UNITED STATES SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, DC 20549
FORM 10-K
   
þ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the fiscal year ended DECEMBER 31, 20082009
OR
   
o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the transition period from                    to                    
Commission file number: 0-24274
LA JOLLA PHARMACEUTICAL COMPANY
(Exact name of registrant as specified in its charter)
   
Delaware 33-0361285
(State or other jurisdiction(I.R.S. Employer

of incorporation or organization)
 (I.R.S. Employer
Identification Number)
6455 Nancy Ridge4365 Executive Drive, Suite 300, San Diego, CA 92121
(Address of principal executive offices, including Zip Code)
Registrant’s telephone number, including area code:(858) 452-6600
Securities registered pursuant to Section 12(b) of the Act:
Title of each class:Name of each exchange on which registered:
Common Stock, par value $0.01 per shareThe Nasdaq Global Market
Securities registered pursuant to Section 12(g) of the Act:
NoneCommon Stock, Par Value $0.01 per share
Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yeso Noþ
Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act. Yeso Noþ
Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yesþ Noo
Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yeso Noo
Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of the Form 10-K or any amendment to this Form 10-K.o
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):
       
Large accelerated filero Accelerated filerþo Non-accelerated filero Smaller reporting companyoþ
    (Do not check if a smaller reporting company)  
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yeso Noþ
The aggregate market value of voting and non-voting common stock held by non-affiliates of the registrant as of June 30, 20082009 totaled approximately $69,285,000$12,042,000 based on the closing price of $2.18$0.19 as reported by the Nasdaq Global Market. As of March 19, 2009,April 6, 2010, there were 55,549,52865,722,648 shares of the Company’s common stock ($0.01 par value) outstanding.
DOCUMENTS INCORPORATED BY REFERENCE
     Portions of the annual stockholders’ report for the year ended December 31, 2008 are incorporated by reference into Parts I and II. Portions of the proxy statement for the 2009 annual stockholders’ meeting are incorporated by reference into Part III.None
 
 

 


 

TABLE OF CONTENTS
     
    
     
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 EX-10.57Exhibit 21.1
 EX-10.58Exhibit 23.1
 EX-10.59Exhibit 31.1
 EX-10.60Exhibit 31.2
 EX-10.61
EX-10.62
EX-10.63
EX-10.64
EX-10.65
EX-23.1
EX-31.1
EX-31.2
EX-32.1Exhibit 32.1

 


FORWARD-LOOKING STATEMENTS
The forward-looking statements in this report involve significant risks, assumptions and uncertainties, and a number of factors, both foreseen and unforeseen, could cause actual results to differ materially from our current expectations. Forward-looking statements include those that express a plan, belief, expectation, estimation, anticipation, intent, contingency, future development or similar expression. The analysis of the data from our Phase 3 ASPEN trial of Riquent showed that the trial did not reach statistical significance with respect to its primary endpoint, delaying time to renal flare or for either secondary endpoint, improvement in proteinuria or time to major SLE flare and we decided to stop the study. Additional risk factors include the uncertainty and timing of initiating a strategic transaction to maximize the value of our remaining assets and continuing as a going concern. Accordingly, you should not rely upon forward-looking statements as predictions of future events. The outcome of the events described in these forward-looking statements are subject to the risks, uncertainties and other factors described in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and in the “Risk Factors” contained in this Annual Report on Form 10-K, and in other reports and registration statements that we file with the Securities and Exchange Commission from time to time. We expressly disclaim any intent to update forward-looking statements.

 


PART I
In this report, all references to “we,” “our,” “us” and “the Company” refer to La Jolla Pharmaceutical Company, a Delaware corporation, and our wholly owned subsidiary.subsidiaries La Jolla Limited (dissolved during October 2009) and Jewel Merger Sub, Inc.
Item 1. Business
Item 1.Business
Overview
La Jolla Pharmaceutical Company was incorporated in Delaware in 1989. We are a biopharmaceutical company that has historically focused on the development and testing of Riquent as a treatment for Lupus nephritis. Lupus is an antibody-mediated disease caused by abnormal B cell production of antibodies that attack healthy tissues. Current treatments for this autoimmune disorder often address only symptoms of the disease, or nonspecifically suppress the normal operation of the immune system, which can result in severe, negative side effects and hospitalization. From August 2004 to February 2009, Riquent was being studied in a double-blinded multicenter Phase 3 clinical trial, called the “ASPEN” trial.
On January 4, 2009, we entered into a development and commercialization agreement (the “Development Agreement”) with BioMarin CF Limited (“BioMarin CF”), a wholly-owned subsidiary of BioMarin Pharmaceutical Inc. (“BioMarin Pharma”). Under the terms of the Development Agreement, BioMarin CF was granted co-exclusive rights to develop and commercialize Riquent in the United States, Europe and all other territories of the world, excluding the Asia Pacific region, and the non-exclusive right to manufacture Riquent anywhere in the world. In January 2009, BioMarin CF paid us a non-refundable commencement payment of $7.5 million and BioMarin Pharma purchased $7.5 million of a newly designated series of our preferred stock. As described below, this agreement was terminated on March 27, 2009. See Note 104 to our audited consolidated financial statements included in Part IV.
In February 2009, we were informed by an Independent Monitoring Board for the Riquent Phase 3 ASPEN study that the monitoring board completed their review of the first interim efficacy analysis of Riquent and determined that continuing the study was futile. We subsequently unblinded the data and found that there was no statistical difference in the primary endpoint, delaying time to renal flare, between the Riquent-treated group and the placebo-treated group, although there was a significant difference in the reduction of antibodies to double-stranded DNA. There were 56 renal flares in 587 patients treated with either 300-mg or 900-mg of Riquent, and 28 renal flares in 283 patients treated with placebo.
Based on these results, we immediately discontinued the Riquent Phase 3 ASPEN study and the further development of Riquent. We had previously devoted substantially all of our research, development and clinical efforts and financial resources toward the development of Riquent. In connection with the termination of our clinical trials for Riquent, we subsequently initiatedtook steps to significantly reduce our operating costs, including a planned substantial reduction in personnel, which we expect will be effected earlywas completed in the second quarter ofApril 2009. We have also ceased the manufacture of Riquent at our former facility in San Diego, California.California as well as all regulatory activities associated with Riquent. See Note 6 to our consolidated financial statements included in Part IV.
Following the futile results of the first interim efficacy analysis of Riquent, BioMarin CF has elected to not exercise its full license rights to the Riquent program under the Development Agreement. Thus, the Development Agreement between the parties terminated on March 27, 2009 in accordance with its terms. Pursuant to the Securities Purchase Agreement between us and BioMarin Pharma, all of the Company’s preferred shares purchased by BioMarin Pharma were converted into common shares. Additionally, all rights to Riquent have beenwere returned to us. See Note 4 to our consolidated financial statements included in Part IV.
In July 2009, we announced that, in light of the alternatives available to us at that time, a wind down of our business would be in the best interest of our stockholders. Although our Board of Directors approved a Plan of Complete Liquidation and Dissolution (the “Plan of Dissolution”) in September 2009, it was subject to approval by holders of at least a majority in voting power of our outstanding shares. We called a special meeting of stockholders to vote on the Plan of Dissolution; however, the majority of our stockholders failed to return their proxy cards or otherwise indicate their votes with respect to this proposal. As a result, in November 2009, we cancelled the special meeting of stockholders and began to evaluate other strategic opportunities.

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In December 2009, we signed a definitive merger agreement with Adamis Pharmaceuticals Corporation (“Adamis”) and our direct wholly-owned subsidiary, Jewel Merger Sub, Inc. (“Merger Sub”) wherein Merger Sub would merge with and into Adamis and Adamis would survive the merger as a wholly-owned subsidiary of La Jolla. The merger required certain proposals to be approved by our stockholders including the issuance of our common stock to Adamis stockholders and effecting a significant reverse split of our common stock. We called a special meeting of stockholders to vote on the merger-related proposals. In early March 2010, the Company and Adamis agreed to terminate the Merger Agreement as a result of too few of our stockholders voting on the proposals related to the Merger such that we did not have the requisite quorum to hold the stockholders’ meeting.
In light of our decisionapparent inability to discontinue development of our Riquent clinical program,complete a strategic transaction that requires stockholder approval, we are seekingcurrently evaluating what options are available to us to maximize the value of our remaining assets. We are currently evaluating our strategic alternatives,assets, which may include the following:
Sell or out-license our remaining assets, including our SSAO compounds, although we do not expect to receive any substantive value for them;
Pursue potential other strategic transactions, which could include mergers, license agreements or other collaborations, with third parties; or
Sell or out-license our Riquent program, although we may not receive any significant value upon any such sale or license;

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Pursue potential other strategic transactions for new technologies, which could include mergers, license agreements or other collaborations, with third parties where we acquire new compounds for development and seek additional capital; or
Implement an orderlya wind down of the Company if other alternatives are not deemed viable and in the best interests of the Company.
Following the negative results of the ASPEN trial, we recorded a significant charge for the impairment of our Riquent assets, including our Riquent-related patents, and it is unlikely that we willmay not realize any substantivesignificant value from these assets in the future. Additionally, there is a substantial risk that we may not successfully implement any of these strategic alternatives, and even if we determine to pursue one or more of these alternatives, we may be unable to do so on acceptable terms. Any such transactions may be highly dilutive to our existing stockholders and may deplete our limited remaining capital resources.

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About Lupus
     Lupus is a life-threatening, antibody-mediated disease in which disease-causing antibodies damage various tissues. According to recent statistics compiled by the Lupus Foundation of America, epidemiological studies and other sources, the number of lupus patients in the United States is estimated to be between 500,000 and 1,000,000, and approximately 16,000 new cases are diagnosed each year. Approximately nine out of 10 lupus patients are women, who usually develop the disease during their childbearing years. Lupus is characterized by a multitude of symptoms that can include kidney inflammation, which can lead to kidney failure (lupus nephritis), serious episodes of cardiac and central-nervous-system inflammation, as well as extreme fatigue, arthritis and rashes. Approximately 80% of all lupus patients progress to serious symptoms. Approximately 40-45% of lupus patients will develop kidney disease, which is a leading cause of death in lupus.
     Lupus nephritis is characterized by periods of extreme, acute inflammation called “renal flares” which often require aggressive treatment with high-dose corticosteroids, immunosuppressive agents, and hospitalization. Patients not experiencing a renal flare often have less severe, chronic inflammation which can also contribute to the morbidity and mortality of lupus nephritis. Patients experiencing a renal flare have more severe inflammation as evidenced by indicators of diminished kidney function such as elevated serum creatinine or increased proteinuria. Proteinuria, or protein in the urine, is believed to be a pathological indicator of renal disease. The reduction of proteinuria is one of the goals for the treatment of lupus patients with renal disease. Monitoring the level of a patient’s proteinuria is a routine and important way to help determine the severity and progression of renal disease. Over time, lupus nephritis can lead to deterioration of kidney function and to end-stage kidney disease, requiring long-term renal dialysis or kidney transplantation to sustain a patient’s life.
     Current treatments for lupus patients who have a renal flare often involve repeated administration of corticosteroids, often at high levels, that can lead to serious side effects when used long-term. Many patients with renal flares are also treated with immunosuppressive therapy, including anti-cancer or transplantation drugs, which can have a general suppressive effect on the immune system, may be carcinogenic and/or can cause birth defects. Treatment with immunosuppressive therapies can leave patients vulnerable to serious infection, which is a significant cause of sickness and death in these patients. Importantly, many patients do not respond adequately to treatment with immunosuppressive therapies and fail to achieve full remission, a return to normal renal function or the level of renal function prior to the flare. As a result, low to moderate levels of inflammation remain as evidenced by elevated urine protein (proteinuria), elevated serum creatinine, and other markers of abnormal kidney function. This incomplete response to treatment with immunosuppressive therapies increases the risk of additional renal flares as well as the risk of end-stage kidney disease and death.

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Riquent Clinical Trial History
Early clinical studies:
     We have conducted several clinical studies of Riquent, including a Phase 1 trial in healthy volunteers and four Phase 2 trials in lupus patients. The first tested a single dose, the second was a repeat dose-escalating clinical trial in two patients. In 1995, we conducted a double-blind, placebo-controlled dose-ranging trial, in which 58 lupus patients with mild lupus symptoms were treated for a four-month period with Riquent or placebo, and then were monitored for two months. Patients in the weekly treatment groups showed a dose-response correlation between increasing doses of Riquent and reductions of levels of antibodies to dsDNA. In 1999, we completed a second double-blind, placebo-controlled dose-ranging trial, in which 74 lupus patients received weekly injections of 10–, 50– or 100–mg of Riquent or placebo for a 12-week period.
     In December 1996, we initiated a double-blind, placebo-controlled, multi-center Phase 2/3 clinical trial of Riquent in which lupus patients with a history of lupus nephritis received placebo or weekly doses of 100–mg of Riquent for the first 16 weeks of the trial. More than 200 patients at more than 50 sites in North America and Europe enrolled in the trial. In May 1999, an interim analysis of the Phase 2/3 trial indicated that the trial was unlikely to reach statistical significance for the primary endpoint, time to renal flare, and the trial was stopped.
Previous Phase 3 trial
     Based on the observations from our Phase 2/3 trial and following discussions with the FDA, we initiated a Phase 3 clinical trial in September 2000 to further evaluate the safety and efficacy of Riquent in the treatment of lupus renal disease. Patients in the trial were treated weekly with either 100-mg of Riquent or placebo for a period of up to 22 months. The trial data indicated that treatment with Riquent did not increase length of time to renal flare, the primary endpoint, or time to treatment with HDCC, the secondary endpoint, in a statistically significant manner when compared with placebo through the end of the study.
     Notwithstanding the failure to reach the primary or secondary endpoints in the earlier Phase 3 trial, in 2004, we filed a New Drug Application (“NDA”) for Riquent with the FDA. Our NDA submission was prepared on our understanding that the FDA could potentially approve Riquent on the basis of our clinical trial results or under the accelerated approval regulation known as Subpart H. In October 2004, we received a letter from the FDA indicating that Riquent is approvable, but that an additional, randomized, double-blind study demonstrating the clinical benefit of Riquent would need to be completed prior to approval. The FDA letter indicated that the successful completion of the clinical trial that we initiated in August 2004 would appear to satisfy this requirement.

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Phase 3 ASPEN trial
     A placebo-controlled Phase 3 clinical benefit trial, designed to meet the FDA’s requirement that we conduct an additional randomized, double-blind study, was initiated in August 2004 under a Special Protocol Assessment (“SPA”). The FDA confirmed that the primary endpoint required to establish efficacy is the time to renal flare for the combined population of patients treated with weekly Riquent doses of 300-mg and 900-mg, compared with placebo. In February 2009, an interim efficacy analysis of the Phase 3 ASPEN study indicated that the trial was unlikely to reach statistical significance for the primary endpoint, delaying time to renal flare, and was stopped. We also stopped further development of Riquent.
     The results from the Phase 3 study indicated that there was no statistical difference in delaying time to renal flare between the Riquent-treated group and the placebo-treated group, although there was a statistically significant reduction in antibodies to double-stranded DNA, which caused us to question our general hypothesis that reductions in double-stranded DNA would delay the time to renal flare. There were 56 renal flares in 587 patients treated with either 300-mg or 900-mg of Riquent and 28 renal flares in 283 patients treated with placebo. No statistical difference was observed between Riquent-treated and placebo-treated patients for either secondary endpoint, percent of patients with a 50% reduction in proteinuria at 12 months or time to Major SLE Flare. Riquent appeared to be well tolerated. The analysis included data from 870 patients who were treated for up to 18 months. Approximately 90% of the patients were female and the median age was 32. Approximately fifty percent of the patients were from Asia; the remaining 50% were from the United States, Mexico, Latin America and Europe.
Inflammatory Program
SSAO Inflammation Program
     On December 2, 2003, we announced the discovery of novel, orally-active small molecules for the treatment of autoimmune diseases and acute and chronic inflammatory disorders. Our scientists have generated highly selective inhibitors of SSAO, an enzyme that has been implicated in inflammatory responses in many tissues and organs. SSAO, also known as vascular adhesion protein-1 or VAP-1, was recently discovered to be a dual-function molecule with enzymatic and cell adhesion activities. SSAO on blood vessels contributes to inflammation by helping white blood cells leave the blood and penetrate inflamed tissue. The enzyme also contributes to the production of molecules that exacerbate inflammation, including formaldehyde and oxygen free radicals. SSAO inhibitors are designed to reduce inflammation by blocking the white blood cells and reducing the levels of inflammatory mediators.
     Increases in the levels of plasma or membrane-associated SSAO have been reported for many inflammation-associated diseases including rheumatoid arthritis, inflammatory bowel disease, diabetes, atherosclerosis psoriasis and chronic heart failure. In addition, treatment of animals with SSAO inhibitors has been shown to provide significant benefit in several inflammation-based diseases.
     Data published by our scientists in 2005 and 2006 in peer-reviewed articles show that these novel, orally-active small molecule inhibitors of SSAO/VAP-1 may provide clinical benefit for the treatment of stroke, ulcerative colitis, and other autoimmune diseases and inflammatory disorders. Peer-reviewed data published in 2007 identified and characterized a lead compound and described its role in inhibiting inflammation in the lungs of rodents.
     Substantially all of our resources have historically been devoted to the development of Riquent and we have therefore not committed significant resources to this program in the past. We expect that SSAO would only be developed further if we were to sell or out-license the compound or engage in a strategic transaction, such as a merger, where the other party has resources to fund its continued development. At present, we do not have the resources to advance this program.
Manufacturing
     Our manufacturing activities have historically consisted of the manufacture of Riquent. In February 2009, we ceased all drug manufacturing activities as a result of the futility determination of the Riquent Phase 3 ASPEN study and we stopped further development of Riquent.

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Patents and Proprietary Technologies
     We fileAll of our issued and pending patents were written off or sold during the year ended December 31, 2009. In order to conserve cash, we have stopped paying patent applicationsmaintenance and prosecution costs on our Riquent related patents, and will need to either reinstate these patents by paying back fees or let them lapse. At the present time, we are considering whether there continues to be potential value in the United States andRiquent patent estate. To the extent that there is believed to be value with these assets, we would need to pay approximately $0.1 million in foreign countries for the protection of our proprietary technologies and drug candidates as we deem appropriate. We currently own 133 issuedfees to reinstate these patents and have 29 pending patent applications in the United States and in foreign countries covering various technologies and drug candidates, including Riquent (Toleragens), our SSAO inhibitor technology (currently there are no issued patents to our SSAO inhibitor technology), our antibody-mediated thrombosis drug candidates (Toleragens), our Tolerance Technology, and our carrier platform and linkage technologies for our Toleragens. As noted above, following the futility finding in the ASPEN trial, we recorded significant impairment charges for our Riquent-related patents and have written down the value of these assets to near zero as of December 31, 2008. Our issued patents, substantially all of which relate to Riquent, include:
Lupus Toleragens — eight issued United States patents, three issued Australian patents, one granted Portuguese patent, two granted Norwegian patents, one granted European patent (which has been unbundled as 13 European national patents), a second granted European patent (which has been unbundled as 15 European national patents), two granted Chinese patents, one granted Hong Kong patent, one granted South Korean patent, two granted Canadian patents, two granted Finnish patents, one granted Irish patent, and one granted Japanese patent (expiring between 2010 and 2020); and
Tolerance Technology — five issued United States patents, one issued Australian patent, one granted European patent (which has been unbundled as 15 European national patents), one granted Japanese patent, two granted Canadian patents, one granted South Korean patent and one granted Irish patent (expiring between 2011 and 2012).
applications.
Competition
The biotechnology and pharmaceutical industries are subject to rapid technological change. Competition from domestic and foreign biotechnologyextremely competitive. Many companies large pharmaceutical companies and other institutions has historically been intense and may increase. A number of companies are pursuing the development of pharmaceuticals in our targeted areas. These include companies that are conducting clinical trials and pre-clinical studies for the treatment of lupus.
     In addition, there are a number of academic institutions, both public and private, engaged in activities relating to the research and development of therapeutics for autoimmune, inflammatory and other diseases. Most of these companies and institutions have substantially greater facilities,financial and other resources research and development capabilities, regulatory compliance expertise, and manufacturing and marketing capabilities than we do. In addition, they may have substantially more experience in effecting strategic combinations, in-licensing technology, developing drugs, obtaining regulatory approvals, and manufacturing and marketing products. We cannot give any assurances that we can effectively compete with these other technologies may in the future be the basis of competitive products. There can be no assurance that our competitors will not develop or obtain regulatory approval for products that would render our technologypharmaceutical and any potential products obsolete or noncompetitive.biotechnology companies.

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Government Regulation
United States
     BiotechnologyGovernmental authorities in the U.S. and other countries extensively regulate, among other things, the research, and development, activities and the manufacturingtesting, manufacture, labeling, promotion, advertising, distribution, and marketing of products are subject to significant regulationproduced by numerous government authorities inthe biotechnology and pharmaceutical industry. In the United States the Food and other countries. In the United States,Drug Administration (the “FDA”) regulates drugs under the Federal Food, Drug, and Cosmetic Act and its implementing regulations. Outside the Public Health Service Act governU.S., the testing, manufacture, safety, efficacy, labeling, storage, record keeping, approval, advertising and promotion, and distribution of our drug candidates and any products we may develop. In addition to FDA regulations, we have historically been subject to other federal, state and local regulations, such as the Occupational Safety and Health Act and the Environmental Protection Act, as well as regulations governing the handling, use and disposal of radioactive and other hazardous materials used in our research activities. Product development and approval within this regulatory framework takes a number of years and involves the expenditure of substantial resources. In addition, this regulatory framework is subject to changes that may adversely affect approval, delay an application or require additional expenditures.
     The steps required before a pharmaceutical compound may be marketed in the United States include: pre-clinical laboratory and animal testing; submission to the FDA of an Investigational New Drug application, which must become effective before clinical trials may commence; conducting adequate and well-controlled clinical trials to establish the safety and efficacy of the drug; submission to the FDA of an NDA or Biologic License Application (“BLA”) for biologics; satisfactory completion of an FDA preapproval inspection of the manufacturing facilities to assess compliance with cGMPs; and FDA approval of the NDA or BLA prior to any commercial sale or shipment of the drug. In addition to obtaining FDA approval for each product, each drug-manufacturing establishment must be registered with the FDA and be operated in conformity with cGMPs. Drug product manufacturing facilities located in California also must be licensed by the State of California in compliance with separate regulatory requirements.
     Pre-clinical testing includes laboratory evaluation of product chemistry and animal studies to assess the safety and efficacy of the product and its formulation. The results of pre-clinical testing are submitted to the FDA as part of an Investigational New Drug Application and, unless the FDA objects, the Investigational New Drug Application becomes effective 30 days following its receipt by the FDA.
     Clinical trials involve administration of the drug to healthy volunteers and to patients diagnosed with the condition for which the drug is being tested under the supervision of a qualified clinical investigator. Clinical trials are conducted in accordance with protocols that detail the objectives of the study, the parameters to be used to monitor safety, and the efficacy criteria to be evaluated. Each protocol is submitted to the FDA as part of the Investigational New Drug application. Each clinical trial is conducted under the auspices of an independent Institutional Review Board (“IRB”) in the United States or Ethics Committee (“EC”) outside the United States for each trial site. The IRB or EC considers, among other matters, ethical factors and the safety of human subjects.
     Clinical trials are typically conducted in three sequential phases, but the phases may overlap or be repeated. In Phase 1, the phase in which the drug is initially introduced into healthy human subjects or patients, the drug is tested for adverse effects, dosage tolerance, metabolism, distribution, excretion and clinical pharmacology. Phase 2 trials involve the testing of a limited patient population in order to characterize the actions of the drug in targeted indications, to determine drug tolerance and optimal dosage, and to identify possible adverse side effects and safety risks. When a compound appears to be effective and to have an acceptable safety profile in Phase 2 clinical trials, Phase 3 clinical trials are undertaken to further evaluate and confirm clinical efficacy and safety within an expanded patient population at multiple clinical trial sites. The FDA reviews the clinical plans and monitors the results of the trials and may discontinue the trials at any time if significant safety issues arise. Similarly, an IRB may suspend or terminate a trial at a study site which is not being conducted in accordance with the IRB’s requirements or which has been associated with unexpected serious harm to subjects.
     The results of pre-clinical testing and clinical trials are submitted to the FDA in the form of an NDA or BLA for marketing approval. The submission of an NDA or BLA also is subject to the payment of user fees, but a waiver of the fees may be obtained under specified circumstances. The testing and approval process is likely to require substantial time and effort and there can be no assurance that any approval will be granted on a timely basis, if at all, or that conditions of any approval, such as warnings, contraindications, or scope of indications will not materially

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impact the potential market acceptance and profitability of the drug product. Data obtained from clinical trials are not always conclusive and the FDA may interpret data differently than we interpret the same data. The FDA may refer the application to an advisory committee for review, evaluation and recommendation as to whether the application should be approved and under what conditions. The FDA is not bound by the recommendations of an advisory committee, but it generally follows such recommendations. The approval process is affected by a number of factors, including the severity of the disease, the availability of alternative treatments, and the risks and benefits of the product demonstrated in clinical trials.
     Additional pre-clinical testing or clinical trials may be requested during the FDA review period and may delay any marketing approval. After FDA approval for the initial indications, further clinical trials may be necessary to gain approval for the use of the product for additional indications. In addition, after approval, some types of changes to the approved product, such as manufacturing changes, are subject to further FDA review and approval. The FDA mandates that adverse effects be reported to the FDA and may also require post-marketing testing to monitor for adverse effects, which can involve significant expense. Adverse effects observed during the commercial use of a drug product or which arise in the course of post-marketing testing can result in the need for labeling revisions, including additional warnings and contraindications, and, if the findings significantly alter the risk/benefit assessment, the potential withdrawal of the drug from the market.
     Among the conditions for FDA approval is the requirement that the prospective manufacturer’s quality control and manufacturing procedures conform to the FDA’s cGMP requirements. Domestic manufacturing facilities are subject to biannual FDA inspections and foreign manufacturing facilities are subject to periodic inspections by the FDA or foreign regulatory authorities. If the FDA finds that a company is not operating in compliance with cGMPs, the continued availability of the product can be interrupted until compliance is achieved and, if the deficiencies are not corrected within a reasonable time frame, the drug could be withdrawn from the market. In addition, the FDA strictly regulates labeling, advertising and promotion of drugs. Failure to conform to requirements relating to licensing, manufacturing, and promoting drug products can result in informal or formal sanctions, including warning letters, injunctions, seizures, civil and criminal penalties, adverse publicity and withdrawal of approval.
Foreign
     Biotechnology research and development activities and the manufacturing and marketing of products are also subject to numerous and varying foreign regulatory requirements governing the design and conduct of clinical trials and marketing approval for pharmaceutical productsauthorization vary widely from country to be marketed outsidecountry, but involve a similar degree of the United States. The approval process varies among countriesoversight and regions and can involve additional testing, and the time required to obtain approval may differ from that required to obtain FDA approval.
     The steps to obtain approval to market a pharmaceutical compoundrigor as in the European Union include: pre-clinical laboratory and animal testing; conducting adequate and well controlled clinical trials to establish safety and efficacy; submission of a Marketing Authorization Application (the “MAA”); and the issuance of a product marketing license by the European Commission prior to any commercial sale or shipment of drug. In addition to obtaining a product marketing license for each product, each drug manufacturing establishment must be registered with the European Medicines Agency (the “EMEA”) must operate in conformity with European good manufacturing practice, and must pass inspections by the European health authorities.
     Upon receiving the MAA, the Committee for Human Medicinal Products (the “CHMP”), a division of the EMEA, will review the MAA and may respond with a list of questions or objections. The answers to the questions posed by the CHMP may require additional tests to be conducted. Responses to the list of questions or objections must be provided to and deemed sufficient by the CHMP within a defined timeframe. Ultimately, a representative from each of the European Member States will vote whether to approve the MAA.
     Foreign regulatory approval processes include all of the risks associated with obtaining FDA approval, and approval by the FDA does not ensure approval by the health authorities of any other country.U.S.

