Small molecule inhibitors of the sodium channel are common pharmacological agents used to treat a variety of cardiac and nervous system pathologies. They act on the channel via binding within the pore to directly block the sodium conduction pathway and/or modulate the channel to favor a non-conductive state. Despite their abundant clinical use, we lack specific knowledge of their protein–drug interactions and the subtle variations between different compound structures. This study investigates the binding and accessibility of nine different compounds in the pore cavity of the Nav1.5 sodium channel using enhanced sampling simulations. We find that most compounds share a common location of pore binding—near the mouth of the DII–III fenestration—associated with the high number of aromatic residues in this region. In contrast, some other compounds prefer binding within the lateral fenestrations where they compete with lipids, rather than binding in the central cavity. Overall, our simulation results suggest that the drug binding within the pore is highly promiscuous, with most drugs having multiple low-affinity binding sites. Access to the pore interior via two out of four of the hydrophobic fenestrations is favorable for the majority of compounds. Our results indicate that the polyspecific and diffuse binding of inhibitors in the pore contributes to the varied nature of their inhibitory effects and can be exploited for future drug discovery and optimization.
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Voltage-Gated Na Channels|
January 07 2025
Drugs exhibit diverse binding modes and access routes in the Nav1.5 cardiac sodium channel pore
Elaine Tao
,
(Conceptualization, Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review & editing)
1Division of Biomedical Science and Biochemistry, Research School of Biology,
Australian National University
, Canberra, Australia
Elaine Tao: [email protected]
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Ben Corry
1Division of Biomedical Science and Biochemistry, Research School of Biology,
Australian National University
, Canberra, Australia
Correspondence to Ben Corry: [email protected]
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Elaine Tao
Conceptualization, Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review & editing
1Division of Biomedical Science and Biochemistry, Research School of Biology,
Australian National University
, Canberra, Australia
Correspondence to Ben Corry: [email protected]
Elaine Tao: [email protected]
Disclosures: The authors declare no competing interests exist.
Received:
August 26 2024
Revision Received:
November 05 2024
Accepted:
December 07 2024
Online ISSN: 1540-7748
Print ISSN: 0022-1295
Funder(s):
Australian Government Research Training Program
© 2025 Tao and Corry
2025
Tao and Corry
This article is distributed under the terms as described at https://rupress.org/pages/terms102024/.
J Gen Physiol (2025) 157 (2): e202413658.
Article history
Received:
August 26 2024
Revision Received:
November 05 2024
Accepted:
December 07 2024
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Citation
Elaine Tao, Ben Corry; Drugs exhibit diverse binding modes and access routes in the Nav1.5 cardiac sodium channel pore. J Gen Physiol 3 March 2025; 157 (2): e202413658. doi: https://doi.org/10.1085/jgp.202413658
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