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Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV
The main protease (M(pro)) of SARS-CoV-2 is essential for viral replication, which suggests that the M(pro) is a critical target in the development of small molecules to treat COVID-19. This study used an in-silico prediction approach to investigate the complex structure of SARS-CoV-2 M(pro) in comp...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier B.V.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10264167/ https://www.ncbi.nlm.nih.gov/pubmed/37321487 http://dx.doi.org/10.1016/j.antiviral.2023.105653 |
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author | Chang, Yu-Jen Le, Uyen Nguyen Phuong Liu, Jia-Jun Li, Sin-Rong Chao, Shao-Ting Lai, Hsueh-Chou Lin, Yu-Feng Hsu, Kai-Cheng Lu, Chih-Hao Lin, Cheng-Wen |
author_facet | Chang, Yu-Jen Le, Uyen Nguyen Phuong Liu, Jia-Jun Li, Sin-Rong Chao, Shao-Ting Lai, Hsueh-Chou Lin, Yu-Feng Hsu, Kai-Cheng Lu, Chih-Hao Lin, Cheng-Wen |
author_sort | Chang, Yu-Jen |
collection | PubMed |
description | The main protease (M(pro)) of SARS-CoV-2 is essential for viral replication, which suggests that the M(pro) is a critical target in the development of small molecules to treat COVID-19. This study used an in-silico prediction approach to investigate the complex structure of SARS-CoV-2 M(pro) in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 M(pro) in cis- and trans-cleavage proteolytic assays. Virtual screening of ∼280,000 compounds from the NCI database identified 10 compounds with highest site-moiety map scores. Compound NSC89640 (coded C1) showed marked inhibitory activity against the SARS-CoV-2 M(pro) in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 M(pro) enzymatic activity, with a half maximal inhibitory concentration (IC(50)) of 2.69 μM and a selectivity index (SI) of >74.35. The C1 structure served as a template to identify structural analogs based on AtomPair fingerprints to refine and verify structure-function associations. M(pro)-mediated cis-/trans-cleavage assays conducted with the structural analogs revealed that compound NSC89641 (coded D2) exhibited the highest inhibitory potency against SARS-CoV-2 M(pro) enzymatic activity, with an IC(50) of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC(50) of <3.5 μM. Thus, C1 shows potential as an effective M(pro) inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 M(pro) and MERS-CoV M(pro). |
format | Online Article Text |
id | pubmed-10264167 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-102641672023-06-14 Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV Chang, Yu-Jen Le, Uyen Nguyen Phuong Liu, Jia-Jun Li, Sin-Rong Chao, Shao-Ting Lai, Hsueh-Chou Lin, Yu-Feng Hsu, Kai-Cheng Lu, Chih-Hao Lin, Cheng-Wen Antiviral Res Article The main protease (M(pro)) of SARS-CoV-2 is essential for viral replication, which suggests that the M(pro) is a critical target in the development of small molecules to treat COVID-19. This study used an in-silico prediction approach to investigate the complex structure of SARS-CoV-2 M(pro) in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 M(pro) in cis- and trans-cleavage proteolytic assays. Virtual screening of ∼280,000 compounds from the NCI database identified 10 compounds with highest site-moiety map scores. Compound NSC89640 (coded C1) showed marked inhibitory activity against the SARS-CoV-2 M(pro) in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 M(pro) enzymatic activity, with a half maximal inhibitory concentration (IC(50)) of 2.69 μM and a selectivity index (SI) of >74.35. The C1 structure served as a template to identify structural analogs based on AtomPair fingerprints to refine and verify structure-function associations. M(pro)-mediated cis-/trans-cleavage assays conducted with the structural analogs revealed that compound NSC89641 (coded D2) exhibited the highest inhibitory potency against SARS-CoV-2 M(pro) enzymatic activity, with an IC(50) of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC(50) of <3.5 μM. Thus, C1 shows potential as an effective M(pro) inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 M(pro) and MERS-CoV M(pro). Elsevier B.V. 2023-08 2023-06-14 /pmc/articles/PMC10264167/ /pubmed/37321487 http://dx.doi.org/10.1016/j.antiviral.2023.105653 Text en © 2023 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 Chang, Yu-Jen Le, Uyen Nguyen Phuong Liu, Jia-Jun Li, Sin-Rong Chao, Shao-Ting Lai, Hsueh-Chou Lin, Yu-Feng Hsu, Kai-Cheng Lu, Chih-Hao Lin, Cheng-Wen Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title | Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title_full | Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title_fullStr | Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title_full_unstemmed | Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title_short | Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV |
title_sort | combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of sars-cov-2 and mers-cov |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10264167/ https://www.ncbi.nlm.nih.gov/pubmed/37321487 http://dx.doi.org/10.1016/j.antiviral.2023.105653 |
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