Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance

Wohlkonig, A.; Chan, Pan F.; Fosberry, Andrew; Homes, Paul; Huang, Jianzhong; Kranz, Michael; Leydon, Vaughan R.; Miles, Timothy J.; Pearson, Neil D.; Perera, Rajika L.; Shillings, Anthony; Gwynn, Michael N.; Bax, Benjamin

doi:10.1038/nsmb.1892

Cited by 269 publications

(361 citation statements)

References 13 publications

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“…The residues lining the thiophene compoundbinding pocket are conserved among bacteria, perhaps because the pocket needs to open and close during the bacterial catalytic cycle, as observed when the two A. baumannii topo IV structures are compared (SI Appendix, Figs. S8 and S9) (25). This finding suggests that the opening and closing of this Aα1 hinge pocket may be coupled to the binding, cleavage, religation, and release of DNA from the DNA gate.…”

Section: Discussionmentioning

confidence: 84%

“…These structural data showed that compound 1 bound to the protein at a site remote from the DNA-cleavage site and devoid of any direct DNA contacts. As far as we know, neither of these features has been previously reported in topoisomerase II poisons (15,19,25,26). The binding pocket lies at the interface between the GyrB topoisomerase-primase (TOPRIM) domain (27) and GyrA winged helix domain (WHD) and opens as a groove toward the outer side of the enzyme (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The thiophene compound-binding pocket does not exist in a 2.2-Å apo A. baumannii crystal structure due to a hinge movement around R33 of the ParC subunit (25), which moves the TOPRIM domain relative to the WHD (SI Appendix, Figs. S8 and S9).…”

Section: Discussionmentioning

confidence: 99%

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Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Chan

Germe

Bax

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase–DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

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Section: Discussionmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

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Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Chan

Germe

Bax

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…This bridge is formed by a divalent metal ion that is chelated by the C3/C4 keto acid of the drug and stabilized by four water molecules (19). Two of these water molecules are coordinated by a conserved serine and acidic residue (located four positions downstream) in the A subunit of the enzyme.…”

Section: D94gmentioning

confidence: 99%

“…Recent structural (19) and functional (20,21) studies with topoisomerase IV indicate that quinolones interact with bacterial type II enzymes primarily through a water-metal ion bridge. This bridge is formed by a divalent metal ion that is chelated by the C3/C4 keto acid of the drug and stabilized by four water molecules (19).…”

Section: D94gmentioning

confidence: 99%

Fluoroquinolone interactions with Mycobacterium tuberculosis gyrase: Enhancing drug activity against wild-type and resistant gyrase

Aldred

Blower

Kerns

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

122

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Mycobacterium tuberculosis is a significant source of global morbidity and mortality. Moxifloxacin and other fluoroquinolones are important therapeutic agents for the treatment of tuberculosis, particularly multidrug-resistant infections. To guide the development of new quinolone-based agents, it is critical to understand the basis of drug action against M. tuberculosis gyrase and how mutations in the enzyme cause resistance. Therefore, we characterized interactions of fluoroquinolones and related drugs with WT gyrase and enzymes carrying mutations at GyrA A90 and GyrA D94. M. tuberculosis gyrase lacks a conserved serine that anchors a water-metal ion bridge that is critical for quinolone interactions with other bacterial type II topoisomerases. Despite the fact that the serine is replaced by an alanine (i.e., GyrA A90 ) in M. tuberculosis gyrase, the bridge still forms and plays a functional role in mediating quinolone-gyrase interactions. Clinically relevant mutations at GyrA A90 and GyrA D94 cause quinolone resistance by disrupting the bridge-enzyme interaction, thereby decreasing drug affinity. Fluoroquinolone activity against WT and resistant enzymes is enhanced by the introduction of specific groups at the C7 and C8 positions. By dissecting fluoroquinolone-enzyme interactions, we determined that an 8-methyl-moxifloxacin derivative induces high levels of stable cleavage complexes with WT gyrase and two common resistant enzymes, GyrA A90V and GyrA D94G. 8-Methyl-moxifloxacin was more potent than moxifloxacin against WT M. tuberculosis gyrase and displayed higher activity against the mutant enzymes than moxifloxacin did against WT gyrase. This chemical biology approach to defining drug-enzyme interactions has the potential to identify novel drugs with improved activity against tuberculosis.Mycobacterium tuberculosis | fluoroquinolones | antibiotic resistance | gyrase | complex stability

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Fluoroquinolone Resistance

Drlica¹,

Zhao²,

Malik³

et al. 2019

Bacterial Resistance to Antibiotics – From Molecules to Man

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Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance

Cited by 269 publications

References 13 publications

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase

Fluoroquinolone interactions with Mycobacterium tuberculosis gyrase: Enhancing drug activity against wild-type and resistant gyrase

Fluoroquinolone Resistance

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