Structure–Activity Relationship (SAR) Development and Discovery of Potent Indole-Based Inhibitors of the Hepatitis C Virus (HCV) NS5B Polymerase

Abstract

Starting with the indole-based C-3 pyridone lead HCV polymerase inhibitor 2, extensive SAR studies were performed at different positions of the indole core. The best C-5 groups were found to be compact and nonpolar moieties and that the C-6 attachments were not affecting potency. Limited N-1 benzyl-type substituent studies indicated that the best substitutions were fluoro or methyl groups at 2' or 5' positions of the benzyl group. To improve pharmacokinetic (PK) properties, acylsulfonamides were incorporated as acid isosteres at the C-2 position. Further optimization of the combination at N-1, C-2, C-5, and C-6 resulted in the identification of compound 56, which had an excellent potency in both NS5B enzyme (IC(50) = 0.008 μM) and cell-based replicon (EC(50) = 0.02 μM) assays and a good oral PK profile with area-under-the curve (AUC) of 14 and 8 μM·h in rats and dogs, respectively. X-ray structure of inhibitor 56 bound to the enzyme was also reported.

A review on HCV inhibitors: Significance of non-structural polyproteins

“…The peptide based derivatives (29) (IC 50 ¼ 70 nm), heterocyclic compounds like thiaphene dihydroxy pyrimidine derivatives (30, [57], thiaphene dihydroxy pyrimidine derivatives (31 & 32, IC 50 ¼ 0.14 & 0.15 mM) [57], thiazline dihydroxy pyrimidine derivatives (33, IC 50 ¼ 0.76 mM), were evaluated as HCV NS5B inhibitors (29 to 33) ( Fig. 11).…”

Design and synthesis of l- and d-phenylalanine derived rhodanines with novel C5-arylidenes as inhibitors of HCV NS5B polymerase

“…16 To rule out any bias, each of the five reported NS5B allosteric binding pockets TP-I (PDB ID: 2XWY), 11 TP-II (PDB ID: 3FRZ), 12 PP-I (PDB ID: 3TYV) 27 , PP-II (PDB ID: 3FQL), 14 and PP-III, that significantly overlaps with PP-II (large grid box created around PP-II bound HCV-796 to obtain docking pose at PP-III), was examined for inhibitor binding. Analysis of the binding energy data (Glidescores) for all single digit µM inhibitors at each allosteric site revealed that they bind with affinity in the order PP-I>PP-II>PP-III>TP-I>TP-II.…”

“…To gain insight into the molecular mechanism of inhibition, we analyzed the interactions of the docked conformation of compound L- 34 (panel A) and for comparison D- 45 (panel B) within the PP-I of NS5B (PDB ID: 3TYV) 27 as shown in Fig. 2.…”

“…3D Structures of target compounds 17–39 and 41–45 were constructed using the fragment dictionary of Maestro 9.0 (Schrodinger, LLC, New York, NY) and geometry was optimized by Macromodel program v9.5 using the OPLS-AA force field with the steepest descent followed by truncated Newton conjugate gradient protocol. The X-ray crystal structure of NS5B polymerase in complex with MK-3281 (PDB ID: 2XWY) 11 , with PF-868554 (PDB ID: 3FRZ) 12 , with indole C2-acyl sulfonamide (PDB ID: 3TYV) 27 , with HCV-796 (PDB ID: 3FQL) 14 and palm pocket (PP)-III, that significantly overlaps with PP-II (large grid box created around PP-II bound HCV-796 to obtain docking pose at PP-III) representing thumb pocket (TP)-I, TP-II, palm pocket (PP)-I, PP-II and PP-III pockets, respectively, obtained from the RCSB Protein Data Bank (PDB), were used in this study. The protein was optimized for docking using the “Protein Preparation Wizard” and “Prime-Refinement Utility” of Maestro 9.0.…”

Structure-Activity Relationships in the Development of Allosteric Hepatitis C Virus RNA-Dependent RNA Polymerase Inhibitors: Ten Years of Research

“…It is worth noting that position 5 of the indole core was moreover very permissive in terms of nature and size, as methyl, ethyl, bromo, tert‐butyl, or cyclopropyl substituents all led to compounds exhibiting IC 50 below 10 nM. Finally, sulfonamide analogues induced an increase of activity, reaching an IC 50 of 3 nM for compound 38h . Interestingly, N −1 substitution with 2‐fluoro‐5‐nitrobenyl leads to a reaction between the phenyl ring and residue Cys366.…”