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Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang KO. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr 2024; 12:e0337223. [PMID: 38466127 PMCID: PMC10986521 DOI: 10.1128/spectrum.03372-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/18/2024] [Indexed: 03/12/2024] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family Picornaviridae and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway.IMPORTANCEFood-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Emma Pool
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Eunji Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - David K. Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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2
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Chen X, Huang X, Ma Q, Kuzmič P, Zhou B, Zhang S, Chen J, Xu J, Liu B, Jiang H, Zhang W, Yang C, Wu S, Huang J, Li H, Long C, Zhao X, Xu H, Sheng Y, Guo Y, Niu C, Xue L, Xu Y, Liu J, Zhang T, Spencer J, Zhu Z, Deng W, Chen X, Chen SH, Zhong N, Xiong X, Yang Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol 2024; 9:1075-1088. [PMID: 38553607 PMCID: PMC10994847 DOI: 10.1038/s41564-024-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 01/22/2024] [Indexed: 04/06/2024]
Abstract
Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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Affiliation(s)
- Xiaoxin Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xiaodong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Biao Zhou
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Sai Zhang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjie Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunguang Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiguan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Haijun Li
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Chaofeng Long
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China
| | - Hongrui Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanan Sheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaoting Guo
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
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3
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Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CTK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med 2024; 16:eadi0979. [PMID: 38478629 DOI: 10.1126/scitranslmed.adi0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/21/2024] [Indexed: 05/09/2024]
Abstract
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
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Affiliation(s)
- Michael Westberg
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Yichi Su
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Pinghan Huang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jaishree Garhyan
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University, Stanford, CA 94305, USA
| | - Puja Bhavesh Patel
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University, Stanford, CA 94305, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA 94305, USA
| | - Yan Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Chenzhou Hao
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Chieh-Wen Lo
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marwah Karim
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Vivian Tat
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shirit Einav
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Catherine Blish
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
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4
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Dayan Elshan NGR, Wolff KC, Riva L, Woods AK, Grabovyi G, Wilson K, Pedroarena J, Ghorai S, Nazarian A, Weiss F, Liu Y, Mazumdar W, Song L, Okwor N, Malvin J, Bakowski MA, Beutler N, Kirkpatrick MG, Gebara-Lamb A, Huang E, Nguyen-Tran VTB, Chi V, Li S, Rogers TF, McNamara CW, Gupta AK, Rahimi A, Chen JJ, Joseph SB, Schultz PG, Chatterjee AK. Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Warhead. J Med Chem 2024; 67:2369-2378. [PMID: 38335279 PMCID: PMC10895651 DOI: 10.1021/acs.jmedchem.3c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by an increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof toward human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLpro inhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = Paxlovid), CMX990 has distinctly differentiated potency (∼5× more potent in primary cells) and human in vitro clearance (>4× better microsomal clearance and >10× better hepatocyte clearance), with good in vitro-to-in vivo correlation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.
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Affiliation(s)
- N G R Dayan Elshan
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Karen C Wolff
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laura Riva
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley K Woods
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gennadii Grabovyi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Katy Wilson
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Pedroarena
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sourav Ghorai
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Armen Nazarian
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Frank Weiss
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuyin Liu
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Wrickban Mazumdar
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lirui Song
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Neechi Okwor
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jacqueline Malvin
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Malina A Bakowski
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Melanie G Kirkpatrick
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amal Gebara-Lamb
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Edward Huang
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vân T B Nguyen-Tran
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Victor Chi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shuangwei Li
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Case W McNamara
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anil Kumar Gupta
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alireza Rahimi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jian Jeffrey Chen
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean B Joseph
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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5
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Barton LS, Callahan JF, Cantizani J, Concha NO, Cotillo Torrejon I, Goodwin NC, Joshi-Pangu A, Kiesow TJ, McAtee JJ, Mellinger M, Nixon CJ, Padrón-Barthe L, Patterson JR, Pearson ND, Pouliot JJ, Rendina AR, Buitrago Santanilla A, Schneck JL, Sanz O, Thalji RK, Ward P, Williams SP, King BW. Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement. Bioorg Med Chem 2024; 100:117618. [PMID: 38309201 DOI: 10.1016/j.bmc.2024.117618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The virally encoded 3C-like protease (3CLpro) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CLpro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CLpro in SARS-CoV-2 virus is described herein.
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Affiliation(s)
- Linda S Barton
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States.
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Juan Cantizani
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Nestor O Concha
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Nicole C Goodwin
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Amruta Joshi-Pangu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Terry J Kiesow
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeff J McAtee
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Mark Mellinger
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Christopher J Nixon
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jaclyn R Patterson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Neil D Pearson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeffrey J Pouliot
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Alan R Rendina
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jessica L Schneck
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Olalla Sanz
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Reema K Thalji
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Paris Ward
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Shawn P Williams
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Bryan W King
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
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6
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Gutti G, He Y, Coldren WH, Lalisse RF, Border SE, Hadad CM, McElroy CA, Ekici ÖD. In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19. J Biomol Struct Dyn 2024; 42:1733-1750. [PMID: 37114441 DOI: 10.1080/07391102.2023.2202247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and β-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopichand Gutti
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yiran He
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - William H Coldren
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah E Border
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Özlem Doğan Ekici
- Department of Chemistry and Biochemistry, The Ohio State University, Newark, Ohio, USA
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7
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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8
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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9
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Dobrikov MI, Dobrikova EY, Nardone-White DT, McKay ZP, Brown MC, Gromeier M. Early enterovirus translation deficits extend viral RNA replication and elicit sustained MDA5-directed innate signaling. mBio 2023; 14:e0191523. [PMID: 37962360 PMCID: PMC10746184 DOI: 10.1128/mbio.01915-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/02/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Multiple pattern recognition receptors sense vRNAs and initiate downstream innate signaling: endosomal Toll-like receptors (TLRs) 3, 7, and 8 and cytoplasmic RIG-I-like receptors (RLRs) RIG-I, and MDA5. They engage distinct signaling scaffolds: mitochondrial antiviral signaling protein (RLR), MyD88, and TLR-adaptor interacting with SLC15A4 on the lysosome (TLR7 and TLR8) and toll/IL-1R domain-containing adaptor inducing IFN (TLR3). By virtue of their unusual vRNA structure and direct host cell entry path, the innate response to EVs uniquely is orchestrated by MDA5. We reported that PVSRIPO's profound attenuation and loss of cytopathogenicity triggers MDA5-directed polar TBK1-IRF3 signaling that generates priming of polyfunctional antitumor CD8+ T-cell responses and durable antitumor surveillance in vivo. Here we unraveled EV-host relations that control suppression of host type-I IFN responses and show that PVSRIPO's deficient immediate host eIF4G cleavage generates unopposed MDA5-directed downstream signaling cascades resulting in sustained type-I IFN release.
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Affiliation(s)
- Mikhail I. Dobrikov
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Elena Y. Dobrikova
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Dasean T. Nardone-White
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical School, Durham, North Carolina, USA
| | - Zachary P. McKay
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Michael C. Brown
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
| | - Matthias Gromeier
- Department of Neurosurgery, Duke University Medical School, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical School, Durham, North Carolina, USA
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10
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Ngo C, Fried W, Aliyari S, Feng J, Qin C, Zhang S, Yang H, Shanaa J, Feng P, Cheng G, Chen XS, Zhang C. Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease. J Med Chem 2023; 66:12237-12248. [PMID: 37595260 PMCID: PMC10510381 DOI: 10.1021/acs.jmedchem.3c00810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/20/2023]
Abstract
There is an urgent need for improved therapy to better control the ongoing COVID-19 pandemic. The main protease Mpro plays a pivotal role in SARS-CoV-2 replications, thereby representing an attractive target for antiviral development. We seek to identify novel electrophilic warheads for efficient, covalent inhibition of Mpro. By comparing the efficacy of a panel of warheads installed on a common scaffold against Mpro, we discovered that the terminal alkyne could covalently modify Mpro as a latent warhead. Our biochemical and X-ray structural analyses revealed the irreversible formation of the vinyl-sulfide linkage between the alkyne and the catalytic cysteine of Mpro. Clickable probes based on the alkyne inhibitors were developed to measure target engagement, drug residence time, and off-target effects. The best alkyne-containing inhibitors potently inhibited SARS-CoV-2 infection in cell infection models. Our findings highlight great potentials of alkyne as a latent warhead to target cystine proteases in viruses and beyond.
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Affiliation(s)
- Chau Ngo
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - William Fried
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Saba Aliyari
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joshua Feng
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Qin
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shilei Zhang
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Hanjing Yang
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Jean Shanaa
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Pinghui Feng
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Genhong Cheng
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Xiaojiang S. Chen
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
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11
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Stubbing LA, Hubert JG, Bell-Tyrer J, Hermant YO, Yang SH, McSweeney AM, McKenzie-Goldsmith GM, Ward VK, Furkert DP, Brimble MA. P 1 Glutamine isosteres in the design of inhibitors of 3C/3CL protease of human viruses of the Pisoniviricetes class. RSC Chem Biol 2023; 4:533-547. [PMID: 37547456 PMCID: PMC10398354 DOI: 10.1039/d3cb00075c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Viral infections are one of the leading causes of acute morbidity in humans and much endeavour has been made by the synthetic community for the development of drugs to treat associated diseases. Peptide-based enzyme inhibitors, usually short sequences of three or four residues, are one of the classes of compounds currently under development for enhancement of their activity and pharmaceutical properties. This review reports the advances made in the design of inhibitors targeting the family of highly conserved viral proteases 3C/3CLpro, which play a key role in viral replication and present minimal homology with mammalian proteases. Particular focus is put on the reported development of P1 glutamine isosteres to generate potent inhibitors mimicking the natural substrate sequence at the site of recognition.'
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Affiliation(s)
- Louise A Stubbing
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Jonathan G Hubert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Joseph Bell-Tyrer
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Yann O Hermant
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Sung Hyun Yang
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Alice M McSweeney
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Geena M McKenzie-Goldsmith
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Vernon K Ward
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
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12
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Miura T, Malla TR, Owen CD, Tumber A, Brewitz L, McDonough MA, Salah E, Terasaka N, Katoh T, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Kawamura A, Schofield CJ, Suga H. In vitro selection of macrocyclic peptide inhibitors containing cyclic γ 2,4-amino acids targeting the SARS-CoV-2 main protease. Nat Chem 2023:10.1038/s41557-023-01205-1. [PMID: 37217786 DOI: 10.1038/s41557-023-01205-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1' catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.
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Affiliation(s)
- Takashi Miura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tika R Malla
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - C David Owen
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Lennart Brewitz
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Michael A McDonough
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Petra Lukacik
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Halina Mikolajek
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, UK
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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13
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Masmoudi F, Santos-Ferreira N, Pajkrt D, Wolthers KC, DeGroot J, Vlaming MLH, Rocha-Pereira J, Buti L. Evaluation of 3D Human Intestinal Organoids as a Platform for EV-A71 Antiviral Drug Discovery. Cells 2023; 12:cells12081138. [PMID: 37190047 DOI: 10.3390/cells12081138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/24/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Enteroviruses are a leading cause of upper respiratory tract, gastrointestinal, and neurological infections. Management of enterovirus-related diseases has been hindered by the lack of specific antiviral treatment. The pre-clinical and clinical development of such antivirals has been challenging, calling for novel model systems and strategies to identify suitable pre-clinical candidates. Organoids represent a new and outstanding opportunity to test antiviral agents in a more physiologically relevant system. However, dedicated studies addressing the validation and direct comparison of organoids versus commonly used cell lines are lacking. Here, we described the use of human small intestinal organoids (HIOs) as a model to study antiviral treatment against human enterovirus 71 (EV-A71) infection and compared this model to EV-A71-infected RD cells. We used reference antiviral compounds such as enviroxime, rupintrivir, and 2'-C-methylcytidine (2'CMC) to assess their effects on cell viability, virus-induced cytopathic effect, and viral RNA yield in EV-A71-infected HIOs and cell line. The results indicated a difference in the activity of the tested compounds between the two models, with HIOs being more sensitive to infection and drug treatment. In conclusion, the outcome reveals the value added by using the organoid model in virus and antiviral studies.
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Affiliation(s)
- Fatma Masmoudi
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC Location Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Nanci Santos-Ferreira
- Laboratory of Virology and Chemotherapy, KU Leuven-Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Dasja Pajkrt
- OrganoVIR Labs, Pediatric Infectious Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Katja C Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC Location Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Jeroen DeGroot
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
| | | | - Joana Rocha-Pereira
- Laboratory of Virology and Chemotherapy, KU Leuven-Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Ludovico Buti
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
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14
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Bulut H. Drug development targeting SARS-CoV-2 main protease. Glob Health Med 2022; 4:296-300. [PMID: 36589216 PMCID: PMC9773221 DOI: 10.35772/ghm.2022.01066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic with more than 6.5 million deaths since 2019. Although a number of vaccines significantly reduced the mortality rate, a large number of the world population is yet being infected with highly contagious omicron variants/subvarints. Additional therapeutic interventions are needed to reduce hospitalization and curb the ongoing pandemic. The activity of the SARS-CoV-2 enzyme; chymotrypsin-like main protease (Mpro) is essential for the cleavage of viral nonstructural polypeptides into individual functional proteins and therefore Mpro is an attractive drug target. The aim of this review is to summarize recent progress toward the development of therapeutic drugs against Mpro protease.
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Affiliation(s)
- Haydar Bulut
- Address correspondence to:Haydar Bulut, The Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. E-mail:
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15
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Bram Y, Duan X, Nilsson-Payant BE, Chandar V, Wu H, Shore D, Fajardo A, Sinha S, Hassan N, Weinstein H, TenOever BR, Chen S, Schwartz RE. Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path. ACS BIO & MED CHEM AU 2022; 2:627-641. [PMID: 36570071 PMCID: PMC9603010 DOI: 10.1021/acsbiomedchemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
The SARS-CoV-2 pandemic is an ongoing threat to global health, and the continuing emergence of contagious variants highlights the urgent need for additional antiviral therapy to attenuate COVID-19 disease. The SARS-CoV-2 main protease (3CLpro) presents an attractive target for such therapy due to its high sequence conservation and key role in the viral life cycle. In this study, we designed a fluorescent-luminescent cell-based reporter for the detection and quantification of 3CLpro intracellular activity. Employing this platform, we examined the efficiency of known protease inhibitors against 3CLpro and further identified potent inhibitors through high-throughput chemical screening. Computational analysis confirmed a direct interaction of the lead compounds with the protease catalytic site and identified a prototype for efficient allosteric inhibition. These developments address a pressing need for a convenient sensor and specific targets for both virus detection and rapid discovery of potential inhibitors.
