A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study

作者：Sima Mihael; Pureber Kaja; Kristan Katja; Urleb Uro'S; Kocjan Darko^*; Grdadolnik Simona Golit

来源：European Journal of Medicinal Chemistry, 2014, 83: 92-101.

DOI：10.1016/j.ejmech.2014.06.021

• MurD ligase
• 2-Oxoindolinylidene inhibitor
• Steady-state enzyme kinetics
• NMR
• Molecular dynamics

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 C-13 selectively labeled MurD enzyme from E. coli and evaluated the binding interactions of the new compound using the H-1/C-13-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.

• 出版日期2014-8-18