Case Studies in Modern Drug Discovery and Development

Xianhai Huang, PhD, is a Principal Scientist at Merck Research Laboratories. Dr. Huang is the inventor or co-inventor on more than forty patents and patent applications. As a mentor in the Schering-Plough chemistry postdoctoral program, Dr. Huang and his group discovered novel synthetic applications of (diacetoxyiodo) benzene and successfully applied the methodology to the total synthesis of psymberin, an antitumor natural product. Robert G. Aslanian, PhD, is an adjunct professor of chemistry at William Paterson University and was formerly a Senior Director of Medicinal Chemistry with the Schering-Plough Research Institute and Merck Research Laboratories. Dr. Aslanian has over twenty-five years of experience in the pharmaceutical industry. He is co-inventor on thirty-eight U.S. patents and coauthor on sixty-seven scientific articles and reviews.

Preface xv

Contributors xvii

Chapter 1 Introduction: Drug Discovery in Difficult Times 1
Malcolm MacCoss

Chapter 2 Discovery and Development of The DPP-4 Inhibitor Januvia® (SITA-GLIPTIN) 10
Emma R. Parmee, Ranabir SinhaRoy, Feng Xu, Jeffrey C. Givand, and Lawrence A. Rosen

2.1 Introduction 10

2.2 DPP-4 Inhibition as a Therapy for Type 2 Diabetes: Identification of Key Determinants for Efficacy and Safety 10

2.2.1 Incretin-Based Therapy for T2DM 10

2.2.2 Biological Rationale: DPP-4 is a Key Regulator of Incretin Activity 11

2.2.3 Injectable GLP-1 Mimetics for the Treatment of T2DM 12

2.2.4 DPP-4 Inhibition as Oral Incretin-Based Therapy for T2DM 12

2.2.5 Investigation of DPP-4 Biology: Identification of Candidate Substrates 13

2.2.6 Preclinical Toxicities of In-Licensed DPP-4 Inhibitors 15

2.2.7 Correlation of Preclinical Toxicity with Off-Target Inhibition of Pro-Specific Dipeptidase Activity 16

2.2.8 Identification of Pro-Specific Dipeptidases Differentially Inhibited by the Probiodrug Compounds 17

2.2.9 A Highly Selective DPP-4 Inhibitor is Safe and Well Tolerated in Preclinical Species 19

2.2.10 A Highly Selective DPP-4 Inhibitor Does Not Inhibit T-Cell Proliferation in vitro 19

2.2.11 DPP-4 Inhibitor Selectivity as a Key Parameter for Drug Development 20

2.3 Medicinal Chemistry Program 20

2.3.1 Lead Generation Approaches 20

2.3.2 Cyclohexyl Glycine α-Amino Acid Series of DPP-4 Inhibitors 20

2.3.3 Improving Selectivity of theα-Amino Acid Series 22

2.3.4 Identification and Optimization of the β-Amino Acid Series 22

2.4 Synthetic and Manufacturing Routes to Sitagliptin 27

2.4.1 Medicinal Chemistry Route to Sitagliptin and Early Modifications 27

2.4.2 An Asymmetric Hydrogenation Manufacturing Route to Sitagliptin 28

2.4.3 A “Greener” Manufacturing Route to Sitagliptin Employing Biocatalytic Transamination 31

2.5 Drug Product Development 33

2.5.1 Overview 33

2.5.2 Composition Development 33

2.5.3 Manufacturing Process Development 33

2.6 Clinical Studies 36

2.6.1 Preclinical PD Studies and Early Clinical Development of Sitagliptin 36

2.6.2 Summary of Phase II/III Clinical Trials 38

2.7 Summary 39

References 39

Chapter 3 Olmesartan Medoxomil: An Angiotensin II Receptor Blocker 45
Hiroaki Yanagisawa, Hiroyuki Koike, and Shin-ichiro Miura

