Most antiretroviral medical treatments were developed and tested principally on HIV-1 B nonrecombinant strain, which represents less than 10% of the worldwide HIV-1-infected population. HIV-1 circulating recombinant form CRF02_AG is prevalent in West Africa and is becoming more frequent in other countries. Previous studies suggested that the HIV-1 polymorphisms might be associated to variable susceptibility to antiretrovirals. This study is pointed to compare the susceptibility to integrase (IN) inhibitors of HIV-1 subtype CRF02_AG IN respectively to HIV-1 B. Structural models of B and CRF02_AG HIV-1 INs as unbound enzymes and in complex with the DNA substrate were built by homology modeling. IN inhibitors—raltegravir (RAL), elvitegravir (ELV) and L731,988—were docked onto the models, and their binding affinity for both HIV-1 B and CRF02_AG INs was compared. CRF02_AG INs were cloned and expressed from plasma of integrase strand transfer inhibitor (INSTI)-na？ve infected patients. Our in silico and in vitro studies showed that the sequence variations between the INs of CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. The binding modes and affinities of INSTI inhibitors to B and CRF02_AG INs were found to be similar. Although previous studies suggested that several naturally occurring variations of CRF02_AG IN might alter either IN/vDNA interactions or INSTIs binding, our study demonstrate that these variations do affect neither IN activity nor its susceptibility to INSTIs. 1. Introduction The pol-encoded HIV-1 integrase (IN) is a key enzyme in the replication mechanism of retroviruses. It catalyses the covalent insertion of the viral cDNA into the chromosomes of the infected cells . Two reactions are required for covalent integration of viral DNA. First, IN binds to a short sequence located at either end of the long terminal repeat (LTR) of the vDNA and catalyzes an endonucleotide cleavage, 3′-processing reaction, resulting in the removal of two nucleotides from each of the 3′-ends of LTR and the delivery of hydroxy groups for nucleophilic attacks. The trimmed DNA is then used as a substrate for strand transfer (ST) reaction, leading to the covalent insertion of the DNA into the host genome . Inhibitors of the strand transfer reaction—INSTIs—constitute a novel family of antiretroviral (ARV) drugs, with raltegravir (RAL) at the cape, which is a first INSTI approved for AIDS treatment. Other inhibitors in advanced phase of development are
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