In-silico prediction of domain involved in chilli protein interaction with chilli leaf curl virus and associated betasatellite encoded protein

The begomovirus-caused chilli leaf curl disease (ChiLCD) is a significant hindrance to the production of chilies (Capsicum annuum) in many chilli-growing regions worldwide. Begomoviruses are involved in protein interactions with plants to disrupt their host’s defence mechanisms. Our earlier research demonstrated that the betasatellite monopartite association on chilli plants increases the activity of the AV2 gene. Here, we predict the interacting regions among chilli-begomovirus proteins. In this study, we used seven begomoviral proteins encoded by the chilli leaf curl virus (ChiLCV Acc. No. MZ540908) and chilli leaf curl betasatellite (ChLCuB Acc. No. MZ540909) that interacted with the host proteins adenylate kinase (ADK), glycoxalases (GLO1), suppressor of gene silencing 3 (SGS3), and S-phase kinase-associated protein 1 (SKP1). We applied a range of computational approaches, including physiochemical analysis, homology modeling, domain prediction, binding site, and interface prediction. Several in silico interaction prediction approaches based on sequence and structure indicated a significant potential binding with the host proteins GLO1 and ADK. Our findings showed that the interactions between ChiLCV-A and ChCLuB are mediated by the ADK and GLO1 domains encoded by C. annuum. Similarly, in HADDOCK the AC1 and AV1 complexes with GLO1 and ADK had the lowest binding energies, respectively. The optimum and lowest binding energies for the βC1 interaction were found in the PyRx tool. We also predicted and validated the deletion and substitution sites within ADK and GLO1 proteins. This is the first systematic investigation of the interactions between the ADK, GLO1, SGS3, and SKP1 chilli proteins and ChiLCV-A and ChCLuB-encoded proteins. The findings of the present study will assist researchers in comprehending the role of viral proteins in chilli leaf curl disease.