title: Type IIA topoisomerase inhibition by a new class of antibacterial agents.
abstract: 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 A 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.
authors.affiliation: Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. benjamin.d.bax@gsk.com
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Bax
authors.forename: Pan F
authors.initials: PF
authors.lastname: Chan
authors.forename: Drake S
authors.initials: DS
authors.lastname: Eggleston
authors.forename: Andrew
authors.initials: A
authors.lastname: Fosberry
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Gentry
authors.forename: Fabrice
authors.initials: F
authors.lastname: Gorrec
authors.forename: Ilaria
authors.initials: I
authors.lastname: Giordano
authors.forename: Michael M
authors.initials: MM
authors.lastname: Hann
authors.forename: Alan
authors.initials: A
authors.lastname: Hennessy
authors.forename: Martin
authors.initials: M
authors.lastname: Hibbs
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Huang
authors.forename: Emma
authors.initials: E
authors.lastname: Jones
authors.forename: Jo
authors.initials: J
authors.lastname: Jones
authors.forename: Kristin Koretke
authors.initials: KK
authors.lastname: Brown
authors.forename: Ceri J
authors.initials: CJ
authors.lastname: Lewis
authors.forename: Earl W
authors.initials: EW
authors.lastname: May
authors.forename: Martin R
authors.initials: MR
authors.lastname: Saunders
authors.forename: Onkar
authors.initials: O
authors.lastname: Singh
authors.forename: Claus E
authors.initials: CE
authors.lastname: Spitzfaden
authors.forename: Carol
authors.initials: C
authors.lastname: Shen
authors.forename: Anthony
authors.initials: A
authors.lastname: Shillings
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Theobald
authors.forename: Alexandre
authors.initials: A
authors.lastname: Wohlkonig
authors.forename: Neil D
authors.initials: ND
authors.lastname: Pearson
authors.forename: Michael N
authors.initials: MN
authors.lastname: Gwynn
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D001051:Apoenzymes / Q000737:chemistry / Q000378:metabolism; D001120:Arginine / Q000378:metabolism; D001224:Aspartic Acid / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D002939:Ciprofloxacin / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D053837:DNA Cleavage; D027081:DNA Gyrase / Q000737:chemistry* / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D004351:Drug Resistance; D004926:Escherichia coli / Q000201:enzymology; D008345:Manganese / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D011804:Quinolines / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D015363:Quinolones / Q000737:chemistry / Q000378:metabolism; D013211:Staphylococcus aureus / Q000201:enzymology*; D013329:Structure-Activity Relationship; D059005:Topoisomerase II Inhibitors
chemical_list: D000900:Anti-Bacterial Agents; D001051:Apoenzymes; D004278:DNA, Superhelical; C552628:GSK299423; D011804:Quinolines; D015363:Quinolones; D059005:Topoisomerase II Inhibitors; D001224:Aspartic Acid; D008345:Manganese; D002939:Ciprofloxacin; D004247:DNA; D001120:Arginine; D027081:DNA Gyrase