1
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Khan U, Mubariz M, Khlidj Y, Nasir MM, Ramadan S, Saeed F, Muhammad A, Abuelazm M. Safety and Efficacy of Camostat Mesylate for Covid-19: a systematic review and Meta-analysis of Randomized controlled trials. BMC Infect Dis 2024; 24:709. [PMID: 39030491 PMCID: PMC11264738 DOI: 10.1186/s12879-024-09468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 06/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Camostat mesylate, an oral serine protease inhibitor, is a powerful TMPRSS2 inhibitor and has been reported as a possible antiviral treatment against COVID-19. Therefore, we aim to assess the safety and efficacy of camostat mesylate for COVID-19 treatment. METHODS A systematic review and meta-analysis synthesizing randomized controlled trials from PubMed, Scopus, Embase, Cochrane, Web of Science, clinical trials.gov, and medrxiv until June 2023. The outcomes were pooled using Mean difference (MD) for continuous outcomes and risk ratio (RR) for dichotomous outcomes. The protocol is registered in PROSPERO with ID CRD42023439633. RESULTS Nine RCTs, including 1,623 patients, were included in this analysis. There was no difference between camostat mesylate and placebo in producing negative PCR test results at 1-7 days (RR: 0.76, 95% CI: [0.54, 1.06] P = 0.1), 8-14 days (RR: 1.02, 95% CI: [0.84, 1.23] P = 0.87), or 15-21 days (RR: 0.99, 95% CI: [0.82, 1.19] P = 0.90); clinical resolution of symptoms at 1-7 days (RR: 0.94 (95% CI: 0.58, 1.53) P = 0.81), 8-14 days (RR: 0.91, 95% CI: [0.74, 1.11] P = 0.33, ), or 15-21 days (RR: 0.77, 95% CI: [0.40, 1.51] P = 0.45); and time to symptom improvement (MD:-0.38 weeks (95% CI: [-1.42, 0.66] P = 0.47, I2 = 85%). CONCLUSION Camostat mesylate did not improve clinical outcomes in patients with COVID-19, compared to placebo.
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Affiliation(s)
- Ubaid Khan
- King Edward Medical University, Lahore, Pakistan.
| | | | - Yehya Khlidj
- Faculty of medicine, Algiers University, Alger Centre, Algeria
| | | | | | - Fatima Saeed
- King Edward Medical University, Lahore, Pakistan
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2
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Lan Q, Yan Y, Zhang G, Xia S, Zhou J, Lu L, Jiang S. Clinical development of antivirals against SARS-CoV-2 and its variants. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100208. [PMID: 38149085 PMCID: PMC10750039 DOI: 10.1016/j.crmicr.2023.100208] [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] [Indexed: 12/28/2023] Open
Abstract
The unceasing global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) calls for the development of novel therapeutics. Although many newly developed antivirals and repurposed antivirals have been applied to the treatment of coronavirus disease 2019 (COVID-19), antivirals showing satisfactory clinical efficacy are few in number. In addition, the loss of sensitivity to variants of concern (VOCs) and lack of oral bioavailability have also limited the clinical application of some antivirals. These facts remind us to develop more potent and broad-spectrum antivirals with better pharmacokinetic/pharmacodynamic properties to fight against infections from SARS-CoV-2, its variants, and other human coronaviruses (HCoVs). In this review, we summarize the latest advancements in the clinical development of antivirals against infections by SARS-CoV-2 and its variants.
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Affiliation(s)
- Qiaoshuai Lan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Yan Yan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Guangxu Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jie Zhou
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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3
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Cesar-Silva D, Pereira-Dutra FS, Giannini ALM, Maya-Monteiro CM, de Almeida CJG. Lipid compartments and lipid metabolism as therapeutic targets against coronavirus. Front Immunol 2023; 14:1268854. [PMID: 38106410 PMCID: PMC10722172 DOI: 10.3389/fimmu.2023.1268854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023] Open
Abstract
Lipids perform a series of cellular functions, establishing cell and organelles' boundaries, organizing signaling platforms, and creating compartments where specific reactions occur. Moreover, lipids store energy and act as secondary messengers whose distribution is tightly regulated. Disruption of lipid metabolism is associated with many diseases, including those caused by viruses. In this scenario, lipids can favor virus replication and are not solely used as pathogens' energy source. In contrast, cells can counteract viruses using lipids as weapons. In this review, we discuss the available data on how coronaviruses profit from cellular lipid compartments and why targeting lipid metabolism may be a powerful strategy to fight these cellular parasites. We also provide a formidable collection of data on the pharmacological approaches targeting lipid metabolism to impair and treat coronavirus infection.
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Affiliation(s)
- Daniella Cesar-Silva
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Filipe S. Pereira-Dutra
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Lucia Moraes Giannini
- Laboratory of Functional Genomics and Signal Transduction, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa M. Maya-Monteiro
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratory of Endocrinology and Department of Endocrinology and Metabolism, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Cecília Jacques G. de Almeida
- Laboratory of Immunopharmacology, Department of Genetics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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4
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Padmanabhan P, Dixit NM. Modelling how increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin B/L inhibitors. J Theor Biol 2023; 572:111568. [PMID: 37393986 DOI: 10.1016/j.jtbi.2023.111568] [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: 02/13/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
The SARS-CoV-2 Omicron variant harbours many mutations in its spike protein compared to the original SARS-CoV-2 strain, which may alter its ability to enter cells, cell tropism, and response to interventions blocking virus entry. To elucidate these effects, we developed a mathematical model of SARS-CoV-2 entry into target cells and applied it to analyse recent in vitro data. SARS-CoV-2 can enter cells via two pathways, one using the host proteases Cathepsin B/L and the other using the host protease TMPRSS2. We found enhanced entry efficiency of the Omicron variant in cells where the original strain preferentially used Cathepsin B/L and reduced efficiency where it used TMPRSS2. The Omicron variant thus appears to have evolved to use the Cathepsin B/L pathway better but at the expense of its ability to use the TMPRSS2 pathway compared to the original strain. We estimated >4-fold enhanced efficiency of the Omicron variant in entry via the Cathepsin B/L pathway and >3-fold reduced efficiency via the TMPRSS2 pathway compared to the original or other strains in a cell type-dependent manner. Our model predicted that Cathepsin B/L inhibitors would be more efficacious and TMPRSS2 inhibitors less efficacious in blocking Omicron variant entry into cells than the original strain. Furthermore, model predictions suggested that drugs simultaneously targeting the two pathways would exhibit synergy. The maximum synergy and drug concentrations yielding it would differ for the Omicron variant compared to the original strain. Our findings provide insights into the cell entry mechanisms of the Omicron variant and have implications for intervention targeting these mechanisms.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia.
