Bioinspired Designs, Molecular Premise and Tools for Evaluating the Ecological Importance of Antimicrobial Peptides

Abstract

This review article provides an overview of recent developments in antimicrobial peptides (AMPs), summarizing structural diversity, potential new applications, activity targets and microbial killing responses in general. The use of artificial and natural AMPs as templates for rational design of peptidomimetics are also discussed and some strategies are put forward to curtail cytotoxic effects against eukaryotic cells. Considering the heat-resistant nature, chemical and proteolytic stability of AMPs, we attempt to summarize their molecular targets, examine how these macromolecules may contribute to potential environmental risks vis-à-vis the activities of the peptides. We further point out the evolutional characteristics of the macromolecules and indicate how they can be useful in designing target-specific peptides. Methods are suggested that may help to assess toxic mechanisms of AMPs and possible solutions are discussed to promote the development and application of AMPs in medicine. Even if there is wide exposure to the environment like in the hospital settings, AMPs may instead contribute to prevent healthcare-associated infections so long as ecotoxicological aspects are considered.

Keywords: antimicrobial peptides; bacteriocins; ecotoxicity; membrane disruption; polyproline helix; therapeutic.

Figure 1

3D structures of selected AMPs, depicting four structural families based secondary structures found in the compound: alpha, beta, alphabeta and non-alphabeta. Structures were edited with protein workshop using the solution NMR structural data for Human cathelicidin LL-37 (PDB: 2K6O), lactoferricin B (PDB: 1LFC), plant defensin Psd1 (PDB: 1JKZ) and bovine indolicidin (PDB: 1G89).

Figure 2

Number of AMPs isolated from natural sources since 2003 (information was extracted from the AMP database (http://aps.unmc.edu/AP).

Figure 3

Diversified schematic structures of natural and artificial AMPs. (a) EeCentrocin 2 is an α-helical heterodimeric peptide with a heavy and a light chain connected via a disulfide bridge (helix-stabilizing residues are indicated in light brown). (b) EPrAMP1 has three disulfide bridges and three strands of beta-sheet (shown in violet). (c) BnPRP1 is a proline-rich peptide. (d) G3KL is a tree-like synthetic polymer composing of alternating residues of lysine and leucine. Red arrows indicate direction of crossing in the peptide chain.

Figure 4

Structure of selected peptides from bacterial sources. (a) Lasso peptides sviceucin, showing two intramolecular disulfide bridges. (b) Circular peptide carnocyclin A, showing N- to C-terminal peptidyl linkage between Leu1 and Leu60. (c) Glycocin peptide sublancin 168, showing a glucose moiety linked to Cys22 and two intramolecular disulfide bridges. (d) Sactipeptides subtilosin A, showing the coordination of the sulfur-α-carbon bridges. (e) NAI-107 has 5 intramolecular thioether cross-linkages, additional 5-chloro-trypthopan, mono-/bis-hydroxylated proline and a c-terminal aminovinylcysteine. (f) Pediocin-like curvacin A, showing the N-terminal YGNGVXC conserved motif, the N-terminal intramolecular disulfide bridge between to Cys10 and Cys15, and the distinct C-terminal helical region. (g) Non-pediocin-like single-peptide lactococcin 972. (h) Non-ribosomally synthesized peptide teixobactin compose of four d-amino acids, enduracididine and an N-terminal methylphenylalanine. Structures were edited with protein workshop using the solution NMR structural data for each molecule.

Figure 5

Membrane penetration mechanisms and mode of action of AMPs. Shaded region illustrates a structural model of the molecular interaction of an AMP with the phospholipid bilayer. A, Barrel-stave pore membrane disruption mechanism where the peptides line the hollow pore, and are oriented parallel to the phospholipid chains. B, Carpet mechanism where the peptides have a detergent-like effect on the membrane. C, Toroidal pore where the lumen of the pore constitutes a mixture of peptide and phospholipids resulting from perpendicular insertion of the peptides in the bilayer. Non-invasive mechanisms of AMPs include binding to: (i) DnaK, (ii) duplex DNA helices (iii) RNA polymerase, (iv) 70S ribosome, (v) undecaprenyl pyrophosphate phosphatase (UppP), (vi) mannose phosphotransferase system (Man-PTS), (vii) maltose transporter (MLT), (viii) Lipoteichoic acid (LTA), (ix) lipid II, inhibiting cell wall biosynthesis, and (x) LPS. The abbreviations PGN, peptidoglycan; OM, outer membrane.