(ACHN) Initiation of ACH-3422 Dosing in HCV-Infected Patients

Initial cohort of HCV-infected patients begin dosing with ACH-3422 for seven days

Clinical trials may continue evaluating 200 mg of sovaprevir for HCV-infected patients

Timelines for reporting proof-of-concept results with ACH-3422, a proprietary uridine-analog nucleotide polymerase inhibitor, during the fall of 2014 and initiating all-oral combination studies by the end of 2014 remain on track

NEW HAVEN, Conn., June 10, 2014  — Achillion Pharmaceuticals, Inc. (Nasdaq:ACHN) today announced the Company has begun dosing ACH-3422, a uridine-analog nucleotide polymerase inhibitor, for seven days in patients with genotype 1 chronic hepatitis C viral infection (HCV) in its ongoing Phase 1 clinical trial. Proof-of-concept results from this trial are expected to be reported during the fall of 2014. Furthermore, Achillion announced today that the U.S. Food and Drug Administration (FDA) has removed the clinical hold on sovaprevir, an NS3/4A protease inhibitor, to permit the conduct of trials in patients with HCV. Sovaprevir doses of 200 mg once daily, the previously evaluated dose that was well-tolerated with clinical activity in two completed Phase 2 studies, may be used in additional therapeutic clinical trials.

“We believe Achillion is uniquely positioned with clinical candidates in each of the nucleotide, NS5A and protease inhibitor categories needed to advance both dual and triple commercially competitive combination therapies that can treat the spectrum of patients with HCV. We remain focused on developing regimens utilizing ACH-3422 and ACH-3102, our second-generation Phase 2 NS5A inhibitor, and the second half of 2014 will feature multiple milestones in that program,” commented Milind Deshpande, Ph.D., President and Chief Executive Officer. “Our HCV pipeline also provides the opportunity to add a NS3/4A protease inhibitor, such as sovaprevir or ACH-2684, in order to explore triple-direct acting antiviral regimens that can potentially shorten treatment durations to less than 8 weeks. We will determine how best to integrate our protease inhibitors into our combination development programs as data from our on-going trials emerge.”

“With the start of patient dosing with ACH-3422, our Phase 1 uridine-analog nucleotide, we remain on track to report proof-of-concept results in the fall, and plan on initiating all oral combination studies with ACH-3422 by the end of 2014. We are also very pleased that the effort by the Achillion team, working in collaboration with the FDA, has resulted in this response for the sovaprevir program,” commented David Apelian, M.D., Ph.D., Executive Vice President and Chief Medical Officer.

Sovaprevir is a Phase 2 NS3/4A protease inhibitor being developed for the potential treatment of chronic HCV infection. To date, approximately 550 subjects have been exposed to sovaprevir with clinical activity reported in two Phase 2 12-week treatment duration studies, one in combination with pegylated-interferon/ribavirin and one in combination with ACH-3102 in which the combination achieved 100% SVR12 in patients with genotype 1b HCV. The FDA removed the clinical hold to permit the conduct of therapeutic trials with a maximum of 200 mg once daily of sovaprevir in HCV patients and in single dose trials in healthy volunteers, but maintained a partial clinical hold for multiple dose studies that may be conducted in healthy volunteers, requiring prior review and approval of the protocol by the FDA. Achillion expects to continue to work collaboratively with the FDA on the continued clinical development of sovaprevir.

About HCV

The hepatitis C virus is the most common cause of viral hepatitis, which is an inflammation of the liver. It is currently estimated that more than 150 million people are infected with HCV worldwide including more than 5 million people in the United States. Three-fourths of the HCV patient population is undiagnosed; it is a silent epidemic and a major global health threat. Chronic hepatitis, if left untreated, can lead to permanent liver damage that can result in the development of liver cancer, liver failure or death. Few therapeutic options currently exist for the treatment of HCV infection.

About Achillion Pharmaceuticals

Achillion is an innovative pharmaceutical company dedicated to bringing important new treatments to patients with infectious disease. Achillion’s discovery, clinical development, and commercial teams have advanced multiple novel product candidates with proven mechanisms of action into studies and toward the market. Achillion is focused on solutions for the most challenging problems in infectious disease including HCV and resistant bacterial infections. For more information on Achillion Pharmaceuticals, please visit www.achillion.com or call 1-203-624-7000.

Cautionary Note Regarding Forward-Looking Statements

This press release includes forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995 that are subject to risks, uncertainties and other important factors that could cause actual results to differ materially from those indicated by such forward-looking statements, including statements with respect to: the Company’s expectations that the phase I study of ACH-3422 will inform the potential initiation of combination studies of ACH-3422 and ACH-3102; the Company’s expectations that it may report preliminary results from its Phase 1 program during the fall of 2014 and begin combination studies by the end of 2014; the Company’s goal to safely and expeditiously advance its all-oral regimens for the treatment of HCV and its expectation that the breadth of its portfolio could enable it to potentially develop commercially-competitive regimens that can be safe, effective, ribavirin-free and that can be used for eight weeks or less to potentially cure HCV. Achillion may use words such as “expect,” “anticipate,” “project,” “intend,” “plan,” “aim,” “believe,” “seek,” ” estimate,” “can,” “focus,” “will,” and “may” and similar expressions to identify such forward-looking statements. Among the important factors that could cause actual results to differ materially from those indicated by such forward-looking statements are risks relating to, among other things Achillion’s ability to: demonstrate in any current and future clinical trials the requisite safety, efficacy and combinability of its drug candidates; advance the preclinical and clinical development of its drug candidates, including ACH-3422, ACH-3102 and its protease inhibitors, under the timelines it projects in current and future clinical trials; satisfactorily respond to the partial clinical hold placed on sovaprevir by the FDA; obtain and maintain necessary regulatory approvals; obtain and maintain patent protection for its drug candidates and the freedom to operate under third party intellectual property; establish commercial manufacturing arrangements; identify, enter into and maintain collaboration agreements with appropriate third-parties; compete successfully with other companies that are seeking to develop improved therapies for the treatment of HCV; manage expenses; manage litigation; raise the substantial additional capital needed to achieve its business objectives; and successfully execute on its business strategies. These and other risks are described in the reports filed by Achillion with the U.S. Securities and Exchange Commission, including its Annual Report on Form 10-K for the year ended December 31, 2013, and its subsequent SEC filings.

In addition, any forward-looking statement in this press release represents Achillion’s views only as of the date of this press release and should not be relied upon as representing its views as of any subsequent date. Achillion disclaims any duty to update any forward-looking statement, except as required by applicable law.

CONTACT: Company Contact:
         Glenn Schulman
         Achillion Pharmaceuticals, Inc.
         Tel. (203) 624-7000
         gschulman@achillion.com

         Media:
         Emily Johnson
         Ogilvy PR
         Tel. (212) 880-5316
         emily.johnson@ogilvy.com

         Investors:
         Mary Kay Fenton
         Achillion Pharmaceuticals, Inc.
         Tel. (203) 624-7000
         mfenton@achillion.com

         Investors:
         Tricia Truehart
         The Trout Group, LLC
         Tel. (646) 378-2953
         ttruehart@troutgroup.com