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Escherichia coli topoisomerase IV","volume":"53","author":"Aldred","year":"2014","journal-title":"Biochemistry"},{"key":"10.1016\/j.bmcl.2018.03.085_b0135","doi-asserted-by":"crossref","first-page":"4628","DOI":"10.1093\/nar\/gkt124","article-title":"Topoisomerase IV-quinolone interactions are mediated through a water-metal ion bridge: mechanistic basis of quinolone resistance","volume":"41","author":"Aldred","year":"2013","journal-title":"Nucl Acids Res"},{"key":"10.1016\/j.bmcl.2018.03.085_b0140","doi-asserted-by":"crossref","first-page":"12300","DOI":"10.1074\/jbc.M113.529164","article-title":"Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding","volume":"289","author":"Mustaev","year":"2014","journal-title":"J Biol Chem"},{"key":"10.1016\/j.bmcl.2018.03.085_b0145","unstructured":"The structure of the A. baumannii topoisomerase IV-moxifloxacin-DNA ternary complex was obtained from PDB ID: 2XKK. Most of the compounds synthesized for this study were docked into the moxifloxacin binding site of the PDB ID: 2XKK structure using the SYBYL-X docking suite (Certara USA Inc, Princeton, NJ, U.S.A.). The binding pocket was created automatically by the software using the natively bound moxifloxacin ligand to determine the location of the binding site. The caged surface shown in Figure 2 represents the binding pocket that was determined by SYBYL based on the location of the ligand (moxifloxacin) from the native crystal structure."},{"key":"10.1016\/j.bmcl.2018.03.085_b0150","doi-asserted-by":"crossref","first-page":"3855","DOI":"10.1016\/j.tetlet.2005.03.181","article-title":"Arylation of nitromethane: masked nucleophilic formylation of fluoroquinolones","volume":"46","author":"Zhang","year":"2005","journal-title":"Tetrahedron Lett"},{"key":"10.1016\/j.bmcl.2018.03.085_b0155","unstructured":"Wild type GyrA and GyrB, two subunits of E. coli DNA gyrase, were separately expressed and purified, and the active DNA gyrase was reconstituted using the protocol described by Shea and Hiasa.34 E. coli DNA gyrase purchased from New England Biolabs was also used. The activity of each preparation of DNA gyrase was measured under the reaction conditions described below and one unit was defined as the amount of DNA gyrase required to completely supercoil 0.3 \u03bcg of the relaxed DNA at 37\u00b0C in 15 min. The relaxed DNA was prepared by incubating negatively supercoiled pBR322 DNA with E. coli topoisomerase I and used as the substrate in the supercoiling assay. Supercoiling reaction mixtures (20 \u03bcL) contained 50 mM Tris-HCl (pH 8.0 at 23\u00b0C), 10 mM MgCl2, 100 mM potassium glutamate, 10 mM dithiothreitol, 50 \u03bcg\/ml bovine serum albumin, 1 mM ATP, 0.3 \u03bcg of the relaxed DNA, 1 unit of E. coli gyrase, and the various concentrations of fluoroquinolones. Reaction mixtures were incubated at 37\u00b0C for 15 min and terminated by adding EDTA to 25 mM and further incubating at 37\u00b0C for 5 min. The DNA products were analyzed by electrophoresis through vertical 1.2% agarose gels (14 x 10 x 0.3 cm) at 2 V\/cm for 15 h a running buffer of 50 mM Tris-HCl (pH 7.9 at 23\u00b0C), 40 mM sodium acetate, and 1 mM EDTA (TAE buffer). Gels were stained with 0.5 \u03bcg\/ml ethidium bromide, and then photographed and quantified using a MyECL Imager (Thermo Fisher Scientific)."},{"key":"10.1016\/j.bmcl.2018.03.085_b0160","doi-asserted-by":"crossref","first-page":"3011","DOI":"10.1128\/AAC.00190-10","article-title":"Comparison of in vitro activities of fluoroquinolone-Like 2,4- and 1,3-diones","volume":"54","author":"Oppegard","year":"2010","journal-title":"Antimicrobial Agents Chemother"},{"key":"10.1016\/j.bmcl.2018.03.085_b0165","unstructured":"The poisoning effect of a fluoroquinolone on DNA gyrase can be measured by a DNA cleavage assay, where a DNA gyrase-fluoroquinolone-DNA ternary complex is converted to a double-strand break. The concentrations of DNA gyrase and N-1 fluoroquinolones were chosen to limit multiple cleavages of the plasmid DNA (data not shown), so that only one ternary complex is formed on each plasmid DNA molecule. This allows us to measure the poisoning of DNA gyrase by an N-1 fluoroquinolone as an increase in the amount of the full-length linear plasmid DNA. DNA cleavage reaction mixtures (20 \u03bcl) contained 50 mM Tris-HCl (pH 8.0 at 23 & #xB0;C), 10 mM MgCl2, 10 mM dithiothreitol, 50 \u03bcg\/mL bovine serum albumin, 1 mM ATP, 5 \u03bcg\/mL tRNA, 0.3 \u03bcg of the supercoiled pBR322 DNA, 5 units of E. coli gyrase, and the various concentrations of fluoroquinolones. Reaction mixtures were incubated at 37\u00b0C for 10 min. SDS was added to a concentration of 1%, and the reaction mixtures were further incubated at 37\u00b0C for 5 min. EDTA and proteinase K were then added to 25 mM and 100 \u03bcg\/mL, respectively, and the incubation was continued for an additional 15 min at 37\u00b0C. The DNA products were purified by extraction with phenol\/chloroform\/isoamyl alcohol (25:24:1, v\/v) and then analyzed by electrophoresis through vertical 1.2% agarose gels at 2 V\/cm for 15 hours in TAE buffer that contained 0.5 \u03bcg\/mL ethidium bromide. After destaining in water, gels were photographed and quantified using a MyECL Imager."},{"key":"10.1016\/j.bmcl.2018.03.085_b0170","doi-asserted-by":"crossref","first-page":"34780","DOI":"10.1074\/jbc.M001608200","article-title":"DNA gyrase-mediated wrapping of the DNA strand is required for the replication fork arrest by the DNA gyrase-quinolone-DNA ternary complex","volume":"275","author":"Hiasa","year":"2000","journal-title":"J Biol Chem"},{"key":"10.1016\/j.bmcl.2018.03.085_b0175","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1007\/s10637-008-9209-1","article-title":"Anti-proliferative effects of simocyclinone D8 (SD8), a novel catalytic inhibitor of topoisomerase II","volume":"28","author":"Sadiq","year":"2010","journal-title":"Invest New Drugs"}],"container-title":["Bioorganic & Medicinal Chemistry Letters"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960894X18302907?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0960894X18302907?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T07:25:45Z","timestamp":1760772345000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0960894X18302907"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6]]},"references-count":35,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2018,6]]}},"alternative-id":["S0960894X18302907"],"URL":"https:\/\/doi.org\/10.1016\/j.bmcl.2018.03.085","relation":{},"ISSN":["0960-894X"],"issn-type":[{"value":"0960-894X","type":"print"}],"subject":[],"published":{"date-parts":[[2018,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Design, synthesis, and evaluation of novel N-1 fluoroquinolone derivatives: Probing for binding contact with the active site tyrosine of gyrase","name":"articletitle","label":"Article Title"},{"value":"Bioorganic & Medicinal Chemistry Letters","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bmcl.2018.03.085","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2018 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}