Effect of Linear and Cyclic Lysine-Lysine-Tryptophan- Tryptophan -Lysine-Phenylalanine Antimicrobial Peptide on Sodium Dodecyl Sulfate Micelle as Cell Membrane Mimetic: Molecular Dynamics Simulation Study

Drug resistance has limited the synthesis of new antibiotics. Therefore, the use of compounds that do not have drug resistance has been considered. Antimicrobial peptides are among the compounds for which drug resistance has not been reported. On the other hand, it has been found that the activity of these compounds is less than that of antibiotics. Therefore, the design of appropriate antimicrobial peptides is challenging. To address this challenge, efforts have been made to understand their mechanism of action. However, their mechanism of action is not well understood. In this work, the interaction of two cyclic and linear antimicrobial peptides with sodium dodecyl sulfate micelles as cell membrane mimetics method has been studied by molecular dynamics simulation. The micellar radius of gyration shows good agreement with the experimental results and the results of other simulations performed. Calculation of the conformational factor shows that cyclic antimicrobial peptide has a greater affinity for interaction with micelles. Charged and aromatic residues are involved in the interaction of cyclic antimicrobial peptides with micelles. Whereas, only charged residues are effective in the interaction of the linear antimicrobial peptides with micelle.