# Molecular docking and simulation analysis of nimbolide with poly-galacturonase from Aspergillus niger: Managing black mold disease for Allium cepa

## TL;DR

This study explores how nimbolide interacts with a key protein in black mold disease to potentially develop new fungicides for onions.

## Contribution

The study identifies nimbolide as a novel inhibitor of poly-galacturonase in Aspergillus niger using molecular docking and simulation.

## Key findings

- Nimbolide showed the highest affinity for poly-galacturonase with -8.0 kcal/mol binding energy.
- Nimbolide formed four hydrogen bonds with residues Gln205, Gln261, and Tyr262.
- Molecular dynamics simulations confirmed the stability of the nimbolide-polygalacturonase complex.

## Abstract

Black mold disease is a major post-harvest issue in Allium cepa caused by Aspergillus niger.
Therefore, it is of interest to describe the molecular docking and simulation analysis of poly-galacturonase protein from
Aspergillus niger 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.