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Leborgne NG, Devisme C, Kozarac N, Berenguer Veiga I, Ebert N, Godel A, Grau-Roma L, Scherer M, Plattet P, Thiel V, Zimmer G, Taddeo A, Benarafa C. Neutrophil proteases are protective against SARS-CoV-2 by degrading the spike protein and dampening virus-mediated inflammation. JCI Insight 2024; 9:e174133. [PMID: 38470488 DOI: 10.1172/jci.insight.174133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Studies on severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) have highlighted the crucial role of host proteases for viral replication and the immune response. The serine proteases furin and TMPRSS2 and lysosomal cysteine proteases facilitate viral entry by limited proteolytic processing of the spike (S) protein. While neutrophils are recruited to the lungs during COVID-19 pneumonia, little is known about the role of the neutrophil serine proteases (NSPs) cathepsin G (CatG), elastase (NE), and proteinase 3 (PR3) on SARS-CoV-2 entry and replication. Furthermore, the current paradigm is that NSPs may contribute to the pathogenesis of severe COVID-19. Here, we show that these proteases cleaved the S protein at multiple sites and abrogated viral entry and replication in vitro. In mouse models, CatG significantly inhibited viral replication in the lung. Importantly, lung inflammation and pathology were increased in mice deficient in NE and/or CatG. These results reveal that NSPs contribute to innate defenses against SARS-CoV-2 infection via proteolytic inactivation of the S protein and that NE and CatG limit lung inflammation in vivo. We conclude that therapeutic interventions aiming to reduce the activity of NSPs may interfere with viral clearance and inflammation in COVID-19 patients.
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Affiliation(s)
- Nathan Gf Leborgne
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Christelle Devisme
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Nedim Kozarac
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
- Graduate School for Cellular and Biomedical Sciences
| | - Inês Berenguer Veiga
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Nadine Ebert
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Aurélie Godel
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | | | - Melanie Scherer
- Graduate School for Cellular and Biomedical Sciences
- Division of Neurological Sciences, Vetsuisse Faculty, and
| | - Philippe Plattet
- Division of Neurological Sciences, Vetsuisse Faculty, and
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Adriano Taddeo
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
| | - Charaf Benarafa
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland
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2
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Sun Y, Li YY, Leung CK, Hu P. iNGNN-DTI: prediction of drug-target interaction with interpretable nested graph neural network and pretrained molecule models. Bioinformatics 2024; 40:btae135. [PMID: 38449285 PMCID: PMC10957515 DOI: 10.1093/bioinformatics/btae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/31/2023] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
MOTIVATION Drug-target interaction (DTI) prediction aims to identify interactions between drugs and protein targets. Deep learning can automatically learn discriminative features from drug and protein target representations for DTI prediction, but challenges remain, making it an open question. Existing approaches encode drugs and targets into features using deep learning models, but they often lack explanations for underlying interactions. Moreover, limited labeled DTIs in the chemical space can hinder model generalization. RESULTS We propose an interpretable nested graph neural network for DTI prediction (iNGNN-DTI) using pre-trained molecule and protein models. The analysis is conducted on graph data representing drugs and targets by using a specific type of nested graph neural network, in which the target graphs are created based on 3D structures using Alphafold2. This architecture is highly expressive in capturing substructures of the graph data. We use a cross-attention module to capture interaction information between the substructures of drugs and targets. To improve feature representations, we integrate features learned by models that are pre-trained on large unlabeled small molecule and protein datasets, respectively. We evaluate our model on three benchmark datasets, and it shows a consistent improvement on all baseline models in all datasets. We also run an experiment with previously unseen drugs or targets in the test set, and our model outperforms all of the baselines. Furthermore, the iNGNN-DTI can provide more insights into the interaction by visualizing the weights learned by the cross-attention module. AVAILABILITY AND IMPLEMENTATION The source code of the algorithm is available at https://github.com/syan1992/iNGNN-DTI.
