ABSTRACT
New antibacterials are needed to tackle antibiotic-resistant bacteria. Type IIA topoisomerases (topo2As), the targets of fluoroquinolones, regulate DNA topology by creating transient double-strand DNA breaks. Here we report the first co-crystal structures of the antibacterial QPT-1 and the anticancer drug etoposide with Staphylococcus aureus DNA gyrase, showing binding at the same sites in the cleaved DNA as the fluoroquinolone moxifloxacin. Unlike moxifloxacin, QPT-1 and etoposide interact with conserved GyrB TOPRIM residues rationalizing why QPT-1 can overcome fluoroquinolone resistance. Our data show etoposide's antibacterial activity is due to DNA gyrase inhibition and suggests other anticancer agents act similarly. Analysis of multiple DNA gyrase co-crystal structures, including asymmetric cleavage complexes, led to a 'pair of swing-doors' hypothesis in which the movement of one DNA segment regulates cleavage and religation of the second DNA duplex. This mechanism can explain QPT-1's bacterial specificity. Structure-based strategies for developing topo2A antibacterials are suggested.
Subject(s)
Anti-Bacterial Agents/chemistry , Antineoplastic Agents/chemistry , DNA Gyrase/chemistry , Etoposide/chemistry , Fluoroquinolones/chemistry , Staphylococcus aureus/enzymology , Topoisomerase II Inhibitors/chemistry , Anti-Bacterial Agents/pharmacology , Antineoplastic Agents/pharmacology , DNA Gyrase/genetics , DNA Gyrase/metabolism , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Bacterial/metabolism , Drug Resistance, Bacterial , Etoposide/pharmacology , Fluoroquinolones/pharmacology , Models, Molecular , Molecular Structure , Moxifloxacin , Staphylococcus aureus/chemistry , Staphylococcus aureus/drug effects , Topoisomerase II Inhibitors/pharmacologyABSTRACT
Quinolone antibacterials have been used to treat bacterial infections for over 40 years. A crystal structure of moxifloxacin in complex with Acinetobacter baumannii topoisomerase IV now shows the wedge-shaped quinolone stacking between base pairs at the DNA cleavage site and binding conserved residues in the DNA cleavage domain through chelation of a noncatalytic magnesium ion. This provides a molecular basis for the quinolone inhibition mechanism, resistance mutations and invariant quinolone antibacterial structural features.
