Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach

Abstract

Bursaphelenchus xylophilus is a destructive phytophagous nematode that mainly infects pine species and causes pine wilt disease (PWD). PWD is one of the most devastating diseases that has damaged the pine forests of eastern Asia and Portugal for the last four decades. B. xylophilus infects healthy pine trees through Monochamus beetles and its subsequent proliferation results in destruction of the infected pine trees. The poor water solubility and high cost of currently used trunk-injected chemicals such as avermectin and abamectin for the prevention of PWD are major concerns. Thus, for the identification of new compounds targeting the different targets, five proteins including cathepsin L-like cystein proteinase, peroxiredoxins, hsp90, venome allergen protein and tubulin that are known to be important for development and pathogenicity of B. xylophilus were selected. The compounds were virtually screened against five proposed targets through molecular docking into hypothetical binding sites located in a homology-built protein model. Of the fifteen nematicides screened, amocarzine, mebendazole and flubendazole were judged to bind best. For these best docked compounds, structural and electronic properties were calculated through density functional theory studies. The results emphasize that these compounds could be potential lead compounds that can be further developed into nematicidal chemical against B. xylophilus. However, further studies are required to ascertain the nematicidal activity of these compounds against phytophagous nematode.

Molecular Docking and Dynamics Simulation of Protein β-Tubulin and Antifungal Cyclic Lipopeptides

“…For example, in the fungus Fusarium oxysporum , 2,4-di- tert -butylphenol, a compound that effectively inhibits spore germination and hyphal growth in vitro, was discovered through molecular docking analyses to potentially bind to β-tubulin protein at the HIS 118 and THR 117 residues [17]. In the plant parasitic nematode Bursaphelenchus xylophilus , the compounds amocarzine, mebendazole, and flubendazole were revealed to bind various target sites, including β-tubulin, by analyzing hypothetical binding sites in a protein model constructed through molecular docking [18].…”

In Silico Identification of Potential Inhibitor Against a Fungal Histone Deacetylase, RPD3 from Magnaporthe Oryzae

“…The hydrophobic non-bonded interactions are formed with Pro42, His191, and Phe218 (Figure 3c). Generally, the non-bonded interaction is involved in making the protein-ligand complex more stable and establishing non-bonded force (Vander Waal’s) to make the ligands achieve its stable conformation for better activity [38].…”

Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection

“…Further, advancement in the bioinformatics assisted molecular and dynamics simulation studies can also help to decipher the molecular and biochemical mechanisms. Moreover, several reports have already been initiated on the structure prediction and their possible interaction with different cellular protein/enzyme targets [207][208][209][210]. Cob-Calan et al [211] demonstrated the interactions of the cyclic lipopeptides iturin A, fengycin, and surfactin with β-tubulin using molecular docking and molecular dynamics simulation.…”