Drug Metabolism Handbook

Ala F. Nassar, PhD, is a faculty member at Yale University. He leads and executes ADME-Tox experiments supporting grant projects. He has served on numerous editorial boards and is the editor of the previous edition of Drug Metabolism Handbook: Concepts and Applications and Biotransformation and Metabolite Elucidation of Xenobiotics: Characterization and Identification.

Paul F. Hollenberg, PhD, was the Maurice H. Seevers Professor and Chair of Pharmacology at the University of Michigan for more than 20 years. His research focused on the active sites of P450s and their catalytic function. He was cofounder and Associate Editor of Chemical Research in Toxicology and has served on numerous editorial boards and review panels.

JoAnn Scatina, PhD has over 30 years of experience in Drug Metabolism and Preclinical Drug Development with leadership roles in both big pharma (Wyeth) and smaller biotech firms. She also provides expert drug development advice as a consultant to biotech and academic institutions.

Soumen Kanti Manna, PhD, is an Associate Professor in the Biophysics and Structural Genomics Division of Saha Institute of Nuclear Physics, Kolkata. His doctoral work involved cytochrome P450 and other metalloproteins. His current research activities include unravelling of metabolic reprogramming associated with gene-environment interaction and cancer as well as RNA modification and biomarker discovery.

Su Zeng, PhD, is a Professor and Director of Institute of Drug Metabolism and Pharmaceutical Analysis at College of Pharmaceutical Sciences, Zhejiang University. His research focuses on the regulation mechanism of drug ADME-Tox by using epigenetic models, transgenic cells expressing drug metabolizing enzymes, or transporters.

Volume 1

Preface xiii

List of contributors xv

Part I. Introduction 1

1. Historical Perspective 3
Roberta S. King

1.1 Controversies Spanning Past, Present, and Future 3

1.2 1800s: Discovery of Major Drug Metabolism Pathways (Conti and Bickel, 1977) 5

1.3 1900–1950s: Confirmation of Major Pathways and Mechanistic Studies 8

1.4 1950s–1980: Modern Drug Metabolism Emerges, with Enzymatic Basis 9

1.5 1980–2005: Field Driven by Improved Technologies 10

1.6 2005+: High Technology 10

References 10

2. Factors Affecting Metabolism 13
Roberta S. King

References 16

3. Biotransformations in Drug Metabolism 17
Roberta S. King

3.1 Drug Metabolism in Drug Development and Drug Therapy 17

3.2 Prediction of Metabolite and Enzyme Responsible 20

3.3 Functional Group Biotransformations: Phase I, Phase II, and Catalysis 21

3.4 Oxidations and Cytochrome P450 23

3.5 Enzymology and Modifiers of Cytochrome P450s 34

References 39

4. A Comprehensive Picture of Biotransformation in Drug Discovery 41
Joe R. Cannon, Prakash Vachaspati, and Yang Yuan

4.1 Introduction 41

4.2 Rate of Metabolism 43

4.3 Metabolism of Small Molecules 46

4.4 Analytical Technologies in Drug Metabolism 65

4.5 Biotransformation for Novel Modalities – Peptides and Protein Degraders 79

4.6 Conclusion 93

References 93

5. In Vivo Drug Metabolite Kinetics 103
Zheng Yang

5.1 Introduction 103

5.2 In Vivo Drug Metabolite Kinetic Concepts and Principles 105

5.3 Effect of Inhibition and Induction on Metabolite Kinetics 122

5.4 Determination of Formation and Elimination Clearance of

Metabolite 127

5.5 Incorporation of Pharmacologically Active Metabolite(s) in

Pharmacokinetic/Pharmacodynamic Modeling 130

5.6 Summary 135

Abbreviations 135

References 137

6. LC-MS/MS-Based Proteomics Methods for Quantifying Drug-Metabolizing Enzymes and Transporters 143
Logan S. Smith, Sun Min Jung, Jiapeng Li, and Hao-Jie Zhu

