Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations

Abstract

The spread of acquired immune deficiency syndrome has increasingly become a great concern owing largely to the failure of chemotherapies. The G48V is considered the key signature residue mutation of HIV-1 protease developing with saquinavir therapy. Molecular dynamics simulations of the wild-type and the G48V HIV-1 protease complexed with saquinavir were carried out to explore structure and interactions of the drug resistance. The molecular dynamics results combined with the quantum-based and molecular mechanics Poisson-Boltzmann surface area calculations indicated a monoprotonation took place on D25, one of the triad active site residues. The inhibitor binding of the triad residues and its interaction energy in the mutant were similar to those in the wild-type. The overall structure of both complexes is almost identical. However, the steric conflict of the substituted valine results in the conformational change of the P2 subsite and the disruption of hydrogen bonding between the -NH of the P2 subsite and the backbone -CO of the mutated residue. The magnitude of interaction energy changes was comparable to the experimental K(i) data. The designing for a new drug should consider a reduction of steric repulsion on P2 to enhance the activity toward this mutant strain.

FIGURE 1

Schematic representation of saquinavir (A) and the wild-type HIV-1 protease-saquinavir complex (B). According to a conventional classification of the protease subsites, the binding pockets are designated by the inhibitor side chains P1, P2, P3, P1′, and P2′.

FIGURE 2

MD snapshots showing interactions in the binding pocket of the wt and G48V for various protonation states: diprotonation (dipro), monoprotonation of D25 (mono25), monoprotonation of D25′ (mono25′), and unprotonation (unpro). Saquinavir (SQV) and the active site residues D25 and D25′ of the enzyme are shown in stick mode. Chain A and B of the enzyme are colored as blue and green.

FIGURE 3

ΔE_cpx between the triad residues and saquinavir of the wt and the G48V complexes for the dipro, mono25, and mono25′ systems.

FIGURE 4

Plots of the energies (A) and RMSDs (B) versus the simulation time for the wt and G48V-SQV complex. The obtained RMSD was computed using the structure at t = 0 as a reference.

FIGURE 5

Backbone RMSD between the wild-type and the G48V structure.

FIGURE 6

HIV-1 PR flap structures of the wt (green) and the G48V (yellow and blue). Some selected residues and saquinavir are presented in stick mode. Hydrogen atoms of the enzyme are not shown for simplification.

FIGURE 7

Fluctuation of χ_P1, χ_P1′, χ_P2, χ_P2′, and χ_P3 corresponding to the dihedral angles of the inhibitor side chains P1, P1′, P2, P2′, and P3, respectively.

FIGURE 8

Conformational change of SQV at the P2 side chain. The rotation of the P2 subsite and the hydrogen bonds are illustrated.

FIGURE 9

Distance trajectories of hydrogen bonding involving the CO backbone of residue 48.

FIGURE 10

Schematic representation of the three-layer ONIOM extrapolation scheme.

FIGURE 11

Schematic representation for the structure of HIV-1PR-SQV with the three partitioned layers.