Discovery of bioactive inhibitors targeting onion yellow dwarf virus coat protein based on molecular docking and...

Onion yellow dwarf virus (OYDV), a devastating pathogen affecting garlic (Allium sativum), causes significant agricultural losses worldwide. Current management strategies rely on chemical pesticides that pose environmental and toxicity concerns, hence emphasizing the urgent need for eco-friendly alternatives.

This study aimed to discover plant-derived inhibitors of OYDV by targeting its coat protein through several computational approaches. The CP of OYDV was characterized, and a high-quality 3D model was validated. Through high-throughput molecular docking of 46 plant-based metabolites, four compounds were selected: hypericin, celastrol, sanguinarine, and asiatic acid with superior binding affinities (below - 9 kcal/mol). These four had exceptionally high docking scores, outperforming the commercial antivirals ribavirin and ningnanmycin. These top ligands have been proven to be less hazardous via in silico toxicity profiling, which makes them suitable for the development of biopesticides. DFT analysis and MD simulations validated the stability and structural flexibility of the hypericin and coat protein, respectively.

These computational findings suggest hypericin could be a promising lead compound for developing sustainable OYDV management strategies.