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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5
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Kant R, Kareinen L, Ojha R, Strandin T, Saber SH, Lesnikova A, Kuivanen S, Sirnonen T, Joensuu M, Vapalahti O, Kirchhausen T, Kipar A, Balistreri G. Complete Protection from SARS-CoV-2 Lung Infection in Mice Through Combined Intranasal Delivery of PIKfyve Kinase and TMPRSS2 Protease Inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549731. [PMID: 37503261 PMCID: PMC10370096 DOI: 10.1101/2023.07.19.549731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Emerging variants of concern of SARS-CoV-2 can significantly reduce the prophylactic and therapeutic efficacy of vaccines and neutralizing antibodies due to mutations in the viral genome. Targeting cell host factors required for infection provides a complementary strategy to overcome this problem since the host genome is less susceptible to variation during the life span of infection. The enzymatic activities of the endosomal PIKfyve phosphoinositide kinase and the serine protease TMPRSS2 are essential to meditate infection in two complementary viral entry pathways. Simultaneous inhibition in cultured cells of their enzymatic activities with the small molecule inhibitors apilimod dimesylate and nafamostat mesylate synergistically prevent viral entry and infection of native SARS-CoV-2 and vesicular stomatitis virus (VSV)-SARS-CoV-2 chimeras expressing the SARS-CoV-2 surface spike (S) protein and of variants of concern. We now report prophylactic prevention of lung infection in mice intranasally infected with SARS-CoV-2 beta by combined intranasal delivery of very low doses of apilimod dimesylate and nafamostat mesylate, in a formulation that is stable for over 3 months at room temperature. Administration of these drugs up to 6 hours post infection did not inhibit infection of the lungs but substantially reduced death of infected airway epithelial cells. The efficiency and simplicity of formulation of the drug combination suggests its suitability as prophylactic or therapeutic treatment against SARS-CoV-2 infection in households, point of care facilities, and under conditions where refrigeration would not be readily available.
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Affiliation(s)
- Ravi Kant
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Lauri Kareinen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Helsinki, Finland
| | - Ravi Ojha
- Medicum Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Medicum Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Saber Hassan Saber
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Angelina Lesnikova
- Medicum Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Tarja Sirnonen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Merja Joensuu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Olli Vapalahti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Medicum Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Anja Kipar
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Giuseppe Balistreri
- Medicum Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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6
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Sengar A, Cervantes M, Bondalapati ST, Hess T, Kasson PM. Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry. J Virol 2023; 97:e0199222. [PMID: 37133381 DOI: 10.1128/jvi.01992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to cell surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here, we used single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We found that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases is used to activate the virus. This suggests that the fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2 in which the subcellular location of entry likely depends on the differential activity of airway, cellsurface, and endosomal proteases, but all support infection. Inhibition of any single host protease may thus reduce infection in some cells but may be less clinically robust. IMPORTANCE SARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we used single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effects. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.
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Affiliation(s)
- Anjali Sengar
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Marcos Cervantes
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Sai T Bondalapati
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Tobin Hess
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Peter M Kasson
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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7
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Yang K, Wang C, Kreutzberger AJB, White KI, Pfuetzner RA, Esquivies L, Kirchhausen T, Brunger AT. Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor. Proc Natl Acad Sci U S A 2023; 120:e2300360120. [PMID: 36940324 PMCID: PMC10068829 DOI: 10.1073/pnas.2300360120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 03/22/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical for its membrane fusion activity. We show that one of these mutations, N969K induces a substantial displacement in the structure of the heptad repeat 2 (HR2) backbone in the HR1HR2 postfusion bundle. Due to this mutation, fusion-entry peptide inhibitors based on the Wuhan strain sequence are less efficacious. Here, we report an Omicron-specific peptide inhibitor designed based on the structure of the Omicron HR1HR2 postfusion bundle. Specifically, we inserted an additional residue in HR2 near the Omicron HR1 K969 residue to better accommodate the N969K mutation and relieve the distortion in the structure of the HR1HR2 postfusion bundle it introduced. The designed inhibitor recovers the loss of inhibition activity of the original longHR2_42 peptide with the Wuhan strain sequence against the Omicron variant in both a cell-cell fusion assay and a vesicular stomatitis virus (VSV)-SARS-CoV-2 chimera infection assay, suggesting that a similar approach could be used to combat future variants. From a mechanistic perspective, our work suggests the interactions in the extended region of HR2 may mediate the initial landing of HR2 onto HR1 during the transition of the S protein from the prehairpin intermediate to the postfusion state.
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Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Alex J. B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Tomas Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
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8
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Doijen J, Temmerman K, Van den Eynde C, Diels A, Van den Broeck N, Van Gool M, Heo I, Jaensch S, Zwaagstra M, Diosa Toro M, Chiu W, De Jonghe S, Leyssen P, Bojkova D, Ciesek S, Cinatl J, Verschueren L, Buyck C, Van Kuppeveld F, Neyts J, Van Loock M, Van Damme E. Identification of Z-Tyr-Ala-CHN 2, a Cathepsin L Inhibitor with Broad-Spectrum Cell-Specific Activity against Coronaviruses, including SARS-CoV-2. Microorganisms 2023; 11:717. [PMID: 36985290 PMCID: PMC10055926 DOI: 10.3390/microorganisms11030717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
The ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is partly under control by vaccination. However, highly potent and safe antiviral drugs for SARS-CoV-2 are still needed to avoid development of severe COVID-19. We report the discovery of a small molecule, Z-Tyr-Ala-CHN2, which was identified in a cell-based antiviral screen. The molecule exerts sub-micromolar antiviral activity against SARS-CoV-2, SARS-CoV-1, and human coronavirus 229E. Time-of-addition studies reveal that Z-Tyr-Ala-CHN2 acts at the early phase of the infection cycle, which is in line with the observation that the molecule inhibits cathepsin L. This results in antiviral activity against SARS-CoV-2 in VeroE6, A549-hACE2, and HeLa-hACE2 cells, but not in Caco-2 cells or primary human nasal epithelial cells since the latter two cell types also permit entry via transmembrane protease serine subtype 2 (TMPRSS2). Given their cell-specific activity, cathepsin L inhibitors still need to prove their value in the clinic; nevertheless, the activity profile of Z-Tyr-Ala-CHN2 makes it an interesting tool compound for studying the biology of coronavirus entry and replication.
