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Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment
The coronavirus disease-19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rampant in the world and is a serious threat to global health. The SARS-CoV-2 RNA has been detected in various environmental media, which speeds up the pace of the virus becom...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Author(s). Published by Elsevier Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133531/ https://www.ncbi.nlm.nih.gov/pubmed/34044308 http://dx.doi.org/10.1016/j.ecoenv.2021.112357 |
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author | Zhang, Fan Wang, Zhuang Vijver, Martina G. Peijnenburg, Willie J.G.M. |
author_facet | Zhang, Fan Wang, Zhuang Vijver, Martina G. Peijnenburg, Willie J.G.M. |
author_sort | Zhang, Fan |
collection | PubMed |
description | The coronavirus disease-19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rampant in the world and is a serious threat to global health. The SARS-CoV-2 RNA has been detected in various environmental media, which speeds up the pace of the virus becoming a global biological pollutant. Because many engineered nanomaterials (ENMs) are capable of inducing anti-microbial activity, ENMs provide excellent solutions to overcome the virus pandemic, for instance by application as protective coatings, biosensors, or nano-agents. To tackle some mechanistic issues related to the impact of ENMs on SARS-CoV-2, we investigated the molecular interactions between carbon nanoparticles (CNPs) and a SARS-CoV-2 RNA fragment (i.e., a model molecule of frameshift stimulation element from the SARS-CoV-2 RNA genome) using molecular mechanics simulations. The interaction affinity between the CNPs and the SARS-CoV-2 RNA fragment increased in the order of fullerenes < graphenes < carbon nanotubes. Furthermore, we developed quantitative structure–activity relationship (QSAR) models to describe the interactions of 17 different types of CNPs from three dimensions with the SARS-CoV-2 RNA fragment. The QSAR models on the interaction energies of CNPs with the SARS-CoV-2 RNA fragment show high goodness-of-fit and robustness. Molecular weight, surface area, and the sum of degrees of every carbon atom were found to be the primary structural descriptors of CNPs determining the interactions. Our research not only offers a theoretical insight into the adsorption/separation and inactivation of SARS-CoV-2, but also allows to design novel ENMs which act efficiently on the genetic material RNA of SARS-CoV-2. This contributes to minimizing the challenge of time-consuming and labor-intensive virus experiments under high risk of infection, whilst meeting our precautionary demand for options to handle any new versions of the coronavirus that might emerge in the future. |
format | Online Article Text |
id | pubmed-8133531 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Author(s). Published by Elsevier Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-81335312021-05-20 Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment Zhang, Fan Wang, Zhuang Vijver, Martina G. Peijnenburg, Willie J.G.M. Ecotoxicol Environ Saf Article The coronavirus disease-19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rampant in the world and is a serious threat to global health. The SARS-CoV-2 RNA has been detected in various environmental media, which speeds up the pace of the virus becoming a global biological pollutant. Because many engineered nanomaterials (ENMs) are capable of inducing anti-microbial activity, ENMs provide excellent solutions to overcome the virus pandemic, for instance by application as protective coatings, biosensors, or nano-agents. To tackle some mechanistic issues related to the impact of ENMs on SARS-CoV-2, we investigated the molecular interactions between carbon nanoparticles (CNPs) and a SARS-CoV-2 RNA fragment (i.e., a model molecule of frameshift stimulation element from the SARS-CoV-2 RNA genome) using molecular mechanics simulations. The interaction affinity between the CNPs and the SARS-CoV-2 RNA fragment increased in the order of fullerenes < graphenes < carbon nanotubes. Furthermore, we developed quantitative structure–activity relationship (QSAR) models to describe the interactions of 17 different types of CNPs from three dimensions with the SARS-CoV-2 RNA fragment. The QSAR models on the interaction energies of CNPs with the SARS-CoV-2 RNA fragment show high goodness-of-fit and robustness. Molecular weight, surface area, and the sum of degrees of every carbon atom were found to be the primary structural descriptors of CNPs determining the interactions. Our research not only offers a theoretical insight into the adsorption/separation and inactivation of SARS-CoV-2, but also allows to design novel ENMs which act efficiently on the genetic material RNA of SARS-CoV-2. This contributes to minimizing the challenge of time-consuming and labor-intensive virus experiments under high risk of infection, whilst meeting our precautionary demand for options to handle any new versions of the coronavirus that might emerge in the future. The Author(s). Published by Elsevier Inc. 2021-08 2021-05-19 /pmc/articles/PMC8133531/ /pubmed/34044308 http://dx.doi.org/10.1016/j.ecoenv.2021.112357 Text en © 2021 The Authors Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Zhang, Fan Wang, Zhuang Vijver, Martina G. Peijnenburg, Willie J.G.M. Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title | Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title_full | Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title_fullStr | Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title_full_unstemmed | Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title_short | Probing nano-QSAR to assess the interactions between carbon nanoparticles and a SARS-CoV-2 RNA fragment |
title_sort | probing nano-qsar to assess the interactions between carbon nanoparticles and a sars-cov-2 rna fragment |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133531/ https://www.ncbi.nlm.nih.gov/pubmed/34044308 http://dx.doi.org/10.1016/j.ecoenv.2021.112357 |
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