of Valortim® and of our co-development arrangement with Medarex, our partner in the development of Valortim®, which would have an adverse effect upon our business. We have completed one Phase I clinical trial for Valortim® with our development partner, Medarex, without any reported drug-related significant adverse events. However, before we may begin selling any doses of Valortim®, we will need to conduct more comprehensive safety trials in a significantly larger group of human subjects. We will be required to expend a significant amount to finalize manufacturing capability through a contract manufacturer to provide material to conduct the pivotal safety and efficacy trials. If our contract manufacturer is unable to produce sufficient quantities at a reasonable cost, or has any other obstacles to production, such as volatile manufacturing, then we will be unable to commence these required clinical trials and studies. Even after we expend sufficient funds to complete the development of Valortim® and if and when we enter into an agreement to supply Valortim® to the U.S. government, we will be required to share any and all profits from the sale of products with our partner in accordance with a pre-determined formula.For example, we have an agreement with Medarex to develop Valortim®, a fully human monoclonal antibody product designed to protect against and treat inhalation anthrax. Under the agreement with Medarex, we will be entitled to a variable percentage of profits derived from sales of Valortim®, if any, depending, in part, on the amount of our investment. In addition, we have entered into licensing and research and development agreements with a number of other parties and collaborators. There can be no assurances that the research and development conducted pursuant to these agreements will result in revenue generating product candidates. If our suppliers, vendors, licensors, or other collaboration partners experience financial difficulties as a result of the current credit crisis and weakening of the globalweak economy, or if they are acquired as part of the current wave of consolidations in the pharmaceutical industry (such as, for example, with the pending acquisitionacquisitions of Medarex by Bristol Myers Squibb)Bristol-Myers Squibb and Diosynth RTP, Inc.’s parent company by Merck & Co., Inc. in 2009 and of Avecia’s CMO subsidiary (Avecia Biologics) by Merck & Co., Inc. in 2010 and the subsequent recently announced pending sale of these two entities by Merck to Fujifilm), their priorities or our working relationship with them might change. As a result, they might shift resources away from the research, development and/or manufacturing efforts intended to benefit our products, which could lead to significant delays in our development programs and potential future sales. In addition, we currently only have a research license from our partner for the work on the AES for rBChE. There can be no assurance that we will be able to secure exclusive rights from our collaborator to develop and commercialize this technology. Finally, our current licensing, research and development, and supply agreements may expire and may not be renewable or could be terminated if we do not meet our obligations.In order forFor our future collaboration efforts to be successful, we must first identify partners whose capabilities complement and integrate well with ours. We face, and will continue to face, significant competition in seeking appropriate collaborators. Collaboration arrangements are complex and time consuming to negotiate, document and implement. We may not be successful in our efforts to establish and implement collaborations or other similar arrangements. The terms of any collaboration or other arrangements that we establish may not be favorable to us. Furthermore, technologies to which we gain access may prove ineffective or unsafe or our partners may prove difficult to work with or less skilled than we originally expected. In addition, any past collaborative successes are no indication of potential future success.6“Risk Factors -“—Legislation limiting or restricting liability for medical products used to fight bioterrorism is new, and we cannot be certain that any such protection will apply to our products or if applied what the scope of any such coverage will bebe.” below. Additionally, we are considering applying for indemnification under the U.S. Support Anti-terrorism by Fostering Effective Technologies (SAFETY) Act of 2002 which preempts and modifies tort laws so as to limit the claims and damages potentially faced by companies who provide certain “qualified” anti-terrorism products. However, we cannot be certain that we will be able to obtain or maintain coverage under the SAFETY Act or adequate insurance coverage on acceptable terms, if at all.Mostgrants.grants to supply the U.S. or other governments with our products. The process of obtaining government contracts is lengthy and uncertain and we will have to compete with other companies for each contract. For example, while RFP-BARDA-08-15 for an rPA vaccine for the SNS initially indicated that the government would make an award by September 26, 2008 (later extended to December 31, 2008), as of the date this Registration Statement is filed, the government has still not issued an award under that solicitation. There can be no assurances that we will be awarded any contracts to supply the U.S. or other governments with our products as such awards may be made, in whole or in part, to our competitors. uncertain.future contract awards to our competitors, rather than to us, for the supply to the U.S. emergency stockpile, of a competing product, our business will be harmed and it is unlikely that we will ultimately be able to supply that particular treatment or product to foreign governments or other third parties. Further, changes in government budgets and agendas, funding strategies, cost overruns in our programs, or advances by our competitors, may result in changes in the timing of funding for, a decreased and de-prioritized emphasis on, procuringor termination of, government contracts that support the development and/or procurement of the biodefense products we are developing. For example, while RFP-BARDA-08-15 for an rPA-based anthrax vaccine for the U.S. government has selected a plague vaccine product candidate from a competitor for advanced development funding, and we do not anticipateSNS initially indicated that the U.S. government will provide additional fundingwould make an award by September 26, 2008, the award was delayed multiple times and ultimately canceled in the futureDecember 2009.or procure RypVax™. Furthermore, given the limited future prospects for RypVax™ at this time, we are in discussions with the U.S. government regarding potential early termination of our current contract. Under the terms of our 2006 contract with the U.S. Department of Defense regarding Protexia®, the Department of Defense may elect not to continue development assistance of this nerve agent countermeasure after initial funding of $41 million has been received (which decision we anticipate may occur by the end of the fourth quarter of 2009 or early 2010), or, if the Department of Defense does so elect to continue funding and we meet all development milestones, it may nevertheless choose not to procure any doses of Protexia®.Duemulti-year contracts. More generally, due to the currentongoing economic downturn, the accompanying fall in tax revenues and the U.S. government’s efforts to stabilize the economy, the U.S. government may be forced or choose further to reduce or delay spending in the biodefense field or eliminate