The Naphthoquinone Diospyrin Is an Inhibitor of DNA Gyrase with a Novel Mechanism of Action

Shantanu Karkare,Terence T.H Chung,Frederic Collin,Lesley A Mitchenall,Adam R Mckay,Sandra J Greive,Jacobus J.M Meyer,Namrita Lall,Anthony Maxwell

doi:10.1074/jbc.m112.419069

Abstract

Tuberculosis and other bacterial diseases represent a significant threat to human health. The DNA topoisomerases are excellent targets for chemotherapy, and DNA gyrase in particular is a well-validated target for antibacterial agents. Naphthoquinones (e.g. diospyrin and 7-methyljuglone) have been shown to have therapeutic potential, particularly against Mycobacterium tuberculosis. We have found that these compounds are inhibitors of the supercoiling reaction catalyzed by M. tuberculosis gyrase and other gyrases. Our evidence strongly suggests that the compounds bind to the N-terminal domain of GyrB, which contains the ATPase active site, but are not competitive inhibitors of the ATPase reaction. We propose that naphthoquinones bind to GyrB at a novel site close to the ATPase site. This novel mode of action could be exploited to develop new antibacterial agents.

Highlights

New antibacterial compounds are urgently needed; DNA gyrase is a well-validated target
Inhibition of DNA Gyrase by Naphthoquinones—To determine whether diospyrin and 7-methyljugolone might target M. tuberculosis DNA gyrase, we assessed their effect on the gyrase supercoiling reaction (Fig. 2)
Both compounds inhibit this reaction with IC50 values of ϳ15 ␮M and ϳ30 ␮M (7-methyljugolone); other naphthoquinones were tested in this reaction (Table 1; the IC50 values of novobiocin and ciprofloxacin against M. tuberculosis gyrase are given for comparison)

Summary

Background

New antibacterial compounds are urgently needed; DNA gyrase is a well-validated target. We propose that naphthoquinones bind to GyrB at a novel site close to the ATPase site This novel mode of action could be exploited to develop new antibacterial agents. Recent advances in M. tuberculosis gyrase have included the structures of the N- and C-terminal domains of GyrA and the C-terminal domain of GyrB [12,13,14], the identification of DNA-binding residues in the C-terminal domain of GyrA [15], and the development of monoclonal antibodies that target the enzyme as potential therapeutic agents [16]. The lack of a clear target definition and the observation of the efficacy of diospyrin against drug-sensitive and drug-resistance strains of M. tuberculosis [19], prompted us to test this and other naphthoquinones against M. tuberculosis DNA gyrase. We have found that these compounds can inhibit gyrase and that they target the enzyme by a novel mechanism, raising the possibility of developing these compounds as potential anti-TB agents

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION