cladinose and desosamine

Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given.

Topics: Algorithms; Amino Sugars; Anti-Bacterial Agents; Azithromycin; Binding Sites; Erythromycin; Escherichia coli; Hexoses; Ketolides; Macrolides; Molecular Dynamics Simulation; Ribosomes; Static Electricity; Thermodynamics; Thermus thermophilus; Water

The work presented in this second part of a two-part series on the accelerated transformation of erythromycin in superheated water focuses on the chemical nature and resultant antimicrobial implications of the overall reaction observed. Analyses of reactor effluents employing infrared spectroscopy and liquid chromatography/mass spectrometry indicated that the initial step in the decomposition pathway is one of dehydration. Subsequent hydrolysis in the presence of an acetate buffer appeared to result in the loss of the sugar cladinose. Chemical transformation under superheated conditions was tied to the loss of antibiotic function by an agar dilution test. The sensitivity of this test was verified by determination of the minimum inhibitory concentration (MIC) of erythromycin corresponding to each of two test microorganisms. MIC values for the selected strains of Escherichia coli and Bacillus subtilis were 35 and 0.5 mg/L, respectively. To relate the loss of antimicrobial activity to increased reaction temperature and thus to increased extent of parent compound transformation to microbially benign intermediates, bioassays using E. coli as test microorganism were performed on flow reactor effluents resulting from reaction of initial erythromycin concentrations of 75-150 mg/L.

Topics: Amino Sugars; Anti-Bacterial Agents; Bacillus subtilis; Biological Assay; Chromatography, High Pressure Liquid; Chromatography, Liquid; Colony Count, Microbial; Erythromycin; Escherichia coli; Hexoses; Hot Temperature; Kinetics; Mass Spectrometry; Microbial Sensitivity Tests; Spectroscopy, Fourier Transform Infrared; Water Pollution, Chemical