title: The binding mode of second-generation sulfonamide inhibitors of MurD: clues for rational design of potent MurD inhibitors.
abstract: A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using (1)H/(13)C heteronuclear single quantum correlation. The MurD protein was selectively (13)C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand-MurD complexes and its influence on ligand-enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors.
authors.affiliation: EN-FIST Centre of Excellence, Ljubljana, Slovenia ; Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia.
authors.forename: Mihael
authors.initials: M
authors.lastname: Simčič
authors.forename: Izidor
authors.initials: I
authors.lastname: Sosič
authors.forename: Milan
authors.initials: M
authors.lastname: Hodošček
authors.forename: Hélène
authors.initials: H
authors.lastname: Barreteau
authors.forename: Didier
authors.initials: D
authors.lastname: Blanot
authors.forename: Stanislav
authors.initials: S
authors.lastname: Gobec
authors.forename: Simona Golič
authors.initials: SG
authors.lastname: Grdadolnik
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D018604:Epitope Mapping; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010453:Peptide Synthases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D013449:Sulfonamides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*
chemical_list: D000900:Anti-Bacterial Agents; D008024:Ligands; D013449:Sulfonamides; D010453:Peptide Synthases; C053379:UDP-N-acetylmuramoylalanine-D-glutamate ligase