Antimicrobial Peptides: Challenges and Future Perspectives

Front Cover
Antimicrobial Peptides
Copyright Page
Contents
List of contributors
Preface
1 Historical developments of antimicrobial peptide research
1.1 Introduction
1.2 History and development of antimicrobial peptides
1.3 Antimicrobial peptides as host innate defense barricade
1.4 Peptide-based database: barn house for AMPs
1.5 Current timeline of antimicrobial peptide approvals
1.6 Chemical developments in AMPs
1.7 Antimicrobial peptides modification for medical application
1.8 Antimicrobial peptides modification for industrial applications
1.9 An interdisciplinary upgrade to AMPs
1.10 Conclusion
References
2 Biosynthesis of peptide antibiotics and innate immunity
2.1 Introduction
2.2 Antimicrobial peptides in innate immunity
2.3 Biosynthesis of nonribosomal and ribosomal peptides
2.3.1 Nonribosomal peptides
2.3.2 Ribosomally synthesized and posttranslationally modified peptides
2.4 Summary and conclusion
References
3 Antimicrobial peptides: features and modes of action
3.1 Introduction
3.2 Historical perspective
3.3 Features of antimicrobial peptides
3.3.1 Diversity
3.3.2 Cationicity and amphipathicity
3.3.3 Structure
3.3.3.1 The α-helical antimicrobial peptides
3.3.3.2 β-Sheet antimicrobial peptides
3.3.3.3 αβ-Antimicrobial peptides
3.3.3.4 Non-αβ (extended structure)
3.4 Biosynthesis and regulation
3.5 Some common families of antimicrobial peptides
3.5.1 Cathelicidins
3.5.2 Defensins
3.5.3 Thionins
3.5.4 Antimicrobial peptides rich in specific amino acids
3.5.4.1 Tryptophan-rich antimicrobial peptides
3.5.4.2 Proline-rich antimicrobial peptides
3.5.4.3 Histatins
3.5.4.4 Unusual amino acid containing ribosomally synthesized antimicrobial peptides
3.6 Relationship of structure with function
3.7 Modes of action
3.7.1 Membrane-mediated action
3.7.1.1 Barrel-stave model
3.7.1.2 Toroidal pore model
3.7.1.3 Carpet model
3.7.1.4 Detergent model
3.7.2 Membrane-independent/nonmembrane-disruptive mechanism
3.8 Multifaceted roles of antimicrobial peptides
3.8.1 Anticancer antimicrobial peptides
3.8.2 Wound-healing antimicrobial peptides
3.8.3 Antidiabetogenic peptides
3.8.4 Antiinflammatory and immunomodulatory peptides
3.8.5 Spermicidal peptides
3.9 Limitations and challenges
3.9.1 Stability
3.9.2 Toxicity
3.9.3 Salt sensitivity
3.9.4 Aggregation propensity
3.10 Conclusion
References
4 Purification and characterization of antimicrobial peptides
4.1 Purification techniques
4.1.1 Solid-phase extraction on C18 column
4.1.2 Ion-exchange chromatography
4.1.3 Gel permeation chromatography
4.1.4 Affinity chromatography
4.1.5 Membrane filtration
4.1.6 High-performance liquid chromatography
4.1.6.1 High-performance gel permeation chromatography
4.1.6.2 Cation-exchange high-performance liquid chromatography
4.1.6.3 Reversed-phase high-performance liquid chromatography
4.2 Characterization techniques
4.2.1 Amino acid analysis
4.2.2 Sequencing—Edman procedure
4.2.3 Two dimensional—poly acrylamide gel electrophoresis
4.2.4 Mass spectrometry
4.2.4.1 Sequence by tandem mass spectrometry
References
5 Antimicrobial lipopeptides of bacterial origin—the molecules of future antimicrobial chemotherapy
5.1 Introduction
5.2 Lipopeptides
5.2.1 Types of lipopeptides produced by different bacterial genera
5.2.1.1 Daptomycin
5.2.1.2 Polymyxins
5.2.1.3 Surfactin
5.2.1.4 Kannurin
5.2.1.5 Lichenysin
5.2.1.6 Iturin
5.2.1.7 Mycosubtilin
5.2.1.8 Bacillomycin L
5.2.1.9 Fengycin
5.2.1.10 WAP-8294A2 (WAP)
5.2.1.11 Tridecaptins
5.2.1.12 Edeines
5.2.1.13 Bogorol cationic peptides
5.2.1.14 Kurstakin
5.2.1.15 Gramicidins
5.2.1.16 Circulocins
5.2.1.17 Amphomycin (Amp)
5.2.1.18 Pseudomonas antimicrobial peptides
5.2.1.18.1 Viscosin
5.2.1.18.2 Amphisin
5.2.1.18.3 Tolaasin
5.2.1.18.4 Syringomycin
5.2.2 Structure–activity relationship of lipopeptides
5.2.3 Mechanism of action of lipopeptides
5.2.3.1 Daptomycin—mode of action
5.2.3.2 Polymyxin—mode of action
5.2.3.3 Mode of action for other lipopeptides
5.2.4 Antiadhesion and antibiofilm activities of lipopeptides
5.2.5 Natural role of lipopeptides
5.2.6 Lipopeptides in the treatment of multidrug-resistant infections
5.3 Conclusion
References
6 Antimicrobial peptides of fungal origin
6.1 Introduction
6.2 Fungi-producing antimicrobial peptides
6.3 Fungal peptides
6.4 Mode of action and biological activities
6.5 Mechanisms of synthesis
