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

  1. Marc Kschonsak

    Structural Biology, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  2. Christine C Jao

    Structural Biology, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  3. Christopher P Arthur

    Structural Biology, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  4. Alexis L Rohou

    Structural Biology, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  5. Philippe Bergeron

    Discovery Chemistry, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  6. Daniel F Ortwine

    Discovery Chemistry, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  7. Steven J McKerrall

    Discovery Chemistry, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  8. David H Hackos

    Neuroscience, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  9. Lunbin Deng

    Neuroscience, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  10. Jun Chen

    Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  11. Tianbo Li

    Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
    Competing interests
    Tianbo Li, Genentech employee.
  12. Peter S Dragovich

    Discovery Chemistry, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  13. Matthew Volgraf

    Discovery Chemistry, Genentech, Inc, South San Francsico, United States
    Competing interests
    No competing interests declared.
  14. Matthew R Wright

    Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, United States
    Competing interests
    No competing interests declared.
  15. Jian Payandeh

    Structural Biology, Genentech, Inc, South San Francisco, United States
    For correspondence
    jpayandeh@exelixis.com
    Competing interests
    No competing interests declared.
  16. Claudio Ciferri

    Structural Biology, Genentech, Inc, South San Francisco, United States
    For correspondence
    ciferri.claudio@gene.com
    Competing interests
    Claudio Ciferri, MK, CCJ, ALR, DFO, DHH, LD, JC, PSD, MW, CC and JCT are Genentech employees. All authors declare no competing financial interest..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0804-2411
  17. John C Tellis

    Discovery Chemistry, Genentech, Inc, South San Francisco, United States
    For correspondence
    tellis.john@gene.com
    Competing interests
    No competing interests declared.

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

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.

Metrics

  • 4,129
    views
  • 634
    downloads
  • 15
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Marc Kschonsak
  2. Christine C Jao
  3. Christopher P Arthur
  4. Alexis L Rohou
  5. Philippe Bergeron
  6. Daniel F Ortwine
  7. Steven J McKerrall
  8. David H Hackos
  9. Lunbin Deng
  10. Jun Chen
  11. Tianbo Li
  12. Peter S Dragovich
  13. Matthew Volgraf
  14. Matthew R Wright
  15. Jian Payandeh
  16. Claudio Ciferri
  17. John C Tellis
(2023)
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

Share this article

https://doi.org/10.7554/eLife.84151

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Joar Esteban Pinto Torres, Mathieu Claes ... Yann G-J Sterckx
    Research Article

    African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.

    1. Structural Biology and Molecular Biophysics
    Manming Xu, Sarath Chandra Dantu ... Shozeb Haider
    Research Article

    The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins’ performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue–residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings—residue pairs with critical dynamical interactions that have been preserved during evolution—DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.