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Binding Moiety Mapping by Saturation Transfer Difference NMR

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Rational Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1824))

Abstract

Saturation transfer difference (STD) NMR has emerged as one of the key technologies in lead optimization during drug design. Unlike most biophysical assays which report only on the binding affinity, STD NMR reports simultaneously on both the binding affinity and the structure of the binding ligand/protein complex. The STD experiment drives magnetization from a protein to a bound small molecule ligand which carries away the memory of the saturation signal when it dissociates. Since the transfer of saturation is distance dependent, STD NMR can be used to map the specific atoms on the ligand in contact with a protein receptor allowing the impact of any structural change in the binding site to be mapped directly on to the individual functional groups responsible when a suitable compound library is screened. Because the signal is detected from the free ligand and not the bound complex, it can be used on a much wider range of systems than protein-detected NMR and has the advantage of more directly reporting on distances than changes in chemical shifts alone. The STD experiment, while deceptively simple, is very sensitive to both sample conditions and acquisition parameters. We present a general protocol for setting up and STD NMR experiment with a particular focus on how choices in sample conditions and acquisition parameters affect the outcome of the experiment.

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Authors and Affiliations

  1. Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Jeffrey R. Brender

  2. Department of Biosciences, Jimma University, Jimma, ET, USA

    Janarthanan Krishnamoorthy

  3. Department of Biophysics, Bose Institute, Kolkata, India

    Anirban Ghosh & Anirban Bhunia

Authors
  1. Jeffrey R. Brender
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  2. Janarthanan Krishnamoorthy
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  3. Anirban Ghosh
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  4. Anirban Bhunia
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Corresponding author

Correspondence to Jeffrey R. Brender .

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Editors and Affiliations

  1. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Thomas Mavromoustakos

  2. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Tahsin F. Kellici

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Brender, J.R., Krishnamoorthy, J., Ghosh, A., Bhunia, A. (2018). Binding Moiety Mapping by Saturation Transfer Difference NMR. In: Mavromoustakos, T., Kellici, T. (eds) Rational Drug Design. Methods in Molecular Biology, vol 1824. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8630-9_4

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  • DOI: https://doi.org/10.1007/978-1-4939-8630-9_4

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  • Print ISBN: 978-1-4939-8629-3

  • Online ISBN: 978-1-4939-8630-9

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