Cover
Preface
1 Basic Properties
1. 1.1 INTRODUCTION
2. 1.2 PROPERTIES OF AMINO ACIDS
3. 1.3 THE PEPTIDE BOND
4. 1.4 SECONDARY STRUCTURES
5. 1.5 PEPTIDE STRUCTURE AND CONFORMATION CHARACTERIZATION METHODS
6. 1.6 PEPTIDE DATABASES AND WEB SOFTWARE
7. BIBLIOGRAPHY
2 Synthesis
1. 2.1 INTRODUCTION
2. 2.2 SOLID‐PHASE PEPTIDE SYNTHESIS
3. 2.3 SOLUTION‐PHASE PEPTIDE SYNTHESIS
4. 2.4 METHODS TO PREPARE LONGER PEPTIDES
5. 2.5 PEPTIDE LIBRARY SYNTHESIS
6. 2.6 SYNTHESIS OF CYCLIC PEPTIDES
7. 2.7 PEPTIDOMIMETICS
8. 2.8 POST‐TRANSLATIONAL MODIFICATIONS
9. 2.9 LIPIDATION
10. 2.10 GLYCOSYLATION
11. 2.11 POLYPEPTIDE POLYMERS AND CONJUGATES OF PEPTIDES AND POLYMERS
12. 2.12 NON‐RIBOSOMAL PEPTIDE SYNTHESIS
13. 2.13 PURIFICATION AND ANALYSIS METHODS
14. BIBLIOGRAPHY
3 Amyloid and Other Peptide Aggregate Structures
1. 3.1 INTRODUCTION
2. 3.2 AMYLOID
3. 3.3 AMYLOID β
4. 3.4 MECHANISMS AND KINETICS OF AMYLOID AGGREGATION
5. 3.5 TOXICITY AND RELEVANCE TO DISEASE
6. 3.6 FIBRILLIZATION OF SMALL PEPTIDES
7. 3.7 BIOLOGICAL FUNCTIONAL AMYLOID AND BIOENGINEERING APPLICATIONS OF AMYLOID MATERIALS
8. 3.8 FIBRILS FROM α‐HELICES
9. 3.9 PEPTIDE HYDROGELS AND TISSUE SCAFFOLDS
10. 3.10 PEPTIDE NANOTUBES
11. 3.11 PEPTIDE AND PEPTIDE CONJUGATE ASSEMBLIES
12. 3.12 CHARACTERIZATION METHODS FOR PEPTIDE ASSEMBLIES
13. BIBLIOGRAPHY
4 Antimicrobial and Cell‐penetrating Peptides
1. 4.1 INTRODUCTION
2. 4.2 BACTERIAL PATHOGENS, TARGETS OF ANTIBACTERIAL AGENTS, AND ANTIMICROBIAL RESISTANCE PATHWAYS
3. 4.3 TESTING ANTIMICROBIAL ACTIVITY
4. 4.4 BACTERIAL BIOFILMS
5. 4.5 DESIGN OF ANTIMICROBIAL PEPTIDES
6. 4.6 CLASSES OF ANTIBACTERIAL PEPTIDES
7. 4.7 ANTIFUNGAL PEPTIDES
8. 4.8 ANTIVIRAL PEPTIDES
9. 4.9 ANTIPARASITIC PEPTIDES
10. 4.10 MECHANISMS OF ACTIVITY
11. 4.11 CELL‐PENETRATING PEPTIDES
12. BIBLIOGRAPHY
5 Peptide Hormones and Peptide Therapeutics
1. 5.1 INTRODUCTION
2. 5.2 GENERAL PRINCIPLES OF PEPTIDE THERAPEUTICS
3. 5.3 PEPTIDE HORMONES
4. 5.4 NEUROPEPTIDES AND OTHER PEPTIDES IN VIVO
5. 5.5 VENOM‐DERIVED PEPTIDES
6. 5.6 ANTICANCER PEPTIDES
7. 5.7 MISCELLANEOUS PEPTIDE THERAPEUTICS
8. 5.8 COSMETIC PEPTIDES AND LIPOPEPTIDES
9. BIBLIOGRAPHY
Index
End User License Agreement

