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Achillion Pipeline Update<br />

May 30, 2013<br />

1


Forward-Looking Statements<br />

This presentation includes forward-looking statements about Achillion Pharmaceuticals, Inc.<br />

and its business, including, without limitation, statements regarding drug discovery, clinical<br />

development, regulatory approval processes, market opportunities, intellectual property,<br />

competition, and financial results. All statements other than statements relating to historical<br />

matters (including statements to the effect that we “believe,” “expect,” “anticipate,” “plan,”<br />

“target,” “intend” and similar expressions) should be considered forward-looking statements.<br />

These forward looking statements are subject to risks and uncertainties that may cause<br />

actual events or results to differ materially from our current expectations. These risks and<br />

uncertainties are detailed in the "Risk Factors" section of our annual report on Form 10-K for<br />

the year ended December 31, 2012, which was filed with the SEC on February 20, 2013.<br />

All forward-looking statements contained in this presentation speak only as of the date<br />

hereof, and we undertake no obligation to update any of these statements, except as<br />

required by law.<br />

2


Experienced Management Team<br />

Milind Deshpande, Ph.D.<br />

President, Chief Executive Officer<br />

Gautam Shah, Ph.D.<br />

EVP, Chief Regulatory Officer<br />

Mary Kay Fenton<br />

SVP, Chief Financial Officer<br />

Joseph Truitt<br />

SVP, Chief Commercial Officer<br />

David Apelian, MD., Ph.D.<br />

EVP, Chief Medical Officer<br />

TICE Life Sciences<br />

Built on more than 130 years of health science experience.<br />

3


Achillion Pharmaceuticals<br />

HCV Development Portfolio Snapshot<br />

Focused on developing best-in-class compounds and combinations<br />

to form cornerstones of future DAA combinations<br />

Discovery<br />

NS3 Protease Inhibitor Program<br />

Sovaprevir (ACH-1625)<br />

ACH-2684<br />

2 nd Gen NS5A Inhibitor Program<br />

ACH-3102<br />

NS5B Polymerase Program<br />

ACH-3422<br />

Combination Development Program<br />

Sovaprevir / ACH-3102 ± rbv<br />

Preclinical Phase 1 Phase 2<br />

Phase 3<br />

4


HCV Therapeutics: Target Profiles<br />

Sovaprevir ACH-3102<br />

ACH-3422<br />

Mechanism of Action NS3 Protease Inhibitor NS5A Inhibitor NS5B Polymerase Inhibitor<br />

Genotype coverage GT 1 - 6 GT 1 - 6 GT 1 - 6<br />

Barrier to resistance<br />

No emergence of ontreatment<br />

PI resistant<br />

mutations seen to date<br />

Higher barrier to<br />

resistance<br />

High barrier to resistance<br />

Combination with DAAs Additive to synergistic Additive to synergistic Additive to synergistic<br />

Safety High safety margins High safety margins<br />

Efficacy (monotherapy) >3 log 10 drop<br />

>3 log 10 drop<br />

(picomolar potency)<br />

Safe through 14-day<br />

animal studies to date<br />

Dosing schedule QD without boosting QD QD<br />

Safety and tolerability<br />

Superior to<br />

1st-generation PIs<br />

Superior to<br />

1st-generation PIs<br />

Abbreviations: DAA, direct-acting antiviral; GT, HCV genotype; PI, protease inhibitor; QD, once daily.<br />

