Computational study of bindings of HK20 Fab and D5 Fab to HIV-1 gp41

Antibodies HK20 and D5 have been shown to target HIV-1 gp41, thereby inhibiting membrane fusion that facilitates viral entry. The binding picture is static, based on the X-ray crystal structures of the Fab regions and gp41 mimetic five-helix bundle. In this study, we carried out molecular dynamics simulation to provide the dynamic binding picture. Calculated binding free energies are within reasonable range of and follow the trend of the experimental values: −15.28 kcal/mol for HK20 Fab (expt. −11.60 kcal/mol) and −17.90 kcal/mol for D5 Fab (expt. −11.70 kcal/mol). Alanine scanning at protein–protein interface reveals that the highest contributors to binding for HK20 Fab are F54 and I56, both of VH region, as well as R30′ of VL region; whereas for D5 Fab, F54 of VH region, as well as W32′ and Y94′ of VL region. HK20 F54 and I56, as well as D5 I52, F54, and T56, bind to the gp41 hydrophobic binding pocket, an important region targeted by many other fusion inhibitors. Hydrogen bonding analysis also identifies high-occupancy hydrogen bonds at the periphery of gp41 hydrophobic pocket. Considering that almost all interface residues are turn residues, further work may be directed to turn mimics. Pre-orientation by the hydrogen bonds to poise this particular turn towards the binding pocket may also be a point worth pursuing