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Affiliation(s)
- Yaron Bram
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Xiaohua Duan
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Benjamin E. Nilsson-Payant
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States
| | - Vasuretha Chandar
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Hao Wu
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Derek Shore
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Alvaro Fajardo
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Saloni Sinha
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Nora Hassan
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Benjamin R. TenOever
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States,
| | - Shuibing Chen
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Robert E. Schwartz
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
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16
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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17
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Sun J, Wen M, Wang H, Ruan Y, Yang Q, Kang X, Zhang H, Zhang Z, Lu H. Prediction of drug-likeness using graph convolutional attention network. Bioinformatics 2022; 38:5262-5269. [PMID: 36222555 DOI: 10.1093/bioinformatics/btac676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/22/2022] [Accepted: 10/08/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The drug-likeness has been widely used as a criterion to distinguish drug-like molecules from non-drugs. Developing reliable computational methods to predict the drug-likeness of compounds is crucial to triage unpromising molecules and accelerate the drug discovery process. RESULTS In this study, a deep learning method was developed to predict the drug-likeness based on the graph convolutional attention network (D-GCAN) directly from molecular structures. Results showed that the D-GCAN model outperformed other state-of-the-art models for drug-likeness prediction. The combination of graph convolution and attention mechanism made an important contribution to the performance of the model. Specifically, the application of the attention mechanism improved accuracy by 4.0%. The utilization of graph convolution improved the accuracy by 6.1%. Results on the dataset beyond Lipinski's rule of five space and the non-US dataset showed that the model had good versatility. Then, the billion-scale GDB-13 database was used as a case study to screen SARS-CoV-2 3C-like protease inhibitors. Sixty-five drug candidates were screened out, most substructures of which are similar to these of existing oral drugs. Candidates screened from S-GDB13 have higher similarity to existing drugs and better molecular docking performance than those from the rest of GDB-13. The screening speed on S-GDB13 is significantly faster than screening directly on GDB-13. In general, D-GCAN is a promising tool to predict the drug-likeness for selecting potential candidates and accelerating drug discovery by excluding unpromising candidates and avoiding unnecessary biological and clinical testing. AVAILABILITY AND IMPLEMENTATION The source code, model and tutorials are available at https://github.com/JinYSun/D-GCAN. The S-GDB13 database is available at https://doi.org/10.5281/zenodo.7054367. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinyu Sun
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Ming Wen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Huabei Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yuezhe Ruan
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Qiong Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Xiao Kang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Hailiang Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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Tsuji K, Ishii T, Kobayakawa T, Higashi-Kuwata N, Azuma C, Nakayama M, Onishi T, Nakano H, Wada N, Hori M, Shinohara K, Miura Y, Kawada T, Hayashi H, Hattori SI, Bulut H, Das D, Takamune N, Kishimoto N, Saruwatari J, Okamura T, Nakano K, Misumi S, Mitsuya H, Tamamura H. Potent and biostable inhibitors of the main protease of SARS-CoV-2. iScience 2022; 25:105365. [PMID: 36338434 PMCID: PMC9623849 DOI: 10.1016/j.isci.2022.105365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Potent and biostable inhibitors of the main protease (Mpro) of SARS-CoV-2 were designed and synthesized based on an active hit compound 5h (2). Our strategy was based not only on the introduction of fluorine atoms into the inhibitor molecule for an increase of binding affinity for the pocket of Mpro and cell membrane permeability but also on the replacement of the digestible amide bond by a surrogate structure to increase the biostability of the compounds. Compound 3 is highly potent and blocks SARS-CoV-2 infection in vitro without a viral breakthrough. The derivatives, which contain a thioamide surrogate in the P2-P1 amide bond of these compounds (2 and 3), showed remarkably preferable pharmacokinetics in mice compared with the corresponding parent compounds. These data show that compounds 3 and its biostable derivative 4 are potential drugs for treating COVID-19 and that replacement of the digestible amide bond by its thioamide surrogate structure is an effective method.
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Affiliation(s)
- Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Chika Azuma
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miyuki Nakayama
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takato Onishi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroki Nakano
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Naoya Wada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miki Hori
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kouki Shinohara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yutaro Miura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuma Kawada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hironori Hayashi
- Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Shin-ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Junji Saruwatari
- Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kenta Nakano
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
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Nadkarni R, Chu WC, Lee CQE, Mohamud Y, Yap L, Toh GA, Beh S, Lim R, Fan YM, Zhang YL, Robinson K, Tryggvason K, Luo H, Zhong F, Ho L. Viral proteases activate the CARD8 inflammasome in the human cardiovascular system. J Exp Med 2022; 219:213484. [PMID: 36129453 PMCID: PMC9499823 DOI: 10.1084/jem.20212117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/18/2022] [Accepted: 08/08/2022] [Indexed: 01/10/2023] Open
Abstract
Nucleotide-binding oligomerization domain (NBD), leucine-rich repeat (LRR) containing protein family (NLRs) are intracellular pattern recognition receptors that mediate innate immunity against infections. The endothelium is the first line of defense against blood-borne pathogens, but it is unclear which NLRs control endothelial cell (EC) intrinsic immunity. Here, we demonstrate that human ECs simultaneously activate NLRP1 and CARD8 inflammasomes in response to DPP8/9 inhibitor Val-boro-Pro (VbP). Enterovirus Coxsackie virus B3 (CVB3)-the most common cause of viral myocarditis-predominantly activates CARD8 in ECs in a manner that requires viral 2A and 3C protease cleavage at CARD8 p.G38 and proteasome function. Genetic deletion of CARD8 in ECs and human embryonic stem cell-derived cardiomyocytes (HCMs) attenuates CVB3-induced pyroptosis, inflammation, and viral propagation. Furthermore, using a stratified endothelial-cardiomyocyte co-culture system, we demonstrate that deleting CARD8 in ECs reduces CVB3 infection of the underlying cardiomyocytes. Our study uncovers the unique role of CARD8 inflammasome in endothelium-intrinsic anti-viral immunity.
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Affiliation(s)
- Rhea Nadkarni
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Wern Cui Chu
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Cheryl Q E Lee
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lynn Yap
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Sheryl Beh
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Radiance Lim
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Yiyun Michelle Fan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yizhuo Lyanne Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kim Robinson
- Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Karl Tryggvason
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Franklin Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
- Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Lena Ho
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
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20
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Paxlovid: Mechanism of Action, Synthesis, and In Silico Study. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7341493. [PMID: 35845944 PMCID: PMC9283023 DOI: 10.1155/2022/7341493] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 12/19/2022]
Abstract
In this work, the discovery and description of PF-07321332, a major bioavailable oral SARS-CoV-2 protease inhibitor with in vitro human coronavirus antiviral activity, and excellent selection of off-target and in vivo immune profiles are reported. Various drugs and novel compound candidates for the treatment of the COVID-19 pandemic have been developed. PF-07321332 (or nirmatrelvir) is a new oral antiviral drug developed by Pfizer. In response to the pandemic, Pfizer has developed the COVID vaccine and in 2022 will launch its new major anti-SARS-Cov-2 protease inhibitor (PI). The combination of ritonavir and nirmatrelvir is under study in phase III of the clinical trial with a brand name Paxlovid. Paxlovid is an active 3Cl protease inhibitor. Paxlovid exerts its antiviral efficacy by inhibiting a necessary protease in the viral replication procedure. Proteases of coronavirus cleave several sites in the viral polyprotein where pyrrolidone was replaced by flexible glutamine. Due to the coronavirus pandemic, there is high demand for synthesis and development of this novel drug. Herein, we report the synthetic route and the mechanism of action was recently published on nirmatrelvir. Also, a comparison of the performance of two new oral antiviruses (molnupiravir and nirmatrelvir) for the treatment of COVID-19 is described. This review will be helpful for different disciplines such as biochemistry, organic chemistry, medicinal chemistry, and pharmacology.
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21
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Yuan X, Kadowaki T. DWV 3C Protease Uncovers the Diverse Catalytic Triad in Insect RNA Viruses. Microbiol Spectr 2022; 10:e0006822. [PMID: 35575593 PMCID: PMC9241925 DOI: 10.1128/spectrum.00068-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/20/2022] Open
Abstract
Deformed wing virus (DWV) is the most prevalent Iflavirus that is infecting honey bees worldwide. However, the mechanisms of its infection and replication in host cells are poorly understood. In this study, we analyzed the structure and function of DWV 3C protease (3Cpro), which is necessary for the cleavage of the polyprotein to synthesize mature viral proteins. Thus, it is one of the nonstructural viral proteins essential for the replication. We found that the 3Cpros of DWV and picornaviruses share common enzymatic properties, including sensitivity to the same inhibitors, such as rupintrivir. The predicted structure of DWV 3Cpro by AlphaFold2, the predicted rupintrivir binding domain, and the protease activities of mutant proteins revealed that it has a Cys-His-Asn catalytic triad. Moreover, 3Cpros of other Iflaviruses and Dicistrovirus appear to contain Asn, Ser, Asp, or Glu as the third residue of the catalytic triad, suggesting diversity in insect RNA viruses. Both precursor 3Cpro with RNA-dependent RNA polymerase and mature 3Cpro are present in DWV-infected cells, suggesting that they may have different enzymatic properties and functions. DWV 3Cpro is the first 3Cpro characterized among insect RNA viruses, and our study uncovered both the common and unique characteristics among 3Cpros of Picornavirales. Furthermore, it would be possible to use the specific inhibitors of DWV 3Cpro to control DWV infection in honey bees in future. IMPORTANCE The number of managed honey bee (Apis mellifera) colonies has considerably declined in many developed countries in the recent years. Deformed wing virus (DWV) vectored by the mites is the major threat to honey bee colonies and health. To give insight into the mechanism of DWV replication in the host cells, we studied the structure-function relationship of 3C protease (3Cpro), which is necessary to cleave a viral polyprotein at the specific sites to produce the mature proteins. We found that the overall structure, some inhibitors, and processing of 3Cpro are shared between Picornavirales; however, there is diversity in the catalytic triad. DWV 3Cpro is the first viral protease characterized among insect RNA viruses and reveals the evolutionary history of 3Cpro among Picornavirales. Furthermore, DWV 3Cpro inhibitors identified in our study could also be applied to control DWV in honey bees in future.
