1
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Jimmidi R, Chamakuri S, Lu S, Ucisik MN, Chen PJ, Bohren KM, Moghadasi SA, Versteeg L, Nnabuife C, Li JY, Qin X, Chen YC, Faver JC, Nyshadham P, Sharma KL, Sankaran B, Judge A, Yu Z, Li F, Pollet J, Harris RS, Matzuk MM, Palzkill T, Young DW. DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors. Commun Chem 2023; 6:164. [PMID: 37542196 PMCID: PMC10403511 DOI: 10.1038/s42004-023-00961-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023] Open
Abstract
The development of SARS-CoV-2 main protease (Mpro) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate Mpro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of Mpro. An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using Mpro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of Mpro with low nanomolar Ki values. Furthermore, these compounds demonstrate efficacy against mutant forms of Mpro that have shown resistance to the standard-of-care drug nirmatrelvir. Overall, this work demonstrates that DEC-Tec can efficiently generate novel and potent inhibitors without preliminary chemical or structural information.
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Affiliation(s)
- Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Shuo Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Melek Nihan Ucisik
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Peng-Jen Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - Leroy Versteeg
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Christina Nnabuife
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ying-Chu Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - John C Faver
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jeroen Pollet
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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2
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Chou O, Juang YP, Chao TL, Tsai SF, Chiu PF, Chiou CT, Tsai KC, Chang SY, Liang PH, Wong CH. Isolation of Anti-SARS-CoV-2 Natural Products Extracted from Mentha canadensis and the Semi-synthesis of Antiviral Derivatives. JOURNAL OF NATURAL PRODUCTS 2023; 86:1428-1436. [PMID: 37267066 DOI: 10.1021/acs.jnatprod.3c00104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Traditional herbal medicine offers opportunities to discover novel therapeutics against SARS-CoV-2 mutation. The dried aerial part of mint (Mentha canadensis L.) was chosen for bioactivity-guided extraction. Seven constituents were isolated and characterized by nuclear magnetic resonance (NMR) and mass spectrometry (MS). Syringic acid and methyl rosmarinate were evaluated in drug combination treatment. Ten amide derivatives of methyl rosmarinate were synthesized, and the dodecyl (13) and 3-ethylphenyl (19) derivatives demonstrated significant improvement in the anti-SARS-CoV-2 plaque reduction assay, achieving IC50 of 0.77 and 2.70 μM, respectively, against Omicron BA.1 as compared to methyl rosmarinate's IC50 of 57.0 μM. Spike protein binding and 3CLpro inhibition assays were performed to explore the viral inhibition mechanism. Molecular docking of compounds 13 and 19 to 3CLpro was performed to reveal potential interaction. In summary, natural products with anti-Omicron BA.1 activity were isolated from Mentha canadensis and derivatives of methyl rosmarinate were synthesized, showing 21- to 74-fold improvement in antiviral activity against Omicron BA.1.
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Affiliation(s)
- Osbert Chou
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Pu Juang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Sheng-Fa Tsai
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pei-Fang Chiu
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chun-Tang Chiou
- Ministry of Health and Welfare, National Research Institute of Chinese Medicine, Taipei 112, Taiwan
| | - Keng-Chang Tsai
- Ministry of Health and Welfare, National Research Institute of Chinese Medicine, Taipei 112, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- The Genomics Research Center, Academia Sinica, Taipei 128, Taiwan
| | - Chi-Huey Wong
- The Genomics Research Center, Academia Sinica, Taipei 128, Taiwan
- Scripps Research Institute, La Jolla, California 92037, United States
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3
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Li F, Fang T, Guo F, Zhao Z, Zhang J. Comprehensive Understanding of the Kinetic Behaviors of Main Protease from SARS-CoV-2 and SARS-CoV: New Data and Comparison to Published Parameters. Molecules 2023; 28:4605. [PMID: 37375160 DOI: 10.3390/molecules28124605] [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: 04/09/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The main protease (Mpro) is a promising drug target for inhibiting the coronavirus due to its conserved properties and lack of homologous genes in humans. However, previous studies on Mpro's kinetic parameters have been confusing, hindering the selection of accurate inhibitors. Therefore, obtaining a clear view of Mpro's kinetic parameters is necessary. In our study, we investigated the kinetic behaviors of Mpro from SARS-CoV-2 and SARS-CoV using both FRET-based cleavage assay and the LC-MS method, respectively. Our findings indicate that the FRET-based cleavage assay could be used for preliminary screening of Mpro inhibitors, while the LC-MS method should be applied to select the effective inhibitors with higher reliability. Furthermore, we constructed the active site mutants (H41A and C145A) and measured the kinetic parameters to gain a deeper understanding of the atomic-level enzyme efficiency reduction compared to the wild type. Overall, our study provides valuable insights for inhibitor screening and design by offering a comprehensive understanding of Mpro's kinetic behaviors.
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Affiliation(s)
- Fangya Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tingting Fang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Zipeng Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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4
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Dehury B, Mishra S, Pati S. Structural insights into SARS-CoV-2 main protease conformational plasticity. J Cell Biochem 2023. [PMID: 37099673 DOI: 10.1002/jcb.30409] [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: 02/17/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
The spread of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin-like protease (3CL MPRO ), belonging to the class of cysteine hydrolases, plays an indispensable role in processing viral polyproteins that are involved in viral replication and transcription. Studies have successfully demonstrated the role of MPRO as an attractive drug target for designing antiviral treatments because of its importance in the viral life cycle. Herein, we report the structural dynamics of six experimentally solved structures of MPRO (i.e., 6LU7, 6M03, 6WQF, 6Y2E, 6Y84, and 7BUY including both ligand-free and ligand-bound states) at different resolutions. We have employed a structure-based balanced forcefield, CHARMM36m through state-of-the-art all-atoms molecular dynamics simulations at µ-seconds scale at room temperature (303K) and pH 7.0 to explore their structure-function relationship. The helical domain-III responsible for dimerization mostly contributes to the altered conformational states and destabilization of MPRO . A keen observation of the high degree of flexibility in the P5 binding pocket adjoining domain II-III highlights the reason for observation of conformational heterogeneity among the structural ensembles of MPRO . We also observe a differential dynamics of the catalytic pocket residues His41, Cys145, and Asp187, which may lead to catalytic impairment of the monomeric proteases. Among the highly populated conformational states of the six systems, 6LU7 and 7M03 forms the most stable and compact MPRO conformation with intact catalytic site and structural integrity. Altogether, our findings from this extensive study provides a benchmark to identify physiologically relevant structures of such promising drug targets for structure-based drug design and discovery of potent drug-like compounds having clinical potential.
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Affiliation(s)
- Budheswar Dehury
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sarbani Mishra
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Division of Bioinformatics, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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5
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Moghadasi SA, Heilmann E, Khalil AM, Nnabuife C, Kearns FL, Ye C, Moraes SN, Costacurta F, Esler MA, Aihara H, von Laer D, Martinez-Sobrido L, Palzkill T, Amaro RE, Harris RS. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. SCIENCE ADVANCES 2023; 9:eade8778. [PMID: 36989354 PMCID: PMC10058310 DOI: 10.1126/sciadv.ade8778] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/28/2023] [Indexed: 05/05/2023]
Abstract
Vaccines and drugs have helped reduce disease severity and blunt the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus transmission, continuous evolution, and increasing selective pressures have the potential to yield viral variants capable of resisting these interventions. Here, we investigate the susceptibility of natural variants of the main protease [Mpro; 3C-like protease (3CLpro)] of SARS-CoV-2 to protease inhibitors. Multiple single amino acid changes in Mpro confer resistance to nirmatrelvir (the active component of Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different resistance mutation profile. Importantly, phylogenetic analyses indicate that several of these resistant variants have pre-existed the introduction of these drugs into the human population and are capable of spreading. These results encourage the monitoring of resistance variants and the development of additional protease inhibitors and other antiviral drugs with different mechanisms of action and resistance profiles for combinatorial therapy.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Christina Nnabuife
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | | | - Morgan A. Esler
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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6
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Arnaiz A, Guirado-Moreno JC, Guembe-García M, Barros R, Tamayo-Ramos JA, Fernández-Pampín N, García JM, Vallejos S. Lab-on-a-chip for the easy and visual detection of SARS-CoV-2 in saliva based on sensory polymers. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 379:133165. [PMID: 36536612 PMCID: PMC9751010 DOI: 10.1016/j.snb.2022.133165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The initial stages of the pandemic caused by SARS-CoV-2 showed that early detection of the virus in a simple way is the best tool until the development of vaccines. Many different tests are invasive or need the patient to cough up or even drag a sample of mucus from the throat area. Besides, the manufacturing time has proven insufficient in pandemic conditions since they were out of stock in many countries. Here we show a new method of manufacturing virus sensors and a proof of concept with SARS-CoV-2. We found that a fluorogenic peptide substrate of the main protease of the virus (Mpro) can be covalently immobilized in a polymer, with which a cellulose-based material can be coated. These sensory labels fluoresce with a single saliva sample of a positive COVID-19 patient. The results matched with that of the antigen tests in 22 of 26 studied cases (85% success rate).
