Idenix Pharmaceuticals Building a Leading Antiviral Franchise

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Idenix Pharmaceuticals Building a Leading Antiviral Franchise Cowen and Company 7 th Annual Global Healthcare Conference November 7, 2006 Jean-Pierre Sommadossi, Ph.D. Chairman and CEO

Safe Harbor This presentation includes forward-looking statements about Idenix and its business, including without limitation, statements regarding drug discovery, research and clinical development, regulatory approval processes and commercialization activities. These forwardlooking statements are subject to risks and uncertainties that may cause actual events or results to differ materially from our current expectations. These risks and uncertainties are detailed in our filings with the Securities and Exchange Commission. All forward-looking statements speak only as of the date of this presentation and, except as required by law, we undertake no obligation to update such statements. 2 2

Idenix Building a Leading Antiviral Franchise Mission Alliance Discover, develop and commercialize innovative antiviral drugs addressing unmet medical needs in large and growing markets Novartis global alliance enhances commercial and financial position Products 1 U.S. approved product, a robust pipeline of HBV, HCV, and HIV antiviral candidates Global Structure More than 270 employees Financial Position Strong cash position, no debt 3 3

Idenix/Novartis Strategic Alliance Landmark Biotech/Pharma Deal Consummated in May 2003 Equity purchase Novartis currently holds 56% of Idenix Maintained equity position through IPO and follow-on offering Standstill until May 2008 2 of 9 board seats License Agreement First right of refusal to Idenix pipeline Terms for any licensed product Novartis fully funds development from point of license forward License fees, regulatory milestones and sales milestones Co-promotion and profit split in U.S. and 5 major E.U. countries for all licensed products In ROW, payments to Idenix based on product sales 4 4

Alliance Economics Licensed Drug Candidates Hepatitis B Licensed telbivudine and valtorcitabine in May 2003 $110 million in potential licensing fees and regulatory milestone payments Upfront licensing payment of $75 million Up to $35 million in regulatory milestones Hepatitis C Licensed valopicitabine (NM283) in March 2006 $550 in potential license fees and regulatory milestone payments $25 million milestone received June 2004 Up to $70 million in license fees ($25 million paid in March 2006, remainder due upon initiation of phase III trials in U.S.) Up to $455 million in regulatory milestones 5 5

Building a Leading Antiviral Franchise Indication Program Preclinical Phase I Phase II Phase III NDA / U.S. Approval HBV Tyzeka (telbivudine) Valtorcitabine (val-ldc) Valopicitabine HCV (NM283) NV-08 HIV IDX-989 IDX-899 90% of antiviral nucleosides with successful Phase I/II results have led to NDA approval 1 6 1. International Antiviral News Vol.7, No.7 and Vol.8 No.1 (01/00) 6

Hepatitis B Program

TYZEKA TM Building a Commercial Franchise Approved in U.S., Switzerland, India, Brazil and Peru Pending regulatory decisions in key worldwide markets Launches expected soon thereafter Brand names TYZEKA TM in the U.S. SEBIVO in the rest of the world Pre-launch preparations underway U.S. operations in place E.U. operations being built Comprehensive data set available for telbivudine Extensive preclinical data Phase I-IIb clinical data and clinical pharmacology studies 2-year GLOBE data, 1-year adefovir switch/comparative data, 6-month lamivudine switch data now available 8 8

TYZEKA TM Ready for U.S. Launch Competitive product profile Idenix/Novartis alliance is aligned and focused on execution We are prepared for launch Best-in-class sales team recruited, trained, equipped and ready Marketing plans complete with brand positioning, messaging and launch platform developed to support TYZEKA launch U.S. KOL community informed, engaged and supportive Tools and tactics are defined and on track for launch Phase IIIb/IV plan is in place and on-going Operational infrastructure built or contracted Product availability quickly after approval Distribution infrastructure in place Plans for product availability within 30 days Access plans for TYZEKA are in place Managed care formulary access tactics designed to support product adoption Comprehensive reimbursement tools will support access to TYZEKA 9 9

Tyzeka Comprehensive Profile at Launch Demonstrated Antiviral Superiority to Lamivudine and Adefovir Trial GLOBE Study Phase III Registration Trial Decomp Phase III Telbivudine vs. Adefovir Phase IIIb Lamivudine Switch Phase IIIb Design Telbivudine vs. lamivudine, in patients with compensated chronic hepatitis B 1,367 patients from 20 countries Two-year study, with primary endpoint at one year of treatment 240 patients with decompensated cirrhosis Two-year study 120 HBeAg-positive patients One-year study, H-H and switching components Primary endpoint at 6 months of treatment 240 HBeAg+ and HBeAg- patients who have received 3-12 months of lamivudine, randomized to continue lamivudine or switch to telbivudine One-year study Status Telbivudine was superior to lamivudine on all key virologic endpoints at one and two years Achieved superiority on primary therapeutic response endpoint in E+ patients, non-inferiority in E- patients and year one and superior in both at year two Worldwide regulatory applications submitted based on one-year data Over 190 patients enrolled, trial ongoing Fully enrolled, ongoing Telbivudine was superior to adefovir at 6 months Patients switched to telbivudine from adefovir at 24 weeks of therapy achieved marked reductions in HBV DNA by week 52 Fully enrolled, ongoing Six-month data demonstrated a benefit of switching patients from lamivudine to telbivudine 10 10