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Affiliation(s)
- Yan Sun
- Department of Biochemistry, Western University, London, ON, N6G 2V4, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Computer Science, Western University, London, ON, N6G 2V4, Canada
| | - Yan Yi Li
- Division of Biostatistics, University of Toronto, Toronto, ON, M5T 3M7, Canada
| | - Carson K Leung
- Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Pingzhao Hu
- Department of Biochemistry, Western University, London, ON, N6G 2V4, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Computer Science, Western University, London, ON, N6G 2V4, Canada
- Division of Biostatistics, University of Toronto, Toronto, ON, M5T 3M7, Canada
- Department of Oncology, Western University, London, ON, N6G 2V4, Canada
- Department of Epidemiology and Biostatistics, Western University, London, ON, N6G 2V4, Canada
- The Children’s Health Research Institute, Lawson Health Research Institute, London, ON, N6A 4V2, Canada
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3
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Jiang S, Yang H, Sun Z, Zhang Y, Li Y, Li J. The basis of complications in the context of SARS-CoV-2 infection: Pathological activation of ADAM17. Biochem Biophys Res Commun 2023; 679:37-46. [PMID: 37666046 DOI: 10.1016/j.bbrc.2023.08.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
The virulence of SARS-CoV-2 decreases with increasing infectivity, the primary approaches for antiviral treatments will be preventing or minimizing the complications resulting from virus infection. ADAM metallopeptidase domain 17 (ADAM17) activation by SARS-CoV-2 infection has a dual effect on the development of the disease: increased release of inflammatory cytokines and dysregulation of Angiotensin converting enzyme II (ACE2) on cell surfaces, inflammatory cytokine infiltration and loss of ACE2 protective function lead to a significant increase in the incidence of related complications. Importantly, pathologically activated ADAM17 showed superior features than S protein in regulating ACE2 expression and participating in the intra cellular replication of SARS-CoV-2. In short, SARS-CoV-2 elicits only a limited immune response when it promotes its own replication and pathogenicity through ADAM17. Therefore, the pathological activation of ADAM17 may also represent a diminished innate antiviral defense and an altered strategy of SARS-CoV-2 infection. In this review, we summarized recent advances in our understanding of the pathophysiology of ADAM17, with a focus on the new findings that SARS-CoV-2 affects ADAM17 expression through Furin protein converting enzyme and Mitogen-activated protein kinase (MAPK) pathway, and raises the hypothesis that SARS-CoV-2 may mediates the pathological activation of ADAM17 by hijacking the actin regulatory pathway, and discussed the underlying biological principles.
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Affiliation(s)
| | - Hao Yang
- Zunyi Medical University Guizhou, China
| | | | - Yi Zhang
- Zunyi Medical University Guizhou, China
| | - Yan Li
- Zunyi Medical University Guizhou, China
| | - Jida Li
- Zunyi Medical University Guizhou, China; Key Laboratory of Maternal & Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi, Guizhou, China.
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4
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Lushington GH, Linde A, Melgarejo T. Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog. BioTech (Basel) 2023; 12:61. [PMID: 37987478 PMCID: PMC10660736 DOI: 10.3390/biotech12040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.
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Affiliation(s)
| | - Annika Linde
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
| | - Tonatiuh Melgarejo
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766, USA;
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Melano I, Cheng WC, Kuo LL, Liu YM, Chou YC, Hung MC, Lai MMC, Sher YP, Su WC. A disintegrin and metalloproteinase domain 9 facilitates SARS-CoV-2 entry into cells with low ACE2 expression. Microbiol Spectr 2023; 11:e0385422. [PMID: 37713503 PMCID: PMC10581035 DOI: 10.1128/spectrum.03854-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/18/2023] [Indexed: 09/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the Coronavirus disease-19 (COVID-19) pandemic, utilizes angiotensin-converting enzyme 2 (ACE2) as a receptor for virus infection. However, the expression pattern of ACE2 does not coincide with the tissue tropism of SARS-CoV-2, hinting that other host proteins might be involved in facilitating SARS-CoV-2 entry. To explore potential host factors for SARS-CoV-2 entry, we performed an arrayed shRNA screen in H1650 and HEK293T cells. Here, we identified a disintegrin and a metalloproteinase domain 9 (ADAM9) protein as an important host factor for SARS-CoV-2 entry. Our data showed that silencing ADAM9 reduced virus entry, while its overexpression promoted infection. The knockdown of ADAM9 decreased the infectivity of the variants of concern tested-B.1.1.7 (alpha), B.1.617.2 (delta), and B.1.1.529 (omicron). Furthermore, mechanistic studies indicated that ADAM9 is involved in the binding and endocytosis stages of SARS-CoV-2 entry. Through immunoprecipitation experiments, we demonstrated that ADAM9 binds to the S1 subunit of the SARS-CoV-2 Spike. Additionally, ADAM9 can interact with ACE2, and co-expression of both proteins markedly enhances virus infection. Moreover, the enzymatic activity of ADAM9 facilitates virus entry. Our study reveals an insight into the mechanism of SARS-CoV-2 virus entry and elucidates the role of ADAM9 in virus infection. IMPORTANCE COVID-19, an infectious respiratory disease caused by SARS-CoV-2, has greatly impacted global public health and the economy. Extensive vaccination efforts have been launched worldwide over the last couple of years. However, several variants of concern that reduce the efficacy of vaccines have kept emerging. Thereby, further understanding of the mechanism of SARS-CoV-2 entry is indispensable, which will allow the development of an effective antiviral strategy. Here, we identify a disintegrin and metalloproteinase domain 9 (ADAM9) protein as a co-factor of ACE2 important for SARS-CoV-2 entry, even for the variants of concern, and show that ADAM9 interacts with Spike to aid virus entry. This virus-host interaction could be exploited to develop novel therapeutics against COVID-19.