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Affiliation(s)
- Ana Arnaiz
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
- Universidad Politécnica de Madrid, Calle Ramiro de Maeztu, 7, 28040 Madrid, Spain
| | - José Carlos Guirado-Moreno
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Marta Guembe-García
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Rocio Barros
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Fernández-Pampín
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - José M García
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Saúl Vallejos
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
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7
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Hou N, Shuai L, Zhang L, Xie X, Tang K, Zhu Y, Yu Y, Zhang W, Tan Q, Zhong G, Wen Z, Wang C, He X, Huo H, Gao H, Xu Y, Xue J, Peng C, Zou J, Schindewolf C, Menachery V, Su W, Yuan Y, Shen Z, Zhang R, Yuan S, Yu H, Shi PY, Bu Z, Huang J, Hu Q. Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro. ACS CENTRAL SCIENCE 2023; 9:217-227. [PMID: 36844503 PMCID: PMC9885526 DOI: 10.1021/acscentsci.2c01359] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Indexed: 05/31/2023]
Abstract
The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, noncovalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC50 values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment.
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Affiliation(s)
- Ningke Hou
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Westlake University; Center for Infectious Disease Research, Westlake
Laboratory of Life Sciences and Biomedicine; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Lei Shuai
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Lijing Zhang
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
- Zhejiang
University, 866 Yuhangtang
Rd, Hangzhou 310058, Zhejiang, China
| | - Xuping Xie
- Department
of Biochemistry and Molecular Biology, Institute for Human Infection
and Immunity, University of Texas Medical
Branch, Galveston, Texas 77555, United States
| | - Kaiming Tang
- State Key
Laboratory of Emerging Infectious Diseases, Department of Microbiology,
Li Ka Shing Faculty of Medicine, The University
of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yunkai Zhu
- Key Laboratory
of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical
Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory,
Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yin Yu
- Key Laboratory
of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical
Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory,
Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Wenyi Zhang
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Qiaozhu Tan
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Gongxun Zhong
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Zhiyuan Wen
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Chong Wang
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Xijun He
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Hong Huo
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
| | - Haishan Gao
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - You Xu
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Jing Xue
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Chen Peng
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Jing Zou
- Department
of Biochemistry and Molecular Biology, Institute for Human Infection
and Immunity, University of Texas Medical
Branch, Galveston, Texas 77555, United States
| | - Craig Schindewolf
- Department
of Microbiology and Immunology, University
of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Vineet Menachery
- Department
of Microbiology and Immunology, University
of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Wenji Su
- WuXi AppTec
(Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Youlang Yuan
- WuXi AppTec
(Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Zuyuan Shen
- WuXi AppTec
(Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Rong Zhang
- Key Laboratory
of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical
Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory,
Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Shuofeng Yuan
- State Key
Laboratory of Emerging Infectious Diseases, Department of Microbiology,
Li Ka Shing Faculty of Medicine, The University
of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hongtao Yu
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Pei-Yong Shi
- Department
of Biochemistry and Molecular Biology, Institute for Human Infection
and Immunity, University of Texas Medical
Branch, Galveston, Texas 77555, United States
| | - Zhigao Bu
- State
Key
Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, No.678 Haping Road, Xiangfang District, Harbin 150069, China
- National
High Containment Laboratory for Animal Diseases Control and Prevention, Harbin 150069, China
| | - Jing Huang
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
| | - Qi Hu
- Key Laboratory
of Structural Biology of Zhejiang Province, School of Life Sciences,
Center for Infectious Disease Research, Westlake Laboratory of Life
Sciences and Biomedicine, Institute of Biology, Westlake Institute
for Advanced Study, Westlake University, No.18 Shilongshan Road Cloud Town,
Xihu District, Hangzhou 310024, Zhejiang China
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8
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Kawashima S, Matsui Y, Adachi T, Morikawa Y, Inoue K, Takebayashi S, Nobori H, Rokushima M, Tachibana Y, Kato T. Ensitrelvir is effective against SARS-CoV-2 3CL protease mutants circulating globally. Biochem Biophys Res Commun 2023; 645:132-136. [PMID: 36689809 PMCID: PMC9839456 DOI: 10.1016/j.bbrc.2023.01.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health concern worldwide. Ensitrelvir (S-217622) has been evaluated as an antiviral treatment for COVID-19, targeting SARS-CoV-2 3C-like protease (3CLpro). Ensitrelvir has been reported to have comparable antiviral activity against some of the SARS-CoV-2 variants: alpha, beta, gamma, delta, and omicron (BA.1.18). In this paper, we describe that ensitrelvir is effective against newly emerging SARS-CoV-2 variants and globally prevalent 3CLpro mutations. Ensitrelvir exhibited comparable antiviral activity against SARS-CoV-2 variants, including recently emerging ones: omicron (BA1.1, BA.2, BA.2.75, BA.4, BA.5, BQ.1.1, XBB.1, and XE), mu, lambda, and theta. Genetic surveillance of SARS-CoV-2 3CLpro, the target of ensitrelvir, was conducted using a public database and identified 11 major 3CLpro mutations circulating globally (G15S, T21I, T24I, K88R, L89F, K90R, P108S, P132H, A193V, H246Y, and A255V). The 3CLpro mutation from proline to histidine at amino acid position 132 was especially identified in the omicron variant, with prevalence of 99.69%. Enzyme kinetic assay revealed that these 3CLpro mutants have enzymatic activity comparable to that of the wild type (WT). Next, we assessed the inhibitory effect of ensitrelvir against mutated 3CLpro, with it showing inhibitory effects similar to that against the WT. These in vitro data suggest that ensitrelvir will be effective against currently circulating SARS-CoV-2 variants, including omicron variants and those carrying 3CLpro mutations, which emerging novel SARS-CoV-2 variants could carry.
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Affiliation(s)
- Sho Kawashima
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuki Matsui
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Takumi Adachi
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuji Morikawa
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Kae Inoue
- Shionogi TechnoAdvance Research CO., LTD., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Shiori Takebayashi
- Shionogi TechnoAdvance Research CO., LTD., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Haruaki Nobori
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Masatomo Rokushima
- Laboratory for Bio-Drug Discovery, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Yuki Tachibana
- Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Teruhisa Kato
- Laboratory for Drug Discovery and Disease Research, Shionogi & Co., Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan.
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9
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Al Adem K, Ferreira JC, Fadl S, Rabeh WM. pH profiles of 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 elucidate its catalytic mechanism and a histidine residue critical for activity. J Biol Chem 2022; 299:102790. [PMID: 36509143 PMCID: PMC9733303 DOI: 10.1016/j.jbc.2022.102790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
3-Chymotrypsin-like protease (3CLpro) is a promising drug target for coronavirus disease 2019 and related coronavirus diseases because of the essential role of this protease in processing viral polyproteins after infection. Understanding the detailed catalytic mechanism of 3CLpro is essential for designing effective inhibitors of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular dynamics studies have suggested pH-dependent conformational changes of 3CLpro, but experimental pH profiles of SARS-CoV-2 3CLpro and analyses of the conserved active-site histidine residues have not been reported. In this work, pH-dependence studies of the kinetic parameters of SARS-CoV-2 3CLpro revealed a bell-shaped pH profile with 2 pKa values (6.9 ± 0.1 and 9.4 ± 0.1) attributable to ionization of the catalytic dyad His41 and Cys145, respectively. Our investigation of the roles of conserved active-site histidines showed that different amino acid substitutions of His163 produced inactive enzymes, indicating a key role of His163 in maintaining catalytically active SARS-CoV-2 3CLpro. By contrast, the H164A and H172A mutants retained 75% and 26% of the activity of WT, respectively. The alternative amino acid substitutions H172K and H172R did not recover the enzymatic activity, whereas H172Y restored activity to a level similar to that of the WT enzyme. The pH profiles of H164A, H172A, and H172Y were similar to those of the WT enzyme, with comparable pKa values for the catalytic dyad. Taken together, the experimental data support a general base mechanism of SARS-CoV-2 3CLpro and indicate that the neutral states of the catalytic dyad and active-site histidine residues are required for maximum enzyme activity.
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10
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Liang R, Song H, Wang K, Ding F, Xuan D, Miao J, Fei R, Zhang J. Porcine epidemic diarrhea virus 3CLpro causes apoptosis and collapse of mitochondrial membrane potential requiring its protease activity and signaling through MAVS. Vet Microbiol 2022; 275:109596. [DOI: 10.1016/j.vetmic.2022.109596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/30/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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11
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Geethakumari AM, Ahmed WS, Rasool S, Fatima A, Nasir Uddin SM, Aouida M, Biswas KH. A genetically encoded BRET-based SARS-CoV-2 M pro protease activity sensor. Commun Chem 2022; 5:117. [PMID: 36187754 PMCID: PMC9516532 DOI: 10.1038/s42004-022-00731-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
The main protease, Mpro, is critical for SARS-CoV-2 replication and an appealing target for designing anti-SARS-CoV-2 agents. Therefore, there is a demand for the development of improved sensors to monitor its activity. Here, we report a pair of genetically encoded, bioluminescence resonance energy transfer (BRET)-based sensors for detecting Mpro proteolytic activity in live cells as well as in vitro. The sensors were generated by sandwiching peptides containing the Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and NanoLuc proteins. Co-expression of the sensors with Mpro in live cells resulted in their cleavage while mutation of the critical C145 residue (C145A) in Mpro completely abrogated their cleavage. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensors developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.
