Discovery of novel uridine‐based chitin synthase inhibitors: Design, synthesis and structure–activity relationships

Abstract Background Chitin synthase (CHS) enables the construction of fungi cell wall and insect skeleton by catalyzing the formation of chitin. CHS inhibitor (CHSI) disrupts the integrity of these structural barriers, leading to fungal cell lysis. Notably, CHSIs are considered non‐toxic to vertebrates, making CHS a promising target for the development of novel antifungal agents. Results Thirty‐three novel uridine‐based derivatives (UDs) were designed and synthesized through fragment‐based drug design (FBDD) to discover potential CHSIs. Bioassays demonstrated that most of the synthesized compounds exhibited excellent fungicidal activity against Alternaria alternata and Botrytis cinerea , with inhibition rates exceeding 80% at 100 μg mL − 1 . Specifically, compound 5a showed significantly stronger fungicidal activity (EC 50 = 0.78 μg mL − 1 ) than the commercial CHSI fungicide polyoxin B (EC 50 = 46.56 μg mL − 1 ). In vivo antifungal assays revealed that compound 5a effectively suppressed the infection of Alternaria alternata and Botrytis cinerea , outperforming the positive control. SEM and TEM analyses indicated that compound 5a disrupted the fungal cell wall and membrane. Enzyme inhibition assays confirmed that compound 5a exhibited superior CHS inhibitory activity (IC 50 = 1.47 μg mL − 1 ) compared to polyoxin B (IC 50 = 1.84 μg mL − 1 ), and molecular docking simulations demonstrated a stronger binding affinity of compound 5a to CHS relative to polyoxin B. A 3D‐QSAR model was established to elucidate the structure–activity relationships (SARs) and provide guidance for further structural optimization. Toxicity tests showed that compound 5a had no significant inhibitory effect on mung bean seed germination and exhibited low toxicity to zebrafish. Conclusion Compound 5a is a promising antifungal agent with a unique mechanism of action by targeting fungal CHS. This study discovered a series of novel CHSIs with excellent fungicidal activities, offering valuable candidates for fungicide development. © 2026 Society of Chemical Industry.