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Affiliation(s)
- Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Li-Lan Kuo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yuag-Meng Liu
- Department of Internal Medicine, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Changhua Christian Medical Foundation, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Michael M. C. Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taipei, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- International Master’s Program of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Drug Development Center, China Medical University, Taichung, Taiwan
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6
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Aiello A, Najafi-Fard S, Goletti D. Initial immune response after exposure to Mycobacterium tuberculosis or to SARS-COV-2: similarities and differences. Front Immunol 2023; 14:1244556. [PMID: 37662901 PMCID: PMC10470049 DOI: 10.3389/fimmu.2023.1244556] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) and Coronavirus disease-2019 (COVID-19), whose etiologic agent is severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are currently the two deadliest infectious diseases in humans, which together have caused about more than 11 million deaths worldwide in the past 3 years. TB and COVID-19 share several aspects including the droplet- and aerosol-borne transmissibility, the lungs as primary target, some symptoms, and diagnostic tools. However, these two infectious diseases differ in other aspects as their incubation period, immune cells involved, persistence and the immunopathological response. In this review, we highlight the similarities and differences between TB and COVID-19 focusing on the innate and adaptive immune response induced after the exposure to Mtb and SARS-CoV-2 and the pathological pathways linking the two infections. Moreover, we provide a brief overview of the immune response in case of TB-COVID-19 co-infection highlighting the similarities and differences of each individual infection. A comprehensive understanding of the immune response involved in TB and COVID-19 is of utmost importance for the design of effective therapeutic strategies and vaccines for both diseases.
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Affiliation(s)
| | | | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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7
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Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue JI, Kawaguchi Y, Mansour RMA, Anvari A, Farahat AA. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses 2023; 15:1171. [PMID: 37243257 PMCID: PMC10223987 DOI: 10.3390/v15051171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and influenza A virus, require the host proteases to mediate viral entry into cells. Rather than targeting the continuously mutating viral proteins, targeting the conserved host-based entry mechanism could offer advantages. Nafamostat and camostat were discovered as covalent inhibitors of TMPRSS2 protease involved in viral entry. To circumvent their limitations, a reversible inhibitor might be required. Considering nafamostat structure and using pentamidine as a starting point, a small set of structurally diverse rigid analogues were designed and evaluated in silico to guide selection of compounds to be prepared for biological evaluation. Based on the results of in silico study, six compounds were prepared and evaluated in vitro. At the enzyme level, compounds 10-12 triggered potential TMPRSS2 inhibition with low micromolar IC50 concentrations, but they were less effective in cellular assays. Meanwhile, compound 14 did not trigger potential TMPRSS2 inhibition at the enzyme level, but it showed potential cellular activity regarding inhibition of membrane fusion with a low micromolar IC50 value of 10.87 µM, suggesting its action could be mediated by another molecular target. Furthermore, in vitro evaluation showed that compound 14 inhibited pseudovirus entry as well as thrombin and factor Xa. Together, this study presents compound 14 as a hit compound that might serve as a starting point for developing potential viral entry inhibitors with possible application against coronaviruses.
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Affiliation(s)
- Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehisa Matsumoto
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Jun-Ichiro Inoue
- Infection and Advanced Research Center (UTOPIA), The University of Tokyo Pandemic Preparedness, Tokyo 108-8639, Japan
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Reem M A Mansour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abtin Anvari
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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8
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Petersen E, Chudakova D, Erdyneeva D, Zorigt D, Shabalina E, Gudkov D, Karalkin P, Reshetov I, Mynbaev OA. COVID-19-The Shift of Homeostasis into Oncopathology or Chronic Fibrosis in Terms of Female Reproductive System Involvement. Int J Mol Sci 2023; 24:ijms24108579. [PMID: 37239926 DOI: 10.3390/ijms24108579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus remains a global public health concern due to the systemic nature of the infection and its long-term consequences, many of which remain to be elucidated. SARS-CoV-2 targets endothelial cells and blood vessels, altering the tissue microenvironment, its secretion, immune-cell subpopulations, the extracellular matrix, and the molecular composition and mechanical properties. The female reproductive system has high regenerative potential, but can accumulate damage, including due to SARS-CoV-2. COVID-19 is profibrotic and can change the tissue microenvironment toward an oncogenic niche. This makes COVID-19 and its consequences one of the potential regulators of a homeostasis shift toward oncopathology and fibrosis in the tissues of the female reproductive system. We are looking at SARS-CoV-2-induced changes at all levels in the female reproductive system.
