Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors

Abstract

Background: HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations afect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with diferent inhibitors and in diferent background sequence contexts. Results: Using these simulations for alchemical calculations to estimate the efects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ efect on IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis infuences whether the unfavourable efect of L76V on inhibitor binding is sufcient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions: We demonstrate that estimating the efect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their efect on the experimentally measured IC50 values. We show that distant site mutations L76V and N88S afect the hydrogen bond network in the protease’s active site, which ofers an explanation for the indirect efect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they afect inhibitor binding.