Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia.

The Bac2A (RLARIVVIRVAR-NH2) is a linearized counterpart of cationic cyclic peptide Bactenecin-one of the smallest naturally occurring antimicrobial peptides (AMPs), which, however, generally exhibits a low or moderate antibacterial potency against gram-positive bacteria. Here, it is found that the Bac2A and its linear derivates cannot spontaneously fold into a well-defined helical conformation in solution, thus impairing the peptide amphipathicity and antibacterial activity. Hydrocarbon stapling is rationally designed to constrain the helical conformation of these linear peptides. Atomistic dynamics simulations reveal that the membrane-penetrating course of linear and stapled peptides include four distinct phases, during which the stapled peptides can maintain in an ordered helical conformation, while linear peptides are structured from intrinsic disorder in water solution to partially helical state in membrane interior, indicating that lipid environment can help the linear peptide refolding into amphipathic helix, although the refolding process would incur a large configurational entropy penalty. The antibacterial activities of the most potent stapled peptide are determined as MIC = 7.6 and 16 µg/ml against two gram-positive Staphylococcus aureus clinical strains isolated from pyemia. The activity values are improved by 7.1-fold and 5-fold as compared to that of native Bac2A peptide with MIC = 54 and 80 µg/ml, respectively.