Breakthroughs in combinatorial chemistry and molecular biology, as well as an overall industry trend toward accelerated development, mean the rate of sample generation now far exceeds the rate of sample analysis in the pursuit of producing new and better pharmaceuticals. LC/MS is an analytical tool that helps the researcher identify the most promising sample early in the selection process, effectively creating a shortcut to finding new drugs. This book is the first to describe LC/MS applications within the context of drug development, including the discovery, preclinical, clinical, and manufacturing phases. In addition to the thorough technical analysis of this tool,LC/MS Applications in Drug Development provides perspective on the significant changes in strategies for pharmaceutical analysis. A process overview of drug development from an analytical point of view is provided along with essential data required to successfully bring a drug to market. The incorporation of LC/MS is illustrated from target to product. Chapters pertaining to the discovery process itself include:ProteomicsGlycoprotein MappingNatural Products DereplicationLead Identification ScreeningOpen-Access LC/MSIn Vitro Drug Screening

Written for both the analytical chemist who uses LC/MS applications and the pharmaceutical scientist who works with the drugs they produce,LC/MS Applications in Drug Development is the premier reference on the subject.

MIKE S. LEE, PhD, is President of Milestone Development Services, a consulting firm specializing in pharmaceutical analysis and drug development strategies. He lives in Newtown, Pennsylvania.

Preface ix

Acknowledgments xi

1. Introduction 1

Emerging Analytical Needs 1

Integration of LC/MS into Drug Development 3

Partnerships and Acceptance 6

Overview 10

2. Drug Development Overview 11

Analysis Perspectives 11

The Four Stages of Drug Development 12

Drug Discovery 14

Preclinical Development 15

Clinical Development 16

Manufacturing 17

3. Accelerated Drug Development 19

Accelerated Development Strategies 20

Quantitative and Qualitative Process Elements 20

Quantitative Process Pipeline 24

Qualitative Process Pipeline 25

Motivating Factors 27

Analysis Opportunities for Accelerated Development 28

Full-Time Equivalent 28

Sample Throughput Model 29

Elimination Model 29

Rate-Determining Event Model 31

Accelerated Development Perspectives 33

4. LC/MS Development 34

The Elements of LC/MS Application 34

HPLC 35

Mass Spectrometry 35

LC/MS Interface 36

LC/MS Growth 38

5. Strategies 41

Standard Methods 43

Template Structure Identification 46

Databases 49

Screening 50

Integration 53

Miniaturization 55

Parallel Processing 56

Visualization 58

Automation 61

Summary 63

6. LC/MS Applications 65

Drug Discovery 65

Proteomics 68

Protein Expression Profiling 70

Quantitation 76

Glycoprotein Mapping 78

Natural Products Dereplication 83

Lead Identification Screening 88

Bioaffinity Screening 89

Combinatorial Library Screening 92

Open-Access LC/MS 96

Structure Confirmation 97

High Throughput 100

Purification 102

Combinatorial Mixture Screening 103

In Vivo Drug Screening 106

Pharmacokinetics 109

In Vitro Drug Screening 115

Metabolic Stability Screening 118

Membrane Permeability 119

Drug-Drug Interaction 121

Metabolite Identification 122

Preclinical Development 123

Metabolite Identification 125

Impurity Identification 132

Degradant Identification 140

Clinical Development 145

Quantitative BioanalysisSelected Ion Monitoring 148

Quantitative BioanalysisSelected Reaction Monitoring 152

Quantitative BioanalysisAutomated Solid-Phase Extraction 156

Quantitative BioanalysisAutomated On-Line Extraction 162

Metabolite Identification 165

Degradant Identification 168

Manufacturing 171

Impurity Identification Using Data-Dependent Analysis 173

Peptide Mapping in Quality Control 176

Patent Protection 178

7. Future Applications and Prospects 183

Workstations 183

Multidimensional Analysis 186

Miniaturization 187

Information Management 189

Strategic Outsourcing 190

Summary 191

8. Perspectives on the Future Growth of LC/MS 192

9. Conclusions 195

Glossary 197

References 205

Index 235