Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase

Laboratory for Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
Journal of Molecular Modeling (Impact Factor: 1.74). 03/2009; 15(8):983-96. DOI: 10.1007/s00894-009-0455-8
Source: PubMed


The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. Structural studies of N-sulfonyl-glutamic acid inhibitors of MurD have made possible the examination of binding modes of this class of compounds, providing valuable information for the lead optimization phase of the drug discovery cycle. Binding free energies were calculated for a series of MurD N-sulphonyl-Glu inhibitors using the linear interaction energy (LIE) method. Analysis of interaction energy during the 20-ns MD trajectories revealed non-polar van der Waals interactions as the main driving force for the binding of these inhibitors, and excellent agreement with the experimental free energies was obtained. Calculations of binding free energies for selected moieties of compounds in this structural class substantiated even deeper insight into the source of inhibitory activity. These results constitute new valuable information to further assist the lead optimization process.

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Available from: Andrej Perdih
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    • "In this study, as part of our ongoing investigation of the MurD enzyme [11] [16] [18] [21] as a potential bacterial target, we report results of the simulations studies where available off-path replica method was applied, to provide a relative energy difference between the TMD calculated pathways of the C-terminal domain closing motion (1EEH-2UAG and 1E0D-2UAG) [16]. This information can subsequently be utilized as a starting rational selection criterion for the rational choice of the intermediate protein structures in drug design efforts using multiple conformations of the target protein in the essentially static structure-based virtual screening experiments. "
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