6.1 Introduction 143

6.2 Mass Spectrometry Versus Alternative Protein Quantification Methods 144

6.3 Mass Spectrometry Data Acquisition Methods for Proteomics Analysis 145

6.4 Targeted Approaches 146

6.5 Untargeted Proteomics Approaches 147

6.6 Relative Quantification Versus Absolute Quantification 150

6.7 Label-Based Proteomics 152

6.8 Label-Free Proteomics 155

6.9 DMET Protein Quantification Using LC-MS/MS-Based Proteomics 158

6.10 Potential Application of DMET Expression Studies 160

6.11 Considerations of DMET Protein Quantification Utilizing LC-MS/MS Methods 163

6.12 Conclusion 164

References 164

Part II. Technologies for in vitro and in vivo studies 177

7. Mass Spectrometry 179
Thomas R. Sharp

7.1 Introduction 179

7.2 A Brief History 180

7.3 The Mass Spectrometry Literature 182

7.4 Mass Spectrometry Instrumentation 183

7.5 Interpretation:What Does it Mean 211

7.6 Conclusions 254

References 255

8. Accelerating Metabolite Identification Mass Spectrometry Technology Drives Metabolite Identification Studies Forward 267
Ala F. Nassar

8.1 Introduction 267

8.2 Criteria for LC-MS Methods 269

8.3 Matrices Effect 269

8.4 Tool of Choice for Metabolite Characterization 270

8.5 Strategies for Identifying Unknown Metabolites 274

8.6 Online HD-LC-MS 275

8.7 “All-in-One” Radioactivity Detector, Stop Flow, and Dynamic

Flow for Metabolite Identification 282

8.8 Metabolic Activation Studies by Mass Spectrometry 287

8.9 Strategies to Screen for Reactive Metabolites 288

8.10 Summary 289

Abbreviations and Glossary 290

References 299

9. Role of Structural Modifications of Drug Candidates to Enhance Metabolic Stability 303
Ala F. Nassar

9.1 Background 303

9.2 Introduction 304

9.3 Significance of Metabolite Characterization and Structure Modification 305

9.4 Enhance Metabolic Stability 305

9.5 Metabolic Stability and Intrinsic Metabolic Clearance 306

9.6 Advantages of Enhancing Metabolic Stability 307

9.7 Strategies to Enhance Metabolic Stability 307

9.8 Analytical Tools 317

9.9 Case Studies 318

9.10 Conclusions 320

References 320

10. Drug Design Strategies: Role of Structural Modifications of Drug Candidates to Improve PK Parameters of New Drugs 323
Ala F. Nassar

10.1 Active Metabolites 323

10.2 Oral Absorption and Intravenous Dose 333

10.3 PK Analysis 333

10.4 Case Studies 334

10.5 Prodrugs to IncreaseWater Solubility 338

10.6 Conclusion 339

References 340

11. Chemical Structural Alert and Reactive Metabolite Concept as Applied in Medicinal Chemistry to Minimize the Toxicity of Drug Candidates 345
Ala F. Nassar

11.1 Importance of Reactive Intermediates in Drug Discovery and Development 345

11.2 Idiosyncratic Drug Toxicity and Molecular Mechanisms 349

11.3 Key Tools and Strategies to Improve Drug Safety 352

11.4 Peroxidases 357

11.5 Acyl Glucuronidation and S-Acyl-CoA Thioesters 358

11.6 Covalent Binding 359

11.7 Mechanistic Studies 360

11.8 Preclinical Development 363

11.9 Clinical Development: Strategy 364

11.10 Case Studies 364

11.11 Conclusion and Future Possibilities 366

References 367

12. Studies of Reactive Metabolites using Genotoxicity Arrays and Enzyme/DNA Biocolloids – 2021 373
James F. Rusling and Eli G. Hvastkovs

