Unveiling key hub genes in E. coli biofilm formation: An in silico approach integrating differential gene expression, biosurfactant targeting, MD simulation and MM-PBSA free energy calculations

Abstract

Biofilm formation by Escherichia coli is a critical factor in antibiotic resistance and persistent infections, posing significant challenges to public health. In this study, we evaluated the biofilm inhibition potential of two novel biosurfactants, BG2A and BG2B, targeting differentially expressed genes (DEGs) during the maturation stages of biofilm development. Differential gene expression (DGE) analysis revealed significant transcriptional changes in biofilm-associated pathways, with pathway enrichment and Gene Ontology (GO) analyses identifying key biological processes. Protein-protein interaction (PPi) network analysis and hub gene identification pinpointed critical regulatory nodes, such as ibpA, ybeD, and ycjF, which play pivotal roles in biofilm maturation and stability. Molecular docking studies demonstrated strong binding affinities, due to its higher binding energy and stable hydrogen bonding networks. These findings were further corroborated by molecular dynamics (MD) simulations, which demonstrated complex stability through low RMSD and RMSF values. Binding free energy calculations using the Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) approach highlighted substantial van der Waals and electrostatic contributions to binding. Additionally, principal component analysis (PCA) and free energy landscape (FEL) analyses provided insights into the conformational dynamics of the ligand–protein complexes. Taken together, this in silico study suggests that BG2A and BG2B hold promise as potential inhibitors of E. coli biofilm maturation. However, further in vitro and in vivo studies are necessary to experimentally validate their therapeutic potential and establish their efficacy in clinical settings.