Antimicrobial Peptides: Classification, Mechanisms Of Action, Targets And Resistance

Discussion

Antimicrobial peptides are an essential component of the host innate immune system and are called host defense peptides. It consist of a number of amino acids ranging from five to more than hundred and as a result they can be termed as oligopeptides. These are proteins of low molecular weight having a broad spectrum of antimicrobial properties against various pathogenic microorganisms like bacteria, fungi, parasites and viruses (Guilhelmelli et al. 2013).

Antimicrobial peptides can be classified according to the activity of the peptides, their 3D structures and on their chain bonding patterns (Wang 2015; Lee et al. 2015). The mechanism of action of antimicrobial peptides include actions on the cell wall and cell membrane, inhibition of enzyme activity and protein folding. Moreover, antimicrobial peptides can also act at the intracellular level (Bahar and Ren 2013).

This report provides a brief introduction of the antimicrobial peptides, classification of antimicrobial peptides, mechanisms of action, intracellular targets and resistance.

Lysozyme is the first antimicrobial peptide discovered by Alexander Flemming. Later on other antimicrobial peptides were discovered. These are the defensins, cecropins, magainins, among others. The characteristics of an antimicrobial peptide is that it is more than 100 amino acids in length, show antimicrobial properties and originates from bacterial, fungal, viral sources as well as from plants and animals (Pushpanathan, Gunasekaran and Rajendhran 2013).

Antimicrobial peptides can be classified based on their activities, three dimensional structures and on their peptide bonding patterns.

The antimicrobial peptides are an essential component of the innate immune system and function as effective defense systems against the various pathogenic microorganisms. These antimicrobial activities can be classified as antibacterial, antifungal, antiviral and antiparasitic (Wang 2017). Apart from these activities, antimicrobial peptides can function as anticancer agents or for immune modulation and for wound healing purposes (Appendix, Table 1).

The antiviral peptides integrates into the host cell membranes or the viral envelope and causes neutralization of the viruses. Defensins bind to the  viral glycoproteins of Herpes Simplex virus (HSV), thereby preventing it to bid to host surfaces. Lactoferrin binds to heparin sulfate on host cell surface preventing the binding of HSV (Nakatsuji and Gallo 2012; Galdiero et al. 2013).

The antibacterial antimicrobial peptides bind to the cell membranes of bacteria and causes damage to the lipid bilayer. Moreover, antibacterial peptides can also interfere with specific pathways in the bacterial cells like DNA replication, protein synthesis, among others. Antibacterial peptides can also kill antibiotic resistant bacteria. Buforin II binds to the essential components of the bacterial cells like DNA and RNA without affecting the cell membrane (Jang et al. 2012). Other examples are Drosocin, Pyrrhocoricin, apidaecin, among others. Nisin can be used against methicillin resistant Staphylococcus aureus (Dosler and Gerceker 2012).

Antifungal peptides target fungal cell walls or their intracellular components. The antifungal peptides disrupts the fungal membrane integrity by either creating pores or by increasing the permeability of the plasma membrane (van der Weerden, Bleackley and Anderson 2013).

Antiparasitic peptides disrupts the cell membrane of the parasites. Magainin kills Paramecium caudatum, Cathelicidin kills Caenorhabditis elegans (Pretzel et al. 2013).

Classification of antimicrobial peptides

Certain antimicrobial peptides can also function as an anticancer peptide. Aurein 1.2 is an antimicrobial peptide that has been shown to have anticancer activity against 55 types of cancer cell lines. Differences between the cell membranes of cancerous and healthy cells enables the antimicrobial peptides to differentiate between them and thereby kill the cancerous cells, while keeping the normal cells intact (Gaspar, Veiga and Castanho 2013).

The structure of antimicrobial peptides can be determined by carrying out nuclear magnetic resonance spectroscopy as well as X-Ray diffraction. The antimicrobial peptides can be classified under the α helical, β sheet and extended structures (Ebenhan et al. 2014). Moreover, further classification of antimicrobial peptides places them under 4 families. These are the α, β, αβ and the non αβ families. These are classified according to the presence of the secondary structures. In the α family, they consist of α helical structures, those in the β family consists of at least 2 β strands. The αβ family consist of both α and β structures, while the non αβ family lacks both the secondary structures (Figure 1; Appendix, Table 2).

Figure 1: Structure of Antimicrobial peptides

(Source: Wang 2015)

Antimicrobial peptides can also be classified on the basis of the bonding between the polypeptide chains. The Class I included antimicrobial peptides that have a linear structure. They are subjected to chemical modification like amidation, glycosylation, addition of sulphate, bromide or phosphate groups. Examples include LL-37, Piscidin 4, Heliocin, Gramicidin, Cipemycin, among others. The Class II peptides consists of chemical bonds between the peptide side chains. Examples include the lantibiotics, which consist of thioether rings, while the defensins consist of disulfide bonds. The Class III antimicrobial peptides consist of chemical bonds between the backbones and the peptide side chains. These involve the formation of chemical bonds between the backbone of one amino acid to the side chain of another amino acid. The Class IV peptides are circular and consist of peptide bonds between the ends of the peptide backbone that contain an amino and carboxyl terminal group. These peptides may contain other chemical modifications like the presence of disulfide bonds. Examples include Plant Cyclotides, Bacterial Entertocin AS-48, among others (Andersson, Hughes and Kubicek-Sutherland 2016).

