A Novel Class of Highly Potent Irreversible Hepatitis C Virus NS5B Polymerase Inhibitors

Abstract

Starting from indole-based C-3 pyridone HCV NS5B polymerase inhibitor 2, structure-activity relationship (SAR) investigations of the indole N-1 benzyl moiety were performed. This study led to the discovery of irreversible inhibitors with p-fluoro-sulfone- or p-fluoro-nitro-substituted N-1 benzyl groups which achieved breakthrough replicon assay potency (EC(50) = 1 nM). The formation of a covalent bond with adjacent cysteine-366 thiol was was proved by mass spectroscopy and X-ray crystal structure studies. The C-5 ethyl C-2 carboxylic acid derivative 47 had an excellent oral area-under-the-curve (AUC) of 18 μM·h (10 mg/kg). Its oral exposure in monkeys and dogs was also very good. The NMR ALARM assay, mass spectroscopy experiments, in vitro counter screening, and toxicology assays demonstrated that the covalent bond formation between compound 47 and the protein was highly selective and specific. The overall excellent profile of 47 made it an interesting candidate for further investigation.

Drugging the undruggable RAS: Mission Possible?

“…This could result in compounds with low toxicity, providing that small molecules could be discovered that do not bind to other cysteine-containing proteins. In other studies aimed at covalent attachment to cysteine-containing proteins, compounds lacking the electrophile that forms the irreversible bond typically bind very tightly to the protein 42,43 . For the K-Ras inhibitors in this study, however, fragments lacking the electrophile do not appear to bind to K-Ras G12C, suggesting that it might be difficult to achieve the needed selectivity.…”

Development of potent dipeptide-type SARS-CoV 3CL protease inhibitors with novel P3 scaffolds: Design, synthesis, biological evaluation, and docking studies

“…Briefly, the commercially available methyl indole-2-carboxylate 6 underwent O-demethylation in the presence of boron tribromide (BBr 3 ) to produce the corresponding 4hydroxyindole ester 7 [15,16], which was subsequently treated with various alcohols under Mitsunobu conditions using diethyl azodicarboxylate (DEAD) and triphenylphosphine (PPh 3 ) in THF, followed by deprotection with lithium hydroxide$water (LiOH$H 2 O) to furnish the 4-isopropoxy (8i) and/or 4-isobutyloxy indole-2-carboxylic acid (8j), respectively [15,17]. Briefly, the commercially available methyl indole-2-carboxylate 6 underwent O-demethylation in the presence of boron tribromide (BBr 3 ) to produce the corresponding 4hydroxyindole ester 7 [15,16], which was subsequently treated with various alcohols under Mitsunobu conditions using diethyl azodicarboxylate (DEAD) and triphenylphosphine (PPh 3 ) in THF, followed by deprotection with lithium hydroxide$water (LiOH$H 2 O) to furnish the 4-isopropoxy (8i) and/or 4-isobutyloxy indole-2-carboxylic acid (8j), respectively [15,17].…”

The HCV Non-Nucleoside Inhibitor Tegobuvir Utilizes a Novel Mechanism of Action to Inhibit NS5B Polymerase Function

“…To explain the NS5B doublet formation, we suggest that reactive intermediate ( 4 ) undergoes pathway C, with a subsequent addition of GSH and NS5B. The nucleophile of the latter could be the thiol group of an exposed cysteine residue as has been described in earlier reports [22], [23], [24]. In the case of proposed intermediate ( 4 ) from Scheme S2, it is unclear which addition occurs first; initial GSH addition is probable since GSH is much more abundant than NS5B in the cell.…”