funding of certain programs altogether, which could decrease the likelihood of future government contract awards or that the government would procure products from us.unfavorableunilateral termination provisions for the government and are subject to audit and modification by the government at its sole discretion, which will subject us to additional risks. These risks include the ability of the U.S. government unilaterally to:· suspend or prevent us for a set period of time from receiving new contracts or extending existing contracts based on violations or suspected violations of laws or regulations;· terminate our contracts, including if funds become unavailable to the applicable governmental agency;· reduce the scope and value of our contracts;7· suspend or prevent us for a set period of time from receiving new contracts or extending existing contracts based on violations or suspected violations of laws or regulations; · terminate our contracts, including if funds become unavailable or are not provided to the applicable governmental agency; · reduce the scope and value of our contracts and/or revise the timing for work to be performed; · audit and object to our contract-related costs and fees, including allocated indirect costs; · control and potentially prohibit the export of our products; · claim rights to products, including intellectual property, developed under the contract; · change certain terms and conditions in our contracts; and · cancel outstanding RFP solicitations (as was the case with RFP-BARDA-08-15) or BAAs. · audit and object to our contract-related costs and fees, including allocated indirect costs;· control and potentially prohibit the export of our products; and· change certain terms and conditions in our contracts.currentongoing economic downturn, the accompanying fall in tax revenues, and the U.S. government’s efforts to stabilize the economy, the U.S. government may be forced or choose further to reduce or delay spending in the biodefense field or eliminate funding of certain programs altogether, which could decrease the likelihood of future government contract awards, the likelihood that the government will exercise its right to extend any of its existing contracts with us and/or the likelihood that the government would procure products from us.reselectre-evaluate bids. The government could even be directed to award a potential contract to one of the other bidders. AnFor example, is the protest filed byin March 2010, a third-party bidderfiled a bid protest with the GAO challenging the February 2010 decision of the DHHSHHS to eliminate that bidder from further considerationmodify its existing research and development contract with us for the development of SparVax TM . In March 2010 HHS suspended performance under the solicitation for an rPA vaccine for the Strategic National Stockpile (RFP-BARDA-08-15), a result of which was a delaymodification pursuant to the contract award dateautomatic stay provisions of the FAR, pending a decision by the GAO on the protest. While the bid protest was ultimately denied, and the related HHS “stop work” order canceled in June 2010, the protest contributed to a reduction in revenues and cash and cash equivalents over the period that work could not be performed under this solicitation.· termination of contracts;· forfeiture of profits;· suspension of payments;· fines; and· suspension or prohibition from conducting business with the U.S. government.· termination of contracts; · forfeiture of profits; · suspension of payments; · fines; and · suspension or prohibition from conducting business with the U.S. government. 8Regulations,Regulation, or FAR, and agency-specific regulations supplemental to the Federal Acquisition Regulations,Regulation, which comprehensively regulate the procurement, formation, administration and performance of government contracts;· ·· ·We were notified by the contract manufacturer who supplies the pegylation reagent for our Protexia® product candidate that it intends to cease its contract manufacturing operations to focus exclusively on developing its own proprietary product candidates. We are now in the process of searching for an alternative supplier. As part of this process, we will need to negotiate and execute a license to certain intellectual property from our current supplier related to the pegylation process and to engage in a technology transfer process to a new supplier. If we are not successful in these endeavors, our Protexia® development program will be adversely affected. current credit crisis and weakening of the global economy and as such may be more susceptible to being acquired as part of9 increasingly challenging for companies to secure debt capital to fund their operations as financial institutions have significantly curtailed their lending activities. If our third-party suppliers continue to experience financial difficulties as a result of weakeningweak demand for their products or for other reasons and are unable to obtain the capital necessary to continue their present level of operations or are acquired by others, they may have to reduce their activities and/or their priorities or our working relationship with them might change. A material deterioration in their ability or willingness to meet their obligations to us could cause a delay in our development programs and potential future sales and jeopardize our ability to meet our obligations under our contracts with the government or other third parties.As noted above in “- Most of our immediately foreseeable future revenues are contingent upon grants and contracts fromFor example, the U.S. government and we may not achieve sufficient revenues from these agreements to attain profitability,” the U.S. government has selected a plague vaccine product candidate from a competitor for advanced development funding. We are in discussions withfunding, causing us to wind down activities related to the U.S. government regarding potential early terminationdevelopment of our contract for RypVax™, which is currently scheduled to end during the first half of 2011.RypVax TM· ·· ·· ·· ·· ·10partiesparties..sixfive pending U.S. patent applications, and have a limited number of foreign patents and pending international and foreign patents pending.applications. In addition, we have rights under numerous other patents and patent applications pursuant to exclusive and non-exclusive license arrangements with licensors and collaborators. However, there can be no assurance that patent applications owned or licensed by us will result in patents being issued or that the patents, whether existing or issued in the future, will afford protection against competitors with similar technology. Any conflicts resulting from third-party patent applications and patents could significantly reduce the coverage of the patents owned, optioned by or licensed to us or our collaborators and limit our ability or that of our collaborators to obtain meaningful patent protection.We are also aware of pending applications directed to pegylated butyrylcholinesterase. Protexia® incorporates butyrylcholinesterase. If patents are issued to third parties that cover Protexia® or other products, we may be required to obtain a license under such patents or obtain alternative technology. We cannot provide any assurances that such licenses will be available or that the terms thereof will be reasonable or that we will be able to develop alternative technologies. If we do not obtain such a license and if a legal action based on such patent was to be brought against us or our distributors, licensees or collaborators, we cannot provide any assurances that we or our