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Affiliation(s)
- Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Saad Rasool
- Division of Genomics and Precision Medicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - S. M. Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
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12
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X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun 2022; 13:5196. [PMID: 36057636 PMCID: PMC9440467 DOI: 10.1038/s41467-022-32854-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/16/2022] [Indexed: 11/11/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes COVID-19, produces polyproteins 1a and 1ab that contain, respectively, 11 or 16 non-structural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for viral assembly and maturation. Using C-terminally substituted Mpro chimeras, we have determined X-ray crystallographic structures of Mpro in complex with 10 of its 11 viral cleavage sites, bound at full occupancy intermolecularly in trans, within the active site of either the native enzyme and/or a catalytic mutant (C145A). Capture of both acyl-enzyme intermediate and product-like complex forms of a P2(Leu) substrate in the native active site provides direct comparative characterization of these mechanistic steps as well as further informs the basis for enhanced product release of Mpro’s own unique C-terminal P2(Phe) cleavage site to prevent autoinhibition. We characterize the underlying noncovalent interactions governing binding and specificity for this diverse set of substrates, showing remarkable plasticity for subsites beyond the anchoring P1(Gln)-P2(Leu/Val/Phe), representing together a near complete analysis of a multiprocessing viral protease. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for antiviral therapeutic development. The SARS-CoV-2 protease Mpro is essential for viral replication. Here, the authors have determined the structures of Mpro in complex with 10 of the 11 viral cleavage sequences including a covalent acyl-enzyme intermediate, providing mechanistic and structural insights for antiviral development.
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13
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Mahmud S, Afrose S, Biswas S, Nagata A, Paul GK, Mita MA, Hasan MR, Shimu MSS, Zaman S, Uddin MS, Islam MS, Saleh MA. Plant-derived compounds effectively inhibit the main protease of SARS-CoV-2: An in silico approach. PLoS One 2022; 17:e0273341. [PMID: 35998194 PMCID: PMC9398018 DOI: 10.1371/journal.pone.0273341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic, caused by the coronavirus 2 (SARS-CoV-2), involves severe acute respiratory syndrome and poses unprecedented challenges to global health. Structure-based drug design techniques have been developed targeting the main protease of the SARS-CoV-2, responsible for viral replication and transcription, to rapidly identify effective inhibitors and therapeutic targets. Herein, we constructed a phytochemical dataset of 1154 compounds using deep literature mining and explored their potential to bind with and inhibit the main protease of SARS-CoV-2. The three most effective phytochemicals Cosmosiine, Pelargonidin-3-O-glucoside, and Cleomiscosin A had binding energies of -8.4, -8.4, and -8.2 kcal/mol, respectively, in the docking analysis. These molecules could bind to Gln189, Glu166, Cys145, His41, and Met165 residues on the active site of the targeted protein, leading to specific inhibition. The pharmacological characteristics and toxicity of these compounds, examined using absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses, revealed no carcinogenicity or toxicity. Furthermore, the complexes were simulated with molecular dynamics for 100 ns to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen profiles from the simulation trajectories. Our analysis validated the rigidity of the docked protein-ligand. Taken together, our computational study findings might help develop potential drugs to combat the main protease of the SARS-CoV-2 and help alleviate the severity of the pandemic.
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Affiliation(s)
- Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Abir Nagata
- Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Sayeedul Islam
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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14
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Shih PC, Mao YW, Hu JW, Hsieh HY, Shih TM, Lu LP, Chang WH, Huang CH, Lin CH, Lin CH, Tan P, Yang YC, Chien MH, Su CC, Yeh CH, Chuang PY, Hsieh TL, Wang CC, Hsieh PS, Chou TY, Tsai GE. Development of Ultrapure and Potent Tannic Acids as a Pan-coronal Antiviral Therapeutic. ACS Pharmacol Transl Sci 2022; 5:400-412. [PMID: 37582235 PMCID: PMC9128009 DOI: 10.1021/acsptsci.1c00264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rampageous transmission of SARS-CoV-2 has been devastatingly impacting human life and public health since late 2019. The waves of pandemic events caused by distinct coronaviruses at present and over the past decades have prompted the need to develop broad-spectrum antiviral drugs against them. In this study, our Pentarlandir ultrapure and potent tannic acids (UPPTA) showed activities against two coronaviral strains, SARS-CoV-2 and HCoV-OC43, the earliest-known coronaviruses. The mode of inhibition of Pentarlandir UPPTA is likely to act on 3-chymotrypsin-like protease (3CLpro) to prevent viral replication, as supported by results of biochemical analysis, a 3CLpro assay, and a "gain-of-function" 3CLpro overexpressed cell-based method. Even in the 3CLpro overexpressed environment, Pentarlandir UPPTA remained its antiviral characteristic. Utilizing cell-based virucidal and cytotoxicity assays, the 50% effective concentrations (EC50) and 50% cytotoxicity concentration (CC50) of Pentarlandir UPPTA were determined to be ∼0.5 and 52.5 μM against SARS-CoV-2, while they were 1.3 and 205.9 μM against HCoV-OC43, respectively. In the pharmacokinetic studies, Pentarlandir UPPTA was distributable at a high level to the lung tissue with no accumulation in the body, although the distribution was affected by the food effect. With further investigation in toxicology, Pentarlandir UPPTA demonstrated an overall safe toxicology profile. Taking these findings together, Pentarlandir UPPTA is considered to be a safe and efficacious pancoronal antiviral drug candidate that has been advanced to clinical development.
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Affiliation(s)
- Po-Chang Shih
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Yi-Wen Mao
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Jhe-Wei Hu
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Han-Yi Hsieh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Tsai-Miao Shih
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Lu-Ping Lu
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Wei-Hua Chang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chan-Hui Huang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chia-Hung Lin
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chih-Hung Lin
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Peng Tan
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ya-Ching Yang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ming-Hong Chien
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Chen-Che Su
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Cheng-Hsin Yeh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Pei-Yun Chuang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Tien-Lan Hsieh
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Ching-Cheng Wang
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
| | - Po-Shiuan Hsieh
- Institute
of Physiology, National Defense Medical
Center, Taipei
City 11490, Taiwan
- Department
of Medical Research, Tri-Service General
Hospital, Taipei City 114, Taiwan
| | - Teh-Ying Chou
- Department
of Pathology and Laboratory Medicine, Taipei
Veterans General Hospital, Taipei City 112, Taiwan
- Institute
of Clinical Medicine, National Yang-Ming
Chiao Tung University, Taipei City 112304, Taiwan
| | - Guochuan Emil Tsai
- Department
of Research and Development, SyneuRx International
(Taiwan) Corp., New Taipei City 22175, Taiwan
- UCLA School
of Medicine, Los Angeles, California 90095, United States
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15
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Jo S, Signorile L, Kim S, Kim MS, Huertas O, Insa R, Reig N, Shin DH. A Study of Drug Repurposing to Identify SARS-CoV-2 Main Protease (3CLpro) Inhibitors. Int J Mol Sci 2022; 23:ijms23126468. [PMID: 35742913 PMCID: PMC9224295 DOI: 10.3390/ijms23126468] [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: 04/21/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wreaked havoc all over the world. Although vaccines for the disease have recently become available and started to be administered to the population in various countries, there is still a strong and urgent need for treatments to cure COVID-19. One of the safest and fastest strategies is represented by drug repurposing (DRPx). In this study, thirty compounds with known safety profiles were identified from a chemical library of Phase II-and-up compounds through a combination of SOM Biotech's Artificial Intelligence (AI) technology, SOMAIPRO, and in silico docking calculations with third-party software. The selected compounds were then tested in vitro for inhibitory activity against SARS-CoV-2 main protease (3CLpro or Mpro). Of the thirty compounds, three (cynarine, eravacycline, and prexasertib) displayed strong inhibitory activity against SARS-CoV-2 3CLpro. VeroE6 cells infected with SARS-CoV-2 were used to find the cell protection capability of each candidate. Among the three compounds, only eravacycline showed potential antiviral activities with no significant cytotoxicity. A further study is planned for pre-clinical trials.
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Affiliation(s)
- Seri Jo
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul 03760, Korea; (S.J.); (S.K.); (M.-S.K.)
| | - Luca Signorile
- SOM Innovation Biotech SA., Baldiri Reixac, 4, 08028 Barcelona, Spain; (L.S.); (O.H.); (R.I.)
| | - Suwon Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul 03760, Korea; (S.J.); (S.K.); (M.-S.K.)
| | - Mi-Sun Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul 03760, Korea; (S.J.); (S.K.); (M.-S.K.)
| | - Oscar Huertas
- SOM Innovation Biotech SA., Baldiri Reixac, 4, 08028 Barcelona, Spain; (L.S.); (O.H.); (R.I.)
| | - Raúl Insa
- SOM Innovation Biotech SA., Baldiri Reixac, 4, 08028 Barcelona, Spain; (L.S.); (O.H.); (R.I.)
| | - Núria Reig
- SOM Innovation Biotech SA., Baldiri Reixac, 4, 08028 Barcelona, Spain; (L.S.); (O.H.); (R.I.)
- Correspondence: (N.R.); (D.H.S.); Tel.: +34-93-402-0150 (N.R.); +82-2-3277-4502 (D.H.S.); Fax: +34-93-403-4510 (N.R.); +82-2-3277-2851 (D.H.S.)
| | - Dong Hae Shin
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul 03760, Korea; (S.J.); (S.K.); (M.-S.K.)
- Correspondence: (N.R.); (D.H.S.); Tel.: +34-93-402-0150 (N.R.); +82-2-3277-4502 (D.H.S.); Fax: +34-93-403-4510 (N.R.); +82-2-3277-2851 (D.H.S.)
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16
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Ferreira JC, Fadl S, Rabeh WM. Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2. J Biol Chem 2022; 298:102023. [PMID: 35568197 PMCID: PMC9091064 DOI: 10.1016/j.jbc.2022.102023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
3C-like protease (3CLpro) is one of two proteases that process and liberate functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by 2-fold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of SARS-CoV-2 3CLpro.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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17
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Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro. Int J Mol Sci 2022; 23:ijms23095268. [PMID: 35563658 PMCID: PMC9103169 DOI: 10.3390/ijms23095268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022] Open
Abstract
3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic studies with a FRET method revealed that the catalytic domain alone presents enzymatic activity, despite it being approximately 8.6 times less than that in the full domain. The catalytic domain was crystallized and its X-ray crystal structure has been determined to 2.3 Å resolution. There are four protomers in the asymmetric unit. Intriguingly, they were packed as a dimer though the dimerization domain was absent. The RMSD of superimposed two catalytic domains was 0.190 for 182 Cα atoms. A part of the long hinge loop (LH-loop) from Gln189 to Asp197 was not built in the model due to its flexibility. The crystal structure indicates that the decreased proteolytic activity of the catalytic domain was due to the incomplete construction of the substrate binding part built by the LH-loop. A structural survey with other 3CLpros showed that SARS-CoV families do not have interactions between DM-loop due to the conformational difference at the last turn of helix α7 compared with others. Therefore, we can conclude that the monomeric form contains nascent enzyme activity and that its efficiency increases by dimerization. This new insight may contribute to understanding the behavior of SARS-CoV-2 3CLpro and thus be useful in developing anti-COVID-19 agents.
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18
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Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington A, Parks JM, Smith DMA, Daidone I, Coates L, Kovalevsky A, Smith JC. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS Pharmacol Transl Sci 2022; 5:255-265. [PMID: 35434531 PMCID: PMC9003389 DOI: 10.1021/acsptsci.2c00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 11/29/2022]
Abstract
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Inhibition of the SARS-CoV-2 main
protease (Mpro) is
a major focus of drug discovery efforts against COVID-19. Here we
report a hit expansion of non-covalent inhibitors of Mpro. Starting from a recently discovered scaffold (The COVID Moonshot
Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2
Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline
series, we searched a database of over a billion compounds using a
cheminformatics molecular fingerprinting approach. We identified and
tested 48 compounds in enzyme inhibition assays, of which 21 exhibited
inhibitory activity above 50% at 20 μM. Among these,
four compounds with IC50 values around 1 μM
were found. Interestingly, despite the large search space, the isoquinolone
motif was conserved in each of these four strongest binders. Room-temperature
X-ray structures of co-crystallized protein–inhibitor complexes
were determined up to 1.9 Å resolution for two of these
compounds as well as one of the stronger inhibitors in the original
isoquinoline series, revealing essential interactions with the binding
site and water molecules. Molecular dynamics simulations and quantum
chemical calculations further elucidate the binding interactions as
well as electrostatic effects on ligand binding. The results help
explain the strength of this new non-covalent scaffold for Mpro inhibition and inform lead optimization efforts for this series,
while demonstrating the effectiveness of a high-throughput computational
approach to expanding a pharmacophore library.
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Affiliation(s)
- Jens Glaser
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Ada Sedova
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Stephanie Galanie
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Protein Engineering, Merck, 126 East Lincoln Avenue, RY800-C303, Rahway, New Jersey 07065, United States
| | - Daniel W Kneller
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Russell B Davidson
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Elvis Maradzike
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Sara Del Galdo
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Audrey Labbé
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Darren J Hsu
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Rupesh Agarwal
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dmytro Bykov
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Arnold Tharrington
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jerry M Parks
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dayle M A Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Leighton Coates
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Andrey Kovalevsky
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jeremy C Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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19
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Kuo CJ, Liang PH. SARS-CoV-2 3CL pro displays faster self-maturation in vitro than SARS-CoV 3CL pro due to faster C-terminal cleavage. FEBS Lett 2022; 596:1214-1224. [PMID: 35302661 DOI: 10.1002/1873-3468.14337] [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: 09/10/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/06/2022]
Abstract
The coronavirus (CoV) disease 2019 (COVID-19) caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. The 3C-like protease (3CLpro ), which cleaves 11 sites including its own N- and C-termini on the viral polyproteins, is essential for SARS-CoV-2 replication. In this study, we constructed the full-length inactive 3CLpro with N- and C-terminal extensions as substrates for monitoring self-cleavage by wild-type 3CLpro . We found that the rate-limiting C-terminal self-cleavage rate of SARS-CoV-2 3CLpro was 35-fold faster than that of SARS-CoV 3CLpro by using the Trx/GST-tagged C145A 3CLpro substrates. Since self-cleavage of 3CLpro is the initial step for maturation of other viral proteins, our study suggests more facile SARS-CoV-2 replication as compared to SARS-CoV.
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Affiliation(s)
- Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
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20
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Campitelli P, Lu J, Ozkan SB. Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases. Biophys J 2022; 121:1483-1492. [PMID: 35300968 PMCID: PMC8920573 DOI: 10.1016/j.bpj.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/28/2021] [Accepted: 03/08/2022] [Indexed: 11/02/2022] Open
Abstract
The SARS-CoV-2 coronavirus has become one of the most immediate and widely-studied systems since its identification and subsequent global outbreak from 2019-2021. In an effort to understand the biophysical changes as a result of mutations, the mechanistic details of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we first explored the long-range dynamics using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter and intra chain, for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and specific distal residues in the CoV-2 mPro not present in CoV-1. The enhanced long distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the Dynamic Flexibility Index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1 while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, where the new substitutions in CoV-2 induce flexibility and dynamical changes elsewhere in the structure.
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21
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Yamane D, Onitsuka S, Re S, Isogai H, Hamada R, Hiramoto T, Kawanishi E, Mizuguchi K, Shindo N, Ojida A. Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide. Chem Sci 2022; 13:3027-3034. [PMID: 35432850 PMCID: PMC8905997 DOI: 10.1039/d1sc06596c] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) is a promising target for COVID-19 treatment. Here, we report an irreversible SARS-CoV-2 Mpro inhibitor possessing chlorofluoroacetamide (CFA) as a warhead for the covalent modification of Mpro. Ugi multicomponent reaction using chlorofluoroacetic acid enabled the rapid synthesis of dipeptidic CFA derivatives that identified 18 as a potent inhibitor of SARS-CoV-2 Mpro. Among the four stereoisomers, (R,R)-18 exhibited a markedly higher inhibitory activity against Mpro than the other isomers. Reaction kinetics and computational docking studies suggest that the R configuration of the CFA warhead is crucial for the rapid covalent inhibition of Mpro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of proteinous cysteines and provide the basis for improving the potency and selectivity of CFA-based covalent inhibitors.
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Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Satsuki Onitsuka
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan
| | - Hikaru Isogai
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Rui Hamada
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Tadanari Hiramoto
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Eiji Kawanishi
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan.,Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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22
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Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
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Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
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23
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Hasegawa T, Imamura RM, Suzuki T, Hashiguchi T, Nomura T, Otsuguro S, Maenaka K, Sasaki M, Orba Y, Sawa H, Sato A, Okabe T, Nagano T, Kojima H. Application of Acoustic Ejection MS System to High-Throughput Screening for SARS-CoV-2 3CL Protease Inhibitors. Chem Pharm Bull (Tokyo) 2021; 70:199-201. [PMID: 34937844 DOI: 10.1248/cpb.c21-01003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mass spectrometry is a powerful methodology for chemical screening to directly quantify substrates and products of enzymes, but its low throughput has been an issue. Recently, an acoustic liquid-handling apparatus (Echo®) used for rapid nano-dispensing has been coupled to a high-sensitivity mass spectrometer to create the Echo® MS system, and we applied this system to screening of SARS-CoV-2 3CL protease inhibitors. Primary screening of 32,033 chemical samples was completed in 12 hours. Among the hits showing selective, dose-dependent 3CL-inhibitory activity, 8 compounds showed antiviral activity in cell-based assay.
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Affiliation(s)
| | | | - Tateki Suzuki
- Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Takao Hashiguchi
- Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Takao Nomura
- Faculty of Pharmaceutical Sciences, Hokkaido University
| | | | | | - Michihito Sasaki
- International Institute for Zoonosis Control, Hokkaido University
| | - Yasuko Orba
- International Institute for Zoonosis Control, Hokkaido University
| | - Hirofumi Sawa
- International Institute for Zoonosis Control, Hokkaido University
| | - Akihiko Sato
- International Institute for Zoonosis Control, Hokkaido University.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd
| | | | | | | |
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24
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Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem 2021; 64:17366-17383. [PMID: 34705466 PMCID: PMC8565456 DOI: 10.1021/acs.jmedchem.1c01475] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Hui Li
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Audrey Labbé
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Mark A. Arnould
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Austin Clyde
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Computer Science, University of Chicago, Chicago, IL 60615, USA
| | - Heng Ma
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60615
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Martha S. Head
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Peter V. Bonnesen
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
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25
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Razali R, Asis H, Budiman C. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Microorganisms 2021; 9:2481. [PMID: 34946083 PMCID: PMC8706127 DOI: 10.3390/microorganisms9122481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.
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Affiliation(s)
| | | | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (R.R.); (H.A.)
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26
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Theerawatanasirikul S, Thangthamniyom N, Kuo CJ, Semkum P, Phecharat N, Chankeeree P, Lekcharoensuk P. Natural Phytochemicals, Luteolin and Isoginkgetin, Inhibit 3C Protease and Infection of FMDV, In Silico and In Vitro. Viruses 2021; 13:2118. [PMID: 34834926 PMCID: PMC8625466 DOI: 10.3390/v13112118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022] Open
Abstract
Foot-and-mouth-disease virus (FMDV) is a picornavirus that causes a highly contagious disease of cloven-hoofed animals resulting in economic losses worldwide. The 3C protease (3Cpro) is the main protease essential in the picornavirus life cycle, which is an attractive antiviral target. Here, we used computer-aided virtual screening to filter potential anti-FMDV agents from the natural phytochemical compound libraries. The top 23 filtered compounds were examined for anti-FMDV activities by a cell-based assay, two of which possessed antiviral effects. In the viral and post-viral entry experiments, luteolin and isoginkgetin could significantly block FMDV growth with low 50% effective concentrations (EC50). Moreover, these flavonoids could reduce the viral load as determined by RT-qPCR. However, their prophylactic activities were less effective. Both the cell-based and the fluorescence resonance energy transfer (FRET)-based protease assays confirmed that isoginkgetin was a potent FMDV 3Cpro inhibitor with a 50% inhibition concentration (IC50) of 39.03 ± 0.05 and 65.3 ± 1.7 μM, respectively, whereas luteolin was less effective. Analyses of the protein-ligand interactions revealed that both compounds fit in the substrate-binding pocket and reacted to the key enzymatic residues of the 3Cpro. Our findings suggested that luteolin and isoginkgetin are promising antiviral agents for FMDV and other picornaviruses.
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Affiliation(s)
- Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Nattarat Thangthamniyom
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.S.); (N.P.); (P.C.)
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ploypailin Semkum
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.S.); (N.P.); (P.C.)
| | - Nantawan Phecharat
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.S.); (N.P.); (P.C.)
| | - Penpitcha Chankeeree
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.S.); (N.P.); (P.C.)
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.S.); (N.P.); (P.C.)
- Center for Advanced Studies in Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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27
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l-Arginine Improves Solubility and ANTI SARS-CoV-2 Mpro Activity of Rutin but Not the Antiviral Activity in Cells. Molecules 2021; 26:molecules26196062. [PMID: 34641606 PMCID: PMC8512140 DOI: 10.3390/molecules26196062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022] Open
Abstract
The COVID-19 pandemic outbreak prompts an urgent need for efficient therapeutics, and repurposing of known drugs has been extensively used in an attempt to get to anti-SARS-CoV-2 agents in the shortest possible time. The glycoside rutin shows manifold pharmacological activities and, despite its use being limited by its poor solubility in water, it is the active principle of many pharmaceutical preparations. We herein report our in silico and experimental investigations of rutin as a SARS-CoV-2 Mpro inhibitor and of its water solubility improvement obtained by mixing it with l-arginine. Tests of the rutin/l-arginine mixture in a cellular model of SARS-CoV-2 infection highlighted that the mixture still suffers from unfavorable pharmacokinetic properties, but nonetheless, the results of this study suggest that rutin might be a good starting point for hit optimization.
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28
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DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors. Proc Natl Acad Sci U S A 2021; 118:2111172118. [PMID: 34426525 PMCID: PMC8433497 DOI: 10.1073/pnas.2111172118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed more than 4 million humans globally, but there is no bona fide Food and Drug Administration-approved drug-like molecule to impede the COVID-19 pandemic. The sluggish pace of traditional therapeutic discovery is poorly suited to producing targeted treatments against rapidly evolving viruses. Here, we used an affinity-based screen of 4 billion DNA-encoded molecules en masse to identify a potent class of virus-specific inhibitors of the SARS-CoV-2 main protease (Mpro) without extensive and time-consuming medicinal chemistry. CDD-1714, the initial three-building-block screening hit (molecular weight [MW] = 542.5 g/mol), was a potent inhibitor (inhibition constant [K i] = 20 nM). CDD-1713, a smaller two-building-block analog (MW = 353.3 g/mol) of CDD-1714, is a reversible covalent inhibitor of Mpro (K i = 45 nM) that binds in the protease pocket, has specificity over human proteases, and shows in vitro efficacy in a SARS-CoV-2 infectivity model. Subsequently, key regions of CDD-1713 that were necessary for inhibitory activity were identified and a potent (K i = 37 nM), smaller (MW = 323.4 g/mol), and metabolically more stable analog (CDD-1976) was generated. Thus, screening of DNA-encoded chemical libraries can accelerate the discovery of efficacious drug-like inhibitors of emerging viral disease targets.
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29
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Ferreira JC, Fadl S, Ilter M, Pekel H, Rezgui R, Sensoy O, Rabeh WM. Dimethyl sulfoxide reduces the stability but enhances catalytic activity of the main SARS-CoV-2 protease 3CLpro. FASEB J 2021; 35:e21774. [PMID: 34324734 PMCID: PMC8441638 DOI: 10.1096/fj.202100994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is responsible for coronavirus disease 2019 (COVID‐19), one of the most challenging global pandemics of the modern era. Potential treatment strategies against COVID‐19 are yet to be devised. It is crucial that antivirals that interfere with the SARS‐CoV‐2 life cycle be identified and developed. 3‐Chymotrypsin‐like protease (3CLpro) is an attractive antiviral drug target against SARS‐CoV‐2, and coronaviruses in general, because of its role in the processing of viral polyproteins. Inhibitors of 3CLpro activity are screened in enzyme assays before further development of the most promising leads. Dimethyl sulfoxide (DMSO) is a common additive used in such assays and enhances the solubility of assay components. However, it may also potentially affect the stability and efficiency of 3CLpro but, to date, this effect had not been analyzed in detail. Here, we investigated the effect of DMSO on 3CLpro‐catalyzed reaction. While DMSO (5%‐20%) decreased the optimum temperature of catalysis and thermodynamic stability of 3CLpro, it only marginally affected the kinetic stability of the enzyme. Increasing the DMSO concentration up to 20% improved the catalytic efficiency and peptide‐binding affinity of 3CLpro. At such high DMSO concentration, the solubility and stability of peptide substrate were improved because of reduced aggregation. In conclusion, we recommend 20% DMSO as the minimum concentration to be used in screens of 3CLpro inhibitors as lead compounds for the development of antiviral drugs against COVID‐19.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Metehan Ilter
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Hanife Pekel
- Department of Pharmacy Services, Vocational School of Health Services, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Rachid Rezgui
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ozge Sensoy
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Department of Computer Engineering, School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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30
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Zhu W, Shyr Z, Lo DC, Zheng W. Viral Proteases as Targets for Coronavirus Disease 2019 Drug Development. J Pharmacol Exp Ther 2021; 378:166-172. [PMID: 33972366 PMCID: PMC8686716 DOI: 10.1124/jpet.121.000688] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to be a global threat since its emergence. Although several COVID-19 vaccines have become available, the prospective timeframe for achieving effective levels of vaccination across global populations remains uncertain. Moreover, the emergence of SARS-CoV-2 variants presents continuing potential challenges for future vaccination planning. Therefore, development of effective antiviral therapies continues to be an urgent unmet need for COVID-19. Successful antiviral regimens for the treatment of human immunodeficiency virus and hepatitis C virus infections have established viral proteases as validated targets for antiviral drug development. In this context, we review protease targets in drug development, currently available antiviral protease inhibitors, and therapeutic development efforts on SARS-CoV-2 main protease and papain-like protease. SIGNIFICANCE STATEMENT: Coronavirus disease 2019 (COVID-19) continues to be a global threat since its emergence. The development of effective antiviral therapeutics for COVID-19 remains an urgent and long-term need. Because viral proteases are validated drug targets, specific severe acute respiratory syndrome coronavirus 2 protease inhibitors are critical therapeutics to be developed for treatment of COVID-19.
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Affiliation(s)
- Wei Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Zeenat Shyr
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Donald C Lo
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
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31
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Diao M, Lang L, Feng J, Li R. Molecular detections of coronavirus: current and emerging methodologies. Expert Rev Anti Infect Ther 2021; 20:199-210. [PMID: 34225540 DOI: 10.1080/14787210.2021.1949986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Seven coronavirus species have been identified that can infect humans. While human coronavirus infections had been historically associated with only mild respiratory symptoms similar to the common cold, three coronaviruses identified since 2003, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and SARS-CoV-2, cause life-threatening severe respiratory syndromes. The coronavirus disease 2019 (COVID-19) caused by the highly transmissible SARS-CoV-2 has triggered a worldwide health emergency. Due to the lack of effective drugs and vaccination, rapid and reliable detection is of vital importance to control coronavirus epidemics/pandemics.Area covered: A literature search was performed in Pubmed covering the detections and diagnostics of SARS, MERS and SARS-CoV-2. This review summarized the current knowledge of established and emerging methods for coronavirus detection. The characteristics of different diagnostic approaches were described, and the strengths and weaknesses of each method were analyzed and compared. In addition, future trends in the field of coronavirus detection were also discussed.Expert opinion: Nucleic acid-based RT-PCR is the current golden-standard of coronavirus detection, while immunoassays provide history of coronavirus infection besides diagnostic information. Integrated high-throughput system holds the great potential and is the trend of future detection and diagnosis of virus infection.
