Phytochemical Analysis and Binding Interaction of Cotton Seed Cake Derived Compounds with Target Protein of Meloidogyne incognita for Nematicidal Evaluation

Abstract

The root-knot nematode Meloidogyne incognita is one of the most damaging plant-parasitic nematodes and is responsible for significant crop losses worldwide. Rising human health and environmental concerns have led to the withdrawal of commonly used chemical nematicides. There has been a tremendous demand for eco-friendly bio-nematicides with beneficial properties to the nematode hosting plants, which encourages the need for alternative nematode management practices. The current study was undertaken to determine the nematicidal potential of cotton seed cake (CSC) against second-stage juvenile (J2) hatching, J2 mortality, and J2 penetration of M. incognita in tomato plants in vitro. J2s and egg masses of M. incognita were exposed to four concentrations (250, 500, 750, and 1000 mg/L) of CSC extracts. The higher J2 mortality and inhibition of J2 hatching were found at 1000 mg/L, while the least effective result was observed at 250 mg/L of the CSC extract. The CSC extract applied with the concentrations mentioned above also showed inhibition of J2 penetration in tomato roots; 1000 mg/L showed the highest inhibition of penetration, while 250 mg/L displayed the least inhibition. Using gas chromatography-mass spectroscopy, we identified 11 compounds, out of which 9,12-Octadecadienoic acid, Hexadecanoic acid, and Tetradecanoic acid were found as major compounds. Subsequently, in silico molecular docking was conducted to confirm the nematicidal behavior of CSC based on binding interactions of the above three major compounds with the targeted protein acetylcholine esterase (AChE) of M. incognita. The values of binding free energy are -5.3, -4.5, and -4.9 kcal/mol, observed for 9,12-Octadecadienoic acid, n-Hexadecanoic acid, and Tetradecanoic acid, respectively, suggesting that 9,12-Octadecadienoic acid binds with the receptor AChE more efficiently than the other two ligands. This study indicates that CSC has nematicidal potential that can be used to control M. incognita for sustainable agriculture.

Keywords: molecular docking; oil seed cake; phytochemical analysis; plant-parasitic nematodes; sustainable management.

Figure 1

Scanning electron microscopy showing the perineal pattern of M. incognita. The high squared dorsal arch and wavy striae are key features of M. incognita.

Figure 2

GC-MS chromatograms of methanolic extract of cotton seed cake.

Figure 3

The best docked poses of AChE receptor with (a) 9,12-Octadecadienoic acid, (b) n-Hexadecanoic acid, and (c) Tetradecanoic acid. Blue stick represents the ligands, in which carbon and its valanced hydrogen atoms are shown by blue color, whereas oxygen atoms are displayed by red color. The colors present in protein structure are based on the different amino acids, which exhibit in the protein. The 9,12-Octadecadienoic acid, n-Hexadecanoic acid, and Tetradecanoic acid exhibited high affinity with aromatic and basic amino acids present in the active site of AChE. The components with aromatic rings showed high affinity due to their π–π interactions with organic residues in the binding site of AChE. The most common amino acids involved in binding with ligands are Phe, Arg, His, Gly, Ala, Ser, Leu, and Gln. The amide groups and hydroxyl groups of amino acids are involved in making hydrogen bonds with the -COOH group of these ligands.

Figure 4

The 2D and 3D representation of interactions for receptor (AChE) docked with (a) 9,12-Octadecadienoic acid, (b) n-Hexadecanoic acid, and (c) Tetradecanoic acid.

Figure 5

Effect of different concentrations of cotton seed cake on J2 hatching of M. incognita over four days of incubation in vitro.