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Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro

The life cycle of severe acute respiratory syndrome coronavirus 2 includes several steps that are supposedly mediated by liquid–liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and genomic RNA. To facilitate the rational design of LLPS-targeting therapeutics, we modeled N-RNA bio...

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Autores principales: Svetlova, Julia, Knizhnik, Ekaterina, Manuvera, Valentin, Severov, Vyacheslav, Shirokov, Dmitriy, Grafskaia, Ekaterina, Bobrovsky, Pavel, Matyugina, Elena, Khandazhinskaya, Anastasia, Kozlovskaya, Liubov, Miropolskaya, Nataliya, Aralov, Andrey, Khodarovich, Yuri, Tsvetkov, Vladimir, Kochetkov, Sergey, Lazarev, Vassili, Varizhuk, Anna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738865/
https://www.ncbi.nlm.nih.gov/pubmed/36499608
http://dx.doi.org/10.3390/ijms232315281
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author Svetlova, Julia
Knizhnik, Ekaterina
Manuvera, Valentin
Severov, Vyacheslav
Shirokov, Dmitriy
Grafskaia, Ekaterina
Bobrovsky, Pavel
Matyugina, Elena
Khandazhinskaya, Anastasia
Kozlovskaya, Liubov
Miropolskaya, Nataliya
Aralov, Andrey
Khodarovich, Yuri
Tsvetkov, Vladimir
Kochetkov, Sergey
Lazarev, Vassili
Varizhuk, Anna
author_facet Svetlova, Julia
Knizhnik, Ekaterina
Manuvera, Valentin
Severov, Vyacheslav
Shirokov, Dmitriy
Grafskaia, Ekaterina
Bobrovsky, Pavel
Matyugina, Elena
Khandazhinskaya, Anastasia
Kozlovskaya, Liubov
Miropolskaya, Nataliya
Aralov, Andrey
Khodarovich, Yuri
Tsvetkov, Vladimir
Kochetkov, Sergey
Lazarev, Vassili
Varizhuk, Anna
author_sort Svetlova, Julia
collection PubMed
description The life cycle of severe acute respiratory syndrome coronavirus 2 includes several steps that are supposedly mediated by liquid–liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and genomic RNA. To facilitate the rational design of LLPS-targeting therapeutics, we modeled N-RNA biomolecular condensates in vitro and analyzed their sensitivity to several small-molecule antivirals. The model condensates were obtained and visualized under physiological conditions using an optimized RNA sequence enriched with N-binding motifs. The antivirals were selected based on their presumed ability to compete with RNA for specific N sites or interfere with non-specific pi–pi/cation–pi interactions. The set of antivirals included fleximers, 5′-norcarbocyclic nucleoside analogs, and perylene-harboring nucleoside analogs as well as non-nucleoside amphiphilic and hydrophobic perylene derivatives. Most of these antivirals enhanced the formation of N-RNA condensates. Hydrophobic perylene derivatives and 5′-norcarbocyclic derivatives caused up to 50-fold and 15-fold enhancement, respectively. Molecular modeling data argue that hydrophobic compounds do not hamper specific N-RNA interactions and may promote non-specific ones. These findings shed light on the determinants of potent small-molecule modulators of viral LLPS.
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spelling pubmed-97388652022-12-11 Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro Svetlova, Julia Knizhnik, Ekaterina Manuvera, Valentin Severov, Vyacheslav Shirokov, Dmitriy Grafskaia, Ekaterina Bobrovsky, Pavel Matyugina, Elena Khandazhinskaya, Anastasia Kozlovskaya, Liubov Miropolskaya, Nataliya Aralov, Andrey Khodarovich, Yuri Tsvetkov, Vladimir Kochetkov, Sergey Lazarev, Vassili Varizhuk, Anna Int J Mol Sci Article The life cycle of severe acute respiratory syndrome coronavirus 2 includes several steps that are supposedly mediated by liquid–liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and genomic RNA. To facilitate the rational design of LLPS-targeting therapeutics, we modeled N-RNA biomolecular condensates in vitro and analyzed their sensitivity to several small-molecule antivirals. The model condensates were obtained and visualized under physiological conditions using an optimized RNA sequence enriched with N-binding motifs. The antivirals were selected based on their presumed ability to compete with RNA for specific N sites or interfere with non-specific pi–pi/cation–pi interactions. The set of antivirals included fleximers, 5′-norcarbocyclic nucleoside analogs, and perylene-harboring nucleoside analogs as well as non-nucleoside amphiphilic and hydrophobic perylene derivatives. Most of these antivirals enhanced the formation of N-RNA condensates. Hydrophobic perylene derivatives and 5′-norcarbocyclic derivatives caused up to 50-fold and 15-fold enhancement, respectively. Molecular modeling data argue that hydrophobic compounds do not hamper specific N-RNA interactions and may promote non-specific ones. These findings shed light on the determinants of potent small-molecule modulators of viral LLPS. MDPI 2022-12-03 /pmc/articles/PMC9738865/ /pubmed/36499608 http://dx.doi.org/10.3390/ijms232315281 Text en © 2022 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
Svetlova, Julia
Knizhnik, Ekaterina
Manuvera, Valentin
Severov, Vyacheslav
Shirokov, Dmitriy
Grafskaia, Ekaterina
Bobrovsky, Pavel
Matyugina, Elena
Khandazhinskaya, Anastasia
Kozlovskaya, Liubov
Miropolskaya, Nataliya
Aralov, Andrey
Khodarovich, Yuri
Tsvetkov, Vladimir
Kochetkov, Sergey
Lazarev, Vassili
Varizhuk, Anna
Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title_full Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title_fullStr Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title_full_unstemmed Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title_short Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro
title_sort nucleoside analogs and perylene derivatives modulate phase separation of sars-cov-2 n protein and genomic rna in vitro
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738865/
https://www.ncbi.nlm.nih.gov/pubmed/36499608
http://dx.doi.org/10.3390/ijms232315281
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