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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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2
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Al Adem K, Ferreira JC, Villanueva AJ, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso THS, Saksena NK, Rabeh WM. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024; 44:BSR20231395. [PMID: 39036877 DOI: 10.1042/bsr20231395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024] Open
Abstract
Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.
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Affiliation(s)
- Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- 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
| | - Farah El-Sadaany
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Imen Masmoudi
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Yugmee Gidiya
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tariro Gurudza
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Masdar City, Abu Dhabi, United Arab Emirates
| | - Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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3
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Aschenbrenner JC, de Godoy AS, Fairhead M, Tomlinson CWE, Winokan M, Balcomb BH, Capkin E, Chandran AV, Golding M, Koekemoer L, Lithgo RM, Marples PG, Ni X, Thompson W, Wild C, Xavier MAE, Fearon D, von Delft F. Identifying novel chemical matter against the Chikungunya virus nsP3 macrodomain through crystallographic fragment screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609196. [PMID: 39229067 PMCID: PMC11370605 DOI: 10.1101/2024.08.23.609196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Chikungunya virus (CHIKV) causes severe fever, rash and debilitating joint pain that can last for months1,2or even years. Millions of people have been infected with CHIKV, mostly in low and middle-income countries, and the virus continues to spread into new areas due to the geographical expansion of its mosquito hosts. Its genome encodes a macrodomain, which functions as an ADP-ribosyl hydrolase, removing ADPr from viral and host-cell proteins interfering with the innate immune response. Mutational studies have shown that the CHIKV nsP3 macrodomain is necessary for viral replication, making it a potential target for the development of antiviral therapeutics. We, therefore, performed a high-throughput crystallographic fragment screen against the CHIKV nsP3 macrodomain, yielding 109 fragment hits covering the ADPr-binding site and two adjacent subsites that are absent in the homologous macrodomain of SARS-CoV-2 but may be present in other alphaviruses, such as Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV). Finally, a subset of overlapping fragments was used to manually design three fragment merges covering the adenine and oxyanion subsites. The rich dataset of chemical matter and structural information discovered from this fragment screen is publicly available and can be used as a starting point for developing a CHIKV nsP3 macrodomain inhibitor.
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Affiliation(s)
- Jasmin C Aschenbrenner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | | | - Michael Fairhead
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Charles W E Tomlinson
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Max Winokan
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Blake H Balcomb
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Eda Capkin
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Anu V Chandran
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Mathew Golding
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Lizbe Koekemoer
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Ryan M Lithgo
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Peter G Marples
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Xiaomin Ni
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Warren Thompson
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Conor Wild
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Mary-Ann E Xavier
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Daren Fearon
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Frank von Delft
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
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4
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Alvarez N, Adam GC, Howe JA, Sharma V, Zimmerman MD, Dolgov E, Rasheed R, Nizar F, Sahay K, Nelson AM, Park S, Zhou X, Burlein C, Fay JF, Iwamoto DV, Bahnck-Teets CM, Getty KL, Lin Goh S, Salhab I, Smith K, Boyce CW, Cabalu TD, Murgolo N, Fox NG, Mayhood TW, Shurtleff VW, Layton ME, Parish CA, McCauley JA, Olsen DB, Perlin DS. Novel Pan-Coronavirus 3CL Protease Inhibitor MK-7845: Biological and Pharmacological Profiling. Viruses 2024; 16:1158. [PMID: 39066320 PMCID: PMC11281459 DOI: 10.3390/v16071158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) continues to be a global threat due to its ability to evolve and generate new subvariants, leading to new waves of infection. Additionally, other coronaviruses like Middle East respiratory syndrome coronavirus (MERS-CoV, formerly known as hCoV-EMC), which first emerged in 2012, persist and continue to present a threat of severe illness to humans. The continued identification of novel coronaviruses, coupled with the potential for genetic recombination between different strains, raises the possibility of new coronavirus clades of global concern emerging. As a result, there is a pressing need for pan-CoV therapeutic drugs and vaccines. After the extensive optimization of an HCV protease inhibitor screening hit, a novel 3CLPro inhibitor (MK-7845) was discovered and subsequently profiled. MK-7845 exhibited nanomolar in vitro potency with broad spectrum activity against a panel of clinical SARS-CoV-2 subvariants and MERS-CoV. Furthermore, when administered orally, MK-7845 demonstrated a notable reduction in viral burdens by >6 log orders in the lungs of transgenic mice infected with SARS-CoV-2 (K18-hACE2 mice) and MERS-CoV (K18-hDDP4 mice).
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Affiliation(s)
- Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | | | | | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Matthew D. Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Enriko Dolgov
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Risha Rasheed
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Fatima Nizar
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Khushboo Sahay
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Andrew M. Nelson
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA (D.S.P.)
