Peptide Therapeutics: Fundamentals of Design, Development, and Delivery

Description

This book explains how peptide-based drug design works, what steps are needed to develop a peptide-based therapeutic, and challenges in synthesis as well as regulatory issues.  It covers the design concept of peptide therapeutics from fundamental principles using structural biology and computational approaches. The chapters are arranged in a linear fashion. A fresh graduate or a scientist who works on small molecules can use this to follow the design and development of peptide therapeutics to use as understanding the basic concepts. Each chapter is written by experts from academia as well as industry. Rather than covering extensive literature, the book provides concepts of design, synthesis, delivery, as well as regulatory affairs and manufacturing of peptides in a systematic way with examples in each case. The book can be used as a reference for a pharmaceutical or biomedical scientist or graduate student who wants to pursue their career in peptide therapeutics. Some chapters will be written as a combination of basic principles and protocol so that scientists can adopt these methods to their research work. The examples provided can be used to perform peptide formulation considerations for the designed peptides. The book has nine chapters, and each chapter can be read as an independent unit on a particular concept. Preface Contents About the Author Chapter 1: Basic Concepts of Design of Peptide-Based Therapeutics 1.1 Introduction 1.2 Three-Dimensional Structure of Peptides 1.3 Targeting a Biochemical Pathway 1.4 Designing Drug When the Target Receptor Structure Is Known 1.4.1 The Binding Site and 3D Structure of Receptor Cavity/Surface 1.4.2 Agonist or Antagonist? 1.4.3 Pharmacophore Identification 1.5 Peptidomimetic 1.5.1 Backbone or Side-Chain Modification 1.5.2 Secondary Structure Mimics 1.6 Protein-Protein Interaction and Peptide Drug Design 1.7 Peptides from Natural Sources and Modification for Drug Design 1.8 Screening Assays 1.9 Binding Assays 1.10 Examples of Peptide-Based Drug Design 1.10.1 Enzyme-Based Drug Design 1.10.2 Receptor Ligand-Based Drug Design 1.10.2.1 Biochemical Basis of the Design 1.10.2.2 Identification of a Binding Epitope 1.10.2.3 N-Methylation of Cyclic Peptide 1.10.2.4 Preclinical and Clinical Evaluation 1.10.3 Example of a Peptide from Natural Resources: Polymyxin B 1.10.3.1 Mechanism of Action 1.10.3.2 SAR Length of Fatty Acid Chain and Substitution The Positive Charge of Dab Side Chains The Linear Tripeptide Segment The Hydrophobic Motif of the Heptapeptide Ring The Heptapeptide Backbone Formulations and Administration Resistance Toxicity and Modification of Polymyxin 1.10.4 Protein-Protein Interaction and Drug Design 1.10.4.1 Biochemical Pathway 1.10.4.2 Design of Peptides First-Generation Peptides Screening Assay Second-Generation Peptides Third-Generation Design of Grafted Peptides 1.11 Summary References Chapter 2: Peptide Synthesis: Methods and Protocols 2.1 Introduction 2.2 Fundamentals of Peptide Synthesis 2.2.1 Solution-Phase Peptide Synthesis 2.2.2 Solid-Phase Peptide Synthesis 2.3 Practical Aspects of Peptide Synthesis 2.4 Peptide Modifications 2.4.1 Cyclization 2.4.2 Disulfide Bond Formation 2.4.3 Automation of Solid-Phase Peptide Synthesis 2.4.4 Peptide Analysis and Purification 2.4.5 Sustainability in Peptide Synthesis 2.5 Examples of Peptide Syntheses Performed in the Authors’ Laboratory 2.5.1 Linear Peptide EHWSY-dK-LRPG-NH2 2.5.2 Fluorescently Labeled Peptide Ac-RWVOWIO(FAM)QVR-dP-G-NH2 2.5.3 Cyclic Peptide Cyclo (SIAD-dp-PDDIK) 2.5.4 PawS-Derived Peptide Cyclo (C(s-Anapa)RKSIPPR (s-Anapa) CFPDDF) References Chapter 3: Computational Methods for Peptide Macrocycle Drug Design 3.1 Introduction 3.2 Available Computational Tools for Peptide Macrocycle Drug Design 3.2.1 Computational Concepts 3.2.2 Heuristic Approaches 3.2.3 Software Approaches for Peptide Drug Modelling 3.2.3.1 Molecular Dynamics (MD) 3.2.3.2 Quantum Mechanics (QM) 3.2.3.3 The Rosetta Software Suite 3.2.3.4 Other Macromolecular Modelling Software 3.3 Pipelines for Peptide Macrocycle Drug Design 3.3.1 Target Modelling 3.3.2 Initial Stub Identification 3.3.3 Sampling Peptide Conformation 3.3.4 Designing Peptide Sequence 3.3.4.1 Approaches to the Fixed-Backbone Design Problem 3.3.4.2 Approaches for Flexible-Backbone Design 3.3.4.3 Controlling the Design Process 3.3.4.4 Filtering Out Poor Designs 3.3.4.5 Example of RosettaScripts Protocol 3.3.5 