Hit to lead optimization of carbothioate derivatives as novel succinate dehydrogenase inhibitors using a multistep virtual screening approach

BACKGROUND: Succinate dehydrogenase inhibitors (SDHIs) represent one of the most important fungicide subclasses for the chemical control of plant diseases. The identification of novel SDHIs with innovative scaffolds through virtual screening is crucial for pathogenic fungi management and food security. RESULTS: A novel carbothioate hit compound was identified through a hierarchical virtual screening protocol with novel β-ketonitrile fungicidal compound as query structure. The structural optimization resulted optimal compound A12 showed good in vitro broad-spectrum fungicidal activities against Rhizoctonia solani, Sclerotiorum sclerotiorum, Botrytis cinerea and Fusarium graminearum, with EC₅₀ values of 4.38, 10.76, 7.69, and 10.28 μg/mL, respectively. A12 also exhibited promising in vivo protective efficacy against rice sheath blight. Scanning electron microscopy (SEM) observation and SDH enzymatic assays revealed that A12 served as a potent SDH inhibitor, with an IC₅₀ value of 4.53 μM. Computational binding mode research demonstrated that A12 formed H-bonds, cation-π and T-π interaction with SDH. CONCLUSION: The identified optimal carbothioate compound A12 served as a potent lead compound for further structural optimization as potential agricultural SDHI fungicides.