Systematic Analysis of the HIV-1 Protease Active-Site Conformational Space Across 690 Crystal Structures

Abstract

Human Immunodeficiency Virus-1 protease (HIV-1 PR) is among the most extensively studied drug targets in the Protein Data Bank (PDB), with more than 600 structural models predominantly derived by X-ray crystallography. This study presents a comprehensive analysis of the binding-site conformational space across the available structural record: 690 crystal structures deposited in the PDB with ≥90% sequence identity and resolution better than or equal to 2.50 Å, of which 684 were successfully featurized by pipeline. The structural dataset covers wild-type enzyme, crystallographic stabilization mutants, drug-resistant variants, and 452 distinct inhibitor binders. Each binding site was featurized as a volume-filling point cloud with six descriptors (electrostatic potential, lipophilicity, and pharmacophoric features) and represented as a geodesic distance matrix with further embedding in spectral distance space. Affinity propagation clustered all pockets into 16 discrete conformational states, with four dominant states accounting for 85% of all structures. The chemical space of the 452 extracted inhibitors is largely continuous, and its partitioning does not correspond to the receptor's conformational landscape; yet the molecular weight of binders correlates with cavity volume: heavier inhibitors disproportionately populate the largest closed-flap state, while lighter molecules favour a distinct, tighter binding envelope. This analysis provides a structural basis and insights for ensemble-based virtual screening, de novo generation of inhibitors, and the systematic interpretation of evidenced structure–ligand data across the HIV-1 PR inhibitor landscape.