Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut

Abstract

The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.

Metabolic profiling during COVID-19 infection in humans: Identification of potential biomarkers for occurrence, severity and outcomes using machine learning

“…Administration of antibiotics to SARS-CoV-2- infected mice resulted in reduction in certain microbiome that metabolizes primary bile acid to secondary bile acids. This leads to accumulation of primary bile acids, which subsequently were found to inhibit nsp15 endoribonuclease of the virus [ 51 ]. Furthermore, infection with SARS-CoV-2 itself causes reduction in the diversity of gut microbiome as shown in human patients [ 52 ] and primates [ 53 ] and microbiota in human gut are known to process primary bile acids into secondary bile acids such as deoxycholic acid and ursodeoxycholic/ chenodeoxycholic acid [ 54 ].…”

SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity

“…DNA fragments encoding wild-type SARS-CoV-2 nsp15 were amplified by PCR from a pET-32a(+) plasmid carrying the nsp15 gene ( 34 ) and inserted into pET-28a(+) vectors harboring an N-terminal 6 × His tag using a ClonExpress II One Step Cloning kit (Vazyme, China) (complete sequence of the nsp15 expression plasmid is listed in Supplementary Table S1 ). The constructs were transformed into Escherichia coli BL21(DE3)pLysS cells (AngYuBio, China).…”

SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity

“…DNA fragments encoding wild-type SARS-CoV-2 nsp15 were amplified by PCR from a pET-32a(+) plasmid carrying the nsp15 gene (Ma et al, 2022) and inserted into pET-28a(+) vectors harboring an N-terminal 6× His tag using a ClonExpress II One Step Cloning kit (Vazyme, China) (complete sequence of the nsp15 expression plasmid is listed in Table S3). The constructs were transformed into E. coli BL21(DE3)pLysS cells (AngYuBio, China).…”