Structural insights into insect-selective sodium channel toxins drive AI-enhanced biopesticide design

Abstract

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 Na v PaS 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 Na v PaS 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.