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Affiliation(s)
- Xuye Yuan
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
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22
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Kumar Biswas B, Soo Shin J, Malpani YR, Hwang D, Jung E, Bong Han S, Vishakantegowda AG, Jung YS. Enteroviral replication inhibition by N-Alkyl triazolopyrimidinone derivatives through a non-capsid binding mode. Bioorg Med Chem Lett 2022; 64:128673. [PMID: 35292344 DOI: 10.1016/j.bmcl.2022.128673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/14/2022] [Accepted: 03/10/2022] [Indexed: 11/20/2022]
Abstract
Small-molecule inhibitors exhibiting broad-spectrum enteroviral inhibition by targeting viral replication proteins are highly desirable in antiviral drug discovery. We used the previously identified antiviral compound 1 as the starting material to develop a novel compound series with high efficacy against human rhinovirus (hRV). Further optimization of N-substituted triazolopyrimidinone derivatives revealed that the N-alkyl triazolopyrimidinone derivatives (2) had more potent antiviral activity against hRVs than compound 1. The new compounds showed improved selectivity index values, and compound 2c (KR-25210) displayed broad anti-hRV activity, with half-maximal effective concentration values ≤ 2 µM against all tested hRVs. In addition, 2c showed notable activity against other enteroviruses. Drug-likeness elucidation showed that 2c exhibited reasonable human and rat liver microsomal phase-I stability and safe CYP inhibition. Replication studies revealed that 2c is not a capsid inhibitor, and a time-of-addition assay indicated that 2c targets the virus replication stages.
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Affiliation(s)
- Bishyajit Kumar Biswas
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217 Gajeongro, Yuseong, Daejeon 34113, Republic of Korea
| | - Jin Soo Shin
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea
| | - Yashwardhan R Malpani
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217 Gajeongro, Yuseong, Daejeon 34113, Republic of Korea
| | - Dasom Hwang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea
| | - Eunhye Jung
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea
| | - Soo Bong Han
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217 Gajeongro, Yuseong, Daejeon 34113, Republic of Korea
| | - Avinash G Vishakantegowda
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217 Gajeongro, Yuseong, Daejeon 34113, Republic of Korea
| | - Young-Sik Jung
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, 141 Gajeongro, Yuseong, Daejeon 34114, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217 Gajeongro, Yuseong, Daejeon 34113, Republic of Korea.
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Malik P, Jain S, Jain P, Kumawat J, Dwivedi J, Kishore D. A comprehensive update on the structure and synthesis of potential drug targets for combating the coronavirus pandemic caused by SARS-CoV-2. Arch Pharm (Weinheim) 2022; 355:e2100382. [PMID: 35040187 PMCID: PMC9011541 DOI: 10.1002/ardp.202100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/18/2023]
Abstract
The outbreak of the coronavirus pandemic COVID-19 created by its severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) variant, known for producing a very severe acute respiratory syndrome, has created an unprecedented situation by its continual assault around the world. The crisis caused by the SARS-CoV-2 variant has been a global challenge, calling to mitigate this unprecedented pandemic that has engulfed the whole world. Since the outbreak and spread of COVID-19, many researchers globally have been grappling to find new clinically trialed active drugs with anti-COVID-19 activity, from antimalarial drugs to JAK inhibitors, antiviral drugs, immune suppressants, and so forth. This article presents a brief discussion on the activity and synthesis of some active molecules such as favipiravir, hydroxychloroquine, pirfenidone, remdesivir, lopinavir, camostat, chloroquine, baricitinib, molnupiravir, and so forth, which are under trial.
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Affiliation(s)
- Prerna Malik
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Sonika Jain
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Pankaj Jain
- Department of PharmacyBanasthali VidyapithJaipurIndia
| | - Jyoti Kumawat
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Jaya Dwivedi
- Department of ChemistryBanasthali VidyapithJaipurIndia
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24
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Structure and antiviral activity of a pectic polysaccharide from the root of Sanguisorba officinalis against enterovirus 71 in vitro/vivo. Carbohydr Polym 2022; 281:119057. [DOI: 10.1016/j.carbpol.2021.119057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/25/2021] [Indexed: 12/22/2022]
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Sripattaraphan A, Sanachai K, Chavasiri W, Boonyasuppayakorn S, Maitarad P, Rungrotmongkol T. Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061908. [PMID: 35335272 PMCID: PMC8955072 DOI: 10.3390/molecules27061908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/27/2022] [Accepted: 03/10/2022] [Indexed: 12/20/2022]
Abstract
Outbreaks of hand, foot, and mouth disease (HFMD) that occur worldwide are mainly caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71). Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir in phase II clinical trial candidate for rhinovirus showed highly potent antiviral activities against enteroviruses as an inhibitor for 3C protease (3Cpro). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 and EV-A71 3Cpro using computational tools. From their predicted binding affinities, the five compounds with functional group modifications at P1′, P2, P3, and P4 sites, namely P1′-1, P2-m3, P3-4, P4-5, and P4-19, could bind with both CV-A16 and EV-A71 3Cpro better than rupintrivir. Subsequently, these five analogs were studied by 500 ns molecular dynamics simulations. Among them, P2-m3, the derivative with meta-aminomethyl-benzyl group at the P2 site, showed the greatest potential to interact with the 3Cpro target by delivering the highest number of intermolecular hydrogen bonds and contact atoms. It formed the hydrogen bonds with L127 and K130 residues at the P2 site stronger than rupintrivir, supported by significantly lower MM/PB(GB)SA binding free energies. Elucidation of designed rupintrivir analogs in our study provides the basis for developing compounds that can be candidate compounds for further HFMD treatment.
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Affiliation(s)
- Amita Sripattaraphan
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (A.S.); (K.S.)
| | - Kamonpan Sanachai
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (A.S.); (K.S.)
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Siwaporn Boonyasuppayakorn
- Applied Medical Virology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Shanghai University, Shanghai 200444, China;
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (A.S.); (K.S.)
- Ph.D. Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: or
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26
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Dai W, Jochmans D, Xie H, Yang H, Li J, Su H, Chang D, Wang J, Peng J, Zhu L, Nian Y, Hilgenfeld R, Jiang H, Chen K, Zhang L, Xu Y, Neyts J, Liu H. Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2. J Med Chem 2022; 65:2794-2808. [PMID: 33872498 PMCID: PMC8084273 DOI: 10.1021/acs.jmedchem.0c02258] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Indexed: 12/30/2022]
Abstract
A novel series of peptidomimetic aldehydes was designed and synthesized to target 3C protease (3Cpro) of enterovirus 71 (EV71). Most of the compounds exhibited high antiviral activity, and among them, compound 18p demonstrated potent enzyme inhibitory activity and broad-spectrum antiviral activity on a panel of enteroviruses and rhinoviruses. The crystal structure of EV71 3Cpro in complex with 18p determined at a resolution of 1.2 Å revealed that 18p covalently linked to the catalytic Cys147 with an aldehyde group. In addition, these compounds also exhibited good inhibitory activity against the 3CLpro and the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially compound 18p (IC50 = 0.034 μM, EC50 = 0.29 μM). According to our previous work, these compounds have no reasons for concern regarding acute toxicity. Compared with AG7088, compound 18p also exhibited good pharmacokinetic properties and more potent anticoronavirus activity, making it an excellent lead for further development.