distributors, licensees or collaborators would prevail or that we have sufficient funds or resources to defend such claims.licenseeslicensors or collaborators may have a material adverse effect on us. The expense of a protracted infringement suit, even if ultimately favorable, would also have a material adverse effect on us.11(“EAR”)or EAR, administered by the U.S. Department of Commerce and are, in certain instances (such as regarding aspects of our Protexia®nerve agent countermeasure product candidate)candidates) subject to the International Traffic in Arms Regulations, (“ITAR”)or ITAR, administered by the U.S. Department of State. EAR restricts the export of dual-use products and technical data to certain countries, while ITAR restricts the export of defense products, technical data and defense services. The U.S. government agencies responsible for administering EAR and ITAR have significant discretion in the interpretation and enforcement of these regulations. Failure to comply with these regulations can result in criminal and civil penalties and may harm our ability to enter into contracts with the U.S. government. It is also possible that these regulations could adversely affect our ability to sell our products to non-U.S. customers.“Even“Even if we succeed in commercializing our product candidates, they may not become profitable and manufacturing problems or side effects discovered at later stages can further increase costs of commercialization,” we are transferring the manufacturing process for the bulk rPA drug substance from Avecia in the United Kingdom to Fujifilm RTP (which recently acquired Merck RTP), a U.S.-based contract manufacturer. In connection with that transfer, we also anticipate moving our U.K.-based operations to the United States by June 30, 2010. There can be no assurance that we will be able to recruit and hire the necessary staff in the U.S. to complete the transfer of activitiesthe manufacturing process in a timely and cost effective manner.12ourOur Common Stock· a limited availability of market quotations for our securities; · a determination that our common stock is a “penny stock” which will require brokers trading in our common stock to adhere to more stringent rules and possibly result in a reduced level of trading activity in the secondary trading market for our securities; · a limited amount of news and analyst coverage for us; and · a decreased ability to issue additional securities (including pursuant to short-form registration statements on Form S-3 or obtain additional financing in the future. · our perceived prospects; · variations in our operating results and whether we have achieved key business targets; · changes in, or our failure to meet, revenue estimates; · changes in securities analysts’ buy/sell recommendations; · differences between our reported results and those expected by investors and securities analysts; · announcements of new contracts by us or our competitors; · reaction to any acquisitions, joint ventures or strategic investments announced by us or our competitors; and · general economic, political or stock market conditions. conversion and exercise of convertible notes, warrants and options could dilute our shareholders, including the investors in this offering, and depress the market price of our common stock.We will likely seek to raise additional capital and may do so at any time through various financing alternatives, including potentially selling shares of common or preferred stock, notes and/or warrants convertible into, or exercisable for, shares of common or preferred stock. Even following the registered offeringcompleted on March 27, 2009, we could again rely upon the shelfpursuant to this registration statement on Form S-3, which was declared effective on February 12, 2009, in connection with a sale from time to time of common stock, preferred stock or warrants or any combination of those securities, either individually or in units, in one or more offerings for up to $50,000,000 (inclusive of the gross proceeds from our recent public offering of $5.5 million and the $2.1 million we would receive if all of the warrants issued in that offering were exercised). Raising capital in this manner or any other mannerotherwise may depress the market price of our stock, and any such financing(s) will dilute our existing shareholders.June 30, 2009,March 31, 2011 we had outstanding options to purchase approximately 4.45.2 million shares of common stock.stock (not including restricted shares). Additional shares are reserved for issuance under our 2007 Long-Term Incentive Compensation Plan. Our stock options are generally exercisable for ten years, with a significant portion exercisable either immediately or beginning one year after the date of the grant. Furthermore,Convertible Notes inconvertible notes by certain of our affiliates, among other securityholders. The registration statement, which was declared effective on November 25, 2009, only covers the aggregate principal amountresale of $19.3 milliona portion of the shares underlying such notes. We are convertible at $2.541667 per share into between approximately 7.6 million and approximately 9.1 millionobligated under the terms of the related registration rights agreement to continue filing registration statements or amendments thereto covering the resale of the remaining portion of the shares underlying the notes, as well as of the shares issuable upon exercise of the related warrants. The sale by these securityholders of their shares pursuant to the registration statement or otherwise could depress the market price of our common stock, depending on when the notes are converted, and the accompanying warrants are exercisable for up to approximately 2.6 million shares of common stock at $2.50 per share. stock.August 12, 2009, the CompanyMarch 31, 2011, we had issued and outstanding additional warrants to purchase up to an additional 3.6approximately 2.6 million shares of common stock. stock (not including the warrants to purchase approximately 2.6 million shares issued in connection with the issuance of the notes in July 2009 and not including the warrants to purchase approximately 0.4 million shares issued in June 2011).If Shares that we are unable to continue to satisfymay issue in the listing requirementsfuture in connection with certain capital-raising transactions and shares available for future issuance upon exercise of NYSE Amex,warrants and options could dilute our securities could be delisted from trading which could limit investors’ ability to make transactions in our securitiesshareholders and subject us to additional trading restrictions.Our common stock is listed ondepress the NYSE Amex (formerly the NYSE Alternext US or American Stock Exchange), a national securities exchange, which imposes continued listing requirements with respect to listed shares. If we fail to satisfy one or moremarket price of the requirements, such as the policy that issuers that have had losses in their five most recent fiscal years have stockholders’ equity of at least $6,000,000, that issuers have more than 300 public shareholders, or that the aggregate market value of shares publicly held be more than $1,000,000, the NYSE Amex may decide to delist our common stock. If the NYSE Amex delists our securities from trading on its exchange and we are not able to list our securities on another exchange or to have them quoted on Nasdaq, our securities could be quoted on the OTC Bulletin Board or on the “pink sheets”. As a result, we could face significant adverse consequences including:·a limited availability of market quotations for our securities;·a determination