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Employees
As of March 19, 2009,5, 2010, we employed 94three regular full-time employees (including five peopleone person who have a Ph.D.has an M.D.). Other personnel resources are used from time to time as consultants on an as-needed basis. In connection with the termination of the clinical trials for Riquent, we ceased all manufacturing and three people who have an M.D., one of which also has a Ph.D.), 75 of whom are trained in clinical, developmentregulatory activities related to Riquent and manufacturing activities. We are currently takingtook steps to significantly reduce our personnel resources and related expenses and expectoperating costs, including a reduction of force that we will have significantly fewer employees startingresulted in the second quartertermination of 2009 as we reduce the sizemajority of our operationsemployees, primarily in responseApril 2009. See Note 6 to the failure of the ASPEN trial.our consolidated financial statements included in Part IV. None of our employees are covered by collective bargaining agreements and management considers relations with our employees to be good.
Available Information
Our annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K, and amendments to those reports filed with or furnished to the Securities and Exchange Commission pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended, are available free of charge through our website at www.ljpc.com as soon as reasonably practicable after we electronically file or furnish the reports with or to the Securities and Exchange Commission.
Item 1A. Risk Factors
Item 1A.Risk Factors
I. RISK FACTORS RELATING TO LA JOLLA PHARMACEUTICAL COMPANY AND THE INDUSTRY IN WHICH WE OPERATE.
In lightWe have only limited assets, no ongoing clinical trials and no products, and will need to raise additional capital if we are to continue as a going concern.
As of December 31, 2009, we had approximately $4.2 million in working capital, no ongoing clinical trials and no products. Although we retain the rights to the Riquent patent estate, the value of the estate is uncertain and has been written down under United States generally accepted accounting principles (“GAAP”) to nearly zero. As a result, we have only limited assets available to operate and develop our business. If we determine that Riquent has no remaining value, then we would either need to acquire rights to another drug candidate for development or choose to liquidate the Company. If we determine that Riquent does have potential value such that it merits further development efforts, we would need to find a development partner and/or raise significant amounts of additional capital to attempt to develop the compound ourselves. Given the limited working capital that we have available, we will need to raise significant amounts of additional capital if we elect to not liquidate the Company, Raising this capital may not be possible or, if possible, may be on terms that are highly unfavorable. For example, because our stock price is so depressed, raising a significant amount of capital would result in the issuance of a very large number of shares. This would greatly dilute the ownership of our decisionexisting stockholders and would likely provide the new investor with a controlling interest in the Company. Additionally, we may find it necessary to discontinue developmentagree to unfavorable investment terms, with terms such as preemptive rights, anti-dilution adjustments, special approval rights, and other terms that could provide new investors with a greater degree of our Riquent clinical program, we are seeking to maximizecontrol over the Company. The existence of these terms could negatively affect the value of our remaining assets, addresscommon stock and could diminish the rights of our liabilitiesexisting stockholders. We may not continue in business and attemptmay liquidate the Company.
Although we are attempting to pursue mergers or similarpotential strategic transactions.  We may be unable to satisfy our liabilities and can providetransactions, there is no assurancesassurance that we canwill be successful in pursuing a strategic transaction.successful.
     InFollowing the failure of Riquent in February 2009 we were informed by an Independent Monitoring Board for the Riquent Phase 3 ASPEN study that the monitoring board completed their review of the first interim efficacy analysis and determined that continuing the study was futile. Based on these results, we immediately discontinued the Riquent Phase 3 ASPEN study and the development of Riquent. We had previously devoted substantially all of our research, development and clinical efforts and financial resources toward the development of Riquent and, in light of the failure of the trial, we subsequently incurred a significant impairment charge as we wrote down the value of our Riquent assets to near zero. In connection with the termination of our clinical trials for Riquent, we initiated steps to significantly reduce our operating costs including a substantial reduction in personnel. We have also ceased the manufacture of Riquent at our facility in San Diego, California and have begunbeen exploring strategic alternatives to maximize stockholder value, as described above.
There is a substantial risk that we may not successfully implement any of these strategic alternatives, particularly in light of our recent inability to obtain stockholder approval of various transactions, and even if we determine to pursue one or more of these alternatives, we may be unable to do so on acceptable financial terms. Any such transactions may require us to incur non-recurring or other charges and may pose significant integration challenges and/or management and business disruptions, any of which could materially and adversely affect our business and financial results. Additionally, pursuing these transactions would deplete some portion of our limited capital resources and may not result in a transaction that is ultimately consummated. We may be unable to discharge our liabilities or negotiate favorable settlement terms with our creditors.

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Stockholders should recognize that in our efforts to address our liabilities and fund the future development of our Company, we may pursue strategic alternatives that result in the stockholders of the Company having little or no continuing interest in the assets or equity of the Company. We will continue to evaluate our alternatives in light of our cash position, including the possibility that we may need toultimately seek protection under the provisions of the U.S. Bankruptcy Code.
We may need to liquidate the Company in a voluntary dissolution under Delaware law or seek protection underCompany.
If we choose to liquidate the provisions of the U.S. Bankruptcy Code, and in either event,Company, it is unlikely that stockholders would receive any significant value for their shares.
We have not generated any revenues from product sales, and have incurred losses in each year since our inception in 1989. We expect that it will be very difficult to raise capital to continue our operations and our

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independent registered public accounting firm has issued an opinion with an explanatory paragraph to the effect that there is substantial doubt about our ability to continue as a going concern. We do not believe that we could succeed in raising additional capital needed to sustain our operations without some strategic transaction, such as a merger.merger or other third-party collaboration. If we are unable to consummate such a transaction, we expect that we would need to cease all operations and wind down. Although we are currently evaluating our strategic alternatives with respect to all aspects of our business, we cannot assure you that any actions that we take would raise or generate sufficient capital to fully address the uncertainties of our financial position. As a result, we may be unable to realize value from our assets and discharge our liabilities in the normal course of business. If we are unable to settle our obligations to our creditors or if we are unable to consummate a strategic transaction, we would likely need to liquidate the Company in a voluntary dissolution under Delaware law or seek protection under the provisions of the U.S. Bankruptcy Code. In that event, we, or a trustee appointed by the court, may be required to liquidate our assets. In either of these events, we might realize significantly less from our assets than the values at which they are carried on our financial statements.Company. The funds resulting from the liquidation of our assets, net of amounts payable, would be used first to satisfy obligations to creditors before any funds would be available to pay our stockholders, and any shortfall in the proceeds would directly reduce the amounts available for distribution,likely return only a small amount, if any,anything, to our creditors and to our stockholders. In the event we are required to liquidate under Delaware law or the federal bankruptcy laws, it is highly unlikely that stockholders would receive any value for their shares. See “Liquidity and Capital Resources” in Part II, Item 7, “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and Note 1 to our consolidated financial statements included elsewhere in this Annual Report on Form 10-K.
We recorded an impairment loss for the year ended December 31, 2008 and may need to record additional charges in the future.
     In light of our decisions to discontinue the development of Riquent, evaluate the possible sale of our equipment and other personal property assets, reduce our workforce, and consider our strategic alternatives with respect to all aspects of our business, management considered whether, under Statement of Financial Accounting Standards (SFAS) No. 144,Accounting for the Impairment or Disposal of Long-Lived Assets, any events or circumstances had occurred since December 31, 2007 and prior to December 31, 2008 that would indicate an impairment of our long-lived assets. After completing our evaluation and considering all external and internal information available as of the impairment analysis, we concluded that, as of December 31, 2008, the carrying amount of the asset group was not fully recoverable and that a material impairment did exist. Accordingly, our financial statements reflect a non-cash charge of $2.8 million for impairment of assets during the fourth quarter of 2008. As we continue to evaluate our business and our assets under SFAS 144, we may need to reflect additional impairment charges in the future, which would negatively impact our financial results and our overall value of the Company.
We face environmental liabilities related to certain hazardous materials used in our operations.
     Due to the nature of our manufacturing processes, we are subject to stringent federal, state and local laws governing the use, handling and disposal of certain materials and wastes. Historically, in our research and manufacturing activities we have used radioactive and other materials that could be hazardous to human health, safety or the environment. These materials and various wastes resulting from their use are stored at our facility pending ultimate use and disposal. The risk of accidental injury or contamination from these materials cannot be eliminated. In the event of such an accident, we could be held liable for any resulting damages, and any such liability could exceed our resources. Although we maintain general liability insurance, we do not specifically insure against environmental liabilities.

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II. RISK FACTORS RELATED SPECIFICALLY TO OUR STOCK.
The pricerecent delisting of our common stock has been volatilecould have a substantial effect on the price and has declined significantlyliquidity of our common stock.
On March 4, 2010, our common stock was delisted from the Nasdaq Capital Market and we may face delisting from Nasdaq.
     Due to the futility determinationbegan trading on The Pink OTC Markets, Inc. (“The Pink Sheets”). As a result of the Riquent clinical trial, our stock has experienced significant price and volume volatility during February and March 2009.  Our stock is currently trading below $0.25 per share and we could continue to experience further declines in our stock price.  Our stock is currently trading below the minimum bid price, which is in violation of Nasdaq’s continued listing requirements.  Although Nasdaq has suspended the enforcement of rules requiring a minimum $1.00 closing bid price and the rules requiring a minimum market value of publicly held shares, this suspension is currently only in effect through July 19, 2009.  We will likely be non-compliant with Nasdaq’s continued listing requirements when this suspension is lifted.  If our stock continues to trade below $1.00 when the temporary suspension is lifted, Nasdaq may commence delisting procedures against us.  In addition to the minimum bid price rule, the Nasdaq Global Market has several other continued listing requirements. Failure to maintain compliance with any Nasdaq listing requirement could cause our stock to be removed from listing on Nasdaq. If we were delisted,The Pink Sheets, the market liquidity of our common stock couldmay be adversely affected and the market price of our common stock couldmay decrease. Such a delisting couldTrading on The Pink Sheets may also adversely affect our ability to effect a strategic transaction, such as a merger with a third party. In addition, our stockholders’ ability to trade or obtain quotations on our shares couldmay be severely limited because of lower trading volumes and transaction delays. These factors couldmay contribute to lower prices and larger spreads in the bid and ask price for our common stock.
Specifically, you may not be able to resell your shares at or above the price you paid for such shares or at all. In addition, class action litigation has often been instituted against companies whose securities have experienced periods of volatility in market price. Any such litigation brought against us could result in substantial costs and a diversion of management’s attention and resources, which could hurt our business, operating results and financial condition.

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OurThe price of our common stock price ishas been, and will be, volatile and may continue to decline.
Our stock has experienced significant price and volume volatility since February 2009 due to, among other things, the futility determination of the Riquent clinical trial in February 2009 and the termination of our merger agreement with Adamis in March 2010. Our stock is currently trading below $0.10 per share and we could continue to experience further declines in our stock price. The market price of our common stock has been and is likely to continue to be highly volatile. Market prices for securities of biotechnology and pharmaceutical companies, including ours, have historically been highly volatile, and the market has from time to time experienced significant price and volume fluctuations that are unrelated to the operating performance of particular companies. The following factors, among others, can have a significant effect on the market price of our securities:
limited financial resources;
announcements regarding mergers or other strategic transactions;
future sales of significant amounts of our common stock by us or our stockholders;
actions or decisions by the FDA and other comparable agencies;
announcements of technological innovations or new therapeutic products by us or others;
developments in patent or other proprietary rights;
public concern as to the safety of drugs discovered or developed by us or others;
developments concerning potential and existing agreements with collaborators;
general market conditions and comments by securities analysts; and

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government regulation, including any legislation that may impact the price of any commercial products that we may seek to sell.
announcements regarding mergers or other strategic transactions;
future sales of significant amounts of our common stock by us or our stockholders;
developments in patent or other proprietary rights;
developments concerning potential agreements with collaborators; and
general market conditions and comments by securities analysts.
The realization of any of the risks described in these “Risk Factors” could have a negative effect on the market price of our common stock.
Failure to achieve and maintain effective internal control over financial reporting in accordance with Section 404 of the Sarbanes-Oxley Act could have a material adverse effect on our business and stock price.
     Section 404 of the Sarbanes-Oxley Act requires us to evaluate annually the effectiveness of our internal controls over financial reporting as of the end of each fiscal year beginning in 2004 and to include a management report assessing the effectiveness of our internal control over financial reporting in all future annual reports beginning with the annual report on Form 10-K for the fiscal year ended December 31, 2004. Section 404 also requires our independent registered public accounting firm to report on our internal control over financial reporting. We evaluated our internal control over financial reporting as of December 31, 2008 in order to comply with Section 404 and concluded that our disclosure controls and procedures were effective as of such date. If we fail to maintain the adequacy of our internal controls, as such standards are modified, supplemented or amended from time to time, we cannot provide any assurances that we will be able to conclude in the future that we have effective internal control over financial reporting in accordance with Section 404. If we fail to achieve and maintain a system of effective internal control over financial reporting, it could have a material adverse effect on our business and stock price.
Anti-takeover devices may prevent changes in our board of directors and management.
We have in place several anti-takeover devices, including a stockholder rights plan, which may have the effect of delaying or preventing changes in our management or deterring third parties from seeking to acquire significant positions in our common stock. For example, one anti-takeover device provides for a board of directors that is separated into three classes, with their terms in office staggered over three year periods. This has the effect of delaying a change in control of our board of directors without the cooperation of the incumbent board. In addition, our bylaws require stockholders to give us written notice of any proposal or director nomination within a specified period of time prior to the annual stockholder meeting, establish certain qualifications for a person to be elected or appointed to the board of directors during the pendency of certain business combination transactions, and do not allow stockholders to call a special meeting of stockholders.
     We may also issue shares of preferred stock without further stockholder approval and upon terms that our board of directors may determine in the future. The issuance of preferred stock could have the effect of making it more difficult for a third party to acquire a majority of our outstanding stock, and the holders of such preferred stock could have voting, dividend, liquidation and other rights superior to those of holders of our common stock.
Item 1B. Unresolved Staff Comments.
Item 1B.Unresolved Staff Comments.
None.
Item 2. Properties.
Item 2.Properties.
     We lease two adjacent buildings in San Diego, California covering a total of approximately 54,000 square feet. One building contains our research and development laboratories and clinical manufacturing facilities and the other contains our corporate offices and warehouse. Both building leases expire in July 2009. Each lease is subject to an escalation clause that provides for annual rent increases. We believe that these facilities will be adequate to meet our needs for the near term. Over the longer term, management believes that space can be secured at commercially reasonable rates.None.
Item 3. Legal Proceedings.
Item 3.Legal Proceedings.
We are not currently a party to any legal proceedings.

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Item 4. Submission of Matters to a Vote of Security Holders.
     None.
Item 4.Reserved.

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5


PART II
Item 5. Market For Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities.
Item 5.Market For Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities.
Information About Our Common Stock
     OurDuring the year ended December 31, 2009, our common stock tradestraded on the Nasdaq Global Marketand Capital Markets under the symbol “LJPC.” As of March 4, 2010, our common stock was delisted from the Nasdaq Capital Market and began trading on the Pink OTC Markets, under the symbol “LJPC.PK.” Set forth below are the high and low sales prices for our common stock for each full quarterly period within the two most recent fiscal years.
                
 Prices Prices 
 High Low 
Year Ended December 31, 2009 
 
First Quarter $3.20 $0.04 
Second Quarter 0.64 0.13 
Third Quarter 0.36 0.14 
Fourth Quarter 0.32 0.06 
 High Low 
Year Ended December 31, 2008  
  
First Quarter $4.25 $1.45  $4.25 $1.45 
Second Quarter 2.35 1.59  2.35 1.59 
Third Quarter 2.50 1.01  2.50 1.01 
Fourth Quarter 1.20 0.58  1.20 0.43 
 
Year Ended December 31, 2007 
 
First Quarter $8.57 $2.80 
Second Quarter 8.68 4.35 
Third Quarter 5.59 3.15 
Fourth Quarter 4.50 3.15 
We have never paid dividends on our common stock and we do not anticipate paying dividends in the foreseeable future. The number of record holders of our common stock as of March 19, 20095, 2010 was approximately 206.289.
Information About Our Equity Compensation Plans
Information regarding our equity compensation plans is incorporated by reference in Item 12 of Part III of this annual report ofon Form 10-K.

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Stock Performance Graph
     The following graph compares the cumulative total stockholder return on our common stock for the five years ended December 31, 2008 with the Center for Research in Securities Prices (“CRSP”) Total Return Index for the Nasdaq Global Market (U.S. Companies) and the CRSP Total Return Index for Nasdaq Pharmaceutical Stocks (comprising all companies listed in the Nasdaq Global Market under SIC 283). The graph assumes that $100 was invested on December 31, 2003 in our common stock and each index and that all dividends were reinvested. No cash dividends have been declared on our common stock. The comparisons in the graph are required by the Securities and Exchange Commission and are not intended to forecast or be indicative of possible future performance of our common stock.
                                 
     12/31/2003    12/31/2004    12/31/2005    12/31/2006    12/31/2007    12/31/2008  
 
La Jolla Pharmaceutical Company*
  $100   $39.20   $17.37   $14.23   $18.40   $2.72  
 
Nasdaq — US
  $100   $108.84   $111.16   $122.11   $132.42   $63.80  
 
Nasdaq — Pharmaceuticals
  $100   $106.51   $117.29   $114.81   $120.74   $112.34  
 
*Item 6. La Jolla Pharmaceutical Company stock prices have been adjusted to reflect the one-for-five reverse stock split effective December 21, 2005.Selected Financial Data
We are a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and are not required to provide the information required under this item.

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6


Item 6. Selected Financial Data.
     The following Selected Financial Data should be read in conjunction with “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in Item 7 beginning at page 17 and the consolidated financial statements of the Company and related notes thereto beginning at page F-2 of this report.
                     
  Years Ended December 31,
  2008 2007 2006 2005 2004
  (In thousands, except per share amounts)
Consolidated Statements of Operations Data:
                    
                     
Expenses:                    
Research and development $51,025  $46,635  $32,834  $22,598  $33,169 
General and administrative  9,702   9,058   9,287   5,405   7,568 
Asset impairment  2,810      104       
   
Loss from operations  (63,537)  (55,693)  (42,225)  (28,003)  (40,737)
                     
Interest expense  (96)  (82)  (46)  (116)  (190)
Interest income  779   2,699   2,826   756   383 
   
                     
Net loss $(62,854) $(53,076) $(39,445) $(27,363) $(40,544)
           
                     
Basic and diluted net loss per share $(1.26) $(1.40) $(1.21) $(1.77) $(3.40)
           
                     
Shares used in computing basic and diluted net loss per share (1)  49,689   37,818   32,588   15,446   11,941 
           
                     
Balance Sheet Data:
                    
                     
Working capital $2,996  $29,881  $37,673  $70,124  $17,539 
Total assets $20,839  $44,405  $49,525  $80,928  $33,026 
Noncurrent portion of obligations under capital leases and notes payable $213  $388  $196  $142  $716 
Stockholders’ equity $3,390  $33,521  $43,089  $77,130  $26,001 
(1)Item 7. Shares have been adjusted to reflect the one-for-five reverse stock split effective December 21, 2005.Management’s Discussion and Analysis of Financial Condition and Results of Operations.

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Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations.
Introduction
Management’s discussion and analysis of financial condition and results of operations is provided as a supplement to the accompanying consolidated financial statements and footnotes to help provide an understanding of our financial condition, the changes in our financial condition and our results of operations. Our discussion is organized as follows:
  Overview and recent developments. This section provides a general description of our business and operating history and a general description of recent events and significant transactions that we believe are important in understanding our financial condition and results of operations.
  Critical accounting policies and estimates. This section contains a discussion of the accounting policies that we believe are important to our financial condition and results of operations and that require significant judgment and estimates on the part of management in their application. In addition, all of our significant accounting policies, including the critical accounting policies and estimates, are summarized in Note 1 to the accompanying consolidated financial statements.
  Results of operations. This section provides an analysis of our results of operations presented in the accompanying consolidated statements of operations by comparing the results for the year ended December 31, 20082009 to the results for the year ended December 31, 2007 and comparing the results for the year ended December 31, 2007 to the results for the year ended December 31, 2006.2008.
  Liquidity and capital resources. This section provides an analysis of our cash flows and a discussion of our outstanding debt and commitments, both firm and contingent, that existed as of December 31, 2008, as well as material subsequent changes. Included in the discussion of outstanding debt is a discussion of our financial capacity to fund our future commitments and a discussion of other financing arrangements.
Overview and Recent Developments
Since our inception in May 1989, we have devoted substantially all of our resources to the research and development of technology and potential drugs to treat antibody-mediated diseases. We have never generated any revenue from product sales and have relied on public and private offerings of securities, revenue from collaborative agreements, equipment financings and interest income on invested cash balances for our working capital.
On January 4, 2009, we entered into a development and commercialization agreement (the “Development Agreement”) with BioMarin CF Limited (“BioMarin CF”), a wholly-owned subsidiary of BioMarin Pharmaceutical Inc. (“BioMarin Pharma”). Under the terms of the Development Agreement, BioMarin CF was granted co-exclusive rights to develop and commercialize Riquent in the United States, Europe and all other territories of the world, excluding the Asia Pacific region, and the non-exclusive right to manufacture Riquent anywhere in the world. In January 2009, BioMarin CF paid us a non-refundable commencement payment of $7.5 million and BioMarin Pharma purchasedpaid $7.5 million offor a newly designated series of our preferred stock. As described below, this agreement was terminated on March 27, 2009. See Note 104 to our audited consolidated financial statements included in Part IV.
Following the futile results of the first interim efficacy analysis of Riquent, BioMarin CF elected to not exercise its full license rights to the Riquent program under the Development Agreement. Thus, the Development Agreement between the parties terminated on March 27, 2009 in accordance with its terms. Pursuant to the Securities Purchase Agreement between us and BioMarin Pharma, all of the Company’s preferred shares purchased by BioMarin Pharma were converted into common shares upon the termination of the Development Agreement. Additionally, all rights to Riquent were returned to us. See Note 4 to our consolidated financial statements included in Part IV.
In February 2009, we were informed by an Independent Monitoring Board for the Riquent Phase 3 ASPEN study that the monitoring board completed theirits review of the first interim efficacy analysis of Riquent and determined that continuing the study was futile. We subsequently unblinded the data and found that there was no statistical difference in the primary endpoint, delaying time to renal flare, between the Riquent-treated group and the placebo-treated group, although there was a significant difference in the reduction of antibodies to double-stranded DNA. There were 56 renal flares in 587 patients treated with either 300-mg or 900-mg of Riquent, and 28 renal flares in 283 patients treated with placebo.

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Based on these results, we immediately discontinued the Riquent Phase 3 ASPEN study and the further development of Riquent. We had previously devoted substantially all of our research, development and clinical efforts and financial resources toward the development of Riquent. In connection with the termination of our clinical

17


trials for Riquent, we subsequently initiatedtook steps to significantly reduce our operating costs, including a planned substantial reduction in personnel, which we expect will be effected earlywas completed in the second quarter ofApril 2009. We have also ceased the manufacture of Riquent at our former facility in San Diego, California. See Note 6 to our consolidated financial statements included in Part IV.
     Following the futile resultsIn July 2009, we announced that, in light of the first interim efficacy analysisalternatives available to us at the time, a wind down of Riquent, BioMarin CF has electedour business would be in the best interests of the Company and its stockholders. Although the Board of Directors (the “Board”) approved a Plan of Complete Liquidation and Dissolution (the “Plan of Dissolution”) in September 2009, it was subject to approval by holders of at least a majority in voting power of our outstanding shares. We called a special meeting of stockholders to vote on the Plan of Dissolution, but the majority of our stockholders failed to return their proxy cards or otherwise indicate their votes with respect to this proposal. Accordingly, we were not exercise its full license rightsable to obtain the requisite quorum to conduct business at the special meeting and were therefore unable to proceed with dissolution.
Because we were unable to obtain sufficient stockholder votes to proceed with dissolution, we entered into an Agreement and Plan of Reorganization (the “Merger Agreement”) by and among the Company, Jewel Merger Sub, Inc. (“Merger Sub”) and Adamis Pharmaceuticals Corporation (“Adamis”) on December 4, 2009. The transaction contemplated by the Merger Agreement was structured as a reverse triangular merger, in which Merger Sub, a wholly-owned subsidiary of the Company, would merge with and into Adamis, with Adamis surviving (the “Merger”). On March 3, 2010, the Company and Adamis agreed to terminate the Merger Agreement as a result of too few of our stockholders voting on the proposals related to the Riquent program underMerger such that we did not have the Development Agreement. Thus,requisite quorum to hold the Development Agreement betweenstockholders’ meeting to approve the parties terminatedproposals related to the Merger. The solicitation of further votes was cancelled due to the delisting from Nasdaq.
Effective at the open of business on March 27, 2009 in accordance with its terms. Pursuant to the Securities Purchase Agreement between us and BioMarin Pharma, all of4, 2010, the Company’s preferred shares purchased by BioMarin Pharma were converted into common shares. Additionally, all rights to Riquent have been returned to us.stock was suspended and delisted from The NASDAQ Stock Market (“Nasdaq”) and began trading on The Pink OTC Markets, Inc. The delisting was the result of Nasdaq’s determination that the Company had nominal assets, other than cash, and nominal operations.
In light of our decisioninability to discontinue development of our Riquent clinical program,complete a strategic transaction that requires stockholder approval, we are seeking to maximize the value of our remaining assets. We are currently evaluating our strategic alternatives,what options are available to us, which may include the following:
Sell or out-license our remaining assets, including our SSAO compounds, although we do not expect to receive any significant value for them;
Pursue potential other strategic transactions, which could include mergers, license agreements or other collaborations, with third parties; or
Implement an orderly wind down of the Company if other alternatives are not deemed viable and in the best interests of the Company.
Sell or out-license our Riquent program, although we may not receive any significant value upon such a sale or license;
Pursue potential other strategic transactions, which could include mergers, license agreements or other collaborations, with third parties; or
Implement a wind down of the Company if other alternatives are not deemed viable and in the best interests of the Company.
Following the negative results of the ASPEN trial, we recorded a significant charge for the impairment of our Riquent assets, including our Riquent-related patents, and it is unlikely that we willmay not realize any substantivesignificant value from these assets in the future. Additionally, there is a substantial risk that we may not successfully implement any of these strategic alternatives, and even if we determine to pursue one or more of these alternatives, we may be unable to do so on acceptable terms. Any such transactions may be highly dilutive to our existing stockholders and may deplete our limited remaining capital resources.
In January 2009, we sold $10 million of face-value auction rate securities to our broker-dealer, UBS A.G. (“UBS”). As of December 31, 2008, we had recognized a total impairment charge of $2.3 million as a result of the illiquidity of these securities, which was fully offset by a $2.3 million realized gain from UBS’s repurchase agreement that provides for a put option on these securities. Following the sale of these investments, we no longer hold any auction-rate securities.

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     On May 12, 2008, we sold 15.6 million Units (the “Units,” where each Unit consists of one share of common stock, $0.01 par value per share and a warrant to purchase 0.25 shares of Common Stock) in an underwritten public offering at a price of approximately $1.92 per Unit, resulting in net proceeds totalling approximately $28.0 million. The warrants, which represent the right to acquire a total of 3.9 million shares of common stock, are exercisable at a price of $2.15 per share and have a five-year term. Certain of our principal stockholders, including affiliates of certain of our directors, purchased an aggregate of approximately $24.3 million, or approximately 81%, of the Units sold.
Critical Accounting Policies and Estimates
The discussion and analysis of our financial condition and results of operations are based on our consolidated financial statements, which have been prepared in accordance with United States generally accepted accounting principles.GAAP. The preparation of these consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. We evaluate our estimates on an ongoing basis, including those related to patent costs, clinical/regulatory expenses and, effective January 1, 2008, the fair value of our financial instruments.basis. We base our estimates on historical experience and on other assumptions that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from these estimates under different assumptions or conditions.

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We believe the following critical accounting policies involve significant judgments and estimates used in the preparation of our consolidated financial statements (see also Note 1 to our consolidated financial statements included in Part IV).
ImpairmentRevenue recognition

We apply the revenue recognition criteria outlined in theASC Topic of Revenue Recognition. Upfront product and useful livestechnology license fees under multiple-element arrangements are deferred and recognized over the period of such services or performance if such arrangements require on-going services or performance. Non-refundable amounts received for substantive milestones are recognized upon achievement of the milestone. Any amounts received prior to satisfying our revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets.

