Title

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

Authors

Pranshu Dangwal^1,*, Saransh Juyal¹, Arun Bhatt¹, Mamta Baunthiyal¹ & Dev Bukhsh Singh²

Affiliation

¹Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, Uttarakhand-246194, India; ²Department of Biotechnology, Siddharth University, Kapilvastu, Siddharth Nagar, India; *Corresponding author

Email

Pranshu Dangwal - E - mail: pranshu_dangwal@gbpiet.ac.in

Saransh Juyal - E - mail: juyalsaransh2001@gmail.com
Arun Bhatt - E - mail: mailarunbhatt@gmail.com
Mamta Baunthiyal - E - mail: mamtabaunthiyal@yahoo.co.in
Dev Bukhsh Singh - E - mail: answer.dev@gmail.com

Article Type

Research Article

Date

Received May 1, 2025; Revised May 31, 2025; Accepted May 31, 2025, Published May 31, 2025

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.

Keywords

Allium cepa, phytoalexins, nimbolide, polygalacturonase, molecular modelling, molecular docking

Citation

Dangwal et al. Bioinformation 21(5): 1050-1056 (2025)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.