(ACHN) 100% Sustained Virologic Response Rate, Ribavirin-Free ACH-3102 and Sofosbuvir

Achillion to Begin a Six Week Treatment Regimen With Its Second-Generation NS5A Inhibitor ACH-3102 and Sofosbuvir

NEW HAVEN, Conn., Aug. 15, 2014  — Achillion Pharmaceuticals, Inc. (Nasdaq:ACHN) today announced interim results from an ongoing Phase 2 proxy study evaluating ACH-3102, Achillion’s second-generation NS5A inhibitor, in combination with sofosbuvir, without ribavirin, for eight weeks of treatment in patients with treatment-naïve genotype 1 chronic hepatitis C virus (HCV) infection. Of the 12 patients treated, 100 percent (n=12/12) remained HCV RNA undetectable four weeks after completing therapy (SVR4). Based upon these results, 12 additional patients will begin treatment with six weeks of once daily ACH-3102 and sofosbuvir.

“ACH-3102 continues to demonstrate good safety and tolerability through three Phase 2 studies. We believe these studies also confirm a differentiated efficacy profile for an NS5A inhibitor. Achieving 100% SVR4 with eight weeks of treatment with sofosbuvir serving as a nucleotide proxy indicate that dosing 50 mg once daily of ACH-3102 plus a nucleotide inhibitor has the potential to achieve commercially competitive results for curing HCV in a short duration, ribavirin-free doublet,” commented David Apelian, M.D., Ph.D., Executive Vice President and Chief Medical Officer at Achillion. “In addition, understanding how ACH-3102 performs with sofosbuvir provides valuable insight for the design of our proprietary combination trial with ACH-3102 and ACH-3422, a uridine-analog nucleotide that continues to advance through its Phase 1 clinical development program.”

Milind Deshpande, Ph.D., President and Chief Executive Officer of Achillion commented, “As we continue to achieve clinical milestones, we remain focused on execution of the broader clinical development strategy for our HCV portfolio. We expect that Phase 1 proof-of-concept results with ACH-3422 will be reported during the fall of this year, which we anticipate will lead to the start of a Phase 2 combination program to evaluate our proprietary doublet regimen for an eight week, or potentially shorter, treatment regimen for HCV that will begin before the end of 2014.”

ACH-3102 – 017: Phase 2 pilot study evaluating eight week treatment in combination with sofosbuvir for genotype 1 treatment-naïve HCV

Achillion is conducting a Phase 2, open-label, randomized, partial-crossover study to evaluate the efficacy, safety, and tolerability of eight weeks or six weeks of ACH-3102 and sofosbuvir, a marketed nucleotide polymerase inhibitor, without ribavirin, in treatment-naïve genotype 1 HCV-infected patients. The primary objective of the study is determination of sustained viral response 12 weeks (SVR12) after the completion of therapy. Eighteen patients were enrolled, including six observational patients. Twelve patients completed eight weeks of treatment consisting of 50 mg of ACH-3102 and 400 mg of sofosbuvir administered once daily while observational patients received no drug during this phase of the trial. Ten of the 12 patients receiving eight weeks of treatment had genotype 1a HCV with median HCV RNA at baseline of 7.22 log₁₀ (range 5.5 – 7.8 log₁₀). No on-treatment viral breakthrough or post-treatment viral relapse has been observed to date. ACH-3102 and sofosbuvir were well tolerated with no significant adverse events, ECG findings, or lab abnormalities observed during treatment.

Following achievement of the pre-specified response rate of 100 percent, the six observational patients plus six additional patients will be enrolled and receive six weeks of treatment consisting of 50 mg of ACH-3102 and 400 mg of sofosbuvir administered once daily. Achillion anticipates that SVR4 results from the crossover cohort will be reported by the end of 2014.

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.

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 1 study of ACH-3422 could 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; the Company’s plan to initiate a Phase 2 combination study of ACH-3422 with ACH-3102 by year-end 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 sovaprevir, under the timelines it projects in current and future clinical trials; 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:
         Laurie Masonson
         Ogilvy PR
         Tel. (917)459-6164
         laurie.masonson@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