zithromax 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

Novel modifications of the desosamine sugar of 14- and 15-membered antibacterial macrolides, in which the desosamine was fused with N-substituted-1,3-oxazolidin-2-ones, were developed in order to completely suppress antibacterial activity and make them promising agents for other biological targets. The synthesis of such bicyclic desosamine derivatives, especially 1,3-oxazolidin-2-one formation, was optimized and conducted under mild conditions without a need for protection/deprotection steps for other functional groups. A focused series of novel desosamine-modified macrolide derivatives was prepared and their antibacterial activities tested. It was shown that these macrolide derivatives do not possess any residual antibacterial activity.

Topics: Amino Sugars; Anti-Bacterial Agents; Cyclization

A series of new triazole-containing ketolides and 2-fluoro-ketolides in which the 5-O-desosamine was replaced by unnatural sugars were synthesized and evaluated against relevant macrolide-sensitive and macrolide-resistant respiratory pathogens. Excellent in vitro antibacterial activities were demonstrated for ketolide analogues having the 6'-OBz-3'-dimethylamino-glucose and 6'-OBz-4'-deoxy-3'-dimethylamino-glucose substituents.

Topics: Amino Sugars; Anti-Bacterial Agents; Ketolides; Microbial Sensitivity Tests; Molecular Conformation; Stereoisomerism; Structure-Activity Relationship