Research Article: In Silico and In Vitro Comparison of HIV-1 Subtypes B and CRF02_AG Integrases Susceptibility to Integrase Strand Transfer Inhibitors

Date Published: July 5, 2012

Publisher: Hindawi Publishing Corporation

Author(s): Xiaoju Ni, Safwat Abdel-Azeim, Elodie Laine, Rohit Arora, Osamuede Osemwota, Anne-Geneviève Marcelin, Vincent Calvez, Jean-François Mouscadet, Luba Tchertanov.


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)-naïve 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.

Partial Text

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 [1]. 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 [1]. 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 elvitegravir (ELV) and GSK572.

The naturally occurring variations in HIV-1 subtype CRF02_AG IN, such as K14R, V31I, L101I, T112V, T124A, T125A, G134N, I135V, K136T, V201I, T206S, V234I, and S283G, do not affect notably integrase structure, neither in vitro enzymatic activity, 3′-processing, nor strand transfer reaction. Docking results of all the considered inhibitors into the unbound IN model show the considerably low scores respectively, to docking into the pre integration IN·DNA complex. The docking scores and inhibitor poses confirm that the generated structure of the HIV IN·DNA complex is the appropriate biologically relevant model used to explain the inhibition mechanism of the strand transfer inhibitors. All the three studied molecules are polydentate ligands able to wrap around the metal cations in the active site. The results of the docking are in perfect agreement with the proposed mechanism of action for INSTIs. Docking results reveal that the modes of binding and docking conformations of three studied molecules are identical for the HIV-1 IN from B and CRF02_AG strains. The proposed mechanism of the integrase inhibition based on considering of different conformational states, unbound IN, and IN·vDNA complex holds for the two studied strains.




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