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Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication

Authors :
Ekaterina Knizhnik
Stepan Chumakov
Julia Svetlova
Iulia Pavlova
Yuri Khodarovich
Vladimir Brylev
Vjacheslav Severov
Rugiya Alieva
Liubov Kozlovskaya
Dmitry Andreev
Andrey Aralov
Anna Varizhuk
Source :
Biomolecules, Vol 13, Iss 11, p 1660 (2023)
Publication Year :
2023
Publisher :
MDPI AG, 2023.

Abstract

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.

Details

Language :
English
ISSN :
2218273X
Volume :
13
Issue :
11
Database :
Directory of Open Access Journals
Journal :
Biomolecules
Publication Type :
Academic Journal
Accession number :
edsdoj.5a4c58f2e2a34e5ea67bf152380c00dc
Document Type :
article
Full Text :
https://doi.org/10.3390/biom13111660