Quinolones are the most commonly prescribed antibacterials worldwide; however, their clinical utility is threatened by the rising occurrence of resistance. Quinolones kill bacterial cells by increasing the level of DNA breaks generated by the type II topoisomerases gyrase and topoisomerase IV. Target-mediated resistance, which occurs as point mutations in the target topoisomerases, is the most common and clinically significant form of resistance. Although mutations at a specific, highly conserved serine and acidic amino acid residue have long been known to cause quinolone resistance, the mechanism by which these enzyme alterations decrease drug activity has not been previously understood.
The research described in this dissertation demonstrates that the primary interaction between clinically relevant quinolones and topoisomerase IV is mediated through a water-metal ion bridge anchored to the enzyme by the conserved serine and acidic residues. Mutations at these two residues, which are the most common alterations seen in quinolone-resistant bacterial strains, cause resistance by disrupting the water-metal ion bridge interaction. Based on results with a Gram-positive and a Gram-negative topoisomerase IV, it appears that the water-metal ion bridge may be a universal mechanism of quinolone-enzyme interaction. Because this interaction is formed with the drug core, it also explains the tolerance for structurally diverse substituents.
Human topoisomerase IIα is resistant to clinically relevant quinolones because it cannot form the water-metal ion bridge. Quinolones and quinazolinediones that overcome resistance mutations in the bacterial type II enzymes do so by forming novel interactions through their C7 substituents, which can also form interactions with the human enzyme and give undesirable cross-reactivity. However, structure-activity relationship studies indicate that there are differences between the human and bacterial type II topoisomerases that can be sensed at the C7, C8, and N3 positions. Thus, it should be possible to design a quinolone or quinolone-like drug that overcomes the most common forms of target-mediated resistance without cross-reacting with the human enzymes. In addition, it may be possible to develop specific quinolones as anticancer agents.