Structural analysis of lead fullerene-based inhibitor bound to human immunodeficiency virus type 1 protease in solution from molecular dynamics simulations

Abstract

Molecular dynamics (MD) simulations of the HIV-1 protease (HIVP) complexed with lead fullerene-based inhibitor (diphenyl C 60 alcohol) in the three protonated states, unprotonated (Un-), monoprotonated (Mono-), and diprotonated (Di-) states at Asp25 and Asp25′ were performed. As the X-ray structure of the investigated complex is not available, it was built up starting with the X-ray crystallographic structure of the HIVP complexed with non-peptide inhibitor (PDB code: 1AID) and that of the diphenyl C 60 alcohol optimized using the integrated ONIOM molecular orbital calculations. The inhibitor was, then, introduced into the enzyme pocket using a molecular docking method. Change of the HIVP binding cavity for all three states were evaluated in terms of distance between the two catalytic residues, Asp25 and Asp25′ as well as those between the catalytic residues and the flap regions. The torsional angles formed by the O–C–C–O of the two carboxyl groups of the catalytic dyad show the non-planar configuration with the most frequency at about −45° for the Un-, 35° and −95° for the Mono- and 60° for the Di-systems. At equilibrium, different orientations of the fullerene-based inhibitor in the three protonation states were observed. For the Di-state, the OH group of the inhibitor stably forms hydrogen bonds with the two aspartic residues. It turns to the flap region to form hydrogen bonding to the backbone N of Ile50′ for the Un-state. In contrast, the OH group turns to locate between the catalytic and the flap region for the Mono-states. Beside the molecular orientation, the rotation of the OH group of the inhibitor in the Un-state was also detected. In terms of solvation, the carboxylate oxygens of the aspartic residues in the Un- and Mono-states were solvated by one to three water molecules while the OH group in these two states was coordinated by one water molecule. This is in contrast to the Di-state in which no water molecule is available in the radius of 5–6 Å around the oxygen atoms of the carboxylate groups of enzyme and of the OH group of the inhibitor. The simulated results lead to the conclusion that the active site of the HIVP complexed with the diphenyl C 60 alcohol is the diprotonation states on Asp25 and Asp25′.