Molecular docking study on the interaction between fatty acid and retinol binding protein of root knot nematode and indole-3-acetic acid for nematicide action

The root-knot nematode (RKN) Meloidogyne javanica is present in plant roots and destroys numerous economically important plants which include cereals, vegetables, grape wine, and some ornamental plants. Fatty acid and retinol-binding protein (FAR) are important in the development of nematodes in their respective hosts. Therefore, FAR is of major interest as a target for drug development. The three-dimensional structure of the FAR protein was predicted using the MODELLER 9.24, and the homology modeling based predicted model was further validated using the PROCHECK analysis tool. The metabolic product of Fusarium oxysporum a fungus endophytes indole-3-acetic acid was found to bind at the active sites of fatty acid and retinol-binding protein of Meloidogyne javanica with lowest binding energy -6.4 Kcal/mole. The molecular docking interactions analysis of FAR protein with the ligand indole-3-acetic acid using AutoDock Vina allows us to detect the specific amino acid residues like Leu- 59, Asp-72, and Lys-120. Within the FAR proteins binding pockets these amino acids play a crucial role in the ligand-binding process and show the affinity towards ligand. The FAR protein model generated through the homology modeling approach along with structural insights gained from molecular docking analysis will promote the indole-3-acetic acid as a potent nematicide and a novel molecule for the rational drug design process. The present study contributes to the understanding mechanism of the nematicide effect of indole-3-acetic acid. Based on our InSilico findings we hypothesize that indole-3-acetic acid can be inhibitory effects on root-knot nematodes.