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Affiliation(s)
- Jordi Doijen
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Koen Temmerman
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Annick Diels
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | | | - Inha Heo
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Steffen Jaensch
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Mayra Diosa Toro
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Winston Chiu
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Leyssen
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Denisa Bojkova
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Jindrich Cinatl
- Institute for Medical Virology, University Hospital, Paul-Ehrlich-Str. 40, Frankfurt University, 60596 Frankfurt am Main, Germany
| | - Lore Verschueren
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Christophe Buyck
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Frank Van Kuppeveld
- Faculty of Veterinary Medicine, Yalelaan 1, Virology Division, Department of Biomolecular Health Sciences, Infectious Diseases and Immunology, Utrecht University, 3584 Utrecht, The Netherlands
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Herestraat 49, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Marnix Van Loock
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ellen Van Damme
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
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9
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Sun M, Zhang C, Sui D, Yang C, Pyeon D, Huang X, Hu J. Rational Design and Synthesis of D-galactosyl Lysophospholipids as Selective Substrates and non-ATP-competitive Inhibitors of Phosphatidylinositol Phosphate Kinases. Chemistry 2023; 29:e202202083. [PMID: 36424188 PMCID: PMC10099810 DOI: 10.1002/chem.202202083] [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: 07/04/2022] [Indexed: 11/27/2022]
Abstract
Phosphatidylinositol phosphate kinases (PIPKs) produce lipid signaling molecules and have been attracting increasing attention as drug targets for cancer, neurodegenerative diseases, and viral infection. Given the potential cross-inhibition of kinases and other ATP-utilizing enzymes by ATP-competitive inhibitors, targeting the unique lipid substrate binding site represents a superior strategy for PIPK inhibition. Here, by taking advantage of the nearly identical stereochemistry between myo-inositol and D-galactose, we designed and synthesized a panel of D-galactosyl lysophospholipids, one of which was found to be a selective substrate of phosphatidylinositol 4-phosphate 5-kinase. Derivatization of this compound led to the discovery of a human PIKfyve inhibitor with an apparent IC50 of 6.2 μM, which significantly potentiated the inhibitory effect of Apilimod, an ATP-competitive PIKfyve inhibitor under clinical trials against SARS-CoV-2 infection and amyotrophic lateral sclerosis. Our results provide the proof of concept that D-galactose-based phosphoinositide mimetics can be developed into artificial substrates and new inhibitors of PIPKs.
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Affiliation(s)
- Mengxia Sun
- Department of Chemistry, Michigan State University, Michigan, MI 48824, USA
| | - Chi Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, MI 48824, USA
| | - Dexin Sui
- Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, MI 48824, USA
| | - Canchai Yang
- Department of Microbiology & Molecular Genetics, Michigan State University, Michigan, MI 48824, USA
| | - Dohun Pyeon
- Department of Microbiology & Molecular Genetics, Michigan State University, Michigan, MI 48824, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, Michigan, MI 48824, USA.,Department of Biomedical Engineering, Michigan State University, Michigan, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, Michigan, MI 48824, USA
| | - Jian Hu
- Department of Chemistry, Michigan State University, Michigan, MI 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, Michigan, MI 48824, USA
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10
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Pérez-Vargas J, Shapira T, Olmstead AD, Villanueva I, Thompson CAH, Ennis S, Gao G, De Guzman J, Williams DE, Wang M, Chin A, Bautista-Sánchez D, Agafitei O, Levett P, Xie X, Nuzzo G, Freire VF, Quintana-Bulla JI, Bernardi DI, Gubiani JR, Suthiphasilp V, Raksat A, Meesakul P, Polbuppha I, Cheenpracha S, Jaidee W, Kanokmedhakul K, Yenjai C, Chaiyosang B, Teles HL, Manzo E, Fontana A, Leduc R, Boudreault PL, Berlinck RGS, Laphookhieo S, Kanokmedhakul S, Tietjen I, Cherkasov A, Krajden M, Nabi IR, Niikura M, Shi PY, Andersen RJ, Jean F. Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics. Antiviral Res 2023; 209:105484. [PMID: 36503013 PMCID: PMC9729583 DOI: 10.1016/j.antiviral.2022.105484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andrea D Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Meng Wang
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Aaleigha Chin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Diana Bautista-Sánchez
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Vitor F Freire
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Virayu Suthiphasilp
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Achara Raksat
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Pornphimol Meesakul
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Isaraporn Polbuppha
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | | | - Wuttichai Jaidee
- Medicinal Plants Innovation Center of Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kwanjai Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Boonyanoot Chaiyosang
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Helder Lopes Teles
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, CEP 78736-900, Rondonópolis, MT, Brazil
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, 80126, Napoli, Italy
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Surat Laphookhieo
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Somdej Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ian Tietjen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, School of Biomedical Engineering, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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11
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Cryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase. Nat Commun 2022; 13:6955. [PMID: 36376282 PMCID: PMC9663175 DOI: 10.1038/s41467-022-34364-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Enteropeptidase (EP) initiates intestinal digestion by proteolytically processing trypsinogen, generating catalytically active trypsin. EP dysfunction causes a series of pancreatic diseases including acute necrotizing pancreatitis. However, the molecular mechanisms of EP activation and substrate recognition remain elusive, due to the lack of structural information on the EP heavy chain. Here, we report cryo-EM structures of human EP in inactive, active, and substrate-bound states at resolutions from 2.7 to 4.9 Å. The EP heavy chain was observed to clamp the light chain with CUB2 domain for substrate recognition. The EP light chain N-terminus induced a rearrangement of surface-loops from inactive to active conformations, resulting in activated EP. The heavy chain then served as a hinge for light-chain conformational changes to recruit and subsequently cleave substrate. Our study provides structural insights into rearrangements of EP surface-loops and heavy chain dynamics in the EP catalytic cycle, advancing our understanding of EP-associated pancreatitis.