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Affiliation(s)
- Wenhao Dai
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hang Xie
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
| | - Hang Yang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Jian Li
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Haixia Su
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Di Chang
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Jiang Wang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Jingjing Peng
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Yong Nian
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine,
University of Lübeck, 23562 Lübeck,
Germany
- German Center for Infection Research (DZIF),
University of Lübeck, 23562 Lübeck,
Germany
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hong Liu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
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27
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Bai B, Belovodskiy A, Hena M, Kandadai AS, Joyce MA, Saffran HA, Shields JA, Khan MB, Arutyunova E, Lu J, Bajwa SK, Hockman D, Fischer C, Lamer T, Vuong W, van Belkum MJ, Gu Z, Lin F, Du Y, Xu J, Rahim M, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic α-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability. J Med Chem 2022; 65:2905-2925. [PMID: 34242027 PMCID: PMC8291138 DOI: 10.1021/acs.jmedchem.1c00616] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Indexed: 12/11/2022]
Abstract
Recurring coronavirus outbreaks, such as the current COVID-19 pandemic, establish a necessity to develop direct-acting antivirals that can be readily administered and are active against a broad spectrum of coronaviruses. Described in this Article are novel α-acyloxymethylketone warhead peptidomimetic compounds with a six-membered lactam glutamine mimic in P1. Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. Compounds 15e, 15h, and 15l displayed selectivity for SARS-CoV-2 3CL protease over CatB and CatS and superior in vitro SARS-CoV-2 antiviral replication inhibition compared with the reported peptidomimetic inhibitors with other warheads. The cocrystallization of 15l with SARS-CoV-2 3CL protease confirmed the formation of a covalent adduct. α-Acyloxymethylketone compounds also exhibited antiviral activity against an alphacoronavirus and non-SARS betacoronavirus strains with similar potency and a better selectivity index than remdesivir. These findings demonstrate the potential of the substituted heteroaromatic and aliphatic α-acyloxymethylketone warheads as coronavirus inhibitors, and the described results provide a basis for further optimization.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Michael A. Joyce
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Holly A. Saffran
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Justin A. Shields
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Elena Arutyunova
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jimmy Lu
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Sardeev K. Bajwa
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Darren Hockman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Conrad Fischer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marco J. van Belkum
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhengxian Gu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Fusen Lin
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Yanhua Du
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Jia Xu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Mohammad Rahim
- Rane Pharmaceuticals, Inc.
4290 91a Street NW, Edmonton, Alberta T6E 5V2, Canada
| | - Howard S. Young
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - M. Joanne Lemieux
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A. Nieman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
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28
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Ioppolo A, Eccles M, Groth D, Verdile G, Agostino M. Evaluation of Virtual Screening Strategies for the Identification of γ-Secretase Inhibitors and Modulators. Molecules 2021; 27:176. [PMID: 35011410 PMCID: PMC8746326 DOI: 10.3390/molecules27010176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
γ-Secretase is an intramembrane aspartyl protease that is important in regulating normal cell physiology via cleavage of over 100 transmembrane proteins, including Amyloid Precursor Protein (APP) and Notch family receptors. However, aberrant proteolysis of substrates has implications in the progression of disease pathologies, including Alzheimer's disease (AD), cancers, and skin disorders. While several γ-secretase inhibitors have been identified, there has been toxicity observed in clinical trials associated with non-selective enzyme inhibition. To address this, γ-secretase modulators have been identified and pursued as more selective agents. Recent structural evidence has provided an insight into how γ-secretase inhibitors and modulators are recognized by γ-secretase, providing a platform for rational drug design targeting this protease. In this study, docking- and pharmacophore-based screening approaches were evaluated for their ability to identify, from libraries of known inhibitors and modulators with decoys with similar physicochemical properties, γ-secretase inhibitors and modulators. Using these libraries, we defined strategies for identifying both γ-secretase inhibitors and modulators incorporating an initial pharmacophore-based screen followed by a docking-based screen, with each strategy employing distinct γ-secretase structures. Furthermore, known γ-secretase inhibitors and modulators were able to be identified from an external set of bioactive molecules following application of the derived screening strategies. The approaches described herein will inform the discovery of novel small molecules targeting γ-secretase.
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Affiliation(s)
- Alicia Ioppolo
- Curtin Health and Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; (A.I.); (M.E.); (D.G.); (G.V.)
| | - Melissa Eccles
- Curtin Health and Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; (A.I.); (M.E.); (D.G.); (G.V.)
| | - David Groth
- Curtin Health and Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; (A.I.); (M.E.); (D.G.); (G.V.)
| | - Giuseppe Verdile
- Curtin Health and Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; (A.I.); (M.E.); (D.G.); (G.V.)
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Mark Agostino
- Curtin Health and Innovation Research Institute, Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; (A.I.); (M.E.); (D.G.); (G.V.)
- Curtin Institute for Computation, Curtin University, Bentley, WA 6102, Australia
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29
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Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors. Eur J Med Chem 2021; 229:114046. [PMID: 34995923 PMCID: PMC8665847 DOI: 10.1016/j.ejmech.2021.114046] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022]
Abstract
Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.
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30
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A cyclic peptide inhibitor of the SARS-CoV-2 main protease. Eur J Med Chem 2021; 221:113530. [PMID: 34023738 PMCID: PMC8096527 DOI: 10.1016/j.ejmech.2021.113530] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 12/19/2022]
Abstract
This paper presents the design and study of a first-in-class cyclic peptide inhibitor against the SARS-CoV-2 main protease (Mpro). The cyclic peptide inhibitor is designed to mimic the conformation of a substrate at a C-terminal autolytic cleavage site of Mpro. The cyclic peptide contains a [4-(2-aminoethyl)phenyl]-acetic acid (AEPA) linker that is designed to enforce a conformation that mimics a peptide substrate of Mpro. In vitro evaluation of the cyclic peptide inhibitor reveals that the inhibitor exhibits modest activity against Mpro and does not appear to be cleaved by the enzyme. Conformational searching predicts that the cyclic peptide inhibitor is fairly rigid, adopting a favorable conformation for binding to the active site of Mpro. Computational docking to the SARS-CoV-2 Mpro suggests that the cyclic peptide inhibitor can bind the active site of Mpro in the predicted manner. Molecular dynamics simulations provide further insights into how the cyclic peptide inhibitor may bind the active site of Mpro. Although the activity of the cyclic peptide inhibitor is modest, its design and study lays the groundwork for the development of additional cyclic peptide inhibitors against Mpro with improved activities.
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31
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Real-Hohn A, Blaas D. Rhinovirus Inhibitors: Including a New Target, the Viral RNA. Viruses 2021; 13:1784. [PMID: 34578365 PMCID: PMC8473194 DOI: 10.3390/v13091784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Rhinoviruses (RVs) are the main cause of recurrent infections with rather mild symptoms characteristic of the common cold. Nevertheless, RVs give rise to enormous numbers of absences from work and school and may become life-threatening in particular settings. Vaccination is jeopardised by the large number of serotypes eliciting only poorly cross-neutralising antibodies. Conversely, antivirals developed over the years failed FDA approval because of a low efficacy and/or side effects. RV species A, B, and C are now included in the fifteen species of the genus Enteroviruses based upon the high similarity of their genome sequences. As a result of their comparably low pathogenicity, RVs have become a handy model for other, more dangerous members of this genus, e.g., poliovirus and enterovirus 71. We provide a short overview of viral proteins that are considered potential drug targets and their corresponding drug candidates. We briefly mention more recently identified cellular enzymes whose inhibition impacts on RVs and comment novel approaches to interfere with infection via aggregation, virus trapping, or preventing viral access to the cell receptor. Finally, we devote a large part of this article to adding the viral RNA genome to the list of potential drug targets by dwelling on its structure, folding, and the still debated way of its exit from the capsid. Finally, we discuss the recent finding that G-quadruplex stabilising compounds impact on RNA egress possibly via obfuscating the unravelling of stable secondary structural elements.
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Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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32
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Dampalla CS, Zheng J, Perera KD, Wong LYR, Meyerholz DK, Nguyen HN, Kashipathy MM, Battaile KP, Lovell S, Kim Y, Perlman S, Groutas WC, Chang KO. Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2021; 118:e2101555118. [PMID: 34210738 PMCID: PMC8307543 DOI: 10.1073/pnas.2101555118] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease (3CLpro) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small-molecule 3CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme- and the cell-based assays. The K18-hACE2 mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and were proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18-hACE2 mice at 24 h postinfection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2-treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro of SARS-CoV-2 and SARS-CoV with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2.
