Chemical Library Design, 2011 Methods in Molecular Biology Series, Vol. 685

Chemical library technologies have brought about dramatic changes in the drug discovery process, and, though still evolving, they have become an integral part of ongoing drug discovery research. In Chemical Library Design, experts in the field provide methods and detailed protocols delving into this key process of selecting useful, biologically relevant compounds from large pools of synthesizable candidates. This compendium includes chapters on historical overviews, state-of-the-art methodologies, including structure-based and fragment-based library design, practical software tools, and successful and important applications of chemical library design. As a volume in the popular Methods in Molecular Biology? series, the thorough contributions provide the kind of meticulous description and implementation advice that is crucial for getting optimal results. Authoritative and cutting-edge, Chemical Library Design is an ideal reference for all scientists seeking the technology needed to aid in the search for new and vital drugs.

Part I: General Topics 1. Historical Overview of Chemical Library Design Roland E. Dolle 2. Chemoinformatics and Library Design Joe Zhongxiang Zhou 3. Molecular Library Design Using Multi-Objective Optimization Methods Christos A Nicolaou and Christos C. Kannas 4. A Scalable Approach to Combinatorial Library Design Puneet Sharma, Srinivasa Salapaka, and Carolyn Beck 5. Application of Free-Wilson Selectivity Analysis for Combinatorial Library Design Simone Sciabola, Robert V. Stanton, Theresa L. Johnson, and Hualin Xi 6. Application of QSAR and Shape Pharmacophore Modeling Approaches for Targeted Chemical Library Design Jerry O. Ebalunode, Weifan Zheng, and Alexander Tropsha 7. Combinatorial Library Design from Reagent Pharmacophore Fingerprints Hongming Chen, Ola Engkvist, and Niklas Blomberg Part II: Structure-Based Library Design 8. Docking Methods for Structure-Based Library Design Claudio N. Cavasotto and Sharangdhar S. Phatak 9. Structure-Based Library Design in Efficient Discovery of Novel Inhibitors Shunqi Yan and Robert Selliah 10. Structure-Based and Property-Compliant Library Design of 11-HSD1 Adamantyl Amide Inhibitors Genevieve D. Paderes, Klaus Dress, Buwen Huang, Jeff Elleraas, Paul A. Rejto, and Tom Pauly Part III: Fragment-Based Library Design 11. Design of Screening Collections for Successful Fragment-Based Lead Discovery James Na and Qiyue Hu 12. Fragment-Based Drug Design Eric Feyfant, Jason Cross, Kevin Paris, and Désirée H.H. Tsao 13. LEAP into the Pfizer Global Virtual Library (PGVL) Space: Creation of Readily Synthesizable Design Ideas Automatically Qiyue Hu, Zhengwei Peng, Jaroslav Kostrowicki, and Atsuo Kuki Part IV: Library Design for Kinase Family 14. The Design, Annotation, and Application of a Kinase-Targeted-Library Hualin Xi and Elizabeth A. Lunney Part V: Library Design Tools 15. PGVL Hub: An Integrated Desktop Tool for Medicinal Chemists to Streamline Design and Synthesis of Chemical Libraries and Singleton Compounds Zhengwei Peng, Bo Yang, Sarathy Mattaparti, Thom Shulok, Thomas Thacher, James Kong, Jaroslav Kostrowicki, Qiyue Hu, James Na, Joe Zhongxiang Zhou, David Klatte, Bo Chao, Shogo Ito, John Clark, Nunzio Sciammetta, Bob Coner, Chris Waller, and Atsuo Kuki 16. Design of Targeted Libraries Against the Human Chk1 Kinase Using PGVL Hub Zhengwei Peng and Qiyue Hu 17. GLARE: A Tool for Product-Oriented Design of Combinatorial Libraries Jean-François Truchon 18. CLEVER: A General Design Tool for Combinatorial Libraries Tze Hau Lam, Paul H. Bernardo, Christina L. L. Chai, and Joo Chuan Tong