Structure-Based Rational Design of Small α-Helical Peptides with Broad-Spectrum Activity Against Multidrug-Resistant Pathogens

Journal of Medicinal Chemistry. 2023. Vol. 66. No. 1. P. 855–874.

Lohan S., Konshina A. G., Efremov R., Maslennikov I. V., Parang K.

A series of small (7- to 12-mer) amphipathic cationic peptides were designed and synthesized with the ultimate goal of creating a set of short helical peptides with broad-range bactericidal activity and good selectivity toward the bacterial cells. Activity analysis identified a lead 12-mer peptide 8b with broad spectrum activity against Gram-positive (MIC=3.1-6.2 µg/mL) and Gram-negative (MIC=6.2-12.5 µg/mL) bacteria, including multidrug-resistant strains, and good selectivity towards prokaryotic cells versus eukaryotic cells (HC50=280 µg/mL and >75% cell viability at 150 µg/mL). The fast membranolytic action of 8b was demonstrated by a calcein dye leakage assay and confirmed using scanning electron microscopy. Analysis of 8b and its closest analogs by CD and NMR spectroscopy indicated their irregular spatial structure in water. A lipid bilayer induced the formation of an amphipathic helix in 8b and other 12-mer peptides, but not in the shorter peptides. Molecular dynamics simulations provided detailed information about the interaction of 8b and its closest analogs with bacterial and mammalian membranes and revealed the roles of particular amino acids in the peptides’ activity and selectivity.

Keywords: молекулярная динамика, computer modeling, antibiotic resistance, antimicrobial peptides, molecular dynamics, антимикробные пептиды, устойчивость к антибиотикам, Amphipathicity, α-Helical Peptide, Membranolytic Action, амфипатичность, альфа-спиральные пептиды, мембранолитическое действие