Efficacy of Ipflufenoquin Against Strawberry Gray Mold: Insights from AI-driven Structural Modeling and Genome-wide Transcriptomic Analysis

Fungal diseases, particularly gray mold caused by Botrytis cinerea, pose a significant threat to strawberry production. In this study, we evaluated the efficacy of ipflufenoquin, a novel dihydroorotate dehydrogenase (DHODH) inhibitor, against fungal pathogens isolated from Korean strawberry fields in 2023. Ipflufenoquin demonstrated high in vitro sensitivity against B. cinerea and broad-spectrum activity against other key pathogens. Fruit and greenhouse trials confirmed its robust control of gray mold, including strains resistant to different classes of fungicides (SDHIs, QoIs, and benzimidazoles). However, its application led to shifts in the fungal community, promoting less sensitive species like Cladosporium and Rhizopus. To elucidate its mode of action, structural modeling with AlphaFold2 and molecular docking confirmed that ipflufenoquin binds to the quinone binding tunnel of DHODH, showing a strong correlation between binding affinity and fungicide susceptibility. Furthermore, transcriptomic profiling via RNA-seq revealed a dual transcriptomic response in B. cinerea: a widespread shutdown of primary metabolic pathways, coupled with a robust cellular stress response characterized by the up-regulation of potential resistance-related genes, including those encoding detoxification enzymes and drug efflux transporters . This integrated study not only establishes ipflufenoquin as an effective solution for managing gray mold but also provides a multi-faceted understanding of its molecular and cellular impacts, offering crucial data for sustainable disease management strategies.