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5
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de Oliveira Só YA, Bezerra KS, Gargano R, Mendonça FLL, Souto JT, Fulco UL, Pereira Junior ML, Junior LAR. In Silico Comparative Analysis of Ivermectin and Nirmatrelvir Inhibitors Interacting with the SARS-CoV-2 Main Protease. Biomolecules 2024; 14:755. [PMID: 39062468 PMCID: PMC11274663 DOI: 10.3390/biom14070755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 07/28/2024] Open
Abstract
Exploring therapeutic options is crucial in the ongoing COVID-19 pandemic caused by SARS-CoV-2. Nirmatrelvir, which is a potent inhibitor that targets the SARS-CoV-2 Mpro, shows promise as an antiviral treatment. Additionally, Ivermectin, which is a broad-spectrum antiparasitic drug, has demonstrated effectiveness against the virus in laboratory settings. However, its clinical implications are still debated. Using computational methods, such as molecular docking and 100 ns molecular dynamics simulations, we investigated how Nirmatrelvir and Ivermectin interacted with SARS-CoV-2 Mpro(A). Calculations using density functional theory were instrumental in elucidating the behavior of isolated molecules, primarily by analyzing the frontier molecular orbitals. Our analysis revealed distinct binding patterns: Nirmatrelvir formed strong interactions with amino acids, like MET49, MET165, HIS41, HIS163, HIS164, PHE140, CYS145, GLU166, and ASN142, showing stable binding, with a root-mean-square deviation (RMSD) of around 2.0 Å. On the other hand, Ivermectin interacted with THR237, THR239, LEU271, LEU272, and LEU287, displaying an RMSD of 1.87 Å, indicating enduring interactions. Both ligands stabilized Mpro(A), with Ivermectin showing stability and persistent interactions despite forming fewer hydrogen bonds. These findings offer detailed insights into how Nirmatrelvir and Ivermectin bind to the SARS-CoV-2 main protease, providing valuable information for potential therapeutic strategies against COVID-19.
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Affiliation(s)
| | - Katyanna Sales Bezerra
- Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte, Natal 59078-570, Brazil; (K.S.B.); (U.L.F.)
| | - Ricardo Gargano
- Institute of Physics, University of Brasília, Brasília 70910-900, Brazil; (Y.A.d.O.S.); (L.A.R.J.)
| | - Fabio L. L. Mendonça
- Department of Electrical Engineering, College of Technology, University of Brasília, Brasília 70910-900, Brazil; (F.L.L.M.); (M.L.P.J.)
| | - Janeusa Trindade Souto
- Department of Microbiology and Parasitology, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59064-741, Brazil;
| | - Umberto L. Fulco
- Department of Biophysics and Pharmacology, Federal University of Rio Grande do Norte, Natal 59078-570, Brazil; (K.S.B.); (U.L.F.)
| | - Marcelo Lopes Pereira Junior
- Department of Electrical Engineering, College of Technology, University of Brasília, Brasília 70910-900, Brazil; (F.L.L.M.); (M.L.P.J.)
| | - Luiz Antônio Ribeiro Junior
- Institute of Physics, University of Brasília, Brasília 70910-900, Brazil; (Y.A.d.O.S.); (L.A.R.J.)
- Computational Materials Laboratory, University of Brasília, LCCMat, Brasília 70919-970, Brazil
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6
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Krismer L, Schöppe H, Rauch S, Bante D, Sprenger B, Naschberger A, Costacurta F, Fürst A, Sauerwein A, Rupp B, Kaserer T, von Laer D, Heilmann E. Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir. NPJ VIRUSES 2024; 2:23. [PMID: 38933182 PMCID: PMC11196219 DOI: 10.1038/s44298-024-00028-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/14/2024] [Indexed: 06/28/2024]
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35% and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of SARS-CoV-2, MERS-CoV and other main proteases. Nirmatrelvir inhibited several of these proteases, whereas ensitrelvir was less broadly active. To simulate nirmatrelvir's clinical use against MERS-CoV and subsequent resistance development, we applied a safe, surrogate virus-based system. Using the surrogate virus, we previously selected hallmark mutations of SARS-CoV-2-Mpro, such as T21I, M49L, S144A, E166A/K/V and L167F. In the current study, we selected a pool of MERS-CoV-Mpro mutants, characterized the resistance and modelled the steric effect of catalytic site mutants S142G, S142R, S147Y and A171S.
