Systems Chemical Biology: Methods and Protocols

ISBN-13: 9781493988907 / Angielski / Twarda / 2018 / 315 str.

Slava Ziegler; Herbert Waldmann

Spis treści

1.      Cellular thermal shift assay (CETSA)- Molina

2.      Thermal proteome profiling (TPP) – Savitski

3.      Generation and Investigation of drug-related resistant mutations; DrugTargetSeq – Tarun Kapoor

4.      BRET for target engagement – Robers/Stoddard

5.      Raman imaging for small molecule visualization in cells– M. Sodeoka

6.      Target prediction for small molecules using Proteobase – Osada

7.      Target prediction for small molecules using Morphobase- Osada

8.      Predictive chemogenomics based on gene expression profiles – S.Schreiber

9.      Genome-wide mapping of ligand interactions (Chem-seq)- R.A: Young

10.  Cheminformatics to assess drug-target networks –(more than one chapter possible) – G. Schneider (and others)

11.  Yeast-based methods for target identification – Dominic Hoepfner

12.  A genome scale overexpression screen to reveal drug activity in human cells - Guri Giaever and Corey Nislow

13.  High-content phenotypic profiling for compound characterization (ORACL) -  S:J Altschuler, and L.F. Wu

14.  Connectivity map / Drug target prioritization by perturbed gene expression and network information. Lamb and Golubb

15.  Activity-based proteome profiling  (Proteome-wide covalent ligand discovery in native biological systems) – Cravatt

16.  Multiplex Cytological Profiling Assay to Measure Diverse Cellular States (Cell painting) Alykhan F. Shamji

17.  Multidimensional Drug Profiling By Automated Microscopy - N.O. Carragher

18.  ProTacs: New approaches to protein degradation – C. Crews

19.  Bioluminescent sensors /Modulating protein activity using tethered ligands -Kai Johnsson

20.  Spatially resolved proteomic mapping in living cells - Alice Ting

21.  Small molecules approaches for stem cell biology – Sheng Ding, Stephen J. Haggarty, O. Brüstle or Hongkui Deng

22.  Zebrafish for compound activity screening – R.T. Peterson

23.  Employment of Drosophila (cells) to detect inhibitors of lipid droplet formation – M. Beller; Matt Boxer

Blurb

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.