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

IF 2.7 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS SLAS Discovery Pub Date : 2024-02-01 DOI:10.1016/j.slasd.2024.01.006

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

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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.

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利用 RNA 双链解旋试验分析 SARS-CoV-2 Omicron nsp13 R392C 变体的活性和抑制作用。

SARS-CoV-2 nsp13 螺旋酶是病毒复制所必需的酶，也是抗病毒药物开发的一个有希望的靶点。本研究比较了 nsp13 和 Omicron nsp13R392C 变体的双链 RNA（dsRNA）解旋活性，后者在目前的循环系中占主导地位。通过体外凝胶和荧光检测，我们发现 nsp13 和 nsp13R392C 都具有dsRNA 解旋活性，且动力学相当。此外，R392C 突变对 nsp13 特异性螺旋酶抑制剂 SSYA10-001 的效率没有影响。我们还证实了其他几种螺旋酶抑制剂对 nsp13 的活性，包括在纳摩尔浓度下抑制 dsRNA 解旋的 punicalagin。总之，这项研究揭示了使用dsRNA开卷试验筛选小分子对nsp13和Omicron nsp13R392C变体的抗病毒活性的实用性。持续监测新出现的变异体对于考虑先导化合物的耐药性特征至关重要，因为这些化合物正朝着下一代疗法的方向发展。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

SLAS Discovery Chemistry-Analytical Chemistry

CiteScore

7.00

自引率

3.20%

发文量

审稿时长

39 days

期刊介绍： Advancing Life Sciences R&D: SLAS Discovery reports how scientists develop and utilize novel technologies and/or approaches to provide and characterize chemical and biological tools to understand and treat human disease. SLAS Discovery is a peer-reviewed journal that publishes scientific reports that enable and improve target validation, evaluate current drug discovery technologies, provide novel research tools, and incorporate research approaches that enhance depth of knowledge and drug discovery success. SLAS Discovery emphasizes scientific and technical advances in target identification/validation (including chemical probes, RNA silencing, gene editing technologies); biomarker discovery; assay development; virtual, medium- or high-throughput screening (biochemical and biological, biophysical, phenotypic, toxicological, ADME); lead generation/optimization; chemical biology; and informatics (data analysis, image analysis, statistics, bio- and chemo-informatics). Review articles on target biology, new paradigms in drug discovery and advances in drug discovery technologies. SLAS Discovery is of particular interest to those involved in analytical chemistry, applied microbiology, automation, biochemistry, bioengineering, biomedical optics, biotechnology, bioinformatics, cell biology, DNA science and technology, genetics, information technology, medicinal chemistry, molecular biology, natural products chemistry, organic chemistry, pharmacology, spectroscopy, and toxicology. SLAS Discovery is a member of the Committee on Publication Ethics (COPE) and was published previously (1996-2016) as the Journal of Biomolecular Screening (JBS).