title: A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study.
abstract: N-(5-(5-nitro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)4-oxo-2-thioxo-1,3-thiazolidin-3-yl)nicotinamide, a 2-oxoindolinylidene derivative with novel structure scaffold, was evaluated for inhibition potency against the MurD enzyme from Escherichia coli using an enzyme steady-state kinetics study. The compound exerted competitive inhibition with respect to UMA, a MurD substrate, and affected bacterial growth. Furthermore, we isolated and purified (13)C selectively labeled MurD enzyme from E. coli and evaluated the binding interactions of the new compound using the (1)H/(13)C-HSQC 2D NMR method. Molecular dynamics calculations showed stable structure for the MurD-inhibitor complex. The binding mode of novel inhibitor was determined and compared to naphthalene-N-sulfonamide-d-Glu derivatives, transition state mimicking inhibitors, UMA and AMP-PCP, an ATP analog. It binds to the UDP/MurNAc binding region. In contrast to transition state mimicking inhibitors, it does not interact with the enzyme's C-terminal domain, which can be beneficial for ligand binding. A pharmacophore pattern was established for the design of novel drugs having a propensity to inhibit a broad spectrum of Mur enzymes.
authors: EN-FIST Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia; Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
authors: Mihael
authors: M
authors: Simčič
authors: EN-FIST Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia; Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
authors: Kaja
authors: K
authors: Pureber
authors: Sandoz Development Centre Slovenia, Lek Pharmaceuticals, Verovškova 57, 1526 Ljubljana, Slovenia.
authors: Katja
authors: K
authors: Kristan
authors: Sandoz Development Centre Slovenia, Lek Pharmaceuticals, Verovškova 57, 1526 Ljubljana, Slovenia.
authors: Uroš
authors: U
authors: Urleb
authors: EN-FIST Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia; Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia. Electronic address: darko.kocjan@ki.si.
authors: Darko
authors: D
authors: Kocjan
authors: EN-FIST Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia; Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia. Electronic address: simona.grdadolnik@ki.si.
authors: Simona Golič
authors: SG
authors: Grdadolnik
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009536:Niacinamide / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D010453:Peptide Synthases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; C000596333:N-(5-(5-nitro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)4-oxo-2-thioxo-1,3-thiazolidin-3-yl)nicotinamide; D009536:Niacinamide; D010453:Peptide Synthases; C053379:UDP-N-acetylmuramoylalanine-D-glutamate ligase
keywords: 2-Oxoindolinylidene inhibitor; Molecular dynamics; MurD ligase; NMR; Steady-state enzyme kinetics