Inhibitors of hepatitis C virus polymerase: Synthesis and characterization of novel 2-oxy-6-fluoro-N-((S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides

SAR exploration from an initial hit, (S)-N-(2-cyclohexenylethyl)-2-fluoro-6-(2-(1-hydroxy-3-phenylpropan-2-ylamino)-2-oxoethoxy)benzamide (1), identified using our proprietary automated ligand identification system (ALIS),1 has led to a novel series of selective hepatitis C virus (HCV) NS5B polymerase inhibitors with improved in vitro potency as exemplified by (S)-2-fluoro-6-(2-(1-hydroxy-3-phenylpropan-2-ylamino)-2-oxoethoxy)-N-isopentyl-N-methylbenzamidecarboxamide (41) (IC50 = 0.5 μM). The crystal structure of an analogue (44) was solved and provided rationalization of the SAR of this series, which binds in a distinct manner in the palm domain of NS5B, consistent with biochemical analysis using enzyme mutant variants. These data warrant further lead optimization efforts on this novel series of non-nucleoside inhibitors targeting the HCV polymerase.

The crystal structure of NS5B (green) complexed with 44 (yellow). The intramolecular hydrogen bond is shown in orange. The intermolecular hydrogen bond from the inhibitor’s hydroxyl group to the bound water molecule (labeled WAT) is shown in blue. The hydrogen bond network surrounding this water is shown in black. The coordinates have been deposited in the Protein Data Bank (Berman et. al., 2000) with accession code 3lkh. This figure was prepared using PyMOL (Delano, 2002). The mechanism of action of compound 44 has shown fully active (IC50 = 0.6 μM) against primer-initiated RNA synthesis involving multiple cycles of initiation and elongation catalyzed by NS5B, it was ineffective (IC50 >200 μM) in inhibiting the elongation of preformed NS5B enzyme–primer–template complexes.Figure optionsDownload as PowerPoint slide