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Side pockets provide the basis for a new mechanism of Kv channel–specific inhibition

Nature Chemical Biology volume 9, pages 507–513 (2013)Cite this article

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Abstract

Most known small-molecule inhibitors of voltage-gated ion channels have poor subtype specificity because they interact with a highly conserved binding site in the central cavity. Using alanine-scanning mutagenesis, electrophysiological recordings and molecular modeling, we have identified a new drug-binding site in Kv1.x channels. We report that Psora-4 can discriminate between related Kv channel subtypes because, in addition to binding the central pore cavity, it binds a second, less conserved site located in side pockets formed by the backsides of S5 and S6, the S4-S5 linker, part of the voltage sensor and the pore helix. Simultaneous drug occupation of both binding sites results in an extremely stable nonconducting state that confers high affinity, cooperativity, use-dependence and selectivity to Psora-4 inhibition of Kv1.x channels. This new mechanism of inhibition represents a molecular basis for the development of a new class of allosteric and selective voltage-gated channel inhibitors.

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Figure 1: Identification of pore-facing and non–pore-facing amino acids of the Psora-4 binding site.
Figure 2: Psora-4 binding site in the central cavity and side pockets.
Figure 3: Introducing Psora-4 affinity into Kv2.1 channels by creating a Kv1-like side pocket.
Figure 4: Psora-4 in the side pocket interacts with the pore helix.
Figure 5: Psora-4 blocking mechanism.

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Acknowledgements

This work was supported by Deutsche Forschungsgemeinschaft grant DE1482-3/2 to N.D. and by the P.E. Kempkes Stiftung 01/2011 to S.R. and S.M. M.S.P.S. is supported by the Wellcome Trust. M.C.S. was supported by US National Institutes of Health (NIH)–NIH Heart, Lung, and Blood Institute grant HL055236. S.M. was supported by the Studienstiftung des Deutschen Volkes e.V.

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Authors and Affiliations

  1. Institute for Physiology and Pathophysiology, University of Marburg, Marburg, Germany

    Stefanie Marzian, Susanne Rinné & Niels Decher

  2. Structural Bioinformatics and Computational Biochemistry Unit, University of Oxford, Oxford, UK

    Phillip J Stansfeld & Mark S P Sansom

  3. Physiological Institute, University of Kiel, Kiel, Germany

    Markus Rapedius, Ehsan Nematian-Ardestani & Thomas Baukrowitz

  4. Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, USA

    Jennifer L Abbruzzese & Michael C Sanguinetti

  5. Sanofi-Aventis, Therapeutic Strategic Unit–Aging, Frankfurt, Germany

    Klaus Steinmeyer

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Contributions

N.D. conceived the study. S.M. performed the majority of the experiments. P.J.S. and M.S.P.S. performed the ligand dockings and MDSs. M.R., E.N.-A. and T.B. performed the inside-out macropatch clamp experiments. J.L.A. and M.C.S. performed the cut-open oocyte Vaseline gap measurements. S.R. and S.M. acquired funding. N.D., M.C.S., T.B., S.R., K.S. and S.M. wrote the manuscript.

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Correspondence to Niels Decher.

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The authors declare no competing financial interests.

Supplementary information

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Supplementary Results (PDF 1096 kb)

Supplementary Video 1

Linear interpolation between open (KvChim) and closed (MlotiK) Kv1.5 models (MOV 32029 kb)

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Marzian, S., Stansfeld, P., Rapedius, M. et al. Side pockets provide the basis for a new mechanism of Kv channel–specific inhibition. Nat Chem Biol 9, 507–513 (2013). https://doi.org/10.1038/nchembio.1271

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