Chemogenomics

1. Front Matter

   Pages i-x

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2. Organizing Bioactive Compound Discovery in Target Families

   • H. Peter Nestler

   Pages 1-19

3. Compound Library Design for Target Families

   • K. V. Balakin, Y. A. Ivanenkov, N. P. Savchuk

   Pages 21-46

4. Targeting the Purinome

   • Jeremy M. Murray, Dirksen E. Bussiere

   Pages 47-92

5. Cofactor Chemogenomics

   • Ratna Singh, Andrea Mozzarelli

   Pages 93-122

6. Chemogenomics with Protein Secondary-Structure Mimetics

   • Garland R. Marshall, Daniel J. Kuster, Ye Che

   Pages 123-158

7. Database Systems for Knowledge-Based Discovery

   • Sarma A. R. P. Jagarlapudi, K. V. Radha Kishan

   Pages 159-172

8. Knowledge-Based Virtual Screening: Application to the MDM4/p53 Protein–Protein Interaction

   • Edgar Jacoby, Andreas Boettcher, Lorenz M. Mayr, Nathan Brown, Jeremy L. Jenkins, Joerg Kallen et al.

   Pages 173-194

9. Off-Target Networks Derived from Ligand Set Similarity

   • Michael J. Keiser, Jérôme Hert

   Pages 195-205

10. Chemogenomic Analysis of Safety Profiling Data

    • Josef Scheiber, Jeremy L. Jenkins

    Pages 207-223

11. Network and Pathway Analysis of Compound–Protein Interactions

    • Richard J. Brennan, Tatiana Nikolskya, Svetlana Bureeva

    Pages 225-247

12. The Flexible Pocketome Engine for Structural Chemogenomics

    • Ruben Abagyan, Irina Kufareva

    Pages 249-279

13. Structure-Based Chemogenomics: Analysis of Protein Family Landscapes

    • Bernard Pirard

    Pages 281-296

14. Hypothesis-Driven Screening

    • Ulrich Schopfer, Caroline Engeloch, Frank Höhn, Hervé Mees, Jennifer Leeds, Fraser Glickman et al.

    Pages 297-316

15. Back Matter

    Pages 317-320

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Chemogenomics aims toward the systematic identification of small molecules that interact with the products of the genome and modulate their biological function. The establishment, analysis, prediction, and expansion of a comprehensive ligand–target SAR (structure–activity relationship) matrix has followed the elucidation of the human genome and presents a key scientific challenge for the twenty-first century. The anno- tion and knowledge-based exploration of the ligand–target SAR matrix is then expected to impact science greatly. Progress alongside this challenge without a doubt will c- tribute to further the fundamental understanding of the biological function of the individual proteins and ultimately provide a basis for the discovery of new and better therapies for diseases. While historically the chemogenomics approach is based on efforts that systematically explore target gene families, today broader in vitro and in silico approaches are available to encompass wider genomes. In this book, experts from academia and industry outline relevant aspects of ch- istry, biology, and molecular informatics which are the cornerstones of chemogenomics. General introductory chapters are combined with chapters describing methods and pro- cols, which are the gold standard of the Methods in Molecular Biology book series.

• Compound library design
• Drug discovery
• Knowledge-based approaches
• Ligand-target SAR
• Protein kinase inhibitors
• Secondary structure
• Small molecules
• Structure-Activity Relationship matrix
• molecular biology
• protein family
• Combinatorial Libraries

From the reviews: “Provide practical and authoritative reviews on current research topics. … The present book represents an illustrative compendium of up-to-date chemogenomics, with a strong emphasis on bio- and cheminformatic concepts. … It therefore represents a valuable complement to published books that are more ‘chemical biology’ driven. It is of particular interest for the ‘data miners’ of the chemogenomics community, giving them an authoritative overview of current technologies and methods available throughout industry and academia.” (Markus Kaiser, ChemBioChem, Vol. 11, March, 2010)

• Basel, Switzerland

  Edgar Jacoby

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