Cryo-EM reveals an unprecedented binding site for NaV1.7 inhibitors enabling rational design of potent hybrid inhibitors
- Genentech, Inc, United States
Abstract
The voltage-gated sodium (NaV) channel NaV1.7 has been identified as a potential novel analgesic target due to its involvement in human pain syndromes. However, clinically available NaV channel blocking drugs are not selective among the nine NaV channel subtypes, NaV1.1-NaV1.9. Moreover, the two currently known classes of NaV1.7 subtype-selective inhibitors (aryl- and acylsulfonamides) have undesirable characteristics that may limit their development. To this point understanding of the structure-activity relationships of the acylsulfonamide class of NaV1.7 inhibitors, exemplified by the clinical development candidate GDC-0310, has been based solely on a single co-crystal structure of an arylsulfonamide inhibitor bound to voltage-sensing domain 4 (VSD4). To advance inhibitor design targeting the NaV1.7 channel, we pursued high-resolution ligand-bound NaV1.7-VSD4 structures using cryogenic electron microscopy (cryo-EM). Here, we report that GDC-0310 engages the NaV1.7-VSD4 through an unexpected binding mode orthogonal to the arylsulfonamide inhibitor class binding pose, which identifies a previously unknown ligand binding site in NaV channels. This finding enabled the design of a novel hybrid inhibitor series that bridges the aryl- and acylsulfonamide binding pockets and allows for the generation of molecules with substantially differentiated structures and properties. Overall, our study highlights the power of cryo-EM methods to pursue challenging drug targets using iterative and high-resolution structure-guided inhibitor design This work also underscores an important role of the membrane bilayer in the optimization of selective NaV channel modulators targeting VSD4.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files. The NaV1.7-NaVPas/GNE-3565 coordinates and cryo-EM maps were deposited in the PDB entry ID 8F0R and EMDB entry ID EMD-28778, respectively. The NaV1.7-NaVPas/GDC-0310 coordinates and cryo-EM maps were deposited in the PDB entry ID 8F0Q and EMDB entry ID EMD-28777, respectively. The NaV1.7-NaVPas bound to the hybrid molecule 2 (GNE-9296) coordinates and cryo-EM maps were deposited in the PDB entry ID 8F0S and EMDB entry ID EMD-28779, respectively. The NaV1.7-NaVPas bound to the hybrid molecule 4 (GNE-1305) coordinates and cryo-EM maps were deposited in the PDB entry ID 8F0P and EMDB entry ID EMD-28776, respectively.
Article and author information
Author details
Funding
Genentech
- Marc Kschonsak
- Christine C Jao
- Christopher P Arthur
- Alexis L Rohou
- Philippe Bergeron
- Daniel F Ortwine
- Steven J McKerrall
- David H Hackos
- Lunbin Deng
- Jun Chen
- Tianbo Li
- Matthew Volgraf
- Matthew R Wright
- Jian Payandeh
- Claudio Ciferri
- John C Tellis
N/A
Reviewing Editor
- Jon T Sack, University of California, Davis, United States
Version history
- Received: October 12, 2022
- Preprint posted: November 10, 2022 (view preprint)
- Accepted: March 27, 2023
- Accepted Manuscript published: March 28, 2023 (version 1)
- Version of Record published: April 18, 2023 (version 2)
Copyright
© 2023, Kschonsak et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Cryo-EM reveals an unprecedented binding site for NaV1.7 inhibitors enabling rational design of potent hybrid inhibitors
eLife 12:e84151.
https://doi.org/10.7554/eLife.84151
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