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Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening

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Abstract

Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.

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Acknowledgments

This work was supported by Defense Threat Reduction Agency award CBS.MEDBIO.01.10.WR.001. The opinions or assertions contained herein belong to the authors and are not necessarily the official views of the U.S. Navy or the U.S. Department of Defense.

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Authors and Affiliations

  1. NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA

    Xin Hu, Noel Southall, David J. Maloney, Anton Simeonov & Ajit Jadhav

  2. Center of Bio/Molecular Science and Engineering, Naval Research Laboratories, Washington, DC, 20375, USA

    Patricia M. Legler

Authors
  1. Xin Hu
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  2. Patricia M. Legler
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  3. Noel Southall
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  4. David J. Maloney
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Correspondence to Ajit Jadhav.

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Hu, X., Legler, P.M., Southall, N. et al. Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening. J Comput Aided Mol Des 28, 765–778 (2014). https://doi.org/10.1007/s10822-014-9758-7

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  • DOI: https://doi.org/10.1007/s10822-014-9758-7

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