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

Yu Jen Chang; Uyen Nguyen Phuong Le; Jia Jun Liu; Sin Rong Li; Shao Ting Chao; Hsueh Chou Lai; Yu Feng Lin; Kai Cheng Hsu; Chih Hao Lu; Cheng Wen Lin

doi:10.1016/j.antiviral.2023.105653

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

Yu Jen Chang
, Uyen Nguyen Phuong Le
, Jia Jun Liu
, Sin Rong Li
, Shao Ting Chao
, Hsueh Chou Lai
, Yu Feng Lin
, Kai Cheng Hsu
, Chih Hao Lu
, Cheng Wen Lin

Research output: Contribution to journal › Article › peer-review

5 Citations (Scopus)

Abstract

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 (IC₅₀) 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 IC₅₀ of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC₅₀ 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.

Original language	English
Article number	105653
Journal	Antiviral Research
Volume	216
DOIs	https://doi.org/10.1016/j.antiviral.2023.105653
Publication status	Published - Aug 2023

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

cis-/trans-cleavage assay
In-silico prediction
Main protease
MERS-CoV
National cancer institute database
SARS-CoV-2

ASJC Scopus subject areas

Pharmacology
Virology

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10.1016/j.antiviral.2023.105653

Cite this

Chang, Y. J., Le, U. N. P., Liu, J. J., Li, S. R., Chao, S. T., Lai, H. C., Lin, Y. F., Hsu, K. C., Lu, C. H., & Lin, C. W. (2023). 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. Antiviral Research, 216, Article 105653. https://doi.org/10.1016/j.antiviral.2023.105653

@article{eb6eaefe5e5a46ee80a69069c14afa70,

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",

abstract = "The main protease (Mpro) of SARS-CoV-2 is essential for viral replication, which suggests that the Mpro 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 Mpro in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 Mpro 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 Mpro in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 Mpro enzymatic activity, with a half maximal inhibitory concentration (IC50) 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. Mpro-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 Mpro enzymatic activity, with an IC50 of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC50 of <3.5 μM. Thus, C1 shows potential as an effective Mpro inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 Mpro and MERS-CoV Mpro.",

keywords = "cis-/trans-cleavage assay, In-silico prediction, Main protease, MERS-CoV, National cancer institute database, SARS-CoV-2",

author = "Chang, \{Yu Jen\} and Le, \{Uyen Nguyen Phuong\} and Liu, \{Jia Jun\} and Li, \{Sin Rong\} and Chao, \{Shao Ting\} and Lai, \{Hsueh Chou\} and Lin, \{Yu Feng\} and Hsu, \{Kai Cheng\} and Lu, \{Chih Hao\} and Lin, \{Cheng Wen\}",

note = "Funding Information: The study research was supported by Taiwan{\textquoteright}s National Science and Technology Council ( MOST110-2923-B-039-001-MY3 , and MOST111-2923-B-039-001-MY3 ), and by China Medical University ( CMU111-S-1 8) and China Medical University Hospital ( DMR-112-115 , and DMR-112-149 ). The study was also supported by the Drug Development Center, China Medical University , from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education , Taiwan. The experiments and data analysis were performed in the Department of Medical Laboratory Science and Biotechnology, China Medical University, and also in the Medical Research Core Facilities Center, Office of Research \& Development, China Medical University, Taichung, Taiwan. We thank Iona J. MacDonald from China Medical University (Taichung, Taiwan) for her editing of this manuscript. Funding Information: The study research was supported by Taiwan's National Science and Technology Council (MOST110-2923-B-039-001-MY3, and MOST111-2923-B-039-001-MY3), and by China Medical University (CMU111-S-18) and China Medical University Hospital (DMR-112-115, and DMR-112-149). The study was also supported by the Drug Development Center, China Medical University, from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education, Taiwan. The experiments and data analysis were performed in the Department of Medical Laboratory Science and Biotechnology, China Medical University, and also in the Medical Research Core Facilities Center, Office of Research \& Development, China Medical University, Taichung, Taiwan. We thank Iona J. MacDonald from China Medical University (Taichung, Taiwan) for her editing of this manuscript. Publisher Copyright: {\textcopyright} 2023 Elsevier B.V.",