Our sole source of revenue in the accompanying consolidated financial statements related to a January 4, 2009 Development Agreement with BioMarin CF which contained multiple potential revenue elements, including non-refundable upfront fees. The Development Agreement was terminated on March 27, 2009 following the failure of the Phase 3 ASPEN trial at which time we had no remaining on-going services or performance. We recognized $8.1 million as collaboration revenue upon termination of the Development Agreement.

Impairment of long-lived assets
     We regularly review our long-lived assets for impairment. Our long-lived assets include costs incurred to file our patent applications. We evaluateIf indicators of impairment exist, we assess the recoverability of the affected long-lived assets by measuring the carrying amount of the assets against the estimated undiscounted future cash flows associated with them. At the time such evaluations indicate that the future undiscounted cash flows of certain long-lived assets are not sufficient to recoverdetermining whether the carrying value of such assets the assets are adjusted to their fair values. The estimation ofcan be recovered through the undiscounted future operating cash flows associated with long-lived assets requires judgment and assumptions that could differ materially from the actual results.flows.
     Costs related to issued patents are amortized using the straight-line method over the lesser of the remaining useful life of the related technology or the remaining patent life, commencing on the date the patent is issued. Legal costs and expenses incurred in connection with pending patent applications have been capitalized. We expense all costs related to abandoned patent applications. If we elect to abandon any of our currently issued or unissued patents, the related expense could be material to our results of operations for the period of abandonment. The estimation of useful lives for long-lived assets requires judgment and assumptions that could differ materially from the actual results. In addition, our results of operations could be materially impacted if we begin amortizing the costs related to unissued patents.
As a result of the futility determination in the Phase 3 ASPEN trial, we decided to discontinuediscontinued the Riquent Phase 3 ASPEN study and halt the further development of Riquent. We had previously devoted substantially all of our research, development and clinical efforts and financial resources toward the development of Riquent. Therefore,Based on these events, the future cash flows from our Riquent-related patents arewere no longer expected to exceed their carrying values. In addition, during 2009values and the Company expects to sell substantially allassets became impaired as of its laboratory equipment, as well as a large portion of its furniture and fixtures and computer equipment and software.
     We performed a recoverability test of the long-lived assets included in our Riquent asset group in accordance with Statement of Financial Accounting Standards No. (“SFAS”) 144,Accounting for the Impairment or Disposal of Long-Lived Assets(“SFAS 144”). The recoverability test was based on the estimated undiscounted future cash flows expected to result from our long-lived assets. Based on the recoverability analysis performed, management does not believe that the estimated undiscounted future cash flows expected to result from the disposition of certain of the Company’s long-lived assets are sufficient to recover the carrying value of these assets.December 31, 2008. Accordingly, we recorded a non-cash charge for the impairment of long-lived assets of $2.8 million for the year ended December 31, 2008 to write down the value of our long-lived assets to their estimated fair values. We recognized $0 and $0.1 million inAlthough no impairment losses forcharges were recorded during 2009, we sold, disposed of, or wrote off all of our remaining long-lived assets during the yearsyear ended December 31, 2007 and 2006, respectively.2009 for a gain of $0.3 million.
Accrued clinical/regulatory expenses
As a result of the discontinuation of the Riquent Phase 3 ASPEN study and the development of Riquent, all clinical and regulatory activities were ceased and no related accruals were required as of December 31, 2009.
We reviewreviewed and accrueaccrued clinical trial and regulatory-related expenses based on work performed, which reliesrelied on estimates of total costs incurred based on patient enrollment, sites activatedcompletion of studies and other events. We followfollowed this method becausesince reasonably dependable estimates of the costs applicable to various stages of a clinical trial cancould be made. Accrued clinical/regulatory costs are subject to revisions as trials progress to completion. Revisions are charged to expense in the period in which the facts that give rise to the revision become known. Historically, revisions have not resulted in material changes to research and development costs.

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Share-based compensation
     We adopted SFAS 123R,Share-Based Payment,(“SFAS 123R”) using the modified prospective transition method, which requires the application of the accounting standard as of January 1, 2006, the first day of our 2006 fiscal year. Our Consolidated Statement of Operations as of andShare-based compensation expense for the years ended December 31, 2008, 20072009 and 2006 reflect the impact of SFAS 123R. In accordance with the modified prospective transition method, our Consolidated Statements of Operations for prior periods have not been restated to reflect, and do not include, the

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impact of SFAS 123R. Share-based compensation expense recognized under SFAS 123R for the years ended December 31, 2008 and December 31, 2007 was approximately $4.4$2.7 million and $4.8$4.4 million, respectively. As of December 31, 2008,2009, there was approximately $4.9$1.0 million of total unrecognized compensation cost related to non-vested share-based payment awards granted under all equity compensation plans. As share-based compensation expense recognized for fiscal years 2009 and 2008 is based on awards ultimately expected to vest, share-based compensation expense has been reduced for estimated forfeitures. Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Total unrecognized compensation cost will be adjusted for future changes in estimated forfeitures. We currently expect to recognize the remaining unrecognized compensationthat cost over a weighted-average period of 1.20.8 years. Additional share-based compensation expense for any new share-based payment awards granted after December 31, 20082009 under all equity compensation plans cannot be predicted at this time because it will depend on, among other matters, the amounts of share-based payment awards granted in the future.
Option-pricing models were developed for use in estimating the value of traded options that have no vesting or hedging restrictions and are fully transferable. Because the employee and director stock options granted by us have characteristics that are significantly different from traded options, and because changes in the subjective assumptions can materially affect the estimated value, in our opinion the existing valuation models may not provide an accurate measure of the fair value of the employee and director stock options granted by us. Although the fair value of the employee and director stock options granted by us is determined in accordance with SFAS 123R using an option-pricing model, that value may not be indicative of the fair value observed in a willing-buyer/willing-seller market transaction.
Fair value of financial instrumentsNew Accounting Pronouncements
     Effective January 1, 2008, we adopted SFAS No. 157,Fair Value Measurements(“SFAS 157”). In February 2008,June 2009, the Financial Accounting Standards Board (“FASBFASB”) approved the FASB Accounting Standards Codification (“the Codification”) when it issued Statement of Financial Accounting Standards No. 168,The FASB Staff Position (“FSP”) No. SFAS 157-2,Effective Date of FASB Statement No. 157, which provides a one-year deferral of the effective date of SFAS No. 157 for non-financial assets and non-financial liabilities, except those that are recognized or disclosed in the financial statements at fair value at least annually. Therefore, we have adopted the provisions of SFAS 157 with respect to financial assets and liabilities only.
     SFAS 157 defines fair value, establishes a framework for measuring fair value under GAAP and enhances disclosures about fair value measurements. Fair value is defined under SFAS 157 as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value under SFAS 157 must maximize the use of observable inputs and minimize the use of unobservable inputs. The standard describes a fair value hierarchy based on three levels of inputs, of which the first two are considered observableAccounting Standards Codification and the last unobservable, that may be used to measure fair value:
Level 1 — Quoted prices in active markets for identical assets or liabilities.
Level 2 — Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
     The adoption of this statement impacted our calculation of fair value associated with our investments, specifically our auction rate securities, which became illiquid during the first quarter of 2008. In accordance with SFAS 157, we valued these securities using Level 3 hierarchical inputs due to the lack of actively traded market data. These inputs include management’s assumptions of pricing by market participants, including assumptions about risk. We based our fair value determination on estimated discounted future cash flows of interest income over a projected period reflective of the length of time we anticipate it will take the securities to become liquid. We considered any impairment on these investments to be other-than-temporary, thus any changes in fair value were recorded to the audited consolidated statement of operations for the year ended December 31, 2008. Because we were required to value those securities using only Level 3 inputs, our valuation determinations are somewhat subjective and the actual fair values as determined at a later date or by a third party may be different than the fair values we have determined.

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     During the fourth quarter of 2008, our broker-dealer, UBS, offered to repurchase our outstanding auction-rate securities at their par value. We accepted this offer in November 2008 and, in January 2009, we sold all of our auction rate securities to UBS at par value of $10.0 million. As of December 31, 2008, we had recognized a total impairment charge of $2.3 million as a result of the illiquidity of these securities, which was fully offset by a $2.3 million realized gain from UBS’s repurchase agreement that provides for a put option on these securities. (See Notes 2 and 10 to our audited consolidated financial statements included in Part IV)
New Accounting Pronouncements
     On January 1, 2008, we adopted the provisions of SFAS 157. SFAS 157 establishes a framework for measuring fair value and expands disclosures about fair value measurements. The changes to current practice resulting from the application of SFAS 157 relate to the definition of fair value, the methods used to measure fair value, and the expanded disclosures about fair value measurements. The adoption did not have an impact on the audited consolidated financial statements or on our consolidated results of operations and financial condition for the year ended December 31, 2008.
     On January 1, 2008, we adopted the provisions of SFAS No. 159,The Fair Value Option for Financial Assets and Financial Liabilities – Including an amendment of FASB Statement No. 115 (“SFAS 159”). SFAS 159 permits entities to choose to measure many financial assets and financial liabilities at fair value. Unrealized gains and losses on items for which the fair value option has been elected are reported in earnings. At this time, we have not elected to account for any of our financial assets or liabilities using the provisions of SFAS 159. As such, the adoption of SFAS 159 did not have an impact on our consolidated results of operations and financial condition for the year ended December 31, 2008.
     In June 2007, FASB ratified the consensus reached by the Emerging Issues Task Force (“EITF”) on EITF Issue No. 07-3,Accounting for Nonrefundable Advance Payments for Goods or Services to Be Used in Future Research and Development Activities(“EITF 07-3”). EITF 07-3 addresses the diversity that exists with respect to the accounting for the non-refundable portion of a payment made by a research and development entity for future research and development activities. Under EITF 07-3, an entity would defer and capitalize non-refundable advance payments made for research and development activities until the related goods are delivered or the related services are performed. EITF 07-3 is effective for fiscal years beginning after December 15, 2007. On January 1, 2008 we adopted the provisions of EITF 07-3, which did not have an impact on our consolidated results of operations and financial condition for the year ended December 31, 2008.
     In May 2008, the FASB issued SFAS No. 162,The Hierarchy of Generally Accepted Accounting Principles(“SFAS 162”). SFAS 162 identifies the sources of accounting principles and the framework for selecting the principles used, which is included in the preparation of financial statements that are presented in conformity with generally accepted accounting principles. SFAS 162 becomes effective 60 days following the SEC’s approval of the Public CompanyThe Accounting Oversight Board amendments to Statement on Auditing Standards No. 69,The MeaningCodification (“ASC”) Topic of Present Fairly in Conformity With Generally Accepted Accounting Principles(the “Topic”). All existing accounting standard documents, such as FASB, American Institute of Certified Public Accountants, Emerging Issues Task Force and other related literature, excluding guidance from the Securities and Exchange Commission (“SEC”), have been superseded by the Codification. All other non-grandfathered, non-SEC accounting literature not included in the Codification has become non-authoritative. The Codification did not change GAAP, but instead introduced a new structure that combines all authoritative standards into a comprehensive, topically-organized online database. The Topic is effective for financial statements issued for interim and annual periods completedending after January 1,September 15, 2009. We do not expect thatThe Topic impacts our financial statement disclosures as all future references to authoritative accounting literature will be referenced in accordance with the adoptionCodification. As a result of SFAS 162 will have a material effect on our consolidated financial statements.the implementation of the Codification during the quarter ended September 30, 2009, previous references to accounting standards and literature are no longer applicable.
Results of Operations
Years Ended December 31, 2008, 20072009 and 20062008
Revenue.For the year ended December 31, 2009, revenue increased to $8.1 million as a result of the Development Agreement entered into with BioMarin CF in January 2009. The Development Agreement was terminated in March 2009 following the negative results from our Riquent Phase 3 ASPEN study. There were no revenues for the year ended December 31, 2008.

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Expenses. During the year ended December 31, 2009, we negotiated settlements related to accounts payable obligations and accrued liabilities with a majority of our vendors to preserve our remaining cash and other assets. These negotiations resulted in a reduction of approximately $2.7 million to accounts payable obligations and accrued liabilities from amounts originally invoiced and accrued, which were recorded upon the execution of the settlement agreements. As a result of these settlements, during the year ended December 31, 2009, there were decreases of $2.6 million and $0.1 million to research and development and general and administrative expenses, respectively.
Research and Development ExpenseExpense.. OurFor the year ended December 31, 2009, research and development expense increasedexpenses decreased to $9.6 million from $51.0 million for the year ended December 31, 2008 from $46.6as a result of the discontinuation of the Riquent Phase 3 ASPEN study, salary and benefits decreases due to the termination of all research personnel and the settlement of accounts payable obligations and accrued liabilities noted above. This decrease was partially offset by an increase in termination expense, mainly relating to severance, of approximately $0.7 million in 2007. The increase inrecorded as of March 31, 2009, as a result of the termination of 64 research and development expensespersonnel in 2008 from 2007 resulted primarily from an increase in clinical trial expenses of approximately $7.8 million, offset by a decrease in Riquent-related drug production of $4.1 million.
     ResearchApril 2009. We expect minimal research and development expense of $50.8 million forexpenditures going forward.
General and Administrative Expense.For the year ended December 31, 2008 related to lupus research and development-related expense consisting primarily of Riquent-related clinical trial expenses and clinical

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drug supply, salaries and other costs related to manufacturing, clinical and research personnel and fees for consulting and professional outside services.
     Our research and development expense increased to $46.6 million for the year ended December 31, 2007 from $32.9 million in 2006. The increase in research and development expenses in 2007 from 2006 resulted primarily from an increase in Riquent-related drug production and clinical trial expenses of approximately $16.0 million. This increase was partially offset by a decrease of approximately $3.2 million in expenses in 2007 as compared to 2006 for the development of our SSAO program, as all of our resources were being devoted to the development of Riquent and further development of the SSAO program depends on our ability to sell, out-license or enter into a collaborative arrangement for this program.
     We expect that our research and development expense will decrease significantly during 2009, as we discontinued the research, development and manufacturing of Riquent during February 2009 and will be reducing our research and development workforce substantially in the second quarter of 2009. Because we have not yet ascertained which strategic option we may ultimately pursue, we do not know the specific number of personnel reductions that will be made. We do expect, however, that the reductions in force will be substantial.
General and Administrative Expense. Our general and administrative expense increasedexpenses decreased to $7.2 million from $9.7 million for the year ended December 31, 2008 from $9.1 million in 2007.2008. The increasedecrease in general and administrative expense in 2008 from 2007 resultedexpenses is primarily from an increase in general corporate consulting, professional outside services and salaries and wages of approximately $1.0 million, primarily as athe result of our potential partnering efforts for Riquent. This increase was offset by a decreasedecreases in our miscellaneous business expensesconsulting and legal expense related to lower patent abandonments during 2008 compared to 2007 (see 2008 patent impairment discussion below) and a decrease in depreciation as a result of more assets being fully depreciated in 2008.
     Our general and administrative expense decreased to $9.1 millionthe BioMarin partnership for the year ended December 31, 2007 from $9.3 million2009 of $1.8 million. In addition, during April 2009, 10 general and administrative personnel were terminated, resulting in 2006.salary and benefits decreases for the year ended December 31, 2009 of $0.8 million. The decrease in general and administrative expense in 2007 from 2006 resulted primarily from a decrease in termination benefits, which for 2006 were mainly severance of approximately $0.9 million and compensation expense of approximately $0.8 million for accelerated stock option vesting related to the former Chairman and Chief Executive Officer’s departure in the first quarter of 2006. This decreaseyear ended December 31, 2009 was partially offset by the increase in the write-off of selected patent applications for technologies not related to Riquent or our small molecule SSAO inhibitors program of approximately $0.7 million, an increase in share-based compensationtermination expense recorded as of March 31, 2009 relating to severance of approximately $0.5$0.3 million for stock options grantedas a result of the termination of personnel in 2006April 2009 and 2007 and an increase in consulting expenses for business development and market researchretention payments recorded as of approximately $0.4 million.
December 31, 2009 of $0.1 million related to our remaining officers as of December 31, 2009. We expect that ourdecreased general and administrative expense will decrease significantly during 2009 as we discontinued the development of Riquent during February 2009 and will be reducing our general and administrative workforce substantially in the second quarter of 2009.expenditures going forward.
Asset Impairments.We recorded a $2.8 million non-cash impairment charge in 2008 (none in 2007 and $0.1 million in 2006)2009) because we no longer believebelieved that the estimated undiscounted future cash flows expected to result from the disposition of certain of the Company’s long-lived assets arewere sufficient to recover the carrying value of these assets. This impairment charge was due to the negative results from the Riquent Phase 3 ASPEN study announced in February 2009, which iswas an indicator of impairment.
Interest IncomeExpense, Interest and ExpenseOther Income.. Our interestInterest expense decreased for the year ended December 31, 2009 compared to the prior year due to the repayment of our notes payable and capital leases during the quarter ended June 30, 2009. Interest and other income decreased to less than $0.1 million for the year ended December 31, 2009, from $0.8 million for the year ended December 31, 2008 from $2.7 million for 20072008. This decrease is primarily due to lower average balances of cash andmoving all short-term investments and lower average interest rates on our investments as compared to 2007. Our interest income was comparable fornon-interest bearing cash accounts during the yearsquarter ended DecemberMarch 31, 2007 and 2006. Interest expense was comparable for the years ended December 31, 2008, 2007 and 2006.2009.
Net Operating Loss and Research Tax Credit Carryforwards. At December 31, 2008, we had federal and California income tax net operating loss carryforwards that are subject to Internal Revenue Code, or IRC, Section 382/383 limitations of net operating loss and research and development credit carryforwards. In February 2009, we experienced a change in ownership at a time when our enterprise value was minimal. As a result of this ownership change and the low enterprise value, our federal and California net operating loss carryforwards and federal research and development credit carryforwards as of December 31, 20082009 will be subject to limitation under IRC Section 382/383 and more likely than not will expire unused.

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Liquidity and Capital Resources
From inception through December 31, 2008,2009, we have incurred a cumulative net loss of approximately $415.7$424.3 million and have financed our operations through public and private offerings of securities, revenues from collaborative agreements, equipment financings and interest income on invested cash balances. From inception through December 31, 2008,2009, we had raised approximately $404.0$410.8 million in net proceeds from sales of equity securities.

11


     On May 12, 2008, we sold 15.6 million Units (comprised of 15.6 million shares of common stock and common stock warrants to purchase an additional 3.9 million shares) for net proceeds totalling approximately $28.0 million. The warrants are exercisable at a price of $2.15 per share and have a five-year term.
As of December 31, 2008,2009, we had $4.3 million in cash, compared to $19.4 million in cash, cash equivalents and short-term investments as compared to $39.4 million as of December 31, 2007.2008. Our working capital as of December 31, 20082009 was $3.0$4.2 million, as compared to $29.9$3.0 million as of December 31, 2007.2008. The decrease in cash, cash equivalents and short-term investments resulted from the use of our financial resources to fund our clinical trial and manufacturing activities during early 2009 and for other general corporate purposes. This decrease iswas partially offset by the netnon-refundable commencement payment of $7.5 million received from BioMarin CF under the Development Agreement and the proceeds of approximately $28.0$7.5 million from the sale of 15.6 million Units in May 2008. We invest our cash in money market funds invested in U.S. Treasury bills, and AAA rated asset-backed student loan auction rate securities. As of December 31, 2008, all339,104 shares of our investments are classified as available-for-sale securities because we expectpreferred stock to sell themBioMarin Pharma under the concurrently executed Securities Purchase Agreement in order to support our current operations regardless of their maturity dates.January 2009.
     As of December 31, 2008, we classified all of our student loan auction rate securities as short-term available-for-sale securities as we will need additional cash in the near term and may be required to liquidate these auction rate securities in order to continue our operations. As of December 31, 2008, all of our short-term available-for-sale securities have stated maturity dates of more than one year, however, their interest rates are reset periodically within time periods not exceeding 92 days. In the event we need to access the funds that are in an illiquid state, we will not be able to do so without a loss of principal until the securities are settled at par by the broker-dealer, a future auction on these auction rate securities is successful or they are redeemed by the issuer at par. As a result, we have recorded a realized impairment loss on these investments in 2008 of approximately $2.3 million.
     In November 2008, we accepted a redemption offer by UBS to sell all $10.0 million of our outstanding auction rate securities (“ARS Rights agreement”), all of which were maintained by UBS. As of December 31, 2008, the fair value of the ARS Rights were recorded as as a realized gain of $2.3 million and a corresponding short-term investment. The realized gain from recording the ARS Rights fully offsets the realized impairment loss on auction rate securities that was recorded during 2008 (see Note 2 to our audited consolidated financial statements included in Part IV). During January 2009, all of our auction rate securities were sold to UBS at par value of $10.0 million in accordance with the terms of the November 2008 redemption offer from UBS (see Note 102 to our audited consolidated financial statements included in Part IV).
In December 2008, we secured a credit facility (the “Credit Facility”) with UBS in the amount of $6.0 million, fully collateralized by our auction rate securities. There was no net interest cost to us as the interest rate charged by UBS was contractually equal to the coupon rates of the auction rate securities. There were no costs related to the establishment of the Credit Facility. During December 2008, we drew the full $6.0 million available under the Credit Facility, for working capital purposes, of which $5.9 million was outstanding as of December 31, 2008. During January 2009, the amount outstanding on the credit facility aswith UBS of December 31, 2008$5.9 million was settled in full and the Credit Facility agreement with UBS was terminated (see Note 10 to our audited consolidated financial statements included in Part IV).terminated.
     In January 2009, we entered into a development and commercialization agreement with BioMarin CF. Under the terms of the agreement, BioMarin CF paid us a non-refundable commencement payment of $7.5 million and BioMarin Pharma purchased $7.5 million of Series B Preferred Stock. On March 27, 2009 and as a result of the termination of the Development Agreement with BioMarin CF, the Series B Preferred Stock issued to BioMarin Pharma converted into 10,173,120 shares of Common Stock.
     AsOn July 31, 2009, our two building leases expired. Pursuant to the lease for one of these buildings, we were responsible for completing modifications to the leased building prior to lease expiration. In July 2009, approximately $0.3 million was paid in accordance with the lease provisions. We exited the buildings upon the expiration of the leases in July 2009.
During the year ended December 31, 2008, approximately $3.8 million worth of property and equipment ($0.2 million net of depreciation and 2008 impairment charges) secured our2009, we paid off all remaining notes payable and capital lease obligations. We leaseIn addition, we early terminated our office and laboratory facilities and theseoperating leases expire on July 31,during the quarter ended June 30, 2009. We also lease certain equipment under operating leases. We have also entered into non-cancelableNo notes payable, purchase commitments, for an aggregate of $1.3 million with third-party manufacturers of materials to be used in the production of Riquent, approximately $0.8 million of

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which is included in the audited consolidated balance sheetcapital leases or material operating leases existed as of December 31, 2008. We intend to use our current financial resources to fund our obligations under these purchase commitments.2009.
     The following table summarizes our contractual obligations as of December 31, 2008. Long-term debt and capital lease obligations include interest.
                     
      Payment due by period (in thousands)
      Less than         More than
  Total 1 Year 1-3 Years 3-5 Years 5 Years
Credit facility $5,933  $5,933  $  $  $ 
Long-term debt obligations  373   177   196       
Operating lease obligations  658   491   148   19    
Capital lease obligations  55   15   40       
Purchase obligations  1,290   1,290          
   
Total $8,309  $7,906  $384  $19  $ 
   
We intend to use our financial resources including the $15 million we received from our collaborative agreement and sale of preferred stock in January 2009, to fund our current obligations and to pursue other strategic alternatives that may become available to us. In the future, it is possible that we will not have adequate resources to support continued operations and we will need to cease operations.
Our future capital uses and requirements depend on numerous forward-looking factors. These factors include but are not limited to the following:
our ability to sell, out-license or otherwise dispose of our assets, including our SSAO compound;Riquent program;
our ability to consummate a strategic transaction such as a merger, license agreement or other collaboration with another company;a third party; or
our ability to negotiate favorable settlement terms with our creditors, as well as any actions that may be taken by our creditors, which could force us toimplementation of a wind down of the Company.Company if other alternatives are not deemed viable and in the best interests of the Company;
There can be no assurance that we will be able to enter into any strategic transactions on acceptable terms, if any, and our negotiating position may worsen as we continue to utilize our existing resources.

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Off-Balance Sheet Arrangements
We have no off-balance sheet arrangements that have or are reasonably likely to have a current or future effect on our consolidated financial condition, changes in our consolidated financial condition, expenses, consolidated results of operations, liquidity, capital expenditures or capital resources.
Item 7A. Quantitative and Qualitative Disclosures About Market Risk.
Item 8.Financial Statements and Supplementary Data.
     We invest our excess cash in interest-bearing investment-grade securities, which we sell from time to time to support our current operations. We do not utilize derivative financial instruments, derivative commodity instruments or other market risk sensitive instruments, positions or transactions in any material fashion. We currently do not invest in any securities that are materially and directly affected by foreign currency exchange rates or commodity prices.
     All of our investment securities are classified as available-for-sale and are therefore reported on the balance sheet at market value. Our investment securities consist of money market funds invested in U.S. Treasury bills, and asset-backed student loan auction rate securities. As of December 31, 2008, our short-term investments included $7.7 million (net of a realized impairment loss of $2.3 million) of AAA rated student loan auction rate securities and $2.3 million for the value of our auction rate securities put rights. Our auction rate securities are debt instruments with a long-term maturity and with an interest rate that is reset in short intervals through auctions.
     During November 2008, we executed a written agreement with UBS to participate in the ARS Rights program for all $10.0 million of our outstanding auction rate securities, all of which were maintained by UBS. Under the terms of the ARS Rights agreement, the applicable exercise period began on January 2, 2009 and ends January 4, 2011. ARS Rights represent an asset akin to a put option, whereby the holder has the right to ‘put’ the auction rate securities back to the broker-dealer during the exercise period for a payment equal to the par value of the auction rate securities. As of December 31, 2008, the fair value of the ARS Rights were recorded as a realized gain of $2.3 million and a corresponding short-term investment. The realized gain from recording the ARS Rights fully offsets the realized impairment loss on auction rate securities that was recorded during 2008 (see Note 2 to our audited consolidated financial statements included in Part IV). During January 2009, pursuant to the ARS Rights agreement, all of our auction rate securities were sold to UBS at par value of $10.0 million (see Note 10 to our audited consolidated financial statements included in Part IV).
     Based on our cash, cash equivalents and short-term investments at December 31, 2008, a hypothetical 10% increase or decrease in interest rates would increase or decrease our annual interest income and cash flows by an immaterial amount.
Item 8. Financial Statements and Supplementary Data.
The financial statements and supplementary data required by this item are set forth above under the caption “Quarterly Results of Operations”“Selected Quarterly Financial Data” on page F-26F-21 and at the end of this report beginning on page F-2 and is incorporated herein by reference.
Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure.
     None.

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Item 9A. Controls and Procedures.
Item 9.Changes in and Disagreements with Accountants on Accounting and Financial Disclosure.
None.
Item 9A(T).Controls and Procedures.
(a) Disclosure Controls and Procedures; Changes in Internal Control Over Financial Reporting
Our management, with the participation of our principal executive and principal financial officers, has evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934 (the “Exchange Act”)) as of December 31, 2008.2009. Based on this evaluation, our principal executive and principal financial officers concluded that our disclosure controls and procedures were effective as of December 31, 2008.2009.
There was no change in our internal control over financial reporting during the quarter ended December 31, 20082009 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.
(b) Management Report on Internal Control Over Financial Reporting
Our management is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is defined in Rule 13a-15(f) and Rule 15d-15(f) promulgated under the Exchange Act as a process designed by, or under the supervision of, our principal executive and principal financial officers and effected by our board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that:
Pertain to the maintenance of records that in reasonable detail accurately and fairly reflect the transactions and dispositions of our assets;
Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures are being made only in accordance with authorizations of our management and directors; and
Provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material effect on our financial statements.
Pertain to the maintenance of records that in reasonable detail accurately and fairly reflect the transactions and dispositions of our assets;
Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures are being made only in accordance with authorizations of our management and directors; and
Provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material effect on our financial statements.
Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.
Our management assessed the effectiveness of our internal control over financial reporting as of December 31, 2008.2009. In making this assessment, our management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in Internal Control-Integrated Framework.
Based on our assessment, management concluded that, as of December 31, 2008,2009, our internal control over financial reporting was effective based on those criteria.
     The independentThis annual report does not include an attestation report of the Company’s registered public accounting firm that audited the consolidated financial statements that are included in this Annual Report on Form 10-K has issued an audit report on ourregarding internal control over financial reporting. TheManagement’s report appears below.was not subject to attestation by the Company’s registered public accounting firm pursuant to temporary rules of the Securities and Exchange Commission that permit the Company to provide only management’s report in this annual report.