3.1 Background 45

3.1.1 Introduction 45

3.1.2 Prototype of Orally Active ARBs 46

3.2 The Discovery of Olmesartan Medoxomil (Benicar) 47

3.2.1 Lead Generation 47

3.2.2 Lead Optimization 49

3.3 Characteristics of Olmesartan 53

3.4 Binding Sites of Omlersartan to the AT1 Receptor and Its Inverse Agonoist Activity 56

3.4.1 Binding Sites of Olmesartan to the AT1 Receptor 56

3.4.2 Inverse Agonist Activity of Olmesartan 56

3.4.3 Molecular Model of the Interaction between Olmesartan and the AT1 Receptor 57

3.5 Practical Preparation of Olmesartan Medoxomil 58

3.6 Preclinical Studies 58

3.6.1 AT1 Receptor Blocking Action 58

3.6.2 Inhibition of Ang II-Induced Vascular Contraction 59

3.6.3 Inhibition of the Pressor Response to Ang II 60

3.6.4 Blood Pressure Lowering Effects 60

3.6.5 Organ Protection 61

3.7 Clinical Studies 62

3.7.1 Antihypertensive Efficacy and Safety 62

3.7.2 Organ Protection 63

3.8 Conclusion 63

References 64

Chapter 4 Discovery of Heterocyclic Phosphonic Acids as Novelampmimics That Are Potent and Selective Fructose-1,6-Bisphosphatase Inhibitors and Elicit Potent Glucose-Lowering Effects in Diabetic Animals and Humans 67
Qun Dang and Mark D. Erion

4.1 Introduction 67

4.2 The Discovery of MB06322 69

4.2.1 Research Operation Plan 69

4.2.2 Discovery of Nonnucleotide AMP Mimics as FBPase Inhibitors 69

4.2.3 Discovery of Benzimidazole Phosphonic Acids as FBPase Inhibitors 74

4.2.4 Discovery of Thiazole Phosphonic Acids as Potent and Selective FBPase Inhibitors 77

4.2.5 The Discovery of MB06322 Through Prodrug Strategy 80

4.3 Pharmacokinetic Studies of MB06322 82

4.4 Synthetic Routes to MB06322 83

4.5 Clinical Studies of MB06322 83

4.5.1 Efficacy Study of Thiazole 12.6 in Rodent Models of T2DM 83

4.5.2 Phase I/II Clinical Studies 84

4.6 Summary 84

References 85

Chapter 5 Setting The Paradigm of Targeted Drugs for The Treatment of Cancer: Imatinib and Nilotinib, Therapies for Chronic Myelogenous Leukemia 88
Paul W. Manley and Jurg Zimmermann

5.1 Introduction 88

5.2 Chronic Myelogenous Leukemia (CML) and Early Treatment of the Disease 89

5.3 Imatinib: A Treatment for Chronic Myelogenous Leukemia (CML) 92

5.4 The Need for New Inhibitorts of BCR-ABL1 and Development of Nilotinib 94

5.5 Conclusion 99

References 100

Chapter 6 Amrubicin, A Completely Synthetic 9-Aminoanthracycline for Extensive-Disease Small-Cell Lung Cancer 103
Mitsuharu Hanada

6.1 Introduction 103

6.2 The Discovery of Amrubicin: The First Completely Synthetic Anthracycline 106

6.3 Toxicological Profile of Amrubicin 107

6.4 DNA Topoisomerase II Inhibition and Apoptosis Induction by Amrubicin 110

6.5 Amrubicin Metabolism: The Discovery of Amrubicinol 113

6.5.1 Amrubicinol Functions as an Active Metabolite of Amrubicin 113

6.5.2 Tumor-Selective Metabolism of Amrubicin to Amrubicinol 115

6.6 Improved Usage of Amrubicin 116

6.7 Clinical Trials 118

6.7.1 Clinical Trials of Amrubicin as First-line Therapy in Patients with ED-SCLC 118

6.7.2 Clinical Trials of Amrubicin as Second-Line Therapy in Patients with ED-SCLC 121

6.8 Conclusions 122

References 123

Chapter 7 The Discovery of Dual IGF-1R and IR Inhibitor FQIT for the Treatment of Cancer 127
Meizhong Jin, Elizabeth Buck, and Mark J. Mulvihill