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Affiliation(s)
| | - Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242
| | - David K Meyerholz
- Department of Pathology, The University of Iowa, Iowa City, IA 52242
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, KS 67260
| | | | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506;
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242;
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260;
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506;
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33
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Coultas JA, Cafferkey J, Mallia P, Johnston SL. Experimental Antiviral Therapeutic Studies for Human Rhinovirus Infections. J Exp Pharmacol 2021; 13:645-659. [PMID: 34276229 PMCID: PMC8277446 DOI: 10.2147/jep.s255211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022] Open
Abstract
Rhinovirus infection is common and usually causes mild, self-limiting upper respiratory tract symptoms. Rhinoviruses can cause exacerbation of chronic respiratory diseases, such as asthma or chronic obstructive pulmonary disease, leading to a significant burden of morbidity and mortality. There has been a great deal of progress in efforts to understand the immunological basis of rhinovirus infection. However, despite a number of in vitro and in vivo attempts, there have been no effective treatments developed. This review article summarises the up to date virological and immunological understanding of these infections. We discuss the challenges researchers face, and key solutions, in their work to investigate potential therapies including in vivo rhinovirus challenge studies. Finally, we explore past and present experimental therapeutic strategies employed in the treatment of rhinovirus infections and highlight promising areas of future work.
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Affiliation(s)
- James A Coultas
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John Cafferkey
- Respiratory Medicine, St Mary's Hospital, Imperial College Healthcare Foundation Trust, London, UK
| | - Patrick Mallia
- National Heart and Lung Institute, Imperial College London, London, UK
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34
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Synthetic and computational efforts towards the development of peptidomimetics and small-molecule SARS-CoV 3CLpro inhibitors. Bioorg Med Chem 2021; 46:116301. [PMID: 34332853 PMCID: PMC8254399 DOI: 10.1016/j.bmc.2021.116301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 12/24/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is a severe febrile respiratory disease caused by the beta genus of human coronavirus, known as SARS-CoV. Last year, 2019-n-CoV (COVID-19) was a global threat for everyone caused by the outbreak of SARS-CoV-2. 3CLpro, chymotrypsin-like protease, is a major cysteine protease that substantially contributes throughout the viral life cycle of SARS-CoV and SARS-CoV-2. It is a prospective target for the development of SARS-CoV inhibitors by applying a repurposing strategy. This review focuses on a detailed overview of the chemical synthesis and computational chemistry perspectives of peptidomimetic inhibitors (PIs) and small-molecule inhibitors (SMIs) targeting viral proteinase discovered from 2004 to 2020. The PIs and SMIs are one of the primary therapeutic inventions for SARS-CoV. The journey of different analogues towards the evolution of SARS-CoV 3CLpro inhibitors and complete synthetic preparation of nineteen derivatives of PIs and ten derivatives of SMIs and their computational chemistry perspectives were reviewed. From each class of derivatives, we have identified and highlighted the most compelling PIs and SMIs for SARS-CoV 3CLpro. The protein-ligand interaction of 29 inhibitors were also studied that involved with the 3CLpro inhibition, and the frequent amino acid residues of the protease were also analyzed that are responsible for the interactions with the inhibitors. This work will provide an initiative to encourage further research for the development of effective and drug-like 3CLpro inhibitors against coronaviruses in the near future.
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Vatansever EC, Yang KS, Drelich AK, Kratch KC, Cho CC, Kempaiah KR, Hsu JC, Mellott DM, Xu S, Tseng CTK, Liu WR. Bepridil is potent against SARS-CoV-2 in vitro. Proc Natl Acad Sci U S A 2021; 118:e2012201118. [PMID: 33597253 PMCID: PMC7958448 DOI: 10.1073/pnas.2012201118] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Guided by a computational docking analysis, about 30 Food and Drug Administration/European Medicines Agency (FDA/EMA)-approved small-molecule medicines were characterized on their inhibition of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). Of these small molecules tested, six displayed a concentration that inhibits response by 50% (IC50) value below 100 μM in inhibiting Mpro, and, importantly, three, that is, pimozide, ebastine, and bepridil, are basic molecules that potentiate dual functions by both raising endosomal pH to interfere with SARS-CoV-2 entry into the human cell host and inhibiting Mpro in infected cells. A live virus-based modified microneutralization assay revealed that bepridil possesses significant anti-SARS-CoV-2 activity in both Vero E6 and A459/ACE2 cells in a dose-dependent manner with low micromolar effective concentration, 50% (EC50) values. Therefore, the current study urges serious considerations of using bepridil in COVID-19 clinical tests.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Kai S Yang
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Aleksandra K Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kaci C Kratch
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Chia-Chuan Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Jason C Hsu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555;
- Center of Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843;
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843
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36
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Qiao J, Li YS, Zeng R, Liu FL, Luo RH, Huang C, Wang YF, Zhang J, Quan B, Shen C, Mao X, Liu X, Sun W, Yang W, Ni X, Wang K, Xu L, Duan ZL, Zou QC, Zhang HL, Qu W, Long YHP, Li MH, Yang RC, Liu X, You J, Zhou Y, Yao R, Li WP, Liu JM, Chen P, Liu Y, Lin GF, Yang X, Zou J, Li L, Hu Y, Lu GW, Li WM, Wei YQ, Zheng YT, Lei J, Yang S. SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Science 2021; 371:1374-1378. [PMID: 33602867 PMCID: PMC8099175 DOI: 10.1126/science.abf1611] [Citation(s) in RCA: 295] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/12/2021] [Indexed: 02/05/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing Mpro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 Mpro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of Mpro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.
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Affiliation(s)
- Jingxin Qiao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yue-Shan Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Zeng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Chong Huang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi-Fei Wang
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoxue Quan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenjian Shen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Mao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xinlei Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Weining Sun
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xincheng Ni
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Kai Wang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Zi-Lei Duan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Hai-Lin Zhang
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wang Qu
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Yang-Hao-Peng Long
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Rui-Cheng Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaolong Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing You
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yangli Zhou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Yao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wen-Pei Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing-Ming Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Pei Chen
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Gui-Feng Lin
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jun Zou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yiguo Hu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Guang-Wen Lu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei-Min Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. .,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Jian Lei
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. .,National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Liu C, Boland S, Scholle MD, Bardiot D, Marchand A, Chaltin P, Blatt LM, Beigelman L, Symons JA, Raboisson P, Gurard-Levin ZA, Vandyck K, Deval J. Dual inhibition of SARS-CoV-2 and human rhinovirus with protease inhibitors in clinical development. Antiviral Res 2021; 187:105020. [PMID: 33515606 PMCID: PMC7839511 DOI: 10.1016/j.antiviral.2021.105020] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/05/2021] [Accepted: 01/17/2021] [Indexed: 12/14/2022]
Abstract
The 3-chymotrypsin-like cysteine protease (3CLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered a major target for the discovery of direct antiviral agents. We previously reported the evaluation of SARS-CoV-2 3CLpro inhibitors in a novel self-assembled monolayer desorption ionization mass spectrometry (SAMDI-MS) enzymatic assay (Gurard-Levin et al., 2020). The assay was further improved by adding the rhinovirus HRV3C protease to the same well as the SARS-CoV-2 3CLpro enzyme. High substrate specificity for each enzyme allowed the proteases to be combined in a single assay reaction without interfering with their individual activities. This novel duplex assay was used to profile a diverse set of reference protease inhibitors. The protease inhibitors were grouped into three categories based on their relative potency against 3CLpro and HRV3C including those that are: equipotent against 3CLpro and HRV3C (GC376 and calpain inhibitor II), selective for 3CLpro (PF-00835231, calpain inhibitor XII, boceprevir), and selective for HRV3C (rupintrivir). Structural analysis showed that the combination of minimal interactions, conformational flexibility, and limited bulk allows GC376 and calpain inhibitor II to potently inhibit both enzymes. In contrast, bulkier compounds interacting more tightly with pockets P2, P3, and P4 due to optimization for a specific target display a more selective inhibition profile. Consistently, the most selective viral protease inhibitors were relatively weak inhibitors of human cathepsin L. Taken together, these results can guide the design of cysteine protease inhibitors that are either virus-specific or retain a broad antiviral spectrum against coronaviruses and rhinoviruses.
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Affiliation(s)
- Cheng Liu
- Aligos Therapeutics, Inc., South San Francisco, USA
| | | | | | | | | | - Patrick Chaltin
- Cistim, Leuven, Belgium; Centre for Drug Design and Discovery (CD3), KU Leuven, Leuven, Belgium
| | | | | | | | | | | | | | - Jerome Deval
- Aligos Therapeutics, Inc., South San Francisco, USA.
