In-silico Studies Calculated a New Chitin Oligomer Binding Site Inside Vicilin: A Potent Antifungal and Insecticidal Agent

Ahsan Saeed; Zahra Rafiq; Muhammad Imran; Qamar Saeed; Muhammad Q Saeed; Zahid Ali; Rana K Iqbal; Saber Hussain; Binish Khaliq; Sohaib Mehmood; Ahmed Akrem

doi:10.1177/15593258221108280

In-silico Studies Calculated a New Chitin Oligomer Binding Site Inside Vicilin: A Potent Antifungal and Insecticidal Agent

Dose Response. 2022 Jun 16;20(2):15593258221108280. doi: 10.1177/15593258221108280. eCollection 2022 Apr-Jun.

Authors

Affiliations

¹ Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan.
² Forman Christian College (A Chartered University), Lahore, Pakistan.
³ Department of Entomology, Bahauddin Zakariya University, Multan, Pakistan.
⁴ Department of Microbiology, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan.
⁵ Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University, Islamabad, Pakistan.
⁶ Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.
⁷ Department of Botany, University of Okara, Okara, Pakistan.

Abstract

Vicilins are major seed storage proteins and show differential binding affinities toward sugar moieties of fungal cell wall and insect gut epithelium. Hence, purpose of study is the thorough in-silico characterization of interactions between vicilin and chitin oligomer followed by fungal and insecticidal bioassays. This work covers the molecular simulation studies explaining the interactions between Pisum sativum vicilin (PsV) and chitin oligomer followed by protein bioassay against different pathogens. LC-MS/MS of purified PsV (∼50 kDa) generated residual data along high pea vicilin homology (UniProtKB ID; P13918). Predicted model (PsV) indicated the characteristic homotrimer joined through head-to-tail association and each monomer is containing a bicupin domain. PsV site map analysis showed a new site (Site 4) into which molecular docking confirmed the strong binding of chitin oligomer (GlcNAc)₄. Molecular dynamics simulation data (50 ns) indicated that chitin-binding site was comprised of 8 residues (DKEDRNEN). However, aspartate and glutamate significantly contributed in the stability of ligand binding. Computational findings were further verified via significant growth inhibition of Aspergillus flavus, A. niger, and Fusarium oxysporum against PsV. Additionally, the substantial adult population of Brevicoryne brassicae was reduced and different life stages of Tribolium castaneum also showed significant mortality.

Keywords: Pisum sativum; antifungal; insecticidal; molecular dynamics simulation; vicilin.