title: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic-ribosome complex supervised by experiment and electronic structure methods.
abstract: We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a) the isolated and b) the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants). The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.
authors.affiliation: Institut für Organische Chemie, Hagenring30, TU-Braunschweig, 38106 Braunschweig, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Grunenberg
authors.affiliation: Institut für Organische Chemie, Hagenring30, TU-Braunschweig, 38106 Braunschweig, Germany; Physical Chemistry Department, Sciences II, University of Geneva , 30, Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Licari
keywords: compliance constants; computational chemistry; drug design; molecular recognition; relaxed force constants