Molecular dynamics study of interactions of polymyxin B3 and its ALA-mutants with lipopolysaccharide

Анотація

Introduction. Emergence of nosocomial bacterial pathogens (especially Gram-negative bacteria) with multiple resistance against almost all available antibiotics is a growing medical problem. No novel drugs targeting multidrug-resistant Gram-negative bacteria have been developed in recent years. In this context, there has been greatly renewed interest to cyclic lipodecapeptides polymyxins. Polymyxins exhibit rapid bactericidal activity, they are specific and highly potent against Gram-negative bacteria, but have potential nephrotoxic side effects. So polymyxins are attractive lead compounds to develop analogues with improved microbiological, pharmacological and toxicological properties. A detailed knowledge of the molecular mechanisms of polymyxin interactions with its cell targets is a prerequisite for the purposeful improvement of its therapeutic properties. The primary cell target of a polymyxin is a lipopolysaccharide (LPS)in the outer membrane of Gram-negative bacteria. The binding site of polymyxin on LPS has been supposed to be Kdo2-lipid A fragment. Methods.For all molecular modeling and molecular dynamics simulation experiments the YASARA suite of programs was used. Complex of antimicrobial peptide polymyxin В₃ (PmB₃) with Kdo2-lipid A portion of E. coli lipopolysaccharide was constructed by rigid docking with flexible side chains of the peptide. By alanine scanning of polymyxin В₃ bound to LPS followed by simulated annealing minimization of the complexes in explicit water environment, the molecular aspects ofPmB₃-LPS binding have beenstudied by 20 ns molecular dynamics simulations at 298 K and pH 7.0. The AMBER03 force field was used with a 1.05 nm force cutoff. To treat long range electrostatic interactions the Particle Mesh Ewald algorithm was used. Results. Ala-mutations of polymyxin’s residues Dab1, Dab3, Dab5, Dab8 and Dab9 in the PmB₃-LPScomplex caused sustained structural changes resulting in the notable loss in stability of LPS complexes with Ala-mutants of PmB₃. The mutations disturbed the characteristic hydrogen-bond network of PmB₃-LPScomplex. Ala-mutations of Dab1, Dab8 and Dab9 amino acid residues of PmB₃destabilized PmB₃-LPS complex to a greater extent: the values of binding energy for these mutants showed increase and large-amplitude irregular fluctuations.

Conclusions. Hydrogen bonding of polymyxin B with the lipopolysaccharide is an important factor of the stability of PmB₃-LPScomplex. Detailed knowledge of the peculiarities of molecular interactions of polymyxins with its primary target on the outer membrane of Gram-negative bacteria is a prerequisite of a purposeful design of novel polymyxin-like lipopeptides.