that our common stock is a “penny stock” which will require brokers trading in our common stock to adhere to more stringent rules and possibly result in a reduced level of trading activity in the secondary trading market for our securities;·a limited amount of news and analyst coverage for us; and·a decreased ability to issue additional securities or obtain additional financing in the future.In addition, a delisting by the NYSE Amex of our securities from trading may trigger an event of default under the 10% Convertible Notes, in which case holders of not less than a majority of the aggregate principal amount of the notes then outstanding may declare the notes immediately due and payable.makegive no assurances that we will ever pay dividends.2007,2010, 2009 or 2008 and the first half of 2009 and do not intend to declare any dividends in the foreseeable future. While subject to periodic review, our current policy is to retain all earnings, if any, primarily to finance our future growth. We make no assurances that we will ever pay dividends, cash or otherwise. Whether we pay any dividends in the future will depend on our financial condition, results of operations, and other factors that we will consider.13STATEMENTScontainsand any related prospectus supplement and the information incorporated by reference herein and therein contain 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.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 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 the Company’s development programs, including without limitation our bid related to SparVax™ under the DHHS Request for Proposals for an Anthrax Recombinant Protective Antigen (rPA) Vaccine for the Strategic National Stockpile, 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, 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, · funding delays, reductions in or elimination of U.S. government funding and/or non-renewal of expiring funding for one or more of our development programs, · the award of government contracts to our competitors or delays caused by third parties challenging government contract awards to us, · 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, from time to time in PharmAthene’s Forms 10-K and 10-Q under the caption ��Risk“Risk Factors” in this prospectus supplement and in itsour other reports filed with the SEC from time to time hereafter. In particular, there can be no assurance that we will prevail in our lawsuit against SIGA, or that even if the court rules in our favor, the court will award monetary damages or other remedies adequate to fully compensate us for our losses. Further, significant additional non-clinical animal studies, human clinical trials, and manufacturing development work remain to be completed for Valortim®. At this point there can be no assurance that the U.S. Securitiesgovernment will renew its contract with us to fund the development of Valortim® beyond January 2012 or that Valortim® will be shown to be safe and Exchange Commission (the “SEC”). effective and approved by regulatory authorities for use in humans.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”). to:· statements about potential future government contract or grant awards, · potential payments under government contracts or grants, · potential regulatory approvals, · future product advancements, and · anticipated financial or operational results. statements.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.receivedno present commitments or agreements for any such transactions. The amounts and timing of our actual expenditures for each purpose may vary significantly depending upon numerous factors, including the actual amount of proceeds we receive, the status of approximately $10.5 millionour research and product development efforts, regulatory approvals, competition and economic or other conditions.10% Convertible Notes and warrants and we will receive the exercise pricerelated series of $2.50 per share upon exercise of any warrants. We will use any proceeds from the exercisepreferred stock. This description of the warrants forpreferred stock in the satisfactioncertificate of existing obligationsdesignations and for general working capital. We will not receive any of the proceeds from the sale of our common stock offered by the selling stockholders named in this prospectus.14· · the title and stated value of the preferred stock; dividend rights, including dividend rates, periods, or payment dates, or methods of calculation of dividends applicable to the preferred stock; whether dividends will be cumulative or non-cumulative, and if cumulative the date from which distributions on the preferred stock shall accumulate; right to convert the preferred stock into a different type of security; voting rights, if any, attributable to the preferred stock; rights and preferences upon our liquidation or winding up of our affairs; terms of redemption; · preemption rights, if any; · the procedures for any auction and remarketing, if any, for the preferred stock; · the provisions for a sinking fund, if any, for the preferred stock; · any listing of the preferred stock on any securities exchange; · the terms and conditions, if applicable, upon which the preferred stock will be convertible into our common stock, including the conversion price (or manner of calculation thereof); SELLING STOCKHOLDERSAn aggregatea discussion of federal income tax considerations applicable to the preferred stock, if material; the relative ranking and preferences of the preferred stock as to dividend or other distribution rights and rights if we liquidate, dissolve or wind up our affairs; any limitations on issuance of any series of preferred stock ranking senior to or on a parity with the series of preferred stock being offered as to distribution rights and rights upon the liquidation, dissolution or winding up or our affairs; and any other specific terms, preferences, rights, limitations or restrictions of the preferred stock. 11,685,031this prospectus, shares of our commonpreferred stock will be registered for resale by the selling stockholders under this prospectus, including (i)may rank, with respect to payment of distributions and rights upon our liquidation, dissolution or winding up, to 9,112,256 shares of common stock issuable upon conversion of all of the 10% Convertible Notes issued to investors pursuant to the Note and Warrant Purchase Agreement, and (ii) 2,572,775sharesallocation of our earnings and losses:· senior to all classes or series of our common stock, and to all of our equity securities ranking junior to the preferred stock; · equally with all equity securities issued by us, the terms of which specifically provide that these equity securities rank on a parity, or equally, with the preferred stock; or · junior to all equity securities issued by us, the terms of which specifically provide that these equity securities rank senior to the preferred stock. issuable upon exerciseor series of all of the warrants issued pursuant to that agreement. Of the 9,112,256 shares of common stock, issuable upon conversion of the 10% Convertible Notes, up to 7,591,780 shares are issuable in respect of the aggregate principal amount of the notes and up to 1,520,476 shares are issuable in respect of interest that accrues on the notes, assuming conversion of all of the notes on the date of maturity. All of the shares referred to in (i) and (ii) above were issued or will be issued by us, if at all, pursuant to exemptions from registration under Section 4(2) of the Securities Act. The description of the 10% Convertible Notes and the warrants is set forth in our Current Reports