Identification and Biological Evaluation of a Series of 1H-Benzo[de]isoquinoline-1,3(2H)-diones as Hepatitis C Virus NS5B Polymerase Inhibitors

Abstract

The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for inhibition. Herein, we present 1H-benzo[de]isoquinoline-1,3(2H)-diones as a new series of selective inhibitors of HCV NS5B polymerase. The HTS hit 1 shows submicromolar potency in two different HCV replicons (1b and 2b) and displays no activity on other polymerases (HIV-RT, Polio-pol, GBV-b-pol). These inhibitors act during the pre-elongation phase by binding to NS5B non-nucleoside binding site Thumb Site II as demonstrated by crystal structure of compound 1 with the DeltaC55-1b and DeltaC21-2b enzymes and by mutagenesis studies. SAR in this new series reveals inhibitors, such as 20, with low micromolar activity in the HCV replicon and with good activity/toxicity window in cells.

Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase

“…1) (15)(16)(17)(18)(19)(20)(21)(22)(23)(24). We will refer to NNI-1 and -2 as ''thumb inhibitors'' while NNI-3 and -4 will be referred to as ''palm inhibitors''.…”

Allosteric inhibitors of hepatitis C virus NS5B polymerase thumb domain site II: Structure-based design and synthesis of new templates

“…To further improve the window between EC 50 and CC 50 , in compound 7c the basic amine was removed from the side chain and the benzyl moiety replaced by a carboxylic group. 9 While 7c showed modest potency, loosing both in enzymatic and cells assays and mainly with respect to genotype 1b, it was less cytotoxic (SI = 8). The beneficial effect of the carboxylic acid presence was not general since CO other analogs in the series exhibited a lower selectivity index (data not shown).…”

“…7 Several small molecules acting as allosteric inhibitors of NS5B have been disclosed during the past years reflecting the major effort in this area from pharmaceutical industries and academia. 8 Recently, we disclosed a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as allosteric inhibitors of NS5B polymerase 9 (Table 1). The lead compound 1a showed nanomolar activity on the main NS5B polymerase genotypes (1b, 2b), while activity was in the micromolar range in the cell based assays (Table 1).…”

“…The tricyclic core interacts with a flat lipophilic surface, the bromophenyl substituent makes extensive Van der Waals and hydrophobic interactions, whereas the imide oxygens and heteroatoms of the ethanolamine side chain are involved in direct or water mediated H-bonds. 9 The bromine present in 1a can be replaced with a chlorine as in 1b without changing the activity profile both on the enzyme and in the cell based assay. The structural information gained with X-ray guided the SAR studies that culminated in the identification of the more active compound 2 in which the ethanolamine side chain had been substituted by a benzylpiperidine moiety.…”

Combination of pharmacophore hypothesis and molecular docking to identify novel inhibitors of HCV NS5B polymerase

“…Eighteen molecules [15,17,20,21,26,[28][29][30][31]34,35,38,44] with diverse structures (Fig. 1) and a fourfold activity spread (0.002-92 µM) were used to develop a pharmacophore model.…”