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(c) Report
Item 9B.Other Information.
We called a special meeting of Independent Registered Public Accounting Firm
The Board of Directors and Stockholders of La Jolla Pharmaceutical Company
     We have audited La Jolla Pharmaceutical Company’s internal control over financial reporting as of December 31, 2008, based on criteria establishedstockholders in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (the “COSO criteria”). La Jolla Pharmaceutical Company’s management is responsible for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Report on Internal Control Over Financial Reporting. Our responsibility isOctober 2009 to express an opinionvote on the company’s internal control over financial reporting based onPlan of Dissolution. However, the majority of our audit.
     We conducted our audit in accordancestockholders failed to return their proxy cards or otherwise indicate their votes with the standards of the Public Company Accounting Oversight Board (United States). Those standards require thatrespect to this proposal. As a result, we plan and perform the auditwere unable to obtain reasonable assurance about whether effective internal control over financial reporting was maintainedthe requisite quorum to conduct business at the special meeting and thus we cancelled the special meeting in all material respects. Our audit included obtaining an understandingNovember 2009.
We called a special meeting of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control basedstockholders in February 2010 to vote on the assessed risk,Merger with Adamis. However, the majority of our stockholders failed to return their proxy cards or otherwise indicate their votes with respect to this proposal. As a result, we were unable to obtain the requisite quorum to conduct business at the special meeting and performing such other procedures asthus we considered necessarycancelled the special meeting in the circumstances. We believe that our audit provides a reasonable basis for our opinion.
     A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.
     Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.
     In our opinion, La Jolla Pharmaceutical Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2008 based on the COSO criteria.
     We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the consolidated balance sheets of La Jolla Pharmaceutical Company as of December 31, 2008 and 2007, and the related consolidated statements of operations, stockholders’ equity, and cash flows for each of the three years in the period ended December 31, 2008 and our report dated March 27, 2009 expressed an unqualified opinion thereon that included an explanatory paragraph regarding La Jolla Pharmaceutical Company’s ability to continue as a going concern.
/s/ Ernst & Young LLP
San Diego, California
March 27, 20092010.

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Item 9B. Other Information.
     None.
PART III
Item 10.Directors, Executive Officers and Corporate Governance.
Our directors and executive officers and their ages as of March 5, 2010 are set forth below.
NameAgePosition(s)
Craig R. Smith, M.D.64Director, Chairman of the Board
Deirdre Y. Gillespie, M.D.53President, Chief Executive Officer and Assistant Secretary
Gail A. Sloan, CPA47Vice President of Finance and Secretary
Robert A. Fildes, Ph.D.71Director
Stephen M. Martin63Director
Frank E. Young, M.D., Ph.D.78Director
The biographies of our directors and executive officers appear below.
Item 10. Directors,Craig R. Smith, M.D.has been a director since 2004 and Chairman of the Board since 2006. Dr. Smith is currently Executive OfficersVice President, Chief Operating Officer and Corporate Governance.director of Algenol Biofuels Inc., a privately held industrial biotechnology company, and the President of Williston Consulting, LLC, a consulting firm providing advisory services to pharmaceutical and biotechnology companies. From 1993 to 2004, Dr. Smith served as Chairman, President and Chief Executive Officer of Guilford Pharmaceuticals, Inc., a publicly held pharmaceutical company. From 1988 to 1992, Dr. Smith was Vice President of Clinical Research and from 1992 to 1993, Senior Vice President of Business and Market Development at Centocor, Inc., a publicly held biotechnology company, which is now a wholly-owned subsidiary of Johnson & Johnson. From 1975 to 1988, he served on the faculty of the Department of Medicine at the Johns Hopkins University School of Medicine. Dr. Smith is a member of the Johns Hopkins Alliance for Science and a member of the board of directors of Adams Express Company, a publicly held closed-end equity investment company, Petroleum & Resources Corporation, a publicly held equity investment company specializing in energy and natural resources, and Depomed, Inc., a publicly held specialty pharmaceutical company. Dr. Smith holds an M.D. from the State University of New York at Buffalo and trained in Internal Medicine at the Johns Hopkins Hospital from 1972 to 1975. Based on Dr. Smith’s executive experience and service on other boards of directors in the biotechnology and pharmaceutical industries, as well as his experience in medicine and academia, the Board believes Dr. Smith has the appropriate set of skills to serve as a member of our Board.
Deirdre Y. Gillespie,M.D., President, Chief Executive Officer and Assistant Secretary, joined us in March 2006 as a director, and as President and Chief Executive Officer. She was appointed Assistant Secretary in February 2007. Dr. Gillespie previously served as the President and Chief Executive Officer of Oxxon Therapeutics, Inc., a privately held pharmaceutical company, from 2001 to 2005. Prior to that, she served as Chief Operating Officer of Vical, Inc., from 2000 to 2001, and Executive Vice President & Chief Business Officer, from 1998 to 2000. Dr. Gillespie also held a number of positions at DuPont Merck Pharmaceutical Company, including Vice President of Marketing, from 1991 to 1996. Dr. Gillespie received her M.B.A. from the London Business School and her M.D. and B.Sc. from London University.
Gail A. Sloan,CPA, Vice President of Finance and Secretary, joined us in 1996 as Assistant Controller, was promoted to Controller in 1997, to Senior Director of Finance in 2002 and to Vice President of Finance in 2004. She was appointed Secretary in 1999. Prior to joining us, from 1993 to 1996, Ms. Sloan served as Assistant Controller at Affymax Research Institute, a publicly held drug-discovery research company and formerly a part of the Glaxo Wellcome Group. From 1985 to 1993, she progressed to the position of Audit Manager with Ernst & Young LLP. Ms. Sloan holds a B.S. in Business Administration from California Polytechnic State University, San Luis Obispo and is a Certified Public Accountant.

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Robert A. Fildes,Ph.D.has been a director since 1991. Since January 1998, Dr. Fildes has served as President of SB2, Inc., a privately held company that licenses antibody technology. From June to December 1998, Dr. Fildes served as Chief Executive Officer of Atlantic Pharmaceuticals, a publicly held company in the field of biotechnology. From 1993 to 1997, Dr. Fildes was the Chairman and Chief Executive Officer of Scotgen Biopharmaceuticals, Inc., a privately held company in the field of human monoclonal antibody technology. From 1990 to 1993, Dr. Fildes was an independent consultant in the biopharmaceutical industry. He was the president and Chief Executive Officer of Cetus Corporation, a publicly held biotechnology company, from 1982 to 1990. From 1980 to 1982, Dr. Fildes was the President of Biogen, Inc., which merged with IDEC Pharmaceuticals Corporation in 2003 to form Biogen Idec, a publicly held biopharmaceutical company, and from 1975 to 1980, he was the Vice President of Operations for the Industrial Division of Bristol-Myers Squibb Company . From April 2002 to April 2003, Dr. Fildes was a director of Polymerat Pty. Ltd., a privately held company (now Anteo Diagnostics Ltd., a publicly held company) that develops surfaces for carrying out biological reactions. Dr. Fildes is currently a director of Inimex Pharmaceuticals, Inc., a privately held Canadian biotechnology company. Dr. Fildes holds a D.C.C. degree in Microbial Biochemistry and a Ph.D. in Biochemical Genetics from the University of London. Based on Dr. Fildes’ executive experience, specifically his experience as Chief Executive Officer at numerous companies in the biotechnology industry, as well as his service on other boards of directors in the biotechnology industries, the Board believes Dr. Fildes has the appropriate set of skills to serve as a member of our Board.
Stephen M. Martinhas been a director since April 2000. Mr. Martin is currently CEO Partner of Hi Tech Partners, LLC, a privately held consulting firm for executive management of early stage technology businesses. In April 2009, he joined QSpex Technologies, Inc., an early-stage private Ophthalmic (Spectacle) Lens manufacturing company as Chief Business Officer and was promoted to Chief Executive Officer in June 2009. In June 2001, Mr. Martin retired from CIBA Vision Corporation, a Novartis Company engaged in the research, manufacture and sale of contact lenses, lens care products and ophthalmic pharmaceuticals. Mr. Martin founded CIBA Vision in 1980. Mr. Martin was President of CIBA Vision Corporation, USA from 1995 to 1998 and President of Ciba Vision Ophthalmics, USA, the company’s ophthalmic pharmaceutical division, which he founded, from 1990 until 1998. He served as CIBA Vision’s Vice President of Venture Opportunities from 1998 until his retirement in 2001. Mr. Martin currently serves as a director of QSpex Technologies, Inc., a privately held spectacle manufacturing company, OcuCure Therapeutics, Inc., a privately held ophthalmic pharmaceutical development company and NeoVista, Inc., a privately held medical device company. From 2003 to 2005, Mr. Martin served as a director of Alimera Sciences, Inc., a privately held ophthalmic pharmaceutical company. Mr. Martin is the inventor on six issued U.S. patents and a number of European patents. Mr. Martin holds a B.A. degree from Wake Forest University and attended the Woodrow Wilson College of Law. Based on Mr. Martin’s executive experience, including his experience in senior management positions in business development, as well as his service on other boards of directors, the Board believes Mr. Martin has the appropriate set of skills to serve as a member of our Board.
Frank E. Young,M.D.,Ph.D.has been a director since 2005. Dr. Young is a former Commissioner of the United States Food and Drug Administration (“FDA”) and has had over a 40-year career in medicine, academia and government. After numerous academic appointments, Dr. Young served as Chairman of the Department of Microbiology and Professor of Microbiology, of Pathology, and of Radiation Biology and Biophysics at the University of Rochester, New York. Subsequently, he became Dean of the School of Medicine and Dentistry, Director of the Medical Center and Vice President for Health Affairs at the University of Rochester. Dr. Young joined the Department of Health and Human Services as Commissioner of the FDA and Assistant Surgeon General (Rear Admiral, USPHS) in 1984. Under Presidents Ronald Reagan, George H.W. Bush, and William J. Clinton, Dr. Young served as Commissioner of the FDA, Deputy Assistant Secretary and Director of the Office of Emergency Preparedness, Director of the National Disaster Medical System and as a member of the Executive Board of the World Health Organization (presidential appointee). Dr. Young currently serves as the Chief Executive Officer of Cosmos Alliance and is a partner of Essex Woodlands Health Ventures. In addition, Dr. Young is Vice Chairman of the board of Agennix AG, a publicly traded company, and serves on the boards of the following private companies: Elusys Therapeutics, Inc. and Light Sciences Oncology. Dr. Young attended Union College and holds an M.D. degree from the University of the State of New York, Upstate Medical Center, where he graduated cum laude, and a Ph.D. degree from Case Western Reserve University. Based on Dr. Young’s experience as a Commissioner of the FDA, his experience in medicine and academia, and his service on other boards of directors in the biotechnology industry, the Board believes Dr. Young has the appropriate set of skills to serve as a member of our Board.

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Director Independence
     Information requiredOur Board has previously determined that each of Doctors Fildes, Smith and Young, and Mr. Martin are “independent” within the meaning of Nasdaq Marketplace Rules 5605(b) and 5605(a)(2) as adopted by this item willthe Nasdaq Stock Market, Inc. (“Nasdaq”). Dr. Gillespie was not deemed to be “independent” because she is our President and Chief Executive Officer.
Committees of the Board of Directors
Our Board has three standing committees: an audit committee; a compensation committee; and a corporate governance and nominating committee. As discussed above, all committee members have been previously determined by our Board to be “independent.” The committees operate under written charters that are available for viewing on our website at www.ljpc.com, then “Investor Relations.”
Audit Committee. It is the responsibility of the audit committee to oversee our accounting and financial reporting processes and the audits of our financial statements. In addition, the audit committee assists the Board in its oversight of our compliance with legal and regulatory requirements. The specific duties of the audit committee include: monitoring the integrity of our financial process and systems of internal controls regarding finance, accounting and legal compliance; selecting our independent auditor; monitoring the independence and performance of our independent auditor; and providing an avenue of communication among the independent auditor, our management and our Board. The audit committee has the authority to conduct any investigation appropriate to fulfill its responsibilities, and it has direct access to all of our employees and to the independent auditor. The audit committee also has the ability to retain, at our expense and without further approval of the Board, special legal, accounting or other consultants or experts that it deems necessary in the performance of its duties.
The audit committee met five times during 2009, and otherwise accomplished its business without formal meetings. The members of the audit committee are Mr. Martin and Doctors Fildes and Smith. Mr. Martin currently serves as the chairman of the audit committee. Our Board has previously determined that each of Doctors Fildes and Smith and Mr. Martin is “independent” within the meaning of the enhanced independence standards contained in our Definitive Proxy Statement for our 2009 Annual MeetingNasdaq Marketplace Rule 5605(c)(2)(A) and Rule 10A-3 under the Exchange Act that relate specifically to members of Stockholders,audit committees.
Our Board has also previously determined that Dr. Smith has sufficient relevant attributes to be filed pursuantdeemed the audit committee’s “audit committee financial expert” as defined in Item 407 of Regulation S-K.
Compensation Committee. It is the responsibility of the compensation committee to Regulation 14Aassist the Board in discharging the Board of Director’s responsibilities regarding the compensation of our employees and directors. The specific duties of the compensation committee include: making recommendations to the Board regarding the corporate goals and objectives relevant to executive compensation; evaluating our executive officers’ performance in light of such goals and objectives; recommending compensation levels to the Board based upon such evaluations; administering our incentive compensation plans, including our equity-based incentive plans; making recommendations to the Board regarding our overall compensation structure, policies and programs; and reviewing the Company’s compensation disclosures. Additional information regarding the processes and procedures of the compensation committee is provided in Item 11 “Executive Compensation.”
The compensation committee met three times during 2009, and otherwise accomplished its business without formal meetings. The members of the compensation committee through September 3, 2009 were Doctors Fildes, Adams and Topper, and Mr. Martin. After the resignations of Doctors Adams and Topper on September 3, 2009, the compensation committee was comprised of Dr. Fildes and Mr. Martin. Dr. Fildes currently serves as the chairman of the compensation committee.

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Corporate Governance and Nominating Committee. It is the responsibility of the corporate governance and nominating committee to assist the Board: to identify qualified individuals to become Board members; to determine the composition of the Board and its committees; and to monitor and assess the effectiveness of the Board and its committees. The specific duties of the corporate governance and nominating committee include: identifying, screening and recommending to the Board candidates for election to the Board; reviewing director candidates recommended by our stockholders; assisting in attracting qualified director candidates to serve on the Board; monitoring the independence of current directors and nominees; and monitoring and assessing the relationship between the Board and our management with respect to the Board’s ability to function independently of management.
The corporate governance and nominating committee did not meet during 2009, but accomplished its business without formal meetings. The members of the corporate governance and nominating committee through September 3, 2009 were Doctors Young and Topper and Mr. Sutter. After the resignations of Dr. Topper and Mr. Sutter on September 3, 2009, the corporate governance and nominating committee was comprised of Dr. Young,
Meetings of Non-Management Directors. The non-management members of the Board regularly meet without any members of management present during regularly scheduled executive sessions of meetings of the Board.
Section 16(a) Beneficial Ownership Reporting Compliance
Under the securities laws of the United States, our directors and officers and persons who own more than 10% of our equity securities are required to report their initial ownership of our equity securities and any subsequent changes in that ownership to the Securities and Exchange Commission (“SEC”) within 120 days ofand the Nasdaq Capital Market. Specific due dates for these reports have been established, and we are required to disclose any late filings during the fiscal year ended December 31, 2008. Such information is incorporated herein2009. To our knowledge, based solely upon our review of the copies of such reports required to be furnished to us during the fiscal year ended December 31, 2009, all of these reports were timely filed, except one report filed in March 2009 by reference.former named executive officer Josefina Elchico reporting the sale of common stock that occurred during February 2009.
Code of Conduct
We have adopted a code of conduct that appliesdescribes the ethical and legal responsibilities of all of our employees and, to the extent applicable, members of our Board. This code includes (but is not limited to) the requirements of the Sarbanes-Oxley Act of 2002 pertaining to codes of ethics for chief executives and senior financial and accounting officers. Our Board has reviewed and approved this code. Our employees agree in writing to comply with the code at commencement of employment and periodically thereafter. Our employees are encouraged to report suspected violations of the code. Our code of conduct is available for viewing on our website at www.ljpc.com, then “Investor Relations.” If we make substantive amendments to the code or grant any waiver, including any implicit waiver, to our principal executive, financial or accounting officer, or persons performing similar functions, we will disclose the nature of such amendment or waiver on our website and/or in a report on Form 8-K in accordance with applicable rules and regulations.
Item 11.Executive Compensation.
Equity Compensation.Under the 2004 Equity Incentive Plan, the Compensation Committee may grant stock options, restricted stock, stock appreciation rights and performance awards. In granting these awards, the Committee may establish any conditions or restrictions it deems appropriate. The grant of options is unrelated to any anticipated major announcements made by the Company and is thus not influenced by any material, non-public information that may exist at the time of grant.
The exercise price of stock options is set at the fair market value on the grant date using the closing market price on the date of grant. New hire stock option awards granted in 2009 vest with respect to 25% of the underlying shares on the one-year anniversary from the date of grant and with respect to the remaining 75% of the underlying shares on a monthly pro rata basis over the next three years. Stock option awards granted in 2009 as a part of the annual performance review process vest monthly on a pro rata basis over 4 years.

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The annual stock option awards for executive performance in fiscal 2008 were made on January 22, 2009. No annual stock option awards for executive performance in fiscal 2009 were made.
On December 31, 2009, we granted 2,021,024 restricted stock units (“RSUs”) to our three remaining employees where each RSU represents a contingent right to receive one share of the Company’s common stock. The RSUs vest upon the closing of the Merger, subject to the continued employment of the recipient through the closing date of the Merger. The RSUs were valued at the fair market value of the Company’s common stock on the grant date. The value of the RSUs on December 31, 2009 was $344,000 and no compensation expense for these RSUs was recognized during 2009. The RSUs were cancelled in March 2010 as a result of the termination of the Merger in March 2010.
Benefits.Our 1995 Employee Stock Purchase Plan (the “1995 Plan”) provides employees with an opportunity to acquire increased equity ownership in the Company over time through periodic purchases of shares. Our 1995 Plan allows employees, including the Named Executive Officers, to purchase common stock every three months (in an amount not exceeding 10% of each employee’s base salary, or hourly compensation, and any cash bonus paid, subject to certain limitations) over the offering period at 85% of the fair market value of the common stock at specified dates. The offering period may not exceed 24 months. No purchases under the 1995 Plan occurred during 2009.
Our retirement savings plan (“401(k) Plan”) was terminated in March 2009. Prior to its termination, our retirement savings plan was a tax-qualified retirement savings plan, pursuant to which all employees, including the Named Executive Officers, were able to contribute the lesser of 50% of their annual compensation or the limit prescribed by the Internal Revenue Service to the 401(k) Plan on a before-tax basis. We did not match employee contributions or otherwise contribute to the 401(k) Plan.
Our health and welfare programs were terminated in April 2009.
We have not historically provided special benefits or perquisites to our executives and did not do so in 2009.
Retention and Separation Agreements.
On December 4, 2009, we entered into Retention and Separation Agreements and General Release of All Claims (the “Retention Agreements”) with our current Named Executive Officers. Our current Named Executive Officers are our Chief Executive Officer and our Vice President of Finance. The Retention Agreements supersede the severance provisions of the employment agreements with the current Named Executive Officers that were effective prior to the signing of the Retention Agreements (the “Prior Employment Agreements”), but otherwise the terms of the Prior Employment Agreements remain in full force and effect. The Retention Agreements do not alter the amount of severance that was to be awarded under the Prior Employment Agreements, but rather change the events that trigger such payments.
Pursuant to the Retention Agreements, on December 18, 2009 we made retention payments to the current Named Executive Officers (the “Retention Payments”) in the amounts of $202,800 to our Chief Executive Officer Principal Financial Officer, Principal Accounting Officer, and $66,184 to allour Vice President of our other officers, directors, employees and agents. The codeFinance. If the current Named Executive Officers voluntarily resigned their employment prior to the earlier to occur of conduct is available at(a) the Corporate Governance sectionclosing of the Investor Relations pageMerger or (b) March 31, 2010, they were to immediately repay the Retention Payments to us. The date under (a) and (b) shall be referred to as the “Separation Date.”
Under the Retention Agreements, each of the current Named Executive Officers agreed to execute an amendment to the Retention Agreements (the “Amendment”) on our website at www.ljpc.com. We intendor about the Separation Date to disclose future amendmentsextend and reaffirm the promises and covenants made by them in the Retention Agreements through the Separation Date. The Retention Agreements also provided for severance payments to certainthe Named Executive Officers (“Severance Payments”) payable in a lump sum on the eighth day after the current Named Executive Officers signed the Amendment.

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In April 2010, the Compensation Committee confirmed that pursuant to the terms of the Retention Agreements, the Retention Payments and Severance Payments were earned as of March 31, 2010 and agreed that the existing employment terms would remain in effect beyond March 31, 2010. As an incentive to retain the current Named Executive Officers to pursue a strategic transaction such as a merger, license agreement, third party collaboration or wind down of the Company, the Compensation Committee also approved a retention bonus for a total of up to approximately $600,000, depending on the type of strategic transaction completed.
In addition to the provisions of our codethe Retention Agreements described above, effective information regarding applicable payments under the Prior Employment Agreements for the current Named Executive Officers is provided below.
Deirdre Y. Gillespie, M.D.Dr. Gillespie is entitled to (i) an annual base salary of conduct$375,000 (which amount has increased since her commencement of employment with us such that her current annual base salary is $405,600); (ii) a discretionary annual bonus with a target amount equal to 40% of her annual base salary (this target percentage has been increased to 50% as of December 31, 2008, although the exact amount will be determined each year based on Dr. Gillespie’s and the Company’s performance with respect to performance objectives established by the compensation committee); and (iii) a grant of an option to purchase 800,000 shares of common stock of the Company, with the option vesting with respect to 200,000 of the underlying shares on the above website within four business days followingfirst anniversary of the date of the agreement and 1/36th of the remaining option to purchase 600,000 shares vesting each month thereafter. The agreements contain non-competition and non-interference provisions; and all post-employment benefits are in exchange for a release agreement. If (i) the Company terminates Dr. Gillespie for cause, all options held by her, whether or not vested, will immediately terminate and become unexercisable (ii) Dr. Gillespie voluntarily resigns, all unvested options held by her will immediately terminate and become unexercisable and all vested options will remain exercisable until three months after the date of termination in the case of incentive stock options or six months in the case of non-qualified stock options, (iii) Dr. Gillespie’s employment ceases as a result of her death or disability, then all unvested options held by her will immediately terminate and become unexercisable and all vested options will remain exercisable until the one year anniversary of the date of cessation of service; (iv) the Company terminates her employment without cause or if she terminates her employment due to a constructive termination, then: (a) one-half of all of her then unvested options will immediately vest and become exercisable; (b) the other one-half of her then unvested options will immediately terminate and become unexercisable; and (c) all vested options (including those which vested pursuant to clause (a) shall expire on the two-year anniversary of the termination date; (v) Dr. Gillespie’s position is reduced such amendmentthat she no longer serves as CEO of the company on or waiver.within 360 days after the consummation of a change in control, then all of her unvested options shall immediately vest and become exercisable; and (vi) notwithstanding the foregoing, in no event shall any option be exercisable after the date of expiration set forth in the Plan.
Item 11. Executive Compensation.
     Information required by this itemGail A. SloanMs. Sloan is entitled to an annual base salary of $198,551 and a discretionary annual bonus in a target amount equal to 30% of her base salary. Ms. Sloan is also eligible to receive periodic equity awards under the Company’s equity compensation plans. Ms. Sloan’s employment will be contained in our Definitive Proxy Statement for our 2009 Annual Meeting of Stockholders,deemed to be filedterminated in connection with a change in control if, within 180 days of the date of the change in control: (i) her employment is terminated; (ii) her position is eliminated as a result of a reduction in force made to reduce over-capacity or unnecessary duplication of personnel and she is not offered a replacement position with the Company or its successor as a vice president with compensation and functional duties substantially similar to the compensation and duties in effect immediately before the change in control; or (iii) she resigns because she is required to be employed more than 50 miles from our current headquarters. Also, all employee stock options granted to Ms. Sloan prior to her termination date will automatically vest and become fully exercisable as of her termination date if her termination of employment is without cause or is in connection with a change in control, and will remain exercisable for a period of one year from her termination date or such longer period as provided by the applicable plan or grant pursuant to Regulation 14Awhich the options were granted.

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Summary Compensation Table
                                 
                      Non-Equity       
              Stock  Option  Incentive Plan  All Other    
Name and     Salary      Awards  Awards  Compensation  Compensation  Total 
Principal Position Year  ($)  Bonus ($) (1)  ($)  ($) (2)  ($) (3)  ($)  ($) 
                                 
Current Officers
Deirdre Y. Gillespie, M.D.
  2009  $421,200  $202,800  $  $1,167,161  $  $  $1,791,161 
President, Chief Executive Officer and Assistant Secretary  2008   402,600         1,093,763   200,772      1,697,135 
                                 
Gail A. Sloan
  2009   206,187   66,184      71,785         344,156 
Vice President of Finance and Secretary  2008   196,906         307,483   53,609      557,998 
                                 
Former Officers*
Niv E. Caviar
  2009   124,734   211,612      635,453         971,799 
Executive Vice President, Chief Business and Financial Officer  2008   280,775         226,995   111,097   25,000(4)  643,867 
                                 
Michael Tansey, M.D., Ph.D.
  2009   113,402   251,063      572,250         936,715 
Executive Vice President and Chief Medical Officer  2008   332,875         387,029   90,383      810,287 
*These former officers were terminated on April 20, 2009 as part of the Company’s restructuring activities, as described above.
(1)The amounts for Dr. Gillespie and Ms. Sloan are retention payments made on December 18, 2009 in accordance with the Retention Agreements dated December 4, 2009. See Note 6 to our audited consolidated financial statements. The amount for Mr. Caviar is severance equal to nine months of Mr. Caviar’s annual base salary at December 31, 2008 pursuant to his employment agreement dated May 10, 2007. The amount for Dr. Tansey is severance equal to nine months of Dr. Tansey’s annual base salary at December 31, 2008 pursuant to his employment agreement dated December 4, 2006. These severance payments were made to Mr. Caviar and Dr. Tansey following their respective terminations on April 20, 2009.
(2)The amounts in this column reflect the dollar amount recognized for financial statement reporting purposes for the fiscal years ended December 31, 2009 and December 31, 2008, for awards and thus may include amounts from awards granted in and prior to 2008. Assumptions used in the calculation of these amounts are included in Note 1 to our audited consolidated financial statements.
(3)These amounts represent the 2008 performance-based bonus awards which were paid in fiscal year 2009.
(4)This amount represents a signing bonus paid to Mr. Caviar in January 2008 in accordance with his employment agreement.

