In silico characterization unveils Helicobacter pylori protein HP0973 as a novel EGFR-interacting virulence factor

Abstract

Helicobacter pylori infection induces gastric inflammation and carcinogenesis through multiple virulence factors. However, a substantial proportion of its genome encodes hypothetical proteins with unknown function. Characterizing these proteins is crucial to expanding our understanding of bacterial pathogenesis. This study presents comprehensive in silico characterization of the hypothetical secreted protein HP0973. Physicochemical and virulence profiling revealed HP0973 as basic, stable, non-toxic, and highly antigenic protein. Sequence alignment and phylogenetic analysis confirmed conservation among H. pylori strains with a soluble lytic transglycolase (SLT) domain (Met90 - Trp181). Protein-protein interaction networks positioned HP0973 centrally with metabolic, translational, and stress-response partners. Secondary structure mostly contained α-helical structure elements, whereas tertiary modelling favoured SWISS-MODEL structure (ERRAT 96.17%; QMEAN -1.00). Molecular docking revealed binding of HP0973 to DI/DIII domains of Epidermal Growth Factor Receptor (EGFR), competing with Epidermal Growth Factor (EGF), as confirmed by reciprocal docking. 200 ns MD simulations affirmed complex stability (RMSD: 1.015 ± 0.11 nm, RMSF 0.363 ± 0.24 nm; RoG 2.911 ± 0.04 nm), sustained H-bonds (12.12 ± 4.18), and favourable MM/GBSA binding free energy (-89.64 kcal/mol), dominated by van der Waals forces. These findings suggest HP0973 as a novel EGFR modulator in H. pylori-driven pathogenesis, warranting experimental validation for therapeutic targeting.