12.1 Introduction 373

12.2 On Demand Metabolic Reactions 374

12.3 Arrays with Electrochemical Detection 376

12.4 Electrochemiluminescent Arrays 379

12.5 ECL Arrays can Measure Both DNA Oxidation and Nucleobase Adduction 388

12.6 Detecting Site-Specific Damage to TUMOR SUPPRESSORGenes 392

12.7 Emerging Technologies and Methods 394

12.8 Conclusions and Future Outlook 398

Acknowledgments 399

Biographies 399

References 399

Part III. Drug interactions 407

13. Enzyme Inhibition 409
Paul F. Hollenberg

13.1 Introduction 409

13.2 Mechanisms of Enzyme Inhibition 411

13.3 Competitive Inhibition 412

13.4 Noncompetitive Inhibition 413

13.5 Uncompetitive Inhibition 414

13.6 Product Inhibition 414

13.7 Transition-State Analogs 415

13.8 Slow, Tight-Binding Inhibitors 415

13.9 Mechanism-Based Inactivators 415

13.10 Inhibitors that are Metabolized to Reactive Products that Covalently Attach to the Enzyme 418

13.11 Substrate Inhibition 419

13.12 Partial Inhibition 419

13.13 Inhibition of Cytochrome P450 Enzymes 420

13.14 Reversible Inhibitors 421

13.15 Quasi-Irreversible Inhibitors 421

13.16 Mechanism-Based Inactivators 422

References 424

14. Xenobiotic Receptor-Mediated Gene Regulation in Drug Metabolism and Disposition 427
Hongbing Wang and Wen Xie

14.1 Introduction 427

14.2 Pregnane X Receptor 429

14.3 Constitutive Androstane/Activated Receptor (CAR) 441

14.4 Closing Remarks and Perspectives 452

Acknowledgments 453

References 453

15. Characterization of Cytochrome P450 Mechanism Based Inhibition 465
Dan A. Rock and Larry C. Wienkers

15.1 Introduction 465

15.2 Inhibitors that Upon Activation Bind Covalently to the P450 Apoprotein 475

15.3 Inhibitors that Interact in a Pseudoirreversible Manner with Heme Iron 478

15.4 Inactivation that Cause Destruction of the Prosthetic Heme Group, Often Times Leading to Heme-Derived Products that Covalently Modify the Apoprotein 480

References 515

16. An Introduction to Metabolic Reaction-Phenotyping 527
Carl Davis

16.1 Introduction 527

16.2 Significant Drug-Metabolizing Enzymes 528

16.3 Common In VitroMethods to Assess Drug Metabolism 534

16.4 In Vitroto In VivoExtrapolation of Metabolic Clearance 539

16.5 Summary 546

References 546

17. Epigenetic Regulation of Drug-Metabolizing Enzymes in Cancer 553
Jiaqi Wang, Xiaoli Zheng, and Su Zeng

17.1 Introduction 553

17.2 DNA Methylation of DMEs 554

17.3 Histone Modification 558

17.4 Noncoding RNA 559

17.5 RNA Methylation 561

17.6 Closing Remarks and Perspectives 563

Acknowledgments 564

References 564

18. Epigenetic Regulation of Drug Transporters in Cancer 573
Yingying Wang, Ying Zhou, Yu Wang, Lushan Yu, and Su Zeng

18.1 Introduction 573

18.2 DNA Methylation 575

18.3 Histone Modifications 579

18.4 Noncoding RNAs 581

18.5 Closing Remarks and Perspectives 591

Acknowledgments 592

References 592

Volume 2

Preface xi

List of contributors xiii

Part IV. Toxicity 605

19. The Role of Drug Metabolism in Toxicity 607
Umesh M. Hanumegowda and Carl Davis

20. Allergic Reactions to Drugs 677
Mark P. Grillo

21. Chemical Mechanisms in Toxicology 703
Mark P. Grillo

22. Role of Bioactivation Reactions in Chemically Induced Nephrotoxicity 745
Lawrence H. Lash

Part V. Applications 773

23. Mapping the Heterogeneous Distribution of Cancer Drugs by Imaging Mass Spectrometry 775
Purva S. Damale and Shibdas Banerjee

24. Systemic Metabolomic Changes Associated with Chemotherapy: Role in Personalized Therapy 811
Bhargab Kalita, Ganesh K. Barik, Tanisha Sharma, Khushman Taunk, Praneeta P. Bhavsar, Manas K. Santra, and Srikanth Rapole

25. Metabolic Reprogramming in Cancer 841
Debasish Prusty and Soumen Kanti Manna

26. Case Study: Metabolism and Reactions of Alkylating Agents in Cancer Therapy 893
Ala F. Nassar, Adam V. Wisnewski, and Ivan King

27. Rewiring of Drug Metabolism and Its Cross-talk with Metabolic Reprogramming in Cancer 923
Subhabrata Majumder and Soumen Kanti Manna

28. Principles of Drug Metabolism and Interactions in Cardio-Oncology 967
Sherry-Ann Brown, Craig Beavers, Sailaja Kamaraju, Meera Mohan, Olubadewa Fatunde, Gift Echefu, Svetlana Zaharova, Brianna Wallace, and Carolyn Oxencis

Index 993