Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase.

Marko Oblak , Simona Golic Grdadolnik , Miha Kotnik , Arnaud Poterszman (1) , Robert Andrew Atkinson (2) , Helene Nierengarten , Dominique Desplancq (2) , Dino Moras (1) , Tom Solmajer

1 IGBMC - Institut de génétique et biologie moléculaire et cellulaire
2 Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique

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.

Domaines: Biologie moléculaire

Marko Oblak, Simona Golic Grdadolnik, Miha Kotnik, Arnaud Poterszman, Robert Andrew Atkinson, et al.. Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase.. Biochemical and Biophysical Research Communications, 2006, 349 (4), pp.1206-13. ⟨10.1016/j.bbrc.2006.08.172⟩. ⟨hal-00188088⟩