ABSTRACT
Third generation Hepatitis C virus (HCV) NS3/4A protease inhibitors (PIs), glecaprevir and voxilaprevir, are highly effective across genotypes and against many resistant variants. Unlike earlier PIs, these compounds have fluorine substitutions on the P2-P4 macrocycle and P1 moieties. Fluorination has long been used in medicinal chemistry as a strategy to improve physicochemical properties and potency. However, the molecular basis by which fluorination improves potency and resistance profile of HCV NS3/4A PIs is not well understood. To systematically analyze the contribution of fluorine substitutions to inhibitor potency and resistance profile, we used a multi-disciplinary approach involving inhibitor design and synthesis, enzyme inhibition assays, co-crystallography, and structural analysis. A panel of inhibitors in matched pairs were designed with and without P4 cap fluorination, tested against WT protease and the D168A resistant variant, and a total of 22 high-resolution co-crystal structures were determined. While fluorination did not significantly improve potency against the WT protease, PIs with fluorinated P4 caps retained much better potency against the D168A protease variant. Detailed analysis of the co-crystal structures revealed that PIs with fluorinated P4 caps can sample alternate binding conformations that enable adapting to structural changes induced by the D168A substitution. Our results elucidate molecular mechanisms of fluorine-specific inhibitor interactions that can be leveraged in avoiding drug resistance.
Subject(s)
Aminoisobutyric Acids , Cyclopropanes , Drug Design , Drug Resistance, Viral , HCV NS3-4A Protease Inhibitors , Lactams, Macrocyclic , Leucine/analogs & derivatives , Proline/analogs & derivatives , Quinoxalines , Sulfonamides , Viral Proteases , Aminoisobutyric Acids/chemistry , Aminoisobutyric Acids/pharmacology , Cyclopropanes/chemistry , Cyclopropanes/pharmacology , Drug Resistance, Viral/genetics , Fluorine/chemistry , HCV NS3-4A Protease Inhibitors/chemistry , HCV NS3-4A Protease Inhibitors/pharmacology , Halogenation , Hepacivirus/drug effects , Hepacivirus/enzymology , Hepacivirus/genetics , Humans , Lactams, Macrocyclic/chemistry , Lactams, Macrocyclic/pharmacology , Leucine/chemistry , Leucine/genetics , Leucine/pharmacology , Proline/chemistry , Proline/genetics , Proline/pharmacology , Quinoxalines/chemistry , Quinoxalines/pharmacology , Sulfonamides/chemistry , Sulfonamides/pharmacology , Viral Proteases/chemistry , Viral Proteases/geneticsABSTRACT
The approval of combination therapies with direct-acting antiviral (DAA) regimens has led to significant progress in the field of hepatitis C virus (HCV) treatment. Although most patients treated with these agents achieve a virological cure, resistance to DAAs is a major issue. The rapid emergence of resistance-associated substitutions (RASs), in particular in the context of incomplete drug pressure, has an impact on sustained virological response (SVR) rates. Several RASs in NS3, NS5A and NS5B have been linked with reduced susceptibility to DAAs. RAS vary based on HCV characteristics and the different drug classes. DAA-resistant HCV variant haplotypes (RVs) are dominant in cases of virological failure. Viruses with resistance to NS3-4A protease inhibitors are only detected in the peripheral blood in a time frame ranging from weeks to months following completion of treatment, whereas NS5A inhibitor-resistant viruses may persist for years. Novel agents have been developed that demonstrate promising results in DAA-experienced patients. The recent approval of broad-spectrum drug combinations with a high genetic barrier to resistance and antiviral potency may overcome the problem of resistance.