7.1 Biological Rational for Targeting the IGF-1R/IR Pathway for Anti-Cancer Therapy 127

7.2 Discovery of OSI-906 128

7.2.1 Summary of OSI-906 Discovery 128

7.2.2 OSI-906 Clinical Aspects 129

7.3 OSI-906 Back Up Efforts 131

7.4 The Discovery of FQIT 131

7.4.1 Lead Generation Strategy 131

7.4.2 Small Molecule Dual IGF-1R/IR Inhibitor Drug Discovery Cascade 133

7.4.3 Initial Proof-of-Concept Compounds 134

7.4.4 Synthesis of 5,7-Disubstituted Imidazo[5,1-f][1,2,4] Triazines 135

7.4.5 Lead Imidazo[5,1-f][1,2,4] Triazine IGF-1R/IR Inhibitors and Emergence of FQIT 139

7.5 In Vitro Profile of FQIT 140

7.5.1 Cellular and Antiproliferative Effects as a Result of IGF-1R and IR Inhibition 140

7.5.2 Cellular Potency in the Presence of Plasma Proteins 141

7.5.3 In Vitro Metabolism and CYP450 Profile 143

7.6 Pharmacokinetic Properties of FQIT 144

7.6.1 formulation and Salt Study 144

7.6.2 Pharmacokinetics Following Intravenous Administration 144

7.6.3 Pharmacokinetics Following Oral Administration 145

7.7 In Vivo Profile of FQIT 146

7.7.1 In Vivo Pharmacodynamic and PK/PD Correlation 146

7.7.2 In Vivo Efficacy 146

7.8 Safety Assessment and Selectivity Profile of FQIT 148

7.8.1 Effects on Blood Glucose and Insulin Levels 148

7.8.2 Oral Glucose Tolerance Test 148

7.8.3 Ames, Rodent, and Nonrodent Toxicology Studies 149

7.8.4 Selectivity Profile of FQIT 149

7.9 Summary 150

Acknowledgments 151

References 151

Chapter 8 Discovery and Development of Montelukast (Singulair®) 154
Robert N. Young

8.1 Introduction 154

8.2 Drug Development Strategies 158

8.3 LTD4 Antagonist Program 159

8.3.1 Lead Generation and Optimization 159

8.3.2 In Vitro and In Vivo Assays 159

8.4 The Discovery of Montelukast (Singulair®) 160

8.4.1 First-Generation Antagonists (Figure 8.3) 160

8.4.2 Discovery of MK-571 163

8.4.3 Discovery of MK-0679 (29) 168

8.4.4 Discovery of Montelukast (L-706,631, MK-0476, Singulair®) 171

8.5 Synthesis of Montelukast 174

8.5.1 Medicinal Chemistry Synthesis 174

8.5.2 Process Chemistry Synthesis [104, 105] (Schemes 8.5 and 8.6) 176

8.6 ADME Studies with MK-0476 (Montelukast) 179

8.7 Safety Assessment of Montelukast 180

8.8 Clinical Development of Montelukast 180

8.8.1 Human Pharmacokinetics, Safety, and Tolerability 180

8.8.2 Human Pharmacology 181

8.8.3 Phase 2 Studies in Asthma 182

8.8.4 Phase 3 Studies in Asthma 182

8.8.5 Effects of Montelukast on Inflammation 185

8.8.6 Montelukast and Allergic Rhinitis 185

8.9 Summary 185

8.9.1 Impact on Society 185

8.9.2 Lessons Learned 186

8.10 Personal Impact 187

References 188

Chapter 9 Discovery and Development of Maraviroc, A CCR5 Antagonist for the Treatment of HIV Infection 196
Patrick Dorr, Blanda Stammen, and Elna van der Ryst

