Peptide Drug Discovery and Development: Translational Research in Academia and Industry

Filling a real knowledge gap, this handbook and ready reference is both modern and forward-looking in its emphasis on the "bench to bedside" translational approach to drug development. Clearly structured into three major parts, the book stakes out the boundaries of peptide drug development in the preclinical as well as clinical stages. The first part provides a general background and focuses on the characteristic strengths and weaknesses of peptide drugs. The second section contains five cases studies of peptides from diverse therapeutic fields, and the lessons to be learned from them, while the final part looks at new targets and opportunities, discussing several drug targets and diseases for which peptide drugs are currently being developed.

Table of Contents:
Preface xiii List of Contributors xv Part I The Academia - Market Bouncing of Peptide Drugs - Challenges and Strategies in Translational Research with Peptide Drugs 1 1 Peptides as Leads for Drug Discovery 3 Paul J. Edwards, and Steven R. LaPlante 1.1 Introduction 3 1.2 Overview of Process for Transforming Peptides to Peptidomimetics 5 1.3 HCMV Protease 7 1.3.1 HCMV Protease: Identification and Characterization of Antiviral Inhibitors Targeting the Serine Protease Domain of the Human Cytomegalovirus (HCMV Protease) 7 1.3.2 Mapping Essential Elements of the Substrate Peptides and Determining Structures of Ligands Bound to HCMV 8 1.3.3 Improving Peptide Activity to Allow SAR Studies 10 1.3.4 Elucidation of the Binding Mode of the Optimized Peptidyl Segment 10 1.3.5 Ligand Adaptations upon Binding 12 1.3.6 Strategic Summary for HCMV Peptide Mimic Design Process 14 1.4 HCV Protease 15 1.4.1 HCV Protease as an Antiviral Target 15 1.4.2 NS3 Serine Protease Possesses a Chymotrypsin-Like Fold 16 1.4.3 Discovery of the Peptide DDIVPC as an Inhibitor of NS3 Protease 16 1.4.4 "Sensemaking" and Knowledge Building: Mapping of the Critical Binding Residues of the Peptide and Creation of an Inhibitor-Protease Model 18 1.4.5 Knowledge Building: Monitoring Ligand Flexibility in the Free-State and Changes Upon Binding - P3 Rigidification 18 1.4.6 N-Terminal Truncation and Improved P1, P2 and P5 Substituents 22 1.4.7 Macrocyclization: Linking the Flexible P1 Side-Chain to P3 25 1.4.8 HCV Protease Inhibitor BI00201335 29 1.5 Herpes Simplex Virus 32 1.5.1 Herpes Simplex Virus-Encoded Ribonucleotide Reductase Inhibitors 32 1.6 Renin 38 1.6.1 Aspartyl Protease Renin as a Target 38 1.7 HIV 45 1.7.1 HIV Protease Inhibitors 45 1.8 Conclusions 47 2 Marketing Antimicrobial Peptides: A Critical Academic Point of View 57 Eduard Bardaji' 2.1 Introduction 57 2.2 Basic Research: Antimicrobial Peptides 58 2.3 Patents 61 2.4 Potential Applications of AMPs 63 2.5 Technology Transfer: Valorization, Licensing, or Spin-Off Creation 64 2.6 Spin-Off Creation: An Academic Point of View 66 3 Oral Peptide Drug Delivery: Strategies to Overcome Challenges 71 Hamman, Josias H. and Steenekamp, Jan H. 3.1 Introduction 71 3.2 Challenges Associated with Oral Peptide Delivery 72 3.2.1 Transport Pathways Across the Intestinal Epithelium 72 3.2.2 Unfavorable Physicochemical Properties of Peptide Drugs 73 3.2.2.1 Molecular Size, Hydrophilicity, and Physical Stability 73 3.2.3 Physical Barriers of the Gastrointestinal Tract 73 3.2.3.1 Transcellular Pathway 73 3.2.3.2 Paracellular Pathway 75 3.2.4 Biochemical Barriers of the Gastrointestinal Tract 75 3.2.4.1 Luminal Enzymes 76 3.2.4.2 Brush Border Membrane Bound Enzymes and Intracellular Enzymes 76 3.2.5 Efflux Transport Systems 76 3.2.6 Gastrointestinal Transit Time and Site-Specific