Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease

Abstract

Background: Drug resistance is a severe problem in HIV treatment. HIV protease is a common target for the design of new drugs for treating HIV infection. Previous studies have shown that the crystallographic structures of the HIV-2 protease (PR2) in bound and unbound forms exhibit structural asymmetry that is important for ligand recognition and binding. Here, we investigated the effects of resistance mutations on the structural asymmetry of PR2. Due to the lack of structural data on PR2 mutants, the 3D structures of 30 PR2 mutants of interest have been modeled using an in silico protocol. Structural asymmetry analysis was carried out with an in-house structural-alphabet-based approach. Results: The systematic comparison of the asymmetry of the wild-type structure and a large number of mutants highlighted crucial residues for PR2 structure and function. In addition, our results revealed structural changes induced by PR2 flexibility or resistance mutations. The analysis of the highlighted structural changes showed that some mutations alter protein stability or inhibitor binding. Conclusions: This work consists of a structural analysis of the impact of a large number of PR2 resistant mutants based on modeled structures. It suggests three possible resistance mechanisms of PR2, in which structural changes induced by resistance mutations lead to modifications in the dimerization interface, ligand recognition or inhibitor binding.

Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease

“…This structural asymmetry of PR2 could result from crystal packing, ligand binding, and intrinsic flexibility of PR2 [ 11 ], and may be involved in the structural changes of PR2, particularly upon ligand recognition and binding [ 11 , 12 , 41 , 42 ]. Our results are in agreement with previous findings that have showed that drug-resistance mutations could modify PR2 structural asymmetry [ 31 ]. Thus, as PR2 is an asymmetric protein, resistance mutations do not always have the same impact on the two chains.…”

“…The location onto PR2 structure of MCS atoms highlighted structural deformations that could be linked to resistance mechanisms. First, we observed, in 19 mutant structures, structural deformations in binding pocket residues as reported in Laville et al, 2020 [ 31 ]. Most of these mutations were located in the binding pocket, except the K7R, I54M and L90M mutations.…”

“…In this study, we started from the list of the 30 drug-resistant mutants of PR2 studied in our previous study [ 31 ]. This mutant list was updated and a list of 31 drug-resistant mutants of PR2 was selected.…”

“…In our previous work, we performed the first structural analysis of the impact of 30 drug-resistant mutants of PR2 based on modeled structures. More precisely, we explored the consequences of drug-resistance mutations on PR2 structural asymmetry, an important property for ligand-binding and the target deformation [ 31 ]. Our findings suggested three possible resistance mechanisms of PR2: (i) mutations that induce structural changes in the binding pocket that could directly alter PI-binding, (ii) mutations that could impact the properties and conformation of the binding pocket by inducing structural changes in residues outside of the binding pocket but involved in interaction with pocket residues, and (iii) mutations that could modify the PR2 interface and its stability through structural changes in interface residues.…”

“…In this study, we structurally analyzed a set of 31 drug-resistant mutants of PR2 that was updated relative to [ 31 ]. The 3D structure of each mutant was modeled and its structure was compared to the wild-type PR2 to locate structural rearrangements induced by drug-resistance mutations at backbone and side-chain atoms.…”