Molecular docking and simulation analysis of nimbolide with poly-galacturonase from <i>Aspergillus niger</i>: Managing black mold disease for <i>Allium cepa</i>.

Abstract

Black mold disease is a major post-harvest issue in <i>Allium cepa</i> caused by <i>Aspergillus niger</i>. Therefore, it is of interest to describe the molecular docking and simulation analysis of poly-galacturonase protein from <i>Aspergillus niger</i> that is involved in disease progression as a promising molecular target for the identification of novel fungicides. Hence, we used I-TASSER to model the protein and docked it with the naturally occurring phytoalexins, which included nimbolide, nimbolin, Azadiradione, Quercetin and Azadirone. We show that nimbolide has the greatest affinity towards poly-galacturonase as compared to other phytoalexins binding with residues Gln205, Gln261, Tyr262 having four hydrogen bonds and -8.0 kcal/mol binding energy. Further, molecular dynamics simulation of protein and docked nimbolide-polyglacturonase complex was carried out to validate the stability of the system at the atomic level. Based on the study, the molecule shows potential for inhibiting pathogenic proteins, making it a promising candidate for further validation under laboratory and field conditions to ensure food and nutritional security.