Cyclic amide bioisosterism: Strategic application to the design and synthesis of HCV NS5B polymerase inhibitors Hanbiao Yang a, * , Robert T. Hendricks a, * , Nidhi Arora a , Dov Nitzan a , Calvin Yee a,  , Matthew C. Lucas a,  , Yanli Yang b , Amy Fung b , Sonal Rajyaguru b , Seth F. Harris c,à , Vincent J. P. Leveque b , Julie Q. Hang b , Sophie Le Pogam b , Deborah Reuter a , Gisele A. Tavares c,§ a Medicinal Chemistry Department, Roche Palo Alto, LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, United States b Viral Diseases Discovery and Translational Area, Roche Palo Alto, LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, United States c Discovery Technologies X-ray Crystallography Group, Roche Palo Alto, LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, United States article info Article history: Received 4 April 2010 Revised 26 May 2010 Accepted 1 June 2010 Available online 8 June 2010 Keywords: Amide bioisostere Modeling Synthesis HCV NS5B polymerase Thumb Mutant 3mt5 X-ray structure PDB Ruthenium catalyst abstract Conformational modeling has been successfully applied to the design of cyclic bioisosteres used to replace a conformationally rigid amide bond in a series of thiophene carboxylate inhibitors of HCV NS5B polymerase. Select compounds were equipotent with the original amide series. Single-point mutant binding studies, in combination with inhibition structure–activity relationships, suggest this new series interacts at the Thumb-II domain of NS5B. Inhibitor binding at the Thumb-II site was ultimately con- firmed by solving a crystal structure of 8b complexed with NS5B. Ó 2010 Elsevier Ltd. All rights reserved. Hepatitis C virus (HCV) is a major threat to public health world- wide as an estimated 3% of the world’s population is infected. Approximately 15–20% of infected individuals clear the virus with- out treatment, while the remaining 75–85% become chronically in- fected. 1 Chronic HCV infection has become a leading cause of cirrhosis, hepatocellular carcinoma and liver transplantation in the US. 2 The current standard of care treatment for HCV infection consists of a combination dose of pegylated interferon-a (PEG- IFNa) along with the broad spectrum antiviral agent Ribavirin for up to 48 weeks. However, only a moderate sustained virological re- sponse (SVR) of 42–46% is achieved in patients infected with geno- type-1 virus, the genotype which accounts for 70% of cases in the US. In addition, patient compliance is often limited by severe side effects. Based on these limitations, there is still a significant unmet clinical need for safer and more effective anti-HCV therapies. HCV contains a positive-sense, single-strand RNA molecule of 9.6 kb with one open reading frame coding for a large polyprotein of 3000 amino acids. Intracellular processing of the polyprotein yields at least ten individual functional proteins, namely C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B. Although the best path for HCV treatment has yet to be defined, 3 it will likely require a combination therapy approach targeting multiple viral proteins and/or pathways in the HCV lifecycle in order to effectively sup- press resistance. One particular HCV target protein of interest is NS5B, an RNA- dependent RNA polymerase (RdRp) that is essential for the synthe- sis and replication of viral RNA. It has a three-dimensional shape similar to other known RNA polymerases and is often described as a right-handed motif, with distinct Palm, Finger, and Thumb do- mains. Several inhibitors targeting various known binding sites within HCV NS5B polymerase have demonstrated useful efficacy in clinical trials. 4 0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2010.06.008 * Corresponding authors. Tel.: +1 650 361 1595. E-mail addresses: Hanbiaoyang@gmail.com (H. Yang), RTH.Hendricks@gmail.- com (R.T. Hendricks).   Present address: Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, United States. à Present address: Roche Group, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. § Present address: Novartis Pharma AG, NIBR, CHBS, WSJ-210.5.13, Switzerland. Bioorganic & Medicinal Chemistry Letters 20 (2010) 4614–4619 Contents lists available at ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl