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Chang YJ, Le UNP, Liu JJ, Li SR, Chao ST, Lai HC, Lin YF, Hsu KC, Lu CH, Lin CW. 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 Res 2023:105653. [PMID: 37321487 PMCID: PMC10264167 DOI: 10.1016/j.antiviral.2023.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/23/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
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.
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Affiliation(s)
- Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan
| | - Uyen Nguyen Phuong Le
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Graduate Institute of Biological Sciences and Technology, China Medical University, Taichung, Taiwan
| | - Jia-Jun Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Sin-Rong Li
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Ting Chao
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Hsueh-Chou Lai
- Division of Hepato-Gastroenterology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Feng Lin
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
| | - Cheng-Wen Lin
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Graduate Institute of Biological Sciences and Technology, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
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