Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile

• Published in: Nature (London) Vol. 604; no. 7906; pp. 541 - 545
• Main Authors: Cao, Xinyun, Boyaci, Hande, Chen, James, Bao, Yu, Landick, Robert, Campbell, Elizabeth A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21-04-2022; Nature Publishing Group
• Subjects: 101/28; 38/70; 631/326/22/1290; 631/326/421; 631/337/572; 631/45/535/1258/1259; 82; 82/16; 82/80; 82/83; Amino acids; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibiotics; Clostridioides; Clostridioides difficile; Clostridium Infections - drug therapy; Clostridium Infections - microbiology; Commensals; Cryoelectron Microscopy; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases; Drug development; E coli; Electron microscopy; Enzymes; Fidaxomicin - chemistry; Fidaxomicin - pharmacology; Fidaxomicin - therapeutic use; Genetic analysis; Humanities and Social Sciences; Humans; Hydrogen bonds; Infections; Intestinal microflora; Microbiomes; Microbiota; Microscopy; multidisciplinary; Nosocomial infection; RNA polymerase; Science; Science (multidisciplinary); Sensitizing
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-022-04545-z

Fidaxomicin (Fdx) is widely used to treat
Clostridioides difficile
(
Cdiff
) infections, but the molecular basis of its narrow-spectrum activity in the human gut microbiome remains unknown.
Cdiff
infections are a leading cause of nosocomial deaths
1
. Fidaxomicin, which inhibits RNA polymerase, targets
Cdiff
with minimal effects on gut commensals, reducing recurrence of
Cdiff
infection
2
,
3
. Here we present the cryo-electron microscopy structure of
Cdiff
RNA polymerase in complex with fidaxomicin and identify a crucial fidaxomicin-binding determinant of
Cdiff
RNA polymerase that is absent in most gut microbiota such as Proteobacteria and Bacteroidetes. By combining structural, biochemical, genetic and bioinformatic analyses, we establish that a single residue in
Cdiff
RNA polymerase is a sensitizing element for fidaxomicin narrow-spectrum activity. Our results provide a blueprint for targeted drug design against an important human pathogen.
Structural analysis of
Clostridioides difficile
RNA polymerase in complex with fidaxomicin combined with biochemical, genetic and bioinformatic analyses identifies a key residue that determines fidaxomicin sensitivity.