Absorption 77 3.3 Strategies to Overcome the Barriers of the Gastrointestinal Tract 77 3.3.1 Absorption Enhancing Agents 77 3.3.2 Chemical and Physical Modifications 78 3.3.3 Targeting Strategies 81 3.3.3.1 Targeting Specific Regions of the Gastrointestinal Tract 81 3.3.3.2 Targeting Receptors and Transporters 82 3.3.4 Formulation Strategies 83 3.3.4.1 Particulate Carrier Systems 83 3.3.4.2 Enzyme Inhibition 84 3.3.4.3 Mucoadhesive Systems 84 3.4 Conclusions 84 4 Rational Design of Amphipathic a-Helical and Cyclic b-Sheet Antimicrobial Peptides: Specificity and Therapeutic Potential 91 Wendy J. Hartsock and Robert S. Hodges 4.1 Introduction to Antimicrobial Peptides 91 4.2 Antimicrobial and Hemolytic Activities of Amphipathic a-Helical Antimicrobial Peptides: Mechanisms and Selectivity 92 4.3 Structure-Activity Relationship Studies of Amphipathic a-Helical and Cyclic b-Sheet Antimicrobial Peptides: Optimization of Pathogen Selectivity and Prevention of Host Toxicity 94 4.4 Commercialization of Antimicrobial Peptides 112 4.5 Therapeutic Potential 113 5 Conotoxin-Based Leads in Drug Design 119 Muharrem Akcan and David J. Craik 5.1 Introduction 119 5.1.1 Cone Snails 119 5.1.2 Conotoxin Discovery and Characterization (MS, cDNA, Peptide Sequencing) 120 5.1.3 Conotoxin Classification and Targets 121 5.1.4 Posttranslational Modifications (PTMs) 122 5.1.5 Prospects for Drug Discovery 124 5.2 Conotoxin Synthesis, Folding, and Structure 124 5.2.1 Synthesis 124 5.2.2 Folding 127 5.2.3 Structure by NMR and X-Ray 127 5.3 Conotoxins as Drug Leads 128 5.3.1 Overview of Conotoxins in Drug Design 128 5.3.2 o-Conotoxins (MVIIA, CVID) 129 5.3.3 a-Conotoxins (Vc1.1) 129 5.3.4 w-Conotoxins (MrIA) 130 5.3.5 Re-engineered Conotoxins in Drug Design 131 5.4 Conclusions 133 6 Plant Antimicrobial Peptides: From Basic Structures to Applied Research 139 Suzana M. Ribeiro, Simoni C. Dias, and Octavio L. Franco 6.1 Introduction 139 6.2 The Diversity of Plant Antimicrobial Peptides: Focusing on Tissue Localization and Plant Species Distribution 139 6.3 Possible Structural Folds Found in Plant AMPs to Date 140 6.4 New Biotechnological Products Produced from Plant Peptides 144 Part II Peptide Drugs' Translational Tales - Peptide Drugs Before, Through and After Industry Pipelines 157 7 Omiganan Pentahydrochloride: A Novel, Broad-Spectrum Antimicrobial Peptide for Topical Use 159 Evelina Rubinchik and Dominique Dugourd 7.1 Omiganan: A Novel Anti-Infective Agent for Topical Indications 159 7.2 Structure and Mechanism of Action 160 7.3 Spectrum of Activity 163 7.4 Preclinical Efficacy Studies 163 7.5 Preclinical Toxicology Studies 164 7.6 Clinical Studies 165 7.7 Conclusions 167 8 Turning Endogenous Peptides into New Analgesics: The Example of Kyotorphin Derivatives 171 Marta M.B. Ribeiro, Isa D. Serrano, and So'nia Sa' Santos 8.1 Introduction 171 8.2 Peptides as Future Drug Candidates 171 8.3 Central Nervous System Analgesic Peptides 172 8.4 Endogenous Opioid System 173 8.5 Strategies to Deliver Analgesic Peptides to the Brain 174 8.6 Development of New Opioid-Derived Peptides 175 8.7 Kyotorphin - the Potential of an Endogenous Dipeptide 177 8.8 New KTP Derivatives 178 8.9 Assessing BBB Permeability with Peptide - Membrane Partition Studies 179 8.10 Kyotorphins: Partition to the Membrane and Enhanced Analgesic Activity 179 8.11 Academia and Pharmaceutical Industry: Friends or Foes? 183 9 The Development of Romiplostim - a Therapeutic Peptibody Used to Stimulate Platelet Production 189 Graham Molineux and Ping Wei 9.1 Introduction 189 9.2 Thrombopoietin and c-Mpl 189 9.3 Discovery and Optimization of Romiplostim 192 9.4 Pharmacodynamics (PD) and Pharmacokinetics (PK) of Romiplostim 194 9.5 A Brief ITP Primer 199 9.5.1 Diagnosis and Treatment 199 9.5.2 Thrombopoietin and ITP 200 9.6 Romiplostim Clinical Data 201 9.7 Safety and Other Insights Gained from Romiplostim Design and Development 203 10 HIV vs. HIV: Turning HIV-Derived Peptides into Drugs 209 Henri G. Franquelim, Pedro M. Matos, and A. Salome' Veiga 10.1 Introduction 209 10.2 HIV-1 Envelope Protein 209 10.3 HIV Entry and Its Inhibition 210 10.4 HIV-1 Fusion Inhibitors: from Bench to Clinical Administration 211 10.5 New Strategies for Creating New HIV Fusion Inhibitor Peptides 215 10.5.1 Increasing Helicity and Binding to gp41 216 10.5.2 Isomeric Peptides and Resistance to Proteolysis 219 10.5.3 Bacterially Expressed Peptides 220 10.5.4 Modification of Peptides by Derivatization with Lipids or Proteins 220 10.6 Drug-Resistance and Combination Therapy 222 10.7 Concluding Remarks 223 11 Sifuvirtide, A Novel HIV-1 Fusion Inhibitor 231 Xiaobin Zhang, Hao Wu, and Fengshan Wang 11.1 Ideal Drug Target HIV-1 gp41 231 11.2 Structure-Based Drug Design of Sifuvirtide 232 11.3 High Potency of Sifuvirtide 234 11.4 Limited Drug Resistance 235 11.5 Enhancement of the Efficiency of Sifuvirtide by Biomembrane Selectivity 236 11.6 Pharmacokinetics of Sifuvirtide with Long Half-Life 237 11.7 Stratification of Monotherapy 238 11.8 20 mg Sifuvirtide Once Daily vs. 100 mg T20 Twice Daily 239 11.9 Conclusions and Discussion 240 Part III Whither Peptide Drugs? Peptides Shaping the Future of Drug Development 245 12 Endogenous Peptides and Their Receptors as Drug Discovery Targets for the Treatment of Metabolic Disease 247 Mary Ann Pelleymounter, Yuren Wang, and Ning Lee 12.1 Centrally Secreted Neuropeptide Systems 248 12.1.1 Corticotropin Releasing Factor (CRF) Peptides 248 12.1.2 Melanin Concentrating Hormone (MCH) 249 12.1.3 Melanocortins 250 12.1.4 Neuropeptide Y (NPY) 252 12.1.5 Neuromedin U (NMU) and Neuromedin S (NMS) 254 12.1.6 Opioids 255 12.1.7 QRFP 256 12.2 Peripherally Secreted Neuropeptides 256 12.2.1 Amylin 256 12.2.2 Bombesin-Like Peptides (Bombesin and Gastrin-Releasing Peptide) 257 12.2.3 Cholecystokinin (CCK) 258 12.2.4 Ghrelin 259 12.2.5 Glucagon-like Peptide-1 260 12.2.6 Leptin 261 12.2.7 Oxyntomodulin (OXM) 262 12.2.8 PYY3-36 and PP 262 12.3 Summary 263 13 Translation of Motilin and Ghrelin Receptor Agonists into Drugs for Gastrointestinal Disorders 269 Gareth J. Sanger, John Broad, and David H. Alpers 13.1 Introduction 269 13.1.1 Similarities and Differences Between Motilin and Ghrelin 269 13.1.2 Clinical Potential of Motilin and Ghrelin Receptor Agonists 270 13.2 Motilin and Ghrelin Receptor Agonists Under Development 271 13.3 Translational Value of Preclinical Assays 275 13.3.1 Motilin 271 13.3.1.1 Assays Relevant to the Therapeutic Mechanism of Action 271 13.3.1.2 Assays Relevant to Possible Non-GI Activity 275 13.3.2 Ghrelin 276 13.3.2.1 Assays Relevant to the Therapeutic Mechanism of Action 276 13.3.2.2 Assays Relevant to Non-GI Activity 276 13.4 Clinical Translation: Selecting the "Right" Patient Population 277 13.4.1 Critically Ill Patients with Delayed Gastric Emptying 279 13.4.2 Patients with Gastroparesis 279 13.4.2.1 Diabetic Gastroparesis 281 13.4.2.2 Parkinson's Disease 281 13.4.2.3 Cyclic Nausea and Vomiting 282 13.4.2.4 Migraine 282 13.4.2.5 Functional Dyspepsia (FD) 282 13.4.2.6 Gastroesophageal Reflux Disease (GERD) 283 13.4.2.7 Anorexia and Decreased Appetite (Ghrelin Agonists Only) 284 13.5 Clinical Development of Motilin and Ghrelin Receptor Agonists 284 13.6 Conclusions 285 14 Of Mice and Men: Translational Research on Amylin Agonism 295 Jonathan D. Roth, Christine M. Mack, James L. Trevaskis, and