Abstract
One of the most powerful methods for investigating the molecular mechanism of drug action is the use of radioligand binding technique. The method allows investigators to pinpoint the direct target of the drug, and the nature of the interaction in terms of binding affinity, specificity, and cooperativity as well as molar binding ratios. These parameters are crucial for deducing a mechanistic model for the drug’s action and thereby assist in the process of drug design by furthering our understanding of the established structure-activity relationship of that class of compounds. The method has been best exemplified by the investigations of mode of action of quinolone antibacterials that target the bacteria-specific type II DNA topoisomerase, DNA gyrase (reviewed in refs. 1–5).
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References
Cozzarelli N. R. (1980) DNA gyrase and the supercoiling of DNA. Science 207, 953–960.
Gellert M. (1981) DNA topoisomerases. Ann. Rev. Biochem. 50, 879–910.
Wang J. C. (1982) DNA topoisomerases. Sci. Am. 247, 94–109.
Sutcliffe J. A., Gootz T. D., and Barrett J. F. (1989) Biochemical characteristics and physiological significance of major DNA topoisomerases. Antimicrob. Agents Chemother. 33, 2027–2033.
Reece R. J. and Maxwell A. (1991) DNA gyrase: structure and function. Crit. Rev. Biochem. Mol. Biol. 26, 335–375.
Shen L. L. and Pernet A. G. (1985) Mechanism of inhibition of DNA gyrase by analogues of nalidixic acid: the target of the drugs is DNA. Proc. Natl. Acad. Sci. USA 82, 307–311.
Shen L. L., Kohlbrenner W. E., Weigl D., and Baranowski J. (1989) Mechanism of quinolone inhibition of DNA gyrase. Appearance of unique norfloxacin binding sites in enzyme-DNA complexes. J. Biol. Chem. 264, 2973–2978.
Shen L. L., Baranowski J., and Pernet A. G. (1989) Mechanism of inhibition of DNA gyrase by quinolone antibacterials: Specificity and cooperativity of drug binding to DNA. Biochemistry 28, 3879–3885.
Shen L. L., Mitscher L. A., Sharma P. N., O‘Donnell T. J., Chu D. W. T., Cooper C. S., et al. (1989) Mechanism of inhibition of DNA gyrase by quinolone antibacterials. A cooperative drug-DNA binding model. Biochemistry 28, 3886–3894.
Morrissey I., Hoshino K., Sato K., Yoshida A., Hayakawa I., Bures M. G., et al. (1996) Mechanism of the differential activities of ofloxacin enantiomers. Antimicrob. Agents Chemother. 40, 1775–1784.
Paulus H. (1969) A rapid and sensitive method for measuring the binding of radioactive ligands to proteins. Anal. Biochem. 32, 91–100.
Markus G., DePasquale J. L., and Wissler F. C. (1978) Quantitative determination of the binding of β-aminocaproic acid to native plasminogen. J. Biol. Chem. 253, 727–732.
Mizuuchi K., Mizuuchi M., O‘Dea M. H., and Gellert M. (1984) Cloning and simplified purification of Escherichia coli DNA gyrase A and B proteins. J. Biol. Chem. 259, 9199–9201.
Hallett P., Grimshaw A. J., Wigley D. B., and Maxwell A. (1990) Cloning of the DNA gyrase genes under tac promoter control: overproduction of the gyrase A and B proteins. Gene 93, 139–142.
Otter R. and Cozzarelli N. R. (1983) E. coli DNA gyrase. Methods Enzymol. 100B, 171–180.
Sambrook J., Fritsch E. F., and Maniatis T. (1989) Molecular Cloning. A Laboratory Mannual, 2nd ed., vol. 3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1.36–1.46.
Sambrook J., Fritsch E. F., and Maniatis T. (1989) Molecular Cloning. A Laboratory Mannual, 2nd ed., vol. 3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p. E3.
Klotz I. M. (1974) Protein interactions with small molecules. Accounts Chem. Res. 7, 162–168.
Cantor C. R. and Schimmel P. R. (1980) Biophysical Chemistry, part III, W. H. Freeman and Company, New York, pp. 863, 864.
Penefsky H. S. (1977) Reversible binding of Pi by beef heart mitochondrial ad-enosine triphosphatase. J. Biol. Chem. 252, 2891–2899.
Shen L. L., Baranowski J., Wai T., Chu D. T. W., and Pernet A. G. (1989d) The binding of quinolones to DNA: should we worry about it? in International Telesymposium on Quinolones (Fernandes P. B., ed), J. R. Prous Science Publishers, Barcelona, Spain, pp. 159–170.
Shen L. L. (1989) A reply: “Do quinolones bind to DNA?”—yes. Biochem. Pharmacol. 38, 2042–2044.
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Shen, L.L. (2001). Quinolone Interactions with DNA and DNA Gyrase. In: Osheroff, N., Bjornsti, MA. (eds) DNA Topoisomerase Protocols. Methods in Molecular Biology™, vol 95. Humana Press. https://doi.org/10.1385/1-59259-057-8:171
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DOI: https://doi.org/10.1385/1-59259-057-8:171
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