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Identification of the functional binding pocket for compounds targeting small-conductance Ca2+-activated potassium channels

Nature Communications volume 3, Article number: 1021 (2012) | Download Citation

Abstract

Small- and intermediate-conductance Ca2+-activated potassium channels, activated by Ca2+-bound calmodulin, have an important role in regulating membrane excitability. These channels are also linked to clinical abnormalities. A tremendous amount of effort has been devoted to developing small molecule compounds targeting these channels. However, these compounds often suffer from low potency and lack of selectivity, hindering their potential for clinical use. A key contributing factor is the lack of knowledge of the binding site(s) for these compounds. Here we demonstrate by X-ray crystallography that the binding pocket for the compounds of the 1-ethyl-2-benzimidazolinone (1-EBIO) class is located at the calmodulin-channel interface. We show that, based on structure data and molecular docking, mutations of the channel can effectively change the potency of these compounds. Our results provide insight into the molecular nature of the binding pocket and its contribution to the potency and selectivity of the compounds of the 1-EBIO class.

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Acknowledgements

We thank Drs Spike Horn and Pat Loll for their encouragement and helpful discussions; the structural facility of the Kimmel Cancer Center of Thomas Jefferson University for access of equipment in initial protein crystal screening and initial in-house X-ray diffraction; staff at the Beamline facility (X29A and X6A) of the Brookhaven National labs and the SYBILS Beamline 12.3.1 at the Advanced Light Source (Berkeley, CA) for assistance with collection of X-ray diffraction data. The work is supported by grants from NIH to JFZ (R01MH073060 and R01NS39355).

Author information

Affiliations

  1. Department of Molecular Physiology and Biophysics, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.

    • Miao Zhang
    •  & Ji-Fang Zhang
  2. Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.

    • John M. Pascal
  3. Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.

    • Marcel Schumann
    •  & Roger S. Armen
  4. Farber Institute for Neurosciences and Graduate Program in Neuroscience, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA.

    • Ji-Fang Zhang

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Contributions

M.Z. and J.M.P. did experiments of X-ray crystallography and the structure determination. M.S. and R.S.A. performed molecular docking and MD modelling. M.Z. and J.F.Z. carried out experiments of electrophysiology and mutagenesis. M.Z., J.M.P., R.S.A. and J.F.Z. prepared the manuscript and the figures.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ji-Fang Zhang.

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https://doi.org/10.1038/ncomms2017

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