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Affiliation(s)
- Mingkun Diao
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Lang Lang
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Juan Feng
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Rongsong Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
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32
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Milligan JC, Zeisner TU, Papageorgiou G, Joshi D, Soudy C, Ulferts R, Wu M, Lim CT, Tan KW, Weissmann F, Canal B, Fujisawa R, Deegan T, Nagaraj H, Bineva-Todd G, Basier C, Curran JF, Howell M, Beale R, Labib K, O'Reilly N, Diffley JF. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp5 main protease. Biochem J 2021; 478:2499-2515. [PMID: 34198327 PMCID: PMC8286836 DOI: 10.1042/bcj20210197] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro, with IC50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC50. Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.
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Affiliation(s)
- Jennifer C. Milligan
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Theresa U. Zeisner
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - George Papageorgiou
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Dhira Joshi
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Christelle Soudy
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Mary Wu
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Chew Theng Lim
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Kang Wei Tan
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Tom Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Hema Nagaraj
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ganka Bineva-Todd
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Clovis Basier
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Joseph F. Curran
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Michael Howell
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Nicola O'Reilly
- Peptide Chemistry STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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33
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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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34
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Seleno-Functionalization of Quercetin Improves the Non-Covalent Inhibition of M pro and Its Antiviral Activity in Cells against SARS-CoV-2. Int J Mol Sci 2021; 22:ijms22137048. [PMID: 34208928 PMCID: PMC8268238 DOI: 10.3390/ijms22137048] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
The development of new antiviral drugs against SARS-CoV-2 is a valuable long-term strategy to protect the global population from the COVID-19 pandemic complementary to the vaccination. Considering this, the viral main protease (Mpro) is among the most promising molecular targets in light of its importance during the viral replication cycle. The natural flavonoid quercetin 1 has been recently reported to be a potent Mpro inhibitor in vitro, and we explored the effect produced by the introduction of organoselenium functionalities in this scaffold. In particular, we report here a new synthetic method to prepare previously inaccessible C-8 seleno-quercetin derivatives. By screening a small library of flavonols and flavone derivatives, we observed that some compounds inhibit the protease activity in vitro. For the first time, we demonstrate that quercetin (1) and 8-(p-tolylselenyl)quercetin (2d) block SARS-CoV-2 replication in infected cells at non-toxic concentrations, with an IC50 of 192 μM and 8 μM, respectively. Based on docking experiments driven by experimental evidence, we propose a non-covalent mechanism for Mpro inhibition in which a hydrogen bond between the selenium atom and Gln189 residue in the catalytic pocket could explain the higher Mpro activity of 2d and, as a result, its better antiviral profile.
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35
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Guijarro-Real C, Plazas M, Rodríguez-Burruezo A, Prohens J, Fita A. Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CL Pro) Activity. Foods 2021; 10:1503. [PMID: 34209659 PMCID: PMC8304378 DOI: 10.3390/foods10071503] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
Antiviral treatments inhibiting Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication may represent a strategy complementary to vaccination to fight the ongoing Coronavirus disease 19 (COVID-19) pandemic. Molecules or extracts inhibiting the SARS-CoV-2 chymotripsin-like protease (3CLPro) could contribute to reducing or suppressing SARS-CoV-2 replication. Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. Methanolic extracts were evaluated in vitro for inhibition of SARS-CoV-2 3CLPro activity using a quenched fluorescence resonance energy transfer (FRET) assay. Extracts from turmeric (Curcuma longa) rhizomes, mustard (Brassica nigra) seeds, and wall rocket (Diplotaxis erucoides subsp. erucoides) at 500 µg mL-1 displayed significant inhibition of the 3CLPro activity, resulting in residual protease activities of 0.0%, 9.4%, and 14.9%, respectively. Using different extract concentrations, an IC50 value of 15.74 µg mL-1 was calculated for turmeric extract. Commercial curcumin inhibited the 3CLPro activity, but did not fully account for the inhibitory effect of turmeric rhizomes extracts, suggesting that other components of the turmeric extract must also play a main role in inhibiting the 3CLPro activity. Sinigrin, a major glucosinolate present in mustard seeds and wall rocket, did not have relevant 3CLPro inhibitory activity; however, its hydrolysis product allyl isothiocyanate had an IC50 value of 41.43 µg mL-1. The current study identifies plant extracts and molecules that can be of interest in the search for treatments against COVID-19, acting as a basis for future chemical, in vivo, and clinical trials.
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Affiliation(s)
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain; (C.G.-R.); (A.R.-B.); (J.P.); (A.F.)
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36
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Ferreira JC, Fadl S, Villanueva AJ, Rabeh WM. Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Front Chem 2021; 9:692168. [PMID: 34249864 PMCID: PMC8264439 DOI: 10.3389/fchem.2021.692168] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are responsible for multiple pandemics and millions of deaths globally, including the current pandemic of coronavirus disease 2019 (COVID-19). Development of antivirals against coronaviruses, including the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) responsible for COVID-19, is essential for containing the current and future coronavirus outbreaks. SARS-CoV-2 proteases represent important targets for the development of antivirals because of their role in the processing of viral polyproteins. 3-Chymotrypsin-like protease (3CLpro) is one such protease. The cleavage of SARS-CoV-2 polyproteins by 3CLpro is facilitated by a Cys145–His41 catalytic dyad. We here characterized the catalytic roles of the cysteine–histidine pair for improved understanding of the 3CLpro reaction mechanism, to inform the development of more effective antivirals against Sars-CoV-2. The catalytic dyad residues were substituted by site-directed mutagenesis. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. The integrity of the structural fold of enzyme variants was investigated by circular dichroism spectroscopy to test if the catalytic inactivation of 3CLpro was caused by gross changes in the enzyme secondary structure. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. Collectively, the above observations confirm the roles of His41 and Cys145 in the catalytic activity and the overall conformational fold of 3CLpro SARS-CoV-2. We conclude that the cysteine–histidine pair should be targeted for inhibition of 3CLpro and development of antiviral against COVID-19 and coronaviruses.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Dražić T, Kühl N, Leuthold MM, Behnam MA, Klein CD. Efficiency Improvements and Discovery of New Substrates for a SARS-CoV-2 Main Protease FRET Assay. SLAS DISCOVERY 2021; 26:1189-1199. [PMID: 34151620 PMCID: PMC8458682 DOI: 10.1177/24725552211020681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a huge impact on the world. Although several vaccines have recently reached the market, the development of specific antiviral drugs against SARS-CoV-2 is an important additional strategy in fighting the pandemic. One of the most promising pharmacological targets is the viral main protease (Mpro). Here, we present an optimized biochemical assay procedure for SARS-CoV-2 Mpro. We have comprehensively investigated the influence of different buffer components and conditions on the assay performance and characterized Förster resonance energy transfer (FRET) substrates with a preference for 2-Abz/Tyr(3-NO2) FRET pairs. The substrates 2-AbzSAVLQSGTyr(3-NO2)R-OH, a truncated version of the established DABCYL/EDANS FRET substrate, and 2-AbzVVTLQSGTyr(3-NO2)R-OH are promising candidates for screening and inhibitor characterization. In the latter substrate, the incorporation of Val at position P5 improved the catalytic efficiency. Based on the obtained results, we present here a reproducible, reliable assay protocol using highly affordable buffer components.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mila M. Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mira A.M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
- Corresponding Author: Christian D. Klein, Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany.
