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Biophysical Screening for the Discovery of Small-Molecule Ligands

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Protein-Ligand Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1008))

Abstract

Discovering small-molecule chemical probes of protein function has great potential to elucidate biological pathways and to provide early-stage proof-of-concept for target validation. Discovery of such probes therefore underpins many of the chemical biology and drug discovery efforts in both academia and the pharmaceutical industry. The process generally begins with screening small molecules to identify bona fide “hits” that bind non-covalently to a target protein. This chapter is concerned with the application of biophysical and structural techniques to small-molecule ligand screening, and with the validation of hits from both structural (binding mode) and energetic (binding affinity) stand-points. The methods discussed include differential scanning fluorimetry (thermal shift), fluorescence polarization (FP), surface plasmon resonance, ligand-observed NMR spectroscopy, isothermal titration calorimetry, and protein X-ray crystallography. The principles of these techniques and the fundamental nature of the observables used to detect macromolecule-ligand binding are briefly outlined. The practicalities, advantages, and disadvantages of each technique are described, particularly in the context of detecting weak affinities, as relevant to fragment screening. Fluorescence-based methods, which offer an attractive combination of high throughput and low cost are discussed in detail. It is argued that applying a combination of different methods provides the most robust and effective way to identify high-quality starting points for follow-up medicinal chemistry and to build structure–activity relationships that better inform effective development of high-quality, cell-active chemical probes by structure-based drug design.

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Acknowledgments

The author wishes to thank several members of the Ciulli and Abell research groups (Department of Chemistry) and the Blundell research group (Department of Biochemistry) for productive collaboration and invaluable discussions over the years. The Ciulli laboratory is funded primarily but not exclusively by the UK Biotechnology and Biological Sciences Research Council (BBSRC). The author thanks the BBSRC for the award of a David Phillips Fellowship (BB/G023123/1). The author did not receive any financial contribution or writing assistance for the production of this chapter and declares no competing financial interests.

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Authors and Affiliations

  1. College of Life Sciences, University of Dundee, Dundee, UK

    Alessio Ciulli

  2. Division of Biological Chemistry and Drug Discovery, The Wellcome Trust Biocentre, Scotland, UK

    Alessio Ciulli

  3. Department of Chemistry, University of Cambridge, Cambridge, UK

    Alessio Ciulli

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  1. Alessio Ciulli
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Editors and Affiliations

  1. Birbeck, University of London, ISMB Biophysics Centre, Institute of Str, Malet Street, London, WC1E 7HX, United Kingdom

    Mark A. Williams

  2. Birkbeck, University of London, School of Crystallography, ISMB Biophysics Centre, Institute of Str, Malet Street, London, WC1E 7HX, United Kingdom

    Tina Daviter

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Ciulli, A. (2013). Biophysical Screening for the Discovery of Small-Molecule Ligands. In: Williams, M., Daviter, T. (eds) Protein-Ligand Interactions. Methods in Molecular Biology, vol 1008. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-398-5_13

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  • DOI: https://doi.org/10.1007/978-1-62703-398-5_13

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-397-8

  • Online ISBN: 978-1-62703-398-5

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