Computer Applications in Pharmaceutical Research and Development

A unique, holistic approach covering all functions and phases ofpharmaceutical research and development

While there are a number of texts dedicated to individualaspects of pharmaceutical research and development, this uniquecontributed work takes a holistic and integrative approach to theuse of computers in all phases of drug discovery, development, andmarketing. It explains how applications are used at various stages,including bioinformatics, data mining, predicting human response todrugs, and high–throughput screening. By providing a comprehensiveview, the book offers readers a unique framework and systemsperspective from which they can devise strategies to thoroughlyexploit the use of computers in their organizations during allphases of the discovery and development process.

Chapters are organized into the following sections:

Computers in pharmaceutical research and development: a generaloverview Understanding diseases: mining complex systems forknowledge Scientific information handling and enhancing productivity Computers in drug discovery Computers in preclinical development Computers in development decision making, economics, and marketanalysis Computers in clinical development Future applications and future development

Each chapter is written by one or more leading experts in thefield and carefully edited to ensure a consistent structure andapproach throughout the book. Figures are used extensively toillustrate complex concepts and multifaceted processes. Referencesare provided in each chapter to enable readers to continueinvestigating a particular topic in depth. Finally, tables ofsoftware resources are provided in many of the chapters.

This is essential reading for IT professionals and scientists inthe pharmaceutical industry as well as researchers involved ininformatics and ADMET, drug discovery, and technology development.The book′s cross–functional, all–phases approach provides a uniqueopportunity for a holistic analysis and assessment of computerapplications in pharmaceutics.

Preface.

Acknowledgments.

Contributors.

PART I: COMPUTERS IN PHARMACEUTICAL RESEARCH ANDDEVELOPMENT: A GENERAL OVERVIEW.

1. The history of computers in pharmaceutical research anddevelopment: A narrative (Donald B. Boyd and Max M. Marsh).

2. Computers as data analysis and data management tools inpreclinical development (Weiyong Li and Kenneth Banks).

3. Statistical modeling in pharmaceutical research anddevelopment (Andrea de Gaetano, Simona Panuzi, Benoit Beck andBruno Boulanger).

PART II: UNDERSTANDING DISEASES: MINING COMPLEX SYSTEMSFOR KNOWLEDGE.

4. Drug discovery from historic herbal texts (Eric J.Buenz).

5. Contextualizing the impact of bioinformatics on preclinicaldrug and vaccine discovery (Darren R. Flower).

6. Computers and systems biology for pharmaceutical research anddevelopment (Sean Ekins and Craig Giroux).

PART III: SCIENTIFIC INFORMATION HANDLING AND ENHANCINGPRODUCTIVITY.

7. Information management –biodata in life sciences (Richard K.Scott and Anthony Parsons).

8. Chemoinformatics techniques for processing chemical structuredatabases (Valerie J. Gillet and Peter Willett).

9. Electronic Laboratory Notebooks (Alfred Nehme and Robert A.Scoffin).

10. Strategies for using information effectively in early stagedrug discovery (David J. Wild).

11. Improving the pharmaceutical research and developmentprocess: how simulation can support management decision–making(Andrew Chadwick, Jonathan Moore, Maggie A.Z. Hupcey, and RobinPurshouse).

PART IV: COMPUTERS IN DRUG DISCOVERY.

12. Computers and protein crystallography (David J. Edwards andRoderick E. Hubbard).

13. Computers, cheminformatics and the medicinal chemist (WeifanZheng and Michael L. Jones).

14. The challenges of making useful protein–ligand free energypredictions for drug discovery (Jun Shimada).

15. Computer algorithms for selecting molecule libraries forsynthesis (Konstantin V. Balakin, Nikolay P. Savchuk and AlexKiselyov).

16. Success stories of computer–aided design (Hugo Kubinyi).

17. Pharmaceutical research and development productivity: cansoftware help (Christophe Lambert and Stan Young)?

PART V: COMPUTERS IN PRE–CLINICAL DEVELOPMENT.

18. Computer methods for predicting drug metabolism (SeanEkins).

19. Computers in toxicology and risk assessment (John C.Dearden).

20. Computer optimization of biopharmaceutical properties (ChengChang and Peter W. Swaan).

21. Computer simulations in pharmacokinetics andpharmacodynamics.

rediscovering systems physiology in the 21st Century (PaoloVicini).

22. Predictive models for better decisions from understandingphysiology to optimizing trial design (James R. Bosley Jr.).

PART VI: COMPUTERS IN DEVELOPMENT DECISION MAKING,ECONOMICS AND MARKET ANALYSIS.

23. Making pharmaceutical development more efficient (MichaelRosenberg and Richard Farris).

24. Use of interactive software in medical decision making(Renee Arnold).

PART VII: COMPUTERS IN CLINICAL DEVELOPMENT.

25. Clinical data collection and management (MazenAbdellatif).

26. Regulation of computer systems (Sandy Weinberg).

27. A new paradigm for analyzing adverse drug events (AnaSzarfman, Jonathan G. Levine and Joseph M. Tonning).

PART VIII: FURTHER APPLICATIONS AND FUTUREDEVELOPMENT.

28. Computers in pharmaceutical formulation (Raymond C. Rowe andElizabeth A. Colbourn).

29. Legal protection of innovative uses of computers in researchand development (Robert Harrison).

30. The ethics of computing in pharmaceutical research (MatthewK. McGowan and Richard J. McGowan).

31. The UltraLink: An expert system for contextual hyperlinkingin knowledgemanagement (Martin Romacker, Nicolas Grandjean, PierreParisot, Olivier Kreim, Daniel Cronenberger, Th r seVachon and Manuel C. Peitsch).

32. Powerful, predictive and pervasive: The future of computersin the pharmaceutical industry (Nick Davies, Heather Ahlborn,Stuart T. Henderson).

Index.

SEAN EKINS, PHD, DSC, is an Adjunct Associate Professor in the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy. Dr. Ekins is the author of more than seventy peer–reviewed papers and book chapters as well as several patents. He serves on editorial boards for the Journal of Pharmacological and Toxicological Methods, Drug Metabolism and Disposition, Drug Discovery Today, and Pharmaceutical Research.

"Computer Applications in Pharmaceutical Research and Development"is ideal for information technologists who want to understand theapplication of computers across the entire drug research anddevelopment process." ( Journal of Clinical Research BestPractices, September 2008)

"...a well–put–together volume with a lot of very interestingand timely information to convey...it would be a nice addition toindividual, academic, and industrial libraries." (Journal ofMedicinal Chemistry, December 28, 2006)

"...strongly recommended both to the structural and medicinalchemistry community, and also to...computational chemists...thewhole book is really very readable and enjoyable." (StructuralChemistry, December 2006)