Abstract
Many voltage-gated sodium channel-targeting animal peptide toxins are renowned for their potency and selectivity against insects. Understanding why these toxins selectively target insect sodium channels over their mammalian counterparts is crucial for developing safer and more effective pest control agents. Here, we present the cryoelectron microscopy (cryo-EM) structures of the insect sodium channel NavPaS bound to two naturally occurring insect-selective toxins, Av3 from the sea anemone and LqhαIT from the scorpion. Both toxins bind to the voltage-sensing domain 4 (VSD4) of NavPaS and disrupt fast inactivation by stabilizing the S4 segment in a deactivated conformation. While Av3 engages a membrane-embedded site between VSD4 and pore domain 1 (PD1), LqhαIT binds to the classical neurotoxin site 3, illustrating distinct binding modes that converge on a shared mechanism of action. These structures reveal the molecular determinants of insect selectivity and highlight the molecular coevolution of toxin-channel interactions, as corroborated by electrophysiology and toxicity assays. Leveraging these insights, we apply AI-driven protein design tools to increase the insecticidal potency of LqhαIT, resulting in a variant with a remarkable doubling in efficacy, as we confirm by insecticidal bioassays. This study illuminates the diverse mechanisms of sodium channel modulation and provides a framework for the structure-guided, AI-driven design of toxin-based biopesticides.
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Data availability
The cryo-EM maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession codes EMD-63108 (NavPaS-Av3); and EMD-63189 (NavPaS-LqhαIT). The atomic coordinates have been deposited in the Protein Data Bank (PDB) under accession codes 9LHZ (NavPaS-Av3); and 9LKZ (NavPaS-LqhαIT). The structures used in this paper are available in the PDB database under accession codes 1ANS, 2ASC, 5X0M, 6NT4, 7DTD, 6J8E, 7W77, 6AGF, 7DTC, 8FHD, 7WE4, 7TJ9, and 5XSY. Source data are provided with this paper.
Code availability
The ComplexDDG code has been deposited in the Zenodo database (https://doi.org/10.5281/zenodo.18150075)69. All other computational tools, including ESM-2 and A3D 2.0, are publicly available as described in references48,49.
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Acknowledgements
This research was funded by Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (no. JYB2025XDXM503 to Z.Y.), the National Natural Science Foundation of China (no. 32372580 to Z.Y., no. 32260666 to S.W. and no. 92156025 to J.M.), the National Key Research and Development Program of China (no. 2025YFC3409400 to Z.Y.), and the Emerging Frontiers Cultivation Program of Tianjin University Interdisciplinary Center (to Z.Y.). We thank Jie Shen from the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, for assisting with the SPR analysis.
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Conceptualization: H.J., and Z.Y.; Methodology: H.J., R.G., C.W., K.D., F.V.P., and Z.Y.; Investigations: H.J., R.G., C.W., H.X., S.M., Y.G., L.L., X.L., Y.L., L.Y., and R.L.; Resources: Z.Y.; Data analysis: H.J., R.G., C.W., and H.X.; Writing - original draft: H.J., R.G., C.W., H.X., Y.L., and Z.Y.; Writing - review and editing: H.J., J.X., K.D., F.V.P., Z.L., S.W., and Z.Y.; Supervision: Z.L., S.W., and Z.Y.; Project administration: Z.Y.; Funding acquisition: J.M., S.W., and Z.Y.
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Jiang, H., Gao, R., Xu, H. et al. Structural insights into insect-selective sodium channel toxins drive AI-enhanced biopesticide design. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70190-z
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DOI: https://doi.org/10.1038/s41467-026-70190-z