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TitleStructural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic.
Journal, issue, pagesSci Rep, Vol. 9, Issue 1, Page 5634, Year 2019
Publish dateApr 4, 2019
AuthorsAlain Scaiola / Marc Leibundgut / Daniel Boehringer / Patrick Caspers / Daniel Bur / Hans H Locher / Georg Rueedi / Daniel Ritz /
PubMed AbstractOxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl ...Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with the peptidyl transferase reaction. Cadazolid is the first member of quinoxolidinone antibiotics, which are characterized by combining the pharmacophores of oxazolidinones and fluoroquinolones, and it is evaluated for treatment of Clostridium difficile gastrointestinal infections that frequently occur in hospitalized patients. In vitro protein synthesis inhibition by cadazolid was shown in Escherichia coli and Staphylococcus aureus, including an isolate resistant against linezolid, the prototypical oxazolidinone antibiotic. To better understand the mechanism of inhibition, we determined a 3.0 Å cryo-electron microscopy structure of cadazolid bound to the E. coli ribosome in complex with mRNA and initiator tRNA. Here we show that cadazolid binds with its oxazolidinone moiety in a binding pocket in close vicinity of the PTC as observed previously for linezolid, and that it extends its unique fluoroquinolone moiety towards the A-site of the PTC. In this position, the drug inhibits protein synthesis by interfering with the binding of tRNA to the A-site, suggesting that its chemical features also can enable the inhibition of linezolid-resistant strains.
External linksSci Rep / PubMed:30948752 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.2 Å
Structure data

4638

6qul

EMDB-4638, PDB-6qul:
Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4639:
Structure of a bacterial 70S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-4641:
Structure of a bacterial 70S ribosomal subunit in complex with cadazolid, reconstruction focused around the 30S ribosomal subunit
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

ChemComp-MG:
Unknown entry

ChemComp-A:
ADENOSINE-5'-MONOPHOSPHATE / Adenosine monophosphate

ChemComp-JJH:
cadazolid / antibiotic*YM / Cadazolid

ChemComp-ZN:
Unknown entry

Source
  • escherichia coli (E. coli)
KeywordsANTIBIOTIC / ribosome / cadazolid / quinoxolidinone / 50S

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