Identification of small molecule inhibitors targeting Wheat Dwarf Virus Rep protein by virtual screening

Wheat dwarf virus (WDV) is a prominent cereal pathogen that causes wheat dwarf disease and is transmitted by the leafhopper (Psammotettix alienus). WDV belongs to the Geminiviridae family and genus Mastrevirus. WDV genome comprises virion sense genes encoding coat protein and movement protein, and complementary sense genes such as Rep and Rep A are involved in rolling-circle replication. The Rep protein is highly versatile, and during replication, it plays crucial roles as a site-specific endonuclease, helicase, ATPase, and ligase. WDV infection causes dwarfing and severe yellowing, leading to heavy yield damage and economic losses. Currently, there are no approved insecticides to control leafhoppers, and the emergence of resistance-breaking WDV strains is a real challenge. Hence, small molecule inhibitors that interfere with WDV Rep protein and prevent viral infection are vital. However, small molecule-based inhibition of WDV replication has not been demonstrated and the complete structure of WDV Rep is not elucidated yet. Consequently, this study aimed to predict the full-length Rep protein structure of WDV and virtually screen the small molecules that can bind to the WDV Rep protein. The structure of the WDV Rep protein was modeled using Robetta and further refined to obtain an optimal structure with the help of the ModBase server. Ligands from ATPase inhibitors, helicase inhibitors, and synthetic libraries were screened by molecular docking using Schrodinger-Maestro with a glide module. The selected ligands were subjected to molecular dynamics and simulation for 200 ns using GROMACS v2019.1. The predicted and refined WDV Rep structure showed an excellent ERRAT score and accepted regions in the Ramachandran plot. Ligand SL2 (glide score of – 9.58) and ligand_3275 (glide score of –10.42) showed a better affinity toward the refined WDV Rep structure and were stable compared to other ligands during simulation. Therefore, ligand SL2 and ligand_3275 can act as potential candidates in modulating the activity of the WDV Rep protein and inhibiting WDV replication during infection.