9.1 Background and Rationale 196

9.2 The Discovery of Maraviroc 199

9.2.1 HTS and Biological Screening to Guide Medicinal Chemistry 199

9.2.2 Hit Optimization 200

9.2.3 Overcoming Binding to hERG 201

9.3 Preclinical Studies 201

9.3.1 Metabolism and Pharmacokinetic Characteristics of Maraviroc 201

9.3.2 Maraviroc Preclinical Pharmacology 202

9.3.3 Preclinical Investigations into HIV Resistance 202

9.3.4 Binding of Maraviroc to CCR5 204

9.4 The Synthesis of Maraviroc 205

9.5 Nonclinical Safety and Toxicity Studies 206

9.5.1 Safety Pharmacology 206

9.5.2 Immuno- and Mechanistic Toxicity 206

9.6 Clinical Development of Maraviroc 207

9.6.1 Phase 1 Studies 207

9.6.2 Phase 2a Studies 209

9.6.3 Phase 2b/3 Studies 210

9.6.4 Development of Resistance to CCR5 Antagonists In Vivo 213

9.7 Summary, Future Directions, and Challenges 214

Acknowledgments 217

References 217

Chapter 10 Discovery of Antimalarial Drug Artemisinin and Beyond 227
Weiwei Mao, Yu Zhang, and Ao Zhang

10.1 Introduction: Natural Products in Drug Discovery 227

10.2 Natural Product Drug Discovery in China 227

10.3 Discovery of Artemisinin: Background, Structural Elucidation and Pharmacological Evaluation 228

10.3.1 Background and Biological Rationale 228

10.3.2 The Discovery of Artemisinin through Nontraditional Drug Discovery Process 229

10.3.3 Structural Determination of Artemisinin 231

10.3.4 Pharmacological Evaluation and Clinical Trial Summary of Artemisinin 231

10.4 The Synthesis of Artemisinin 232

10.4.1 Synthesis of Artemisinin using Photooxidation of Cyclic or Acyclic Enol Ether as the Key Step 233

10.4.2 Synthesis of Artemisinin by Photooxidation of Dihydroarteannuic Acid 236

10.4.3 Synthesis of Artemisinin by Ozonolysis of a Vinylsilane Intermediate 236

10.5 SAR Studies of Structural Derivatives of Artemisinin: The Discovery of Artemether 238

10.5.1 C-10-Derived Artemisinin Analogs 240

10.5.2 C-9 and C-9,10 Double Substituted Analogs 245

10.5.3 C-3 Substituted Analogs 246

10.5.4 C-6 or C-7 Substituted Derivatives 246

10.5.5 C-11-Substituted Analogs 247

10.6 Development of Artemether 248

10.6.1 Profile and Synthesis of Artemether 248

10.6.2 Clinical Studies Aspects of Artemether 249

10.7 Conclusion and Perspective 250

Acknowledgment 250

References 251

Chapter 11 Discovery and Process Development of MK-4965, A Potent Nonnucleoside Reverse Transcriptase Inhibitor 257
Yong-Li Zhong, Thomas J. Tucker, and Jingjun Yin

11.1 Introduction 257

11.2 The Discovery of MK-4965 260

11.2.1 Background Information 260

11.2.2 SAR Studies Leading to the Discovery of MK-4965 262

11.3 Preclinical and Clinical Studies of MK-4965 (19) 266

11.4 Summary of Back-Up SAR Studies of MK-4965 Series 266

11.5 Process Development of MK-4965 (19) 267

11.5.1 Medicinal Chemistry Route 267

11.5.2 Process Development 269

11.6 Conclusion 290

11.6.1 Lessons Learned from the Medicinal Chemistry Effort of MK-4965 Discovery 290

11.6.2 Summary and Lessons Learned from the Process Development of MK-4965 291

Acknowledgments 291

References 291

Chapter 12 Discovery of Boceprevir and Narlaprevir: The First and Second Generation of HCV NS3 Protease Inhibitors 296
Kevin X. Chen and F. George Njoroge