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Outstanding Equity Awards at 2009 Fiscal Year End
                         
                      Market or 
  Number of  Number of              Payout Value of 
  Securities  Securities          Number of  Unearned 
  Underlying  Underlying          Unearned Shares,  Shares, Units or 
  Unexercised  Unexercised  Option      Units or Other  Other Rights 
  Options  Options  Exercise  Option  Rights that have not  that have not 
  (#)  (#)  Price  Expiration  Vested  Vested 
Name Exercisable  Unexercisable  ($)  Date(1)  (#)  ($) 
                         
Current Officers
Deirdre Y. Gillespie
  766,666   33,333(2) $5.26   03/15/2016         
   106,250   43,750(2)  3.08   02/05/2017         
   68,750   81,250(2)  2.42   02/21/2018         
   34,375   115,625(2)  1.42   01/22/2019         
                   1,411,898(3) $240,023(4)
                         
Gail A. Sloan  972      18.44   01/28/2010         
   3,800      35.00   11/20/2010         
   3,000      38.25   07/19/2011         
   2,999      35.50   12/14/2011         
   5,999      25.45   07/18/2012         
   5,999      29.50   11/21/2012         
   5,999      14.85   05/12/2013         
   6,000      23.55   09/18/2013         
   14,000      14.80   05/21/2014         
   10,583      2.40   04/25/2015         
   5,415      2.15   05/19/2015         
   21,199      4.20   10/10/2015         
   184,548      4.46   04/17/2016         
   17,708   7,291(2)  3.08   02/05/2017         
   11,458   13,541(2)  2.42   02/21/2018         
   5,729   19,270(2)  1.42   01/22/2019         
                   483,810(3) $82,248(4)
                         
Former Officer*
Michael J.B. Tansey
  113,000(5)     3.61   07/17/2016         
   87,000(5)     3.23   12/04/2016         
   50,000(5)     5.47   05/23/2017         
   40,000(5)     2.42   02/21/2018         
   200,000(5)     1.82   05/22/2018         
   45,000(5)     1.42   01/22/2019         
*This former officer was terminated on April 20, 2009.
(1)All stock options expire ten years from the date of grant.
(2)The stock options vest and become exercisable ratably on a monthly basis over four years from the date of grant.
(3)These are restricted stock units (“RSUs”) granted on December 31, 2009 where each RSU represents a contingent right to receive one share of our common stock. The RSUs were to vest upon the closing of the Merger, subject to the continued employment of the recipient through the closing date of the Merger; however, the Merger was terminated in March 2010 and accordingly, the RSUs were accordingly cancelled.
(4)The value of each RSU is the closing price of our common stock on the date of grant, which was $0.17.
(5)Pursuant to Dr. Tansey’s employment agreement dated December 4, 2006, all of Dr. Tansey’s unvested options automatically vested upon his termination date of April 20, 2009 and remain exercisable for one year following the termination date. If not exercised by April 20, 2010, all of Dr. Tansey’s stock options will be cancelled on April 20, 2010.
Option Exercises and Stock Vested in Fiscal Year 2009
No named executive officers exercised any options or had any restricted stock vest in fiscal year 2009.

22


Director Compensation Table — 2009
                 
  Fees Earned or          
  Paid in Cash  Stock Awards  Option Awards  Total 
Name ($)  ($)  ($) (1)  ($) 
                 
Thomas H. Adams (2) $24,500  $  $19,139  $43,639 
                 
Robert A. Fildes  37,500      19,139   56,639 
                 
Stephen M. Martin  51,000      19,139   70,139 
                 
Craig R. Smith  62,750      18,619   81,369 
                 
Martin P. Sutter (2)        6,206   6,206 
                 
James N. Topper (2)        6,206   6,206 
                 
Frank E. Young  29,500      6,206   35,706 
(1)The amounts in this column reflect the dollar amount recognized for financial statement reporting purposes for the fiscal year ended December 31, 2009, and thus may include amounts from awards granted in and prior to 2009. Assumptions used in the calculation of these amounts are included in Note 1 to our consolidated financial statements.
(2)Doctors Adams and Topper and Mr. Sutter resigned as directors effective September 3, 2009.
Director Compensation
Retainers and Fees. Directors who are also our employees receive no extra compensation for their service on the Board. In 2009, non-employee directors received $1,500 per Board meeting attended in person and $750 per Board meeting attended telephonically. Non-employee directors also receive $750 per committee meeting attended in person and $500 per committee meeting attended telephonically. Directors are reimbursed for reasonable costs associated with attendance at meetings of the SEC within 120 daysBoard and its committees. Non-employee directors receive an annual retainer of December 31, 2008. Such information$20,000, which is incorporated herein by reference.paid quarterly. The Chairman of the Board, Dr. Smith, receives an additional annual retainer of $25,000, which is paid quarterly. In 2009, the chairman of the audit committee received an annual fee of $10,000. In 2009, the chairman of the compensation committee received an annual fee of $5,000. All chairman fees are paid quarterly. All other members of the audit, compensation and corporate governance and nominating committees receive an annual retainer of $2,000, which is paid quarterly.
Option Grants Under the 2004 Plan. Under the La Jolla Pharmaceutical Company 2004 Equity Incentive Plan, each of our non-employee directors automatically receives, upon becoming a non-employee director, a one-time grant of a non-qualified stock option to purchase up to 40,000 shares of our common stock at an exercise price equal to the fair market value of a share of the common stock on the date of grant. These non-employee director options have a term of 10 years and vest with respect to 25% of the underlying shares on the grant date and with respect to an additional 25% of the underlying shares on the date of each of the first three anniversaries of such grant, but only if the director remains a non-employee director for the entire period from the date of grant to such date. Upon re-election to our Board or upon continuing as a director after an annual meeting without being re-elected due to the classification of the Board, each non-employee director automatically receives a grant of an additional non-qualified stock option to purchase up to 10,000 shares of our common stock. Due to the futility of the Riquent trial, the annual grants for 2009 were not made. These additional non-employee director options have a term of 10 years and vest and become exercisable upon the earlier to occur of the first anniversary of the grant date or immediately prior to the annual meeting of stockholders next following the grant date; provided that the director remains a director for the entire period from the grant date to such earlier date. The exercise price for these additional non-employee director options is the fair market value of our common stock on the date of their grant. All outstanding non-employee director options vest in full immediately prior to any change in control. Each non-employee director is also eligible to receive additional options under the 2004 Plan in the discretion of the compensation committee of the Board. These options vest and become exercisable pursuant to the 2004 Plan and the terms of the option grant. The Chairman of the Board receives an additional annual grant of non-qualified stock options to purchase 20,000 shares of our common stock. Due to the futility of the Riquent trial, this Chairman of the Board annual grant for 2009 was not made. These non-employee director options have a term of 10 years and vest and become exercisable upon the first anniversary of the grant date.

23


Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters.
Equity Compensation Plan Information required by this item will
The following table provides information as of December 31, 2009 with respect to shares of our common stock that may be contained inissued under our Definitive Proxy Statement forequity compensation plans.
             
          Number of 
          Securities 
          Remaining 
          Available for 
  Number of      Future Issuance 
  Securities to be  Weighted-  Under Equity 
  Issued upon  Average Exercise  Compensation 
  Exercise of  Price of  Plans (Excluding 
  Outstanding  Outstanding  Securities 
  Options, Warrants  Options, Warrants  Reflected in 
  and Rights  and Rights  Column (a)) 
Plan Category
            
Equity Compensation plans approved by security holders  5,529,591(1) $6.99   1,082,671(2)
Equity Compensation plans not approved by security holders         
(1)Outstanding options to purchase shares of our common stock under the La Jolla Pharmaceutical Company 1994 Stock Incentive Plan and the 2004 Plan.
(2)Includes 1,065,694 shares subject to the 2004 Plan and 16,977 shares subject to the 1995 Plan (each stated as of December 31, 2009).
Security Ownership of Certain Beneficial Owners and Management
The following table sets forth information regarding beneficial ownership of our 2009 Annual Meetingcommon stock as of Stockholders,March 5, 2010 based on information available to be filed pursuant to Regulation 14Aus and filings with the SEC by:
each of our directors;
each of our “named executive officers” as defined by SEC rules;
all of our current directors and executive officers as a group; and
each person or group of affiliated persons known by us to be the beneficial owner of more than 5% of our common stock.

24


Beneficial ownership and percentage ownership are determined in accordance with the rules of the SEC and include voting or investment power with respect to shares of stock. This information does not necessarily indicate beneficial ownership for any other purpose. Under these rules, shares of our common stock issuable under stock options that are exercisable within 12060 days of December 31, 2008. Such informationMarch 5, 2010 are deemed outstanding for the purpose of computing the percentage ownership of the person holding the options, but are not deemed outstanding for the purpose of computing the percentage ownership of any other person.
Unless otherwise indicated and subject to applicable community property laws, to our knowledge, each stockholder named in the following table possesses sole voting and investment power over their shares of our common stock, except for those jointly owned with that person’s spouse. Percentage of beneficial ownership of our common stock is incorporated herein by reference.based on 65,722,648 shares of common stock outstanding as of March 5, 2010. Unless otherwise noted below, the address of each person listed on the table is c/o La Jolla Pharmaceutical Company, 4365 Executive Drive, Suite 300, San Diego, California 92121.
                 
      Shares       
  Shares of  with Right to       
  Common  Acquire  Total  Percentage 
  Stock  within 60  Beneficial  of Common 
Name and Address Owned  Days  Ownership  Stock 
                 
Essex Woodlands Health Ventures Fund VI, L.P. and affiliates     4,139,014   4,139,014   5.9%
Craig R. Smith, M.D.(1)     123,400   123,400   *%
Robert A. Fildes, Ph.D.(1)     97,759   97,759   *%
Stephen M. Martin(1)  40   105,400   105,440   *%
Frank E. Young, M.D., Ph.D.(1)  5,600   38,000   43,600   *%
Deirdre Y. Gillespie, M.D.(1)(2)     1,046,875   1,046,875   1.6%
Gail A. Sloan(2)     310,686   310,686   *%
Michael J.B. Tansey, M.D.(3)     535,000   535,000   *%
All current executive officers and directors as a group (6 persons)(4)  5,640   1,722,120   1,727,760   2.6%
*Less than one percent.
(1)Current director as of March 5, 2010.
(2)Current executive officer as of March 5, 2010.
(3)Former executive officer terminated April 20, 2009.
(4)The six current executive officers and directors are comprised of Dr. Smith, Dr. Fildes, Mr. Martin, Dr. Young, Dr. Gillespie and Ms. Sloan (each of whom is included within the table above).
Item 13. Certain Relationships
Item 14.Principal Accountant Fees and Services.
The following table presents the aggregate fees agreed to by the Company for the annual and Related Transactions,statutory audits for fiscal years ended December 31, 2008 and Director Independence.2009, and all other fees paid by us during 2008 and 2009 to Ernst & Young LLP:
     Information required
         
  2008  2009 
Audit Fees $298,861  $141,210 
Audit Related Fees      
Tax Fees  87,000   17,000 
All Other Fees  45,000    
       
Total $430,861  $158,210 
       

25


Audit Fees. The fees identified under this caption were for professional services rendered by this item will be containedErnst & Young LLP for the audit of our annual financial statements and internal control over financial reporting and for the review of the financial statements included in our Definitive Proxy Statementquarterly reports on Form 10-Q. The amounts also include fees for services that are normally provided by the auditor in connection with regulatory filings and engagements for the years identified. Audit fees in 2008 include an aggregate of $65,025 in fees paid in connection with our filing of registration statements on Form S-8 and Form S-3. Audit fees in 2009 Annual Meetinginclude an aggregate of Stockholders,$26,210 in fees paid in connection with our filing of registration statements on Form S-3 and S-4.
Tax Fees. Tax fees consist principally of assistance related to be filed pursuanttax compliance and reporting.
All Other Fees.These fees consist primarily of accounting consultation fees related to Regulation 14A withpotential collaborative agreements.
Pre-approval Policy. Our audit committee approves in advance all services provided by our independent registered public accounting firm. All engagements of our independent registered public accounting firm in 2008 and 2009 were pre-approved by the SEC within 120 days of December 31, 2008. Such information is incorporated herein by reference.
Item 14. Principal Accountant Fees and Services.
     Information required by this item will be contained in our Definitive Proxy Statement for our 2009 Annual Meeting of Stockholders, to be filed pursuant to Regulation 14A with the SEC within 120 days of December 31, 2008. Such information is incorporated herein by reference.audit committee.

28

26


PART IV
Item 15. Exhibits, Financial Statement Schedules.
(a) Documents filed as part of this report.
1. The following consolidated financial statements of La Jolla Pharmaceutical Company are filed as part of this report under Item 8 — Financial Statements and Supplementary Data:
     
  F-1 
     
  F-2 
     
  F-3 
     
  F-4 
     
  F-5 
     
  F-6 
2.Financial Statement Schedules.
These schedules are omitted because they are not required, or are not applicable, or the required information is shown in the consolidated financial statements or notes thereto.
3.Exhibits.
2. Financial Statement Schedules.
These schedules are omitted because they are not required, or are not applicable, or the required information is shown in the consolidated financial statements or notes thereto.
3. Exhibits.
The exhibit index attached to this report is incorporated by reference herein.

29

27


SIGNATURES
Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.
     
 LA JOLLA PHARMACEUTICAL COMPANY
 
 
March 30, 2009 By:  /s/ Deirdre Y. Gillespie   
April 15, 2010  Deirdre Y. Gillespie, M.D.  
  President, Chief Executive Officer and Assistant Secretary  
 
Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.
     
Signature Title Date
     
     /s/
/s/ Deirdre Y. Gillespie
Deirdre Y. Gillespie, M.D
 President, Chief Executive Officer and Assistant
Deirdre Y. Gillespie, M.D
 Secretary (Principal Executive Officer) March 30, 2009April 15, 2010
     
     /s/ Niv E. CaviarExecutive Vice President, Chief Business Officer
/s/ Gail A. Sloan
 
Niv E. CaviarGail A. Sloan
 Vice President of Finance and ChiefSecretary (Principal Financial Officer (Principal Financialand Accounting Officer) March 30, 2009April 15, 2010
     
     /s/ Gail
/s/ Robert A. Sloan
Vice President of Finance and Secretary (Principal
Fildes
 
GailRobert A. SloanFildes, Ph.D.
  Accounting Officer)Director  March 30, 2009April 15, 2010
     
     /s/ Thomas H. Adams
/s/ Stephen M. Martin
Stephen M. Martin
 Director March 30, 2009
Thomas H. Adams, Ph.D.
April 15, 2010
     
     /s/ Robert A. Fildes
/s/ Craig R. Smith
Craig R. Smith, M.D.
 Director March 30, 2009
Robert A. Fildes, Ph.D.
April 15, 2010
     
     /s/ Stephen M. MartinDirectorMarch 30, 2009
Stephen M. Martin
     /s/ Craig R. SmithDirectorMarch 30, 2009
Craig R. Smith, M.D.
     /s/ Martin SutterDirectorMarch 30, 2009
Martin Sutter
     /s/ James N. TopperDirectorMarch 30, 2009
James N. Topper, M.D., Ph.D.
     /s//s/ Frank E. YoungDirectorMarch 30, 2009
 
Frank E. Young, M.D., Ph.D.
 Director  April 15, 2010

30

28


Report of Independent Registered Public Accounting Firm
The Board of Directors and Stockholders of La Jolla Pharmaceutical Company
We have audited the accompanying consolidated balance sheets of La Jolla Pharmaceutical Company as of December 31, 20082009 and 2007,2008, and the related consolidated statements of operations, stockholders’ equity, and cash flows for each of the threetwo years in the period ended December 31, 2008.2009. These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on these financial statements based on our audits.
We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. We were not engaged to perform an audit of the Company’s internal control over financial reporting. Our audits included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements. An audit also includesstatements, assessing the accounting principles used and significant estimates made by management, as well asand evaluating the overall financial statement presentation. We believe that our audits provide a reasonable basis for our opinion.
In our opinion, the financial statements referred to above present fairly, in all material respects, the consolidated financial position of La Jolla Pharmaceutical Company at December 31, 20082009 and 2007,2008, and the consolidated results of its operations and its cash flows for each of the threetwo years in the period ended December 31, 2008,2009, in conformity with U.S. generally accepted accounting principles.
The accompanying financial statements have been prepared assuming that La Jolla Pharmaceutical Company will continue as a going concern. As more fully described in Note 1, La Jolla Pharmaceutical Company has incurred recurring operating losses, an accumulated deficit of $415.7$424.3 million and working capitalas of $3.0 million at December 31, 2008.2009 and has no current source of revenues or financing. These conditions, among others, as discussed in Note 1 to the consolidated financial statements, raise substantial doubt about La Jolla Pharmaceutical Company’s ability to continue as a going concern. Management’s plans in regard to these matters also are described in Note 1. The 20082009 consolidated financial statements do not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classifications of liabilities that may result from the outcome of this uncertainty.
     We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), La Jolla Pharmaceutical Company’s internal control over financial reporting as of December 31, 2008, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission and our report dated March 27, 2009 expressed an unqualified opinion thereon.
/s/ Ernst & Young LLP
San Diego, California
March 27, 2009April 15, 2010

F-1


La Jolla Pharmaceutical Company
Consolidated Balance Sheets
(In thousands, except share and par value amounts)
        
 December 31,        
 2008 2007 December 31, 
   2009 2008 
Assets
  
Current assets:  
Cash and cash equivalents $9,447 $4,373  $4,254 $9,447 
Short-term investments, available-for-sale 10,000 34,986   10,000 
Prepaids and other current assets 785 1,018  586 785 
       
Total current assets 20,232 40,377  4,840 20,232 
 
Property and equipment, net 357 1,271   357 
Patent costs and other assets, net 250 2,757   250 
       
 $20,839 $44,405  $4,840 $20,839 
       
  
Liabilities and stockholders’ equity
  
Current liabilities:  
Accounts payable $4,626 $2,203  $125 $4,626 
Accrued clinical/regulatory expenses 3,957 6,282   3,957 
Accrued expenses 1,008 664  323 1,008 
Accrued payroll and related expenses 1,549 1,199  173 1,549 
Credit facility 5,933    5,933 
Current portion of obligations under notes payable 152 138   152 
Current portion of obligations under capital leases 11 10   11 
       
Total current liabilities 17,236 10,496  621 17,236 
  
Non-current portion of obligations under notes payable 179 344   179 
Non-current portion of obligations under capital leases 34 44   34 
  
Commitments  
  
Stockholders’ equity:  
Preferred stock, $0.01 par value; 8,000,000 shares authorized, no shares issued or outstanding      
Common stock, $0.01 par value; 225,000,000 shares authorized, 55,549,528 and 39,629,660 shares issued and outstanding at December 31, 2008 and 2007, respectively 555 396 
Common stock, $0.01 par value; 225,000,000 shares authorized, 65,722,648 and 55,549,528 shares issued and outstanding at December 31, 2009 and 2008, respectively 657 555 
Additional paid-in capital 418,522 385,944  427,883 418,522 
Other comprehensive income  14 
Accumulated deficit  (415,687)  (352,833)  (424,321)  (415,687)
       
Total stockholders’ equity 3,390 33,521  4,219 3,390 
       
 $20,839 $44,405  $4,840 $20,839 
       
See accompanying notes.

F-2


La Jolla Pharmaceutical Company
Consolidated Statements of Operations
(In thousands, except per share amounts)
                    
 Years Ended December 31, Years Ended December 31, 
 2008 2007 2006 2009 2008 
 
Revenue from collaboration agreement $8,125 $ 
   
Expenses:  
Research and development $51,025 $46,635 $32,834  9,576 51,025 
General and administrative 9,702 9,058 9,287  7,193 9,702 
Asset impairments 2,810  104   2,810 
       
Total expenses 63,537 55,693 42,225  16,769 63,537 
       
  
Loss from operations  (63,537)  (55,693)  (42,225)  (8,644)  (63,537)
  
Interest expense  (96)  (82)  (46)  (13)  (96)
Interest income  779 2,699 2,826 
Interest and other income 23 779 
     
Net loss $(62,854) $(53,076) $(39,445) $(8,634) $(62,854)
       
  
Basic and diluted net loss per share $(1.26) $(1.40) $(1.21) $(0.14) $(1.26)
       
  
Shares used in computing basic and diluted net loss per share 49,689 37,818 32,588  63,326 49,689 
       
See accompanying notes.

F-3


La Jolla Pharmaceutical Company
Consolidated Statements of Stockholders’ Equity
For the Years Ended December 31, 2006, 20072008 and 20082009
(In thousands)
                                         
 Additional Other Total Additional Other   Total 
 Common stock paid-in comprehensive Accumulated stockholders’ Preferred stock Common stock paid-in comprehensive Accumulated stockholders’ 
 Shares Amount capital income (loss) deficit equity
  
Balance at December 31, 2005 32,533 $325 $337,117 $ $(260,312) $77,130 
Issuance of common stock under Employee Stock Purchase Plan 80 1 226   227 
Exercise of stock options 56 1 125   126 
Share-based compensation expense 24  5,051   5,051 
Net loss      (39,445)  (39,445)
  
Balance at December 31, 2006 32,693 327 342,519   (299,757) 43,089 
Issuance of common stock, net 6,670 67 37,845   37,912 
Issuance of common stock under Employee Stock Purchase Plan 97 1 260   261 
Exercise of stock options 166 1 499   500 
Share-based compensation expense 4  4,821   4,821 
Net loss      (53,076)  (53,076)
Net unrealized gains on available-for-sale securities    14  14 
   
Comprehensive loss  (53,062)
   Shares Amount Shares Amount capital income (loss) deficit equity 
Balance at December 31, 2007 39,630 396 385,944 14  (352,833) 33,521   $ 39,630 $396 $385,944 $14 $(352,833) $33,521 
Issuance of common stock, net 15,615 156 27,877   28,033    15,615 156 27,877   28,033 
Issuance of common stock under Employee Stock Purchase Plan 304 3 287   290    304 3 287   290 
Exercise of stock options 1  3   3    1  3   3 
Share-based compensation expense   4,411   4,411      4,411   4,411 
Net loss      (62,854)  (62,854)        (62,854)  (62,854)
Net unrealized losses on available-for-sale securities     (14)   (14)       (14)   (14)
      
Comprehensive loss  (62,868)  (62,868)
                   
Balance at December 31, 2008 55,550 $555 $418,522 $ $(415,687) $3,390    55,550 555 418,522   (415,687) 3,390 
Issuance of preferred stock 339 3   6,807   6,810 
Conversion of preferred stock, net  (339)  (3) 10,173 102  (99)    
Share-based compensation expense     2,653   2,653 
Net loss        (8,634)  (8,634)
                   
Balance at December 31, 2009  $ 65,723 $657 $427,883 $ $(424,321) $4,219 
                 
See accompanying notes.

F-4


La Jolla Pharmaceutical Company
Consolidated Statements of Cash Flows
(In thousands)
            
 Years Ended December 31,         
 2008 2007 2006  Years Ended December 31, 
   2009 2008 
Operating activities
  
Net loss $(62,854) $(53,076) $(39,445) $(8,634) $(62,854)
Adjustments to reconcile net loss to net cash used for operating activities:  
Depreciation and amortization 990 1,687 1,987  117 990 
Loss on write-off/disposal of patents, property and equipment and licenses 243 934 316 
(Gain) loss on write-off/disposal of patents, property and equipment  (347) 199 
Loss on impairment of patents, property and equipment and licenses 2,810  104   2,810 
Share-based compensation expense 4,411 4,821 5,051  2,653 4,411 
Amortization (accretion) of investment premium/discount 240  (227) 36 
Expense reduction from settlement of vendor obligations  (2,743)  
Amortization of investment premium/discount  240 
Changes in operating assets and liabilities:      
Prepaids and other current assets 233  (14)  (101) 199 233 
Accounts payable 2,423 78 1,259 
Accrued clinical/regulatory expenses  (2,325) 4,752 1,303 
Accrued expenses 344  (473)  (147)
Accounts payable and accrued liabilities  (6,400) 442 
Accrued payroll and related expenses 350  (66) 487   (1,376) 350 
       
Net cash used for operating activities  (53,135)  (41,584)  (29,150)  (16,531)  (53,179)
  
Investing activities
  
Purchases of short-term investments   (51,415)  (16,700)
Sales of short-term investments 24,665 55,750 44,050  10,000 24,665 
Net proceeds from sale of patents and property and equipment 861 44 
Additions to property and equipment  (506)  (354)  (335)  (18)  (506)
Increase in patent costs and other assets  (116)  (628)  (536)  (6)  (116)
       
Net cash provided by investing activities 24,043 3,353 26,479  10,837 24,087 
  
Financing activities
  
Net proceeds from issuance of common stock 28,326 38,673 353   28,326 
Net proceeds from issuance of preferred stock 6,810  
Proceeds from credit facility 6,000     6,000 
Proceeds from issuance of notes payable  312 263 
Payments on credit facility  (5,933)  
Payments on obligations under notes payable  (151)  (209)  (527)  (331)  (151)
Payments on obligations under capital leases  (9)  (1)    (45)  (9)
       
Net cash provided by financing activities 34,166 38,775 89  501 34,166 
       
  
Increase (decrease) in cash and cash equivalents 5,074 544  (2,582)
(Decrease) increase in cash and cash equivalents  (5,193) 5,074 
Cash and cash equivalents at beginning of period 4,373 3,829 6,411  9,447 4,373 
       
Cash and cash equivalents at end of period $9,447 $4,373 $3,829  $4,254 $9,447 
       
  
Supplemental disclosure of cash flow information:
  
Interest paid $96 $82 $46  $13 $96 
       
Supplemental schedule of noncash investing and financing activities:
 
Capital lease obligations incurred for property and equipment $ $55 $ 
  
See accompanying notes.

F-5


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies
Organization and Business Activity
La Jolla Pharmaceutical Company (the “Company”) is a biopharmaceutical company dedicatedformed to improvingimprove and preservingpreserve human life by developing innovative pharmaceutical products.
Basis of Presentation
The accompanying consolidated financial statements have been prepared assuming that the Company will continue as a going concern. This basis of accounting contemplates the recovery of the Company’s assets and the satisfaction of liabilities in the normal course of business and does not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classification of liabilities that might be necessary should the Company be unable to continue as a going concern. While the basis of presentation remains that of a going concern, the Company has a history of recurring losses from operations, had an accumulated deficit of $424,321,000 as of December 31, 2009, and currently has no source of revenues or financing. The Company is currently evaluating strategic alternatives which may include mergers, license agreements, third party collaborations to develop new products or a wind down of the Company. The Company’s current inability to generate future cash flows and recent inability to consummate a strategic transaction raise substantial doubt about the Company’s ability to continue as a going concern.
On January 4, 2009, the Company entered into a development and commercialization agreement (the “Development Agreement”) with BioMarin CF, a wholly-owned subsidiary of BioMarin Pharmaceutical Inc. (“BioMarin Pharma”), granting BioMarin CF co-exclusive rights to develop and commercialize Riquent (and certain potential follow-on products) (collectively, “Riquent”) in the “Territory,” and the non-exclusive right to manufacture Riquent anywhere in the world. The “Territory” includes all countries of the world except the “Asia-Pacific Territory” (i.e., all countries of East Asia, Southeast Asia, South Asia, Australia, New Zealand, and other countries of Oceania). Under the terms of the Development Agreement, BioMarin CF paid the Company a non-refundable commencement payment of $7,500,000 and through BioMarin Pharma, paid $7,500,000 for a newly designated series of preferred stock (the “Series B-1 Preferred Stock”), pursuant to a related securities purchase agreement described more fully at Note 4, below.
In February 2009, the Company announced that an Independent Monitoring Board for the Riquent® Phase 3 ASPEN study had completed theits review of theirthe first interim efficacy analysis and determined that continuing the study was futile. Based on these results, the Company immediately discontinued the Riquent Phase 3 ASPEN study and the development of Riquent. The Company had previously devoted substantially all of its research, development and clinical efforts and financial resources toward the development of Riquent. In connection with the termination of the clinical trials for Riquent, the Company subsequently initiated steps to significantly reducereduced its operating costs, includingceased all Riquent manufacturing and regulatory activities and effected a planned substantial reduction in personnel,force in April 2009 (see Note 6).
Following the futile results of the first interim efficacy analysis of Riquent received in February 2009, BioMarin CF elected not to exercise its full license rights to the Riquent program under the Development Agreement. Thus, the Development Agreement between the parties terminated on March 27, 2009 in accordance with its terms. Pursuant to the Securities Purchase Agreement between the Company and BioMarin Pharma, all of the Company’s preferred shares purchased by BioMarin Pharma were converted into common shares. All rights to Riquent were returned to the Company.
In July 2009, the Company announced that, in light of the alternatives available to the Company at the time, a wind down of the Company’s business would be in the best interests of the Company and its stockholders. Although the Board of Directors (the “Board”) approved a Plan of Complete Liquidation and Dissolution (the “Plan of Dissolution”) in September 2009, it was subject to approval by holders of at least a majority in voting power of the Company’s outstanding shares. The Company called a special meeting of stockholders to vote on the Plan of Dissolution, but the majority of the Company’s stockholders failed to return their proxy cards or otherwise indicate their votes with respect to this proposal. As a result, the Company was not able to obtain the requisite quorum to conduct business at the special meeting and the special meeting was therefore cancelled.

