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.

FIGURE 1

Orientation of residues 66 and 154 (a) in the crystal structure and (b) in the initial model of T66I/M154I HIV-1 IN complex.

FIGURE 2

5CITEP and L-731,988 HIV-1 IN inhibitors.

FIGURE 3

Ribbon diagram of the (a) wild-type and (b) T66I/M154I HIV-1 IN complexes from average structures over the entire simulations. The figures were prepared using the program MOLMOL (Koradi et al., 1996).

FIGURE 4

Root-mean-square deviation (RMSD) of the C_α atoms for the (a) wild-type and (b) T66I/M154I IN complexes as a function of simulation time.

FIGURE 5

Plots of the experimental and calculated B-factors of the C_α atoms as a function of residue number along the chain. The positions of residues 66 and 154 are marked in the original crystal structure.

FIGURE 6

RMSD over the trajectory of the C_α atoms of the loop 138–149 taking as the reference frame the starting structure.

FIGURE 7

Superimposed average structures from the MD simulations of the wild-type (black) and double mutant (gray) IN.

FIGURE 8

RMSD from the initial structure for all nonhydrogen 5CITEP atoms as a function of simulation time.

FIGURE 9

Time evolution of the distance between the fixed center of the catalytic triad (D64, D116, and E152) and the center of the indole and tetrazole rings of the ligand for the (a) wild-type and the (b) double mutant complexes.

FIGURE 10

The largest correlated motions for the HIV IN catalytic core domains of (a) wild-type and (b) double mutant with a bound inhibitor, 5CITEP. For each figure, two protein trace structures from the maximal and minimal projections along the largest eigenvector were superimposed to show the largest correlated motions (maximum in black and minimum in gray). The two major moving loops, designated as Loop A and Loop B, are highlighted in thick black. Each structure was slightly rotated to show each loop structure clearly. For quantitative comparisons of the two structures, the 154 C_α-C_α distances of each maximal and minimal structure were measured (c).

FIGURE 11

Comparison of the average structures from the (a) wild-type and the (b) double mutant T66I/M154I IN complex MD simulations.

FIGURE 12

Hypothetical proposed mechanism for the HIV-1 IN inhibition (a) 5CITEP/wild-type IN complex, and (b) drug resistant 5CITEP/T66I/M154I IN complex, by MD studies.