Strong Growth Driven by Novel Antiviral Therapies Global HBV Antiviral Sales Forecast (USD millions) 1,500 2,000 Anti-virals: Lamivudine Adefovir Entecavir Telbivudine Other anti-virals Key Market Drivers 2006 2010 Launch of more potent therapies Significant expansion of diagnosed/treated patient population Increased use of combination therapy 300 2004 2010 2015 11 Source: IMS, Decision Resources 11

12 HBV Nucleoside U.S. Market Strong Market Growth 7,000 6,000 5,000 Hepsera Epivir-HBV Baraclude Total Nucleoside 4,000 3,000 2,000 1,000 0 12 Total Rx Nov-02 Aug-02 May-03 Feb-03 Nov-03 Aug-03 Nov-06 Aug-06 May-06 Feb-06 Nov-05 Aug-05 May-05 Feb-05 Nov-04 Aug-04 May-04 Feb-04 Source: IMS Weekly Oral Nucleoside Rx Data through October 2006

Comprehensive HBV Development Program Valtorcitabine Second Drug Candidate for the Treatment of HBV Being developed as a fixed-dose combination with telbivudine for those patients for whom treatment with a single agent may not be adequate Preclinical data demonstrated synergy between two agents Currently in ongoing 48-week phase IIb proof-of-concept clinical trial in combination with telbivudine Phase III go/no-go decision will be made in 2007 based on phase IIb data 13 13

Hepatitis C Program

Chronic HCV Market Innovation Proven to Drive Market Expansion 3500 50% 3000 Global HCV Market Sustained Viral Response Rate Pegylated Interferon + RBV 42-46% Interferon + RBV 40% 2500 33-36% Global Sales ($MM) 2000 1500 1000 Interferon 48 Weeks 20% Interferon 24 Weeks 12% 30% 20% SVR Rate (Genotype 1) 10% 500 0 0% 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 15 Sources: Schering-Plough Quarterly Reports, Hoffman La Roche Quarterly Reports, InterMune Quarterly Reports Credit Suisse First Boston: Hepatitis C Market-Competition Intensifies, March 2003 Pockros, P.J. Developments in the treatment of chronic hepatitis C. Expert Opinion on Investigational Drugs 11(4) 515-528, 2002 15

Comparisons Between HCV and HIV Similarities Both are RNA viruses discovered in the 1980s Both replicate and mutate rapidly Vaccines do not exist for either Rapid emergence of resistance has been demonstrated with monotherapy Targets for drugs in development overlap Protease inhibitors (nucleosides, non-nucleosides) Polymerase inhibitors Differences HIV is a retrovirus and integrates; HCV is a flavivirus and doesn t integrate HIV treatment is a long-term chronic therapy cannot eliminate integrated HIV with any therapy HCV treatment today is 48 weeks or shorter (dependent on genotype) no integrants or other stable viral forms, virus can be eliminated with successful treatment 16 Sources: World Health Organization Hepatitis C Fact Sheet NIH: HIV and AIDS: An Overview NIAID Fact Sheet; Brown, et. al., Scope of Worldwide Hepatitis C Problem. Liver Transplantation. November 2003 Food and Drug Administration HIV/AIDS Timeline accessed at www.fda.gov 16

Potential Evolution of HCV Therapy for Genotype 1 Small Molecules will be Added in an Effort to Improve SVR Rates Estimated 60-70% ate R R SV Interferon Estimated 85-90% 42-50% Peg-Interferon +/10% Ribavirin OR Nucleoside polymerase Inhibitor +/- 1st Stage 1989-1998 Protease Inhibitor Other Direct Antivirals All Oral Therapy 17 Estimated 85-90% 35% +/+/- 6th Stage 2015+ 2nd Stage 1998-2001 3rd Stage 2001 - present 4th Stage 2009-2010 5th Stage 2011-2015 17

Valopicitabine (NM283) Clinical Development First-in-Class Polymerase Inhibitor Current Development Status Two Phase IIb trials Treatment-naïve patients Treatment-refractory patients Drug-Drug Interaction study Primary PK/PD endpoint at day 36, study will continue to week 12 followed by 36 weeks of standard of care 90 treatment-naïve patients, 3 arms: 200 mg/d NM283 + peg 200 mg/d NM283 + peg + weightbased dosing of RBV placebo + peg + weight-based dosing of RBV Path Forward Idenix will continue to gain additional safety and efficacy data from ongoing phase IIb trials and drug-drug interaction study Define optimal dosing regimen and phase III development plan Evaluate additional populations HCV/HIV co-infected patients Valopicitabine is an investigational compound for the treatment of hepatitis C that is currently being evaluated in ongoing clinical trials. The most commonly occurring adverse events are gastrointestinal side effects. 18 18