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38
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Mattenberger F, Latorre V, Tirosh O, Stern A, Geller R. Globally defining the effects of mutations in a picornavirus capsid. eLife 2021; 10:64256. [PMID: 33432927 PMCID: PMC7861617 DOI: 10.7554/elife.64256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
The capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral fitness across different structural and functional attributes of the capsid is lacking. To address this limitation, we globally define the effects of mutations across the capsid of a human picornavirus. Using this resource, we identify structural and sequence determinants that accurately predict mutational fitness effects, refine evolutionary analyses, and define the sequence specificity of key capsid-encoded motifs. Furthermore, capitalizing on the derived sequence requirements for capsid-encoded protease cleavage sites, we implement a bioinformatic approach for identifying novel host proteins targeted by viral proteases. Our findings represent the most comprehensive investigation of mutational fitness effects in a picornavirus capsid to date and illuminate important aspects of viral biology, evolution, and host interactions. A virus is made up of genetic material that is encased with a protective protein coat called the capsid. The capsid also helps the virus to infect host cells by binding to the host receptor proteins and releasing its genetic material. Inside the cell, the virus hitchhikes the infected cell’s machinery to grow or replicate its own genetic material. Viral capsids are the main target of the host’s defence system, and therefore, continuously change in an attempt to escape the immune system by introducing alterations (known as mutations) into the genes encoding viral capsid proteins. Mutations occur randomly, and so while some changes to the viral capsid might confer an advantage, others may have no effect at all, or even weaken the virus. To better understand the effect of capsid mutations on the virus’ ability to infect host cells, Mattenberger et al. studied the Coxsackievirus B3, which is linked to heart problems and acute heart failure in humans. The researchers analysed around 90% of possible amino acid mutations (over 14,800 mutations) and correlated each mutation to how it influenced the virus’ ability to replicate in human cells grown in the laboratory. Based on these results, Mattenberger et al. developed a computer model to predict how a particular mutation might affect the virus. The analysis also identified specific amino acid sequences of capsid proteins that are essential for certain tasks, such as building the capsid. It also included an analysis of sequences in the capsid that allow it to be recognized by another viral protein, which cuts the capsid proteins into the right size from a larger precursor. By looking for similar sequences in human genes, the researchers identified several ones that the virus may attack and inactivate to support its own replication. These findings may help identify potential drug targets to develop new antiviral therapies. For example, proteins of the capsid that are less likely to mutate will provide a better target as they lower the possibility of the virus to become resistant to the treatment. They also highlight new proteins in human cells that could potentially block the virus in cells.
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Affiliation(s)
- Florian Mattenberger
- Institute for Integrative Systems Biology, I2SysBio (Universitat de València-CSIC), Paterna, Spain
| | - Victor Latorre
- Institute for Integrative Systems Biology, I2SysBio (Universitat de València-CSIC), Paterna, Spain
| | - Omer Tirosh
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Ron Geller
- Institute for Integrative Systems Biology, I2SysBio (Universitat de València-CSIC), Paterna, Spain
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Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C-like protease? Rev Med Virol 2021; 31:1-22. [PMID: 33624382 PMCID: PMC7883238 DOI: 10.1002/rmv.2206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 is the etiological agent of the ongoing pandemic of coronavirus disease-2019, a multi-organ disease that has triggered an unprecedented global health and economic crisis. The virally encoded 3C-like protease (3CLpro ), which is named after picornaviral 3C protease (3Cpro ) due to their similarities in substrate recognition and enzymatic activity, is essential for viral replication and has been considered as the primary drug target. However, information regarding the cellular substrates of 3CLpro and its interaction with the host remains scarce, though recent work has begun to shape our understanding more clearly. Here we summarized and compared the mechanisms by which picornaviruses and coronaviruses have evolved to evade innate immune surveillance, with a focus on the established role of 3Cpro in this process. Through this comparison, we hope to highlight the potential action and mechanisms that are conserved and shared between 3Cpro and 3CLpro . In this review, we also briefly discussed current advances in the development of broad-spectrum antivirals targeting both 3Cpro and 3CLpro .
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Honglin Luo
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
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Khanna M, Gautam A, Rajput R, Sharma L. Natural Products as a Paradigm for the Treatment of Coxsackievirus - induced Myocarditis. Curr Top Med Chem 2020; 20:607-616. [PMID: 31995007 DOI: 10.2174/1568026620666200129094516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Coxsackievirus B3 (CVB3), a member of the Picornaviridae family, is considered to be one of the most important infectious agents to cause virus-induced myocarditis. Despite improvements in studying viral pathology, structure and molecular biology, as well as diagnosis of this disease, there is still no virus-specific drug in clinical use. Structural and nonstructural proteins produced during the coxsackievirus life cycle have been identified as potential targets for blocking viral replication at the step of attachment, entry, uncoating, RNA and protein synthesis by synthetic or natural compounds. Moreover, WIN (for Winthrop) compounds and application of nucleic-acid based strategies were shown to target viral capsid, entry and viral proteases, but have not reached to the clinical trials as a successful antiviral agent. There is an urgent need for diverse molecular libraries for phenotype-selective and high-throughput screening.
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Affiliation(s)
- Madhu Khanna
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Anju Gautam
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Roopali Rajput
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Latika Sharma
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
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41
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Arafet K, Serrano-Aparicio N, Lodola A, Mulholland AJ, González FV, Świderek K, Moliner V. Mechanism of inhibition of SARS-CoV-2 M pro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity. Chem Sci 2020; 12:1433-1444. [PMID: 34163906 PMCID: PMC8179034 DOI: 10.1039/d0sc06195f] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | | | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma Italy
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol UK
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I 12071 Castelló Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
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42
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Hoffman RL, Kania RS, Brothers MA, Davies JF, Ferre RA, Gajiwala KS, He M, Hogan RJ, Kozminski K, Li LY, Lockner JW, Lou J, Marra MT, Mitchell LJ, Murray BW, Nieman JA, Noell S, Planken SP, Rowe T, Ryan K, Smith GJ, Solowiej JE, Steppan CM, Taggart B. Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19. J Med Chem 2020; 63:12725-12747. [PMID: 33054210 PMCID: PMC7571312 DOI: 10.1021/acs.jmedchem.0c01063] [Citation(s) in RCA: 320] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 01/16/2023]
Abstract
The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins, which are cleaved at specific sites by a 3C-like cysteine protease (3CLpro) in a post-translational processing step that is critical for coronavirus replication. The 3CLpro sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CLpro employing ligand-protease structures solved by X-ray crystallography led to the identification of 3 and 4. Preclinical experiments reveal 4 (PF-00835231) as a potent inhibitor of CoV-2 3CLpro with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19.
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Affiliation(s)
- Robert L. Hoffman
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Robert S. Kania
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Mary A. Brothers
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jay F. Davies
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Rose A. Ferre
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Ketan S. Gajiwala
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Mingying He
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Robert J. Hogan
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
| | - Kirk Kozminski
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Lilian Y. Li
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jonathan W. Lockner
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Jihong Lou
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Michelle T. Marra
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Lennert J. Mitchell
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Brion W. Murray
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - James A. Nieman
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Stephen Noell
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Simon P. Planken
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Thomas Rowe
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
| | - Kevin Ryan
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - George J. Smith
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - James E. Solowiej
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Claire M. Steppan
- Pfizer Worldwide Research
and Development, 10770 Science Center Drive, San
Diego, California 92121 United States
| | - Barbara Taggart
- Southern Research
Institute, 2000 9th Avenue South, Birmingham,
Alabama 35205 United States
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43
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Comparative Antiviral Efficacy of Viral Protease Inhibitors against the Novel SARS-CoV-2 In Vitro. Virol Sin 2020; 35:776-784. [PMID: 32910347 PMCID: PMC7481761 DOI: 10.1007/s12250-020-00288-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
The recent outbreak of novel coronavirus pneumonia (COVID-19) caused by a new coronavirus has posed a great threat to public health. Identifying safe and effective antivirals is of urgent demand to cure the huge number of patients. Virus-encoded proteases are considered potential drug targets. The human immunodeficiency virus protease inhibitors (lopinavir/ritonavir) has been recommended in the global Solidarity Trial in March launched by World Health Organization. However, there is currently no experimental evidence to support or against its clinical use. We evaluated the antiviral efficacy of lopinavir/ritonavir along with other two viral protease inhibitors in vitro, and discussed the possible inhibitory mechanism in silico. The in vitro to in vivo extrapolation was carried out to assess whether lopinavir/ritonavir could be effective in clinical. Among the four tested compounds, lopinavir showed the best inhibitory effect against the novel coronavirus infection. However, further in vitro to in vivo extrapolation of pharmacokinetics suggested that lopinavir/ritonavir could not reach effective concentration under standard dosing regimen [marketed as Kaletra®, contained lopinavir/ritonavir (200 mg/50 mg) tablets, recommended dosage is 400 mg/10 mg (2 tablets) twice daily]. This research concluded that lopinavir/ritonavir should be stopped for clinical use due to the huge gap between in vitro IC50 and free plasma concentration. Nevertheless, the structure–activity relationship analysis of the four inhibitors provided further information for de novel design of future viral protease inhibitors of SARS-CoV-2.
