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

LBPA, CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France.
Journal of Molecular Recognition (Impact Factor: 2.15). 11/2009; 22(6):480-94. DOI: 10.1002/jmr.970
Source: PubMed


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.

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    • "Interaction with DNA is probably impaired owing to an unfavorable orientation when Y143 is mutated in R, an orientation which is more favorable when Y143 is mutated in C. This is in agreement with the work of Mouscadet et al [25] who propose that native residues in wild-type enzyme involved in resistance (N155 and Q148) have a clear preference for adenine recognition, while mutations of N155 in H or of Q148 in H, R or K give mutants that favor pyrimidines. It might be that RAL inhibits HIV replication by mimicking adenine. "
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    ABSTRACT: Resistance to HIV-1 integrase (IN) inhibitor raltegravir (RAL), is encoded by mutations in the IN region of the pol gene. The emergence of the N155H mutation was replaced by a pattern including the Y143R/C/H mutations in three patients with anti-HIV treatment failure. Cloning analysis of the IN gene showed an independent selection of the mutations at loci 155 and 143. Characterization of the phenotypic evolution showed that the switch from N155H to Y143C/R was linked to an increase in resistance to RAL. Wild-type (WT) IN and IN with mutations Y143C or Y143R were assayed in vitro in 3'end-processing, strand transfer and concerted integration assays. Activities of mutants were moderately impaired for 3'end-processing and severely affected for strand transfer. Concerted integration assay demonstrated a decrease in mutant activities using an uncleaved substrate. With 3'end-processing assay, IC(50) were 0.4 microM, 0.9 microM (FC = 2.25) and 1.2 microM (FC = 3) for WT, IN Y143C and IN Y143R, respectively. An FC of 2 was observed only for IN Y143R in the strand transfer assay. In concerted integration, integrases were less sensitive to RAL than in ST or 3'P but mutants were more resistant to RAL than WT.
    Full-text · Article · Apr 2010 · PLoS ONE
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    • "Only one IFD pose of raltegravir at the catalytic site of SIVmac251 (Fig. 7) came out from the IFD protocol, and it was similar to one of the two conformations of the drug at the HIV-1 IN catalytic site, as described in the previous IFD study [27]. This IFD pose clearly showed raltegravir as an ideal prosecution of the 3' DNA strand of 3'processed viral DNA, consistently with the hypothesis [52] that this drug acts as a nucleotide mimic (Fig. 8A). The three pharmacophoric oxygens of the drug were engaged in bidentate chelation of the two Mg2+ ions within the catalytic cavity (Fig. 8B), while the substituted benzyl group deeply occupied a pocket mainly defined by IN residues Q148, E152 and H156, and viral nucleotides dG18, dC19, dA20, dG24 and dC25, as previously described in docking simulations at the HIV-1 IN CCD [27] [see Additional file 5]. "
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    ABSTRACT: In this study we successfully created a new approach to ART in SIVmac251 infected nonhuman primates. This drug regimen is entirely based on drugs affecting the pre-integration stages of replication and consists of only two nucleotidic/nucleosidic reverse transcriptase inhibitors (Nt/NRTIs) and raltegravir, a promising new drug belonging to the integrase strand transfer inhibitor (INSTI) class. In acutely infected human lymphoid CD4+ T-cell lines MT-4 and CEMx174, SIVmac251 replication was efficiently inhibited by raltegravir, which showed an EC90 in the low nanomolar range. This result was confirmed in primary macaque PBMCs and enriched CD4+ T cell fractions. In vivo monotherapy with raltegravir for only ten days resulted in reproducible decreases in viral load in two different groups of animals. When emtricitabine (FTC) and tenofovir (PMPA) were added to treatment, undetectable viral load was reached in two weeks, and a parallel increase in CD4 counts was observed. In contrast, the levels of proviral DNA did not change significantly during the treatment period, thus showing persistence of this lentiviral reservoir during therapy. In line with the high conservation of the three main amino acids Y143, Q148 and N155 (responsible for raltegravir binding) and molecular docking simulations showing similar binding modes of raltegravir at the SIVmac251 and HIV-1 IN active sites, raltegravir is capable of inhibiting SIVmac251 replication both in tissue culture and in vivo. This finding may help to develop effective ART regimens for the simian AIDS model entirely based on drugs adopted for treatment in humans. This ART-treated AIDS nonhuman primate model could be employed to find possible strategies for virus eradication from the body.
    Full-text · Article · Mar 2010 · Retrovirology
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    • "The strand-transfer reaction that leads to HIV DNA integration into host cellular DNA is catalysed by a dynamic complex associating an IN tetramer and the two ends of the linear viral DNA molecule [1,13,14,19,25,30,38]. Studies conducted using INSTIs have found that the binding site for this family of drugs is constituted both by elements of the enzyme itself and by elements of viral DNA. "
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    ABSTRACT: Similar to all antiretroviral drugs, failure of raltegravir-based treatment regimens to fully supress HIV replication almost invariably results in emergence of HIV resistance to this new drug. HIV resistance to raltegravir is the consequence of mutations located close to the integrase active site, which can be divided into three main evolutionary pathways: the N155H, the Q148R/H/K and the Y143R/C pathways. Each of these primary mutations can be accompanied by a variety of secondary mutations that both increase resistance and compensate for the variable loss of viral replicative capacity that is often associated with primary resistance mutations. One unique property of HIV resistance to raltegravir is that each of these different resistance pathways are mutually exclusive and appear to evolve separately on distinct viral genomes. Resistance is frequently initiated by viruses carrying mutations of the N155H pathway, followed by emergence and further dominance of viral genomes carrying mutations of the Q148R/H/K or of the Y143R/C pathways, which express higher levels of resistance. Even if some natural integrase polymorphisms can be part of this evolution process, these polymorphisms do not affect HIV susceptibility in the absence of primary mutations. Therefore, all HIV-1 subtypes and groups, together with HIV-2, are naturally susceptible to raltegravir. Finally, because interaction of integrase strand transfer inhibitors with the HIV integrase active site is comparable from one compound to another, raltegravir-resistant viruses express significant cross resistance to most other compounds of this new class of antiretroviral drugs.
    Preview · Article · Nov 2009 · European journal of medical research
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