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

Khachatryan, Hamlet

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

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ISSN:

0321-1339 ; e-3045-3151

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Contributor(s):

Պատ․ խմբ.՝ Վ. Հ․ Համբարձումյան (1944-1959) ; Մ․ Մ․ Ջրբաշյան (1960-1965) ; Ա․ Գ․ Նազարով (1966-1983) ; Պատ․ խմբ․ տեղակալ՝ Վ․ Հ․ Ղազարյան (1983-1986) ; Պատ․ խմբ․՝ Դ․ Մ․ Սեդրակյան (1987-1999) ; Գլխավոր խմբ․՝ Ս․ Ա․ Համբարձումյան (2000-2004) ; Վ․ Ս․ Զաքարյան (2005-2018) ; Ռ․ Մ․ Մարտիրոսյան (2018-2025) ; Ա․ Ս․ Սաղյան (2026-)

Coverage:

1-11

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.