Absolute HCV RNA to Week 24 Valopicitabine Phase IIb Treatment-Naïve Study Mean log 10 Absolute HCV RNA (IU/mL) 7 6 5 4 3 2 1 peg-ifnα initiated arms A-D NM283 initiated in arm A NM283 dose reduction Week 24 HCV RNA Change from Baseline: A (400-800 mg @D29) = -4.17 (n= 34) B (200 mg @D1) = -4.24 (n= 34) C (400-800 mg @D1) = -4.24 (n= 34) D (800 mg @D1) = -4.56 (n= 36) E (800 mg) = -3.90 (n= 35) Amplicor LLOQ (<600 IU/mL) TaqMan LLOD (<20 IU/mL) 19 0 0 4 8 12 16 20 24 Week 19

Week 12 and 24 HCV RNA Responses Valopicitabine Phase IIb Treatment-Naïve Study Mean from Baseline (log 10 IU/mL) Amplicor LLOQ <600 IU/mL (%) TaqMan LLOD <20 IU/mL (%) Group n Wk 12 n Wk 24 Wk 12 Wk 24 Wk 12 Wk 24 A 34-4.10 34-4.17 68 74 59 62 B 34-3.86 34-4.24 68 71 44 68 C 34-4.11 34-4.24 74 71 44 59 D 36-4.55 36-4.56 81 81 67 67 E 35-4.04 35-3.90 69 63 54 49 C+D+E* 105-4.24 105-4.24 74 71 55 58 *Pooled Data from 3 NM283 800 mg arms ITT Analysis; missing data imputed to Week 24 using Last Observation Carried Forward (LOCF) 20 20

Building the Pipeline

HIV Discovery Program NNRTI clinical candidates selected based on: Antiviral potency Lack of cross resistance with other currently approved NNRTIs Favorable pharmacological properties in a variety of animal species Two lead candidates with indistinguishable antiviral activity in vitro have been identified Exploratory IND filed for both HIV clinical candidates (IDX-989 and IDX- 899) Exploratory IND process will provide critical human pharmacokinetic and metabolic data to help select the most promising drug candidate Ongoing discovery efforts for complementary drugs with different mechanisms of action 22 22

HCV Discovery Program Focused on discovering next-generation HCV drug candidates Discovery and business development activity in a variety of classes Nucleoside polymerase inhibitors Non-nucleoside polymerase inhibitors Protease inhibitors Goal is to develop drug candidates that are complementary to valopicitabine Collaboration with Metabasis strengthens our Hepatitis C research engine and accelerates the NV-08 program to clinical proof-of-concept stage 23 23

Cash Flow Summary $ in millions 12/31/05 Cash Balance, incl. marketable sec. $242.2 1Q 06 Cash Flow Valopicitabine license fee ($22.3) $25.0 3/31/06 Cash Balance, incl. marketable sec. $244.8 2Q 06 Cash Flow ($18.1) 6/30/06 Cash Balance, incl. marketable sec. $226.7 3Q 06 Cash Flow ($17.1) 9/30/06 Cash Balance, incl. marketable sec. $209.6 Expect to end 2006 with between $170 million and $190 million of cash, cash equivalents and marketable securities 24 24

2006 Milestones Expected to Drive Value Telbivudine Global regulatory filings 1Q Data from phase IIIb studies Telbivudine vs. adefovir 1H Lamivudine switch 2H 2-year GLOBE study data 2H U.S. approval 2H Valopicitabine (NM283) In-licensing decision by Novartis 1Q Phase IIb in treatment-refractory population 24-week data Spring Phase IIb in treatment-naïve population 12-week data Spring 24-week data Fall Initiate ribavirin drug-drug interaction study 2H Preclinical File exploratory IND for HIV drug candidates (IDX-989 and IDX-899) 2H 25 25

2007 Momentum is Building HBV Anticipated approval and launch of SEBIVO in Europe Anticipated approval and launch of SEBIVO in Asia Phase III go/no-go decision for valtorcitabine HCV Results from drug-drug interaction study of valopicitabine with ribavirin Initiation of phase III registration trials of valopicitabine Final data from ongoing phase IIb studies of valopictabine Target new IND for complementary HCV program HIV Phase Ib/IIa dose-ranging study of selected compound Proof-of-concept study in HIV infected patients 26 26

Idenix Pharmaceuticals: Building a Leading Antiviral Franchise Investor Contact: Amy Sullivan Vice President, Corporate Communications 617-995-9838 investor@idenix.com www.idenix.com