Molecular docking and dynamics simulation studies uncover the host–pathogen protein–protein interactions in soybean (Glycine max (L.) Merr.) and Groundnut bud necrosis virus: first report

Abstract

Background Soybean is a widely consumed oilseed crop with economic importance. It is enriched with numerous bioactive compounds that have health-promoting properties. Groundnut bud necrosis virus (GBNV) affects many agriculturally important crops, such as soybean, resulting in crop losses. GBNV is a single-stranded RNA virus from the genus Orthotospovirus and family Bunyaviridae. It is transmitted by insect vectors (thrips) and is further aggravated by secondary transmission from infected plants to others in the same field. There are no commercially available drugs against GBNV; thus, there is a need to explore phytomolecules that control the infection. This study utilizes soybean proteins (CAM, CDK1, Cul1, GSK3, HSP70, LOX, PCNA, and TCP) and GBNV proteins (CP, EGP, MP, NSP, NS, and RDRP) for the analysis of their inhibitory interactions. Physicochemical properties for both protein groups were examined. The molecular basis for the selective predictive association of these protein interactions was evaluated using in silico molecular docking approaches, dynamics simulations analysis, and post-simulation computational analyses. Results The results indicate that among these 50 protein–protein interactions, heat shock protein 70 (HSP70) exhibited potential inhibitory action against the RNA-dependent RNA polymerase (RDRP) with −12.12 kcal/mol binding affinity (z-score: 0.0). RDRP is an essential enzyme required for the transcription and replication of the viral genome. HSPs function in both abiotic and biotic stresses. Although further studies are required, these preliminary findings will be useful for developing new therapeutic agents against the virus, thus paving the way for researchers to find better alternatives. Conclusion This is the first study to combine prediction, structural validation, and interface analysis of the interaction between soybean and GBNV proteins.