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Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targ...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10597523/ https://www.ncbi.nlm.nih.gov/pubmed/37874836 http://dx.doi.org/10.1371/journal.pone.0293263 |
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author | Longsompurana, Phoomintara Rungrotmongkol, Thanyada Plongthongkum, Nongluk Wangkanont, Kittikhun Wolschann, Peter Poo-arporn, Rungtiva P. |
author_facet | Longsompurana, Phoomintara Rungrotmongkol, Thanyada Plongthongkum, Nongluk Wangkanont, Kittikhun Wolschann, Peter Poo-arporn, Rungtiva P. |
author_sort | Longsompurana, Phoomintara |
collection | PubMed |
description | The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2. |
format | Online Article Text |
id | pubmed-10597523 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-105975232023-10-25 Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 Longsompurana, Phoomintara Rungrotmongkol, Thanyada Plongthongkum, Nongluk Wangkanont, Kittikhun Wolschann, Peter Poo-arporn, Rungtiva P. PLoS One Research Article The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of numerous variants of concern (VOCs) has made it challenging to develop targeted therapies that are broadly specific in neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs) using computational techniques that can effectively neutralize the receptor-binding domain (RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein docking programs and identified HDOCK as the most suitable program for Nb/RBD docking with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with key amino acids of the RBDs, resulting in higher binding affinity than human angiotensin-converting enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful development of these Nbs demonstrates the potential of molecular modeling as a low-cost and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2. Public Library of Science 2023-10-24 /pmc/articles/PMC10597523/ /pubmed/37874836 http://dx.doi.org/10.1371/journal.pone.0293263 Text en © 2023 Longsompurana et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Longsompurana, Phoomintara Rungrotmongkol, Thanyada Plongthongkum, Nongluk Wangkanont, Kittikhun Wolschann, Peter Poo-arporn, Rungtiva P. Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title_full | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title_fullStr | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title_full_unstemmed | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title_short | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 |
title_sort | computational design of novel nanobodies targeting the receptor binding domain of variants of concern of sars-cov-2 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10597523/ https://www.ncbi.nlm.nih.gov/pubmed/37874836 http://dx.doi.org/10.1371/journal.pone.0293263 |
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