Discovery of (7R)-14-Cyclohexyl-7-{[2-(dimethylamino)ethyl](methyl) amino}-7,8-dihydro-6H-indolo[1,2-e][1,5]benzoxazocine-11-carboxylic Acid (MK-3281), a Potent and Orally Bioavailable Finger-Loop Inhibitor of the Hepatitis C Virus NS5B Polymerase

Abstract

Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral genome and has been a prime target for drug discovery efforts. Here, we report on the further development of tetracyclic indole inhibitors, binding to an allosteric site on the thumb domain. Structure-activity relationship (SAR) studies around an indolo-benzoxazocine scaffold led to the identification of compound 33 (MK-3281), an inhibitor with good potency in the HCV subgenomic replication assay and attractive molecular properties suitable for a clinical candidate. The compound caused a consistent decrease in viremia in vivo using the chimeric mouse model of HCV infection.

A randomized, double blind, dose escalation, first time in human study to assess the safety, tolerability, pharmacokinetics, and antiviral activity of single doses of GSK2485852 in chronically infected hepatitis C subjects

“…11 Internal analysis of published clinical data sets of HCV NNIs showed correlation between the maintenance of NNI inhibitor concentrations above the protein adjusted EC 90 value and declines in HCV RNA levels (data not shown), therefore, the protein adjusted EC 90 for genotype 1b NS5B C316N replicon PA EC 90 (124 nM ¼ 69 ng/mL) was selected as the minimum target exposure at which antiviral activity was like to occur. [22][23][24][25][26][27][28] The similar in vitro potencies of these compounds and the predictions made by Reddy et al suggested the desired drop in viral load would require substantially higher and more frequent GSK2485852 doses so plasma concentrations many multiples above the PA EC 90 would be maintained in the majority of subjects. HCV-infected subjects exposed to the 420 mg dose had GSK2485852 concentrations that exceeded the PA EC 90 for 7.4-16 hours and had significant decline of À1.33 log 10 IU/ mL in HCV RNA levels.…”

Hepatitis C virus infection and related liver disease: the quest for the best animal model

“…Quasispecies population before and after treatment as well as selection of mutations leading to the appearance of resistant variants were also analyzed by ultra deep sequencing in these animals (Shi et al, 2013). Furthermore, several other compounds with an effect on viral replication have also been tested with success as monotherapy against HCV infection (Nakagawa et al, 2007; Kneteman et al, 2009; Narjes et al, 2011). …”

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.…”

“…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.…”

“…9 The combination of crystallographic, biochemical and mutagenesis studies have allowed the identification of at least five nonnucleoside inhibitor (NNI) binding sites on NS5B enzyme. 10 MK-3281 bound to thumb pocket (TP)-I 11 and PF-868554 bound to TP-II 12 of NS5B are located in the thumb domain, whereas acylpyrrolidine bound to palm pocket (PP)-I 13 , HCV-796 bound to PP-II 14 and GS9190 bound to PP-III 15 of NS5B are partially overlapped and are located between the thumb and the palm domains, in close proximity to the active site. Several inhibitors targeting these binding sites on NS5B have demonstrated strong efficacy in clinical trials.…”