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12
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Luo S, Zhang J, Kreutzberger AJ, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW. An antibody from single human V H-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Sci Immunol 2022; 7:eadd5446. [PMID: 35951767 PMCID: PMC9407951 DOI: 10.1126/sciimmunol.add5446] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 Omicron subvariants have generated a worldwide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of vaccination-induced antibodies. To manage Omicron subvariants and prepare for new ones, additional means of isolating broad and potent humanized SARS-CoV-2 neutralizing antibodies are desirable. Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vκ1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact CDR3 sequences generated by nontemplated junctional modifications during V(D)J recombination. Immunizing this mouse model with SARS-CoV-2 (Wuhan-Hu-1) spike protein immunogens elicited several VH1-2/Vκ1-33-based neutralizing antibodies that bound RBD in a different mode from each other and from those of many prior patient-derived VH1-2-based neutralizing antibodies. Of these, SP1-77 potently and broadly neutralized all SARS-CoV-2 variants through BA.5. Cryo-EM studies revealed that SP1-77 bound RBD away from the receptor-binding motif via a CDR3-dominated recognition mode. Lattice light-sheet microscopy-based studies showed that SP1-77 did not block ACE2-mediated viral attachment or endocytosis but rather blocked viral-host membrane fusion. The broad and potent SP1-77 neutralization activity and nontraditional mechanism of action suggest that it might have therapeutic potential. Likewise, the SP1-77 binding epitope may inform vaccine strategies. Last, the type of humanized mouse models that we have described may contribute to identifying therapeutic antibodies against future SARS-CoV-2 variants and other pathogens.
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Affiliation(s)
- Sai Luo
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Alex J.B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Changbin Jing
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Aimee Chapdelaine Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lucas Vieira Francisco
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anand Saminathan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Himanshu Batra
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hidde Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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13
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Wagoner J, Herring S, Hsiang TY, Ianevski A, Biering SB, Xu S, Hoffmann M, Pöhlmann S, Gale M, Aittokallio T, Schiffer JT, White JM, Polyak SJ. Combinations of Host- and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2. Microbiol Spectr 2022; 10:e0333122. [PMID: 36190406 PMCID: PMC9718484 DOI: 10.1128/spectrum.03331-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 02/08/2023] Open
Abstract
Three directly acting antivirals (DAAs) demonstrated substantial reduction in COVID-19 hospitalizations and deaths in clinical trials. However, these agents did not completely prevent severe illness and are associated with cases of rebound illness and viral shedding. Combination regimens can enhance antiviral potency, reduce the emergence of drug-resistant variants, and lower the dose of each component in the combination. Concurrently targeting virus entry and virus replication offers opportunities to discover synergistic drug combinations. While combination antiviral drug treatments are standard for chronic RNA virus infections, no antiviral combination therapy has been approved for SARS-CoV-2. Here, we demonstrate that combining host-targeting antivirals (HTAs) that target TMPRSS2 and hence SARS-CoV-2 entry, with the DAA molnupiravir, which targets SARS-CoV-2 replication, synergistically suppresses SARS-CoV-2 infection in Calu-3 lung epithelial cells. Strong synergy was observed when molnupiravir, an oral drug, was combined with three TMPRSS2 (HTA) oral or inhaled inhibitors: camostat, avoralstat, or nafamostat. The combination of camostat plus molnupiravir was also effective against the beta and delta variants of concern. The pyrimidine biosynthesis inhibitor brequinar combined with molnupiravir also conferred robust synergistic inhibition. These HTA+DAA combinations had similar potency to the synergistic all-DAA combination of molnupiravir plus nirmatrelvir, the protease inhibitor found in paxlovid. Pharmacodynamic modeling allowed estimates of antiviral potency at all possible concentrations of each agent within plausible therapeutic ranges, suggesting possible in vivo efficacy. The triple combination of camostat, brequinar, and molnupiravir further increased antiviral potency. These findings support the development of HTA+DAA combinations for pandemic response and preparedness. IMPORTANCE Imagine a future viral pandemic where if you test positive for the new virus, you can quickly take some medicines at home for a few days so that you do not get too sick. To date, only single drugs have been approved for outpatient use against SARS-CoV-2, and we are learning that these have some limitations and may succumb to drug resistance. Here, we show that combinations of two oral drugs are better than the single ones in blocking SARS-CoV-2, and we use mathematical modeling to show that these drug combinations are likely to work in people. We also show that a combination of three oral drugs works even better at eradicating the virus. Our findings therefore bode well for the development of oral drug cocktails for at home use at the first sign of an infection by a coronavirus or other emerging viral pathogens.
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Affiliation(s)
- Jessica Wagoner
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Shawn Herring
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Tien-Ying Hsiang
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California—Berkeley, Berkeley, California, USA
| | - Shuang Xu
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University of Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University of Göttingen, Göttingen, Germany
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Judith M. White
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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14
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Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein. Proc Natl Acad Sci U S A 2022; 119:e2210990119. [PMID: 36122200 PMCID: PMC9546559 DOI: 10.1073/pnas.2210990119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ∼100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.
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Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Alex J. B. Kreutzberger
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Ravi Ojha
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Suvi Kuivanen
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Sergio Couoh-Cardel
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Serena Muratcioglu
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Timothy J. Eisen
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Richard G. Held
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Subu Subramanian
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Kendra Marcus
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Catherine A. Doyle
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22903
| | - John Kuriyan
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki 00290, Finland
- Helsinki University Hospital Diagnostic Center, Clinical Microbiology, University of Helsinki, Helsinki 00290, Finland
| | | | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
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15
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Abstract
Infection by SARS-CoV-2 depends upon the large spike (S) protein decorating the virions and is responsible for receptor engagement and subsequent fusion of viral and cellular membranes allowing release of virion contents into the cell. Using new single-particle imaging tools to visualize and track the successive steps from virion attachment to fusion, combined with chemical and genetic perturbations of the cells, we provide direct evidence for the cellular uptake routes of productive infection in multiple cell types and their dependence on proteolysis of S by cell surface or endosomal proteases. We show that fusion and content release always require the acidic environment from endosomes, preceded by liberation of the S1 fragment which depends on angiotensin converting enzyme receptor engagement. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cell entry starts with membrane attachment and ends with spike (S) protein–catalyzed membrane fusion depending on two cleavage steps, namely, one usually by furin in producing cells and the second by TMPRSS2 on target cells. Endosomal cathepsins can carry out both. Using real-time three-dimensional single-virion tracking, we show that fusion and genome penetration require virion exposure to an acidic milieu of pH 6.2 to 6.8, even when furin and TMPRSS2 cleavages have occurred. We detect the sequential steps of S1-fragment dissociation, fusion, and content release from the cell surface in TMPRRS2-overexpressing cells only when exposed to acidic pH. We define a key role of an acidic environment for successful infection, found in endosomal compartments and at the surface of TMPRSS2-expressing cells in the acidic milieu of the nasal cavity.
