Chemical biology: methods and protocols / ed. by J.E.Hempel et al. - New York: Springer Science+Business Media: Humana press, 2015. - xiv, 333 p.: ill., tab. - (Methods in molecular biology; 1263) (Springer protocols). - Bibliogr. at the end of the chapters. - Ind.: p.329-333. - ISBN 978-1-4939-2268-0; ISSN 1064-3745 Шифр: (Pr 852/N 1263) 02  Место хранения:   02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents

Preface ......................................................... v Contributors ................................................... xi Part I. In Vitro Chemical Genetic Screening 1 Identification of Therapeutic Small-Molecule Leads in Cultured Cells Using Multiplexed Pathway Reporter Readouts ... 3 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 ..................................................... 15 Ari D. Brettman, Pauline H. Tan, Khoa Tran, and Stanley Y. Shaw 3 Construction and Application of a Photo-Cross-Linked Chemical Array .............................................. 29 Yasumitsu Kondoh, Kaori Honda, and Hiroyuki Osada 4 High Content Screening for Modulators of Cardiac Differentiation in Human Pluripotent Stem Cells ............. 43 Sean Spiering, Herman Davidovics, Paul J. Bushway, Mark Mercola, and Erik Willems 5 Small-Molecule High-Throughput Screening Utilizing Xenopus Egg Extract ......................................... 63 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 ................................... 77 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 .......................... 93 Jessica Stephan and Ann E. Ehrenhofer-Murray 8 Protocols for the Routine Screening of Drug Sensitivity in the Human Parasite Trichomonas vaginalis ................ 103 Manal J. Natto, Anthonius A. Eze, and Harry P. de Koning 9 Chemical Genetic Screens Using Arabidopsis thaliana Seedlings Grown on Solid Medium ............................ 111 Thanh Theresa Dinh and Xuemei Chen 10 Small-Molecule Screening Using Drosophila Models of Human Neurological Disorders ............................ 127 Mickael Poidevin, Feiran Zhang, and Peng Jin 11 High-Throughput Small-Molecule Screening in Caenorhabditis elegans ..................................... 139 Sunitha Rangaraju, Gregory M. Solis, and Michael Petrascheck 12 Whole-Organism Screening for Modulators of Fasting Metabolism Using Transgenic Zebrafish ...................... 157 Philipp Gut and Didier Y.R. Stainier 13 High Content Screening for Modulators of Cardiovascular or Global Developmental Pathways in Zebrafish .............. 167 Charles H. Williams and Charles C. Hong Part III. Small Molecules in Chemical Biology 14 Extraction Methods of Natural Products from Traditional Chinese Medicines .......................................... 177 Jingyu Zhang, Jianying Han, Ayokunmi Oyeleye, Miaomiao Liu, Xueting Liu, and Lixin Zhang 15 Bioassay-Guided Identification of Bioactive Molecules from Traditional Chinese Medicines ......................... 187 Jianying Han, Jingyu Zhang, Wenni He, Pet Huang, Ayokunmi Oyeleye, Xueting Liu, and Lixin Zhang 16 NMR Screening in Fragment-Based Drug Design: A Practical Guide ...................................................... 197 Hai-Young Kim and Daniel F. Wyss 17 Practical Strategies for Small-Molecule Probe Development in Chemical Biology ........................................ 209 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 .................................................. 225 Todd A. Wenderski, Christopher F. Stratton, Renato A. Bauer, Felix Kopp, and Derek S. Tan 19 Small-Molecule Library Screening by Docking with PyRx ...... 243 Sargis Dallakyan and Arthur J. Olson Part IV. Small Molecule Target Identification 20 Fluorous Photoaffinity Labeling to Probe Protein-Small Molecule Interactions ...................................... 253 Weigang Huang and Qisheng Zhang 21 Identification of the Targets of Biologically Active Small Molecules Using Quantitative Proteomics .............. 263 Gloria Vendrell-Navarro, Andreas Brockmeyer, Herbert Waldmann, Petra Janning, and Slava Ziegler 22 Drug Affinity Responsive Target Stability (DARTS) for Small-Molecule Target Identification ....................... 287 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 ............................ 299 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 ............. 319 Shinsuke Ohnuki, Hiroki Okada, and Toshikazu Ohya Index ......................................................... 329