F-6


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
On December 4, 2009, the Company entered into an Agreement and Plan of Reorganization (the “Merger Agreement”) by and among the Company, Jewel Merger Sub, Inc. (“Merger Sub”) and Adamis Pharmaceuticals Corporation (“Adamis”). The transaction contemplated by the Merger Agreement was structured as a reverse triangular merger, in which is expectedMerger Sub, a wholly-owned subsidiary of the Company, would merge with and into Adamis, with Adamis surviving (the “Merger”). On March 3, 2010, the Company and Adamis agreed to terminate the Merger Agreement as a result of the failure of the Company’s stockholders to vote in sufficient quantities for there to be effected early ina quorum to hold the second quarterstockholders’ meeting to approve the proposals related to the Merger. The solicitation of 2009. The Company has also ceasedfurther votes was cancelled due to the manufacturedelisting of Riquent. In addition, the Company has incurred a net loss of $62.9 million in 2008, has had cumulative net losses of $415.7 million from inception to date and has limited financial resources at December 31, 2008.
These events raise substantial doubt about the Company’s ability to continue as a going concern.common stock from Nasdaq.
Effective at the open of business on March 4, 2010, the Company’s common stock was suspended and delisted from The accompanying consolidated financial statements have been prepared assumingNASDAQ Stock Market (“Nasdaq”) and began trading on The Pink OTC Markets, Inc. The delisting was the result of Nasdaq’s determination that the Company will continue as a going concern. This basis of accounting contemplates the recovery of the Company’shad nominal assets, other than cash, and the satisfaction of liabilities in the normal course of business and this does not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classification of liabilities that might be necessary should the Company be unable to continue as a going concern.
In light of the Company’s decision to discontinue development of the Riquent clinical program, the Company is seeking to maximize the value of its remaining assets. The Company is currently evaluating its strategic alternatives, which include the following:
Sell or out-license the Company’s remaining assets, including the Company’s SSAO compounds;
Pursue potential other strategic transactions, which could include mergers, license agreements or other collaborations, with third parties; or
Implement an orderly wind down of the Company if other alternatives are not deemed viable and in the best interests of the Company.
had nominal operations.
Principles of Consolidation
The accompanying consolidated financial statements include the accounts of theLa Jolla Pharmaceutical Company and its wholly-owned subsidiary,subsidiaries, La Jolla Limited, which was incorporated in England in October 2004.2004, and Jewel Merger Sub, Inc., which was incorporated in Delaware in December 2009. There have been no significant transactions related to either subsidiary since their inception. La Jolla Limited since its inception.was formally dissolved during October 2009 with no resulting accounting consequences.
Use of Estimates
The preparation of consolidated financial statements in conformity with United States generally accepted accounting principles (“GAAP”) requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and disclosures made in the accompanying notes to the consolidated financial statements. Actual results could differ materially from those estimates.
Cash, Cash Equivalents and Short-Term Investments
Cash and cash equivalents consist of cash and short-term,The Company considers all highly liquid investments which include money market funds and debt securities with maturities from purchase datea maturity of three months or less and are stated at estimated fair value.when purchased to be cash equivalents. Short-term investments mainly consist of debt securities with maturities from purchase date of greater than three months. In accordance with Statement of Financial Accounting Standard (“SFAS”) No. 115,Accounting for Certain Investments in Debt and Equity Securities, management hasare classified the Company’s cash equivalents and

F-6


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)
short-term investments as available-for-sale securities in the accompanying consolidated financial statements.accordance withThe ASC Topic of Investments. Available-for-sale securities are recordedcarried at estimated fair value, with the unrealized gains and losses reported in other comprehensive income (loss). The amortized cost of debt securities in this category is adjusted for amortization of premiums and accretion of discounts to maturity. Such amortization is included in interest income. Realized gains and losses and declines in value judged to be other-than-temporary, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific identification method. Interest and dividends on securities classified as available-for-sale are included in interest income.
ConcentrationRevenue Recognition

The Company applies the revenue recognition criteria outlined in theASC Topic of Risk

Cash, cash equivalentsRevenue Recognition. Upfront product and short-term investmentstechnology license fees under multiple-element arrangements are deferred and recognized over the period of such services or performance if such arrangements require on-going services or performance. Non-refundable amounts received for substantive milestones are recognized upon achievement of the milestone. Any amounts received prior to satisfying the Company’s revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets.

The Company’s sole source of revenue in the consolidated financial instrumentsstatements related to a January 4, 2009 Development Agreement with BioMarin CF which potentially subjectcontained multiple potential revenue elements, including non-refundable upfront fees. The Development Agreement was terminated on March 27, 2009 following the failure of the Phase 3 ASPEN trial at which time the Company to concentrations of credit risk.had no remaining on-going services or performance. The Company deposits its cash in financial institutions. At times, such deposits may be in excessrecognized $8,125,000 as collaboration revenue upon termination of insured limits. The Company invests its excess cash primarily in government-asset-backed securities, and money market funds invested in U.S. Treasury bills. The Company has established guidelines relative to the diversification of its cash investments and their maturities in an effort to maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates.

As of December 31, 2008, there was insufficient demand at auctions for the Company’s student loan auction rate securities, representing a par value of approximately $10,000,000. During January 2009, the Company sold all of these auction rate securities to its broker-dealer at par value of $10,000,000 (see Notes 2 and 10).
Development Agreement.
Impairment of Long-Lived Assets and Assets to Be Disposed Of
In accordance with SFAS No. 144,Accounting for the Impairment or Disposal of Long-Lived Assets, ifIf indicators of impairment exist, the Company assesses the recoverability of the affected long-lived assets by determining whether the carrying value of such assets can be recovered through the undiscounted future operating cash flows. If impairment is indicated, the

F-7


La Jolla Pharmaceutical Company measures the amount of such impairment by comparing the carrying value of the asset
Notes to the fair value of the asset and records the impairment as a reduction in the carrying value of the related asset and a charge to operating results. Estimating the undiscounted future cash flows associated with long-lived assets requires judgment and assumptions that could differ materially from the actual results.Consolidated Financial Statements
As a result of the futility determination in the Phase 3 ASPEN trial, the Company discontinued the Riquent Phase 3 ASPEN study and the development of Riquent. Based on these events, the future cash flows from the Company’s Riquent-related patents arewere no longer expected to exceed their carrying values and the assets became impaired. This rendered substantially allimpaired as of the Company’s laboratory equipment, as well as a large portion of its furniture and fixtures and computer equipment and software impaired.
The Company performed a recoverability test of its long-lived assets in accordance with SFAS No. 144. The recoverability test was based on the estimated undiscounted future cash flows expected to result from the Company’s long-lived assets. Based on the recoverability analysis performed, management does not believe that the estimated undiscounted future cash flows expected to result from the disposition of certain of the Company’s long-lived assets are sufficient to recover the carrying value of these assets.December 31, 2008. Accordingly, the Company recorded a non-cash charge for the impairment of long-lived assets of $2,810,000 for the year ended December 31, 2008 to write down the value of the Company’s long-lived assets to their estimated fair values. Impairment charges included $2,061,000 for patents, $724,000 for property and equipment, and $25,000 for licenses. TheAlthough no impairment charges were recorded during 2009, the Company recognized $0 and $104,000 in impairment losses forsold, disposed of, or wrote off all of its remaining long-lived assets during the yearsyear ended December 31, 2007 and 2006, respectively.

F-7


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary2009 for a gain of Significant Accounting Policies (continued)$347,000.
Property and Equipment
Property and equipment is stated at cost and has been depreciated using the straight-line method over the estimated useful lives of the assets (primarily five years). Leasehold improvements and equipment under capital leases are stated at cost and have been depreciated on a straight-line basis over the shorter of the estimated useful life or the lease term.
Property and equipment is comprised of the following (in thousands):
        
 December 31,        
 2008 2007 December 31, 
   2009 2008 
Laboratory equipment $6,171 $6,498  $ $6,171 
Computer equipment and software 4,654 4,727  2,186 4,654 
Furniture and fixtures 477 491   477 
Leasehold improvements 3,275 3,273   3,275 
       
 14,577 14,989  2,186 14,577 
Less: Accumulated depreciation  (14,220)  (13,718)  (2,186)  (14,220)
       
 $357 $1,271  $ $357 
       
Depreciation expense for the years ended December 31, 2009 and 2008 2007was $115,000 and 2006 was $737,000, $1,471,000, and $1,840,000, respectively. Impairment charges of $724,000 during 2008 were reflected as a reduction to the above noted 2008 costs.
Patents
TheDuring 2009, all remaining patents were sold, disposed of, or written off.
Prior to 2009, the Company hashad filed numerous patent applications with the United States Patent and Trademark Office and in foreign countries. Legal costs and expenses incurred in connection with pending patent applications have beenwere capitalized. Costs related to issued patents arewere amortized using the straight-line method over the lesser of the remaining useful life of the related technology or the remaining patent life, commencing on the date the patent iswas issued. Total
As a result of the sale, disposal, or write-off of all remaining patents as of December 31, 2009, total issued and pending patent application costs and accumulated amortization were $0 as of December 31, 2009. As of December 31, 2008, total issued patent application costs (net of 2008 impairment charges) and accumulated amortization were $1,159,000 and $1,116,000, at December 31, 2008 and $2,492,000 and $911,000 at December 31, 2007, respectively. Total pending patent application costs (less 2008 impairment charges) were $207,000 and $1,004,000 at December 31, 2008 and 2007, respectively.2008. Capitalized costs related to patent applications arewere charged to operations at the time a determination is made not to pursue such applications or they become impaired. Amortization expense for the years ended December 31, 2009 and 2008 2007was $2,000 and 2006 was $245,000, $207,000, and $139,000, respectively.
Accrued Clinical/Regulatory Expenses
As a result of the Company discontinuing the Riquent Phase 3 ASPEN study and the development of Riquent, all clinical and regulatory activities were ceased and no related accruals were required as of December 31, 2009.

F-8


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
The Company reviewsreviewed and accruesaccrued clinical trial and regulatory-related expenses based on work performed, which reliesrelied on estimates of total costs incurred based on patient enrollment, completion of studies and other events. The Company followsfollowed this method since reasonably dependable estimates of the costs applicable to various stages of a clinical trial cancould be made. Accrued clinical/regulatory costs are subject to revisions as trials progress to completion. Revisions are charged to expense in the period in which the facts that give rise to the revision become known. Historically, revisions have not resulted in material changes to research and development costs.
Share-Based Compensation
On January 1, 2006, the Company adopted SFAS No. 123R,Share-Based Payment(“SFAS 123R”), which is a revision of SFAS No. 123,Accounting and Disclosure of Stock-Based Compensation (“SFAS 123”). SFAS 123R requires the measurement and recognition of compensation expense for all share-based payment awards made to employees and directors, including stock options, restricted stock and purchases under the La Jolla Pharmaceutical Company 1995 Employee Stock Purchase Plan (the “ESPP”), based on estimated fair values. SFAS 123R supersedes the Company’s previous accounting under Accounting Principles Board Opinion (“APB”) No. 25,

F-8


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)
Accounting for Stock Issued to Employees(“APB 25”), and SFAS 123, for periods beginning in fiscal 2006. In March 2005, the Securities and Exchange Commission (“SEC”) issued Staff Accounting Bulletin (“SAB”) No. 107 (“SAB 107”), which discusses the interaction between SFAS 123R and certain SEC rules and regulations and provides the SEC’s staff views regarding the valuation of share-based payment arrangements for public companies.
The Company has applied the provisions of SAB 107, related to the calculation of its expected term, in its adoption of SFAS 123R and for the period permitted by SAB 107.
Share-based compensation expense recognized under SFAS 123R for the years ended December 31, 2008, 20072009 and 2006, respectively2008 was approximately $2,653,000 and $4,422,000, $4,810,000 and $5,048,000.respectively. As of December 31, 2008,2009, there was approximately $4,940,000$976,000 of total unrecognized compensation cost related to non-vested share-based payment awards granted under all equity compensation plans. As share-based compensation expense recognized in the Consolidated Statement of Operations for the fiscal years 2008, 20072009 and 20062008 is based on awards ultimately expected to vest, share-based compensation expense has been reduced for estimated forfeitures. SFAS 123R requires forfeitures to beForfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Total unrecognized compensation cost will be adjusted for future changes in estimated forfeitures. The Company expects to recognize that cost over a weighted-average period of 1.20.8 years.
Compensation expenseDeferred charges for options or stock awards issuedgranted to non-employees, other than non-employee directors, has been determined in accordance with Emerging Issues Task Force 96-18,Accounting for Equity Instruments That Are Issued to Other Than Employees for Acquiring, or in Conjunction with Selling, Goods or Services. Deferred charges for options granted to such non-employees are periodically remeasured as the options vest. In December 2008, the Company granted non-qualified stock options to purchase a total of 15,000 shares of common stock to a consultant at an exercise price equal to the fair market value of the stock at the date of the grant. The Company recognized compensation expense for these stock option grants of approximately ($1,000) and $1,000 for the yearyears ended December 31, 2008.2009 and 2008, respectively. In September and October 2007, the Company granted non-qualified stock options to purchase a total of 12,000 shares of common stock to consultants at an exercise price equal to the fair market value of the stock at the date of each grant. For the yearsyear ended December 31, 2008, and 2007, the Company recognized compensation (credit) expense for these stock option grants of approximately ($11,000) and $11,000, respectively. In January 2006, the Company granted a non-qualified stock option to purchase 1,000 shares of common stock to a consultant at an exercise price equal to the fair market value of the stock at the date of the grant. The Company recognized. No compensation expense for these stock option grants of approximately $3,000 forwas recognized during the year ended December 31, 2006.2009.
As permitted by SFAS 123R, theThe Company utilizes the Black-Scholes option-pricing model as its method of valuation for stock options and purchases under the ESPP. The Black-Scholes model was previously utilized for the Company’s pro forma information required under SFAS 123. The Company’s determination of the fair value of share-based payment awards on the date of grant using an option-pricing model is affected by the Company’s stock price as well as assumptions regarding a number of highly complex and subjective variables. These variables include, but are not limited to, the Company’s expected stock price volatility over the term of the awards and actual and projected employee stock option exercise behaviors.
Share-Based Award Valuation and Expense Information Under SFAS 123R and APB 25
The following table summarizes share-based compensation expense (in thousands) related to employee and director stock options and restricted stock and ESPP purchases under SFAS 123R for the years ended December 31, 2009 and 2008, 2007as well as share-based compensation expense related to ESPP purchases for the year ended December 31, 2008:
         
  December 31, 
  2009  2008 
Research and development $632  $1,961 
General and administrative  2,021   2,461 
       
Share-based compensation expense included in operating expenses $2,653  $4,422 
       
For the years ended December 31, 2009 and 2006:2008, the Company estimated the fair value of each option grant on the date of grant using the Black-Scholes option-pricing model with the following weighted-average assumptions:
             
  December 31, 
  2008  2007  2006 
Research and development $1,961  $1,907  $1,833 
General and administrative  2,461   2,903   3,215 
          
Share-based compensation expense included in operating expenses $4,422  $4,810  $5,048 
          

F-9


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)Options:
         
  December 31, 
  2009  2008 
Risk-free interest rate  0.6%  3.2%
Dividend yield  0.0%  0.0%
Volatility  295.0%  115.1%
Expected life (years)  5.6   5.6 
For the yearsyear ended December 31, 2008, 2007, and 2006, the Company estimated the fair value of each option grant and ESPP purchase rightrights on the date of grant using the Black-Scholes option-pricing model with the following weighted-average assumptions:
Options:
             
  December 31,
  2008 2007 2006
Risk-free interest rate  3.2%  4.7%  4.8%
Dividend yield  0.0%  0.0%  0.0%
Volatility  115.1%  118.0%  113.7%
Expected life (years)  5.6   6.0   5.9 

F-10


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)
ESPP:
             
  December 31,
  2008 2007 2006
Risk-free interest rate  1.1%  4.5%  4.8%
Dividend yield  0.0%  0.0%  0.0%
Volatility  99.6%  67.8%  46.4%
Expected life (years) 3 months 3 months 3 months
December 31,
2008
Risk-free interest rate1.1%
Dividend yield0.0%
Volatility99.6%
Expected life3 months
The weighted-average fair values of options granted were $1.70, $3.71$1.72 and $3.92$1.70 for the years ended December 31, 2008, 20072009 and 2006,2008, respectively. The weighted-average purchase pricesprice of shares purchased through the ESPP werewas $0.95 $2.69 and $2.98 for the yearsyear ended December 31, 2008, 2007 and 2006, respectively.2008. No ESPP purchases were made during 2009.
The risk-free interest rate assumption is based on observed interest rates appropriate for the term of the Company’s employee and director stock options and ESPP purchases. The dividend yield assumption is based on the Company’s history and expectation of dividend payouts. The Company has never paid dividends on its common stock and the Company does not anticipate paying dividends in the foreseeable future.
The Company used historical stock price volatility as the expected volatility assumption required in the Black-Scholes option-pricing model consistent with SFAS 123R.model. The selection of the historical volatility approach was based on the availability of historical stock prices for the duration of the awards’ expected term and the Company’s assessment that historical volatility is more representative of future stock price trends than other available methods.
The expected life of employee and director stock options represents the weighted-average period the stock options are expected to remain outstanding. Under SAB 107, the simplified method is an acceptable method of calculating the expected life of options granted through December 31, 2007. However, for options granted after December 31, 2007, companies are expected to use more detailed information about employee exercise behavior, if available, to calculate the expected life of options under SAB 107 rather than the simplified method. For option grants made during 2008, the Company calculated the expected life usingUsing historical option exercise data. Under this method of calculating the expected life of option grants,data, the expected life for option grants made during the yearyears ended December 31, 2009 and 2008 was 5.6 years for the new and existing employee grants and the director grants. Under the SAB 107 simplified method, the expected life calculated by the Company for option grants made during the year ended December 31, 2007 was 6.0 — 6.1 years for the new and existing employee grants and 5.5 years for the director grants. The expected life calculated by the Company for option grants made during the year ended December 31, 2006 was 5.8 years for the new and existing employee grants, 6.1 years for the new officer grants, and 5.3 — 6.0 years for the director grants. The expected life for ESPP purchase rights represents the length of each purchase period. Because employees purchase stock quarterly, the expected term for ESPP purchase rights is three months for shares purchased during the yearsyear ended December 31, 2008, 2007 and 2006.2008. No ESPP purchases were made during 2009.
Because share-based compensation expense recognized in the Consolidated Statement of Operations for fiscal years 2008, 20072009 and 20062008 is based on awards ultimately expected to vest, it has been reduced for estimated forfeitures. SFAS 123R requires forfeitures to beForfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Forfeitures were estimated based on historical experience.experience for compensation expense recognized for fiscal year 2008. During 2009, forfeitures were estimated based on actual events; primarily the reduction in force that occurred during April 2009 (see Note 6).
Restricted Stock
There was no restricted stock issued during the years ended December 31, 2009 and 2008. In addition, no compensation expense related to restricted stock was recognized during the years ended December 31, 2009 and 2008.

F-11

F-10


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)
Restricted Stock Units
On December 14, 2005,31, 2009, the Company issued 83,518 shares ofgranted 2,021,024 restricted stock units (“RSUs”) to certain membersthe Company’s three remaining employees where each RSU represented a contingent right to receive one share of management in exchange for services provided over the vesting period, pursuantCompany’s common stock. The RSUs were to certain retention agreements dated October 6, 2005. The sharesvest upon the closing of restricted stock fully vested (i.e., the restrictions lapsed) one year fromMerger, subject to the continued employment of the recipient through the closing date of grant andthe Merger. The RSUs were subject to repurchase byvalued at the Company until the one-year anniversaryfair market value of the dateCompany’s common stock on the grant date. The value of issuance. Pursuant to a separation agreement dated March 17, 2006, the Company’s repurchase right with respect to 29,120 shares of restricted stock granted to the former Chairman and Chief Executive Officer immediately lapsed upon his resignation on March 14, 2006. As such and in accordance with his retention agreement, the Company accelerated the vesting of these shares of restricted stock. In addition, the remaining 54,398 shares of restricted stock fully vestedRSUs on December 14, 2006, the one-year anniversary of the date of issuance,31, 2009 was $344,000 and therefore the Company’s repurchase right with respect to these shares of restricted stock has lapsed.
On March 15, 2006, the Company issued 20,000 shares of restricted stock to the new Chairman of the Board in exchange for services provided over the vesting period. The shares of restricted stock vested with respect to 10,000 shares six months after the issuance date and with respect to the remaining 10,000 shares upon the first anniversary of the issuance date. On September 15, 2006 and March 15, 2007, the vesting provisions with respect to the 20,000 shares of restricted stock were met and therefore the Company’s repurchase rights lapsed.
In both December 2006 and March 2007, the Company issued an additional 3,600 shares of restricted stock to the Chairman of the Board in accordance with the Chairman Compensation Policy approved by the Board of Directors on March 14, 2006 regarding the tax liability associated with the restricted stock issued on March 15, 2006 and vested on September 15, 2006 and March 15, 2007. All of these additional shares of restricted stock immediately vested on the date of issuance.
There was no restricted stock issued in 2008.
In accordance with SFAS 123R, the Company recognized approximately $36,000, and $381,000, respectively, in compensation expense for these RSUs was recognized during 2009. As a result of the restricted stock grants noted above fortermination of the years ended December 31, 2007, and 2006, which includes compensation expense forMerger in March 2010, the acceleration of vesting. There was no compensation expense related to restricted stock grants during the year ended December 31, 2008.RSUs were cancelled.
Net Loss Per Share
Basic and diluted net loss per share is computed using the weighted-average number of common shares outstanding during the periods in accordance with SFAS No. 128,periods. Earnings per Shareand SAB No. 98. Basic earnings per share (“EPS”) is calculated by dividing the net income or loss by the weighted-average number of common shares outstanding for the period, without consideration for common share equivalents. Diluted EPS is computed by dividing the net income or loss by the weighted-average number of common share equivalents outstanding for the period determined using the treasury-stock method. For purposes of this calculation, stock options common stock subject to repurchase by the Company, and warrants are considered to be common stock equivalents and are only included in the calculation of diluted earnings per share when their effect is dilutive.

F-12


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
1. Organization and Summary of Significant Accounting Policies (continued)
Because the Company has incurred a net loss for all threeboth of the two years presented in the Consolidated Statements of Operations, stock options common stock subject to repurchase and warrants are not included in the computation of net loss per share because their effect is anti-dilutive. The shares used to compute basic and diluted net loss per share represent the weighted-average common shares outstanding, reduced by the weighted-average unvested common shares subject to repurchase. There were no unvested common shares subject to repurchase for the years ended December 31, 2008 and 2007. The number of weighted-average unvested common shares subject to repurchase for the year ended December 31, 2006 was 8,000.outstanding.
Comprehensive Loss
In accordance with SFAS No. 130,Reporting Comprehensive Income (Loss), unrealizedUnrealized gains and losses on available-for-sale securities are included in other comprehensive income.income (loss).
Recently Issued Accounting Standards
On January 1, 2008,In June 2009, the Company adoptedFinancial Accounting Standards Board (“FASB”) approved the provisionsFASB Accounting Standards Codification (“the Codification”) when it issued Statement of Financial Accounting Standards Board (“FASB”) SFAS No. 157,168,Fair Value Measurements(“SFAS 157”). SFAS 157 establishes a framework for measuring fair value and expands disclosures about fair value measurements. The changes to current practice resulting from the application of SFAS 157 relate to the definition of fair value, the methods used to measure fair value,FASB Accounting Standards Codification and the expanded disclosures about fair value measurements. See Note 3 for further details on the impact of the adoption of SFAS 157 on the Company’s consolidated results of operations and financial condition for the year ended December 31, 2008.
On January 1, 2008, the Company adopted the provisions of FASB SFAS No. 159,The Fair Value Option for Financial Assets and Financial Liabilities – Including an amendment of FASB Statement No. 115 (“SFAS 159”). SFAS 159 permits entities to choose to measure many financial assets and financial liabilities at fair value. Unrealized gains and losses on items for which the fair value option has been elected are reported in earnings. At this time, the Company has not elected to account for any of its financial assets or liabilities using the provisions of SFAS 159. As such, the adoption of SFAS 159 did not have an impact on the Company’s consolidated results of operations and financial condition for the year ended December 31, 2008.
In June 2007, FASB ratified the consensus reached by the Emerging Issues Task Force (“EITF”) on EITF Issue No. 07-3,Accounting for Nonrefundable Advance Payments for Goods or Services to Be Used in Future Research and Development Activities(“EITF 07-3”). EITF 07-3 addresses the diversity that exists with respect to the accounting for the non-refundable portion of a payment made by a research and development entity for future research and development activities. Under EITF 07-3, an entity would defer and capitalize non-refundable advance payments made for research and development activities until the related goods are delivered or the related services are performed. EITF 07-3 is effective for fiscal years beginning after December 15, 2007. On January 1, 2008 the Company adopted the provisions of EITF 07-3, which did not have an impact on the Company’s consolidated results of operations and financial condition for the year ended December 31, 2008.
In May 2008, the FASB issued SFAS No. 162,The Hierarchy of Generally Accepted Accounting Principles(“SFAS 162”). SFAS 162 identifies the sources of accounting principles and the framework for selecting the principles used, which is included in the preparation of financial statements that are presented in conformity with generally accepted accounting principles. SFAS 162 becomes effective 60 days following the SEC’s approval of the Public CompanyThe Accounting Oversight Board amendments to Statement on Auditing Standards No. 69,The MeaningCodification (“ASC”) Topic of Present Fairly in Conformity With Generally Accepted Accounting Principles(the “Topic”). All existing accounting standard documents, such as FASB, American Institute of Certified Public Accountants, Emerging Issues Task Force and other related literature, excluding guidance from the Securities and Exchange Commission (“SEC”), have been superseded by the Codification. All other non-grandfathered, non-SEC accounting literature not included in the Codification has become non-authoritative. The Codification did not change GAAP, but instead introduced a new structure that combines all authoritative standards into a comprehensive, topically-organized online database. The Topic is effective for financial statements issued for interim and annual periods completedending after January 1,September 15, 2009. The Company does not expect the adoption of SFAS 162 to have a material effect onTopic impacts the Company’s consolidated financial statements.statement disclosures as all future references to authoritative accounting literature will be referenced in accordance with the Codification. As a result of the implementation of the Codification during the quarter ended September 30, 2009, previous references to accounting standards and literature are no longer applicable.

