The development of new effective antibiotics by inspiring from natural peptide antibiotics

Antimicrobial peptides produced by a wide spectrum of organisms from insects to humans, are natural antibiotics, which may be important alternative therapy agents for infections caused by organisms resistant to classical antimicrobials. Inspired from conserved motifs of natural antimicrobial peptides we aimed to design short, easy to produce peptides, which show antibacterial activity. We have determined the conserved regions of natural antimicrobial peptides and analyzed their three-dimensional structure. This revealed that these short peptide regions consisted of repeating hydrophobic and positively charged amino acids that form alpha-helix structures and position positively charged amino acids on one side of the helix. We have designed and obtained peptides similar to these structures and determined their antibacterial activity on different species of bacteria and studied their relation to bacterial membranes by molecular dynamics modeling, which helped us to understand their mechanism of action. Including arginine in peptides as a positively charged amino acid produced better antibacterial activity compared to lysine. Having positively charged amino acids at both ends created better activity to E. coli (MIC 2.0 μg/ml) compared to Staphylococcus aureus (MIC 16.0 μg/ml). Having positively charged amino-acid only at one end created equal activity to both of these organisms (MIC 4.0 μg/ml). The positioning of arginines on one side of the molecule in a zigzag form increased the activity prominently compared to positioning on an almost linear axis. Increasing the number of hydrophobic amino acids from 3 to 6 at one end resulted to self-binding and eliminated completely the antibacterial activity of the peptide. Molecular dynamic simulations suggested that asymmetric positioning of hydrophobic and positively charged amino acids buries the hydrophobic part into the lipid bilayer of the membranes and positively charged parts fix it to the negatively charged phosphate groups of phospholipids on both sides of the lipid bilayer. Thus, a single molecule is able to create hydrophilic channel, which results the leak of water and hydrophilic molecules. Electron microscopic examination of staphylococci treated with these peptides revealed that the bacteria split into almost two equal halves from the middle where active cell wall synthesis occur. Additionally, docking studies revealed that there was strong binding of the peptides to major peptidoglycan synthesizing zare protein, transglycosylase, indicating that they may also be inhibiting the cell wall synthesis. All peptides were susceptible to proteinase K. Development of their synthetic similar derivatives resistant to proteases, will increase their clinical usefulness. Once their safety is proven, these peptides may be promising drugs against organisms resistant to other antibiotics.