on Form 8-K and Form 8-K/A filed with the SEC on July 30, 2009 and August 3, 2009, respectively, and are incorporated herein by reference.To the extent permitted by law, the selling stockholders listed below may resell shares pursuant to this prospectus. We have registered the sale of the shares to permit the selling stockholders and their respective permitted transferees or other successors in interest that receive their shares from the selling stockholders after the date of this prospectus to resell the shares.The following table sets forth the name of the selling stockholders, the number and percentage of sharesholders of our commonpreferred stock beneficially ownedmay be entitled to receive distributions, when and as authorized by eachour board of the selling stockholders asdirectors, out of August 25, 2009(1)legally available funds, and immediately after the offering (assuming that all shares offered in this prospectus are sold) andshare pro rata based on the number of shares of ourpreferred stock, common stock being offered byand other equity securities outstanding.selling stockholders (assuming conversionapplicable supplement to this prospectus, and as otherwise required under Delaware law, holders of our preferred stock may or may not have voting rights.notescorresponding amounts payable on all of our stock of other classes or series of equity security ranking on a parity with the datepreferred stock in the distribution of maturity). The selling stockholdersassets upon liquidation, dissolution or winding up, then the holders of our preferred stock and all other such classes or series of equity securities may sell all, some or noneshare ratably in the distribution of the shares being offered. Accordingly, no estimate can be given asassets in proportion to the full liquidating distributions to which they would otherwise be respectively entitled.thatof stock.held by the selling stockholders upon consummation of any sales. In addition, the selling stockholders listedset forth in the table below may have acquired, sold or transferred, in transactions exempt from registration, some or allapplicable supplement to this prospectus. These terms will include the amount and type of their shares since the date as ofsecurity into which the informationshares of preferred stock are convertible, the conversion price (or manner of calculation thereof), the conversion period, provisions as to whether conversion will be at the option of the holders of the preferred stock or us, the events, if any, requiring an adjustment of the conversion price and provisions, if any, affecting conversion in the table is presented.All information with respect to share ownership has been furnished byevent of the selling stockholders, obtained from our transfer agent and/or obtained from certain beneficial ownership filings made by the selling stockholders with the SEC. Each selling stockholderredemption of that is an affiliate of a broker-dealer has informed us that it purchased the shares being registered for resalepreferred stock.ordinary course of businessapplicable supplement to this prospectus, our preferred stock will be subject to mandatory redemption or redemption at our option, in whole or in part, in each case upon the terms, at the times and at the time ofredemption prices set forth in such purchase, it had no agreements or understandings, directly or indirectly,supplement to this prospectus.any person to distribute the shares. From time to time, additional information concerning ownershipwe may include in any applicable prospectus supplements, summarizes the material terms and provisions of the shareswarrants that we may offer under this prospectus. While the terms we have summarized below will apply generally to any warrants that we may offer under this prospectus, we will describe the particular terms of common stockany series of warrants in more detail in the applicable prospectus supplement. The terms of any warrants offered under a prospectus supplement may restdiffer from the terms described below.holdersthe SEC, the form of warrant agreement, which may include a form of warrant certificate, that describes the terms of the shares not namedparticular series of warrants we are offering. The following summary of material provisions of the warrants and the warrant agreements are subject to all the provisions of the warrant agreement and warrant certificate applicable to a particular series of warrants. We urge you to read the applicable prospectus supplements related to the particular series of warrants that we sell under this prospectus, as well as the complete warrant agreements and/or warrant certificates that contain the terms of the warrants.table below and of whom we are unaware.15* Less than 1%(1)Based·the offering price and aggregate number of warrants offered; · if applicable, the designation and terms of the securities with which the warrants are issued and the number of warrants issued with each such security or each principal amount of such security; · if applicable, the date on 28,427,950 sharesand after which the warrants and the related securities will be separately transferable;· in the case of ourwarrants to purchase common stock outstanding as of August 25, 2009. Beneficial ownership is determined in accordance with the rules and regulations of the SEC. In computingor preferred stock, the number of shares beneficially owned by a personof common stock or preferred stock, as the case may be, purchasable upon the exercise of one warrant and the percentage ownership of that person,price at which these shares of our common stock underlying warrants, shares of our common stock underlying may be purchased upon such exercise;· the principal amount of 10% Convertible Notes or subject to options held by that person that are currently exercisable/convertible or exercisable/convertible within 60 days of the date hereof, are deemed outstanding. Such shares, however, are not deemed outstanding for the purposes of computing the percentage ownershipterms of any other person. Except as indicated pursuantrights to applicable community property laws, each stockholder namedredeem or call the warrants;· any provisions for changes to or adjustments in the table has sole voting and investment power with respect to the shares set forth opposite such stockholder’s name.(2)In accordance with the definitionexercise price or number of beneficial ownership, this number (i) includes the shares issuable in respect of the principal amount of the 10% Convertible Notes and the shares issuable in respect of interest on such notes that will accrue within 60 days of August 25, 2009 and (ii) does not include shares of common stocksecurities issuable upon exercise of the warrants. Thewarrants;· the dates on which the right to exercise the warrants are not exercisable until January 28, 2010.will commence and expire;· the manner in which the warrant agreements and warrants may be modified; (3)The number·federal income tax consequences of shares underlyingholding or exercising the 10% Convertible Notes in this column represents warrants, if material;· the sum of (i) the shares issuable in respectterms of the principal amount of the notes held by an investor and (ii) the shares issuable in respect of interest that accrues on the notes, assuming that the investor converts all of its notes on the date of maturity. If an investor converts notes prior to maturity, a lesser number of shares will be issued in respect of accrued interest.(4)The warrants are not exercisable until, and the shares of common stock underlying the warrants therefore will not be issued prior to, January 28, 2010.