Type IIA topoisomerase inhibition by a new class of antibacterial agents

Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action. Here we report the 2.1 Å crystal structure of a potent, new class, broad-spectrum antibacterial agent in complex with Staphylococcus aureus DNA gyrase and DNA, showing a new mode of inhibition that circumvents fluoroquinolone resistance in this clinically important drug target. The inhibitor ‘bridges’ the DNA and a transient non-catalytic pocket on the two-fold axis at the GyrA dimer interface, and is close to the active sites and fluoroquinolone binding sites. In the inhibitor complex the active site seems poised to cleave the DNA, with a single metal ion observed between the TOPRIM (topoisomerase/primase) domain and the scissile phosphate. This work provides new insights into the mechanism of topoisomerase action and a platform for structure-based drug design of a new class of antibacterial agents against a clinically proven, but conformationally flexible, enzyme class. Topoisomerase inhibition Enzymes that move along a DNA strand, such as DNA and RNA polymerases, tend to cause the build-up of supercoiling ahead of their motion. Unchecked, this would cause the DNA to become overwound, like a twisted rubber band. Topoisomerases relieve this stress by first cleaving and then re-ligating the DNA. Topoisomerase inhibitors are used as antibacterial and anticancer drugs — for example, antibacterials of the quinolone family have been in clinical use since 1962, but are now compromised by the emergence of multidrug-resistant bacteria. The crystal structure of a type II topoisomerase from Staphylococcus aureus , DNA gyrase, has now been determined in a complex with DNA and with the broad-spectrum antibiotic GSK299423. This is an example of a new class of antibiotics that interact with the same targets as fluoroquinolones, but are structurally and mechanistically distinct from them. The structure reveals a mechanism that circumvents fluoroquinolone resistance and opens up strategies of exploiting alternative inhibition mechanisms for clinically validated targets. Enzymes that move along DNA, such as DNA and RNA polymerases, cause the DNA ahead of them to become