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Affiliation(s)
- Elena Petersen
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Daria Chudakova
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Daiana Erdyneeva
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Dulamsuren Zorigt
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | | | - Denis Gudkov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Pavel Karalkin
- P.A. Herzen Moscow Research Institute of Oncology, 125284 Moscow, Russia
- Institute of Cluster Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Igor Reshetov
- Institute of Cluster Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Ospan A Mynbaev
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Li Y, Wang K, Sun H, Wu S, Wang H, Shi Y, Li X, Yan H, Yang G, Wu M, Li Y, Ding X, Si S, Jiang J, Du Y, Li Y, Hong B. Omicsynin B4 potently blocks coronavirus infection by inhibiting host proteases cathepsin L and TMPRSS2. Antiviral Res 2023; 214:105606. [PMID: 37076089 PMCID: PMC10110284 DOI: 10.1016/j.antiviral.2023.105606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/21/2023]
Abstract
The emergence of SARS-CoV-2 variants represents a major threat to public health and requires identification of novel therapeutic agents to address the unmet medical needs. Small molecules impeding viral entry through inhibition of spike protein priming proteases could have potent antiviral effects against SARS-CoV-2 infection. Omicsynin B4, a pseudo-tetrapeptides identified from Streptomyces sp. 1647, has potent antiviral activity against influenza A viruses in our previous study. Here, we found omicsynin B4 exhibited broad-spectrum anti-coronavirus activity against HCoV-229E, HCoV-OC43 and SARS-CoV-2 prototype and its variants in multiple cell lines. Further investigations revealed omicsynin B4 blocked the viral entry and might be related to the inhibition of host proteases. SARS-CoV-2 spike protein mediated pseudovirus assay supported the inhibitory activity on viral entry of omicsynin B4 with a more potent inhibition of Omicron variant, especially when overexpression of human TMPRSS2. Moreover, omicsynin B4 exhibited superior inhibitory activity in the sub-nanomolar range against CTSL, and a sub-micromolar inhibition against TMPRSS2 in biochemical assays. The molecular docking analysis confirmed that omicsynin B4 fits well in the substrate binding sites and forms a covalent bond to Cys25 and Ser441 in CTSL and TMPRSS2, respectively. In conclusion, we found that omicsynin B4 may serve as a natural protease inhibitor for CTSL and TMPRSS2, blocking various coronavirus S protein-driven entry into cells. These results further highlight the potential of omicsynin B4 as an attractive candidate as a broad-spectrum anti-coronavirus agent that could rapidly respond to emerging variants of SARS-CoV-2.
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Affiliation(s)
- Yihua Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kun Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongmin Sun
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuo Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Huiqiang Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xingxing Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Haiyan Yan
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Mengyuan Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiaotian Ding
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuyi Si
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jiandong Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yu Du
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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10
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Chan JFW, Huang X, Hu B, Chai Y, Shi H, Zhu T, Yuen TTT, Liu Y, Liu H, Shi J, Wen L, Shuai H, Hou Y, Yoon C, Cai JP, Zhang AJ, Zhou J, Yin F, Yuan S, Zhang BZ, Brindley MA, Shi ZL, Yuen KY, Chu H. Altered host protease determinants for SARS-CoV-2 Omicron. Sci Adv 2023; 9:eadd3867. [PMID: 36662861 PMCID: PMC9858505 DOI: 10.1126/sciadv.add3867] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/19/2022] [Indexed: 05/02/2023]
Abstract
Successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requires proteolytic cleavage of the viral spike protein. While the role of the host transmembrane protease serine 2 in SARS-CoV-2 infection is widely recognized, the involvement of other proteases capable of facilitating SARS-CoV-2 entry remains incompletely explored. Here, we show that multiple members from the membrane-type matrix metalloproteinase (MT-MMP) and a disintegrin and metalloproteinase families can mediate SARS-CoV-2 entry. Inhibition of MT-MMPs significantly reduces SARS-CoV-2 replication in vitro and in vivo. Mechanistically, we show that MT-MMPs can cleave SARS-CoV-2 spike and angiotensin-converting enzyme 2 and facilitate spike-mediated fusion. We further demonstrate that Omicron BA.1 has an increased efficiency on MT-MMP usage, while an altered efficiency on transmembrane serine protease usage for virus entry compared with that of ancestral SARS-CoV-2. These results reveal additional protease determinants for SARS-CoV-2 infection and enhance our understanding on the biology of coronavirus entry.
