Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: Flap dynamics and binding mechanism

Abstract

Inhibitors of HIV-1 protease (HIV-1-pr) generally only bind to the active site of the protease. However, for some mutants such as V32I and M46L the TMC114 can bind not only to the active cavity also to the groove of the flexible flaps. Although the second binding site suggests the higher efficiency of the drug against HIV-1-pr, the drug resistance in HIV-1-pr due to mutations cannot be ignored, which prompts us to investigate the molecular mechanisms of drug resistance and behavior of double bound TMC114 to HIV-1-pr. The conformational dynamics of HIV-1-pr and the binding of TMC114 to the WT, V32I and M46L mutants were investigated with all-atom molecular dynamic (MD) simulation. The 20 ns MD simulation shows many fascinating effects of the inhibitor binding to the WT and mutant proteases. MM-PBSA calculations explain the binding free energies unfavorable for the M46L and V32I mutants as compared to the WT. For the single binding the less binding affinity can be attributed to the entropic loss for both V32I-1T and M46L-1T. Although the second binding of TMC114 with flap does increase binding energy for the mutants (V32I-2T and M46L-2T), the considerable entropy loss results in the lower binding Gibbs free energies. Thus, binding of TMC114 in the flap region doesn't help much in the total gain in binding affinity of the system, which was verified from this study and thereby validating experiments.

Conformational variation of an extreme drug resistant mutant of HIV protease

“…The PR20MD simulation equilibrated to the highest RMS deviation of 2.4 ± 0.3 Å; while PR20 D25N MD gave the lowest RMS value of 1.5 ± 0.1 Å. The scale of the fluctuations is similar to the range described in previous simulations of HIV-1 protease and its mutants by other groups [20; 49–51]. …”

“…The relationship between drug resistant mutations and flap dynamics is complex. Recently; for example; the effects of single mutations V32I and M46L were studied by molecular dynamics in [20]. However; the observation of widely separated flaps in the structures of drug resistant mutants such as PR20 [13] and MDR769 [21] suggests that altered flap flexibility contributes to resistance.…”

Interactions of the α3β2 Nicotinic Acetylcholine Receptor Interfaces with α-Conotoxin LsIA and its Carboxylated C-terminus Analogue: Molecular Dynamics Simulations

“…Positive values represent enhanced flexibility of the backbone of the LsIA bound complex, whereas lower flexibility (relative to LsIA#) is demonstrated by negative values. Only residues that show differences in RMSF values greater than 0.5 (Å) were included, as this value has been used as a cut-off point in previous MD simulation studies comparing similar proteins in different states [ 48 , 49 ].…”

“…Positive values represent enhanced flexibility of the backbone of the LsIA bound complex, whereas lower flexibility (relative to LsIA#) is demonstrated by negative values. Only residues that show differences in RMSF values greater than 0.5 (Å) were included, as this value has been used as a cut-off point in previous MD simulation studies comparing similar proteins in different states [48,49]. We also compared the differences in RMSF results between LsIA-and LsIA#-α3β2 complexes, by subtracting the RMSF values of LsIA# bound α3β2 nAChR from those of the LsIA bound complex ( Figure 3A).…”

Recent Developments and Applications of the MMPBSA Method

“…Other efforts focused on HIV viruses, including HIV-1 protease (Li D. et al, 2014 ; Tzoupis et al, 2014 ; Chen J. Z. et al, 2015 ; Meher and Wang, 2015 ; Chen, 2016 ; Hu et al, 2016 ; Sroczynski et al, 2016 ; Xanthopoulos et al, 2016 ), gp120 (Wang J. H. et al, 2015 ), gp41 (Song et al, 2014 ), reverse transcriptase (Bernardo and Silva, 2014 ), HIV integrase (Quevedo et al, 2014 ; Han et al, 2016 ), and a comparative analysis of inhibitors for HIV-1 and HIV-2 proteases (Chen et al, 2014a ). Wright et al studied 9 inhibitor-bound HIV-1 proteases and compared the absolute binding free energies computed via MMPBSA and MMGBSA with and without normal mode-derived configurational entropy.…”