Binding differences of fluxapyroxad with succinate dehydrogenase across species: insights from in silico simulations

Abstract BACKGROUND Elucidating the species selectivity mechanism of succinate dehydrogenase (SDH) inhibitors (SDHIs) is crucial for the discovery novel eco‐friendly SDHI fungicides. Fluxapyroxad (FLX), a representative SDHI, was investigated through in silico study to identify species‐specific differences in its binding modes with SDH. RESULTS SDH structure models of six species were constructed, and the model predicted by Discovery Studio 3.5 was selected based on multidimensional quality assessments, compared with those from SWISS‐MODEL and AlphaFold. All SDH–FLX complexes were then subjected to 100 ns molecular dynamics, based on docking results and virtual amino acid mutations. Residues C_025, C_030 and C_034 were considered as potential differences sites across species in relation to FLX binding. At the C_025 position, the interaction between FLX and phenylalanine or leucine might be replaceable, as evidenced by the similar binding free energy, π–π interaction and H‐bond occupancy rates in Rhizoctonia solani _F025L and other fungal systems. Tryptophan at the C_030 position in Sus scrofa and Danio rerio systems, and at the C_034 position in R. solani , Zymoseptoria tritici , and Botrytis cinerea systems, exhibited similar π–π interactions that contributed to stable inhibitor binding. In Apis mellifera , S. scrofa _W030I, and Z. tritici_ W034S systems, the absence of SDHC tryptophan at C_030 and C_034 was reflected by weaker binding free energy. CONCLUSION The binding differences of FLX with SDH across species might be attributed to the π–π interaction provided by SDHC tryptophan. This study revealed the probable binding modes of FLX with SDH, which might facilitate the future design of selective SDHIs. © 2025 Society of Chemical Industry.