TBD<br />

TBD<br />

5


Sovaprevir + ACH-3102<br />

Phase 2: Combination Development Program<br />

2013 2014<br />

1Q 2Q 3Q 4Q 1Q 2Q 3Q<br />

• All trials evaluating<br />

sovaprevir and ACH-3102<br />

• Phase 2 program will have<br />

treated over 400 patients by<br />

3Q14<br />

007- IIa<br />

Gt 1a/b treatment-naïve<br />

(n = 30-50)<br />

No rbv 8/12 wk<br />

(n = TBD)<br />

• First study results expected in<br />

summer 2013<br />

Graphical representation.<br />

Does not indicate specific dates within each quarter<br />

Apollo-C IIb Trial<br />

Worldwide (+rbv)<br />

Gt 1a/b tx-naïve<br />

(n = ~200)<br />

HIV co-infected trial<br />

Gt 1a/b treatment-naïve<br />

(n = TBD)<br />

Non-genotype 1 trial<br />

Gt 2, 3, 4 treatment-naïve<br />

(n = TBD)<br />

Cirrhotic Trial<br />

Compensated cirrhosis<br />

(n = TBD)<br />

6


Sovaprevir + ACH-3102 +/- RBV<br />

Phase 2a: -007 Study Overview<br />

Segment 1<br />

Segment 2<br />

RVR EOT<br />

Treatment naive, GT1<br />

N = 15 (10 active/5 placebo)<br />

Sovaprevir (200) + 3102 (150/50) + RBV<br />

Treatment naive, GT1<br />

N = 15 (10 active/5 placebo)<br />

Sovaprevir (400) + 3102 (150/50) + RBV<br />

Treatment naive, GT1<br />

N = TBD<br />

Sovaprevir (TBD) + 3102 (TBD) + RBV<br />

Follow-up<br />

Week 0 Week 4<br />

Week 12<br />

Week 24<br />

• Randomized, double-blind, placebo-controlled, GT1a/1b balanced<br />

• Determine efficacy including RVR, ETR and SVR<br />

• WW study being conducted in the US, Canada, Australia, and NZ<br />

• RVR results anticipated during 3Q13 and SVR during 4Q13<br />

SVR 4<br />

Follow-up<br />

Follow-up<br />

SVR 12<br />

7


NS5B Polymerase Inhibitor<br />

ACH-3422<br />

8


ACH-3422<br />

NS5B Polymerase Nucleotide Inhibitor<br />

• ACH-3422 is a nucleotide prodrug of uridine analog<br />

• Virology<br />

– Specific for HCV polymerase<br />

– Highly potent (EC 50 : GT 1a 65nM, GT 1b 50 nM, GT 2a 85 nM)<br />

– Highly specific for HCV<br />

– Pan-genotypic activity with a high barrier to resistance<br />

• PK and Metabolism<br />

– Rapid conversion of prodrug to monophosphate in microsomes and<br />

in hepatocytes<br />

– PK profiles suggests once-daily (QD) dosing<br />

• Safety<br />

– 14-day animal tox completed<br />

– High exposure of triphosphate in liver<br />

– No significant findings at the highest dose tested<br />

9


ACH-3422<br />

Preclinical Profile<br />

• Potent anti-HCV activity<br />

Inhibitor EC 50 (uM)<br />

• Specific for inhibition of HCV<br />

• Moderate shift in EC 50 in presence of S282T mutation<br />

in NS5B polymerase<br />

– ACH-3422: 5.7-fold shift<br />

– Sofosbuvir: 7.6-fold shift<br />

GT-1b GT-1a GT-2a (JFH-1)<br />

ACH-3422 0.05 0.065 0.085<br />

Sofosbuvir 0.15 0.24 0.091<br />

10


ACH-3422<br />

Preclinical Profile<br />

• Rapid conversion of prodrug to monophosphate in<br />

microsomes and in hepatocytes<br />

• Conversion of ACH-3422 to corresponding<br />

triphosphate is comparable to the conversion of<br />

sofosbuvir to triphosphate<br />

– Human hepatocytes/24 h incubation<br />

Inhibitor Parent<br />

Triphosphate<br />

(uM)<br />

Triphosphate<br />

(% of 20uM dose)<br />

ACH-3422 ND 5.15 26<br />

Sofosbuvir ND 5.84 29<br />

11


ACH-3422<br />

Preclinical Profile<br />

• Potent in vitro NS5B polymerase inhibition<br />

• Minimal in vitro cytotoxicity<br />

Inhibitor<br />

Inhibitor<br />

IC 50 (uM)<br />

[ 32 P]-CTP [ 32 P]-UTP<br />

ACH-3422-TP 1.15 1.45<br />

Sofosbuvir-TP 1.58 1.11<br />

CC 50 (uM)<br />

HeLa HepG2 Huh-7 CEMss Hepatocytes<br />

(rat)<br />

Hepatocytes<br />

(monkey)<br />

ACH-3422 >50 13.6 32 52 48 88<br />

12


Capitalization and Liquidity<br />

Balance Sheet Metrics As of 3/31/2013<br />

Cash and equivalents $200.9 million<br />

Debt obligations $0.6 million<br />

Shares outstanding 96.6 million<br />

Top 5 Shareholders *<br />

Fidelity Management & Research 13.2 million (13%)<br />

QVT Funds 11 million (11%)<br />

Domain Partners 5.8 million (6%)<br />

BlackRock Fund Advisors 5.1 million (5%)<br />

Vanguard Group 4.0 million (4%)<br />

* Based upon most recent SEC filings and confirmed positions<br />

13


HCV Development Strategy<br />

• Strategic portfolio that aims to provide optimal<br />

outcomes and treatment duration for all HCV patients<br />

• -007 sova/ACH-3102/rbv 12-wk combination trial for<br />

GT 1 ongoing with interim results anticipated 3Q13<br />

• Modifying existing studies in order to evaluate 8-wk<br />

and 12-wk treatment regimens without rbv expected<br />

to begin summer 2013<br />

• Continue to accelerate development program with<br />

keen focus on initiating Phase 3 in 2H 2014<br />

• Advancing nucleotide NS5B polymerase inhibitor<br />

toward IND 1Q14<br />

14


Achillion Pharmaceuticals, Inc.<br />

NASDAQ: <strong>ACHN</strong><br />

15

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