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Chemogenomics

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Daniel Merk

    1. Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Apirat Chaikuad

    1. Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2706)

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About this book

This volume presents both theoretical guidance and protocols on chemogenomics including chemogenomics library assembly, compound profiling, and phenotypic assays. The chapters in this book cover topics such as the assembly and use of Kinase Chemogenomics; data mining for chemogenomic compound candidates; protocols for protein family-focused assay systems to profile chemogenomic compounds; functional and target engagement assays in cellular settings for broad characterization; and a discussion on phenotypic assays where chemogenomic sets may be applied. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Chemogenomics: Methods and Protocols is a valuable resource for all researchers whoare interested in learning more about this diverse and developing field. 


Keywords

Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. An Introduction to Chemogenomics

    • Apirat Chaikuad, Daniel Merk
    Pages 1-10

  3. Developing a Kinase Chemogenomic Set: Facilitating Investigation into Kinase Biology by Linking Phenotypes to Targets

    • Carrow I. Wells, David H. Drewry
    Pages 11-24

  4. Compilation of Custom Compound/Bioactivity Datasets from Public Repositories

    • Laura Isigkeit, Daniel Merk
    Pages 25-50

  5. Quality Control of Chemogenomic Library Using LC-MS

    • Václav Němec, Stefan Knapp
    Pages 51-58

  6. Annotation of the Effect of Chemogenomic Compounds on Cell Health Using High-Content Microscopy in Live-Cell Mode

    • Amelie Tjaden, Stefan Knapp, Susanne Müller
    Pages 59-73

  7. Characterization of Cellular Viability Using Label-Free Brightfield Live-Cell Imaging

    • Lewis Elson, Amelie Tjaden, Stefan Knapp, Susanne Müller
    Pages 75-88

  8. Plate-Based Screening for DUB Inhibitors

    • Stephan Scherpe, Aysegul Sapmaz, Monique P. C. Mulder
    Pages 89-96

  9. NanoBRET™ Live-Cell Kinase Selectivity Profiling Adapted for High-Throughput Screening

    • Amanda N. Nieman, Kaitlin K. Dunn Hoffman, Elizabeth R. Dominguez, Jennifer Wilkinson, James D. Vasta, Matthew B. Robers et al.
    Pages 97-124

  10. A Fluorescence-Based Reporter Gene Assay to Characterize Nuclear Receptor Modulators

    • Espen Schallmayer, Daniel Merk
    Pages 125-135

  11. Measuring Protein–Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay

    • Magdalena M. Szewczyk, Dominic D. G. Owens, Dalia Barsyte-Lovejoy
    Pages 137-148

  12. HiBiT Cellular Thermal Shift Assay (HiBiT CETSA)

    • Sarath Ramachandran, Magdalena Szewczyk, Samir H. Barghout, Alessio Ciulli, Dalia Barsyte-Lovejoy, Victoria Vu
    Pages 149-165

  13. Detection of Cellular Target Engagement for Small-Molecule Modulators of Striatal-Enriched Protein Tyrosine Phosphatase (STEP)

    • Ye Na Han, Lester J. Lambert, Laurent J. S. De Backer, Jiaqian Wu, Nicholas D. P. Cosford, Lutz Tautz
    Pages 167-175

  14. Target Deconvolution by Limited Proteolysis Coupled to Mass Spectrometry

    • Viviane Reber, Matthias Gstaiger
    Pages 177-190

  15. Global Assessment of Drug Target Engagement and Selectivity of Covalent Cysteine-Reactive Inhibitors Using Alkyne-Functionalized Probes

    • Elisabeth M. Rothweiler, Kilian V. M. Huber
    Pages 191-200

  16. 3D Spheroid Invasion Assay for High-Throughput Screening of Small-Molecule Libraries

    • Kunal Karve, Stephanie Poon, Panagiotis Prinos, Laurie Ailles
    Pages 201-214

  17. Live-Cell High-Throughput Screen for Monitoring Autophagy Flux

    • Sara Cano-Franco, Hung Ho-Xuan, Lorene Brunello, Alexandra Stolz
    Pages 215-224

  18. Phenotypic Chemical Screening in CD4+ T Cells to Identify Epigenetic Inhibitors

    • Adam P. Cribbs, Udo Oppermann
    Pages 225-231

  19. Back Matter

    Pages 233-234
    Download chapter PDF
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Editors and Affiliations

  • Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany

    Daniel Merk

  • Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany

    Apirat Chaikuad

Bibliographic Information

  • Book Title: Chemogenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Daniel Merk, Apirat Chaikuad

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3397-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-3396-0Published: 10 August 2023

  • Softcover ISBN: 978-1-0716-3399-1Due: 10 September 2023

  • eBook ISBN: 978-1-0716-3397-7Published: 09 August 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 234

  • Number of Illustrations: 2 b/w illustrations, 60 illustrations in colour

  • Topics: Genetics and Genomics, Pharmacology/Toxicology

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