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A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing

The alarming pandemic situation of Coronavirus infectious disease COVID-19, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a critical threat to public health. The unexpected outbreak and unrealistic progression of COVID-19 have generated an utmost need to real...

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Detalles Bibliográficos
Autores principales: K., Deepthi, A.S., Jereesh, Liu, Yuansheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8492370/
https://www.ncbi.nlm.nih.gov/pubmed/34630000
http://dx.doi.org/10.1016/j.asoc.2021.107945
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author K., Deepthi
A.S., Jereesh
Liu, Yuansheng
author_facet K., Deepthi
A.S., Jereesh
Liu, Yuansheng
author_sort K., Deepthi
collection PubMed
description The alarming pandemic situation of Coronavirus infectious disease COVID-19, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a critical threat to public health. The unexpected outbreak and unrealistic progression of COVID-19 have generated an utmost need to realize promising therapeutic strategies to fight the pandemic. Drug repurposing-an efficient drug discovery technique from approved drugs is an emerging tactic to face the immediate global challenge. It​ offers a time-efficient and cost-effective way to find potential therapeutic agents for the disease. Artificial Intelligence-empowered deep learning models enable the rapid identification of potentially repurposable drug candidates against diseases. This study presents a deep learning ensemble model to prioritize clinically validated anti-viral drugs for their potential efficacy against SARS-CoV-2. The method integrates the similarities of drug chemical structures and virus genome sequences to generate feature vectors. The best combination of features is retrieved by the convolutional neural network in a deep learning manner. The extracted deep features are classified by the extreme gradient boosting classifier to infer potential virus–drug associations. The method could achieve an AUC of 0.8897 with 0.8571 prediction accuracy and 0.8394 sensitivity under the fivefold cross-validation. The experimental results and case studies demonstrate the suggested deep learning ensemble system yields competitive results compared with the state-of-the-art approaches. The top-ranked drugs are released for further wet-lab researches.
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spelling pubmed-84923702021-10-06 A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing K., Deepthi A.S., Jereesh Liu, Yuansheng Appl Soft Comput Article The alarming pandemic situation of Coronavirus infectious disease COVID-19, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has become a critical threat to public health. The unexpected outbreak and unrealistic progression of COVID-19 have generated an utmost need to realize promising therapeutic strategies to fight the pandemic. Drug repurposing-an efficient drug discovery technique from approved drugs is an emerging tactic to face the immediate global challenge. It​ offers a time-efficient and cost-effective way to find potential therapeutic agents for the disease. Artificial Intelligence-empowered deep learning models enable the rapid identification of potentially repurposable drug candidates against diseases. This study presents a deep learning ensemble model to prioritize clinically validated anti-viral drugs for their potential efficacy against SARS-CoV-2. The method integrates the similarities of drug chemical structures and virus genome sequences to generate feature vectors. The best combination of features is retrieved by the convolutional neural network in a deep learning manner. The extracted deep features are classified by the extreme gradient boosting classifier to infer potential virus–drug associations. The method could achieve an AUC of 0.8897 with 0.8571 prediction accuracy and 0.8394 sensitivity under the fivefold cross-validation. The experimental results and case studies demonstrate the suggested deep learning ensemble system yields competitive results compared with the state-of-the-art approaches. The top-ranked drugs are released for further wet-lab researches. Elsevier B.V. 2021-12 2021-10-06 /pmc/articles/PMC8492370/ /pubmed/34630000 http://dx.doi.org/10.1016/j.asoc.2021.107945 Text en © 2021 Elsevier B.V. All rights reserved. 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
K., Deepthi
A.S., Jereesh
Liu, Yuansheng
A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title_full A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title_fullStr A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title_full_unstemmed A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title_short A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing
title_sort deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus sars-cov-2 for covid-19 drug repurposing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8492370/
https://www.ncbi.nlm.nih.gov/pubmed/34630000
http://dx.doi.org/10.1016/j.asoc.2021.107945
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