Nimbolide as a natural fungicide against Black Mold disease of Allium cepa: A molecular docking and simulation-based study

Black mold disease provoked by Aspergillus niger is one of the major postharvest diseases in Allium cepa . In the present study, efforts have been made to model the polygalacturonase protein of Aspergillus niger that is involved in disease progression as a promising molecular target for the identification of novel fungicides through computational approach. We used I-TASSER to determine the 3D structure of the target protein and docked it with naturally occurring phytoalexins which included nimbolide, nimbolin, Azadiradione, Quercetin and Azadirone. The result of present study revealed that nimbolide has the greatest affinity towards polygalacturonase as compared to other phytoalexins which binds the protein at amino acid residues Gln205, Gln261, Tyr262 with 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, this may lead to inhibition of pathogenic protein. Thus, it is of interest to consider the molecule for further validation at lab and field conditions for ensuring food and nutritional security.