F-13

F-11


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
2. Cash Equivalents and Short-term Investments
As of December 31, 2009, the Company held cash of $4,254,000 and held no available-for-sale securities or short-term investments.
The following is a summary of the Company’s available-for-sale securities as of December 31, 2008 (in thousands):
                         
      Gross Gross      
  Amortized Unrealized Unrealized Realized Realized Estimated Fair
  Cost Gains Losses Gains Losses Value
   
December 31, 2008
                        
Money market accounts $2,686  $  $  $  $  $2,686 
Asset-backed auction rate securities  10,000            (2,270)  7,730 
Auction security rights           2,270      2,270 
   
  $12,686  $  $  $2,270  $(2,270) $12,686 
   
                                     
 Gross Gross       Gross Gross       
 Amortized Unrealized Unrealized Realized Realized Estimated Fair Amortized Unrealized Unrealized Realized Realized Estimated Fair 
 Cost Gains Losses Gains Losses Value Cost Gains Losses Gains Losses Value 
  
December 31, 2007
 
December 31, 2008
 
Money market accounts $2,051 $ $ $ $ $2,051  $2,686 $ $ $ $ $2,686 
Obligations of United States government agencies 6,916 14    6,930 
Asset-backed auction rate securities 28,056     28,056  10,000     (2,270) 7,730 
Auction rate security rights    2,270  2,270 
               
 $37,023 $14 $ $ $ $37,037  $12,686 $ $ $2,270 $(2,270) $12,686 
               
The amortized cost of debt securities isheld as of December 31, 2008 was adjusted for amortization of premiums and accretion of discounts to maturity. Included in cash and cash equivalents at December 31, 2008 and 2007 were $2,686,000 and $2,051,000, respectively, of securities classified as available-for-sale as the Company expects to sell them in orderwhich were sold during 2009 to support its current operations regardless of their maturity date.operations. As of December 31, 2008, available-for-sale securities and cash equivalents of $2,686,000 mature inhad a maturity date of one year or less and $10,000,000 arewere due after one year. Securities that have a maturity date greater than one year have their interest rate reset periodically within time periods not exceeding 92 days.
As of December 31, 2008, the Company’s cash, cash equivalents and short-term investments total $19,447,000. The Company’s investment securities consistconsisted of money market funds invested in U.S. Treasury bills and student loan auction rate securities. There has beenDuring 2008, there was insufficient demand at auction for all four of the Company’s auction rate securities during 2008.securities. As a result, these securities are currentlywere not liquid. In the event the Company needs to access the funds that are in an illiquid state, it will not be able to do so without a loss of principal until a future auction on these auction rate securities is successful, the securities are settled at par by the broker-dealer or they are redeemed by the issuer. The Company may incur a loss of principal if the Company is required to sell or borrow against these securities in a privately negotiated transaction. As a result, the Company has recorded a realized impairment loss on these securities of $2,270,000 in 2008. This realized loss was determined in accordance with SFAS 157, which was adopted by the Company on January 1, 2008 (see Note 3). The Company’s auction rate securities arewere classified as short-term investments, and the realized impairment loss iswas included in the Company’s statement of operations. operations for the year ended December 31, 2008.
During the fourth quarter of 2008, the Company’s broker-dealer, UBS, extended an offer of Auction Rate Securities Rights (“ARS Rights”) to holders of illiquid auction rate securities that were maintained by UBS as of February 13, 2008. The ARS Rights provideprovided the holder with the ability to sell the auction rate securities, along with the ARS Rights, to UBS at the par value of the auction rate securities, during an applicable exercise period. The ARS Rights arewere not transferable, not tradeable, and willwere not be quoted or listed on any securities exchange or other trading network.
During November 2008, the Company executed a written agreement with UBS to participate in the ARS Rights program for all $10,000,000 of its outstanding auction rate securities, all of which were maintained by UBS. Under the terms of the ARS Rights agreement, the applicable exercise period began on January 2, 2009 and ends January 4, 2011. ARS Rights represent an asset akin to a put option, whereby the Company has the right to ‘put’ the auction rate securities back to the broker-dealer during the exercise period for a payment equal to the par value of the auction rate securities. As of December 31, 2008, the fair value of the ARS Rights were recorded as a realized gain

F-14


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
2. Cash Equivalents and Short-term Investments (continued)
of $2,270,000 and a corresponding short-term investment. The realized gain from recording the ARS Rights fully offsetsoffset the realized impairment loss on auction rate securities that was recorded during 2008. During January 2009, all of the Company’s auction rate securities were sold to UBS at par value of $10,000,000 pursuant to the ARS Rights agreement (see Note 10).
3. Fair Value of Financial Instruments
As a basis for considering market participant assumptions in fair value measurements, SFAS 157 establishes a fair value hierarchy that prioritizes the inputs to valuation techniques used to measure fair value into three broad levels. The fair value hierarchy gives the highest priority to quoted prices in active markets for identical assets or liabilities (Level 1) and the lowest priority to unobservable inputs (Level 3). Due to the lack of actively traded market data for the Company’s student loan auction rate securities, the value of these securities and resulting realized impairment loss was determined using Level 3 hierarchical inputs. These inputs include management’s assumptions of pricing by market participants, including assumptions about risk. In accordance with SFAS 157, the Company used the concepts of fair value based on estimated discounted future cash flows of interest income over a projected five-year period reflective of the length of time the Company anticipates it will take the securities to become liquid. Discount rates ranging from approximately 5% to 10% were utilized when preparing this model. The Company classified all of the student loan auction rate securities as short-term available-for-sale securities as the Company will need additional cash in the near term and may be required to liquidate these auction rate securities in order to continue operations. Because of the Company’s inability to hold these securities until their maturity (which ranges between 20-30 years), the Company believes the impairment of these securities is other-than-temporary. See Notes 1 and 10 for further details.
The Company measures the following financial assets at fair value on a recurring basis. The fair value of these financial assets at December 31, 2008 (in thousands) are as follows:
                 
      Fair Value Measurements at Reporting Date Using
      Quoted prices in      
      active markets     Significant
      for identical Significant other unobservable
  Balance at assets observable inputs inputs
Description December 31, 2008 (Level 1) (Level 2) (Level 3)
 
Cash and cash equivalents $9,447  $9,447  $  $ 
Short-term investments  7,730         7,730 
   
ARS Rights (Note 2)  2,270         2,270 
   
Total $19,447  $9,447  $  $10,000 
   
The following table sets forth the change in estimated fair value for the Company’s auction rate securities (in thousands).
     
  Fair Value Measurement Using 
  Significant Unobservable Inputs 
  (Level 3) 
  Year Ended 
  December 31, 2008 
Beginning balance $ 
Transfers in to Level 3    
Auction rate securities  10,000 
ARS Rights  2,270 
Total realized/unrealized losses    
Included in net loss  (2,270)
Included in comprehensive loss   
Purchases, issuances and settlements   
    
Ending balance $10,000 
    
agreement.

F-15

F-12


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
4. Commitments3. Fair Value of Financial Instruments
Fair value is defined underThe ASC Topic of Fair Value Measurements and Disclosuresas the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value underThe ASC Topic of Fair Value Measurements and Disclosuresmust maximize the use of observable inputs and minimize the use of unobservable inputs. The standard describes a fair value hierarchy based on three levels of inputs, of which the first two are considered observable and the last unobservable, that may be used to measure fair value which are the following:
Level 1 — Quoted prices in active markets for identical assets or liabilities.
Level 2 — Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.
As of December 31, 2009, cash and cash equivalents were comprised of cash in checking accounts. The Company held no investments as of December 31, 2009.
As of December 31, 2008, cash and cash equivalents were comprised of short-term, highly liquid investments with maturities of 90 days or less from the date of purchase. Investments were comprised of available-for-sale securities recorded at estimated fair value determined using level 3 inputs. Unrealized gains and losses associated with the Company’s investments, if any, were reported in stockholders’ equity.
At December 31, 2008, short-term investments were comprised of $10,000,000 invested in auction rate securities, which were sold to UBS at par value in January 2009 pursuant to an Auction Rate Securities Agreement executed in November 2008.
Leases4. Development and Stock Purchase Agreements
In July 1992,On January 4, 2009, the Company entered into the Development Agreement with BioMarin CF, a non-cancelable operating leasewholly-owned subsidiary of BioMarin Pharma, granting BioMarin CF co-exclusive rights to develop and commercialize Riquent (and certain potential follow-on products) (collectively, “Riquent”) in the “Territory,” and the non-exclusive right to manufacture Riquent anywhere in the world. The “Territory” includes all countries of the world except the “Asia-Pacific Territory” (i.e., all countries of East Asia, Southeast Asia, South Asia, Australia, New Zealand, and other countries of Oceania).
Under the terms of the Development Agreement, BioMarin CF paid the Company a non-refundable commencement payment of $7,500,000 and, through BioMarin Pharma, paid $7,500,000 for a newly designated series of preferred stock (the “Series B-1 Preferred Stock”), pursuant to a related securities purchase agreement described more fully below. The stated amount paid for the rentalpreferred stock was $625,000 in excess of its research andfair value, such amount was accounted for as additional consideration paid for the development laboratories and clinical manufacturing facilities. In October 1996,arrangement.
Following the Company entered into an additional non-cancelable operating lease for additional office space. In 2004,futile results of the Company exercisedfirst interim efficacy analysis of Riquent received in February 2009, BioMarin CF elected not to exercise its optionsfull license rights to extend these leases until Julythe Riquent program under the Development Agreement. Thus, the Development Agreement between the parties terminated on March 27, 2009 in accordance with its terms. All rights to Riquent were returned to the Company. Accordingly, the $8,125,000 related to the Development Agreement was recorded as revenue in the quarter ended March 2009.
In October 2007, the Company entered into a capital lease agreement for $55,000 to finance the purchase of certain equipment. The agreement is secured by the equipment, bears interest at 10.00% per annum, and is payable in monthly installments of principal and interest of approximately $1,000 for 60 months.

F-16

F-13


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
In connection with the Development Agreement, the Company also entered into a securities purchase agreement, dated as of January 4, 2009 with BioMarin Pharma. In accordance with the terms of the agreement, on January 20, 2009, the Company sold 339,104 shares of Series B-1 Preferred Stock at a price per share of $22.1171 and received $7,500,000 which was in excess of the fair value of the preferred stock. On March 27, 2009, in connection with the termination of the Development Agreement, the Series B-1 Preferred Stock converted into 10,173,120 shares of Common Stock pursuant to the terms of the securities purchase agreement. The premium over the fair value of the stock issued of $625,000 was added to the value of the Development Agreement.
4.5. Commitments (continued)
Annual future minimumThe Company leased two adjacent buildings in San Diego, California covering a total of approximately 54,000 square feet. Both building leases expired in July 2009. Pursuant to one of the leases, the Company was responsible for completing modifications to the leased building prior to lease paymentsexpiration. In July 2009, approximately $315,000 was paid in accordance with the lease provisions upon lease expiration and exit of the buildings.
In addition, the Company early terminated its operating leases during the quarter ended June 30, 2009, and as a result paid a termination fee of $100,000 in September 2009. There were no material operating leases remaining as of December 31, 2008 are as follows (in thousands):
         
  Operating  Capital 
Years ended December 31, Leases  Leases 
 
2009 $491  $15 
2010  66   14 
2011  49   14 
2012  32   12 
2013 and there-after  19    
       
Total $657   55 
        
Less amount representing interest      (10)
        
Present value of net minimum lease payments      45 
Less current portion      (11)
        
Noncurrent portion of capital lease obligations     $34 
        
2009.
Rent expense under all operating leases totaled $900,000, $869,000,$590,000 and $1,065,000$900,000 for the years ended December 31, 2009 and 2008, 2007 and 2006, respectively. The Company held no equipment acquired under capital leases as of December 31, 2009. Equipment acquired under capital leases included in property and equipment as of December 31, 2008 totaled $43,000 (net of accumulated amortization of $12,000) and $54,000 (net of accumulated amortization of $1,000) at December 31, 2008 and 2007, respectively. Amortization expense associated with this equipment iswas included in depreciation and amortization expense.
The Company renewed certain of its liability insurance policies in March 2009 covering future periods.
Purchase Obligations6. Restructuring Costs
AsIn connection with the termination of December 31, 2008,the clinical trials for Riquent, the Company had total purchase obligationsceased all manufacturing and regulatory activities related to Riquent and initiated steps to significantly reduce its operating costs, including a reduction of force, resulting in the termination of 74 employees who received notification in February 2009 and were terminated in April 2009. The Company recorded a charge of approximately $1,290,000, which consisted of non-cancelable purchase commitments with third-party manufacturers of materials to be used$1,048,000 in the productionquarter ended March 31, 2009, of Riquent. Forwhich $668,000 was included in research and development and $380,000 was included in general and administrative expense. The $1,048,000 was paid in May 2009.
On December 4, 2009, the year ended December 31, 2008, approximately $459,000Company entered into Retention and Separation Agreements and General Release of All Claims (the “Retention Agreements”) with its two remaining officers (the “Remaining Officers”). The Retention Agreements supersede the severance provisions of the total purchase obligationsemployment agreements with the Remaining Officers that were effective prior to the signing of the Retention Agreements (the “Prior Employment Agreements”), but otherwise the terms of the Prior Employment Agreements remain in full force and effect. The Retention Agreements do not included in the Company’s consolidated financial statements. The Company intends to use its current financial resources to fund its obligations under these purchase commitments.
5. Credit Facility
In December 2008, the Company secured a credit facility (the “Credit Facility”) with UBS inalter the amount of $6,000,000, fully collateralized byseverance that was to be awarded under the Company’s auction rate securities. There was no net interest costPrior Employment Agreements, but rather changes the event that trigger such payments.
Pursuant to the Retention Agreements, on December 18, 2009 the Company paid a total of $269,000, less applicable withholding taxes, to the Remaining Officers (the “Retention Payments”). If the Remaining Officers voluntarily resigned their employment prior to the earlier to occur of (a) the closing of the Merger and (b) March 31, 2010, they were to immediately repay the Retention Payments to the Company. The date under (a) and (b) shall be referred to as the interest rate charged by UBS was contractually equal to the coupon rates“Separation Date.” The unearned portion of the auction rate securities. There were no costspaid Retention Payments, including related to the establishmentemployer taxes, of the Credit Facility. During December 2008, the Company drew the full $6,000,000 available under the Credit Facility, of which $5,933,000$222,000 was outstandingdeferred as of December 31, 2008. During January 2009, all2009.
Under the Retention Agreements, each of the Company’s auction rate securities were soldRemaining Officers agreed to UBS at par value of $10,000,000 pursuantexecute an amendment to the ARS Rights agreement, at which timeRetention Agreements (the “Amendment”) on or about the amount outstandingSeparation Date to extend and reaffirm the promises and covenants made by them in the Retention Agreements through the Separation Date. The Retention Agreements provided for severance payments totaling $538,000, less applicable withholding taxes (the “Severance Payments”) payable in a lump sum on the Credit Facility as of December 31, 2008 was settled in full andeighth day after the Credit Facility agreement was terminated (see Note 10).
6. Long-Term Debt
The following is a summary ofRemaining Officers signed the notes payable obligations that are secured by financed property and equipment of approximately $3,788,000 ($172,000 net of depreciation and 2008 impairment charges) as of December 31, 2008:
         
      Original 
      Note 
  Interest   Amount 
Date of Note Rate (%) Monthly Payments (in thousands) 
 
December 28, 2006 10.56 First 36 months at $8,000; last 12 months at $3,000  263 
June 28, 2007 10.82 First 36 months at $2,000; last 12 months at $500  75 
December 31, 2007 10.55 $6,000 for 48 months  236 
        
      $574 
        
Amendment.

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F-14


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
6. Long-Term Debt (continued)
Annual future minimum notes payable paymentsThe earned portion of the Severance Payments, including related employer taxes, of $94,000 was accrued as of December 31, 2008 are2009.
In April 2010, the Compensation Committee of the Board confirmed that pursuant to the terms of the Retention Agreements, the Retention Payments and Severance Payments were earned as follows (in thousands):
     
  Notes 
Years ended December 31, Payable 
 
2009 $177 
2010  127 
2011  69 
    
Total  373 
Less amount representing interest  (42)
    
Present value of net minimum notes payable payments  331 
Less current portion  (152)
    
Noncurrent portion of notes payable $179 
    
of March 31, 2010 and agreed that the existing employment terms would remain in effect beyond March 31, 2010. As an incentive to retain the current Named Executive Officers to pursue a strategic transaction such as a merger, license agreement, third party collaboration or wind down of the Company, the Compensation Committee also approved a retention bonus for a total of up to approximately $600,000, depending on the type of strategic transaction completed.
7. Settlement of Liabilities
During the year ended December 31, 2009, the Company negotiated settlements related to accounts payable obligations and accrued liabilities with a majority of its vendors. These negotiations resulted in reductions to accounts payable obligations and accrued liabilities from those amounts originally invoiced and accrued of approximately $2,743,000 for the year ended December 31, 2009, which were recorded as expense reductions upon the execution of the settlement agreements. As a result of these settlements, during the year ended December 31, 2009 there were decreases of $2,597,000 and $146,000 to research and development and general and administrative expenses, respectively.
In April 2009, the Company settled its notes payable obligations at face value. No notes payable obligations exist as of December 31, 2009.
8. Stockholders’ Equity
Preferred Stock
As of December 31, 2008,2009, the Company’s Board of Directors is authorized to issue 8,000,000 shares of preferred stock with a par value of $0.01 per share, in one or more series.
The Company’s Certificate of Designation filed with the Secretary of State of the State of Delaware designatesdesignated 500,000 shares of preferred stock as nonredeemable Series A Junior Participating Preferred Stock (“Series A Preferred Stock”). Pursuant to the terms ofStock. These shares were potentially issuable under the Company’s Stockholder Rights Plan, which was terminated in the event of liquidation, each share of Series A Preferred Stock is entitled to receive, subject to certain restrictions, a preferential liquidation payment of $10,000 per share plus the amount of accrued unpaid dividends. The Series A Preferred Stock is subject to certain anti-dilution adjustments, and the holder of each share is entitled to 10,000 votes, subject to adjustments. Cumulative quarterly dividends of the greater of $1.00 or, subject to certain adjustments, 10,000 times any dividend declared on shares of common stock, are payable when, as and if declared by the Board of Directors, from funds legally available for this purpose.
See Note 10 for discussion of preferred stock issued after December 31, 2008.September 2009.
Warrants
In connection with the December 2005 private placement, the Company issued warrants to purchase 4,399,992 shares of the Company’s common stock. The warrants were immediately exercisable upon grant, have an exercise price of $5.00 per share and remain exercisable for five years.
In connection with the May 2008 public offering, the Company issued warrants to purchase 3,903,708 shares of the Company’s common stock. The warrants were immediately exercisable upon grant, have an exercise price of $2.15 per share and remain exercisable for five years.
As of December 31, 2008,2009, all of the warrants were outstanding and 8,303,700 shares of common stock are reserved for issuance upon exercise of the warrants.
Restricted Stock
On December 14, 2005, the Company issued 83,518 shares of restricted stock to certain members of management in exchange for services provided over the vesting period, pursuant to certain retention agreements dated October 6, 2005. The shares of restricted stock fully vested (i.e., the restrictions lapsed) one year from the date of grant and were subject to repurchase by the Company until the one-year anniversary of the date of issuance. Pursuant to a separation agreement dated March 17, 2006, the Company’s repurchase right with respect to 29,120 shares of restricted stock granted to the former Chairman and Chief Executive Officer immediately lapsed upon his resignation on March 14, 2006. As such and in accordance with his retention agreement, the Company accelerated

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F-15


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
7. Stockholder’s Equity (continued)
the vesting of these shares of restricted stock. In addition, the remaining 54,398 shares of restricted stock fully vested on December 14, 2006, the one-year anniversary of the date of issuance, and therefore the Company’s repurchase right with respect to these shares of restricted stock has lapsed.
On March 15, 2006, the Company issued 20,000 shares of restricted stock to the new Chairman of the Board in exchange for services provided over the vesting period. The shares of restricted stock vested with respect to 10,000 shares six months after the issuance date and vested with respect to the remaining 10,000 shares upon the first anniversary of the issuance date. On September 15, 2006 and March 15, 2007, the vesting provisions with respect to the 20,000 shares of restricted stock were met and therefore the Company’s repurchase rights lapsed.
In both December 2006 and March 2007, the Company issued an additional 3,600 shares of restricted stock to the Chairman of the Board in accordance with the Chairman Compensation Policy approved by the Board of Directors on March 14, 2006 regarding tax liability associated with the restricted stock issued on March 15, 2006 and vested on September 15, 2006 and March 15, 2007. All of these additional shares of restricted stock immediately vested on the date of issuance.
There was no restricted stock issued in 2008.
In accordance with SFAS 123R, the Company recognized approximately $36,000, and $381,000, respectively, in compensation expense for the restricted stock grants noted above for the years ended December 31, 2007, and 2006, which includes compensation expense for the acceleration of vesting. There was no compensation expense related to restricted stock grants during the year ended December 31, 2008. The total fair value of the restricted stock grants vested in 2007 was approximately $77,000 of which approximately $41,000 was recognized in 2006 and approximately $36,000 was recognized in 2007. The total fair value of the restricted stock grants vested in 2006 was approximately $352,000 of which approximately $12,000 was recognized in 2005 and approximately $340,000 was recognized in 2006.
Stock Option Plans
In June 1994, the Company adopted the La Jolla Pharmaceutical Company 1994 Stock Incentive Plan (the “1994 Plan”) under which, as amended, 1,640,000 shares of common stock (post-reverse stock split) were authorized for issuance. The 1994 Plan expired in June 2004 and there were 748,612474,504 options outstanding under the 1994 Plan as of December 31, 2008.2009.
In May 2004, the Company adopted the La Jolla Pharmaceutical Company 2004 Equity Incentive Plan (the “2004 Plan”) under which, as amended, 6,400,000 shares of common stock (post-reverse stock split) have been authorized for issuance. The 2004 Plan provides for the grant of incentive and non-qualified stock options, as well as other share-based payment awards, to employees, directors, consultants and advisors of the Company with up to a 10-year contractual life and various vesting periods as determined by the Company’s compensation committee or the board of directors, as well as automatic fixed grants to non-employee directors of the Company. As of December 31, 2008,2009, there were a total of 4,878,3483,034,063 options outstanding and no unvested shares2,021,024 RSUs outstanding. As of restricted stock granted under the 2004 Plan and 1,242,432December 31, 2009, 1,065,694 shares remained available for future grant.grant under the 2004 Plan.
A summary of the Company’s stock option activity (including shares of restricted stock) and related data follows:
             
      Outstanding Options
  Options     Weighted-
  Available Number of Average
  For Grant Shares Exercise Price
   
Balance at December 31, 2005  3,190,231   2,148,028  $16.09 
Granted  (2,450,745)  2,450,745  $4.58 
Restricted stock granted  (23,600)      
Exercised     (56,012) $2.25 
Cancelled  240,382   (240,382) $14.04 

F-19


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
7. Stockholder’s Equity (continued)
             
      Outstanding Options
  Options     Weighted-
  Available Number of Average
  For Grant Shares Exercise Price
Expired  (100,983)    $26.39 
       
Balance at December 31, 2006  855,285   4,302,379  $9.83 
Additional shares authorized  840,000       
Granted  (1,027,973)  1,027,973  $4.30 
Restricted stock granted  (3,600)      
Exercised     (166,280) $3.01 
Cancelled  354,496   (354,496) $14.20 
Expired  (153,808)    $25.80 
       
Balance at December 31, 2007  864,400   4,809,576  $8.56 
Additional shares authorized  1,400,000       
Granted  (1,481,900)  1,481,900  $2.02 
Exercised     (1,097) $2.51 
Cancelled  663,418   (663,418) $8.91 
Expired  (203,486)    $19.80 
       
Balance at December 31, 2008  1,242,432   5,626,961  $6.80 
       
For the year ended December 31, 2008, options cancelled (included in the above table) consisted of approximately 459,932 options forfeited with a weighted-average exercise price of $4.09.
         
  Outstanding Options 
      Weighted- 
  Number of  Average 
  Shares  Exercise Price 
Balance at December 31, 2007  4,809,576  $8.56 
Granted  1,481,900  $2.02 
Exercised  (1,097) $2.51 
Forfeited / Expired  (663,418) $8.91 
        
Balance at December 31, 2008  5,626,961  $6.80 
Granted  691,875  $1.73 
Forfeited / Expired  (2,810,268) $5.31 
        
Balance at December 31, 2009  3,508,568  $6.99 
        
As of December 31, 2008,2009, options exercisable have a weighted-average remaining contractual term of 6.46.0 years. No stock option exercises occurred during the year ended December 31, 2009. The total intrinsic value of stock option exercises, which is the difference between the exercise price and closing price of the Company’s common stock on the date of exercise, during the yearsyear ended December 31, 2008 2007, and 2006 was $2,000, $500,000, and $74,000, respectively.$2,000. As of December 31, 20082009 and 2007,2008, the total intrinsic value, which is the difference between the exercise price and closing price of the Company’s common stock of options outstanding and exercisable, was $0 and $844,000, respectively.$0.
                                        
 Years Ended December 31,   Years Ended December 31, 
 2008 2007 2006 2009 2008 
 Weighted- Weighted- Weighted- Weighted- Weighted- 
 Average Average Average Average Average 
 Exercise Exercise Exercise Exercise Exercise 
 Options Price Options Price Options Price Options Price Options Price 
Exercisable at end of year 3,522,747 $9.08 2,808,588 $11.44 1,859,139 $16.27  3,175,233 $7.47 3,522,747 $9.08 
Weighted-average fair value of options granted during the year $1.70 $3.71 $3.92  $1.72 $1.70 

F-16


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
Exercise prices and weighted-average remaining contractual lives for the options outstanding (excluding shares of restricted stock) as of December 31, 20082009 were:
                             
              Weighted-         Weighted-
              Average         Average
              Remaining Weighted-     Exercise
              Contractual Average     Price of
Options Range of Life Exercise Options Options
Outstanding Exercise Prices (in years) Price Exercisable Exercisable
 
747,759 $0.64     $1.82   9.45  $1.66   9,821  $1.09 
786,614 $1.87     $2.42   8.38  $2.36   286,884  $2.34 
541,869 $3.06     $3.60   8.01  $3.13   288,869  $3.16 
667,678 $3.61     $4.44   7.37  $4.01   554,234  $4.03 
791,568     $4.46       7.29  $4.46   728,778  $4.46 
853,500 $4.60     $5.26   7.27  $5.24   592,750  $5.25 
664,395 $5.36     $14.85   6.68  $9.17   487,833  $10.46 
573,578 $15.70     $60.31   3.00  $29.09   573,578  $29.09 
                            
5,626,961 $0.64     $60.31   7.29  $6.80   3,522,747  $9.08 
                            

F-20


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
7. Stockholder’s Equity (continued)
                     
      Weighted-          Weighted- 
      Average          Average 
      Remaining  Weighted-      Exercise 
      Contractual  Average      Price of 
Options  Range of Life  Exercise  Options  Options 
Outstanding  Exercise Prices (in years)  Price  Exercisable  Exercisable 
 560,000  $0.64 – $1.82  8.71  $1.61   425,104  $1.67 
 539,498  $1.87 – $3.08  7.40  $2.60   374,393  $2.62 
 422,000  $3.23 – $3.99  6.52  $3.67   422,000  $3.67 
 475,105  $4.20 – $4.46  6.10  $4.36   475,105  $4.36 
 810,000  $5.26  6.20  $5.26   776,666  $5.26 
 356,094  $5.47 – $18.75  4.67  $11.11   356,094  $11.11 
 262,872  $19.00 – $35.25  2.24  $27.56   262,872  $27.56 
 15,999  $35.50  1.95  $35.50   15,999  $35.50 
 8,000  $36.75  1.13  $36.75   8,000  $36.75 
 58,999  $38.25  1.55  $38.25   58,999  $38.25 
                  
 3,508,567  $0.64 – $38.25  6.25  $6.99   3,175,232  $7.47 
                  
At December 31, 2008,2009, the Company has reserved 6,869,3934,574,261 shares of common stock for future issuance upon exercise of options granted or to be granted under the 1994 and 2004 Plans.
Restricted Stock Units
Under the 2004 Plan, the Company granted 2,021,024 RSUs to the Company’s three remaining employees on December 31, 2009, where each RSU represents a contingent right to receive one share of the Company’s common stock. The RSUs were to vest upon the closing of the Merger, subject to the continued employment of the recipient through the closing date of the Merger. As a result of the termination of the Merger in March 2010, the RSUs were cancelled.
Stock-based compensation cost of RSUs is measured by the market value of the Company’s common stock on the date of grant. The grant date intrinsic value of awards granted is amortized on a straight-line basis over the requisite service periods of the awards, which are the vesting periods. The weighted average grant date intrinsic value was $0.17 per RSU. No stock-based compensation expense related to these RSUs was recognized during 2009.
A summary of the Company’s RSU activity and related data follows:
         
      Weighted- 
      Average 
      Grant Date 
      Fair Value 
  Shares  per Share 
Restricted stock units outstanding at December 31, 2008    $ 
Granted  2,021,024  $0.17 
       
Restricted stock units outstanding at December 31, 2009  2,021,024  $0.17 
As of December 31, 2009, 2,021,024 shares of common stock are reserved for issuance upon vesting of the RSUs.

