Repurposing the human antiviral phytochemical drug, agathisflavone, for management of begomoviruses infecting plants

Begomoviruses are whitefly-transmitted circular single-stranded DNA viruses causing severe yield losses in economically important crops, particularly in tropical and subtropical regions. Current management strategies depend mainly on pesticide-based vector control and host resistance, which are limited by environmental concerns and frequent resistance breakdown due to rapid viral evolution. This study aimed to identify and validate a small-molecule inhibitor targeting the replication initiator protein (Rep) of tomato leaf curl New Delhi virus (ToLCNDV), a major begomovirus infecting tomato. Fifteen plant-derived phytochemicals with reported antiviral activity against human viruses were screened in silico against the ToLCNDV Rep protein. Molecular docking and molecular dynamics simulations were used to evaluate binding affinity and stability, while protein–DNA docking assessed overlap between inhibitor-binding residues and the viral DNA-binding domain. As agathisflavone showed the most stable binding with Rep, it was isolated from cashew ( Anacardium occidentale ) leaves and formulated as an agathisflavone-enriched formulation (AGT-F). AGT-F was applied as a foliar spray and seed treatment, alone or in combination, under different inoculation regimes. Antiviral efficacy was assessed through symptom development, viral load estimation, and oxidative stress analysis. Agathisflavone emerged as the lead compound, showing high binding affinity (−8.6 kcal/mol) toward Rep and stable interaction during a 100 ns molecular dynamics simulation. Protein–DNA docking revealed overlapping residues between the agathisflavone-binding site and the viral DNA-binding domain of Rep. In planta studies showed delayed symptom development up to 20 days post-inoculation (dpi), compared to 8 dpi in control plants, and up to 99 % reduction in viral accumulation following combined seed treatment and foliar spray. AGT-F also reduced virus-induced oxidative stress and improved antioxidant status and seedling vigour. This study demonstrates cross-kingdom repurposing of agathisflavone as a promising eco-friendly antiviral molecule targeting the Rep protein of ToLCNDV, providing a rational strategy for begomovirus disease management. • This study validated a 3D model of the replication initiator protein, serving as a new framework for understanding begomovirus replication. • Molecular docking and dynamics simulations show that the antiviral compound, agathisflavone (AGT), binds to the Rep protein in a way that directly blocks its ability to interact with viral origin of replication. • Agathisflavone-enriched formulation (AGT-F) significantly reduced viral symptoms and titres in Nicotiana benthamiana and tomato plants through both foliar application and seed priming. • AGT-F not only suppressed viral accumulation but also mitigated virus-induced oxidative stress, suggesting a dual mode of action that enhances host defence and contributes to sustainable virus management.