The competitive binding between inhibitors and substrates of HCV NS3/4A protease: a general mechanism of drug resistance

Hepatitis C virus (HCV) infection is a serious public health problem throughout the world. Great success has been achieved in developing inhibitors targeting the HCV NS3/4A protease over the past decade, but the rapid emergence of drug resistant mutations greatly compromises the efficacy of antiviral drugs or drug candidates. According to the substrate envelope hypothesis (Romano et al., 2010), severe drug resistant mutations would always occur where the inhibitors protrude from the substrate envelope, defined as a consensus volume occupied by the viral substrates in the active site of the NS3/4A protease. However, the substrate envelope hypothesis just qualitatively assesses the impact of mutations to a specific inhibitor, but no quantitative data is obtained. To remedy the weakness, the dynamic binding patterns of HCV NS3/4A protease inhibitors or substrates were investigated by molecular dynamics (MD) simulations and continuum solvation binding affinity predictions in this study. By comparing the quantitative binding profiles between the substrates and inhibitors, derived from the free energy decomposition analysis, we observed most residues involved in drug resistance form stronger interactions with the inhibitors than with the substrates, which is roughly coincident with the substrate envelope hypothesis and supports the general mechanism of drug resistance: the critical resistant mutations impair more to the binding of inhibitors than that of substrates. Furthermore, our predictions illustrate that the natural substrates of NS3/4A form balanced interactions with the strands 135-139 and 154-160 whereas the inhibitors cannot. Therefore, to overcome drug resistance, it may be necessary to restore the interaction balance between the two strands and the drug candidates. To our disappointment, the underlying resistant mechanisms of some mutations could not be well captured by just comparing the binding profiles of inhibitors and substrates, and more studies should be proceeded to propose a general drug resistance mechanism.