In silico docking of natural compounds from plants against Rhizoctonia solani pectate lyase

Sheath blight disease caused by the fungal pathogen Rhizoctonia solani kuhn is one of the most devastating diseases of rice plant. The disease is controlled mostly by management practices and spraying of fungicides like validamycin. However, the development of pesticide resistance in pathogens has become a cause of concern. In addition, the application of pesticides has adverse environmental effects. Thus, efforts are being made to look for biogenic compounds that could be used for disease control. In this context, the present in silico docking study was carried out to find out the effective biogenic compounds found in plants that could antagonize the pectate lyase enzyme, which is one of the most important plant cell wall degrading enzymes. The compounds selected for the study are active ingredients of plant extracts that have been found to have antagonizing effects against R. solani. The amino acid sequence available for R. solani pectate lyase protein was retrieved from the Uniprot database (entry no. A0A0B7F4Q0) and the three-dimensional model was generated using Swiss-model server. The compounds were docked with the protein using Autodock 4.2 tool. The docking study showed that the binding energies varied between − 2.47 and − 7.79. Validamycin which is used for controlling sheath blight disease had a binding energy of − 2.47. The compounds d-5-Avenasterol (− 7.79), β-sitosterol (− 7.72), gedunin (− 7.59), nimbiol (− 7.16), cycloartenol (− 6.98), stigmasterol (− 6.76), nimbolide (− 6.33) were among the compounds with high binding affinity (low binding energy). Among the amino acids, GLU-217, ARG-326, ASP-228 were found to be predominantly involved in the H-bonding formation. Among the compounds, gedunin, nimbiol, nimbolide met all the criteria for pesticide set by the Tice rule. The compounds gedunin, nimbiol, nimbolide found in the neem plant belong to the chemical class triterpenoid (limonoids), are slightly hydrophilic in nature and soluble in alcohols, ketones and esters. The preliminary findings suggest that these compounds could be used for preparing formulations for controlling the sheath blight disease of rice.