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Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China
- Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong, Special Administrative Region, People’s Republic of China
- Academician Workstation of Hainan Province, Hainan Medical University–The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Guangzhou Laboratory, Guangdong Province, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hongyu Shi
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, NY, New York, USA
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lei Wen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Anna Jinxia Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Feifei Yin
- Academician Workstation of Hainan Province, Hainan Medical University–The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan Province, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China
- Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People’s Republic of China
| | - Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
| | - Melinda A. Brindley
- Department of Infectious Diseases and Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, Hubei, People’s Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China
- Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong, Special Administrative Region, People’s Republic of China
- Academician Workstation of Hainan Province, Hainan Medical University–The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China; and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Guangzhou Laboratory, Guangdong Province, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China
- Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People’s Republic of China
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11
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Heindl MR, Böttcher-Friebertshäuser E. The role of influenza-A virus and coronavirus viral glycoprotein cleavage in host adaptation. Curr Opin Virol 2023; 58:101303. [PMID: 36753938 PMCID: PMC9847222 DOI: 10.1016/j.coviro.2023.101303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
While receptor binding is well recognized as a factor in influenza-A virus (IAV) and coronavirus (CoV) host adaptation, the role of viral glycoprotein cleavage has not been studied in detail so far. Interestingly, recent studies suggest that host species may differ in their protease repertoire available for cleavage. Furthermore, it was shown for certain bat-derived CoVs that proteolytic activation provides a critical barrier to infect human cells. Understanding the role of glycoprotein cleavage in different species and how IAV and CoVs adapt to a new protease repertoire may allow evaluating the zoonotic potential and risk posed by these viruses. Here, we summarize the current knowledge on the emergence of a multibasic cleavage site (CS) in the glycoproteins of IAVs and CoVs in different host species. Additionally, we discuss the role of transmembrane serine protease 2 (TMPRSS2) in virus activation and entry and a role of neuropilin-1 in acquisition of a multibasic CS in different hosts.
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12
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Nejat R, Torshizi MF, Najafi DJ. S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review. Vaccines (Basel) 2023; 11:vaccines11020204. [PMID: 36851081 PMCID: PMC9968219 DOI: 10.3390/vaccines11020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Since the spread of the deadly virus SARS-CoV-2 in late 2019, researchers have restlessly sought to unravel how the virus enters the host cells. Some proteins on each side of the interaction between the virus and the host cells are involved as the major contributors to this process: (1) the nano-machine spike protein on behalf of the virus, (2) angiotensin converting enzyme II, the mono-carboxypeptidase and the key component of renin angiotensin system on behalf of the host cell, (3) some host proteases and proteins exploited by SARS-CoV-2. In this review, the complex process of SARS-CoV-2 entrance into the host cells with the contribution of the involved host proteins as well as the sequential conformational changes in the spike protein tending to increase the probability of complexification of the latter with angiotensin converting enzyme II, the receptor of the virus on the host cells, are discussed. Moreover, the release of the catalytic ectodomain of angiotensin converting enzyme II as its soluble form in the extracellular space and its positive or negative impact on the infectivity of the virus are considered.
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Affiliation(s)
- Reza Nejat
- Department of Anesthesiology and Critical Care Medicine, Laleh Hospital, Tehran 1467684595, Iran
- Correspondence:
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13
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Guo X, Cao J, Cai JP, Wu J, Huang J, Asthana P, Wong SKK, Ye ZW, Gurung S, Zhang Y, Wang S, Wang Z, Ge X, Kwan HY, Lyu A, Chan KM, Wong N, Huang J, Zhou Z, Bian ZX, Yuan S, Wong HLX. Control of SARS-CoV-2 infection by MT1-MMP-mediated shedding of ACE2. Nat Commun 2022; 13:7907. [PMID: 36564389 PMCID: PMC9780620 DOI: 10.1038/s41467-022-35590-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for SARS-CoV-2. The full-length membrane form of ACE2 (memACE2) undergoes ectodomain shedding to generate a shed soluble form (solACE2) that mediates SARS-CoV-2 entry via receptor-mediated endocytosis. Currently, it is not known how the physiological regulation of ACE2 shedding contributes to the etiology of COVID-19 in vivo. The present study identifies Membrane-type 1 Matrix Metalloproteinase (MT1-MMP) as a critical host protease for solACE2-mediated SARS-CoV-2 infection. SARS-CoV-2 infection leads to increased activation of MT1-MMP that is colocalized with ACE2 in human lung epithelium. Mechanistically, MT1-MMP directly cleaves memACE2 at M706-S to release solACE218-706 that binds to the SARS-CoV-2 spike proteins (S), thus facilitating cell entry of SARS-CoV-2. Human solACE218-706 enables SARS-CoV-2 infection in both non-permissive cells and naturally insusceptible C57BL/6 mice. Inhibition of MT1-MMP activities suppresses solACE2-directed entry of SARS-CoV-2 in human organoids and aged mice. Both solACE2 and circulating MT1-MMP are positively correlated in plasma of aged mice and humans. Our findings provide in vivo evidence demonstrating the contribution of ACE2 shedding to the etiology of COVID-19.
