Chemical Genomics

About this book

Advances in chemistry, biology, and genomics coupled with laboratory automation and computational technologies have led to the rapid emergence of the multidisciplinary field of chemical genomics. This edited text with contributions from experts in the field discusses evolving concepts, essential techniques, and a wide range of applications to help further the study of chemical genomics. The beginning chapters provide an overview of the basic principles of chemical biology and chemical genomics. This is followed by a technical section that describes the sources of small molecule chemicals, the basics of high-throughput screening technologies, various bioassays for biochemical-, cellular-, and organism-based screens, and computational approaches. The final chapters connect the chemical genomics field with personalized medicine and the druggable genome for future discovery of new therapeutics.

In selected chapters, a resource section is included for further information. Chemical Genomics provides an introduction to the principles of chemical genomics, serves as a resource for the associated technologies, and gives readers general concepts, useful vocabulary, practical techniques, and broad, forward-thinking perspectives. Chemical Genomics will be valuable to researchers, professionals, and students in many fields besides chemical genomics, including biology, biomedicine, chemistry and drug discovery.

Contents

Part I. Overviews
1. Harnessing the power of chemistry for biology and medicine Cheryl L. Meyerkord and Haian Fu
2. Chemical genomics: exploring biology with small organic molecules Nicholas Aberle and Craig M. Crews
3. Chemical proteomics Akihisa Matsuyama, Yoko Yashiroda, and Minoru Yoshida

Part II. Molecules for Chemical Genomics
4. Diversity-oriented synthesis Warren R. J. D. Galloway, Richard J. Spandl, Andreas Bender, Gemma L. Thomas, Monica Diaz-Gavilan, Kieron M. G. O'Connell, and David R. Spring
5. Targeted chemical libraries Gregory P. Tochtrop and Ryan E. Looper
6. Fragment-based ligand discovery Sandra Bartoli, Antonella Squarcia, and Daniela Fattori
7. Basics and principles for building natural product-based libraries for HTS Ronald J. Quinn

Part III. Basics of High Throughput Screening
8. Essentials for high throughput screening operations Stewart P. Rudnicki, James V. Follen, Nicola J. Tolliday, and Caroline E. Shamu
9. High content analysis and screening: basics, instrumentation and applications Paul A. Johnston
10. Phenotypic screens with model organisms Grant N. Wheeler, Robert A. Field, and Matthew L. Tomlinson
11. Screening informatics and ChemInformatics Lestyn Lewis

Part IV. Chemical Genomics Assays and Screens
12. Basics on HTS assay design and optimization Eduard Sergienko
13. Molecular sensors for transcriptional and post-transcriptional assays Douglas S. Auld and Natasha Thorne
14. Fluorescence-based platforms for HTS assays - FP and TR-FRET Yuhong Du and Jonathan Havel
15. Compound profiling with high content screening methodology Thomas Mayer and Stephan Sch#rer
16. Use of transgenic zebrafish in a phenotypic screen for angiogenesis inhibitors Jaeki Min, Yuhong Du, Brenda Bondesen, Brian Revennaugh, Peter Eimon, and Ray Dingledine
17. Flow cytometry multiplexed screening methodologies Virginia M. Salas, J. Jacob Strouse, Zurab Surviladze, Irena Ivnitski-Steele, Bruce S. Edwards, and Larry A. Sklar
18. Basic principles and practices of computer-aided screening and drug design Chao-Yie Yang, Denzil Bernard, and Shaomeng Wang
19. Computational approach for drug target identification Honglin Li, Mingyue Zheng, Xiaofeng Liu, and Hualiang Jiang
20. Label-free biosensor technologies for assay development and HTS Yuhong Du and Arron Xu

Part V. Chemical genomics and medicine
21. Pharmacogenomics to link genetic background with therapeutic efficacy and safety Mark M. Bouzyk, Weining Tang, and Brian Leyland-Jones
22. Drugs, genomic response signatures, and customized cancer therapy Rafael Rosell, Teresa Moran, Miguel Taron

Appendix. Current drug targets and the druggable genome Andreas Russ

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Biography

Haian Fu is a professor of Pharmacology, Hematology, and Medical Oncology at Emory University School of Medicine. He is the Director of the Emory Chemical Biology Discovery Center and leader of the Discovery and Developmental Therapeutics Program at the Winship Cancer Institute of Emory University. Dr Fu serves as a Steering Committee member for the NIH National Cancer Institute Chemical Biology Consortium and is co-founder of the International Chemical Biology Society. His research focuses on protein-protein interactions in signal transduction pathways that control cell survival and death in normal and cancer cells, as well as targeting these interactions for chemical biology studies and drug discovery. He serves on the editorial board of several scientific journals, including Current Chemical Genomics, and edited Protein-Protein Interactions: Methods and Applications (2004).

Dr Fu has received various honors, including the PhRMA Faculty Development Award, the Burroughs Wellcome Fund New Investigator Award, the GRA Distinguished Investigator Award, and the Georgia Cancer Coalition Distinguished Cancer Scholar. He is also a recipient of the Award for Excellence in Mentorship from the Emory Graduate Division of Biological and Biomedical Sciences (2000), the Outstanding Postdoctoral Mentor Award from Emory University (2011), and the Emory Pharmacology Teaching Excellence Award (2006).