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38
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Yan S, Wu G. Potential 3-chymotrypsin-like cysteine protease cleavage sites in the coronavirus polyproteins pp1a and pp1ab and their possible relevance to COVID-19 vaccine and drug development. FASEB J 2021; 35:e21573. [PMID: 33913206 PMCID: PMC8206714 DOI: 10.1096/fj.202100280rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus (CoV) 3-chymotrypsin (C)-like cysteine protease (3CLpro ) is a target for anti-CoV drug development and drug repurposing because along with papain-like protease, it cleaves CoV-encoded polyproteins (pp1a and pp1ab) into nonstructural proteins (nsps) for viral replication. However, the cleavage sites of 3CLpro and their relevant nsps remain unclear, which is the subject of this perspective. Here, we address the subject from three standpoints. First, we explore the inconsistency in the cleavage sites and relevant nsps across CoVs, and investigate the function of nsp11. Second, we consider the nsp16 mRNA overlapping of the spike protein mRNA, and analyze the effect of this overlapping on mRNA vaccines. Finally, we study nsp12, whose existence depends on ribosomal frameshifting, and investigate whether 3CLpro requires a large number of inhibitors to achieve full inhibition. This perspective helps us to clarify viral replication and is useful for developing anti-CoV drugs with 3CLpro as a target in the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
| | - Guang Wu
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. An Updated Review on SARS-CoV-2 Main Proteinase (M Pro): Protein Structure and Small-Molecule Inhibitors. Curr Top Med Chem 2021; 21:442-460. [PMID: 33292134 DOI: 10.2174/1568026620666201207095117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
[Coronaviruses (CoVs) are enveloped positive-stranded RNA viruses with spike (S) protein projections that allow the virus to enter and infect host cells. The S protein is a key virulence factor determining viral pathogenesis, host tropism, and disease pathogenesis. There are currently diverse corona viruses that are known to cause disease in humans. The occurrence of Middle East respiratory syndrome coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), as fatal human CoV diseases, has induced significant interest in the medical field. The novel coronavirus disease (COVID-19) is an infectious disease caused by a novel strain of coronavirus (SAR-CoV-2). The SARS-CoV2 outbreak has been evolved in Wuhan, China, in December 2019, and identified as a pandemic in March 2020, resulting in 53.24 M cases and 1.20M deaths worldwide. SARS-CoV-2 main proteinase (MPro), a key protease of CoV-2, mediates viral replication and transcription. SARS-CoV-2 MPro has been emerged as an attractive target for SARS-CoV-2 drug design and development. Diverse scaffolds have been released targeting SARS-CoV-2 MPro. In this review, we culminate the latest published information about SARS-CoV-2 main proteinase (MPro) and reported inhibitors.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Haizhen A Zhong
- Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182, United States
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Jo S, Kim S, Yoo J, Kim MS, Shin DH. A Study of 3CLpros as Promising Targets against SARS-CoV and SARS-CoV-2. Microorganisms 2021; 9:756. [PMID: 33916747 PMCID: PMC8065850 DOI: 10.3390/microorganisms9040756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/14/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), results in serious chaos all over the world. In addition to the available vaccines, the development of treatments to cure COVID-19 should be done quickly. One of the fastest strategies is to use a drug-repurposing approach. To provide COVID-19 patients with useful information about medicines currently being used in clinical trials, twenty-four compounds, including antiviral agents, were selected and assayed. These compounds were applied to verify the inhibitory activity for the protein function of 3CLpros (main proteases) of SARS-CoV and SARS-CoV-2. Among them, viral reverse-transcriptase inhibitors abacavir and tenofovir revealed a good inhibitory effect on both 3CLpros. Intriguingly, sildenafil, a cGMP-specific phosphodiesterase type 5 inhibitor also showed significant inhibitory function against them. The in silico docking study suggests that the active-site residues located in the S1 and S2 sites play key roles in the interactions with the inhibitors. The result indicates that 3CLpros are promising targets to cope with SAR-CoV-2 and its variants. The information can be helpful to design treatments to cure patients with COVID-19.
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Affiliation(s)
| | | | | | | | - Dong Hae Shin
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, 52, Ewhayeodae-gil, Seoul 03760, Korea; (S.J.); (S.K.); (J.Y.); (M.-S.K.)
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42
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Nguyen TTH, Jung JH, Kim MK, Lim S, Choi JM, Chung B, Kim DW, Kim D. The Inhibitory Effects of Plant Derivate Polyphenols on the Main Protease of SARS Coronavirus 2 and Their Structure-Activity Relationship. Molecules 2021; 26:1924. [PMID: 33808054 PMCID: PMC8036510 DOI: 10.3390/molecules26071924] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
The main protease (Mpro) is a major protease having an important role in viral replication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus that caused the pandemic of 2020. Here, active Mpro was obtained as a 34.5 kDa protein by overexpression in E. coli BL21 (DE3). The optimal pH and temperature of Mpro were 7.5 and 37 °C, respectively. Mpro displayed a Km value of 16 μM with Dabcyl-KTSAVLQ↓SGFRKME-Edans. Black garlic extract and 49 polyphenols were studied for their inhibitory effects on purified Mpro. The IC50 values were 137 μg/mL for black garlic extract and 9-197 μM for 15 polyphenols. The mixtures of tannic acid with puerarin, daidzein, and/or myricetin enhanced the inhibitory effects on Mpro. The structure-activity relationship of these polyphenols revealed that the hydroxyl group in C3', C4', C5' in the B-ring, C3 in the C-ring, C7 in A-ring, the double bond between C2 and C3 in the C-ring, and glycosylation at C8 in the A-ring contributed to inhibitory effects of flavonoids on Mpro.
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Affiliation(s)
- Thi Thanh Hanh Nguyen
- Institutes of Green Bioscience and Technology, Seoul National University, Pyeongchang-gun 25354, Gang-won-do, Korea;
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Engery Research Institute, Jeongeup 56212, Jeollabuk-do, Korea; (J.-H.J.); (M.-K.K.); (S.L.)
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Engery Research Institute, Jeongeup 56212, Jeollabuk-do, Korea; (J.-H.J.); (M.-K.K.); (S.L.)
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Engery Research Institute, Jeongeup 56212, Jeollabuk-do, Korea; (J.-H.J.); (M.-K.K.); (S.L.)
| | - Jae-Myoung Choi
- Ottogi Sesame Mills Co., Ltd., Eumseong-gun 27623, Chungcheongbuk-do, Korea; (J.-M.C.); (B.C.)
| | - Byoungsang Chung
- Ottogi Sesame Mills Co., Ltd., Eumseong-gun 27623, Chungcheongbuk-do, Korea; (J.-M.C.); (B.C.)
| | - Do-Won Kim
- Department of Physics, Gangneung-Wonju National University, Gangneung 25457, Gangwon-do, Korea;
| | - Doman Kim
- Institutes of Green Bioscience and Technology, Seoul National University, Pyeongchang-gun 25354, Gang-won-do, Korea;
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang-gun 25354, Gangwon-do, Korea
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43
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Kinetic Characterization and Inhibitor Screening for the Proteases Leading to Identification of Drugs against SARS-CoV-2. Antimicrob Agents Chemother 2021; 65:AAC.02577-20. [PMID: 33526482 PMCID: PMC8097444 DOI: 10.1128/aac.02577-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
Coronavirus (CoV) disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has claimed many lives worldwide and is still spreading since December 2019. The 3C-like protease (3CLpro) and papain-like protease (PLpro) are essential for maturation of viral polyproteins in SARS-CoV-2 life cycle and thus regarded as key drug targets for the disease. Coronavirus (CoV) disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has claimed many lives worldwide and is still spreading since December 2019. The 3C-like protease (3CLpro) and papain-like protease (PLpro) are essential for maturation of viral polyproteins in SARS-CoV-2 life cycle and thus regarded as key drug targets for the disease. In this study, 3CLpro and PLpro assay platforms were established, and their substrate specificities were characterized. The assays were used to screen collections of 1,068 and 2,701 FDA-approved drugs. After excluding the externally used drugs which are too toxic, we totally identified 12 drugs as 3CLpro inhibitors and 36 drugs as PLpro inhibitors active at 10 μM. Among these inhibitors, six drugs were found to suppress SARS-CoV-2 with the half-maximal effective concentration (EC50) below or close to 10 μM. This study enhances our understanding on the proteases and provides FDA-approved drugs for prevention and/or treatment of COVID-19.
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten J, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 2021; 24:102021. [PMID: 33426509 PMCID: PMC7783459 DOI: 10.1016/j.isci.2020.102021] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kendra E. Leigh
- Max Planck Institute of Biophysics, Frankfurt am Main, Hessen 60438, Germany
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Saarland 66123, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | | | | | - Anthony Calderaio
- VirtualFlow Organization, https://virtual-flow.org/, Boston, MA 02115, USA
| | | | - Alexander Rose
- Mol∗ Consortium, https://molstar.org, San Diego, CA 92109, USA
| | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin 14195, Germany
- Institute of Mathematics, Technical University Berlin, Berlin 10587, Germany
| | - J.J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz 8010, Austria
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Ryan Yust
- Google, Mountain View, CA 94043, USA
| | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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Xiong M, Su H, Zhao W, Xie H, Shao Q, Xu Y. What coronavirus 3C-like protease tells us: From structure, substrate selectivity, to inhibitor design. Med Res Rev 2021; 41:1965-1998. [PMID: 33460213 PMCID: PMC8014231 DOI: 10.1002/med.21783] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
The emergence of a variety of coronaviruses (CoVs) in the last decades has posed huge threats to human health. Especially, the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to more than 70 million infections and over 1.6 million of deaths worldwide in the past few months. None of the efficacious antiviral agents against human CoVs have been approved yet. 3C-like protease (3CLpro ) is an attractive target for antiviral intervention due to its essential role in processing polyproteins translated from viral RNA, and its conserved structural feature and substrate specificity among CoVs in spite of the sequence variation. This review focuses on all available crystal structures of 12 CoV 3CLpro s and their inhibitors, and intends to provide a comprehensive understanding of this protease from multiple aspects including its structural features, substrate specificity, inhibitor binding modes, and more importantly, to recapitulate the similarity and diversity among different CoV 3CLpro s and the structure-activity relationship of various types of inhibitors. Such an attempt could gain a deep insight into the inhibition mechanisms and drive future structure-based drug discovery targeting 3CLpro s.
