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 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.
Bax
Benjamin D
BD
Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. benjamin.d.bax@gsk.com
Chan
Pan F
PF
Eggleston
Drake S
DS
Fosberry
Andrew
A
Gentry
Daniel R
DR
Gorrec
Fabrice
F
Giordano
Ilaria
I
Hann
Michael M
MM
Hennessy
Alan
A
Hibbs
Martin
M
Huang
Jianzhong
J
Jones
Emma
E
Jones
Jo
J
Brown
Kristin Koretke
KK
Lewis
Ceri J
CJ
May
Earl W
EW
Saunders
Martin R
MR
Singh
Onkar
O
Spitzfaden
Claus E
CE
Shen
Carol
C
Shillings
Anthony
A
Theobald
Andrew J
AJ
Wohlkonig
Alexandre
A
Pearson
Neil D
ND
Gwynn
Michael N
MN
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
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