(5)Includes 849,211 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009), the sharessecurities issuable upon exercise of the warrantswarrants; and the shares underlying the options mentioned below. Dr. James Cavanaugh, a member· any other specific terms, preferences, rights or limitations 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 52,483 shares of common stock which were exercisable as of August 25, 2009 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.(6)Includes 2,203,461 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise ofrestrictions on the 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, Dennis16Henner, 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. Steven St. 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.(7)Includes 137,185 restricted shares (included herein irrespective of the vesting date), options to purchase 478,188 shares of common stock (representing the portion of options to purchase a total of 999,388 shares of common stock that was exercisable as of August 25, 2009 or will become exercisable within 60 days thereof), 24,893 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the warrants. Mr. Wright is our President and Chief Executive Officer and a member of our Board of Directors.(8)Includes options to purchase 77,483 shares of common stock (representing the portion of options to purchase a total of 102,759 shares of common stock that was exercisable as of August 25, 2009 or will become exercisable within 60 days thereof), 17,021 shares issuable upon conversion of the 10% convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the warrants. Mr. McCleary is a member of our Board of Directors.(9)Includes 60,573 restricted shares (included herein irrespective of vesting date), options to purchase a total of 207,783 shares of common stock (representing the portion of options to purchase a total of 343,046 shares of common stock that was exercisable as of August 25, 2009 or will become exercisable within 60 days thereof), 6,630 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the warrants.(10)Includes 838,175 shares of our common stock, 2,820,655 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the 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, Inc. after conversion. As a result of this restriction, the number of shares that may be issued on conversion of the notes by the above holders 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 theretofore been converted.(11)Includes options to purchase 50,000 shares of common stock, 402,950 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the warrants. Dr. Schaffer is a member of our Board of Directors.(12)Mary L. Pappajohn is the spouse of John Pappajohn, who is the Chairman of our Board of Directors.(13)Includes 49,308 restricted shares (included herein irrespective of vesting date), options to purchase a total of 151,086 shares of common stock (representing the portion of options to purchase a total of 284,480 shares of common stock that was exercisable as of August 25, 2009 or will become exercisable within 60 days thereof), 4,029 shares issuable upon conversion of the 10% Convertible Notes (including shares underlying interest that will accrue within 60 days of August 25, 2009) and the shares issuable upon exercise of the warrants.17 this prospectus may be offered and sold from time to time by the selling stockholders. The term “selling stockholder” includes pledgees, donees, transferees or other successors in interest selling shares received after the date of this prospectus from each selling stockholder as a pledge, gift, partnership distribution or other non-sale related transfer. The number of shares beneficially owned by a selling stockholder will decrease as and when it effects any such transfers. The plan of distribution for the selling stockholders’ shares sold hereunder will otherwise remain unchanged, except that the transferees, pledgees, donees or other successors will be selling stockholders hereunder. To the extent required, we may amend and supplement this prospectus from time to time to describe a specific plantime. Registration of distribution.The selling stockholdersour securities covered by this prospectus does not mean, however, that those securities will act independently of us in making decisions with respect tonecessarily be offered or sold.timing, manner and size of each sale. The selling stockholders may make these sales at prices and under terms then prevailing or at prices related to the then current market price. The selling stockholders may also make sales in negotiated transactions. The selling stockholders may offer their shares from time to time pursuant to one or more of the following methods:securities covered by this prospectus:·ordinary brokerage transactions·through agents; · through one or more underwriters or dealers in a public offering and transactionssale by them;· through a block trade in which the broker-dealer solicits purchasers;·onebroker or moredealer engaged to handle the block trades in which the broker-dealertrade will attempt to sell the sharessecurities as agent, but may position and resell a portion of the block as principal to facilitate the transaction;purchases by a broker-dealer as principal and resale by the broker-dealer for its account;·an exchange distribution in accordance with the rules of the applicable exchange;·publicly or privately negotiated transactions;·on the NYSE Amex (or through the facilities of any national securities exchange or U.S. inter-dealer quotation system of a registered national securities association, on which the shares are then listed, admitted to unlisted trading privileges or included for quotation);·through underwriters, brokers or dealers (who may act as agents or principals) or directly to one or more purchasers;· in “at the market offerings,” within the meaning of Rule 415(a)(4) of the Securities Act, to or through a market maker or into an existing trading market, on an exchange or otherwise; ·through a combination of any suchof these methods of sale; and·any other method permitted pursuant to applicable law.In connection with distributions· at a fixed exchange ratio in return for other of our securities. shares or otherwise, the selling stockholders may:·enter into hedging transactions with broker-dealers or other financial institutions, which may in turn engage in short sales of the shares in the course of hedging the positions they assume;·sell the shares short and redeliver the shares to close out such short positions;·enter into option or other transactions with broker-dealers or other financial institutions which require the delivery to them of shares offered by this prospectus, which they may in turn resell; and·pledge shares to a broker-dealer or other financial institution, which, upon a default, they may in turn resell.In addition to the foregoing methods, the selling stockholders may offer their sharessecurities from time to time in one or more transactions involving principalsat a fixed price or brokers not otherwise contemplated above, in a combination of such methods or described above or any other lawful methods. The selling stockholdersprices, which may also transfer, donate or assign their shares to lenders, family members and others and each of such persons will be deemed to be a selling stockholder for purposes of this prospectus. The selling stockholders or their successors in interest maychanged from time to time, pledgeat market prices prevailing at the times of sale, at prices related to such prevailing market prices, or grantat negotiated prices. For each offering of securities hereunder, we will describe the method of