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Affiliation(s)
- Muya Xiong
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Su
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenfeng Zhao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hang Xie
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Shao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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46
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Konwar M, Sarma D. Advances in developing small molecule SARS 3CL pro inhibitors as potential remedy for corona virus infection. Tetrahedron 2021; 77:131761. [PMID: 33230349 PMCID: PMC7674993 DOI: 10.1016/j.tet.2020.131761] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/06/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Originated in China, coronavirus disease 2019 (COVID-19)- the highly contagious and fatal respiratory disease caused by SARS-CoV-2 has already infected more than 29 million people worldwide with a mortality rate of 3.15% (according to World Health Organization's (WHO's) report, September 2020) and the number is exponentially increasing with no remedy whatsoever discovered till date. But it is not the first time this infectious viral disease has appeared, in 2002 SARS-CoV infected more than 8000 individuals of which 9.6% patients died and in 2012 approximately 35% of MERS-CoV infected patients have died. Literature reports indicate that a chymotripsin-like cystein protease (3CLpro) is responsible for the replication of the virus inside the host cell. Therefore, design and synthesis of 3CLpro inhibitor molecules play a great impact in drug development against this COVID-19 pandemic. In this review, we are discussing the anti-SARS effect of some small molecule 3CLpro inhibitors with their various binding modes of interactions to the target protein.
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Affiliation(s)
- Manashjyoti Konwar
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
- Department of Chemistry, Dibru College, Dibrugarh, 786003, Assam, India
| | - Diganta Sarma
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
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47
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Jo S, Kim S, Shin DH, Kim MS. Inhibition of SARS-CoV 3CL protease by flavonoids. J Enzyme Inhib Med Chem 2020; 35:145-151. [PMID: 31724441 PMCID: PMC6882434 DOI: 10.1080/14756366.2019.1690480] [Citation(s) in RCA: 412] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022] Open
Abstract
There were severe panics caused by Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome-Coronavirus. Therefore, researches targeting these viruses have been required. Coronaviruses (CoVs) have been rising targets of some flavonoids. The antiviral activity of some flavonoids against CoVs is presumed directly caused by inhibiting 3C-like protease (3CLpro). Here, we applied a flavonoid library to systematically probe inhibitory compounds against SARS-CoV 3CLpro. Herbacetin, rhoifolin and pectolinarin were found to efficiently block the enzymatic activity of SARS-CoV 3CLpro. The interaction of the three flavonoids was confirmed using a tryptophan-based fluorescence method, too. An induced-fit docking analysis indicated that S1, S2 and S3' sites are involved in binding with flavonoids. The comparison with previous studies showed that Triton X-100 played a critical role in objecting false positive or overestimated inhibitory activity of flavonoids. With the systematic analysis, the three flavonoids are suggested to be templates to design functionally improved inhibitors.
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Affiliation(s)
- Seri Jo
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Suwon Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy and Graduates School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
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48
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Abian O, Ortega-Alarcon D, Jimenez-Alesanco A, Ceballos-Laita L, Vega S, Reyburn HT, Rizzuti B, Velazquez-Campoy A. Structural stability of SARS-CoV-2 3CLpro and identification of quercetin as an inhibitor by experimental screening. Int J Biol Macromol 2020; 164:1693-1703. [PMID: 32745548 PMCID: PMC7395220 DOI: 10.1016/j.ijbiomac.2020.07.235] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/19/2022]
Abstract
The global health emergency generated by coronavirus disease 2019 (COVID-19) has prompted the search for preventive and therapeutic treatments for its pathogen, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are many potential targets for drug discovery and development to tackle this disease. One of these targets is the main protease, Mpro or 3CLpro, which is highly conserved among coronaviruses. 3CLpro is an essential player in the viral replication cycle, processing the large viral polyproteins and rendering the individual proteins functional. We report a biophysical characterization of the structural stability and the catalytic activity of 3CLpro from SARS-CoV-2, from which a suitable experimental in vitro molecular screening procedure has been designed. By screening of a small chemical library consisting of about 150 compounds, the natural product quercetin was identified as reasonably potent inhibitor of SARS-CoV-2 3CLpro (Ki ~ 7 μM). Quercetin could be shown to interact with 3CLpro using biophysical techniques and bind to the active site in molecular simulations. Quercetin, with well-known pharmacokinetic and ADMET properties, can be considered as a good candidate for further optimization and development, or repositioned for COVID-19 therapeutic treatment.
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Affiliation(s)
- Olga Abian
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain.
| | - David Ortega-Alarcon
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Jimenez-Alesanco
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Laura Ceballos-Laita
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Hugh T Reyburn
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB), CSIC, 28049 Madrid, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Adrian Velazquez-Campoy
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Fundación ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain.
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49
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Kneller DW, Galanie S, Phillips G, O'Neill HM, Coates L, Kovalevsky A. Malleability of the SARS-CoV-2 3CL M pro Active-Site Cavity Facilitates Binding of Clinical Antivirals. Structure 2020; 28:1313-1320.e3. [PMID: 33152262 PMCID: PMC7584437 DOI: 10.1016/j.str.2020.10.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 requires rapid development of specific therapeutics and vaccines. The main protease of SARS-CoV-2, 3CL Mpro, is an established drug target for the design of inhibitors to stop the virus replication. Repurposing existing clinical drugs can offer a faster route to treatments. Here, we report on the binding mode and inhibition properties of several inhibitors using room temperature X-ray crystallography and in vitro enzyme kinetics. The enzyme active-site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors (telaprevir, narlaprevir, and boceprevir) to bind and inhibit SARS-CoV-2 3CL Mpro. Narlaprevir, boceprevir, and telaprevir are low-micromolar inhibitors, whereas the binding affinity of leupeptin is substantially weaker. Repurposing hepatitis C clinical drugs as COVID-19 treatments may be a useful option to pursue. The observed malleability of the enzyme active-site cavity should be considered for the successful design of specific protease inhibitors.
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Affiliation(s)
- Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA; Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA; Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA; National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
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50
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Tsai KC, Huang YC, Liaw CC, Tsai CI, Chiou CT, Lin CJ, Wei WC, Lin SJS, Tseng YH, Yeh KM, Lin YL, Jan JT, Liang JJ, Liao CC, Chiou WF, Kuo YH, Lee SM, Lee MY, Su YC. A traditional Chinese medicine formula NRICM101 to target COVID-19 through multiple pathways: A bedside-to-bench study. Biomed Pharmacother 2020; 133:111037. [PMID: 33249281 PMCID: PMC7676327 DOI: 10.1016/j.biopha.2020.111037] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
COVID-19 is a global pandemic, with over 50 million confirmed cases and 1.2 million deaths as of November 11, 2020. No therapies or vaccines so far are recommended to treat or prevent the new coronavirus. A novel traditional Chinese medicine formula, Taiwan Chingguan Yihau (NRICM101), has been administered to patients with COVID-19 in Taiwan since April 2020. Its clinical outcomes and pharmacology have been evaluated. Among 33 patients with confirmed COVID-19 admitted in two medical centers, those (n = 12) who were older, sicker, with more co-existing conditions and showing no improvement after 21 days of hospitalization were given NRICM101. They achieved 3 consecutive negative results within a median of 9 days and reported no adverse events. Pharmacological assays demonstrated the effects of the formula in inhibiting the spike protein/ACE2 interaction, 3CL protease activity, viral plaque formation, and production of cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α. This bedside-to-bench study suggests that NRICM101 may disrupt disease progression through its antiviral and anti-inflammatory properties, offering promise as a multi-target agent for the prevention and treatment of COVID-19.
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Affiliation(s)
- Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, No. 250 Wu-Xing Street, Taipei 11031, Taiwan.
| | - Yi-Chia Huang
- Department of Chinese Medicine, Tri-Service General Hospital, National Defense Medical Center, No.325, Section 2, Chenggong Road, Neihu District, Taipei 11490, Taiwan.
| | - Chia-Ching Liaw
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Chia-I Tsai
- Department of Traditional Chinese Medicine, Taichung Veterans General Hospital, No. 1650, Taiwan Boulevard Section 4, Seatwen District, Taichung 407204, Taiwan.
| | - Chun-Tang Chiou
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Chien-Jung Lin
- Department of Chinese Medicine, Tri-Service General Hospital, National Defense Medical Center, No.325, Section 2, Chenggong Road, Neihu District, Taipei 11490, Taiwan.
| | - Wen-Chi Wei
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Sunny Jui-Shan Lin
- Department of Chinese Medicine, Tri-Service General Hospital, National Defense Medical Center, No.325, Section 2, Chenggong Road, Neihu District, Taipei 11490, Taiwan.
| | - Yu-Hwei Tseng
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Chenggong Road, Neihu District, Taipei 11490, Taiwan.
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, No. 128, Section 2, Academia Road, Nankang District, Taipei 11529, Taiwan.
| | - Jia-Tsrong Jan
- Genomic Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nankang District, Taipei, 11529, Taiwan.
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, No. 128, Section 2, Academia Road, Nankang District, Taipei 11529, Taiwan.
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, No. 128, Section 2, Academia Road, Nankang District, Taipei 11529, Taiwan.
| | - Wen-Fei Chiou
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Yao-Haur Kuo
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan.
| | - Shen-Ming Lee
- Department of Statistic, Feng Chia University, No. 100, Wenhwa Road, Seatwen District, Taichung 40724, Taiwan.
| | - Ming-Yung Lee
- Department of Data Science and Big Data Analytics, Providence University, Taichung, No. 200, Section 7, Taiwan Boulevard, Shalu District, Taichung 43301, Taiwan.
| | - Yi-Chang Su
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, No.155-1, Section 2, Linong Street, Beitou District, Taipei 11221, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, No.91, Hsueh-Shih Road, Taichung 40402, Taiwan.
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