HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Abstract

Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified Omega-shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir-resistant viruses.

Impact of Y143 HIV-1 Integrase Mutations on Resistance to Raltegravir In Vitro and In Vivo

“…Although this hypothesis remains a theoretical model owing to the lack of structural data, it is supported by biochemical results showing that both the Y143 and Q148 residues are involved in specifically binding the extremity of viral DNA (13,15,22). The resistance of recombinant IN to RAL in vitro and molecular modeling study suggested that the presence of R or H at position 148 prevents RAL binding while mutated IN is still capable of interacting with DNA (12,31). Thus, the replacement of neighboring Y by R may provide a similar effect, thereby providing an alternative pathway for RAL resistance.…”

“…Three-dimensional (3D) models of raltegravir resistance mutants were built by individual amino acid substitutions, using previously generated models of the catalytic core of wild-type IN, and were optimized as previously described (31). The stereochemical quality of the models was assessed with the ProTable Procheck software program (24), which showed that more than 97% of the nonglycine residues in all models had dihedral angles in the most favored and allowed regions of the Ramachandran plot, consistent with high model quality.…”

“…This proximity in an invariant structure, as well as the high mobility of the loop, suggests comparable roles of these mutations in resistance to RAL. We previously demonstrated that the Q148R/H/K mutation alters the specificity of DNA recognition by IN (31). We thus compared the hydrophobicity and hydrogen-bonding patterns of the WT and mutant proteins, both factors playing key roles in the binding of substrates or inhibitors.…”

Newly approved integrase inhibitors for clinical treatment of AIDS

“…These two mutations also reduced the replication capacity of HIV [37,38]. RAL failure is most associated with mutations via two genetic pathways (N155H, G140S/A or Q148K/R/H) [39,40]. N155H was selected early in the evolution process of RAL resistance in patients and was later replaced by genotype that containging Q148HKR [41].…”

Point Mutations Associated with HIV-1 Drug Resistance, Evasion of the Immune Response and AIDS Pathogenesis

“…E92Q mutation and the two polymorphic mutations L74M and G163R generally occur with N155H, while G140A/S generally occurs with Q148H/R/K (Cooper et al, 2008). Additional mutations (listed in Table 4) have been reported as being selected either in vitro or in vivo by raltegravir and include the non-polymorphic L74R, E138A/K, Y143R/C/H, N155S, H183P, Y226D/F/H, S230R, and D232N and the polymorphic mutations T97A and V151I (Delelis et al, 2011;Malet et al, 2008;Mouscadet et al, 2009). For both raltegravir and elvitegravir, virologic failure has generally been accompanied by 100-fold or greater decreases in susceptibility and the development of two or more INI resistance mutations.…”