List of Tables

Chapter 1
1. Table 1.1 Properties of amino acids.
2. Table 1.2 Side chain protonation depending on pH.
3. Table 1.3 Some non‐standard amino acids.
4. Table 1.4 Bond angles and residue spacings for regular peptide conformations.
5. Table 1.5 Typical FTIR band ranges for peptides.
6. Table 1.6 Examples of useful peptide software and websites.
Chapter 2
1. Table 2.1 Common peptide synthesis resins (resin bead shown as filled circle)...
2. Table 2.2 Typical side chain protecting groups and deprotection conditions.
Chapter 3
1. Table 3.1 Conditions associated with amyloid‐forming peptides and proteins.
2. Table 3.2 Effect on Aβ of APP mutations.
3. Table 3.3 Cell adhesion and related motifs.
4. Table 3.4 Examples of surfactant‐like peptides, peptide bolaamphiphiles, and ...
Chapter 4
1. Table 4.1 List of pathogens identified by WHO as priorities due to antimicrob...
2. Table 4.2 Marketed antimicrobial peptides.
3. Table 4.3 Examples of anionic antimicrobial peptides.
4. Table 4.4 Examples of antifungal peptides.
5. Table 4.5 Examples of antiviral peptides.
6. Table 4.6 Examples of antiparasitic peptides.
7. Table 4.7 Lipid composition of the cell membrane of selected bacteria.
8. Table 4.8 Examples of widely studied cell‐penetrating peptides (CPPs).
Chapter 5
1. Table 5.1 Examples of established peptide hormone‐based therapeutics on the m...
2. Table 5.2 Sequences of GnRH agonists with generic sequence (pG)HWSYxLRPy.
3. Table 5.3 Sequences of human pancreatic polypeptides with PP‐fold related res...
4. Table 5.4 Gut‐related peptide families including neurotransmitters (italicize...
5. Table 5.5 Venom‐derived peptide therapeutics.
6. Table 5.6 Examples of peptides used in skincare products.

