GCMS and Molecular Docking Based Insights into the Antifungal Potential of Bacillus Bs-06 Against Fusarium oxysporum f. sp. lycopersici

Abstract

The utilization of Bacillus spp. as eco-compatible bioresources represented a promising strategy in antifungal biotechnology. In this study, Bacillus subtilis Bs-06, isolated from the rhizosphere of healthy tomato plants, exhibited strong antagonistic activity through the secretion of diverse bioactive metabolites. Gas chromatography–mass spectrometry (GC–MS) analysis of its culture extract identified ten major compounds, including Phenol-3,5-bis(1,1-dimethylethyl), palmitic acid, oleic acid, and octadecanoic acid, which had been widely reported for antimicrobial efficacy. To investigate their Molecular Docking targeted the key virulence proteins of Fusarium oxysporum f.sp. lycopersici Cutinase (5AJH), Avr1/SIX4 (7T6A), and Avr3/SIX1 (7T69). Docking simulations revealed strong binding affinities, with Phenol-3,5-bis(1,1-dimethylethyl) showing the highest interaction energy (− 11.53 kcal/mol) against Avr3. The ligand–protein complexes were stabilized by hydrogen bonding and hydrophobic interactions, suggesting potential inhibition of pathogen virulence functions. Normal mode analysis further demonstrated differential flexibility among protein–ligand complexes, where Avr1 exhibited the highest conformational mobility, while Cutinase displayed the greatest structural rigidity. These findings established Bs-06 as a valuable source of antifungal metabolites capable of targeting virulence determinants at the molecular level. The integration of GC–MS profiling, molecular docking, and dynamic simulations underscored the potential of Bacillus derived metabolites as sustainable biocontrol agents for managing Fusarium wilt in tomato.