Chemical Biology: Methods and Protocols

ISBN-13: 9781493952847 / Angielski / Miękka / 2016 / 333 str.

Jonathan E. Hempel; Charles H. Williams; Charles C. Hong

Opis

This volume seeks to enable the discovery of tools in chemical biology by providing readers with various techniques ranging from initial chemical genetic screening to target identification.

Spis treści

Part I In Vitro Chemical Genetic Screening

1.    Identification of Therapeutic Small Molecule Leads in Cultured Cells Using Multiplexed Pathway Reporter Read-outs

Ozlem Kulak, Kiyoshi Yamaguchi, and Lawrence Lum

2.    Applying the Logic of Genetic Interaction to Discover Small Molecules That Functionally Interact with Human Disease Alleles

Ari D. Brettman, Pauline H. Tan, Khoa Tran, and Stanley Y. Shaw

3.    Construction and Application of a Photo-cross-linked Chemical Array

Yasumitsu Kondoh, Kaori Honda, and Hiroyuki Osada

4.    High Content Screening for Modulators of Cardiac Differentiation in Human Pluripotent Stem Cells

Sean Spiering, Herman Davidovics, Paul J. Bushway, Mark Mercola, and Erik Willems

5.    Small Molecule High-Throughput Screening Utilizing Xenopus Egg Extract

Matthew R. Broadus, P. Renee Yew, Stephen R. Hann, and Ethan Lee

 

Part II In Vivo Chemical Genetic Screening

6.    Fission Yeast-based High-throughput Screens for PKA Pathway Inhibitors and Activators

Ana Santos de Medeiros, Grace Kwak, Jordan Vanderhooft, Sam Rivera, Rachel Gottlieb, and Charles S. Hoffman

7.    A Method for High-throughput Analysis of Chronological Aging in Schizosaccharomyces pombe

Jessica Stephan and Ann E. Ehrenhofer-Murray

8.    Protocols for the Routine Screening of Drug Sensitivity in the Human Parasite Trichomonas vaginalis

Manal J. Natto, Anthonius A. Eze, and Harry P. de Koning

9.    Chemical Genetic Screens Using Arabidopsis thaliana Seedlings Grown on Solid Medium

Thanh Theresa Dinh and Xuemei Chen

10.  Small Molecule Screening Using Drosophila Models of Human Neurological Disorders

Mickael Poidevin, Feiran Zhang, and Peng Jin

11.  High-throughput Small Molecule Screening in Caenorhabditis elegans

Sunitha Rangaraju, Gregory M. Solis, and Michael Petrascheck

12.  Whole-organism Screening for Modulators of Fasting Metabolism Using Transgenic Zebrafish

Philipp Gut and Didier Y.R. Stainier

13.  High Content Screening for Modulators of Cardiovascular or Global Developmental Pathways in Zebrafish

Charles H. Williams III and Charles C. Hong

 

Part III Small Molecules in Chemical Biology

14.  Extraction Methods of Natural Products from Traditional Chinese Medicines

Jingyu Zhang, Jianying Han, Ayokunmi Oyeleye, Miaomiao Liu, Xueting Liu, and Lixin Zhang

15.  Bioassay-guided Identification of Bioactive Molecules from Traditional Chinese Medicines

Jianying Han, Jingyu Zhang, Wenni He, Pei Huang, Ayokunmi Oyeleye, Xueting Liu, and Lixin Zhang

16.  NMR Screening in Fragment-Based Drug Design: A Practical Guide

Hai-Young Kim and Daniel F. Wyss

17.  Practical Strategies for Small Molecule Probe Development in Chemical Biology

Jonathan E. Hempel and Charles C. Hong

18.  Principal Component Analysis as a Tool for Library Design: A Case Study Investigating Natural Products, Brand-name Drugs, Natural Product-like Libraries, and Drug-like Libraries

Todd A. Wenderski, Christopher F. Stratton, Renato A. Bauer, Felix Kopp, and Derek S. Tan

19.  Small Molecule Library Screening by Docking with PyRx

Sargis Dallakyan and Arthur J. Olson

 

Part IV Small Molecule Target Identification

20.  Fluorous Photoaffinity Labeling to Probe Protein-Small Molecule Interactions

Weigang Huang and Qisheng Zhang

21.  Identification of the Targets of Biologically Active Small Molecules Using Quantitative Proteomics

Glòria Vendrell-Navarro, Andreas Brockmeyer, Herbert Waldmann, Petra Janning, and Slava Ziegler

22.  Drug Affinity Responsive Target Stability (DARTS) for Small Molecule Target Identification

Melody Y. Pai, Brett Lomenick, Heejun Hwang, Robert Schiestl, William McBride, Joseph A. Loo, and Jing Huang

23.  Chemical Genomic Profiling via Barcode Sequencing to Predict Compound Mode of Action

Jeff S. Piotrowski, Scott W. Simpkins, Sheena C. Li, Raamesh Deshpande, Sean J. McIlwain, Irene M. Ong, Chad L. Myers, Charlie Boone, and Raymond J. Andersen

24.  Image-Based Prediction of Drug Target in Yeast

Shinsuke Ohnuki, Hiroki Okada, and Yoshikazu Ohya

Blurb

This volume seeks to enable the discovery of tools in chemical biology by providing readers with various techniques ranging from initial chemical genetic screening to target identification. To successfully highlight the essential components of the chemical biology tool discovery process, the book is organized into four parts that focus on platforms for molecular discovery in in vitro cellular systems, in vivo chemical genetic screening protocols, and methods used to discover functional protein targets. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.

Practical and informative, Chemical Biology: Methods and Protocols seeks to improve the success rate of the chemical biology field through the dissemination of detailed and experiential knowledge.