Company’s Proprietary Complement Platform Focuses on Advancing Factor D Inhibitor Drug Candidates That Could Treat Ultra-Rare Diseases Such as Paroxysmal Nocturnal Hemoglobinuria (PNH) and Other Complement-Mediated Diseases

NEW HAVEN, CT, USA I February 11, 2016 I Achillion Pharmaceuticals, Inc. (Nasdaq:ACHN) today announced the initiation of a phase 1 study with ACH-4471, the Company’s first orally-administered, highly potent and specific small molecule that has been shown to inhibit complement factor D. The phase 1 study is being conducted in healthy volunteers and is evaluating single ascending doses of ACH-4471 to assess safety, tolerability, pharmacokinetics (PK) and pharmacodynamics (PD). The Company expects to report interim clinical data from this study during the second quarter of 2016.

“We believe our molecular-level understanding of factor D, based upon proprietary high-resolution x-ray structures, has enabled us to design ACH-4471 with the potential to be the first orally-bioavailable, highly differentiated treatment for PNH and other ultra-rare diseases. We look forward to advancing ACH-4471, with the goal of demonstrating its safety, tolerability, proof-of-mechanism and working to establish its potential benefit for patients,” commented Milind Deshpande, Ph.D., President and Chief Executive Officer.

Dr. Deshpande further stated, “In addition to ACH-4471, we have developed a substantial library of complement factor D inhibitors and are now working to advance distinct small molecule candidates with traits appropriate for ophthalmic administration, to potentially treat dry AMD, and for inhalation, in order to address respiratory indications such as COPD.”

ACH-4471 Phase 1 Healthy Volunteer Development Program

The initial phase 1 trial is a randomized, placebo-controlled, single-ascending dose study of ACH-4471 administered to healthy volunteers. Approximately 28 subjects are expected to be enrolled. The primary endpoint for the trial is evaluation of safety and tolerability. Secondary endpoints include assessments of PK, PD, and evaluation of alternative pathway inhibition in ex vivo laboratory assessments of blood samples from subjects in order to establish a PK/PD relationship for ACH-4471. Interim study results are anticipated during the second quarter of 2016. In addition, a second phase 1 study evaluating multiple-ascending doses in healthy volunteers is expected to be initiated in the second quarter of 2016 with interim results anticipated during the third quarter of 2016.

About Complement Factor D Platform

Achillion has leveraged its internal discovery capabilities and a novel complement-related platform to develop drug candidates that are oral inhibitors of complement factor D. Factor D is an essential serine protease involved in the complement pathway, a part of the innate immune system. Achillion’s complement platform is focused on seeking to advance compounds that inhibit factor D, can be orally-administered, and can potentially be used in the treatment of immune-related diseases in which complement plays a critical role. Potential indications being evaluated for these compounds include paroxysmal nocturnal hemoglobinuria (PNH), atypical hemolytic uremic syndrome (aHUS), dry age-related macular degeneration (dry AMD), and chronic obstructive pulmonary disease (COPD). Achillion anticipates that its platform could play a role in addressing the needs of all PNH patients, including patients who have suboptimal response to, or fail to respond to, the currently available treatments, as well as for patients suffering from other alternative pathway complement-mediated diseases. Achillion nominated ACH-4471 for clinical development in December 2015, and initiated clinical development in February 2016 with a phase 1 healthy volunteer trial assessing single-ascending doses of ACH-4471.

About Achillion Pharmaceuticals

Achillion Pharmaceuticals, Inc. (NASDAQ:ACHN) is a science-driven, patient-focused company seeking to leverage its strengths across the continuum from discovery to commercialization in its goal of providing better treatments for people with serious diseases. The company employs a highly-disciplined discovery and development approach that has allowed it to pursue best-in-class oral antiviral therapy for chronic hepatitis C (HCV) and build a platform of potent and specific complement inhibitors. Achillion is rapidly advancing its efforts to become a fully-integrated pharmaceutical company with a goal of bringing life-saving medicines to patients with rare diseases. More information is available at http://www.achillion.com.

SOURCE: Achillion Pharmaceuticals