Clinical and In Vitro Resistance to GS-9669, a Thumb Site II Nonnucleoside Inhibitor of the Hepatitis C Virus NS5B Polymerase

Abstract

bTreatment with GS-9669, a novel nonnucleoside inhibitor (site II) of hepatitis C virus (HCV) nonstructural 5B (NS5B) polymerase, resulted in significant antiviral activity in HCV genotype (GT) 1 patients dosed at 50 and 500 mg once daily (QD) and at 50, 100, and 500 mg twice daily (BID) for 3 days. This report characterizes the virologic resistance to GS-9669 in vitro and in GT1 HCV-infected patients from a phase I clinical study. An in vitro resistance selection study with GS-9669 revealed substitutions at several NS5B residues that conferred resistance. The M423 variants were selected at low drug concentrations (5؋ the 50% effective concentration [EC 50 ]), and the L419, R422, and I482 variants were selected at higher drug concentrations (20؋ the EC 50 ). H epatitis C virus (HCV) infects an estimated 170 million people worldwide (1). HCV infection can lead to cirrhosis, hepatocellular carcinoma, or other complications. Until recently, the standard of care for the treatment of chronic HCV infection consisted of 24 to 48 weeks of pegylated interferon (PEG-IFN) and ribavirin (RBV) (2), which are associated with significant side effects, including fever, fatigue, anemia, leukopenia, thrombocytopenia, and depression (3, 4). A sustained virologic response (SVR) occurs in only 42% to 53% of patients with genotype (GT) 1 or GT4 HCV and up to 78% to 82% of patients infected with GT2 or GT3 HCV (5, 6). Novel direct-acting antiviral agents (DAAs) are being developed in combination with PEG-IFN-RBV and are also being pursued as components of IFN-free and IFN-and RBV-free regimens to improve efficacy and shorten treatment duration. Two protease inhibitors (PIs) approved for the treatment of HCV, telaprevir and boceprevir, have demonstrated significantly improved SVR rates when given in combination with PEG-IFN-RBV in GT1 patients (60 to 75% for combination compared with 38 to 46% for PEG-IFN-RBV only) (7,8). However, these new agents require thrice-daily dosing and are associated with more frequent occurrences of and severe anemia and rash (9, 10). Two HCV drugs received FDA approval at the end of 2013, simeprevir (Olysio), a nonstructural 3/4A (NS3/4A) protease inhibitor in combination with PEG-IFN-RBV, and sofosbuvir (Sovaldi), a nucleotide inhibitor, which is the first drug that has demonstrated safety and efficacy for treating non-genotype-1 HCV infection without the need to coadminister PEG-IFN.GS-9669 (Fig. 1) is a novel thumb site II nonnucleoside inhibitor (NNI) of the HCV NS5B RNA polymerase, with a binding affinity of 1.4 nM for the GT1b NS5B protein. It is a selective inhibitor of HCV RNA replication, with a mean 50% effective concentration (EC 50 ) of Յ11 nM in GT1 and GT5 replicon assays (11). Other NNIs currently in phase II clinical studies include BI-207127 and BMS-791325 (binding to thumb site I), filibuvir and lomibuvir (binding to thumb site II), setrobuvir, ABT-072, and ABT-333 (binding to palm site I), and tegobuvir (also binding in the palm) (12). In a phase Ib study of filibuvir, resistance-associat...

Insight into the drug resistance mechanisms of GS-9669 caused by mutations of HCV NS5B polymerase via molecular simulation

“…Moreover, the binding energies of these mutation systems increase gradually. The calculation results are consistent with the experimental results [26] , [29] that these mutations will cause resistance and the levels of resistance increases sequentially. Differently, the binding energies of the R422K (−36.46 kcal/mol) and I482L (−36.60 kcal/mol) mutant systems are more negative than that of the WT system.…”

“…Therefore, the M423T mutation mainly affects the interaction between the residue at the mutation site and the inhibitor, but failed to cause large changes in the polymerase-inhibitor interactions. This should be the reason that the M423T mutation produced weak drug resistance in experimental detection [26] , [29] .

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“…1 b), an NNI that binds to the thumb site II, is a promising antiviral drug candidate for the GT1 chronic HCV and has advanced into phase II trials [26] , [27] , [28] . However, resistance variants such as M423T/I/V, L419M, R422K, I482L and so on, were identified to GS-9669 in vitro [26] , [29] , which could reduce its potency. The understanding of the drug resistance mechanism of GS-9669 is very crucial for the design of novel potent agents targeting viral variants.…”

Clinical Resistance to Velpatasvir (GS-5816), a Novel Pan-Genotypic Inhibitor of the Hepatitis C Virus NS5A Protein

“…More substantial suppression of wild-type virus by larger doses resulted in more frequent detection of resistant variants, although RASs may be generated during treatment because of the high error rate of HCV RNA replication. This is consistent with other phase 1 HCV DAA monotherapy studies (28,43,44) and suggests that RASs preexist among patients with pretreatment RASs included Y93H (n ϭ 3 [GT1a, n ϭ 2; GT1b, n ϭ 1]), L31M (n ϭ 11 [GT1a, n ϭ 7; GT2b, n ϭ 4]), H58D (GT3a, n ϭ 3), Q30H (GT1a, n ϭ 2), M28T (GT1a, n ϭ 3), and Q30R (GT1a, n ϭ 2). (B) Changes in frequencies among patients without pretreatment RASs included Y93H (n ϭ 38 [GT1a, n ϭ 18; GT1b, n ϭ 6; GT2b, n ϭ 2; GT3, n ϭ 12]), L31M (n ϭ 16 [GT1a, n ϭ 11; GT1b, n ϭ 4; GT2b, n ϭ 1]), L31V (n ϭ 25 [GT1a, n ϭ 18; GT1b, n ϭ 5; GT2b, n ϭ 1; GT3, n ϭ 1]), H58D (GT1a, n ϭ 5), M28T (GT1a, n ϭ 17), Q30H (GT1a, n ϭ 6), Q30R (GT1a, n ϭ 10), Y93N (n ϭ 21 [GT1a, n ϭ 14; GT1b, n ϭ 2; GT3a, n ϭ 5]).…”

Worldwide Prevalence of Baseline Resistance-Associated Polymorphisms and Resistance Mutations in HCV against Current Direct-Acting Antivirals

“…The L419I in this region was found to be a polymorphism in GT2, 3, 4 and 6. L419M/S was found to confer ≥100-fold resistance increase against radalbuvir in the GT1a and 1b replicon assays [32]. However, resistance information of the L419I mutation is not available.…”