List of Illustrations

Chapter 1
1. Figure 1.1 Enantiomers of amino acid residues in peptides. Left: L‐amino aci...
2. Figure 1.2 Fischer projections and structures of L‐threonine, D‐threonine, L
3. Figure 1.3 Configurations of a peptide bond.
4. Figure 1.4 The standard amino acids.
5. Figure 1.5 Amino acid side chain labelling nomenclature.
6. Figure 1.6 Resonance structures of (a) arginine and (b) histidine.
7. Figure 1.7 Hydrophobicity of amino acids, according to the Wimley–White scal...
8. Figure 1.8 Schematic titration curve for a tetrapeptide NH₂–EGAK–COOH, plott...
9. Figure 1.9 Chou–Fasman scale of α‐helix and β‐sheet propensity for protein a...
10. Figure 1.10 Formation of a peptide bond (amide group highlighted in purple) ...
11. Figure 1.11 Peptide bond geometry with typical angles shown.
12. Figure 1.12 A Ramachandran plot. The shaded areas show the ‘normally allowed...
13. Figure 1.13 Principle regular peptide secondary structures: (a) α‐helix (sho...
14. Figure 1.14 Example of a helical wheel diagram of a α‐helical peptide sequen...
15. Figure 1.15 The coil–helix transition is cooperative, leading to a sigmoidal...
16. Figure 1.16 Example of a β‐hairpin structure.
17. Figure 1.17 Helical peptide secondary structures. (a) PPII structure, (b) PG...
18. Figure 1.18 Examples of β‐ and γ‐turn structures. (a) Classical γ‐turn, (b) ...
19. Figure 1.19 Backbone and side chain interactions that stabilize peptide stru...
20. Figure 1.20 (a) A dimeric coiled coil structure based on the abcdefg heptad ...
21. Figure 1.21 Leucine zipper (bZip) structure involved in DNA transcription.
22. Figure 1.22 Measured CD spectra for peptides. Open circles: Derivative of pe...
23. Figure 1.23 Chemical shift index plot (for ¹Hα) for 56‐residue sequence from...
Chapter 2
1. Figure 2.1 Schematic of sequential process in solid‐phase peptide synthesis....
2. Figure 2.2 Orthogonal protecting groups illustrated for an aspartic acid res...
3. Figure 2.5 Enolization and oxazolone formation cause peptide racemization. X...
4. Figure 2.3 Common coupling reagents in peptide synthesis that generate activ...
5. Figure 2.4 HBTU activation mechanism.
6. Figure 2.6 Aspartimide formation reaction and subsequent reactions including...
7. Figure 2.7 Diketopiperazine formation for an on‐resin sequence with C‐termin...
8. Figure 2.8 Pseudoproline formation strategy: ring‐opening of an oxazolidine ...
9. Figure 2.9 The Hmb reversible backbone protecting group.
10. Figure 2.10 O‐acyl isopeptide conversion into a native peptide.
11. Figure 2.11 Convergent SPPS, for the case of fragment condensation from the ...
12. Figure 2.12 Mechanism of native chemical ligation, here the SR group is pres...
13. Figure 2.13 Recombinant production of peptides/proteins via molecular clonin...
14. Figure 2.14 Schematic showing the steps of spot peptide synthesis.
15. Figure 2.15 Split‐mix peptide synthesis, illustrated for a three monomer syn...
16. Figure 2.16 Schematic of cyclization reactions involving the peptide head (C...
17. Figure 2.17 Strategy for on‐resin head‐to‐tail peptide cyclization using a r...
18. Figure 2.18 Representative peptide side chain cyclization reactions. (a) Dis...
19. Figure 2.19 Molecular structures of two natural bicyclic peptides: (a) phall...
20. Figure 2.20 Structures of some peptidomimetics.
21. Figure 2.21 Production of C‐terminal amide group via oxygenation of a termin...
22. Figure 2.22 Peptide modified at cysteine residue with (a) farnesyl group, (b...
23. Figure 2.23 Lipopeptides prepared by (a) N‐terminal palmitoylation, (b) C‐te...
24. Figure 2.24 Synthesis of amidated peptides using amine‐modified linkers.
25. Figure 2.25 (a) N‐glycosylation of an N residue, (b) O‐glycosylation of S or...
26. Figure 2.26 Synthesis of polypeptides via N‐carboxyanhydride polymerization:...
27. Figure 2.27 Representative coupling chemistries. In general R denotes a pept...
28. Figure 2.28 Side group reactions for peptide functionalization. For lysine a...
29. Figure 2.29 Peptide ion fragmentation labelling system for tandem MS along w...
30. Figure 2.30 Reaction of ninhydrin with primary amines.
31. Figure 2.31 Scheme of the Edman degradation reaction.
Chapter 3
1. Figure 3.1 Hierarchical structure of amyloid fibrils and ‘cross‐β’ X‐ray dif...
2. Figure 3.2 TEM images of amyloid fibrils: (a) negative stain TEM image from ...
3. Figure 3.3 Oligomerization and fibrillization pathways. Species in green are...
4. Figure 3.4 The amyloid hypothesis for AD. LTP (long‐term potentiation)...
5. Figure 3.5 (Box) Amino acid sequences of Aβ peptides Aβ40 and Aβ42, with enz...
6. Figure 3.6 Structure of Aβ42 amyloid fibrils (pdb file 5KK3).
7. Figure 3.7 Concentration of species versus time, showing lag and growth phas...
8. Figure 3.8 Microscopic processes that govern the rate of amyloid fibril form...
