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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 32, Number 1
BKCSDE 32(1)
January 20, 2011 

Understanding Drug-Protein Interactions in Escherichia coli FabI and Various FabI Inhibitor Complexes
Han Myoung Lee*, N. Jiten Singh
Enoyl-acyl carrier protein reductase, ENR inhibitor, ENR-NAD+-ligand interaction, Molecular dynamics
Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl- ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-NAD+ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-NAD+-TCL, while the contribution of NAD+ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and NAD+ have many effective functional groups such as aromatic π rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-π interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.
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