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Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is a devastating epidemic disease on wheat. At present, the control of FHB is mainly dependent on the application of fungicides, such as benzimidazoles, whose targets are β2-tubulin. The aim of this research was to investigate the interaction between β2-tubulin protein of F. graminearum with benzimidazoles. The β2-tubulin structure was obtained by homology modeling method. And structures of β2-tubulin complexed with the small molecular inhibitor: carbendazim, benomyl, thiabendazole and thiophanate-methyl, were built respectively by molecular docking based on the β2-tubulin structure. Molecular docking results showed that the amino acid Phe198 and Val236 in F. graminearum β2-tubulin can directly interact through hydrogen bonds with four benzimidazole molecules, and the amino acid residues at position 50, 134, 165, 167, 198, 200, 236, 237, 239, 240, 250, 253, 257, 314 of F. graminearum β2-tubulin can form a drug binding pocket. In addition, the binding energy of β2-tubulin/carbendazim is lowest(-5.72 kcal/mol)and the affinity is highest, compared with the other three complexes. Then, the sensitivity of F. graminearum to four benzimidazole fungicides were tested using mycelium growth rate method, the results showed that the EC50 value of F. graminearum to carbendazim, benomyl, thiabendazole and thiophanate-methyl was 0.772 mg/L, 0.862 mg/L, 1.088 mg/L, 13.266 mg/L, respectively. This indicated that F. graminearum is more sensitive to carbendazim than to the other three fungicides, which is consistent with the molecular docking results.