The most important mechanism of action of antimicrobial peptides involve the ability to carry out damage to the cell membrane. There are 2 models that describe the mechanism of action of antimicrobial peptides in the disruption of cell membranes. These are the Toroidal model, the barrel-stave model and the carpet model (Figures 2 and 3; Appendix. Table 3).

According to the Toroidal model, the antimicrobial peptides get inserted into the membranes, thereby forming a bundle or pore. This in turn induces the lipid monolayers to bend through the pores. This results in interspersed sections of membrane lipids and peptides giving rise to pores (Bertelsen et al. 2012).

According to this model, the antimicrobial peptides create transmembrane pores by directly inserting into the core lipid region of the target membranes. The antimicrobial peptides binds as a monomer on the surface of the membrane, undergoes subsequent oligomerization, thereby resulting in the formation of pores. The formation of pores results in the leaking of the cellular cytoplasmic contents, ultimately resulting in cell death (Seo et al. 2012; Phoenix, Dennison and Harris 2013).

Classification based on antimicrobial activities

The antimicrobial peptides that follow the carpet model function as detergents and covers the surfaces of the membranes. When the antimicrobial peptide concentration reaches the threshold, the membrane undergoes disintegration and eventual cell lysis. However at low concentration, the peptides form pores in the transmembrane, thereby indicating that the mode of action of the peptide depends on its concentration (Li et al. 2017).

Figure 2: Mechanism of action of antimicrobial peptides

(Source: Jakel et al. 2012)

The intracellular targets of antimicrobial peptides include inhibition of synthesis of cell walls, inhibition of synthesis of nucleic acids and proteins and induction of cell death. Class I bacteriocins kill bacteria by targeting the Lipid II component, thereby inhibiting cell wall synthesis. They can also form pores thereby resulting in efflux of ions and molecules. Nisin is another antimicrobial peptide that binds to the lipid III and IV components, thereby inhibiting the biosynthesis of techoic acid and lipoteichoic acid, which is an important component of bacterial cell walls. Induction of autolysins results in damage to cell walls, resulting in lysis and eventual cell death (Figure 4) (Yount and Yeaman 2013).

Other intracellular targets include proteins and nucleic acids. These antimicrobial peptides inhibit the synthesis of nucleic acids. Some of these peptides are Buforin II, Indolicin, among others. Indolicin inhibits DNA synthesis, thereby resulting in filamentation of bacterial cells. Cathelicidins inhibit both DNA as well as protein synthesis. Bactenecins inhibit RNA nad protein synthesis in bacteria like Klebsiella pneumoniae and Escherichia coli. Microcin C inhibits protein synthesis by targeting the aminoacyl t-RNA synthetase, while Microcidin B17 inhibits DNA replication by affecting the DNA gyrase (Figure 5).

Antimicrobial peptides can also induce cell apoptosis. Magainin increases the levels of reactive oxygen species and increases the activities of caspase 3 that results in apoptosis and cell death. PvD(1) is a plant defensin that kills pathogenic fungi by activation of the oxidative stress responses, which results in the production of reactive oxygen species and nitric oxide (Oyinloye, Adenowo and Kappo 2015).

Figure 3: Antimicrobial peptides killing mechanisms

(Source: Mahlapuu et al. 2016)

Figure 4: Inhibition of cell wall synthesis

(Source: Perez, Perez and Elegado 2015)

Figure 5: Modes of action of antimicrobial peptides

(Source: Martin et al. 2015)

In spite of the presence of a large number of antimicrobial peptides, but still many microbes show resistance to such peptides. The various resistance mechanisms used by them include: bacterial surface remodeling, proteolytic degradation of cationic antimicrobial peptides, downregulation of the expression of antimicrobial genes, antimicrobial resistant biofilm formation, use of efflux pumps, trapping and subsequent neutralization of the antimicrobial peptides (Maria-Neto et al. 2015) (Appendix, Table 4).

Conclusion

Antimicrobial peptides are a class of natural antibiotics having a wide range of activity against various organisms. Antimicrobial peptides have also been shown to have anticancer properties. They are classified on the basis of their activities, on the basis of their secondary structures and on the basis of their peptide bonding patterns. Their mechanism of action is based on three models, which are the barrel-stave, toroidal and carpet models. Apart from damaging the cell membranes, antimicrobial peptides also affect various intracellular targets like inhibition of synthesis of cell walls, proteins and nucleic acids. Moreover, they can also cause apoptosis of cells. Despite their effectiveness, various resistance mechanisms are also present that prevent their proper functioning. Thus, it can be concluded that antimicrobial peptides are an effective component of the host innate immune system.

Antiviral peptides

References

Andersson, D.I., Hughes, D. and Kubicek-Sutherland, J.Z., 2016. Mechanisms and consequences of bacterial resistance to antimicrobial peptides. Drug Resistance Updates, 26, pp.43-57.

