Molecular modeling study of the contributions of side amino acid residues of polymyxin B3 to its binding with E.coli outer membrane lipopolysaccharide
Keywords:
polymyxin, lipopolysaccharide, alanine scanning, binding energyAbstract
Last decades, antimicrobial peptides (AMPs) are the subject of intense investigations aimed to develop effective drugs against extremely resistant nosocomial bacterial pathogens (especially Gram-negative bacteria). In particular, there has been greatly renewed interest to polymyxins, the representatives of AMPs which are specific and highly potent against Gram-negative bacteria, but have potential nephrotoxic side effect. A prerequisite of purposeful enhancement of therapeutic properties of polymyxins is a detailed knowledge of the molecular mechanisms of their interactions with cell targets. Lipopolysaccharide (LPS), the main component of the outer leaflet of outer membrane of gram-negative bacteria, is a primary cell target of polymyxins. The aim of the paper was to study the peculiarities of molecular interactions of polymyxin В3 with lipopolysaccharide of the outer membrane of gram-negative bacterium. Materials and methods. The complexes of polymyxin В3 (PmВ3) and its alanine-derivatives with E. coli outer membrane lipopolysaccharide were built and studied by molecular modeling methods (minimization, simulated annealing, docking). Atom coordinates of polymyxin В3 and LPS structures were taken from nuclear magnetic resonance and X-ray crystallography experiments, respectively. The AMBER03 force field was used with a 1.05 nm force cutoff. Longrange electrostatic interactions were treated by the Particle Mesh Ewald method. Results and discussion. Alanine scanning of PmВ3 molecule has been carried out and the role of its side amino acid residues in the formation of complex with lipopolysaccharide has been investigated. It has been shown that substitutions of polymyxin’s Dab residues in positions 1, 3, 5, 8 and 9 for alanine markedly reduce the binding energy of PmB3-LPS complex, where as the similar substitutions of residues in positions 2, 6, 7 and 10 leave the binding energy virtually unchanged. Structural aspects of antimicrobial action of polymyxins have been analyzed. Changes of minimal inhibitory concentrations (MIC) of alanine-derivatives of polymyxin and binding energies in dependence on the alanine substituent position were parallel, except Ala2- PmВ3 mutant. Conclusions. Polymyxin’s side Dab residues, especially Dab1, Dab5, Dab 8 and Dab9, essentially contribute to the energy of polymyxin В3 binding with LPS of the outer membrane. Contribution of the others polymyxin’s side residues to the binding energy of the complex of polymyxin В3 with LPS was insignificant.
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