Alnylam Pharmaceuticals Reports Second Quarter 2012 Financial Results

Alnylam Pharmaceuticals Reports Second Quarter 2012 Financial Results

Alnylam Pharmaceuticals, Inc.

. (Nasdaq: ALNY), a leading RNAi therapeutics company, today reported its consolidated financial results for the second quarter 2012, and company highlights.

“This was an exceptional quarter and recent period for Alnylam, where we reported positive clinical data from several RNAi therapeutic programs. Within our ‘Alnylam 5x15’ product efforts, we showed that ALN-TTR02 achieves rapid, dose-dependent, durable, and specific knockdown of serum transthyretin - the disease causing protein in transthyretin-mediated amyloidosis - after just a single dose. Specifically, we showed transthyretin knockdown of up to 94% with a nearly 80% level of suppression sustained at one month. We believe these data document an unprecedented level of clinical activity for RNAi therapeutics and serve as an important industry milestone in the advancement of this new class of medicines to patients,” said John Maraganore, Ph.D., Chief Executive Officer of Alnylam. “We also reported encouraging clinical data from our Phase I ALN-PCS trial showing statistically significant and durable knockdown of plasma PCSK9 of up to 84% and lowering of LDL cholesterol of up to 50%. Further, we presented key pre-clinical proof of concept data for ALN-AT3, an RNAi therapeutic targeting antithrombin for the treatment of hemophilia, which employs our conjugate delivery platform enabling subcutaneous dose administration. In aggregate, these important accomplishments give us great confidence in the continued execution of our ‘Alnylam 5x15’ product strategy focused on advancement of RNAi therapeutics toward genetically defined targets for diseases where there are limited treatment options for patients and caregivers.”

“In addition to the important advancements made with our ‘Alnylam 5x15’ programs, we also made notable progress with our partnered RNAi therapeutic programs. We reported top-line results from our Phase IIb trial with ALN-RSV01 - an inhaled RNAi therapeutic for the treatment of respiratory syncytial virus infection in lung transplant patients - which we believe provide important evidence for clinical efficacy toward new or progressive bronchiolitis obliterans syndrome, an irreversible and life-threatening complication of infection in these patients. We look forward to presenting additional data from our ALN-RSV01 study and discussing our results with U.S. and European regulatory authorities,” said Barry Greene, President and Chief Operating Officer of Alnylam. “In addition, we are very pleased to have formed a strategic collaboration with Ascletis, a Chinese biopharmaceutical company, for the continued advancement of ALN-VSP, our RNAi therapeutic program for the treatment of liver cancer that has completed a positive Phase I study. We look forward to working with Ascletis in their efforts to advance this medicine into Phase II trials.”

At June 30, 2012, Alnylam had cash, cash equivalents and total marketable securities of $292.8 million, as compared to $260.8 million at December 31, 2011.

The net loss according to accounting principles generally accepted in the U.S. (GAAP) for the second quarter of 2012 was $13.0 million, or $0.25 per share on both a basic and diluted basis (including $3.1 million, or $0.06 per share of non-cash stock-based compensation expense), as compared to a net loss of $13.8 million, or $0.33 per share on both a basic and diluted basis (including $4.2 million, or $0.10 per share of non-cash stock-based compensation expense), for the same period in the previous year.

Revenues were $20.9 million for the second quarter of 2012, as compared to $20.6 million for the same period last year. Revenues for the second quarter of 2012 included $14.0 million of collaboration revenues related to the company’s alliance with Roche (which assigned its rights and obligations to Arrowhead Research Corporation during 2011), $5.5 million of revenues from the company’s alliance with Takeda Pharmaceuticals Company Limited, and $1.4 million of expense reimbursement, amortization, and/or license fee revenues from Cubist Pharmaceuticals, Inc., InterfeRx™, research reagent and services licensees, and other sources.

Research and development (R&D) expenses were $21.7 million in the second quarter of 2012, which included $2.0 million of non-cash stock-based compensation, as compared to $25.3 million in the second quarter of 2011, which included $2.8 million of non-cash stock-based compensation. The decrease in R&D expenses in the second quarter of 2012 as compared to the prior year period was due primarily to lower clinical trial and manufacturing expenses related to the company’s ALN-RSV and ALN-VSP programs, partially offset by additional expenses related to the advancement of the company’s ALN-TTR program. In addition, external services expenses decreased, due primarily to lower pre-clinical expenses for the company’s ALN-TTR and ALN-PCS programs which were advanced further in the clinic. Compensation and related expenses also decreased due primarily to the reduction in workforce in connection with Alnylam’s January 2012 strategic corporate restructuring. Partially offsetting these decreases were license fees due to certain entities related to drug delivery-related and platform technologies. Alnylam expects R&D expenses will remain consistent for the remainder of 2012.