6.6 Detection methods of antimicrobial peptides
6.7 Peptide databases
6.7.1 Peptaibol database
6.8 Biotechnological applications
6.9 Summary and conclusions
Acknowledgments
References
7 Insect peptides with antimicrobial effects
7.1 Introduction
7.2 The need for antimicrobial peptides
7.3 Classification of insect peptides
7.3.1 Attacins
7.3.2 Cecropins
7.3.3 Defensins
7.3.4 Gloverins
7.3.5 Lebocins
7.3.6 Moricins
7.4 Mode of action
7.5 Concluding remarks
References
8 Amphibian host defense peptides
8.1 Antimicrobial peptides: critical component of innate immune system
8.2 Antimicrobial peptide from amphibians
8.2.1 Antimicrobial peptides isolated from African frogs
8.2.2 Antimicrobial peptide isolated from amphibians in North America
8.2.3 Antimicrobial peptides isolated from amphibians in South America
8.2.4 Antimicrobial peptide isolated from amphibians in Australia
8.2.5 Antimicrobial peptide isolated from amphibians in Europe
8.2.6 Antimicrobial peptide isolated from amphibians in Asia
8.2.6.1 Western Ghats: the treasure house for antimicrobial peptides
8.3 Conclusion
References
9 Plant-derived antimicrobial peptides
9.1 General characteristics of bioactive peptides derived from plants
9.2 Antimicrobial peptides derived from different plant families
9.2.1 Cyclotides
9.2.2 Thionins
9.2.3 Defensins
9.2.4 Snakins
9.2.5 Heveins and hevein-like peptides
9.3 Extraction and identification of plant antimicrobial peptides
9.4 Perspectives in technological and therapeutic applications
9.5 Concluding remarks
References
10 Mammalian antimicrobial peptides
10.1 Introduction
10.2 History of antimicrobial peptides
10.3 Mammalian antimicrobial peptides as first-line defense against invading microbes
10.4 Classification of mammalian antimicrobial peptides
10.4.1 Classification of antimicrobial peptides based on amino acid sequence
10.4.1.1 Proline-rich peptides
10.4.1.2 Tryptophan and arginine-rich antimicrobial peptides
10.4.1.3 Histidine-rich peptides
10.4.1.4 Glycine-rich antimicrobial peptides
10.4.2 Classification of antimicrobial peptides based on the structure
10.4.2.1 Defensins
10.4.2.2 Cathelicidins
10.4.2.3 Histatins
10.4.2.4 Thrombocidin
10.4.3 Classification of antimicrobial peptides based on the activity
10.4.3.1 Antibacterial peptides
10.4.3.2 Antifungal peptides
10.4.3.3 Antiviral peptides
10.4.3.4 Antiparasitic peptides
10.4.3.5 Anticancer peptides
10.4.3.6 Immunomodulatory and chemotactic peptides
10.4.3.7 Antimicrobial peptides in tissue regeneration and wound healing
10.4.3.8 Antimicrobial peptides in ophthalmology
10.4.3.9 Antimicrobial peptides in fertility
10.5 Common mechanism of action of mammalian antimicrobial peptides
10.5.1 Membrane-targeting mechanism
10.5.2 Cell wall-targeting mechanism
10.5.3 Targeting intracellular processes
10.5.4 Immunomodulatory mechanism
10.6 Clinical applications of antimicrobial peptides
10.7 Current and future prospects and challenges in developing antimicrobial peptides
References
11 Antimicrobial peptides from marine environment
11.1 Introduction
11.2 Antimicrobial peptides from marine invertebrates
11.2.1 Antimicrobial peptides from marine sponges
11.2.2 Antimicrobial peptides from marine molluscs
11.2.3 Antimicrobial peptides from ascidians
11.2.3.1 Tunicates
11.2.4 Antimicrobial peptides from crustaceans
11.2.5 Antimicrobial peptides from marine worms
11.2.6 Antimicrobial peptides from Cnidaria
11.2.7 Antimicrobial peptides from Echinodermata
11.3 Antimicrobial peptides from marine microorganisms
11.3.1 Antimicrobial peptides from marine bacteria
11.3.1.1 Ribosomal antimicrobial peptides (bacteriocins) from marine bacteria
11.3.1.2 Nonribosomal antimicrobial peptides from marine bacteria
11.3.2 Antimicrobial peptides from marine actinomycetes
11.3.3 Antimicrobial peptides from marine fungi
11.4 Antimicrobial peptides from marine vertebrates
11.4.1 Antimicrobial peptides from marine fishes
11.5 Antimicrobial peptides from marine algae
11.6 Conclusions
References
12 Peptides with antiviral activities
12.1 Introduction
12.2 Viral life cycle
12.3 Peptides as viral inhibitors
12.4 Mechanism of inhibition
12.4.1 Viral attachment inhibitors
12.4.2 Plasma membrane and viral fusion inhibitors
12.4.3 Endosomal acidification inhibitors
12.4.4 Replication and translation inhibitors
12.5 Peptides as therapeutics
12.6 Challenges and future scope
Acknowledgments
References