9. Figure 3.9 Schematic fibril growth curves, showing effect of the rate consta...
10. Figure 3.10 Homologous versus heterologous seeding. Colour scheme as for Fig...
11. Figure 3.11 Steric zipper structure obtained from single‐crystal X‐ray diffr...
12. Figure 3.12 Formation of filamentous hyphae by fungi and Streptomyces bacter...
13. Figure 3.13 Schematic of self‐assembling fibre peptides due to complementary...
14. Figure 3.14 A peptide hydrogel in a vial with overlaid schematic of microsco...
15. Figure 3.15 Examples of enzymatic reactions using Fmoc‐ and naphthalene‐modi...
16. Figure 3.16 There are multiple cues for cell adhesion with the ECM. These in...
17. Figure 3.17 Three classes of observed peptide nanotube structures: (a) beta‐...
18. Figure 3.18 Closure of helical ribbons (a) into a peptide nanotube comprisin...
19. Figure 3.19 Stacking of alternating D,L‐cyclic peptides to form nanotubes, s...
20. Figure 3.20 Bottom: AFM height images during the time‐dependent aggregation ...
21. Figure 3.21 Lipopeptide self‐assembled nanostructures. (a) Fibrils, (b) mice...
22. Figure 3.22 Schematic phase diagram for lipopeptide assemblies in terms of t...
23. Figure 3.23 Molecular structure of fluorescent probe dyes mentioned in the t...
24. Figure 3.24 Congo red staining of β‐sheet ‘amyloid’ fibrils formed by lipope...
25. Figure 3.25 Representative cryo‐TEM images from different classes of peptide...
26. Figure 3.26 Dynamic shear moduli measured (at a stress σ = 100 Pa) for hydro...
Chapter 4
1. Figure 4.1 Targets for antimicrobials, showing examples for each type includ...
2. Figure 4.2 The distinct cell wall structures of the two different groups of ...
3. Figure 4.3 Antimicrobial resistance mechanisms.
4. Figure 4.4 Measurement of inhibition zone of antimicrobial agent on a Petri ...
5. Figure 4.5 Different classes of antimicrobial agents. (a) Bacteriostatic age...
6. Figure 4.6 Stages in biofilm formation and strategies to prevent/disrupt or ...
7. Figure 4.7 Antimicrobial killing kinetics for cultures showing resistance, t...
8. Figure 4.8 (a) Molecular structure of c‐di‐GMP. (b) Generic molecular struct...
9. Figure 4.9 Molecular structures of some host defence AMPs: (a) human neutrop...
10. Figure 4.10 Bidentate binding of guanidinium groups with acidic XOO⁻ g...
11. Figure 4.11 Molecular structures of some arginine‐rich AMPs: (a) gramicidin ...
12. Figure 4.12 Molecular structures of some AMPs based on cyclic peptides: (a) ...
13. Figure 4.13 Schematic of the cell membrane of fungi.
14. Figure 4.14 Molecular structure of several echinocandins: (a) caspofungin, (...
15. Figure 4.15 Examples of antifungal lipopeptides from among those produced by...
16. Figure 4.16 Membrane‐disruption modes of antimicrobial activity. The peptide...
17. Figure 4.17 Structure of heparin.
18. Figure 4.18 Mechanisms of uptake of CPPs.
Chapter 5
1. Figure 5.1 Number of approved peptide therapeutics according to treatment fi...
2. Figure 5.2 SWOT analysis of peptide therapeutics.
3. Figure 5.3 Delivery routes for marketed peptides.
4. Figure 5.4 Examples of peptide enzyme inhibitors: (a) amastatin, (b) boroleu...
5. Figure 5.5 Schematic of a dose–response curve, showing bioactivity versus co...
6. Figure 5.6 Action of peptide hormones at cell‐surface receptors.
7. Figure 5.7 The hypothalamic–pituitary system, showing key hormones and their...
8. Figure 5.8 Molecular structure of (a) GnRH and (b) thyrotropin‐releasing hor...
9. Figure 5.9 Molecular structure of cetrorelix.
10. Figure 5.10 Molecular structures of: (a) somatostatin, (b) octreotide and la...
11. Figure 5.11 Molecular structure of etelcalcetide.
12. Figure 5.12 Pathways by which insulin and glucagon regulate blood sugar leve...
13. Figure 5.13 (a) Three‐dimensional crystal structure of insulin, showing inte...
14. Figure 5.14 Insulin analogue peptides on the market.
15. Figure 5.15 α‐helical structure of glucagon, obtained from X‐ray diffraction...
16. Figure 5.16 Vasopressin/oxytocin peptide family members. Mpa = 3‐mercaptopro...
17. Figure 5.17 Molecular structures of (a) lisinopril and (b) enalapril.
18. Figure 5.18 Interactions of gut and endocrine hormones with the brain and ho...
19. Figure 5.19 Molecular structures of: (a) GLP‐1 with residues which are subst...
20. Figure 5.20 Molecular structure of macimorelin.
21. Figure 5.21 Venom‐based peptide therapeutics: (a) eptifibatide and (b) bival...
22. Figure 5.22 Molecular structures of (a) ziconotide, (b) linaclotide, and (c)...
23. Figure 5.23 Molecular structures of (a) bortezomib, (b) apicidin, (c) romide...
24. Figure 5.24 Molecular structures of (a) dactinomycin, (b) bleomycin A₂, and ...
25. Figure 5.25 Molecular structure of mifamurtide.
26. Figure 5.26 Molecular structure of cyclosporin.
27. Figure 5.27 Pam_nCSK₄ lipopeptides with n = 1, 2, or 3 palmitoyl chains attac...

