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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