David G. Parkes 14.1 Overview of Amylin Physiology 295 14.2 Pramlintide: An Amylin Agonist 296 14.3 Amylin Agonism: Translational Research in Insulin-Dependent Diabetes 297 14.3.1 Post-Prandial Hyperglucagonemia and Diabetes 297 14.3.2 Amylin Agonism and Glucagon: Preclinical and Clinical Studies 297 14.3.3 Gastric Emptying and Diabetes 298 14.3.4 Amylin Agonism and Gastric Emptying: Preclinical and Clinical Studies 298 14.4 Amylin Agonism: Translational Research in Obesity 299 14.4.1 Food Intake and Body Weight: Role of Endogenous Amylin 299 14.4.2 Food Intake and Body Weight: Pre-clinical Studies 300 14.4.3 Food Intake and Body Weight: Clinical Studies 302 14.4.4 Combination Studies 304 14.4.5 Amylin Agonism and Small Molecule Agents 304 14.4.6 Combined Amylin and Leptin Agonism 305 14.4.7 Future Areas for Amylin Agonism-Based Translational Research 307 15 Peptides and Polypeptides as Immunomodulators and Their Consequential Therapeutic Effect in Multiple Sclerosis and Other Autoimmune Diseases 313 Ruth Arnon, Michael Sela, and Rina Aharoni 15.1 Introduction 313 15.2 Peptides as Antigens and Vaccines 314 15.3 Peptides as Immunomodulators 315 15.4 Development of Copolymer 1 - a Polypeptide Immunomodulator Drug for the Treatment of Multiple Sclerosis 316 15.4.1 Clinical Studies with Cop 1 in MS Patients 317 15.4.2 Immunological Mechanisms Involved in the Mitigation of Disease by Cop 1 318 15.4.3 Immunomodulation by Cop 1 in the CNS 320 15.4.4 Neuroprotection and Augmentation of Neurotropic Factors in the Brain 321 15.4.5 Myelin Repair and Neurogenesis 323 15.4.6 The Effect of Cop 1 on Another Autoimmune Disease - Inflammatory Bowel Disease 326 15.5 Additional Immunomodulatory Peptides as Drug Candidates 327 15.5.1 Peptide Therapy for Type 1 Diabetes 327 15.5.2 Myasthenia Gravis (MG) 328 15.5.3 A Novel Tolerogenic Peptide for the Specific Treatment of Systemic Lupus Erythematosus 328 15.6 Summary and Concluding Remarks 329 16 Development of Antibody Fragments for Therapeutic Applications 337 Sofia Co rte-Real, Frederico Aires da Silva, and Joa"o Gonc- alves 16.1 Antibodies 337 16.1.1 Antibody Structure 338 16.1.2 Antibody Fragments 341 16.1.3 Single-Domain Antibodies 343 16.1.4 Engineering Multivalent, Bispecific, and Bifunctional Fragments 345 16.1.5 Intracellular Antibodies (Intrabodies) 347 16.1.5.1 Immunogenicity of Engineered Antibodies 348 16.1.5.2 Engineering New Protein Scaffolds 349 16.2 Conclusions 350 Index 357

About the Author :
Miguel Castanho is head of the Biochemistry department of the School of Medicine at the University of Lisbon (Portugal). He also leads the Physical Biochemistry research unit at the Institute of Molecular Medicine. His main field of research is the interaction of peptide drugs with lipids, in particular the role of lipid membranes in the mechanism of action of peptide drugs. Nuno C. Santos is the leader of the Biomembranes Unit of the Institute of Molecular Medicine. His research is centered on the specific functions of biological membranes lipids and proteins, with a special focus on their relevance for pathologic processes ranging from viral or bacterial infection to cardiovascular diseases. Together, Miguel Castanho and Nuno C. Santos have been involved in many collaborative drug discovery and development projects with industry partners in Europe, USA, Canada, and China.

Review :
"This book illustrates many of the technical prerequisites and describes model systems in which these objectives have been at least partially achieved. It convincingly shows that peptide-based drug discovery has become a mainstream activity in the drug discovery and development process." (ChemMedChem, 2012)