This edition first published 2020
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Library of Congress Cataloging‐in‐Publication Data

Names: Hamley, Ian W., author.

Title: Introduction to peptide science / Ian W. Hamley.

Description: First edition. | Hoboken, NJ : Wiley, 2020. | Includes bibliographical references and index.

Identifiers: LCCN 2020013505 (print) | LCCN 2020013506 (ebook) | ISBN 9781119698173 (paperback) | ISBN 9781119698180 (adobe pdf) | ISBN 9781119698197 (epub)

Subjects: MESH: Peptides | Antimicrobial Cationic Peptides | Peptide Hormones | Nanotubes, Peptide

Classification: LCC QP552.P4 (print) | LCC QP552.P4 (ebook) | NLM QU 68 | DDC 612/.015756–dc23

LC record available at https://lccn.loc.gov/2020013505

LC ebook record available at https://lccn.loc.gov/2020013506

Preface

Welcome (or welcome back!) to the wonderful world of peptide science. Peptides are fascinating chain molecules, built from amino acids, that nature has evolved to fulfil an incredible range of structural and functional roles. Of particular importance are peptide hormones, a major class of signalling molecules in the body. But there are many other essential peptides ensuring your body keeps working. Peptides crop up everywhere, along with their larger cousins proteins, as components of biological structures in silk, collagen, amyloid, and many other biomaterials. Amyloid is also now implicated as a ‘pathological’ agent in many diseases that are becoming of increasing concern, including neurodegenerative diseases such as Alzheimer's. Peptide hormones are playing an important role in conditions associated with a modern lifestyle, such as diabetes and the related condition of obesity.

Nature uses an alphabet of 20 natural amino acids to build peptides. Peptides have been synthesized in the laboratory for decades and in the last 50 years automated synthesis methods have been introduced, been rapidly developed, and have become established. Scientists are now designing original sequences and incorporating novel residues, functionalities, and configurations into peptides and are also creating conjugates of peptides with lipids, glyco‐saccharides, and polymers.

This book covers the basic properties of peptides, looking at essential synthesis methods and peptide aggregate structures, including amyloid and other nanostructures such as peptide nanotubes and peptide gels. Medically related applications are considered in the final two chapters, devoted to antimicrobial peptides and peptide therapeutics. These are discussed in the context of peptide hormones, from which many of the most important peptide therapeutics introduced into practice (so far) are derived.

This book is intended to provide a broad coverage of peptide science that is otherwise lacking in existing textbooks. There are several excellent books that cover peptide synthesis in detail and a few books cover basic properties, with the best coverage often being in introductory texts on proteins or general biochemistry. There are also specialist texts on peptide therapeutics and antimicrobial peptides, and a very few on amyloid. However, I felt there was a need for a compact introductory text that covers applications such as therapeutics and biomaterials. This book aims to achieve that. In addition, it covers at an introductory level a number of modern developments in the field that are not included in older texts in the areas of synthesis and aggregation/self‐assembly. The book includes aspects of synthetic chemistry, biochemistry, and biophysics relevant to understanding peptide science. This is an interdisciplinary field, so these are not considered to be exclusive terms, nor is this an exhaustive list of disciplines that feed into or from peptide science.

I have intended this book to be an introduction for senior undergraduates of chemistry, biochemistry, or biology and so should be useful as a supplementary text for junior courses in these and allied subjects. In addition it contains, in a compact and easy to reach form, much material that should be a valuable reference source for researchers in the field. All the texts I consulted in the course of writing the book, including existing books in the field along with key articles (mainly review articles) that I referred to, are cited in the Bibliography sections at the end of each chapter. Of course these do not provide a complete reference list on the subject; it would be impossible to compile such a list, given the huge volume of research in this exciting and fast‐moving field.

I apologize in advance for any errors or omissions and would be grateful to be informed of these. I would also be happy to receive any other feedback on the book as this would be very useful if a future edition emerges. At the moment, I will take a justified break from peptide book writing, although I've enjoyed the process and have learnt many useful new things. I hope you enjoy it in a similar style.

I would like to acknowledge my editor Jenny Cossham for supporting this project and my group of great students and postdocs who have helped immensely as we have learned together over the last couple of decades about peptides and their applications. Also thanks to all my many valued collaborators over the years, from around the world. Finally, I am very grateful to my family for their extracurricular support, and in the case of my wife Valeria for curricular support as well!

Ian W. Hamley
University of Reading, UK, 2020