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J. Biol. Chem., Vol. 278, Issue 41, 39435-39442, October 10, 2003

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Specific and Potent Inhibition of NAD⁺-dependent DNA Ligase by Pyridochromanones^*

Heike Brötz-Oesterhelt  , Igor Knezevic , Stephan Bartel ¶, Thomas Lampe ¶, Ute Warnecke-Eberz  ||, Karl Ziegelbauer , Dieter Häbich ¶ and Harald Labischinski 

From the Department of Anti-infectives and ^¶Department of Chemistry, Bayer AG, Bayer Health Care, Pharma Research, Aprather Weg 18a, D-42096 Wuppertal, Germany

Pyridochromanones were identified by high throughput screening as potent inhibitors of NAD⁺-dependent DNA ligase from Escherichia coli. Further characterization revealed that eubacterial DNA ligases from Gramnegative and Gram-positive sources were inhibited at nanomolar concentrations. In contrast, purified human DNA ligase I was not affected (IC₅₀ > 75 µM), demonstrating remarkable specificity for the prokaryotic target. The binding mode is competitive with the eubacteria-specific cofactor NAD⁺, and no intercalation into DNA was detected. Accordingly, the compounds were bactericidal for the prominent human pathogen Staphylococcus aureus in the low µg/ml range, whereas eukaryotic cells were not affected up to 60 µg/ml. The hypothesis that inhibition of DNA ligase is the antibacterial principle was proven in studies with a temperature-sensitive ligase-deficient E. coli strain. This mutant was highly susceptible for pyridochromanones at elevated temperatures but was rescued by heterologous expression of human DNA ligase I. A physiological consequence of ligase inhibition in bacteria was massive DNA degradation, as visualized by fluorescence microscopy of labeled DNA. In summary, the pyridochromanones demonstrate that diverse eubacterial DNA ligases can be addressed by a single inhibitor without affecting eukaryotic ligases or other DNA-binding enzymes, which proves the value of DNA ligase as a novel target in antibacterial therapy.

Received for publication, June 18, 2003 , and in revised form, July 15, 2003.

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^|| Present address: Dept. of Visceral and Vascular Surgery, University of Cologne, Joseph-Stelzmann-Str. 9, D-50931 Cologne, Germany.

To whom correspondence should be addressed. Tel.: 49-202-364561; Fax: 49-202-364116; E-mail: heike.broetz-oesterhelt.hb{at}bayer-ag.de.

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