Stabilization of the integrase‐DNA complex by Mg²⁺ ions and prediction of key residues for binding HIV‐1 integrase inhibitors

Abstract

The HIV-1 integrase is an attractive target for the therapeutics development against AIDS, as no host homologue of this protein has been identified. The integrase strand transfer inhibitors (INSTIs), including raltegravir, specifically target the second catalytic step of the integration process by binding to the DDE motif of the catalytic site and coordinating Mg(2+) ions. Recent X-ray crystallographic structures of the integrase/DNA complex from prototype foamy virus allowed to investigate the role of the different partners (integrase, DNA, Mg(2+) ions, raltegravir) in the complex stability using molecular dynamics (MD) simulations. The presence of Mg(2+) ions is found to be essential for the stability, whereas the simultaneous presence of raltegravir and Mg(2+) ions has a destabilizing influence. A homology model of HIV-1 integrase was built on the basis of the X-ray crystallographic information, and protein marker residues for the ligand binding were detected by clustering the docking poses of known HIV-1 integrase inhibitors on the model. Interestingly, we had already identified some of these residues to be involved in HIV-1 resistance mutations and in the stabilization of the catalytic site during the MD simulations. Classification of protein conformations along MD simulations, as well as of ligand docking poses, was performed by using an original learning method, based on self-organizing maps. This allows us to perform a more in-depth investigation of the free-energy basins populated by the complex in MD simulations on the one hand, and a straightforward classification of ligands according to their binding residues on the other hand.

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

“…The conformations were clustered using a self-organizing map (SOM) approach [ 62 , 63 ], on which the coordinate RMSD values between the conformers obtained by Branch-and-Prune and the corresponding PDB structure, were projected on the SOMs (Figure 6 ). These RMSD values lay in the 1.3-3.2 Å range for 2JMY_1, in the 2.4-4.9 Å range for 2JMY_2, in the 1.5-4.0 Å range for 2KXA, and in the 3.2-6.0 Å for 2KSL.…”

Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives

“…Yu et al [67] selected the final structure based not only on the docking score, but also on the pharmacophore location of the hydrophobic p-fluorobenzyl group. Clustering of docking pose is a post-processing step to identify compounds with diverse chemotypes for further synthesis [60,61]. Importantly, docking can also generate relatively reliable structures for other computational approaches [34,55,63,67].…”

“…Reddy et al [60] incorporated most of the possible stereoisomers into docking procedures to study the activity of individual stereotypes for each ligand. Miri et al [61] prepared different protonation states and semi-empirical charges of ligands to make the conformations more accurate. Quantum mechanics/molecular mechanics (QM/MM) docking was carried out by Reddy et al [30], which improved the partial charges by replacing them with charges derived from QM calculations of ligands in the field of the receptor; QM/MM docking offered significantly enhanced accuracy over pure MM docking.…”

Systematic exploration of protein conformational space using a Distance Geometry approach

“…To scale down the combinatorial of the calculation, a clustering approach, the Self-Organizing Maps (SOM), [58][59][60][61] which are unsupervised neural networks, were used to reduce the number of conformations. The method was implemented through a set of python scripts.…”