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Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication
Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtain...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10668963/ https://www.ncbi.nlm.nih.gov/pubmed/38002341 http://dx.doi.org/10.3390/biom13111660 |
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author | Knizhnik, Ekaterina Chumakov, Stepan Svetlova, Julia Pavlova, Iulia Khodarovich, Yuri Brylev, Vladimir Severov, Vjacheslav Alieva, Rugiya Kozlovskaya, Liubov Andreev, Dmitry Aralov, Andrey Varizhuk, Anna |
author_facet | Knizhnik, Ekaterina Chumakov, Stepan Svetlova, Julia Pavlova, Iulia Khodarovich, Yuri Brylev, Vladimir Severov, Vjacheslav Alieva, Rugiya Kozlovskaya, Liubov Andreev, Dmitry Aralov, Andrey Varizhuk, Anna |
author_sort | Knizhnik, Ekaterina |
collection | PubMed |
description | Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA–DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals. |
format | Online Article Text |
id | pubmed-10668963 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-106689632023-11-17 Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication Knizhnik, Ekaterina Chumakov, Stepan Svetlova, Julia Pavlova, Iulia Khodarovich, Yuri Brylev, Vladimir Severov, Vjacheslav Alieva, Rugiya Kozlovskaya, Liubov Andreev, Dmitry Aralov, Andrey Varizhuk, Anna Biomolecules Article Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA–DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals. MDPI 2023-11-17 /pmc/articles/PMC10668963/ /pubmed/38002341 http://dx.doi.org/10.3390/biom13111660 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Knizhnik, Ekaterina Chumakov, Stepan Svetlova, Julia Pavlova, Iulia Khodarovich, Yuri Brylev, Vladimir Severov, Vjacheslav Alieva, Rugiya Kozlovskaya, Liubov Andreev, Dmitry Aralov, Andrey Varizhuk, Anna Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title | Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title_full | Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title_fullStr | Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title_full_unstemmed | Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title_short | Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication |
title_sort | unwinding the sars-cov-2 ribosomal frameshifting pseudoknot with lna and g-clamp-modified phosphorothioate oligonucleotides inhibits viral replication |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10668963/ https://www.ncbi.nlm.nih.gov/pubmed/38002341 http://dx.doi.org/10.3390/biom13111660 |
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