Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays

Nicole L. Inniss; Margarita Rzhetskaya; Ted Ling-Hu; Ramon Lorenzo-Redondo; Kelly E. Bachta; Karla J.F. Satchell; Judd F. Hultquist

doi:10.1016/j.slasd.2024.01.006

Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays

Nicole L. Inniss, Margarita Rzhetskaya, Ted Ling-Hu, Ramon Lorenzo-Redondo, Kelly E. Bachta, Karla J.F. Satchell^*, Judd F. Hultquist^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13^R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13^R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13^R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.

Original language	English (US)
Article number	100145
Journal	SLAS Discovery
Volume	29
Issue number	3
DOIs	https://doi.org/10.1016/j.slasd.2024.01.006
State	Published - Apr 2024

Funding

This work was supported by a COVID supplement award from the Robert H. Lurie Comprehensive Cancer Center funded by the National Cancer Institute (P30 CA060553), by HHS/NIH/NIAID Contract #75N93022C00035, by the Successful Clinical Response to Pneumonia Therapy (SCRIPT) Center (NIH U19AI135964), by institutional support for the Center for Pathogen Genomics and Microbial Evolution (CPGME), and by a Developmental Award from the Quantitative Biosciences Institute Coronavirus Research Group (QCRG) Antiviral Drug Discovery (AViDD) center (NIH U19AI171110).Jacob VanderVaart is thanked for technical assistance during the early stages of this project. This research was supported in part through the computational resources and staff contributions provided by the Genomics Computer Cluster which is jointly supported by Northwestern University Feinberg School of Medicine, Center for Genetic Medicine, Department of Biochemistry and Molecular Genetics, Office of the Provost, Office for Research, and Information Technology. The Genomics Computer Cluster is part of Quest, Northwestern University's high-performance computing facility, to advance genomics research. Jacob VanderVaart is thanked for technical assistance during the early stages of this project. This research was supported in part through the computational resources and staff contributions provided by the Genomics Computer Cluster which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg's Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Computer Cluster is part of Quest, Northwestern University's high-performance computing facility, to advance genomics research. This work was supported by a COVID supplement award from the Robert H. Lurie Comprehensive Cancer Center funded by the National Cancer Institute ( P30 CA060553 ), by HHS/NIH/NIAID Contract #75N93022C00035, by the Successful Clinical Response to Pneumonia Therapy (SCRIPT) Center ( NIH U19AI135964 ), by institutional support for the Center for Pathogen Genomics and Microbial Evolution (CPGME), and by a Developmental Award from the Quantitative Biosciences Institute Coronavirus Research Group (QCRG) Antiviral Drug Discovery (AViDD) center ( NIH U19AI171110 ).

Keywords

Antiviral drug discovery
COVID-19
Direct-acting antiviral
Helicase
Nsp13
R392C
SARS-CoV-2
Unwinding assay

ASJC Scopus subject areas

Biotechnology
Analytical Chemistry
Biochemistry
Molecular Medicine

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10.1016/j.slasd.2024.01.006

Cite this

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title = "Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays",

abstract = "SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.",

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author = "Inniss, {Nicole L.} and Margarita Rzhetskaya and Ted Ling-Hu and Ramon Lorenzo-Redondo and Bachta, {Kelly E.} and Satchell, {Karla J.F.} and Hultquist, {Judd F.}",

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year = "2024",

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doi = "10.1016/j.slasd.2024.01.006",

language = "English (US)",

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AU - Bachta, Kelly E.

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AU - Hultquist, Judd F.

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AB - SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.

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Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays

Abstract

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Keywords

ASJC Scopus subject areas

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