Development of carboxylic acid replacements in indole-N- acetamide inhibitors of hepatitis C virus NS5B polymerase Ian Stansfield, * Marco Pompei, Immacolata Conte, Caterina Ercolani, Giovanni Migliaccio, Mark Jairaj, Claudio Giuliano, Michael Rowley and Frank Narjes IRBM (Merck Research Laboratories Rome), Via Pontina Km 30,600, 00040 Pomezia, Rome, Italy Received 16 May 2007; revised 28 June 2007; accepted 29 June 2007 Available online 7 July 2007 Abstract—Allosteric inhibition of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase enzyme has recently emerged as a viable strategy toward blocking replication of viral RNA in cell-based systems. We report here 2 series of indole- N-acetamides, bearing physicochemically diverse carboxylic acid replacements, which show potent affinity for the NS5B enzyme with reduced potential for formation of glucuronide conjugates. Preliminary optimization of these series furnished compounds that are potent in the blockade of subgenomic HCV RNA replication in HUH-7 cells. Ó 2007 Elsevier Ltd. All rights reserved. HCV is a major human pathogen associated with chronic hepatitis and liver disease, cirrhosis, hepato-cel- lular carcinoma, and liver failure. 1 Worldwide, there are an estimated 170 million chronic carriers, 2 whilst in the US alone, 4 million have antibodies to HCV, indicating an on-going or previous infection with the virus. For over 10 years, frontline therapies have been based around interferon-a, commonly dosing in conjunction with ribavirin. Despite progress with such therapies (e.g., introduction of pegylated interferon), 3 sustained viral response (SVR) rates are still typically poor, partic- ularly for genotype-1 infections that predominate in Europe, Japan, and the U.S. 4 In addition, therapy is of- ten accompanied by significant adverse side effects 5 — consequently, there is a pressing need for new and broadly effective therapeutics to combat HCV. 3,6 HCV is a small, enveloped, single stranded positive RNA virus in the Flaviviridae family. The genome is approximately 10,000 nucleotides and encodes a single polyprotein of about 3000 amino acids. This polyprotein comprises the structural (C, E1, and E2) and non-struc- tural (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) pro- teins that are required for replication and packaging of viral genomic RNA. NS5B is the viral RNA-dependent RNA polymerase (RdRp). The RdRp activity of NS5B is essential for viral replication 7 and has no functional equivalent in uninfected mammalian cells—thus making the NS5B protein an attractive target for drug discovery. 8 The NS5B RdRp comprises the palm, fingers, and thumb subdomains common to nucleotide polymerizing enzymes. 9 Inhibition of NS5B can be achieved through interaction at the active site, for which both nucleoside ligands 10,11 and non-nucleoside inhibitors have been de- scribed. 11–15 Alternatively, several allosteric inhibitor binding sites on NS5B have been identified distal to the catalytic center. 11,16 Recent reports from our labora- tories documented the development of N-acetamido-in- dole-6-carboxylates, such as 1, as potent inhibitors interacting at one such allosteric site that lies close to a conserved amino acid, proline 495, on the surface of the thumb domain. 17–19 An issue with compounds from this class, however, was that glucuronide conjugates of the carboxylic acid were frequently observed as major circulating metabolites (Fig. 1). To moderate the formation of glucuronide conjugates in the systemic circulation, viable alternatives to the C6-carboxylate were sought. There are a number of moieties documented in the literature as mimetics for carboxylic acids, with diverse physical attributes and spanning a multi-log unit range of pK a values. In this 0960-894X/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2007.06.093 Keywords: Hepatitis C virus; NS5B polymerase; Allosteric inhibition; Indoles; Acid replacements. * Corresponding author. Tel.: +39 06 91093286; fax: +39 06 91093654; e-mail: ian_stansfield@merck.com Bioorganic & Medicinal Chemistry Letters 17 (2007) 5143–5149