title: Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design.
abstract: Widespread fluoroquinolone resistance has drawn attention to quinazolinediones (diones), fluoroquinolone-like topoisomerase poisons that are unaffected by common quinolone-resistance mutations. To better understand differences between quinolones and diones, we examined their impact on the formation of cleaved complexes (drug-topoisomerase-DNA complexes in which the DNA moiety is broken) with gyrase, one of two bacterial targets of the drugs. Formation of cleaved complexes, measured by linearization of a circular DNA substrate, required lower concentrations of quinolone than dione. The reverse reaction, detected as resealing of DNA breaks in cleaved complexes, required higher temperatures and EDTA concentrations for quinolones than diones. The greater stability of quinolone-containing complexes was attributed to the unique ability of the quinolone C3/C4 keto acid to complex with magnesium and form a previously described drug-magnesium-water bridge with GyrA-Ser83 and GyrA-Asp87. A nearby substitution in GyrA (G81C) reduced activity differences between quinolone and dione, indicating that resistance due to this variation derives from perturbation of the magnesium-water bridge. To increase dione activity, we examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is distal to the bridging C3/C4 keto acid substituent of quinolones. The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking, and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins. Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds active against common quinolone-resistant mutants.
authors.affiliation: Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences , 225 Warren Street, Newark, New Jersey 07103, United States.
authors.forename: Karl
authors.initials: K
authors.lastname: Drlica
authors.forename: Arkady
authors.initials: A
authors.lastname: Mustaev
authors.forename: Tyrell R
authors.initials: TR
authors.lastname: Towle
authors.forename: Gan
authors.initials: G
authors.lastname: Luan
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Kerns
authors.forename: James M
authors.initials: JM
authors.lastname: Berger
mesh_terms: D040981:Acinetobacter baumannii / Q000737:chemistry / Q000201:enzymology; D020816:Amino Acid Motifs; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D053960:DNA Breaks; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D027101:DNA Topoisomerase IV / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry*; D024901:Drug Resistance, Multiple, Bacterial; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology; D024841:Fluoroquinolones / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D052999:Quinazolinones / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013296:Streptococcus pneumoniae / Q000737:chemistry / Q000201:enzymology; D013329:Structure-Activity Relationship
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004270:DNA, Circular; D024841:Fluoroquinolones; D052999:Quinazolinones; D011994:Recombinant Proteins; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase; D008274:Magnesium