distribution of such securities in a prospectus supplement. The prospectus supplements will describe the terms of the offerings of the securities, including:· The name or names of any underwriters, if any; · The purchase price of our securities and the proceeds we will receive from the sale; · Any overallotment options under which underwriters may purchase additional securities from us; · Any agency fees or underwriting discounts and other items constituting agents’ or underwriters’ compensation; · Any public offering price; · Any discounts or concessions allowed or reallowed or paid to dealers; and · Any securities exchange or market on which our common stock or other securities may be listed. interestso long as the stabilizing bids do not exceed a specified maximum price.someexcess of the number of shares an underwriter is obligated to purchase, which creates a syndicate short position. The short position may be either a covered short position or alla naked short position. In a covered short position, the number of shares over-allotted by an underwriter is not greater than the number of shares that it may purchase in the over-allotment option. In a naked short position, the number of shares involved is greater than the number of shares in the over-allotment option. An underwriter may close out any short position by either exercising its over-allotment option and/or purchasing shares in the open market.of common stock, and if the selling stockholders default in the performance of their secured obligations, the pledgees or secured parties may offer and sell the shares of common stock from to time under this prospectus; provided howeveropen market after pricing that could adversely affect investors who purchase in the event ofoffering.pledge or then default onselling concession from a secured obligationsyndicate member when the common shares originally sold by the selling stockholder, in order for the shares to be sold under this18registration statement, unless permitted by law, we must distribute a prospectus supplement and/or amendment to this registration statement amending the list of selling stockholders to include the pledgee, secured party or other successors in interest of the selling stockholder under this prospectus.The selling stockholders may also sell their shares pursuant to Rule 144 under the Securities Act, which permits limited resale of sharessyndicate member is purchased in a private placement subjectstabilizing or syndicate covering transaction to cover syndicate short positions.satisfactiondirection or magnitude of certain conditions.Sales through brokersany effect that any of these activities may be madehave on the price of our common stock or, if applicable, the price for any of our other securities. For a description of these activities, see the information under the heading “Underwriting” or “Plan of Distribution” in the applicable prospectus supplement.any methodthe dealers at the time of trading authorized by any stock exchange or market on whichresale. We will include in the shares may be listed or quoted, including block trading in negotiated transactions. Without limitingprospectus supplement the foregoing, such brokers may act as dealers by purchasing any or allnames of the shares covereddealers and the terms of the transaction.thisus to the agent in the prospectus either assupplement. Unless the prospectus supplement states otherwise, any such agent will act on a best-efforts basis for the period of its appointment.for others or as principals for their own accounts, and reselling such sharesunderwriters to solicit offers by certain types of institutional investors to purchase securities from us at the public offering price set forth in the prospectus supplement pursuant to this prospectus. The selling stockholders may effect such transactions directly, or indirectly through underwriters, broker-dealers or agents actingdelayed delivery contracts providing for payment and delivery on their behalf. In effecting sales, broker-dealers or agents engaged bya specified date in the selling stockholders may arrange for other broker-dealersfuture. We will describe the conditions to participate. Broker-dealers or agents may receive commissions, discounts or concessions from the selling stockholders, in amounts to be negotiated immediately prior to the sale (which compensation as to a particular broker-dealer might be in excess of customary commissions for routine market transactions).In offering the shares covered by this prospectus, the selling stockholders, and any broker-dealers and any other participating broker-dealers who execute sales for the selling stockholders, may be deemed to be “underwriters” within the meaning of the Securities Act in connection with these sales. Any profits realized by the selling stockholderscontracts and the compensationcommissions we must pay for solicitation of such broker-dealersthese contracts in the prospectus supplement.be deemedprovide underwriters and agents with indemnification against civil liabilities related to be underwriting discounts and commissions.The Company is required to pay all fees and expenses incident to the registration of the shares.The Company has agreed to indemnify the selling stockholders against certain losses, claims, damages and liabilities,this offering, including liabilities under the Securities Act.York, will pass upon the validity of the common stock offered pursuant to this prospectus.2008,2010, as set forth in their report, which is incorporated by reference in this prospectus and elsewhere in the registration statement. Our financial statements are incorporated by reference in reliance on Ernst & Young LLP’s report, given on their authority as experts in accounting and auditingauditing.specialcurrent reports, proxy statements and other information with the SEC. You may read and copy any materials we file with the SEC at the SEC’s Public Reference Room located at 100 F Street, N.E., Washington, D.C. 20549. Please call the SEC at 1-800-SEC-03301-800-SEC -0330 for further information on the Public Reference Room. You may also access filed documents at the SEC’s website at www.sec.gov.19after the date of the initial registration statement and prior to effectiveness of such registration statement as well as after the date of this prospectus and prior to the termination of the offering shall be deemed incorporated by reference in this prospectus and1934, shall be deemed to be aincorporated by reference in the registration statement and to be part of this prospectusthereof from the date of filing of such documentsinformation and reports.·our Annual Report on Form 10-K for the year ended December 31, 2008 (File No. 001-32587);·Amendment No. 1 to our Annual Report on Formand 10-K/A for the year ended December 31, 20082010 (File No. 001-32587)001 -32587);ReportsReport on Form 10-Q for the quartersquarter ended March 31, 2009 and June 30, 20092011 (File No. 001-32587);ReportsReport on Form 8-K and/or 8-K/A filed with the SEC on January 27, 2009, March 24, 2009, March 27, 2009, March 30, 2009, April 16, 2008, April 23, 2009, April 28, 2009, April 30, 2009, May 15, 2009, June 23, 2009, July 16, 2009, July 30, 2009, August 3, 2009, August 6, 2009, August 13, 2009 and August 17, 2009;·our Preliminary Proxy Statement filed with the SEC on June 18, 2009, including any amendments or supplements filed for the purpose of updating same;10, 2011; andall documents filed by us with the SEC under Section 13(a), 13(c), 14 or 15(d) of the Exchange Act after the date of this prospectus and before the termination of this offering.