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Affiliation(s)
- Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Sprenger
- Institute of Biochemistry, University of Innsbruck, CMBI – Center for Molecular Biosciences Innsbruck, Innsbruck, 6020 Austria
| | - Andreas Naschberger
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | | | - Anna Fürst
- Institute of Molecular Immunology, Technical University of Munich, Munich, 81675 Germany
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
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Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, Gabrielyan Y, Ayvazyan M, Bozdaganyan M, Fakhar Z, Gharaghani S, Zakaryan H. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep 2024; 14:14255. [PMID: 38902397 PMCID: PMC11189913 DOI: 10.1038/s41598-024-65228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024] Open
Abstract
The coronavirus disease 19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health crisis with millions of confirmed cases and related deaths. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and presents an attractive target for drug development. Despite the approval of some drugs, the search for effective treatments continues. In this study, we systematically evaluated 342 holo-crystal structures of Mpro to identify optimal conformations for structure-based virtual screening (SBVS). Our analysis revealed limited structural flexibility among the structures. Three docking programs, AutoDock Vina, rDock, and Glide were employed to assess the efficiency of virtual screening, revealing diverse performances across selected Mpro structures. We found that the structures 5RHE, 7DDC, and 7DPU (PDB Ids) consistently displayed the lowest EF, AUC, and BEDROCK scores. Furthermore, these structures demonstrated the worst pose prediction results in all docking programs. Two structural differences contribute to variations in docking performance: the absence of the S1 subsite in 7DDC and 7DPU, and the presence of a subpocket in the S2 subsite of 7DDC, 7DPU, and 5RHE. These findings underscore the importance of selecting appropriate Mpro conformations for SBVS, providing valuable insights for advancing drug discovery efforts.
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Affiliation(s)
- Hamlet Khachatryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
| | - Mher Matevosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Vardan Harutyunyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Smbat Gevorgyan
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Anastasiya Shavina
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Irina Tirosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Yeva Gabrielyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Marusya Ayvazyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | | | - Zeynab Fakhar
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hovakim Zakaryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
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8
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Xiao YQ, Long J, Zhang SS, Zhu YY, Gu SX. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorg Chem 2024; 147:107380. [PMID: 38636432 DOI: 10.1016/j.bioorg.2024.107380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.
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Affiliation(s)
- Ya-Qi Xiao
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
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9
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Syed YY. Ensitrelvir Fumaric Acid: First Approval. Drugs 2024; 84:721-728. [PMID: 38795314 DOI: 10.1007/s40265-024-02039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 05/27/2024]
Abstract
Ensitrelvir fumaric acid (Xocova®) is an oral SARS-CoV-2 main protease inhibitor developed by Shionogi for the treatment of SARS-CoV-2 infection. It is the first single-entity, nonpeptidic, noncovalent, small molecule antiviral of its kind. Following emergency regulatory approval in Japan in November 2022, ensitrelvir received standard approval in Japan on 5 March 2024 for the treatment of SARS-CoV-2 infection. This article summarizes the milestones in the development of ensitrelvir leading to this first standard approval for SARS-CoV-2 infection.
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Affiliation(s)
- Yahiya Y Syed
- Springer Nature, Mairangi Bay, Private Bag 65901, Auckland, 0754, New Zealand.
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10
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Fukumoto Y, Suzuki N, Hara R, Tanaka YK, Ogra Y. Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine. Int J Mol Sci 2024; 25:5767. [PMID: 38891954 PMCID: PMC11172239 DOI: 10.3390/ijms25115767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
While research has identified several inhibitors of the main protease (Mpro) of SARS-CoV-2, a significant portion of these compounds exhibit reduced activity in the presence of reducing agents, raising concerns about their effectiveness in vivo. Furthermore, the conventional biosafety level 3 (BSL-3) for cellular assays using viral particles poses a limitation for the widespread evaluation of Mpro inhibitor efficacy in a cell-based assay. Here, we established a BSL-1 compatible cellular assay to evaluate the in vivo potential of Mpro inhibitors. This assay utilizes mammalian cells expressing a tagged Mpro construct containing N-terminal glutathione S-transferase (GST) and C-terminal hemagglutinin (HA) tags and monitors Mpro autodigestion. Using this method, GC376 and boceprevir effectively inhibited Mpro autodigestion, suggesting their potential in vivo activity. Conversely, carmofur and ebselen did not exhibit significant inhibitory effects in this assay. We further investigated the inhibitory potential of selenoneine on Mpro using this approach. Computational analyses of binding energies suggest that noncovalent interactions play a critical role in facilitating the covalent modification of the C145 residue, leading to Mpro inhibition. Our method is straightforward, cost-effective, and readily applicable in standard laboratories, making it accessible to researchers with varying levels of expertise in infectious diseases.
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Grants
- 19K07079 Ministry of Education, Culture, Sports, Science and Technology
- 21H04920 Ministry of Education, Culture, Sports, Science and Technology
- 19H05772 Ministry of Education, Culture, Sports, Science and Technology
- 22K05345 Ministry of Education, Culture, Sports, Science and Technology
- 24K09793 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (N.S.); (Y.-k.T.); (Y.O.)