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Affiliation(s)
- Xuanming Guo
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jianli Cao
- grid.194645.b0000000121742757Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jian-Piao Cai
- grid.194645.b0000000121742757State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jiayan Wu
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jiangang Huang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Pallavi Asthana
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Sheung Kin Ken Wong
- grid.194645.b0000000121742757School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zi-Wei Ye
- grid.194645.b0000000121742757Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Susma Gurung
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yijing Zhang
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Sheng Wang
- grid.470187.dRespiratory Department, Jinhua Guangfu Hospital, Jinhua, China
| | - Zening Wang
- grid.267308.80000 0000 9206 2401Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Xin Ge
- grid.267308.80000 0000 9206 2401Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Hiu Yee Kwan
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Aiping Lyu
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Kui Ming Chan
- grid.35030.350000 0004 1792 6846Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Nathalie Wong
- grid.415197.f0000 0004 1764 7206Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, N.T., Hong Kong SAR, China
| | - Jiandong Huang
- grid.194645.b0000000121742757School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhongjun Zhou
- grid.194645.b0000000121742757School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zhao-Xiang Bian
- grid.221309.b0000 0004 1764 5980Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Shuofeng Yuan
- grid.194645.b0000000121742757State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hoi Leong Xavier Wong
- grid.221309.b0000 0004 1764 5980School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
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14
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Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
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Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
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15
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Benlarbi M, Laroche G, Fink C, Fu K, Mulloy RP, Phan A, Ariana A, Stewart CM, Prévost J, Beaudoin-Bussières G, Daniel R, Bo Y, El Ferri O, Yockell-Lelièvre J, Stanford WL, Giguère PM, Mubareka S, Finzi A, Dekaban GA, Dikeakos JD, Côté M. Identification and differential usage of a host metalloproteinase entry pathway by SARS-CoV-2 Delta and Omicron. iScience 2022; 25:105316. [PMID: 36254158 PMCID: PMC9549715 DOI: 10.1016/j.isci.2022.105316] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/05/2022] [Accepted: 10/05/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike glycoprotein (S) binds to angiotensin-converting enzyme 2 (ACE2) to mediate membrane fusion via two distinct pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In this study, we found that SARS-CoV-2 S has a wider protease usage and can also be activated by TMPRSS13 and matrix metalloproteinases (MMPs). We found that MMP-2 and MMP-9 played roles in SARS-CoV-2 S cell-cell fusion and TMPRSS2- and cathepsin-independent viral entry in cells expressing high MMP levels. MMP-dependent viral entry required cleavage at the S1/S2 junction in viral producer cells, and differential processing of variants of concern S dictated its usage; the efficiently processed Delta S preferred metalloproteinase-dependent entry when available, and less processed Omicron S was unable to us metalloproteinases for entry. As MMP-2/9 are released during inflammation, they may play roles in S-mediated cytopathic effects, tropism, and disease outcome. MMP-2 and MMP-9 enable SARS-CoV-2 S-mediated syncytia in the absence of TMPRSS2 SARS-CoV-2 can enter cells via MMPs in a TMPRSS2- and cathepsin-independent manner MMP-dependent S activation requires prior S1/S2 processing Delta S can readily use MMPs for entry while Omicron S cannot
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Affiliation(s)
- Mehdi Benlarbi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Corby Fink
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry Western University, London, ON N6A 5C1, Canada,Molecular Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Kathy Fu
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rory P. Mulloy
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alexandra Phan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Ardeshir Ariana
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Corina M. Stewart
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Redaet Daniel
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Omar El Ferri
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Julien Yockell-Lelièvre
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,The Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - William L. Stanford
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,The Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Patrick M. Giguère
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gregory A. Dekaban
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry Western University, London, ON N6A 5C1, Canada,Molecular Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Jimmy D. Dikeakos
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry Western University, London, ON N6A 5C1, Canada,Molecular Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada,Corresponding author
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16
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Chan SW. Fusion assays for screening of fusion inhibitors targeting SARS-CoV-2 entry and syncytia formation. Front Pharmacol 2022; 13:1007527. [PMID: 36438831 PMCID: PMC9691968 DOI: 10.3389/fphar.2022.1007527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/19/2022] [Indexed: 08/30/2023] Open
Abstract
Virus fusion process is evolutionarily conserved and provides a promising pan-viral target. Cell-cell fusion leads to syncytial formation and has implications in pathogenesis, virus spread and immune evasion. Drugs that target these processes can be developed into anti-virals. Here, we have developed sensitive, rapid, adaptable fusion reporter gene assays as models for plasma membrane and alternative fusion pathways as well as syncytial fusion in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have confirmed their specificity using neutralizing antibodies and specific protease inhibitors. The fusion report gene assays are more sensitive and unbiased than morphological fusion assay. The fusion assays can differentiate between transmembrane serine protease 2 (TMPRSS2)-dependency in TMPRSS2(+) cells and trypsin-dependency in angiotensin-converting enzyme 2 (ACE2)(+)TMPRSS2(-) cells. Moreover, we have identified putative novel fusion processes that are triggered by an acidic pH with and without trypsin. Coupled with morphological fusion criteria, we have found that syncytia formation is enhanced by TMPRSS2 or trypsin. By testing against our top drug hits previously shown to inhibit SARS-CoV-2 pseudovirus infection, we have identified several fusion inhibitors including structurally related lopsided kite-shaped molecules. Our results have important implications in the development of universal blockers and synergistic therapeutics and the small molecule inhibitors can provide important tools in elucidating the fusion process.