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16
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Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD. Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. J Med Chem 2022; 65:12860-12882. [PMID: 36111834 PMCID: PMC9574855 DOI: 10.1021/acs.jmedchem.2c00697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
From a designed library of indolyl pyrimidinamines, we
identified
a highly potent and cell-active chemical probe (17) that
inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive
evaluation of inhibitor selectivity confirmed that this PIKfyve probe
demonstrates excellent kinome-wide selectivity. A structurally related
indolyl pyrimidinamine (30) was characterized as a negative
control that lacks PIKfyve inhibitory activity and exhibits exquisite
selectivity when profiled broadly. Chemical probe 17 disrupts
multiple phases of the lifecycle of β-coronaviruses: viral replication
and viral entry. The diverse antiviral roles of PIKfyve have not been
previously probed comprehensively in a single study or using the same
compound set. Our scaffold is a distinct chemotype that lacks the
canonical morpholine hinge-binder of classical lipid kinase inhibitors
and has a non-overlapping kinase off-target profile with known PIKfyve
inhibitors. Our chemical probe set can be used by the community to
further characterize the role of PIKfyve in virology.
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Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances M. Potjewyd
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rebekah J. Dickmander
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sharon Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sophia M. Min
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S. McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J. Moorman
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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17
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Tobback E, Degroote S, Buysse S, Delesie L, Van Dooren L, Vanherrewege S, Barbezange C, Hutse V, Romano M, Thomas I, Padalko E, Callens S, De Scheerder MA. Efficacy and safety of camostat mesylate in early COVID-19 disease in an ambulatory setting: a randomized placebo-controlled phase II trial. Int J Infect Dis 2022; 122:628-635. [PMID: 35803469 PMCID: PMC9254441 DOI: 10.1016/j.ijid.2022.06.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES This study aimed to assess the efficacy and safety of 300 mg camostat mesylate three times daily in a fasted state to treat early phase COVID-19 in an ambulatory setting. METHODS We conducted a phase II randomized controlled trial in symptomatic (maximum 5 days) and asymptomatic patients with confirmed COVID-19 infection. Patients were randomly assigned in a 2:1 ratio to receive either camostat mesylate or a placebo. Outcomes included change in nasopharyngeal viral load, time to clinical improvement, the presence of neutralizing antibodies, and safety. RESULTS Of 96 participants randomized between November 2020 and June 2021, analyses were performed on the data of 90 participants who completed treatment (N = 61 camostat mesylate, N = 29 placebo). The estimated mean change in cycle threshold between day 1 and day 5 between the camostat and placebo group was 1.183 (P = 0.511). The unadjusted hazard ratio for clinical improvement in the camostat group was 0.965 (95% confidence interval, 0.480-1.942, P = 0.921 by Cox regression). The percentage distribution of the 50% neutralizing antibody titer at day 28 visit and frequency of adverse events were similar between the two groups. CONCLUSION Under this protocol, camostat mesylate was not found to be effective as an antiviral drug against SARS-CoV-2. TRIAL REGISTRATION ClinicalTrials.gov NCT04625114; November 12, 2020.
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Affiliation(s)
- Els Tobback
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Sophie Degroote
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Sabine Buysse
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Liesbeth Delesie
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Lucas Van Dooren
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Sophie Vanherrewege
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Cyril Barbezange
- National Influenza Centre, Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Veronik Hutse
- National Influenza Centre, Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Marta Romano
- Immune Response Service, Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Isabelle Thomas
- National Influenza Centre, Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium.
| | - Elizaveta Padalko
- Department of Laboratory Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
| | - Marie-Angélique De Scheerder
- Department of General Internal Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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18
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The Key Role of Lysosomal Protease Cathepsins in Viral Infections. Int J Mol Sci 2022; 23:ijms23169089. [PMID: 36012353 PMCID: PMC9409221 DOI: 10.3390/ijms23169089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Cathepsins encompass a family of lysosomal proteases that mediate protein degradation and turnover. Although mainly localized in the endolysosomal compartment, cathepsins are also found in the cytoplasm, nucleus, and extracellular space, where they are involved in cell signaling, extracellular matrix assembly/disassembly, and protein processing and trafficking through the plasma and nuclear membrane and between intracellular organelles. Ubiquitously expressed in the body, cathepsins play regulatory roles in a wide range of physiological processes including coagulation, hormone secretion, immune responses, and others. A dysregulation of cathepsin expression and/or activity has been associated with many human diseases, including cancer, diabetes, obesity, cardiovascular and inflammatory diseases, kidney dysfunctions, and neurodegenerative disorders, as well as infectious diseases. In viral infections, cathepsins may promote (1) activation of the viral attachment glycoproteins and entry of the virus into target cells; (2) antigen processing and presentation, enabling the virus to replicate in infected cells; (3) up-regulation and processing of heparanase that facilitates the release of viral progeny and the spread of infection; and (4) activation of cell death that may either favor viral clearance or assist viral propagation. In this review, we report the most relevant findings on the molecular mechanisms underlying cathepsin involvement in viral infection physiopathology, and we discuss the potential of cathepsin inhibitors for therapeutical applications in viral infectious diseases.