·1-800-SEC-0330.1-800-SEC -0330. The SEC also maintains an Internet site that contains reports, proxy and information statements, and other information regarding issuers, like PharmAthene, that file electronically with the SEC at http://www.sec.gov.20table sets forthis a statement of the estimated costs and expenses, payableother than underwriting compensation, incurred or expected to be incurred by the Registrantus in connection with the issuance and distribution of the securities being registered pursuant to this registration statement. All of the amounts shown are estimates except for the SEC registration fee. The amounts do not include the costs of preparing any prospectus supplements, NYSE Amex listing fees, FINRA filing fees, transfer agent fees or other expenses relating to the sale and distribution of theparticular securities registered hereby:SEC Registration Fee $ 11,610 Accounting Fees and Expenses $ 50,000 Legal Fees and Expenses $ 50,000 Miscellaneous Fees and Expenses $ 5,000 Total: $ 116,305 certificateAmended and Restated Certificate of incorporationIncorporation, as amended, provides that the Company, to the full extent permitted by Section 145 of the Delaware General Corporation Law, as amended from time to time, shall indemnify all persons whom it may indemnify pursuant thereto.such law. It further provides that expenses (including attorneys’ fees) incurred by an officer or director in defending any civil, criminal, administrative, or investigative action, suit or proceeding for which such officer or director may be entitled to indemnification hereunderunder our Amended and Restated Certificate of Incorporation, as amended, shall be paid by the Company in advance of the final disposition of such action, suit or proceeding upon receipt of an undertaking by or on behalf of such director or officer to repay such amount if it shall ultimately be determined that he is not entitled to be indemnified by the Company as authorized thereby.bylawsBylaws, as amended, provide the Company with the power to indemnify its officers, directors, employees and agents or any person serving at the Company’s request as a director, officer, employee or agent of another corporation, partnership, joint venture, trust or other enterprise to the fullest extent permitted by Delaware law.Insofar as indemnification for liabilities arising under the Securities Act may be permitted to the Registrant’s directors, officers, and controlling persons pursuant to the foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the Commission such indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment of expenses incurred or paid by a director, officer or controlling person in a successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to the court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.(A)Registrantregistrant hereby undertakes:Registration Statement:1933;Registration Statementregistration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forthII-1Registration Statement.registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than 20 percent change in the maximum aggregate offering price set forth in the “Calculation of Registration Fee” table in the effective Registration Statement;Registration Statementregistration statement or any material change to such information in the Registration Statement;(A)(a)(1)(i), (A)(a)(1)(ii) and (a)(1)(iii) do not apply if the information required to be included in a post-effectivepost- effective amendment by those paragraphs is contained in periodic reports filed with or furnished to the Commission by the registrant pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”) that are incorporated by reference in the Registration Statementregistration statement or is contained in a form of prospectus pursuant to Rule 424(b) that is part of the Registration Statement;of 1933, each such post-effective amendment shall be deemed to be a new Registration Statementregistration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initialbona fide offering thereof; andRegistration Statementregistration statement shall be deemed to be a new Registration Statementregistration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initialbona fide offering thereof.(C)II-2August 27, 2009.July 7, 2011.By:/s/ David P. WrightBy: David P. WrightChief Executive Officer David P. Wright,Eric I. Richman, Charles A. Reinhart III and Jordan P. Karp, and each of them, as attorneys-in-fact and agents, with full power of substitution and resubstitution, for and in the name, place and stead of the undersigned, in any and all capacities, to sign any and all amendments (including post-effectivepost- effective amendments) to this Registration Statement or any Registration Statement for this offering that is to be effective upon the filing pursuant to Rule 462(b) under the Securities Act of 1933, as amended, and all post-effective amendments thereto, and to file the same, with all exhibits thereto and all other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents full power and authority to do and perform each and every act and thing requisite and necessary to be done in and about the premises, as fully to all intents and purposes as the undersigned might or could do in person, hereby ratifying and confirming all that each of said attorney-in-fact or substitute or substitutes, may lawfully do or cause to be done by virtue hereof.August 27, 2009.July 7, 2011.David P. Wright Eric I. Richman Chief Executive Officer and Director David P. WrightChief Financial Officer(Principal Financial Officer and Principal Accounting Officer) /s/ John Pappajohn /s/ John PappajohnJohn Pappajohn/s/ Derace Schaffer, M.D. Derace Schaffer, M.D. Director /s/ Derace Schaffer, MDDirectorDerace Schaffer, MDM. GillDirectorII-3/s/ James H. Cavanaugh, Ph.D.James H. Cavanaugh, Ph.D.DirectorDirector DirectorDirector /s/ Jeffrey W. Runge, M.D. Jeffrey W. Runge, M.D. Director /s/ Mitchel Sayare, Ph.D. Mitchel Sayare, Ph.D. Director 3.11.1 Form of Underwriting Agreement.* 3.1 incorporatedas amended. Incorporated by reference to Exhibit 3.1the Company’s current report on Form 8-K filed on November 4, 2009.3.2 Registrant’s Current Report on Form 8-K filed June 19, 2008 (File No. 001-32587).by the Registrant on May 2, 2008.3.2By-laws, incorporatedCertificate of Designations with respect to Preferred Stock.*4.1 Exhibit 3.1 to the Registrant’s Current Report on Form 8-K filed May 2, 2008 (File No. 001-32587).by the Registrant on September 24, 2007.4.1Form of 10% Unsecured Senior Convertible Note, incorporated by reference to Exhibit 4.9 to the Registrant’s Current Report on Form 8-K/A, filed August 3, 2009 (File No. 001-32587).4.2To Purchase Common Stock, incorporated by reference to Exhibit 4.10 to the Registrant’s Current Report onand/or Form 8-K/A, filed August 3, 2009 (File No. 001-32587).Sonnenschein, Nath & RosenthalSNR Denton US LLP.10.1Note and Warrant Purchase Agreement, dated as of July 24, 2009 by and among PharmAthene, Inc. and the investors named therein, as amended by Amendment No. 1 to Note and Warrant Purchase Agreement, dated as of July 26, 2009 and Amendment No. 2 to Note and Warrant Purchase Agreement, dated as of July 28, 2009, incorporated by reference to Exhibit 10.50 to the Registrant’s Current Report on Form 8-K/A, filed August 3, 2009 (File No. 001-32587).10.2Registration Rights Agreement, dated as of July 26, 2009 by and among PharmAthene, Inc. and the investors named therein, incorporated by reference to Exhibit 10.51 to the Registrant’s Current Report on Form 8-K/A, filed August 3, 2009 (File No. 001-32587).23.1Sonnenschein, Nath & RosenthalSNR Denton US LLP (included in Exhibit 5.1).independent registered public accounting firm.