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44
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Wu X, Qu J, Chen Y. Quinim: A New Ligand Scaffold Enables Nickel-Catalyzed Enantioselective Synthesis of α-Alkylated γ-Lactam. J Am Chem Soc 2020; 142:15654-15660. [DOI: 10.1021/jacs.0c07126] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xianqing Wu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jingping Qu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yifeng Chen
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
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45
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Rathnayake AD, Zheng J, Kim Y, Perera KD, Mackin S, Meyerholz DK, Kashipathy MM, Battaile KP, Lovell S, Perlman S, Groutas WC, Chang KO. 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Sci Transl Med 2020; 12:scitranslmed.abc5332. [PMID: 32747425 PMCID: PMC7574915 DOI: 10.1126/scitranslmed.abc5332] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus 3C-like proteases (3CLpro) are attractive therapeutic targets because they play a vital role in coronavirus replication. Rathnayake et al. now report a series of optimized coronavirus 3CLpro inhibitors that blocked replication of the human coronaviruses MERS-CoV and SARS-CoV-2 in cultured cells. Administration of a lead compound to a MERS-CoV mouse model demonstrated proof-of-concept efficacy. These findings suggest that this lead compound should be investigated further as a potential therapeutic for human coronavirus infection. Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.
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Affiliation(s)
- Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Samantha Mackin
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - David K Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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46
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Yuan S, Fan K, Chen Z, Sun Y, Hou H, Zhu L. Structure of the HRV-C 3C-Rupintrivir Complex Provides New Insights for Inhibitor Design. Virol Sin 2020; 35:445-454. [PMID: 32103448 PMCID: PMC7462945 DOI: 10.1007/s12250-020-00196-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/25/2019] [Indexed: 10/24/2022] Open
Abstract
Human rhinoviruses (HRVs) are the predominant infectious agents for the common cold worldwide. The HRV-C species cause severe illnesses in children and are closely related to acute exacerbations of asthma. 3C protease, a highly conserved enzyme, cleaves the viral polyprotein during replication and assists the virus in escaping the host immune system. These key roles make 3C protease an important drug target. A few structures of 3Cs complexed with an irreversible inhibitor rupintrivir have been determined. These structures shed light on the determinants of drug specificity. Here we describe the structures of HRV-C15 3C in free and inhibitor-bound forms. The volume-decreased S1' subsite and half-closed S2 subsite, which were thought to be unique features of enterovirus A 3C proteases, appear in the HRV-C 3C protease. Rupintrivir assumes an "intermediate" conformation in the complex, which might open up additional avenues for the design of potent antiviral inhibitors. Analysis of the features of the three-dimensional structures and the amino acid sequences of 3C proteases suggest new applications for existing drugs.
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Affiliation(s)
- Shuai Yuan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Kaiyue Fan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Zhonghao Chen
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yao Sun
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai Hou
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Ling Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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47
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Vatansever EC, Yang K, Kratch KC, Drelich A, Cho CC, Mellott DM, Xu S, Tseng CTK, Liu WR. Bepridil is potent against SARS-CoV-2 In Vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511370 PMCID: PMC7263498 DOI: 10.1101/2020.05.23.112235] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Guided by a computational docking analysis, about 30 FDA/EMA-approved small molecule medicines were characterized on their inhibition of the SARS-CoV-2 main protease (MPro). Of these tested small molecule medicines, six displayed an IC50 value in inhibiting MPro below 100 μM. Three medicines pimozide, ebastine, and bepridil are basic small molecules. Their uses in COVID-19 patients potentiate dual functions by both raising endosomal pH to slow SARS-CoV-2 entry into the human cell host and inhibiting MPro in infected cells. A live virus-based microneutralization assay showed that bepridil inhibited cytopathogenic effect induced by SARS-CoV-2 in Vero E6 cells completely at and dose-dependently below 5 μM and in A549 cells completely at and dose-dependently below 6.25 μM. Therefore, the current study urges serious considerations of using bepridil in COVID-19 clinical tests.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kai Yang
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kaci C Kratch
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chuan Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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48
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Cobalt-catalyzed highly enantioselective hydrogenation of α,β-unsaturated carboxylic acids. Nat Commun 2020; 11:3239. [PMID: 32591536 PMCID: PMC7319995 DOI: 10.1038/s41467-020-17057-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/03/2020] [Indexed: 11/15/2022] Open
Abstract
Asymmetric hydrogenation of α,β-unsaturated acids catalyzed by noble metals has been well established, whereas, the asymmetric hydrogenation with earth-abundant-metal was rarely reported. Here, we describe a cobalt-catalyzed asymmetric hydrogenation of α,β-unsaturated carboxylic acids. By using chiral cobalt catalyst bearing electron-donating diphosphine ligand, high activity (up to 1860 TON) and excellent enantioselectivity (up to >99% ee) are observed. Furthermore, the cobalt-catalyzed asymmetric hydrogenation is successfully applied to a broad spectrum of α,β-unsaturated carboxylic acids, such as various α-aryl and α-alkyl cinnamic acid derivatives, α-oxy-functionalized α,β-unsaturated acids, α-substituted acrylic acids and heterocyclic α,β-unsaturated acids (30 examples). The synthetic utility of the protocol is highlighted by the synthesis of key intermediates for chiral drugs (6 cases). Preliminary mechanistic studies reveal that the carboxy group may be involved in the control of the reactivity and enantioselectivity through an interaction with the metal centre. A large number of marketed drugs contains a chiral carboxylic acid scaffold. Here, the authors report the asymmetric hydrogenation of α,β-unsaturated carboxylic acids to α-chiral carboxylic acids using a cobalt catalyst bearing an electron-donating chiral diphosphine ligand.
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49
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Synthesizing Chiral Drug Intermediates by Biocatalysis. Appl Biochem Biotechnol 2020; 192:146-179. [DOI: 10.1007/s12010-020-03272-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/13/2020] [Indexed: 01/16/2023]
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50
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Frecer V, Miertus S. Antiviral agents against COVID-19: structure-based design of specific peptidomimetic inhibitors of SARS-CoV-2 main protease. RSC Adv 2020; 10:40244-40263. [PMID: 35520818 PMCID: PMC9057467 DOI: 10.1039/d0ra08304f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/30/2020] [Indexed: 11/21/2022] Open
Abstract
Despite the intense development of vaccines and antiviral therapeutics, no specific treatment of coronavirus disease 2019 (COVID-19), caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently available. Recently, X-ray crystallographic structures of a validated pharmacological target of SARS-CoV-2, the main protease (Mpro also called 3CLpro) in complex with peptide-like irreversible inhibitors have been published. We have carried out computer-aided structure-based design and optimization of peptidomimetic irreversible α-ketoamide Mpro inhibitors and their analogues using MM, MD and QM/MM methodology, with the goal to propose lead compounds with improved binding affinity to SARS-CoV-2 Mpro, enhanced specificity for pathogenic coronaviruses, decreased peptidic character, and favourable drug-like properties. The best inhibitor candidates designed in this work show largely improved interaction energies towards the Mpro and enhanced specificity due to 6 additional hydrogen bonds to the active site residues. The presented results on new SARS-CoV-2 Mpro inhibitors are expected to stimulate further research towards the development of specific anti-COVID-19 drugs. Structure-based design of SARS-CoV-2 main protease inhibitors identified hydantoin, benzothiazine and cresol moieties as promising residues of new peptidomimetic inhibitors.![]()
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Affiliation(s)
- Vladimir Frecer
- Department of Physical Chemistry of Drugs
- Faculty of Pharmacy
- Comenius University in Bratislava
- Bratislava
- Slovakia
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology (ICARST)
- Bratislava
- Slovakia
- Department of Biotechnology
- Faculty of Natural Sciences
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