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11
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Voget R, Breidenbach J, Claff T, Hingst A, Sylvester K, Steinebach C, Vu LP, Weiße RH, Bartz U, Sträter N, Müller CE, Gütschow M. Development of an active-site titrant for SARS-CoV-2 main protease as an indispensable tool for evaluating enzyme kinetics. Acta Pharm Sin B 2024; 14:2349-2357. [PMID: 38799620 PMCID: PMC11121168 DOI: 10.1016/j.apsb.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 05/29/2024] Open
Abstract
A titrant for the SARS-CoV-2 main protease (Mpro) was developed that enables, for the first time, the exact determination of the concentration of the enzymatically active Mpro by active-site titration. The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme-titrant complex. Four fluorogenic substrates of Mpro, including a prototypical, internally quenched Dabcyl-EDANS peptide, were compared in terms of solubility under typical assay conditions. By exploiting the new titrant, key kinetic parameters for the Mpro-catalyzed cleavage of these substrates were determined.
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Affiliation(s)
- Rabea Voget
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Julian Breidenbach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Alexandra Hingst
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Katharina Sylvester
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Lan Phuong Vu
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Renato H. Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach 53359, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Christa E. Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn 53121, Germany
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12
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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13
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Ibrahim M, Sun X, de Oliveira VM, Liu R, Clayton J, Kilani HE, Shen J, Hilgenfeld R. Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583178. [PMID: 38496596 PMCID: PMC10942327 DOI: 10.1101/2024.03.04.583178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
During the continuing evolution of SARS-CoV-2, the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November that year. Along with its sublineages, it has maintained a prominent role ever since. The Nsp5 main protease (Mpro) of the Omicron virus is characterized by a single dominant mutation, P132H. Here we determined the X-ray crystal structures of the P132H mutant (or O-Mpro) as free enzyme and in complex with the Mpro inhibitor, the alpha-ketoamide 13b-K, and we conducted enzymology, biophysical as well as theoretical studies to characterize the O-Mpro. We found that O-Mpro has a similar overall structure and binding with 13b-K; however, it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro (with "WT" referring to the original Wuhan-1 strain). Intriguingly, the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here. The empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to the less favorable van der Waals interactions and backbone conformation in the individual protomers. The all-atom continuous constant pH molecular dynamics (MD) simulations reveal that His132 and Glu240 display coupled titration. At pH 7, His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged. In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations, we also determined crystal structures of the relatively frequent P132H+T169S double mutant but found little evidence for a correlation between the two sites.
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Affiliation(s)
- Mohamed Ibrahim
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Vinicius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Joseph Clayton
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Haifa El Kilani
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, 23562 Lübeck, Germany
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Furuya C, Yasuda H, Hiki M, Shirane S, Yamana T, Uchimura A, Inano T, Takaku T, Hamano Y, Ando M. Case report: Ensitrelvir for treatment of persistent COVID-19 in lymphoma patients: a report of two cases. Front Immunol 2024; 15:1287300. [PMID: 38333218 PMCID: PMC10850233 DOI: 10.3389/fimmu.2024.1287300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Persistent COVID-19 is a well recognized issue of concern in patients with hematological malignancies. Such patients are not only at risk of mortality due to the infection itself, but are also at risk of suboptimal malignancy-related outcomes because of delays and terminations of chemotherapy. We report two lymphoma patients with heavily pretreated persistent COVID-19 in which ensitrelvir brought about radical changes in the clinical course leading to rapid remissions. Patient 1 was on ibrutinib treatment for mantle cell lymphoma when he developed COVID-19 pneumonia which was severe and ongoing for 2 months despite therapy with molnupiravir, multiple courses of remdesivir, one course of sotrovimab, tocilizumab, and steroids. Patient 2 was administered R-CHOP therapy for diffuse large B-cell lymphoma when he developed COVID-19 which was ongoing for a month despite treatment with multiple courses of remdesivir and one course of sotrovimab. A 5-day administration of ensitrelvir promptly resolved the persistent COVID-19 accommodated by negative conversions of RT-qPCR tests in both patients within days. Ensitrelvir is a novel COVID-19 therapeutic that accelerates viral clearance through inhibition of the main protease of SARS-CoV-2, 3-chymotrypsin-like protease, which is vital for viral replication. Ensitrelvir is a promising treatment approach for immunocompromised lymphoma patients suffering from persisting and severe COVID-19.
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Affiliation(s)
- Chiho Furuya
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hajime Yasuda
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Makoto Hiki
- Department of Cardiovascular Biology and Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuichi Shirane
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomohito Yamana
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ayana Uchimura
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tadaaki Inano
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoiku Takaku
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasuharu Hamano
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miki Ando
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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