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Affiliation(s)
- Shiu-Wan Chan
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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17
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Abdul F, Ribaux P, Caillon A, Malézieux-Picard A, Prendki V, Vernaz N, Zhukovsky N, Delhaes F, Krause KH, Preynat-Seauve O. A Cellular Assay for Spike/ACE2 Fusion: Quantification of Fusion-Inhibitory Antibodies after COVID-19 and Vaccination. Viruses 2022; 14:v14102118. [PMID: 36298674 PMCID: PMC9609042 DOI: 10.3390/v14102118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Not all antibodies against SARS-CoV-2 inhibit viral entry, and hence, infection. Neutralizing antibodies are more likely to reflect real immunity; however, certain tests investigate protein/protein interaction rather than the fusion event. Viral and pseudoviral entry assays detect functionally active antibodies but are limited by biosafety and standardization issues. We have developed a Spike/ACE2-dependent fusion assay, based on a split luciferase. Hela cells stably transduced with Spike and a large fragment of luciferase were co-cultured with Hela cells transduced with ACE2 and the complementary small fragment of luciferase. Cell fusion occurred rapidly allowing the measurement of luminescence. Light emission was abolished in the absence of Spike and reduced in the presence of proteases. Sera from COVID-19-negative, non-vaccinated individuals or from patients at the moment of first symptoms did not lead to a significant reduction of fusion. Sera from COVID-19-positive patients as well as from vaccinated individuals reduced the fusion. This assay was more correlated to pseudotyped-based entry assay rather than serology or competitive ELISA. In conclusion, we report a new method measuring fusion-inhibitory antibodies in serum, combining the advantage of a complete Spike/ACE2 interaction active on entry with a high degree of standardization, easily allowing automation in a standard bio-safety environment.
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Affiliation(s)
- Fabien Abdul
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Pascale Ribaux
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Aurélie Caillon
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Astrid Malézieux-Picard
- Division of Internal Medicine for the Aged, Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Chemin du Pont Bochet 3, 1226 Thônex, Switzerland
| | - Virginie Prendki
- Division of Internal Medicine for the Aged, Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Chemin du Pont Bochet 3, 1226 Thônex, Switzerland
| | - Nathalie Vernaz
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
- Medical Directorate, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland
| | | | - Flavien Delhaes
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Medicine, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
- Correspondence:
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18
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Harte JV, Wakerlin SL, Lindsay AJ, McCarthy JV, Coleman-Vaughan C. Metalloprotease-Dependent S2′-Activation Promotes Cell–Cell Fusion and Syncytiation of SARS-CoV-2. Viruses 2022; 14:v14102094. [PMID: 36298651 PMCID: PMC9608990 DOI: 10.3390/v14102094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 cell–cell fusion and syncytiation is an emerging pathomechanism in COVID-19, but the precise factors contributing to the process remain ill-defined. In this study, we show that metalloproteases promote SARS-CoV-2 spike protein-induced syncytiation in the absence of established serine proteases using in vitro cell–cell fusion assays. We also show that metalloproteases promote S2′-activation of the SARS-CoV-2 spike protein, and that metalloprotease inhibition significantly reduces the syncytiation of SARS-CoV-2 variants of concern. In the presence of serine proteases, however, metalloprotease inhibition does not reduce spike protein-induced syncytiation and a combination of metalloprotease and serine protease inhibition is necessitated. Moreover, we show that the spike protein induces metalloprotease-dependent ectodomain shedding of the ACE2 receptor and that ACE2 shedding contributes to spike protein-induced syncytiation. These observations suggest a benefit to the incorporation of pharmacological inhibitors of metalloproteases into treatment strategies for patients with COVID-19.