12.1 Introduction 296

12.2 HCV NS3 Protease Inhibitors 298

12.3 Research Operation Plan and Biological Assays 302

12.3.1 Research Operation Plan 302

12.3.2 Enzyme Assay 302

12.3.3 Replicon Assay 302

12.3.4 Measure of Selectivity 303

12.4 Discovery of Boceprevir 303

12.4.1 Initial Lead Generation Through Structure-Based Drug Design 303

12.4.2 SAR Studies Focusing on Truncation, Depeptization, and Macrocyclisation 304

12.4.3 Individual Amino Acid Residue Modifications 307

12.4.4 Correlations Between P1, P3, and P3 Capping: The Identification of Boceprevir 315

12.5 Profile of Boceprevir 317

12.5.1 In Vitro Characterization of Boceprevir 317

12.5.2 Pharmacokinetics of Boceprevir 317

12.5.3 The Interaction of Boceprevir with NS3 Protease 318

12.6 Clinical Development and Approval of Boceprevir 319

12.7 Synthesis of Boceprevir 319

12.8 Discovery of Narlaprevir 322

12.8.1 Criteria for the Back-up Program of Boceprevir 322

12.8.2 SAR Studies 322

12.8.3 Profile of Narlaprevir 326

12.8.4 Clinical Development Aspects of Narlaprevir 327

12.8.5 Synthesis of Narlaprevir 327

12.9 Summary 329

References 330

Chapter 13 The Discoveryofsamsca® (Tolvaptan): Thefirst Oral Nonpeptide Vasopressin Receptor Antagonist 336
Kazumi Kondo and Yoshitaka Yamamura

13.1 Background Information about the Disease 336

13.2 Biological Rational 337

13.3 Lead Generation Strategies: The Discovery of Mozavaptan 338

13.4 Lead Optimization: From Mozavaptan to Tolvaptan 347

13.5 Pharmacological Profiles of Tolvaptan 350

13.5.1 Antagonistic Affinities of Tolvaptan for AVP Receptors 350

13.5.2 Aquaretic Effect Following a Single Dose in Conscious Rats 352

13.6 Drug Development 353

13.6.1 Synthetic Route of Discovery and Commercial Synthesis [10a] 353

13.6.2 Nonclinical Toxicology 353

13.6.3 Clinical Studies 355

13.7 Summary Focusing on Lessons Learned 356

Acknowledgments 357

References 357

Chapter 14 Silodosin (Urief®, Rapaflo®, Thrupas®, Urorec®, Silodix®): A Selective α1A Adrenoceptor Antagonist for the Treatment of Benign Prostatic Hyperplasia 360
Masaki Yoshida, Imao Mikoshiba, Katsuyoshi Akiyama, and Junzo Kudoh

14.1 Background Information 360

14.1.1 Benign Prostatic Hyperplasia 360

14.1.2 α1-Adrenergic Receptors 361

14.2 The Discovery of Silodosin 362

14.2.1 Medicinal Chemistry 362

14.2.2 The Synthesis of Silodosin (Discovery Route) 363

14.2.3 Receptor Binding Studies 365

14.3 Pharmacology of Silodosin 369

14.3.1 Action Against Noradrenalin-Induced Contraction of Lower Urinary Tract Tissue 369

14.3.2 Actions Against Phenylephrine-Induced Increase in Intraurethral Pressure and Blood Pressure 371

14.3.3 Actions Against Intraurethral Pressure Increased by Stimulating Hypogastric Nerve and Blood Pressure in Dogs with Benign Prostatic Hyperplasia 372

14.3.4 Safety Pharmacology 373

14.4 Metabolism of Silodosin 373

14.5 Pharmacokinetics of Silodosin 376

14.5.1 Absorption 376

14.5.2 Organ Distribution 377

14.5.3 Excretion 378

14.6 Toxicology of Silodosin 379

14.7 Clinical Trials 382

14.7.1 Phase I Studies 382

14.7.2 Phase III Randomized, Placebo-Controlled, Double-Blind Study 383

14.7.3 Long-Term Administration Study 385

14.8 Summary: Key Lessons Learned 388

References 389

Chapter 15 Raloxifene: A Selective Estrogen Receptor Modulator (SERM) 392
Jeffrey A. Dodge and Henry U. Bryant

15.1 Introduction: SERMs 392

15.2 The Benzothiophene Scaffold: A New Class of SERMs 394

15.3 Assays for Biological Evaluation of Tissue Selectivity 394

15.4 Benzothiophene Structure Activity 395

15.5 The Synthesis of Raloxifene 401

15.6 SERM Mechanism 402

15.7 Raloxifene Pharmacology 405

15.7.1 Skeletal System 405

15.7.2 Reproductive System—Uterus 407

15.7.3 Reproductive System—Mammary 408

15.7.4 General Safety Profile and Other Pharmacological Considerations 410

15.8 Summary 411

References 411

Appendix I Small Molecule Drug Discovery and Development Paradigm 417

Appendix II Glossary 419

Appendix III Abbreviations 432

Index 443