year = "2023",

month = aug,

doi = "10.1016/j.antiviral.2023.105653",

language = "English",

volume = "216",

journal = "Antiviral Research",

issn = "0166-3542",

publisher = "Elsevier B.V.",

}

TY - JOUR

T1 - 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

AU - Chang, Yu Jen

AU - Le, Uyen Nguyen Phuong

AU - Liu, Jia Jun

AU - Li, Sin Rong

AU - Chao, Shao Ting

AU - Lai, Hsueh Chou

AU - Lin, Yu Feng

AU - Hsu, Kai Cheng

AU - Lu, Chih Hao

AU - Lin, Cheng Wen

N1 - Funding Information: The study research was supported by Taiwan’s National Science and Technology Council ( MOST110-2923-B-039-001-MY3 , and MOST111-2923-B-039-001-MY3 ), and by China Medical University ( CMU111-S-1 8) and China Medical University Hospital ( DMR-112-115 , and DMR-112-149 ). The study was also supported by the Drug Development Center, China Medical University , from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education , Taiwan. The experiments and data analysis were performed in the Department of Medical Laboratory Science and Biotechnology, China Medical University, and also in the Medical Research Core Facilities Center, Office of Research & Development, China Medical University, Taichung, Taiwan. We thank Iona J. MacDonald from China Medical University (Taichung, Taiwan) for her editing of this manuscript. Funding Information: The study research was supported by Taiwan's National Science and Technology Council (MOST110-2923-B-039-001-MY3, and MOST111-2923-B-039-001-MY3), and by China Medical University (CMU111-S-18) and China Medical University Hospital (DMR-112-115, and DMR-112-149). The study was also supported by the Drug Development Center, China Medical University, from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education, Taiwan. The experiments and data analysis were performed in the Department of Medical Laboratory Science and Biotechnology, China Medical University, and also in the Medical Research Core Facilities Center, Office of Research & Development, China Medical University, Taichung, Taiwan. We thank Iona J. MacDonald from China Medical University (Taichung, Taiwan) for her editing of this manuscript. Publisher Copyright: © 2023 Elsevier B.V.

PY - 2023/8

Y1 - 2023/8

N2 - The main protease (Mpro) of SARS-CoV-2 is essential for viral replication, which suggests that the Mpro 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 Mpro in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 Mpro 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 Mpro in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 Mpro enzymatic activity, with a half maximal inhibitory concentration (IC50) 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. Mpro-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 Mpro enzymatic activity, with an IC50 of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC50 of <3.5 μM. Thus, C1 shows potential as an effective Mpro inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 Mpro and MERS-CoV Mpro.

AB - The main protease (Mpro) of SARS-CoV-2 is essential for viral replication, which suggests that the Mpro 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 Mpro in compounds from the United States National Cancer Institute (NCI) database, then validate potential inhibitory compounds against the SARS-CoV-2 Mpro 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 Mpro in cis-/trans-cleavage assays. C1 strongly inhibited SARS-CoV-2 Mpro enzymatic activity, with a half maximal inhibitory concentration (IC50) 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. Mpro-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 Mpro enzymatic activity, with an IC50 of 3.05 μM and a SI of >65.57. Compounds C1 and D2 also displayed inhibitory activity against MERS-CoV-2 with an IC50 of <3.5 μM. Thus, C1 shows potential as an effective Mpro inhibitor of SARS-CoV-2 and MERS-CoV. Our rigorous study framework efficiently identified lead compounds targeting the SARS-CoV-2 Mpro and MERS-CoV Mpro.

KW - cis-/trans-cleavage assay

KW - In-silico prediction

KW - Main protease

KW - MERS-CoV

KW - National cancer institute database

KW - SARS-CoV-2

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DO - 10.1016/j.antiviral.2023.105653

M3 - Article

C2 - 37321487

AN - SCOPUS:85161962425

SN - 0166-3542

VL - 216

JO - Antiviral Research

JF - Antiviral Research

M1 - 105653

ER -

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

Abstract

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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