Bahar, A.A. and Ren, D., 2013. Antimicrobial peptides. Pharmaceuticals, 6(12), pp.1543-1575.

Bertelsen, K., Dorosz, J., Hansen, S.K., Nielsen, N.C. and Vosegaard, T., 2012. Mechanisms of peptide-induced pore formation in lipid bilayers investigated by oriented 31P solid-state NMR spectroscopy. PloS one, 7(10), p.e47745.

Dosler, S. and Gerceker, A.A., 2012. In vitro activities of antimicrobial cationic peptides; melittin and nisin, alone or in combination with antibiotics against Gram-positive bacteria. Journal of Chemotherapy, 24(3), pp.137-143.

Ebenhan, T., Gheysens, O., Kruger, H.G., Zeevaart, J.R. and Sathekge, M.M., 2014. Antimicrobial peptides: their role as infection-selective tracers for molecular imaging. BioMed research international, 2014.

Galdiero, S., Falanga, A., Tarallo, R., Russo, L., Galdiero, E., Cantisani, M., Morelli, G. and Galdiero, M., 2013. Peptide inhibitors against herpes simplex virus infections. Journal of Peptide Science, 19(3), pp.148-158. 

Gaspar, D., Veiga, A.S. and Castanho, M.A., 2013. From antimicrobial to anticancer peptides. A review. Frontiers in microbiology, 4.

Guilhelmelli, F., Vilela, N., Albuquerque, P., Derengowski, L.D.S., Silva-Pereira, I. and Kyaw, C.M., 2013. Antibiotic development challenges: the various mechanisms of action of antimicrobial peptides and of bacterial resistance. Frontiers in microbiology, 4.

Jäkel, C.E., Meschenmoser, K., Kim, Y., Weiher, H. and Schmidt-Wolf, I.G., 2012. Efficacy of a proapoptotic peptide towards cancer cells. in vivo, 26(3), pp.419-426.

Jang, S.A., Kim, H., Lee, J.Y., Shin, J.R., Cho, J.H. and Kim, S.C., 2012. Mechanism of action and specificity of antimicrobial peptides designed based on buforin IIb. Peptides, 34(2), pp.283-289. 

Lee, H.T., Lee, C.C., Yang, J.R., Lai, J.Z. and Chang, K.Y., 2015. A large-scale structural classification of antimicrobial peptides. BioMed research international, 2015.

Li, J., Koh, J.J., Liu, S., Lakshminarayanan, R., Verma, C.S. and Beuerman, R.W., 2017. Membrane active antimicrobial peptides: Translating mechanistic insights to design. Frontiers in neuroscience, 11.

Mahlapuu, M., Håkansson, J., Ringstad, L. and Björn, C., 2016. Antimicrobial peptides: an emerging category of therapeutic agents. Frontiers in cellular and infection microbiology, 6.

Maria-Neto, S., de Almeida, K.C., Macedo, M.L.R. and Franco, O.L., 2015. Understanding bacterial resistance to antimicrobial peptides: From the surface to deep inside. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1848(11), pp.3078-3088.

Martin, L., van Meegern, A., Doemming, S. and Schuerholz, T., 2015. Antimicrobial peptides in human sepsis. Frontiers in immunology, 6.

Nakatsuji, T. and Gallo, R.L., 2012. Antimicrobial peptides: old molecules with new ideas. Journal of Investigative Dermatology, 132(3), pp.887-895.

Oyinloye, B.E., Adenowo, A.F. and Kappo, A.P., 2015. Reactive oxygen species, apoptosis, antimicrobial peptides and human inflammatory diseases. Pharmaceuticals, 8(2), pp.151-175.

Phoenix, D.A., Dennison, S.R. and Harris, F., 2013. Models for the membrane interactions of antimicrobial peptides. Antimicrobial Peptides, pp.145-180.

Pretzel, J., Mohring, F., Rahlfs, S. and Becker, K., 2013. Antiparasitic peptides. In Yellow Biotechnology I (pp. 157-192). Springer Berlin Heidelberg.

Pushpanathan, M., Gunasekaran, P. and Rajendhran, J., 2013. Antimicrobial peptides: versatile biological properties. International journal of peptides, 2013.

Seo, M.D., Won, H.S., Kim, J.H., Mishig-Ochir, T. and Lee, B.J., 2012. Antimicrobial peptides for therapeutic applications: a review. Molecules, 17(10), pp.12276-12286.

van der Weerden, N.L., Bleackley, M.R. and Anderson, M.A., 2013. Properties and mechanisms of action of naturally occurring antifungal peptides. Cellular and molecular life sciences, 70(19), pp.3545-3570.

Wang, G. ed., 2017. Antimicrobial peptides: discovery, design and novel therapeutic strategies. Cabi.

Wang, G., 2015. Improved methods for classification, prediction, and design of antimicrobial peptides. Computational Peptidology, pp.43-66.

Yount, N.Y. and Yeaman, M.R., 2013. Peptide antimicrobials: cell wall as a bacterial target. Annals of the New York Academy of sciences, 1277(1), pp.127-138.