Identification of a Novel Druggable Pocket in the HIV-1 gp120 C5 Domain at the Conformational Relay Junction

Abstract

HIV-1 entry requires a conformational relay that transmits the receptor-engagement signal to membrane fusion activation, yet no approved drug targets this transmission step. Here I report a novel druggable pocket in the gp120 C5 domain (Arg465-Arg472, sequence RPGGGDMR) at this relay junction, identified through computational analysis of the gp120-CD4-CCR5 ternary complex (PDB 6MEO, 3.9 Å cryo-EM). The motif is 100% conserved across 360 solved gp120 structures and untouched by all 28 known entry-inhibitor resistance mutations. The pocket passes all five Halgren druggability criteria, and molecular docking of BMS-626529 yields -6.81 kcal/mol across a 20-frame MD ensemble. Half-microsecond simulations of four independent SOSIP trimer structures from multiple clades confirm the pocket as a conformational anchor: sub-2 Å internal RMSD (1.29-1.98 Å), 0th RMSF percentile in three of four structures, kinematically decoupled from global backbone dynamics. Alchemical free energy perturbation (3 replicas, 9 legs, 1,440 ns) reveals strong negative allosteric coupling between the drug and CD4, with ΔΔG = +3.9 kcal/mol — the first measurement of the conformational relay signal strength. Umbrella sampling (29 windows, 290 ns) confirms a ~6.8-8.0 kcal/mol unbinding barrier. These results identify the gp120 C5 relay pocket as a first-in-class drug target: a molecule in this pocket terminates the conformational relay, permitting normal receptor engagement while blocking fusion activation.