Molecular Dynamics Studies of the Wild-Type and Double Mutant HIV-1 Integrase Complexed with the 5CITEP Inhibitor: Mechanism for Inhibition and Drug Resistance

Abstract

The human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the life cycle of the virus and is an attractive target for the development of new drugs useful in acquired immunodeficiency syndrome multidrug therapy. Starting from the crystal structure of the 5CITEP inhibitor bound to the active site in the catalytic domain of the HIV-1 IN, two different molecular dynamics simulations in water have been carried out. In the first simulation the wild-type IN was used, whereas in the second one the double mutation T66I/M154I, described to lead to drug resistance, was introduced in the protein. Compelling differences have been observed in these two structures during analyses of the molecular dynamics trajectories, particularly in the inhibitor binding modes and in the conformational flexibility of the loop (residues 138-149) located near the three catalytic residues in the active site (Asp(64), Asp(116), Glu(152)). Because the conformational flexibility of this region is important for efficient biological activity and its behavior is quite different in the two models, we suggest a hypothetical mechanism for the inhibition and drug resistance of HIV-1 IN. These results can be useful for the rational design of more potent and selective integrase inhibitors and may allow for the design of inhibitors that will be more robust against known resistance mutations.

Human Immunodeficiency Virus Type 1 (HIV-1) Integrase: Resistance to Diketo Acid Integrase Inhibitors Impairs HIV-1 Replication and Integration and Confers Cross-Resistance to l -Chicoric Acid

“…In addition to I66 preventing normal hydrogen bonding interactions, in the context of the double mutation T66I-M154I, the side chain of catalytic core residue E152 is oriented toward D64 and D116, whereas it is oriented away in reference IN. The hydrogen bonding interactions of E152 are also altered (2). Therefore, based on crystal structure and molecular dynamics data, in combination with viral and enzymatic data presented here, we hypothesize that both proteins are attenuated for catalytic activity due to (i) disrupted interaction of the viral DNA ends with the catalytic site of IN and (ii) altered orientation of active-site residues.…”

“…Thus, while both G140S and T66I-M154I resistance mutations affect the mobility of the same region and lead to resistance to both the dicaffeoyltartaric acids and diketo acids, they may confer resistance via two distinct mechanisms. The end product may be the same, however, as impaired loop mobility resulting from a G140 mutation could impair hydrogen bonding of E152 in a manner similar to that hypothesized for T66I-M154I (2).…”

“…The G140S may also impair loop mobility, as evident by the mutant's impaired viral integration and enzymatic activities (35). In contrast, by molecular dynamics simulations, T66I-M154I conferred increased loop flexibility compared to reference IN (2). Indeed, the flexibility of the double mutant in the presence of 5-CITEP matched that of reference IN alone and was substantially greater than that observed for reference IN with inhibitor (2).…”

“…T66I and T66I-M154I conferred an approximately twofold decrease in specific activity compared to reference IN, confirming that the T66I mutation attenuates catalytic activity (Table 3) course of this simulation, T66 transiently interacted first with I73, N155, and H67 and next with K159. In contrast, in the context of the T66I-M154I double mutation, I66 interacted only with I73 throughout the course of the study (2). In addition to I66 preventing normal hydrogen bonding interactions, in the context of the double mutation T66I-M154I, the side chain of catalytic core residue E152 is oriented toward D64 and D116, whereas it is oriented away in reference IN.…”

Computational and synthetic approaches for the discovery of HIV-1 integrase inhibitors

“…Even if several molecular dynamics studies of HIV-1 IN had already been published, [49][50][51][52][53][54] no attempts to perform MD simulations of IN/DNA complex had been reported. It is worth underlying that in our structure, looking at the catalytic core domains both of subunits A and B, only the catalytic core of subunit B made direct contacts with the viral DNA.…”