Computational Validation of Designs 3.3.5.1 Ranking Designs by Computed Interaction Energy with the Target 3.3.5.2 Ranking Designs by Computed Rigidity in the Binding-Competent Conformation 3.3.6 Experimental Validation of Top Designs 3.4 Emerging Technologies 3.4.1 Deep Neural Networks and Other Machine Learning Methods 3.4.2 Quantum Computing 3.5 Conclusions Appendixes Appendix A: Running Examples Obtaining and Compiling the Rosetta Software Obtaining Example XML Scripts and Inputs Running Example XML Scripts Appendix B: Code Listings References Chapter 4: Strategies to Optimize Peptide Stability and Prolong Half-Life 4.1 Introduction 4.2 Strategies to Improve Proteolytic Peptide Stability and Prolong Half-Life 4.3 Replacing L-Amino Acids with D-Amino Acids or Unnatural Amino Acids 4.4 Other Backbone Modification Strategies 4.5 Protection of N- and C-Termini 4.6 Cyclization 4.7 Increase Molecular Weight 4.8 Noncovalent π–π Interactions 4.9 Enzyme Inhibition 4.10 Flip-Flop Kinetics 4.11 Methods to Assess Peptide Stability 4.12 Blood, Serum, and Plasma Stability Assays 4.13 Hepatic Stability Assays 4.14 Kidney and Tissue Stability Assays 4.15 Gastric Intestinal Stability Assays 4.16 Conclusions References Chapter 5: Therapeutic Peptide Delivery: Fundamentals, Formulations, and Recent Advances 5.1 Introduction 5.2 Peptide Therapeutics Administered via Parenteral Route 5.3 Peptide Therapeutics Administered via Oral Route 5.4 Peptide Therapeutics Administered via Pulmonary Route 5.5 Peptide Therapeutics Administered via Transdermal Route 5.6 Peptide Therapeutics Administered via Other Routes 5.7 Summary References Chapter 6: Liposome Nanocarriers for Peptide Drug Delivery 6.1 Introduction 6.1.1 Limitations of Peptides as Therapeutics 6.2 Nanoparticle in Drug Delivery 6.2.1 Dendrimers 6.2.2 Micelles 6.2.3 Carbon Nanotubes 6.2.4 Quantum Dots 6.2.5 Liposomes 6.3 Liposome 6.4 Formulation and Manufacturing Strategies of Liposome 6.5 Characterization of Liposomes 6.6 Liposome Stabilization Strategy with Lyophilization 6.7 Liposomal Nanocarrier System for Peptide Drug Delivery 6.8 Types of Liposome 6.8.1 Active Targeting Liposomes 6.8.2 Stimuli-Responsive Liposomes 6.8.3 Temperature-Sensitive Liposomes (Thermosensitive Liposomes) 6.8.4 pH-Sensitive Liposomes 6.8.5 Magnetic Field-Responsive Liposomes 6.8.6 Ultrasound-Responsive Liposomes 6.8.7 Light-Sensitive Liposomes 6.9 Limitation of Liposomes 6.9.1 Reticuloendothelial System (RES) and Liposome Clearance 6.9.2 Accelerated Blood Clearance Phenomenon 6.9.3 High Serum Protein Binding 6.9.4 Masking of Surface Ligands by Polymers 6.9.5 Difficulty in the Accurate Characterization of Surface-Functionalized Liposomes 6.9.6 Large-Scale Production of Surface-Functionalized Liposomes 6.9.7 Stringent Storage Conditions 6.9.8 Aggregation of Liposomes 6.9.9 High Cost 6.9.10 Recent Examples of Liposome-Mediated Peptide Drug Delivery in Clinical Trials 6.10 Summary References Chapter 7: Peptides and Their Delivery to the Brain 7.1 Introduction 7.2 Structure of the BBB and In Vitro and In Vivo Models for Brain Delivery 7.2.1 Method for Assessing BBB Permeability 7.3 Passive Diffusion Across the BBB via Transcellular Pathway 7.4 Receptor-Mediated Transcytosis of Peptides Through the BBB 7.5 Peptide Conjugates for Delivering Drugs Across the BBB 7.6 Brain Drug Delivery Using Nanoparticles 7.7 Modulation of the BBB to Improve Delivery via Paracellular Pathways 7.7.1 Osmotic Blood-Brain Barrier Disruption (BBBD) Method 7.7.2 Blood-Brain Barrier Modulators (BBBMs) of the Intercellular Junction Proteins 7.8 Nasal Delivery of Peptides 7.9 Conclusions References Chapter 8: Emerging Peptide Drug Modalities for Intracellular Target Space 8.1 Introduction 8.2 Intracellularly Targeted Peptides: Some Historical Milestones 8.3 Expanding Intracellular Target Space: Emerging Peptide Modalities 8.4 Unlocking the Secrets of Cell Permeability: Exploiting Innovative Tools 8.5 Future Intracellularly Targeted Peptide Drugs: Clinical Trials and Beyond References Chapter 9: Regulatory Issues for Peptide Drugs 9.1 Introduction 9.2 Definition of Biologics, Peptide, Polypeptide, and Protein Drugs 9.3 Investigational New Drug (IND) Application 9.4 New Drug Application (NDA) 9.4.1 Chemistry 9.4.2 Raw Material Impurities 9.4.3 Process-Related Impurities 9.4.4 Stability 9.4.5 Nonclinical Pharmacology and Toxicology 9.4.6 Immunogenicity and Immunotoxicity 9.5 Abbreviated New Drug Application 9.6 Approval Process 9.7 Post-approval References Index