Structural and biochemical insights into the antibiofilm activity of cationic lipoamino acid ester against methicillin-resistant Staphylococcus aureus

Abstract

Three-dimensional structures, primarily derived from X-ray crystallography, are crucial for understanding the solid-state properties of active pharmaceuticals and for enabling structure-based drug design. Herein, we report the first single crystal X-ray structure of cationic lipoaminoacid ester [(2-((N-(2-methoxy-2-oxoethyl)tetradecanamido)methyl)-1-methylpyridin-1-ium iodide, QPyN14Ge]. QPyN14Ge crystallized in the triclinic space group P1̄. QPyN14Ge has a highly ordered and coherent packing arrangement due to tail-to-tail interdigitation of hydrophobic layers, stabilization by planar trans-amide head groups, controlled flexibility at the distal ends of the hydrocarbon chains, and heavy-atom anchoring by iodine near the polar region. QPyN14Ge exhibits antimicrobial activity against Methicillin-resistant Staphylococcus aureus by compromising membrane integrity. Molecular docking reveals that QPyN14Ge binds to the Staphylococcal protein FemX, which is responsible for peptidoglycan biosynthesis. Molecular dynamics simulations support the formation of a stable, energetically favourable FemX-QPyN14Ge complex, suggesting its potential as a cell wall biosynthesis inhibitor. QPyN14Ge shows strong antibiofilm activity at the MIC and can inhibit biofilm formation (40%) even at sub-MIC levels. Confocal microscopy shows that sub-MIC QPyN14Ge reduces the biofilm thickness from 11.88 ± 1.16 µm to 7.01 ± 0.95 µm. The antibiofilm mechanism is attributed to the inhibition of major virulence factors of MRSA, such as cell surface hydrophobicity, slime synthesis, exopolysaccharide production, and staphyloxanthin production. The findings suggest that ability of QPyN14Ge to form interdigitated molecular packing, in which molecules insert themselves between lipid bilayers, thinning and compromising membrane integrity, resulted in antibacterial and antibiofilm activities.