Discovery, classification and functional diversity of antimicrobial peptides.

Antimicrobial peptides and proteins (AMPs), first discovered in 1922, have attracted much research attention since the 1980s. These innate immune molecules are universal and over 2700 have been discovered in all life forms, ranging from bacteria to humans. AMPs can have antibacterial, antiviral, antifungal and antiparasitic activities. The term 'host defence peptide' emphasizes immune modulatory functions such as chemotactic, apoptotic and wound healing properties. With further expansion in the known AMP functions beyond host defence, a natural and general term, 'innate immune peptides', may be used to cover antimicrobial, immune modulation and other functional roles of these molecules. Efforts have also been made in unifying nomenclature and classification of AMPs. While AMPs are normally named based on peptide properties, source organisms, or a combination of both, they can be classified based on source kingdoms, peptide chemical and physical properties, biological functions and mechanisms of action. Importantly, bacterial AMPs, including nisin, gramicidin A, gramicidin S, polymyxin and daptomycin, have been successfully utilized either clinically or as food preservatives. The multiple functions of AMPs provide a basis for developing other potential applications in the future. Antimicrobial peptides and proteins, biopolymers of amino acids, are universal defence molecules of innate immune systems. In invertebrates, they are the major innate defence molecules of innate immunity, whereas in vertebrates they serve as both effectors in the innate immune system and modulators in the adaptive immune system (Epand and Vogel, 1999; Tossi and Sandri, 2002; Zasloff, 2002; Boman, 2003; Brogden et al., 2005; Zanetti, 2005; Amiche et al., 2008; Conlon, 2008; Gallo, 2013; Nuri et al., 2015; Wang et al., 2015; Hancock et al., 2016). The diversity of AMPs in terms of sequence, structure and function continues to expand. Broadly, AMPs include gene-encoded antimicrobial peptides (<100 amino acids), antimicrobial proteins, and non-gene encoded peptide antibiotics. This chapter provides an overview on peptide discovery, nomenclature, classification and functional diversity. Section 1.1 highlights the discovery of important AMPs with a focus on those that have already found medical and industrial applications. Section 1.2 summarizes the main methods for peptide nomenclature. Section 1.3 discusses the classification of AMPs, including a unified and systematic classification, which is independent of peptide biological source, activity and three-dimensional structure. Finally, Section 1.4 describes a variety of functional roles of these innate immune peptides.