F-17


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
Employee Stock Purchase Plan
Effective August 1, 1995, the Company adopted the ESPP under which, as amended, 850,000 shares of common stock are reserved for sale to eligible employees, as defined in the ESPP. Employees may purchase common stock under the ESPP every three months (up to but not exceeding 10% of each employee’s base salary, or hourly compensation, and any cash bonus paid, subject to certain limitations) over the offering period at 85% of the fair market value of the common stock at specified dates. The offering period may not exceed 24 months. During the years ended December 31, 2008 and 2007, 303,937 and 97,104No shares of common stock were issued under the ESPP respectively.during the year ended December 31, 2009 and 303,937 shares of common stock were issued under the ESPP during the year ended December 31, 2008. As of December 31, 2008,2009, 833,023 shares of common stock have been issued under the ESPP and 16,977 shares of common stock are available for future issuance.
             
  Years Ended December 31,
  2008 2007 2006
Weighted-average fair value of Employee Stock Purchase Plan purchases $0.71  $1.47  $1.48 

F-21


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
7. Stockholder’s Equity (continued)
     
  Year Ended 
  December 31, 
  2008 
Weighted-average fair value of Employee Stock Purchase Plan purchases $0.71 
Stockholder Rights Plan
The Company hashad adopted a Stockholder Rights Plan (the “Rights Plan”), which was amended and restated in December 2008, and subsequently amended in January 2009 and terminated in September 2009. TheAmong other provisions, the Rights Plan providesprovided for a dividend of one right (a “Right”) to purchase fractions of shares of the Company’s Series A Preferred Stock for each share of the Company’s common stock. Under certain conditions involving an acquisition by any person or group of 15% or more of the common stock (or in the case of Grandfathered Persons, as defined in the Rights Plan, the acquisition of common stock in excess of the applicable Grandfathered Percentage, as defined in the Rights Plan; or, in the case of BioMarin, 15% or more of shares not issued under the securities purchase agreement between BioMarin and the Company), the Rights permit the holders (other than the 15% holder, or, in the case of Grandfathered Persons, as defined in the Rights Plan, the acquisition of common stock in excess of the applicable Grandfathered Percentage, as defined in the Rights Plan; or, in the case of BioMarin, 15% or more of shares issued under the securities purchase agreement between BioMarin and the Company) to purchase the Company’s common stock at a 50% discount upon payment of an exercise price of $30 per Right. In addition, in the event of certain business combinations, the Rights permit the purchase of the common stock of an acquirer at a 50% discount. Under certain conditions, the Rights may be redeemed by the Board of Directors in whole, but not in part, at a price of $0.001 per Right. The Rights have no voting privileges and are attached to and automatically trade with the Company’s common stock. The Rights expire on December 2, 2018.
8.9. 401(k) Plan
The Company has establishedhad a 401(k) defined contribution retirement plan (the “401(k) Plan”), which was amendedterminated in May 1999 to cover all employees. The 401(k) Plan was also amended in December 2003 to increase the voluntary employee contributions from a maximum of 20% to 50% of annual compensation (as defined). This increase was effective beginning January 1, 2004.March 2009. The Company doesdid not match employee contributions or otherwise contribute to the 401(k) Plan. In March 2009, the Company terminated the 401(k) Plan.
9.10. Income Taxes
The Company adopted the provisionsASC Topic of FASB Interpretation No. 48,Accounting for Uncertainty in Income Taxes —an Interpretation of FASB Statement No. 109 (“FIN 48”) on January 1, 2007. FIN 48 prescribes a recognition threshold and measurement attribute criteria for the financial statement recognition and measurement of tax positions taken or expected to be taken in a tax return. For those benefits to be recognized, a tax position must be more-likely-than-not to be sustained upon examination by taxing authorities. Upon implementation, the Company hadAn uncertain income tax position will not be recognized if it has less than a 50% likelihood of being sustained. There were no unrecognized tax benefits.benefits as of the date of adoption. As of December 31, 2009 and 2008, there are nothe total liability for unrecognized tax benefits was $45,000 and $0, respectively, and is included in current liabilities.
A reconciliation of the beginning and ending amounts of unrecognized tax benefits is as follows (in thousands):
     
  Amount 
Unrecognized tax benefits balance at December 31, 2008 $ 
Increases related to current and prior year tax positions  45 
Settlements and lapses in statutes of limitations   
    
Unrecognized tax benefits balance at December 31, 2009 $45 
    
Included in the balance sheetof unrecognized tax benefits at December 31, 2009 are $45,000 of tax benefits that, would, if recognized, would affect the Company’s effective tax rate.

F-18


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
The Company is subject to taxation in the United States and various state jurisdictions. The Company’s tax years for 19931995 and forward are subject to examination by the United States and California tax authorities due to the carry forward of unutilized net operating losses and research and development credits.

F-22


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
9. Income Taxes (continued)
The Company has not completed its Section 382/383 analysis regarding the limitation of net operating loss and research and development credit carryforwards. The Company does not presently plan to complete its Section 382/383 analysis and unless and until this analysis has been completed, the Company has removed the deferred tax assets for net operating losses and research and development credits generated through 20082009 from its deferred tax asset schedule and has recorded a corresponding decrease to its valuation allowanceallowance.
At December 31, 2008,2009, the Company had federal and California income tax net operating loss carryforwards of approximately $362,037,000$360,563,000 and $202,859,000,$223,465,000, respectively. The difference between the federal and California tax loss carryforwards is primarily attributable to the capitalization of research and development expenses for California income tax purposes. In addition, the Company has federal and California research and development tax credit carryforwards of $16,483,000$16,372,000 and $9,729,000,$10,050,000, respectively. The federal net operating loss, and research tax credit carryforwards will begin to expire in 2009 unless previously utilized. Theand California net operating loss carryforwards will begin to expire in 2010 unless previously utilized. The California research and development credit carryforwards will carry forward indefinitely until utilized. In February 2009, the Company experienced a change in ownership at a time when its enterprise value was minimal. As a result of this ownership change and the low enterprise value, the Company’s federal and California net operating loss carryforwards and federal research and development credit carryforwards as of December 31, 20082009 will be subject to limitation under IRC Section 382/383 and more likely than not will expire unused.
Significant components of the Company’s deferred tax assets as of December 31, 20082009 and 20072008 are listed below. A valuation allowance of $14,330,000$12,881,000 and $10,923,000$14,330,000 at December 31, 20082009 and 2007,2008, respectively, has been recognized to offset the net deferred tax assets as realization of such assets is uncertain. Amounts are shown in thousands as of December 31 of the respective years:years (in thousands):
        
 December 31,         
 2008 2007  December 31, 
   2009 2008 
Deferred tax assets:  
Net operating loss carryforwards $ $  $ $ 
Research and development credits      
Capitalized research and development and other 14,330 10,923  12,881 14,330 
       
Total deferred tax assets 14,330 10,923  12,881 14,330 
       
Net deferred tax assets 14,330 10,923  12,881 14,330 
Valuation allowance for deferred tax assets  (14,330)  (10,923)  (12,881)  (14,330)
       
Net deferred taxes $ $  $ $ 
       
10. Subsequent Events
Development and Stock Purchase Agreement
On January 4, 2009 (the “Effective Date”),Income taxes computed by applying the Company entered into a development and commercialization agreement (the “Development Agreement”) with BioMarin CF Limited (“BioMarin CF”), a wholly-owned subsidiary of BioMarin Pharmaceutical Inc. (“BioMarin Pharma”), granting BioMarin CF co-exclusive rightsU.S. Federal Statutory rates to develop and commercialize Riquent (and certain potential follow-on products) (collectively, “Riquent”)income from continuing operations before income taxes are reconciled to the provision for income taxes set forth in the “Territory,” and the non-exclusive right to manufacture Riquent anywhere in the world. The “Territory” includes all countriesstatement of the world except the “Asia-Pacific Territory” (i.e., all countries of East Asia, Southeast Asia, South Asia, Australia, New Zealand, and other countries of Oceania).operations as follows (in thousands):
Under the terms of the Development Agreement, BioMarin CF paid the Company a non-refundable commencement payment of $7,500,000 and purchased, through BioMarin Pharma, $7,500,000 of a newly designated series of preferred stock (the “Series B Preferred Stock”), pursuant to a securities purchase agreement described more fully below.
Following the futile results of the first interim efficacy analysis of Riquent, BioMarin CF has elected to not exercise its full license rights to the Riquent program under the Development Agreement. Thus, the Development Agreement between the parties terminated on March 27, 2009 in accordance with its terms. All rights to Riquent have been returned to the Company.
         
  2009  2008 
Tax benefit at statutory federal rate $(3,022) $(21,999)
State tax benefit, net of federal  (496)  (3,612)
Generation of research and development credits  (347)  (1,461)
Expired tax attributes  4,347   3,069 
Removal of net operating losses and research and development credits  767   19,696 
Stock compensation expense  281   733 
Other  (81)  166 
Change in valuation allowance  (1,449)  3,408 
       
  $  $ 
       

F-23


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
10. Subsequent Events (continued)
In connection with the Development Agreement, the Company also entered into a securities purchase agreement, dated as of January 4, 2009 (the “Purchase Agreement”) with BioMarin Pharma. In accordance with the terms of the agreement, on January 20, 2009, the Company sold 339,104 shares of Series B Preferred Stock at a price per share of $22.1171 for gross proceeds totaling $7,500,000. On March 27, 2009, in connection with the termination of the Development Agreement, the Series B Preferred Stock converted into 10,173,120 shares of Common Stock.
Auction Rate Securities
During January 2009, all of the Company’s auction rate securities were sold to UBS at par value of $10,000,000 pursuant to the ARS Rights agreement (see Note 2). Upon the sale of these auction rate securities, the amount outstanding on the Credit Facility agreement as of December 31, 2008 was settled in full and the Credit Facility was terminated.

F-24


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
10. Subsequent Events (continued)
Interim Efficacy Analysis Results and Restructuring Activities
In February 2009, the Company announced that an Independent Monitoring Board for the Riquent Phase 3 ASPEN study had completed the review of their first interim efficacy analysis of Riquent and determined that continuing the study was futile. The Company subsequently unblinded the data and found that there was no statistical difference in the primary endpoint, delaying time to renal flare, between the Riquent-treated group and the placebo-treated group, although there was a significant difference in the reduction of antibodies to double-stranded DNA. There were 56 renal flares in 587 patients treated with either 300-mg or 900-mg of Riquent, and 28 renal flares in 283 patients treated with placebo.
Based on these results, the Company immediately discontinued the Riquent Phase 3 ASPEN study and the further development of Riquent. The Company had previously devoted substantially all of its research, development and clinical efforts and financial resources toward the development of Riquent. In connection with the termination of the clinical trials for Riquent, the Company subsequently initiated steps to significantly reduce its operating costs, including a planned substantial reduction in personnel, which is expected to be effected early in the second quarter of 2009. The Company has also ceased the manufacture of Riquent at its facility in San Diego, California.

F-25F-19


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
11. Subsequent Events
On March 3, 2010, the Company and Adamis agreed to terminate the Merger Agreement as a result of the failure of the Company’s stockholders to vote in sufficient quantities for there to be a quorum to hold the stockholders’ meeting to approve the proposals related to the Merger. The solicitation of further votes was cancelled due to the Company’s delisting from Nasdaq.
As a result of the termination of the Merger with Adamis, the RSUs granted in December 2009 were cancelled in March 2010.
Effective at the open of business on March 4, 2010, the Company’s common stock was suspended and delisted from Nasdaq and began trading on The Pink OTC Markets, Inc. The delisting was the result of Nasdaq’s determination that the Company had nominal assets, other than cash, and had nominal operations.

F-20


La Jolla Pharmaceutical Company
Notes to Consolidated Financial Statements
12. Selected Quarterly Financial Data (unaudited)
The following is a summary of the unaudited quarterly results of operations for the years ended December 31, 20082009 and 20072008 (in thousands except per share amounts):
                                
 Quarters Ended Quarters Ended 
 Mar. 31, Jun. 30, Sept. 30, Dec. 31, 
2009
 
Revenue from collaborative agreement: $8,125 $ $ $ 
 
Expenses: 
Research and development 9,893  (85)  (240) 8 
General and administrative 2,487 2,124 992 1,590 
         
Total expenses 12,380 2,039 752 1,598 
         
 
Loss from operations  (4,255)  (2,039)  (752)  (1,598)
 
Interest and other income (expense), net 3  (4) 54  (43)
         
 
Net loss $(4,252) $(2,043) $(698) $(1,641)
         
 
Basic and diluted net loss per share $(0.08) $(0.03) $(0.01) $(0.02)
         
 
Shares used in computing basic and diluted net loss per share 56,115 65,723 65,723 65,723 
 Mar. 31, Jun. 30, Sept. 30, Dec. 31,         
   
2008
  
Expenses:  
Research and development $11,338 $12,732 $14,099 $12,856  $11,338 $12,732 $14,099 $12,856 
General and administrative 1,906 2,069 2,791 2,936  1,906 2,069 2,791 2,936 
Asset impairment 2,810  2,810 
           
Loss from operations  (13,244)  (14,801)  (16,890)  (18,602)  (13,244)  (14,801)  (16,890)  (18,602)
  
Interest income (expense), net  (393)  (134)  (244) 1,454   (393)  (134)  (244) 1,454 
           
  
Net loss $(13,637) $(14,935) $(17,134) $(17,148) $(13,637) $(14,935) $(17,134) $(17,148)
           
  
Basic and diluted net loss per share $(0.34) $(0.31) $(0.31) $(0.31) $(0.34) $(0.31) $(0.31) $(0.31)
           
  
Shares used in computing basic and diluted net loss per share 39,631 48,252 55,327 55,423  39,631 48,252 55,327 55,423 
           
 
2007
 
Expenses: 
Research and development $10,375 $12,186 $11,448 $12,626 
General and administrative 1,980 2,112 2,585 2,381 
  
Loss from operations  (12,355)  (14,298)  (14,033)  (15,007)
 
Interest income, net 485 781 744 607 
  
 
Net loss $(11,870) $(13,517) $(13,289) $(14,400)
  
 
Basic and diluted net loss per share $(0.36) $(0.34) $(0.34) $(0.36)
  
 
Shares used in computing basic and diluted net loss per share 32,737 39,256 39,577 39,607 
  

F-26

F-21


EXHIBIT INDEX
   
Exhibit Number Description
2.1Agreement and Plan of Reorganization, by and among La Jolla Pharmaceutical Company, Adamis Pharmaceuticals Corporation and Jewel Merger Sub, Inc., dated as of December 4, 2009 (16)
3.1 Restated Certificate of Incorporation (1)
   
3.2 Amended and Restated Bylaws (2)
   
3.3Certificate of Designations of Series A Junior Participating Preferred Stock (32)
  
4.1 Form of Common Stock Certificate (3)
   
4.2Rights Agreement, dated as of December 3, 1998, between the Company and American Stock Transfer &
Trust Company (4)
  
4.210.1 Amended and Restated Rights Agreement, dated as of December 2, 2008, between the Company and American Stock Transfer & Trust Company (4)
4.3Amendment No. 1 to Amended and Restated Rights Agreement, dated as of January 20, 2009 between the Company and American Stock Transfer & Trust Company (30)
10.1 Form of Indemnification Agreement (5)(4)*
   
10.2Industrial Real Estate Lease, effective July 27, 1992, by and between the Company and BRE Properties, Inc. (6)
  
10.310.2 First Amendment to Lease, dated March 15, 1993, by and between the Company and BRE Properties, Inc. (6)
10.4Second Amendment to Lease, dated July 18, 1994, by and between the Company and BRE Properties, Inc. (7)
10.5Third Amendment to Lease, dated January 26, 1995, by and between the Company and BRE Properties, Inc. (8)
10.6Fourth Amendment to Lease, dated July 8, 2004, by and between the Company and EOP-Industrial Portfolio, LLC (9)
10.7Building Lease Agreement, effective November 1, 1996, by and between the Company and WCB II-S BRD Limited Partnership (10)
10.8First Amendment to Lease, dated May 4, 2001, by and between the Company and Spieker Properties, L.P. (9)
10.9Second Amendment to Lease, dated July 8, 2004, by and between the Company and EOP-Industrial Portfolio, LLC (9)
10.10 La Jolla Pharmaceutical Company 1994 Stock Incentive Plan (Amended and Restated as of May 16, 2003) (11)(5)*


   
Exhibit Number10.3 Description
10.11 La Jolla Pharmaceutical Company 1995 Employee Stock Purchase Plan (Amended and Restated as of June 20, 2008)
(33) (6)*
   
10.1210.4 La Jolla Pharmaceutical Company 2004 Equity Incentive Plan (Amended and Restated as of June 20, 2008) (33)(6)*
   
10.1310.5 Form of Option Grant under the La Jolla Pharmaceutical Company 2004 Equity Incentive Plan (12)*
10.14Steven B. Engle Employment Agreement (6)*
   
10.15Amendment No. 1 to Steven B. Engle Employment Agreement (13)*
  
10.1610.6 Amendment No. 2 to Steven B. Engle Employment Agreement (14)*
10.17Amendment No. 3 to Steven B. Engle Employment Agreement (11)*
10.18Amended and Restated Employment Agreement, dated February 23, 2006, by and between the Company and Bruce Bennett, Jr. (1)*
10.19 Amended and Restated Employment Agreement, dated February 23, 2006, by and between the Company and Josefina Elchico (1)*
   
10.20Amended and Restated Employment Agreement, dated February 23, 2006, by and between the Company and Paul Jenn, Ph.D. (1)*
  
10.2110.7 Amended and Restated Employment Agreement, dated February 23, 2006, by and between the Company and Theodora Reilly (1)*
10.22 Amended and Restated Employment Agreement, dated February 23, 2006, by and between the Company and Gail Sloan (1)*
   
10.23Retention Agreement, dated October 6, 2005, by and between the Company and Steven B. Engle (15)*
  
10.2410.8Retention Agreement, dated October 6, 2005, by and between the Company and Matthew Linnik, Ph.D. (15)*
  
10.25Retention Agreement, dated October 6, 2005, by and between the Company and Bruce Bennett (15)*
10.26Retention Agreement, dated October 6, 2005, by and between the Company and Josefina T. Elchico (15)*
10.27Retention Agreement, dated October 6, 2005, by and between the Company and Paul Jenn, Ph.D. (15)*


Exhibit NumberDescription
10.28Retention Agreement, dated October 6, 2005, by and between the Company and Theodora Reilly (15)*
10.29Retention Agreement, dated October 6, 2005, by and between the Company and Gail Sloan (15)*
10.30Retention Agreement, dated October 6, 2005, by and between the Company and Andrew Wiseman, Ph.D. (15)*
10.31Retention Agreement, dated October 6, 2005, by and between the Company and Lisa Koch (24)*
10.32Master Security Agreement, effective as of September 6, 2002, by and between the Company and General Electric Capital Corporation (17)
10.33Promissory Note, dated as of December 28, 2006, by and between the Company and General Electric Capital
Corporation (23)
10.34Promissory Note, dated as of September 28, 2004, by and between the Company and General Electric Capital
Corporation (18)
10.35Promissory Note, dated as June 25, 2004, between the Company and General Electric Capital Corporation (9)


Exhibit NumberDescription
10.36Promissory Note, dated as March 31, 2003, between the Company and General Electric Capital Corporation (19)
10.37Promissory Note, dated as of December 18, 2003, between the Company and General Electric Capital Corporation (20)
10.38Promissory Note, dated as of September 26, 2003, between the Company and General Electric Capital Corporation (16)
10.39Promissory Note, dated as of June 27, 2003, between the Company and General Electric Capital Corporation (11)
10.40Promissory Note, dated as of April 23, 2003, between the Company and General Electric Capital Corporation (21)
10.41Promissory Note, dated as of December 30, 2002, between the Company and General Electric Capital Corporation (21)
10.42Amendment to Promissory Note, dated as of September 27, 2002, by and between the Company and General Electric Capital Corporation (17)
10.43Promissory Note, dated as of September 26, 2002, by and between the Company and General Electric Capital
Corporation (17)
10.44Chief Executive Officer Employment Agreement, dated March 15, 2006, by and between the Company and Deirdre Y. Gillespie, M.D. (22)(7)*
   
10.45Separation Agreement, dated March 17, 2006, by and between the Company and Steven B. Engle (22)*
  
10.4610.9 Employment Offer Letter, dated July 10, 2006 and executed July 14, 2006, by and between the Company and Michael Tansey, M.D. (25)(8)*
   
10.4710.10 Employment Agreement, dated December 4, 2006, by and between the Company and Michael Tansey, M.D. (23)(9)*
   
10.48Underwriting Agreement, dated as of March 29, 2007, between the Company and Needham & Company, LLC and A.G. Edwards & Sons, Inc. (29)
  
10.4910.11 Executive Employment Agreement, dated May 10, 2007, by and between the Company and Niv Caviar (27)(10)*
   
10.50Promissory Note, dated as of June 28, 2007, between the Company and General Electric Capital Corporation (6)
  
10.5110.12 First Amendment to Chief Executive Officer Employment Agreement, (6)dated July 31, 2007, by and between the Company and Deirdre Y. Gillespie (11)*
   
10.52Promissory Note, dated as of December 31, 2007, between the Company and General Electric Capital Corporation (31)
  
10.5310.13 Employment Agreement,Offer Letter, dated March 4, 2008, by and between the Company and Luke Seikkula (28)(12)*
   
10.5410.14 Underwriting Agreement, dated as of May 6, 2008, between the Company and UBS Securities, LLC and Canaccord Adams, Inc. (34)(13)
   
10.5510.15 Form of Warrant Agreement (34)(13)

F-22


   
10.56Exhibit Number ReservedDescription
 10.16 
10.57 Employment Agreement,Offer Letter, dated March 4, 2008, by and between the Company and Lisa Koch-Hulle **(14)*
   
10.5810.17 First Amendment to Executive Employment Agreement, dated December 24, 2008, by and between the Company and Gail Sloan.*(14)*
   
10.5910.18 First Amendment to Executive Officer Employment Agreement, dated December 24, 2008, by and between the Company and Niv Caviar.*(14)*
   
10.6010.19 First Amendment to Employment Agreement,Offer Letter, dated December 26, 2008, by and between the Company and Vicki Motte.*(14)*
   
10.6110.20 First Amendment to Employment Agreement,Offer Letter, dated December 26, 2008, by and between the Company and Luke Seikkula.*(14)*
   
10.6210.21 First Amendment to Executive Employment Agreement, dated December 29, 2008, by and between the Company and Josefina Elchico.*(14)*
   
10.6310.22 First Amendment to Employment Agreement,Offer Letter, dated December 29, 2008, by and between the Company and Lisa Koch-Hulle.*(14)*
   
10.6410.23 First Amendment to Executive Employment Agreement, dated December 30, 2008, by and between the Company and Michael Tansey.*(14)*
   
10.6510.24 FirstSecond Amendment to Chief Executive Officer Employment Agreement, dated December 31, 2008, by and between the Company and Deirdre Gillespie.*(14)*
   


10.25Development and Commercialization Agreement, dated as of January 4, 2009, by and between the Company and BioMarin CF Limited (15)†
   
Exhibit Number10.26 DescriptionSecurities Purchase Agreement, dated as of January 4, 2009, by and between the Company and BioMarin Pharmaceutical Inc.(15)†
10.27Amendment No. 1 to Development and Commercialization Agreement, dated as of January 4, 2009, by and between the Company and BioMarin CF Limited (15)
10.28Amendment No. 1 to Securities Purchase Agreement, dated as of January 4, 2009, by and between the Company and BioMarin Pharmaceutical Inc.(15)
10.29Retention and Separation Agreement and General Release of All Claims, dated December 4, 2009, by and between the Company and Deirdre Y. Gillespie, M.D. (16)*
10.30Retention and Separation Agreement and General Release of All Claims, dated December 4, 2009, by and between the Company and Gail A. Sloan (16)*
10.31Form of Voting Agreement (16)
21.1 Subsidiaries of La Jolla Pharmaceutical Company (12)**
   
23.1 Consent of Independent Registered Public Accounting Firm **
   
31.1 Certification Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 **
   
31.2 Certification Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 **
   
32.1 Certification Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 **
 
* This exhibit is a management contract or compensatory plan or arrangement.

F-23


 
** Filed herewith.
Confidential treatment for certain provisions of this exhibit.
 
(1) Previously filed with the Company’s Current Report on Form 8-K filed March 1, 2006 and incorporated by reference herein.
 
(2) Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2000 and incorporated by reference herein.
 
(3) Previously filed with the Company’s Registration Statement on Form S-3 (Registration No. 333-131246) filed January 24, 2006 and incorporated by reference herein.


(4)Previously filed with the Company’s Current Report on Form 8-K filed December 4, 2008 and incorporated by reference herein.
 
(5)(4) Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2005 and incorporated by reference herein.
 
(6)Previously filed with the Company’s Registration Statement on Form S-1 (Registration No. 33-76480) filed June 3, 1994 and incorporated by reference herein.
(7)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 1994 and incorporated by reference herein.
(8)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 1995 and incorporated by reference herein.
(9)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2004 and incorporated by reference herein.
(10)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 1996 and incorporated by reference herein.
(11)(5) Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2003 and incorporated by reference herein.
 
(12)(6) Previously filed with the Company’s Annual ReportRegistration Statement on Form 10-K for the year ended December 31, 2004S-8 (Registration No. 333-151825) filed June 20, 2008 and incorporated by reference herein.
 
(13)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 1997 and incorporated by reference herein.
(14)Previously filed with the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 1999 and incorporated by reference herein.
(15)Previously filed with the Company’s Current Report on Form 8-K filed October 7, 2005 and incorporated by reference herein.


(16)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2003 and incorporated by reference herein.
(17)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2002 and incorporated by reference herein.
(18)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2004 and incorporated by reference herein.
(19)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2004 and incorporated by reference herein.
(20)Previously filed with the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2003 and incorporated by reference herein.
(21)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2003 and incorporated by reference herein.
(22)(7) Previously filed with the Company’s Current Report on Form 8-K filed March 20, 2006 and incorporated by reference herein.
 
(23)(8)Previously filed with the Company’s Current Report on Form 8-K filed July 18, 2006 and incorporated by reference herein.
(9) Previously filed with the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2006 and incorporated by reference herein.
 
(24)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2006 and incorporated by reference herein.
(25)Previously filed with the Company’s Current Report on Form 8-K filed July 18, 2006 and incorporated by reference herein.
(26)Previously filed with the Company’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2007 and incorporated by reference herein.
(27)(10) Previously filed with the Company’s Current Report on Form 8-K filed May 10, 2007 and incorporated by reference herein.
 
(28)(11)Previously filed with the Company’s Registration Statement on Form S-1 (Registration No. 33-76480) filed June 3, 1994 and incorporated by reference herein.
(12) Previously filed with the Company’s Current Report on Form 8-K filed March 4, 2008 and incorporated by reference herein.
 
(29)Previously filed with the Company’s Current Report on Form 8-K filed March 30, 2007 and incorporated by reference herein.


(30)Previously filed with the Company’s Registration Statement on Form 8-A (Registration No. 000-24274) filed January 26, 2009 and incorporated by reference herein.
(31)Previously filed with the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2007 and incorporated by reference herein.
(32)Previously filed with the Company’s Current Report on Form 8-A12G filed December 4, 2008 and incorporated by reference herein.
(33)Previously filed with the Company’s Registration Statement on Form S-8 (Registration No. 333-151825) filed June 20, 2008 and incorporated by reference herein.
(34)(13) Previously filed with the Company’s Current Report on Form 8-K filed May 7, 2008 and incorporated by reference herein.
(14)Previously filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2008 and incorporated by reference herein.
(15)Previously file with the Company’s Quarterly Report on Form 10-Q for the quarter ended March 31, 2009 and incorporated by reference herein.
(16)Previously filed with the Company’s Current Report on Form 8-K filed on December 7, 2009 and incorporated by reference herein.

 

F-23