SNAP output for PDB entry 6qul [SNAP web server]

PDB-id

6qul; SNAP-derived features in text and JSON formats; DNAproDB

Class

antibiotic

Method

cryo-EM (3.0 Å)

Summary

Structure of a bacterial 50s ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid

Reference

Scaiola A, Leibundgut M, Boehringer D, Caspers P, Bur D, Locher HH, Rueedi G, Ritz D (2019): "Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic." Sci Rep, 9, 5634. doi: 10.1038/s41598-019-42155-4.

Abstract

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.