Structural basis for modulation of human NaV1.3 by clinical drug and selective antagonist

Xiaojing Li,Yiwei Gao,Yan Zhao,Daohua Jiang,Hongwei Zhang,Xuejun Cai Zhang,Feng Xu,Yanchun Zheng,Yanli Dong,Bei Yang,Shuli Zhang,Hao Xu,Jianyuan Sun

doi:10.1038/s41467-022-28808-5

Abstract

Voltage-gated sodium (NaV) channels play fundamental roles in initiating and propagating action potentials. NaV1.3 is involved in numerous physiological processes including neuronal development, hormone secretion and pain perception. Here we report structures of human NaV1.3/β1/β2 in complex with clinically-used drug bulleyaconitine A and selective antagonist ICA121431. Bulleyaconitine A is located around domain I-II fenestration, providing the detailed view of the site-2 neurotoxin binding site. It partially blocks ion path and expands the pore-lining helices, elucidating how the bulleyaconitine A reduces peak amplitude but improves channel open probability. In contrast, ICA121431 preferentially binds to activated domain IV voltage-sensor, consequently strengthens the Ile-Phe-Met motif binding to its receptor site, stabilizes the channel in inactivated state, revealing an allosterically inhibitory mechanism of NaV channels. Our results provide structural details of distinct small-molecular modulators binding sites, elucidate molecular mechanisms of their action on NaV channels and pave a way for subtype-selective therapeutic development.

Highlights

Voltage-gated sodium (NaV) channels play fundamental roles in initiating and propagating action potentials
Emergent evidence indicates NaV1.3 is important for fetal neuronal development, and mutations in NaV1.3 are related to focal epilepsies and polymicrogyria[6–8]
We first examined the functional characteristics of human NaV1.3/β1/β2 co-expressed in human embryonic kidney (HEK) 293 cells by whole-cell voltage clamp recording

Summary

Introduction

Voltage-gated sodium (NaV) channels play fundamental roles in initiating and propagating action potentials. Bulleyaconitine A is located around domain I-II fenestration, providing the detailed view of the site-2 neurotoxin binding site It partially blocks ion path and expands the porelining helices, elucidating how the bulleyaconitine A reduces peak amplitude but improves channel open probability. Our results provide structural details of distinct small-molecular modulators binding sites, elucidate molecular mechanisms of their action on NaV channels and pave a way for subtype-selective therapeutic development. NaV1.1, NaV1.2, NaV1.3 and NaV1.6, encoded by SCN1A, SCN2A, SCN3A and SCN8A, are highly expressed in the central nervous system (CNS)[2,3] Pathogenic variants of these NaVs are associated with neurological disorders including epilepsy, migraine and neuropathic pain[4,5]. New drug binding sites on NaVs and isoform-selective drugs are eagerly awaited to minimize potential off-target side effects

Methods

Results

Conclusion