In the present work, the mechanism of resistance to aminoglycoside antibiotics was investigated. We examined the conformational changes of the O-phosphotransferase-IIIa enzyme, complexed with the antibiotics using MD simulations. The inhibitory effects of a group of antibacterial peptides against the enzyme were also examined, among which CP10A showed the highest affinity and the results correlated with the measured IC50 values. The regioselectivity of the phosphorylation reaction was shown to be in favor of the OH at the 5″ position versus the 3' of the antibiotic. The binding mode of CP10A was evaluated by means of MD simulation that resulted in recognizing its Trp8 and Arg13 residues binding near to where residues at the 3' and 5″ positions of the antibiotic would bind; thus, they are essential for the peptide inhibitory effect. The major open, semi-open, and closed conformations of the binding sites were identified throughout the MD trajectory, which enable the enzyme to regulate the influx of molecules into these sites. Based on the enzyme crystal structure, it was assumed that the 'antibiotic loop' of the enzyme is stable in its liganded mode; however, MD results revealed that the loop is highly flexible in both liganded and ligand-free modes.
Keywords: IC50; aminoglycoside-modifying enzyme; antibacterial peptide inhibitors; antibiotic resistance; deoxystreptamine-containing aminoglycosides; molecular dynamics simulations; phosphorylation.
© 2016 John Wiley & Sons A/S.