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Systems Chemical Biology

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Slava Ziegler

    1. Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Herbert Waldmann

    1. Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1888)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. PREDECT Protocols for Complex 2D/3D Cultures

    • Suzana Vidic, Marta F. Estrada, Kjersti Gjerde, Vítor E. Santo, Annika Osswald, Michaël Barbier et al.
    Pages 1-20

  3. Phenotypic Screening Using Mouse and Human Stem Cell-Based Models of Neuroinflammation and Gene Expression Analysis to Study Drug Responses

    • Masin Abo-Rady, Jessica Bellmann, Michael Glatza, Lara Marrone, Lydia Reinhardt, Santiago Tena et al.
    Pages 21-43

  4. Quantitative, Real-Time Measurements of Intracellular Target Engagement Using Energy Transfer

    • Matthew B. Robers, James D. Vasta, Cesear R. Corona, Rachel Friedman Ohana, Robin Hurst, Manisha A. Jhala et al.
    Pages 45-71Open Access

  5. Target Engagement of Small Molecules: Thermal Profiling Approaches on Different Levels

    • Elena S. Reckzeh, Andreas Brockmeyer, Malte Metz, Herbert Waldmann, Petra Janning
    Pages 73-98

  6. Visualizing Bioactive Small Molecules by Alkyne Tagging and Slit-Scanning Raman Microscopy

    • Jun Ando, Kosuke Dodo, Katsumasa Fujita, Mikiko Sodeoka
    Pages 99-114

  7. The Cell Painting Assay as a Screening Tool for the Discovery of Bioactivities in New Chemical Matter

    • Axel Pahl, Sonja Sievers
    Pages 115-126

  8. Proteomic Profiling for Target Identification of Biologically Active Small Molecules Using 2D DIGE

    • Makoto Muroi, Hiroyuki Osada
    Pages 127-139

  9. Examining Cellular Responses to Kinase Drug Inhibition Through Phosphoproteome Mapping of Substrates

    • Daniel Bucio-Noble, Crystal Semaan, Mark P. Molloy
    Pages 141-152

  10. CRISPR/Cas9-Based Chemogenomic Profiling in Mammalian Cells

    • Dominic Hoepfner, Gregory McAllister, Gregory R. Hoffman
    Pages 153-174

  11. Exome Sequencing of Drug-Resistant Clones for Target Identification

    • Ting Han, Deepak Nijhawan
    Pages 175-187

  12. The Use of Large-Scale Chemically-Induced Transcriptome Data Acquired from LINCS to Study Small Molecules

    • Michio Iwata, Yoshihiro Yamanishi
    Pages 189-203

  13. Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer

    • Alok Jaiswal, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio
    Pages 205-217

  14. Predicting Drug Interactions From Chemogenomics Using INDIGO

    • Sriram Chandrasekaran
    Pages 219-231

  15. Computational Analyses Connect Small-Molecule Sensitivity to Cellular Features Using Large Panels of Cancer Cell Lines

    • Matthew G. Rees, Brinton Seashore-Ludlow, Paul A. Clemons
    Pages 233-254

  16. Web-Based Tools for Polypharmacology Prediction

    • Mahendra Awale, Jean-Louis Reymond
    Pages 255-272

  17. In Silico Target Prediction for Small Molecules

    • Ryan Byrne, Gisbert Schneider
    Pages 273-309

  18. Back Matter

    Pages 311-315
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Keywords

About this book

This volume explores the latest available wet-lab techniques and computational methods to study in-cell small-molecule behavior and interactions with their targets. The chapters in this book discuss topics such as disease-relevant models for chemical biology studies, target engagement using cellular thermal shift assay or bioluminescence resonance energy transfer; visualization of bio-active small molecules Raman microscopy; (phospho-)proteomics and transcriptomics for mode-of-action studies, CRISPR/Cas9-based chemogenomic profiling in mammalian cells; predicting drug interactions using computational approaches; comparison of compound-induced profiles using high-content imaging or cancer cell line panels and web-based tools for polypharmacology prediction. 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, Systems Chemical Biology: Methods and Protocols is a valuable resource for novice or expert scientists and researchers trying to initiate or continue their chemical biology studies at a systems level.

Editors and Affiliations

  • Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

    Slava Ziegler, Herbert Waldmann

Bibliographic Information

  • Book Title: Systems Chemical Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Slava Ziegler, Herbert Waldmann

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8891-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-8890-7Published: 06 December 2018

  • eBook ISBN: 978-1-4939-8891-4Published: 05 December 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 315

  • Number of Illustrations: 22 b/w illustrations, 43 illustrations in colour

  • Topics: Bioinformatics

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