In-silico prediction, characterization, molecular docking and dynamic simulation studies for screening potential fungicides against leaf rust of Triticum aestivum

• Published in: Journal of biomolecular structure & dynamics Vol. 42; no. 19; pp. 9993 - 10005
• Main Authors: Gosavi, Gokul, Jade, Dhananjay, Ponnambalam, Sreenivasan, Harrison, Michael A., Zhou, Huanbin
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 02-12-2024
• Subjects: Basidiomycota; Binding Sites; Computer Simulation; Fungicides, Industrial - chemistry; Fungicides, Industrial - metabolism; Fungicides, Industrial - pharmacology; MAP kinase 1; molecular docking; Molecular Docking Simulation; molecular dynamic simulation; Molecular Dynamics Simulation; molecular modeling; Plant Diseases - microbiology; Plant Leaves - chemistry; Plant Leaves - metabolism; Plant Leaves - microbiology; Protein Binding; Puccinia - chemistry; Puccinia triticina; Triticum - microbiology; virtual screening; Puccinia triticina; molecular docking; virtual screening; molecular dynamic simulation; molecular modeling; MAP kinase 1
• ISSN: 0739-1102; 1538-0254; 1538-0254
• DOI: 10.1080/07391102.2023.2254410

Triticum aestivum is an important crop worldwide, which is a large source of food grain. T.aestivum demands on developed countries will grow every year, this increase in the demand is profoundly serious especially in the light climate change which would lead to a 29% reduction in final productivity. Rust fungus attacks the T.aestivum, specifically newly planted T.aestivum plants, which block the vascular system, stun, and finally damage grain and tillers. In present study we predict the 3D structure then find the binding pocket and conserved domains for MAPkinase-1 of Puccinia triticina. After that, screen the FungiPAD, PubChem, NPAtlas databases by physicochemical properties, docking, clustering, ADME (Absorption, distribution, metabolism, and excretion) and PAINS (pan assay interference compounds) filter analysis. Through this screening process screen the nine compounds, which are benzovindiflupyr, furametpyr, isopyrazam, fenaminstrobin, and flumorph from Fungicide database: zoxamide, vinclozolin, pentachloronitrobenzene, and dithianon from PubChem database, based on the binding energy, clustering, ADME and PAINS analysis. All these nine compounds bind in the same pocket and show the same pattern of interaction. Among these nine compounds, select the two compounds (PubChem:122087 (-6.96 kcal/mol) and FDBD02904 (-8.62 kcal/mol)) based on binding energy for 100 ns MD simulation and free energy calculation. MD simulation shows stability throughout the simulation, and it shows the sable interaction when compounds bind to the MAPKinase 1 protein which may help to protein kinase pathways in plant defense response. This result helps to design alternative fungicide against the wheat rust disease.
Communicated by Ramaswamy H. Sarma