Abstract
β−1,3-glucan synthase is the molecular target for triterpenoid and echinocandin antifungal drugs in clinical. It catalyzes the formation of β−1,3-glucan, which is the primary component of the fungal cell wall. However, the inhibition mechanism of β−1,3-glucan synthase by triterpenoid drugs remains unclear. In this study, we report cryo-electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae β−1,3-glucan synthase Fks1 and Fks2 in the apo state, the triterpenoid drug enfumafungin-bound state, and an open state. Structural analysis along with mutagenesis reveals the enfumafungin binding site, and the mechanism of the clinical drug-resistant mutations of the β−1,3-glucan synthases. Remarkably, the enfumafungin attaches on a single transmembrane helix TM5 of the β−1,3-glucan synthases, reorganizes its nearby lipid environment, and stabilizes the enzyme in a specific basal state with intact active site. Moreover, we elucidate that both the basal state and the open state are essential for FKS’s glycosyltransferase activity. Our research also shows that Fks2 is highly conserved with Fks1 in terms of structure, activity, and drug inhibition. These findings provide deep insights into the fungal cell wall synthesis, and will facilitate the development of antifungal drugs targeting β−1,3-glucan synthase.
Data availability
The cryo-EM 3D maps and the corresponding atomic models of the Fks1 and Fks2 have been deposited at the EMDB database and the RCSB PDB with the respective accession codes of EMD-66359 and 9WY1 (Fks1 in apo state), EMD-66409 and 9WZU (Fks1 in complex with enfumafungin), EMD-66410 and 9WZV (Fks1 with intact active site), EMD-66411 and 9WZX (Fks1 in open state), EMD-66408 and 9WZT (Fks2 in apo state), EMD-66407 and 9WZS (Fks2 in complex with enfumafungin), EMD-66419 and 9X04 (Fks2 with intact active site). PDB codes of previously published structures used in this study are 8WLA and 7YUY. MD simulation input, parameter, and output files are provided in Supplementary Data 1. Source data are provided as a Source Data file. Source data are provided with this paper.
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Acknowledgments
Cryo-EM data were collected in the Peking University Health Science Center Cryo-Electron Microscopy Facility. We thank Dandan Chen and Lihong Chen for facilitating data collection. We thank Yong Wang for facilitating the MD analysis. This work was supported by grants from the National Natural Science Foundation of China (32571451 and 92578126 to L.B.), Beijing Natural Science Foundation (7252080 to L.B.), and Peking University (to L.B.).
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Z.Y. and L.B. conceived and designed the experiments. Z.Y., L.S., L.W., Y.N., R.L., D.C., T.S., and L.B. performed the experiments. Z.Y., L.S., L.W., C.Y., Y.S., and L.B. analyzed the data. Z.Y. and L.B. wrote the paper with input from all authors.
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You, ZL., Sun, L., Wang, LX. et al. Inhibition mechanism of the fungal β−1,3-glucan synthases by triterpenoid antifungal drugs. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69114-8
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DOI: https://doi.org/10.1038/s41467-026-69114-8
