Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase.
Fighting bacterial resistance is a challenging task in the field of medicinal chemistry. DNA gyrase represents a validated antibacterial target and has drawn much interest in recent years. By a structure-based approach we have previously discovered compound 1, an indolinone derivative, possessing inhibitory activity against DNA gyrase. In the present paper, a detailed biophysical characterization of this inhibitor is described. Using mass spectrometry, NMR spectroscopy, and fluorescence experiments we have demonstrated that compound 1 binds reversibly to the ATP-binding site of the 24 kDa N-terminal fragment of DNA gyrase B from Escherichia coli (GyrB24) with low micromolar affinity. Based on these data, a plausible molecular model of compound 1 in the active site of GyrB24 was constructed. The predicted binding mode explains the competitive inhibitory mechanism with respect to ATP and forms a useful basis for further development of potent DNA gyrase inhibitors.
Oblak
Marko
M
Laboratory of Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, POB660, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
Grdadolnik
Simona Golic
SG
Kotnik
Miha
M
Poterszman
Arnaud
A
Atkinson
R Andrew
RA
Nierengarten
Helene
H
Desplancq
Dominique
D
Moras
Dino
D
Solmajer
Tom
T
D000255:Adenosine Triphosphate / Q000737:chemistry*; D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D003198:Computer Simulation; D027081:DNA Gyrase / Q000737:chemistry*; D007211:Indoles / Q000037:antagonists & inhibitors*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation
D007211:Indoles; C057812:indoline; D000255:Adenosine Triphosphate; D027081:DNA Gyrase