General and administrative (G&A) expenses were $11.2 million in the second quarter of 2012, which included $1.1 million of non-cash stock-based compensation, as compared to $8.4 million in the second quarter of 2011, which included $1.4 million of non-cash stock-based compensation. The increase in G&A expenses for the second quarter of 2012 as compared to the prior year period was due primarily to an increase in consulting and professional services related to business and legal activities. Alnylam expects G&A expenses will remain consistent for the remainder of 2012.

Equity in loss of joint venture was $1.1 million and $1.0 million for the second quarter of 2012 and 2011, respectively, related to our share of the net losses incurred by Regulus.

Interest income was $0.3 million for the second quarter of 2012 and 2011.

Alnylam expects that its cash, cash equivalents and total marketable securities balance will be greater than $250 million at December 31, 2012.

“Alnylam continues to maintain a solid financial profile, ending the second quarter with approximately $293 million in cash,” said Michael Mason, Vice President, Finance and Treasurer of Alnylam. “We believe we will end 2012 with greater than $250 million in cash, which will continue to provide us with a strong balance sheet as we advance our RNAi therapeutics through clinical trials and toward the market.”

Management will provide an update on the company, discuss second quarter 2012 results, and discuss expectations for the future via conference call on Monday, August 6, 2012 at 4:30 p.m. ET. A corporate slide presentation will also be available on the News & Investors page of the company’s website, , to accompany the conference call. To access the call, please dial 866-383-8008 (domestic) or 617-597-5341 (international) five minutes prior to the start time and provide the passcode 97579609. A replay of the call will be available beginning at 6:30 p.m. ET on Monday, August 6, 2012. To access the replay, please dial 888-286-8010 (domestic) or 617-801-6888 (international), and provide the passcode 83717981.

A live audio webcast of the call will also be available on the News & Investors page of the company’s website, . An archived webcast will be available on the Alnylam website approximately two hours after the event.

RNAi (RNA interference) is a revolution in biology, representing a breakthrough in understanding how genes are turned on and off in cells, and a completely new approach to drug discovery and development. Its discovery has been heralded as “a major scientific breakthrough that happens once every decade or so,” and represents one of the most promising and rapidly advancing frontiers in biology and drug discovery today which was awarded the 2006 Nobel Prize for Physiology or Medicine. RNAi is a natural process of gene silencing that occurs in organisms ranging from plants to mammals. By harnessing the natural biological process of RNAi occurring in our cells, the creation of a major new class of medicines, known as RNAi therapeutics, is on the horizon. Small interfering RNA (siRNA), the molecules that mediate RNAi and comprise Alnylam’s RNAi therapeutic platform, target the cause of diseases by potently silencing specific mRNAs, thereby preventing disease-causing proteins from being made. RNAi therapeutics have the potential to treat disease and help patients in a fundamentally new way.

Alnylam is a biopharmaceutical company developing novel therapeutics based on RNA interference, or RNAi. The company is leading the translation of RNAi as a new class of innovative medicines with a core focus on RNAi therapeutics for the treatment of genetically defined diseases, including ALN-TTR for the treatment of transthyretin-mediated amyloidosis (ATTR), ALN-AT3 for the treatment of hemophilia, ALN-PCS for the treatment of severe hypercholesterolemia, ALN-HPN for the treatment of refractory anemia, and ALN-TMP for the treatment of hemoglobinopathies. As part of its “Alnylam 5x15” strategy, the company expects to have five RNAi therapeutic products for genetically defined diseases in clinical development, including programs in advanced stages, on its own or with a partner by the end of 2015. Alnylam has additional partnered programs in clinical or development stages, including ALN-RSV01 for the treatment of respiratory syncytial virus (RSV) infection, ALN-VSP for the treatment of liver cancers, and ALN-HTT for the treatment of Huntington’s disease. The company’s leadership position on RNAi therapeutics and intellectual property have enabled it to form major alliances with leading companies including Merck, Medtronic, Novartis, Biogen Idec, Roche, Takeda, Kyowa Hakko Kirin, Cubist, and Ascletis. In addition, Alnylam and Isis co-founded Regulus Therapeutics Inc., a company focused on discovery, development, and commercialization of microRNA therapeutics; Regulus has formed partnerships with GlaxoSmithKline and Sanofi. Alnylam has also formed Alnylam Biotherapeutics, a division of the company focused on the development of RNAi technologies for applications in biologics manufacturing, including recombinant proteins and monoclonal antibodies. Alnylam’s VaxiRNA™ platform applies RNAi technology to improve the manufacturing processes for vaccines; GlaxoSmithKline is a collaborator in this effort. Alnylam scientists and collaborators have published their research on RNAi therapeutics in over 100 peer-reviewed papers, including many in the world’s top scientific journals such as , , , and . Founded in 2002, Alnylam maintains headquarters in Cambridge, Massachusetts. For more information, please visit .