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19
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Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the pre-hairpin intermediate of the spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503553. [PMID: 35982670 PMCID: PMC9387137 DOI: 10.1101/2022.08.11.503553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors which block formation of the so-called HR1HR2 six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. Here we performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic SARS-CoV-2 infection assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ~100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a pre-hairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the pre-hairpin intermediate of the S protein. Significance Statement SARS-CoV-2 infection requires fusion of viral and host membranes, mediated by the viral spike glycoprotein (S). Due to the importance of viral membrane fusion, S has been a popular target for developing vaccines and therapeutics. We discovered a simple peptide that inhibits infection by all major variants of SARS-CoV-2 with nanomolar efficacies. In marked contrast, widely used shorter peptides that lack a key N-terminal extension are about 100 x less potent than this peptide. Our results suggest that a simple peptide with a suitable sequence can be a potent and cost-effective therapeutic against COVID-19 and they provide new insights at the virus entry mechanism.
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20
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Inhibitors of Deubiquitinating Enzymes Interfere with the SARS-CoV-2 Papain-like Protease and Block Virus Replication In Vitro. Viruses 2022; 14:v14071404. [PMID: 35891385 PMCID: PMC9324251 DOI: 10.3390/v14071404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/01/2023] Open
Abstract
The ubiquitin proteasome system (UPS), particularly its deubiquitinating enzymes (DUBs), play a key role in the replication cycle of coronaviruses. The SARS-CoV-2 papain-like protease (Plpro) is known to process the viral polyproteins to form the replicase transcriptase complex and to counteract the host viral response. Recently, it was shown that this viral protease can also act as a deubiquitinating enzyme. In this study, we demonstrate that certain DUB-Inhibitors (DIs) interfere with SARS-CoV-2 replication. The DIs PR-619 and HBX41108 restrict SARS-CoV-2 in both Vero B4 and human Calu-3 lung cells where cells were infected with a Multiplicity of Infection (MOI) of 0.02. An in vitro protease assay using recombinant Plpro and Amido-4-methylcoumarin (AMC)-conjugated substrate revealed that PR-619 and HBX41108 are able to block the protease at concentrations where the interventions restricted virus replication. In contrast, DIs that do not inhibit Plpro had no influence on virus replication, which indicated that the protease might be at least one major target. Future vertical studies that would gain more insights into the mechanisms of how DUBs effect the replication of SARS-CoV-2 will further validate them as a potential therapeutic target.
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21
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SARS-CoV-2 requires acidic pH to infect cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35702155 PMCID: PMC9196115 DOI: 10.1101/2022.06.09.495472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 cell entry starts with membrane attachment and ends with spike-protein (S) catalyzed membrane fusion depending on two cleavage steps, one usually by furin in producing cells and the second by TMPRSS2 on target cells. Endosomal cathepsins can carry out both. Using real-time 3D single virion tracking, we show fusion and genome penetration requires virion exposure to an acidic milieu of pH 6.2-6.8, even when furin and TMPRSS2 cleavages have occurred. We detect the sequential steps of S1-fragment dissociation, fusion, and content release from the cell surface in TMPRRS2 overexpressing cells only when exposed to acidic pH. We define a key role of an acidic environment for successful infection, found in endosomal compartments and at the surface of TMPRSS2 expressing cells in the acidic milieu of the nasal cavity. Significance Statement Infection by SARS-CoV-2 depends upon the S large spike protein decorating the virions and is responsible for receptor engagement and subsequent fusion of viral and cellular membranes allowing release of virion contents into the cell. Using new single particle imaging tools, to visualize and track the successive steps from virion attachment to fusion, combined with chemical and genetic perturbations of the cells, we provide the first direct evidence for the cellular uptake routes of productive infection in multiple cell types and their dependence on proteolysis of S by cell surface or endosomal proteases. We show that fusion and content release always require the acidic environment from endosomes, preceded by liberation of the S1 fragment which depends on ACE2 receptor engagement. One sentence summary Detailed molecular snapshots of the productive infectious entry pathway of SARS-CoV-2 into cells.
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22
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Petrenko VA, Gillespie JW, De Plano LM, Shokhen MA. Phage-Displayed Mimotopes of SARS-CoV-2 Spike Protein Targeted to Authentic and Alternative Cellular Receptors. Viruses 2022; 14:v14020384. [PMID: 35215976 PMCID: PMC8879608 DOI: 10.3390/v14020384] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/11/2022] Open
Abstract
The evolution of the SARS-CoV-2 virus during the COVID-19 pandemic was accompanied by the emergence of new heavily mutated viral variants with increased infectivity and/or resistance to detection by the human immune system. To respond to the urgent need for advanced methods and materials to empower a better understanding of the mechanisms of virus’s adaptation to human host cells and to the immuno-resistant human population, we suggested using recombinant filamentous bacteriophages, displaying on their surface foreign peptides termed “mimotopes”, which mimic the structure of viral receptor-binding sites on the viral spike protein and can serve as molecular probes in the evaluation of molecular mechanisms of virus infectivity. In opposition to spike-binding antibodies that are commonly used in studying the interaction of the ACE2 receptor with SARS-CoV-2 variants in vitro, phage spike mimotopes targeted to other cellular receptors would allow discovery of their role in viral infection in vivo using cell culture, tissue, organs, or the whole organism. Phage mimotopes of the SARS-CoV-2 Spike S1 protein have been developed using a combination of phage display and molecular mimicry concepts, termed here “phage mimicry”, supported by bioinformatics methods. The key elements of the phage mimicry concept include: (1) preparation of a collection of p8-type (landscape) phages, which interact with authentic active receptors of live human cells, presumably mimicking the binding interactions of human coronaviruses such as SARS-CoV-2 and its variants; (2) discovery of closely related amino acid clusters with similar 3D structural motifs on the surface of natural ligands (FGF1 and NRP1), of the model receptor of interest FGFR and the S1 spike protein; and (3) an ELISA analysis of the interaction between candidate phage mimotopes with FGFR3 (a potential alternative receptor) in comparison with ACE2 (the authentic receptor).
