Biophysical screening for the discovery of small-molecule ligands

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

    35 Citations (Scopus)

    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.

    Original languageEnglish
    Title of host publicationProtein-ligand interactions
    Subtitle of host publicationmethods and applications
    EditorsMark A. Williams, Tina Daviter
    PublisherHumana Press
    Pages357-388
    Number of pages32
    ISBN (Electronic)9781627033985
    ISBN (Print)9781627033978
    DOIs
    Publication statusPublished - 2013

    Publication series

    NameMethods in Molecular Biology
    PublisherHumana Press
    Volume1008
    ISSN (Print)1064-3745

    Fingerprint

    Ligands
    Fluorometry
    Calorimetry
    Proteins
    Fluorescence Polarization
    Surface Plasmon Resonance
    Pharmaceutical Chemistry
    Drug Design
    X Ray Crystallography
    Drug Industry
    Drug Discovery
    Structure-Activity Relationship
    Magnetic Resonance Spectroscopy
    Hot Temperature
    Fluorescence
    Costs and Cost Analysis

    Cite this

    Ciulli, A. (2013). Biophysical screening for the discovery of small-molecule ligands. In M. A. Williams, & T. Daviter (Eds.), Protein-ligand interactions: methods and applications (pp. 357-388). (Methods in Molecular Biology; Vol. 1008). Humana Press. https://doi.org/10.1007/978-1-62703-398-5_13
    Ciulli, Alessio. / Biophysical screening for the discovery of small-molecule ligands. Protein-ligand interactions: methods and applications. editor / Mark A. Williams ; Tina Daviter. Humana Press, 2013. pp. 357-388 (Methods in Molecular Biology).
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    Ciulli, A 2013, Biophysical screening for the discovery of small-molecule ligands. in MA Williams & T Daviter (eds), Protein-ligand interactions: methods and applications. Methods in Molecular Biology, vol. 1008, Humana Press, pp. 357-388. https://doi.org/10.1007/978-1-62703-398-5_13

    Biophysical screening for the discovery of small-molecule ligands. / Ciulli, Alessio.

    Protein-ligand interactions: methods and applications. ed. / Mark A. Williams; Tina Daviter. Humana Press, 2013. p. 357-388 (Methods in Molecular Biology; Vol. 1008).

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

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    AB - 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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    Ciulli A. Biophysical screening for the discovery of small-molecule ligands. In Williams MA, Daviter T, editors, Protein-ligand interactions: methods and applications. Humana Press. 2013. p. 357-388. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-398-5_13