title: Lincomycin and clindamycin conformations. A fragment shared by macrolides, ketolides and lincosamides determined from TRNOE ribosome-bound conformations.
abstract: Two important lincosamide antibiotics, lincomycin and clindamycin were studied in the complex state with the bacterial ribosome after a conformational analysis by 1H and 13C NMR spectroscopy and molecular modelling of the unbound molecules. Lincosamide-ribosome interactions were investigated using two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY), resulting in a bound structure compatible with the experimental NMR data. The results compared with the conformational analysis of the substrates in solution indicate that specific conformations are preferred in the bound state. Clindamycin, the more bioactive antibiotic studied, displayed a stronger NMR response than lincomycin showing that in lincosamide-ribosome interactions, a low affinity binding level is associated to the tight binding one and is related to biological activity. This study shows that conformation plays an essential role for the low affinity binding site. Superimposition of lincosamide, macrolide and ketolide bound structures exhibited conformational similarities in a particular fragment which is in agreement with a hypothesis of partial overlapping lincosamide and macrolide binding sites.
authors.affiliation: Université René Descartes-Paris V, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (UMR 8601 CNRS), France.
authors.forename: L
authors.initials: L
authors.lastname: Verdier
authors.forename: G
authors.initials: G
authors.lastname: Bertho
authors.forename: J
authors.initials: J
authors.lastname: Gharbi-Benarous
authors.forename: J P
authors.initials: JP
authors.lastname: Girault
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D002981:Clindamycin / Q000737:chemistry* / Q000378:metabolism; D007659:Ketones / Q000737:chemistry; D008034:Lincomycin / Q000737:chemistry* / Q000378:metabolism; D055231:Lincosamides; D018942:Macrolides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D007659:Ketones; D055231:Lincosamides; D018942:Macrolides; D002981:Clindamycin; D008034:Lincomycin