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Affiliation(s)
- Valery A. Petrenko
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Correspondence: (V.A.P.); (J.W.G.); Tel.: +1-334-844-2897 (V.A.P.); +1-334-844-2625 (J.W.G.)
| | - James W. Gillespie
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Correspondence: (V.A.P.); (J.W.G.); Tel.: +1-334-844-2897 (V.A.P.); +1-334-844-2625 (J.W.G.)
| | - Laura Maria De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98122 Messina, Italy;
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23
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Abstract
It is currently unknown if SARS-CoV-2 can spread through cell–cell contacts, and if so, the underlying mechanisms and implications. In this work, we show, by using lentiviral pseudotyped virus, that the spike protein of SARS-CoV-2 mediates the viral cell-to-cell transmission, with an efficiency higher than that of SARS-CoV. We also find that cell–cell fusion contributes to cell-to-cell transmission, yet ACE2 is not absolutely required. While the authentic variants of concern (VOCs) B.1.1.7 (alpha) and B.1.351 (beta) differ in cell-free infectivity from wild type and from each other, these VOCs have similar cell-to-cell transmission capability and exhibit differential sensitivity to neutralization by vaccinee sera. Results from our study will contribute to a better understanding of SARS-CoV-2 spread and pathogenesis. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the global COVID-19 pandemic. Herein, we provide evidence that SARS-CoV-2 spreads through cell–cell contact in cultures, mediated by the spike glycoprotein. SARS-CoV-2 spike is more efficient in facilitating cell-to-cell transmission than is SARS-CoV spike, which reflects, in part, their differential cell–cell fusion activity. Interestingly, treatment of cocultured cells with endosomal entry inhibitors impairs cell-to-cell transmission, implicating endosomal membrane fusion as an underlying mechanism. Compared with cell-free infection, cell-to-cell transmission of SARS-CoV-2 is refractory to inhibition by neutralizing antibody or convalescent sera of COVID-19 patients. While angiotensin-converting enzyme 2 enhances cell-to-cell transmission, we find that it is not absolutely required. Notably, despite differences in cell-free infectivity, the authentic variants of concern (VOCs) B.1.1.7 (alpha) and B.1.351 (beta) have similar cell-to-cell transmission capability. Moreover, B.1.351 is more resistant to neutralization by vaccinee sera in cell-free infection, whereas B.1.1.7 is more resistant to inhibition by vaccinee sera in cell-to-cell transmission. Overall, our study reveals critical features of SARS-CoV-2 spike-mediated cell-to-cell transmission, with important implications for a better understanding of SARS-CoV-2 spread and pathogenesis.
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24
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Chapoval SP, Keegan AD. Perspectives and potential approaches for targeting neuropilin 1 in SARS-CoV-2 infection. Mol Med 2021; 27:162. [PMID: 34961486 PMCID: PMC8711287 DOI: 10.1186/s10020-021-00423-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel type b coronavirus responsible for the COVID-19 pandemic. With over 224 million confirmed infections with this virus and more than 4.6 million people dead because of it, it is critically important to define the immunological processes occurring in the human response to this virus and pathogenetic mechanisms of its deadly manifestation. This perspective focuses on the contribution of the recently discovered interaction of SARS-CoV-2 Spike protein with neuropilin 1 (NRP1) receptor, NRP1 as a virus entry receptor for SARS-CoV-2, its role in different physiologic and pathologic conditions, and the potential to target the Spike-NRP1 interaction to combat virus infectivity and severe disease manifestations.
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Affiliation(s)
- Svetlana P Chapoval
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, 800 West Baltimore Street, Baltimore, MD, 21201, USA.
- Program in Oncology at the Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
- SemaPlex LLC, Ellicott City, MD, USA.
| | - Achsah D Keegan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, 800 West Baltimore Street, Baltimore, MD, 21201, USA
- Program in Oncology at the Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
- VA Maryland Health Care System, Baltimore VA Medical Center, Baltimore, MD, USA
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25
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Serra A, Fratello M, Federico A, Ojha R, Provenzani R, Tasnadi E, Cattelani L, Del Giudice G, Kinaret PAS, Saarimäki LA, Pavel A, Kuivanen S, Cerullo V, Vapalahti O, Horvath P, Lieto AD, Yli-Kauhaluoma J, Balistreri G, Greco D. Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation. Brief Bioinform 2021; 23:6484515. [PMID: 34962256 PMCID: PMC8769897 DOI: 10.1093/bib/bbab507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
The pharmacological arsenal against the COVID-19 pandemic is largely based on generic anti-inflammatory strategies or poorly scalable solutions. Moreover, as the ongoing vaccination campaign is rolling slower than wished, affordable and effective therapeutics are needed. To this end, there is increasing attention toward computational methods for drug repositioning and de novo drug design. Here, multiple data-driven computational approaches are systematically integrated to perform a virtual screening and prioritize candidate drugs for the treatment of COVID-19. From the list of prioritized drugs, a subset of representative candidates to test in human cells is selected. Two compounds, 7-hydroxystaurosporine and bafetinib, show synergistic antiviral effects in vitro and strongly inhibit viral-induced syncytia formation. Moreover, since existing drug repositioning methods provide limited usable information for de novo drug design, the relevant chemical substructures of the identified drugs are extracted to provide a chemical vocabulary that may help to design new effective drugs.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Ravi Ojha
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riccardo Provenzani
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ervin Tasnadi
- Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Giusy Del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Pia A S Kinaret
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura A Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Alisa Pavel
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland
| | - Suvi Kuivanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vincenzo Cerullo
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Horvath
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Synthetic and Systems Biology Unit, Biological Research Centre, Eotvos Lorand Research Network, Szeged, Hungary
| | - Antonio Di Lieto
- Department of Forensic Psychiatry, Aarhus University, Aarhus, Denmark
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giuseppe Balistreri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,BioMediTech Institute, Tampere University, Tampere, Finland.,Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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26
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White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ. Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses. mBio 2021; 12:e0334721. [PMID: 34933447 PMCID: PMC8689562 DOI: 10.1128/mbio.03347-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The world was unprepared for coronavirus disease 2019 (COVID-19) and remains ill-equipped for future pandemics. While unprecedented strides have been made developing vaccines and treatments for COVID-19, there remains a need for highly effective and widely available regimens for ambulatory use for novel coronaviruses and other viral pathogens. We posit that a priority is to develop pan-family drug cocktails to enhance potency, limit toxicity, and avoid drug resistance. We urge cocktail development for all viruses with pandemic potential both in the short term (<1 to 2 years) and longer term with pairs of drugs in advanced clinical testing or repurposed agents approved for other indications. While significant efforts were launched against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in vitro and in the clinic, many studies employed solo drugs and had disappointing results. Here, we review drug combination studies against SARS-CoV-2 and other viruses and introduce a model-driven approach to assess drug pairs with the highest likelihood of clinical efficacy. Where component agents lack sufficient potency, we advocate for synergistic combinations to achieve therapeutic levels. We also discuss issues that stymied therapeutic progress against COVID-19, including testing of agents with low likelihood of efficacy late in clinical disease and lack of focus on developing virologic surrogate endpoints. There is a need to expedite efficient clinical trials testing drug combinations that could be taken at home by recently infected individuals and exposed contacts as early as possible during the next pandemic, whether caused by a coronavirus or another viral pathogen. The approach herein represents a proactive plan for global viral pandemic preparedness.
