The inhibitory activities of the 15 compounds in the E.coli DNA-gyrase superwiling assay and their
ability to facilitate the “cleavable complex” are compared with some known 4-quinolone antibacterials (Table
I). Eight of the 15 flavones tested inhibited the DNA-gyrase catalytic activity. The use of the DNA-gyrase
supcrcoiling inhibition assay has been the classical approach in identifying and quantitating inhibition of
DNA-gyrase by quinolones (9). This assay can detect both Gyr A and Gyr B subunit inhibitors, since the
reaction exposes the holoenzyme to the potential inhibitor. Unfortunately, in a catalytic assay, reaction
conditions such as pH, ionic strength, intercalation, chelation, and other non-specific effects can arise and be
mistakenly read as specific inhibition. Since flavones are known to inhibit several enzymes by non-specific
mechanisms (lo,1 l), one could not conclude based on the results of the inhibition of the catalytic activity,
that these flavones were bonafide inhibitors of the enzyme. A more specific variation on the supercoiling
inhibition assay is the DNA-gyrase “cleavable complex” assay. In this assay, the endpoint is the detection
and quantitation of linearized, cleaved fragments of the starting substrate, as compared to change in topomer
position as with the supercoiling inhibition assay. A major difference in these assays is that the generation
of the linearized fragment requires the catalytic activity of the holoenzyme to remain intact (i.e. free from
non-specific inhibition) in order for the “cleavable complex” intermediate of DNA gyrase*DNAVrug to be
formed, which in turn inhibits the resealing of the DNA. Any activity that prevents the binding or catalytic
The inhibitory activities of the 15 compounds in the E.coli DNA-gyrase superwiling assay and theirability to facilitate the “cleavable complex” are compared with some known 4-quinolone antibacterials (TableI). Eight of the 15 flavones tested inhibited the DNA-gyrase catalytic activity. The use of the DNA-gyrasesupcrcoiling inhibition assay has been the classical approach in identifying and quantitating inhibition ofDNA-gyrase by quinolones (9). This assay can detect both Gyr A and Gyr B subunit inhibitors, since thereaction exposes the holoenzyme to the potential inhibitor. Unfortunately, in a catalytic assay, reactionconditions such as pH, ionic strength, intercalation, chelation, and other non-specific effects can arise and bemistakenly read as specific inhibition. Since flavones are known to inhibit several enzymes by non-specificmechanisms (lo,1 l), one could not conclude based on the results of the inhibition of the catalytic activity,that these flavones were bonafide inhibitors of the enzyme. A more specific variation on the supercoilinginhibition assay is the DNA-gyrase “cleavable complex” assay. In this assay, the endpoint is the detectionand quantitation of linearized, cleaved fragments of the starting substrate, as compared to change in topomerposition as with the supercoiling inhibition assay. A major difference in these assays is that the generationof the linearized fragment requires the catalytic activity of the holoenzyme to remain intact (i.e. free fromnon-specific inhibition) in order for the “cleavable complex” intermediate of DNA gyrase*DNAVrug to be
formed, which in turn inhibits the resealing of the DNA. Any activity that prevents the binding or catalytic
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