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Affiliation(s)
- James V. Harte
- Signal Transduction Laboratory, School of Biochemistry & Cell Biology and the Analytical and Biological Chemistry Research Facility (ABCRF), University College Cork, Western Gateway Building, T12 XF62 Cork, Ireland
| | - Samantha L. Wakerlin
- Signal Transduction Laboratory, School of Biochemistry & Cell Biology and the Analytical and Biological Chemistry Research Facility (ABCRF), University College Cork, Western Gateway Building, T12 XF62 Cork, Ireland
| | - Andrew J. Lindsay
- Membrane Trafficking & Disease Laboratory, Biosciences Institute, School of Biochemistry & Cell Biology, University College Cork, T12 YT20 Cork, Ireland
| | - Justin V. McCarthy
- Signal Transduction Laboratory, School of Biochemistry & Cell Biology and the Analytical and Biological Chemistry Research Facility (ABCRF), University College Cork, Western Gateway Building, T12 XF62 Cork, Ireland
- Correspondence: (J.V.M.); (C.C.-V.)
| | - Caroline Coleman-Vaughan
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland
- Correspondence: (J.V.M.); (C.C.-V.)
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19
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Gellenoncourt S, Saunders N, Robinot R, Auguste L, Rajah MM, Kervevan J, Jeger-Madiot R, Staropoli I, Planchais C, Mouquet H, Buchrieser J, Schwartz O, Chakrabarti LA. The Spike-Stabilizing D614G Mutation Interacts with S1/S2 Cleavage Site Mutations To Promote the Infectious Potential of SARS-CoV-2 Variants. J Virol 2022;:e0130122. [PMID: 36121299 DOI: 10.1128/jvi.01301-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained genetically stable during the first 3 months of the pandemic, before acquiring a D614G spike mutation that rapidly spread worldwide and then generating successive waves of viral variants with increasingly high transmissibility. We set out to evaluate possible epistatic interactions between the early-occurring D614G mutation and the more recently emerged cleavage site mutations present in spike of the Alpha, Delta, and Omicron variants of concern. The P681H/R mutations at the S1/S2 cleavage site increased spike processing and fusogenicity but limited its incorporation into pseudoviruses. In addition, the higher cleavage rate led to higher shedding of the spike S1 subunit, resulting in a lower infectivity of the P681H/R-carrying pseudoviruses compared to those expressing the Wuhan wild-type spike. The D614G mutation increased spike expression at the cell surface and limited S1 shedding from pseudovirions. As a consequence, the D614G mutation preferentially increased the infectivity of P681H/R-carrying pseudoviruses. This enhancement was more marked in cells where the endosomal route predominated, suggesting that more stable spikes could better withstand the endosomal environment. Taken together, these findings suggest that the D614G mutation stabilized S1/S2 association and enabled the selection of mutations that increased S1/S2 cleavage, leading to the emergence of SARS-CoV-2 variants expressing highly fusogenic spikes. IMPORTANCE The first SARS-CoV-2 variant that spread worldwide in early 2020 carried a D614G mutation in the viral spike, making this protein more stable in its cleaved form at the surface of virions. The Alpha and Delta variants, which spread in late 2020 and early 2021, respectively, proved increasingly transmissible and pathogenic compared to the original strain. Interestingly, Alpha and Delta both carried the mutations P681H/R in a cleavage site that made the spike more cleaved and more efficient at mediating viral fusion. We show here that variants with increased spike cleavage due to P681H/R were even more dependent on the stabilizing effect of the D614G mutation, which limited the shedding of cleaved S1 subunits from viral particles. These findings suggest that the worldwide spread of the D614G mutation was a prerequisite for the emergence of more pathogenic SARS-CoV-2 variants with highly fusogenic spikes.
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20
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Aramyan S, McGregor K, Sandeep S, Haczku A. SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK. Front Immunol 2022; 13:945317. [PMID: 36189278 PMCID: PMC9519185 DOI: 10.3389/fimmu.2022.945317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.
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Affiliation(s)
- Sona Aramyan
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Kirk McGregor
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Samarth Sandeep
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
| | - Angela Haczku
- University of California (UC) Davis Lung Center Pulmonary, Critical Care and Sleep Division, Department of Medicine, School of Medicine, University of California, Davis, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
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