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Affiliation(s)
- Judith M. White
- University of Virginia, Department of Cell Biology, Charlottesville, Virginia, USA
- University of Virginia, Department of Microbiology, Charlottesville, Virginia, USA
| | - Joshua T. Schiffer
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Rachel A. Bender Ignacio
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shuang Xu
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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27
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Garg AK, Mittal S, Padmanabhan P, Desikan R, Dixit NM. Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost. Front Immunol 2021; 12:776933. [PMID: 34917089 PMCID: PMC8669483 DOI: 10.3389/fimmu.2021.776933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of COVID-19 vaccines appears to depend in complex ways on the vaccine dosage and the interval between the prime and boost doses. Unexpectedly, lower dose prime and longer prime-boost intervals have yielded higher efficacies in clinical trials. To elucidate the origins of these effects, we developed a stochastic simulation model of the germinal center (GC) reaction and predicted the antibody responses elicited by different vaccination protocols. The simulations predicted that a lower dose prime could increase the selection stringency in GCs due to reduced antigen availability, resulting in the selection of GC B cells with higher affinities for the target antigen. The boost could relax this selection stringency and allow the expansion of the higher affinity GC B cells selected, improving the overall response. With a longer dosing interval, the decay in the antigen with time following the prime could further increase the selection stringency, amplifying this effect. The effect remained in our simulations even when new GCs following the boost had to be seeded by memory B cells formed following the prime. These predictions offer a plausible explanation of the observed paradoxical effects of dosage and dosing interval on vaccine efficacy. Tuning the selection stringency in the GCs using prime-boost dosages and dosing intervals as handles may help improve vaccine efficacies.
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Affiliation(s)
- Amar K. Garg
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Soumya Mittal
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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28
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Islam F, Bibi S, Meem AFK, Islam MM, Rahaman MS, Bepary S, Rahman MM, Rahman MM, Elzaki A, Kajoak S, Osman H, ElSamani M, Khandaker MU, Idris AM, Emran TB. Natural Bioactive Molecules: An Alternative Approach to the Treatment and Control of COVID-19. Int J Mol Sci 2021; 22:12638. [PMID: 34884440 PMCID: PMC8658031 DOI: 10.3390/ijms222312638] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 02/07/2023] Open
Abstract
Several coronaviruses (CoVs) have been associated with serious health hazards in recent decades, resulting in the deaths of thousands around the globe. The recent coronavirus pandemic has emphasized the importance of discovering novel and effective antiviral medicines as quickly as possible to prevent more loss of human lives. Positive-sense RNA viruses with group spikes protruding from their surfaces and an abnormally large RNA genome enclose CoVs. CoVs have already been related to a range of respiratory infectious diseases possibly fatal to humans, such as MERS, SARS, and the current COVID-19 outbreak. As a result, effective prevention, treatment, and medications against human coronavirus (HCoV) is urgently needed. In recent years, many natural substances have been discovered with a variety of biological significance, including antiviral properties. Throughout this work, we reviewed a wide range of natural substances that interrupt the life cycles for MERS and SARS, as well as their potential application in the treatment of COVID-19.
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Affiliation(s)
- Fahadul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Atkia Farzana Khan Meem
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mohaimenul Islam
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Saidur Rahaman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Sristy Bepary
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mizanur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Md. Mominur Rahman
- Department of Pharmacy, Daffodil International University, Dhaka 1207, Bangladesh; (F.I.); (A.F.K.M.); (M.M.I.); (M.S.R.); (S.B.); (M.M.R.); (M.M.R.)
| | - Amin Elzaki
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Samih Kajoak
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Hamid Osman
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mohamed ElSamani
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.E.); (S.K.); (H.O.); (M.E.)
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia;
| | - Abubakr M. Idris
- Department of Chemistry, College of Science, King Khalid University, Abha 62529, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62529, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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29
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Ianevski A, Yao R, Lysvand H, Grødeland G, Legrand N, Oksenych V, Zusinaite E, Tenson T, Bjørås M, Kainov DE. Nafamostat-Interferon-α Combination Suppresses SARS-CoV-2 Infection In Vitro and In Vivo by Cooperatively Targeting Host TMPRSS2. Viruses 2021; 13:1768. [PMID: 34578348 PMCID: PMC8473362 DOI: 10.3390/v13091768] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 and its vaccine/immune-escaping variants continue to pose a serious threat to public health due to a paucity of effective, rapidly deployable, and widely available treatments. Here, we address these challenges by combining Pegasys (IFNα) and nafamostat to effectively suppress SARS-CoV-2 infection in cell culture and hamsters. Our results indicate that Serpin E1 is an important mediator of the antiviral activity of IFNα and that both Serpin E1 and nafamostat can target the same cellular factor TMPRSS2, which plays a critical role in viral replication. The low doses of the drugs in combination may have several clinical advantages, including fewer adverse events and improved patient outcome. Thus, our study may provide a proactive solution for the ongoing pandemic and potential future coronavirus outbreaks, which is still urgently required in many parts of the world.
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Affiliation(s)
- Aleksandr Ianevski
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Rouan Yao
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Hilde Lysvand
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Gunnveig Grødeland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway;
- Institute of Clinical Medicine (KlinMed), University of Oslo, 0318 Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Nicolas Legrand
- Oncodesign, 25 Avenue du Québec, 91140 Villebon Sur Yvette, France;
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Denis E. Kainov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, 00014 Helsinki, Finland
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