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In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people across the globe and created not only a health emergency but also a financial crisis. This virus attacks the angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membr...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8694220/ https://www.ncbi.nlm.nih.gov/pubmed/35424358 http://dx.doi.org/10.1039/d0ra09123e |
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author | Badhe, Yogesh Gupta, Rakesh Rai, Beena |
author_facet | Badhe, Yogesh Gupta, Rakesh Rai, Beena |
author_sort | Badhe, Yogesh |
collection | PubMed |
description | The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people across the globe and created not only a health emergency but also a financial crisis. This virus attacks the angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membrane. The spike protein of the virus binds to this receptor which is a critical step in infection. A molecule which can specifically stop this binding could be a potential therapeutic agent. In this study, we have tested 12 potential peptides which can bind to the receptor binding domain (RBD) of the spike protein of the virus and thus can potentially inhibit the binding of the latter on ACE2 receptors. These peptides are screened based on their binding with the RBD of the spike protein and aqueous stability, obtained using several atomistic molecular dynamic simulations. The potential of mean force calculation of peptides confirmed their binding to the RBD of the spike protein. Furthermore, two potential peptides were tested for use in a biosensing application for SARS-CoV-2 detection. Two types of biosensing platforms, a graphene sheet and a carbon nano tube (CNT) were tested. The peptides were modified in order to functionalize the graphene and CNT. Based on the interaction between the substrate, peptide and spike protein, the utility of the screened peptide for a given bio sensing platform is discussed and recommended. |
format | Online Article Text |
id | pubmed-8694220 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
spelling | pubmed-86942202022-04-13 In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection Badhe, Yogesh Gupta, Rakesh Rai, Beena RSC Adv Chemistry The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people across the globe and created not only a health emergency but also a financial crisis. This virus attacks the angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membrane. The spike protein of the virus binds to this receptor which is a critical step in infection. A molecule which can specifically stop this binding could be a potential therapeutic agent. In this study, we have tested 12 potential peptides which can bind to the receptor binding domain (RBD) of the spike protein of the virus and thus can potentially inhibit the binding of the latter on ACE2 receptors. These peptides are screened based on their binding with the RBD of the spike protein and aqueous stability, obtained using several atomistic molecular dynamic simulations. The potential of mean force calculation of peptides confirmed their binding to the RBD of the spike protein. Furthermore, two potential peptides were tested for use in a biosensing application for SARS-CoV-2 detection. Two types of biosensing platforms, a graphene sheet and a carbon nano tube (CNT) were tested. The peptides were modified in order to functionalize the graphene and CNT. Based on the interaction between the substrate, peptide and spike protein, the utility of the screened peptide for a given bio sensing platform is discussed and recommended. The Royal Society of Chemistry 2021-01-19 /pmc/articles/PMC8694220/ /pubmed/35424358 http://dx.doi.org/10.1039/d0ra09123e Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/ |
spellingShingle | Chemistry Badhe, Yogesh Gupta, Rakesh Rai, Beena In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title |
In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title_full |
In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title_fullStr |
In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title_full_unstemmed |
In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title_short |
In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection |
title_sort | in silico design of peptides with binding to the receptor binding domain (rbd) of the sars-cov-2 and their utility in bio-sensor development for sars-cov-2 detection |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8694220/ https://www.ncbi.nlm.nih.gov/pubmed/35424358 http://dx.doi.org/10.1039/d0ra09123e |
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