The “Alnylam 5x15” strategy, launched in January 2011, establishes a path for development and commercialization of novel RNAi therapeutics to address genetically defined diseases with high unmet medical need. Products arising from this initiative share several key characteristics including: a genetically defined target and disease; the potential to have a major impact in a high unmet need population; the ability to leverage the existing Alnylam RNAi delivery platform; the opportunity to monitor an early biomarker in Phase I clinical trials for human proof of concept; and the existence of clinically relevant endpoints for the filing of a new drug application (NDA) with a focused patient database and possible accelerated paths for commercialization. By the end of 2015, the company expects to have five such RNAi therapeutic programs in clinical development, including programs in advanced stages, on its own or with a partner. The “Alnylam 5x15” programs include ALN-TTR for the treatment of transthyretin-mediated amyloidosis (ATTR), ALN-AT3 for the treatment of hemophilia, ALN-PCS for the treatment of severe hypercholesterolemia, ALN-HPN for the treatment of refractory anemia, and ALN-TMP for the treatment of hemoglobinopathies. Alnylam intends to focus on developing and commercializing certain programs from this product strategy itself in the United States and potentially certain other countries; the company will seek development and commercial alliances for other core programs both in the United States and in other global territories.

Various statements in this release concerning Alnylam’s future expectations, plans and prospects, including without limitation, Alnylam’s expectations regarding its “Alnylam 5x15” product strategy, Alnylam’s views with respect to the potential for RNAi therapeutics, including ALN-TTR02 and ALN-TTRsc, ALN-AT3, ALN-PCS, ALN-VSP and ALN-RSV01, its expectations with respect to the timing and success of its clinical and pre-clinical trials, the expected timing of regulatory filings, including its plan to file IND or IND equivalent applications and initiate clinical trials for ALN-TTR02, ALN-TTRsc and ALN-AT3, its expectations regarding reporting data from its clinical studies, including its ALN-RSV01 study, its plans to seek collaborations for its ALN-PCS program, its expectations regarding the continued development of ALN-VSP in China and the rest of the world, the possibility of Alnylam receiving future milestones and royalties from Ascletis based on the development and commercialization of ALN-VSP in the Ascletis territory, and its expected cash position as of December 31, 2012, constitute forward-looking statements for the purposes of the safe harbor provisions under The Private Securities Litigation Reform Act of 1995. Actual results may differ materially from those indicated by these forward-looking statements as a result of various important factors, including, without limitation, risks and uncertainties related to Alnylam’s ability to successfully implement its strategic corporate restructuring and workforce reduction plan and achieve the estimated cost savings, the impact of the workforce reduction on Alnylam’s business, the ability of Alnylam to attract and retain qualified personnel, Alnylam’s ability to manage operating expenses, Alnylam’s ability to discover and develop novel drug candidates and delivery approaches, successfully demonstrate the efficacy and safety of its drug candidates, the pre-clinical and clinical results for its product candidates, which may not support further development of product candidates, actions of regulatory agencies, which may affect the initiation, timing and progress of clinical trials, obtaining, maintaining and protecting intellectual property, Alnylam’s ability to enforce its patents against infringers and defend its patent portfolio against challenges from third parties, obtaining regulatory approval for products, competition from others using technology similar to Alnylam’s and others developing products for similar uses, Alnylam’s ability to obtain additional funding to support its business activities and establish and maintain strategic business alliances and new business initiatives, Alnylam’s dependence on third parties for development, manufacture, marketing, sales and distribution of products, the outcome of litigation, and unexpected expenditures, as well as those risks more fully discussed in the “Risk Factors” section of its most recent quarterly report on Form 10-Q on file with the Securities and Exchange Commission. In addition, any forward-looking statements represent Alnylam’s views only as of today and should not be relied upon as representing its views as of any subsequent date. Alnylam explicitly disclaims any obligation to update any forward-looking statements.

This selected financial information should be read in conjunction with the consolidated financial statements and notes thereto included in Alnylam’s Annual Report on Form 10-K which includes the audited financial statements for the year ended December 31, 2011.

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