Structural and functional analysis of a novel flavonoid-binding hypothetical protein from Staphylococcus aureus through molecular docking and dynamics

Abstract

Staphylococcus aureus is a significant human pathogen responsible for a wide range of infections, with increasing antibiotic resistance posing a major global health challenge. Despite extensive genomic characterization, many hypothetical proteins remain functionally unannotated, limiting our understanding of bacterial adaptation and pathogenicity. This study aimed to characterize such hypothetical protein, YP_500302.1, to uncover their potential roles and therapeutic relevance. YP_500302.1 was identified as a 495-amino acid transmembrane protein, predicted to function as a glucosyltransferase. Structural and physicochemical analyses indicated its potential involvement in membrane-associated processes. Molecular docking studies with 35 polyphenols revealed that hesperidin (-9.5 kcal mol⁻¹), naringin (-9.3 kcal mol⁻¹), and rutin (-8.9 kcal mol⁻¹) exhibited the strongest binding affinities. Hydrogen bond analysis over a 10 ns molecular dynamics simulation further supported the dynamic interactions of hesperidin with key residues, particularly ASP32 and THR370. These findings highlight the importance of characterizing hypothetical proteins in S. aureus to identify novel drug targets and combat antibiotic resistance.