13 Antimicrobial peptide antibiotics against multidrug-resistant ESKAPE pathogens
13.1 Introduction
13.2 Antibiotic resistance of ESKAPE pathogens
13.2.1 Direct drug interaction
13.2.2 Indirect drug resistance
13.3 Strategies to combat the ESKAPE pathogens
13.3.1 Vaccines
13.3.2 Phage therapy
13.3.3 Antibiotic derivatives
13.3.4 Antimicrobial peptides
13.4 Advantages and disadvantages of cationic antimicrobial peptides
13.5 Antimicrobial peptides to stop ESKAPE pathogens
13.5.1 Structure-based design
13.5.2 Library-based search and peptide mimetics
13.5.3 Peptide conjugates
13.5.4 Combined treatment
13.5.5 Formulated antimicrobial peptides
13.5.6 Surface immobilized antimicrobial peptides
13.6 Mechanisms of bacterial killing by antimicrobial peptides
13.6.1 Bacterial membranes
13.6.2 Cell wall
13.6.3 Bacterial ribosomes
13.7 Efficacies in animal models and clinical use of antimicrobial peptides
13.8 Concluding remarks
Acknowledgment
References
14 Antimicrobial peptide resistance and scope of computational biology in antimicrobial peptide research
14.1 Introduction
14.2 Antimicrobial peptide resistance in gram-positive bacteria
14.2.1 Bacterial cell surface—cell wall and cell membrane
14.2.1.1 Repulsion of antimicrobial peptides
14.2.1.2 Target modification
14.2.1.3 Alterations to membrane composition
14.2.2 Extracellular mechanism of antimicrobial peptide resistance
14.2.2.1 Extracellular proteases
14.2.2.2 Protein-mediated sequestration
14.2.3 Inhibition of antimicrobial peptide activity by surface-associated polysaccharides
14.3 Mechanisms of antimicrobial peptides resistance in gram-negative bacteria
14.3.1 Modifications in the bacterial outer membrane
14.3.1.1 Lipopolysaccharide modifications
14.3.1.2 Phospholipid modifications
14.3.2 Biofilm formation
14.3.3 Efflux pumps
14.3.4 Binding and sequestering cationic antimicrobial peptides
14.3.5 Proteolytic degradation of antimicrobial peptides
14.3.6 Modulation of cationic antimicrobial peptide expression
14.4 Scope of computational biology in antimicrobial peptide research
14.4.1 Antimicrobial peptide databases
14.4.1.1 Data repository of antimicrobial peptides
14.4.1.2 Dragon antimicrobial peptide database
14.4.1.3 The antimicrobial peptide database
14.4.1.4 Database of antimicrobial activity and structure of peptides
14.4.1.5 Collection of antimicrobial peptides
14.4.1.6 A database linking antimicrobial peptides
14.4.1.7 Yet another database of antimicrobial peptides
14.4.1.8 Database of anuran defense peptide
14.4.1.9 Antimicrobial peptide scaffold by property alignment
14.4.1.10 Invertebrate antimicrobial peptide database
14.4.1.11 Database of biofilm-active antimicrobial peptides
14.4.1.12 Bacteria peptide database
14.4.2 Detection of antimicrobial peptides and their resistance patterns by machine learning approach
14.4.3 Recent perspectives on the scope of computational biology in antimicrobial peptide research
14.5 Conclusion
References
15 Recent advances and challenges in peptide drug development
15.1 Introduction
15.2 Historical overview of peptide drug development
15.3 Basic drawbacks of peptide drugs
15.4 Present approaches toward the discovery of protein–protein modulators
15.4.1 High-throughput screening
15.4.2 Fragment-based drug discovery
15.4.3 Structure-based design
15.5 Peptides and protein–protein interactions
15.5.1 Potential developments for intrusive peptides
15.5.2 Computational and experimental methods for determining protein–protein interactions
15.5.3 Computer-assisted docking strategies
15.5.4 Structural-based predictions
15.6 Innovations and computational methods for peptide–protein interactions
15.6.1 Selection of preliminary peptide scaffolds
15.6.2 Molecular docking for peptide–protein interactions
15.6.3 Docking methods at local and global levels
15.6.3.1 Local docking methods
15.6.3.2 Global docking methods
15.6.4 Template-based docking method
15.7 Conclusion
References
16 Future perspective of peptide antibiotic market
16.1 Introduction
16.2 Global antimicrobial peptides market overview
16.3 Applications of antimicrobial peptide
16.3.1 Prospects in medicine
16.3.2 Food industry
16.3.3 Animal husbandry and aquaculture
16.4 Important parameters of market analysis
16.5 Drivers and restraints of the peptide antibiotics market
16.6 Conclusion
References
Index
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