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Cheng S, Feng Y, Li W, Liu T, Lv X, Tong X, Xi G, Ye X, Li X. Development of novel antivrial agents that induce the degradation of the main protease of human-infecting coronaviruses. Eur J Med Chem 2024; 275:116629. [PMID: 38941718 DOI: 10.1016/j.ejmech.2024.116629] [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: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
The family of human-infecting coronaviruses (HCoVs) poses a serious threat to global health and includes several highly pathogenic strains that cause severe respiratory illnesses. It is essential that we develop effective broad-spectrum anti-HCoV agents to prepare for future outbreaks. In this study, we used PROteolysis TArgeting Chimera (PROTAC) technology focused on degradation of the HCoV main protease (Mpro), a conserved enzyme essential for viral replication and pathogenicity. By adapting the Mpro inhibitor GC376, we produced two novel PROTACs, P2 and P3, which showed relatively broad-spectrum activity against the human-infecting CoVs HCoV-229E, HCoV-OC43, and SARS-CoV-2. The concentrations of these PROTACs that reduced virus replication by 50 % ranged from 0.71 to 4.6 μM, and neither showed cytotoxicity at 100 μM. Furthermore, mechanistic binding studies demonstrated that P2 and P3 effectively targeted HCoV-229E, HCoV-OC43, and SARS-CoV-2 by degrading Mpro within cells in vitro. This study highlights the potential of PROTAC technology in the development of broad-spectrum anti-HCoVs agents, presenting a novel approach for dealing with future viral outbreaks, particularly those stemming from CoVs.
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Affiliation(s)
- Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Tong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xun Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xiaomei Tong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Gan Xi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xin Ye
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
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2
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Fischer K, Lulla A, So TY, Pereyra-Gerber P, Raybould MIJ, Kohler TN, Yam-Puc JC, Kaminski TS, Hughes R, Pyeatt GL, Leiss-Maier F, Brear P, Matheson NJ, Deane CM, Hyvönen M, Thaventhiran JED, Hollfelder F. Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells. Nat Biotechnol 2024:10.1038/s41587-024-02346-5. [PMID: 39143416 DOI: 10.1038/s41587-024-02346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/27/2024] [Indexed: 08/16/2024]
Abstract
Monoclonal antibodies are increasingly used to prevent and treat viral infections and are pivotal in pandemic response efforts. Antibody-secreting cells (ASCs; plasma cells and plasmablasts) are an excellent source of high-affinity antibodies with therapeutic potential. Current methods to study antigen-specific ASCs either have low throughput, require expensive and labor-intensive screening or are technically demanding and therefore not widely accessible. Here we present a straightforward technology for the rapid discovery of monoclonal antibodies from ASCs. Our approach combines microfluidic encapsulation of single cells into an antibody capture hydrogel with antigen bait sorting by conventional flow cytometry. With our technology, we screened millions of mouse and human ASCs and obtained monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 with high affinity (<1 pM) and neutralizing capacity (<100 ng ml-1) in 2 weeks with a high hit rate (>85% of characterized antibodies bound the target). By facilitating access to the underexplored ASC compartment, the approach enables efficient antibody discovery and immunological studies into the generation of protective antibodies.
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Affiliation(s)
- Katrin Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tsz Y So
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Hughes
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | | | | | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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3
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Jamal GA, Jahangirian E, Hamblin MR, Mirzaei H, Tarrahimofrad H, Alikowsarzadeh N. Proteases, a powerful biochemical tool in the service of medicine, clinical and pharmaceutical. Prep Biochem Biotechnol 2024:1-25. [PMID: 38909284 DOI: 10.1080/10826068.2024.2364234] [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: 06/24/2024]
Abstract
Proteases, enzymes that hydrolyze peptide bonds, have various applications in medicine, clinical applications, and pharmaceutical development. They are used in cancer treatment, wound debridement, contact lens cleaning, prion degradation, biofilm removal, and fibrinolytic agents. Proteases are also crucial in cardiovascular disease treatment, emphasizing the need for safe, affordable, and effective fibrinolytic drugs. Proteolytic enzymes and protease biosensors are increasingly used in diagnostic and therapeutic applications. Advanced technologies, such as nanomaterials-based sensors, are being developed to enhance the sensitivity, specificity, and versatility of protease biosensors. These biosensors are becoming effective tools for disease detection due to their precision and rapidity. They can detect extracellular and intracellular proteases, as well as fluorescence-based methods for real-time and label-free detection of virus-related proteases. The active utilization of proteolytic enzymatic biosensors is expected to expand significantly in biomedical research, in-vitro model systems, and drug development. We focused on journal articles and books published in English between 1982 and 2024 for this study.
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Affiliation(s)
- Ghadir A Jamal
- Faculty of Allied Health Sciences, Kuwait University, Kuwait City, Kuwait
| | - Ehsan Jahangirian
- Department of Molecular, Zist Tashkhis Farda Company (tBioDx), Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Health Science, Laser Research Center, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Neda Alikowsarzadeh
- Molecular and Life Science Department, Han University of Applied Science, Arnhem, Nederland
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4
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Boston RH, Guan R, Kalmar L, Beier S, Horner EC, Beristain-Covarrubias N, Yam-Puc JC, Pereyra Gerber P, Faria L, Kuroshchenkova A, Lindell AE, Blasche S, Correa-Noguera A, Elmer A, Saunders C, Bermperi A, Jose S, Kingston N, Grigoriadou S, Staples E, Buckland MS, Lear S, Matheson NJ, Benes V, Parkinson C, Thaventhiran JE, Patil KR. Stability of gut microbiome after COVID-19 vaccination in healthy and immuno-compromised individuals. Life Sci Alliance 2024; 7:e202302529. [PMID: 38316462 PMCID: PMC10844540 DOI: 10.26508/lsa.202302529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Bidirectional interactions between the immune system and the gut microbiota are key contributors to various physiological functions. Immune-associated diseases such as cancer and autoimmunity, and efficacy of immunomodulatory therapies, have been linked to microbiome variation. Although COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.
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Affiliation(s)
- Rebecca H Boston
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rui Guan
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lajos Kalmar
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sina Beier
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Juan Carlos Yam-Puc
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra Gerber
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
| | - Luisa Faria
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna E Lindell
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Andrea Correa-Noguera
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | - Areti Bermperi
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Sherly Jose
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Emily Staples
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Matthew S Buckland
- Department of Clinical Immunology, Barts Health, London, UK
- UCL GOSH Institute of Child Health Division of Infection and Immunity, Section of Cellular and Molecular Immunology, London, UK
| | - Sara Lear
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Nicholas J Matheson
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christine Parkinson
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - James Ed Thaventhiran
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Kiran R Patil
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
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5
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Chan HTH, Brewitz L, Lukacik P, Strain-Damerell C, Walsh MA, Schofield CJ, Duarte F. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein. RSC Chem Biol 2024; 5:117-130. [PMID: 38333195 PMCID: PMC10849127 DOI: 10.1039/d3cb00128h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 02/10/2024] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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6
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Jackson HK, Long HM, Yam‐Puc JC, Palmulli R, Haigh TA, Gerber PP, Lee JS, Matheson NJ, Young L, Trowsdale J, Lo M, Taylor GS, Thaventhiran JE, Edgar JR. Bioengineered small extracellular vesicles deliver multiple SARS-CoV-2 antigenic fragments and drive a broad immunological response. J Extracell Vesicles 2024; 13:e12412. [PMID: 38339765 PMCID: PMC10858312 DOI: 10.1002/jev2.12412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The COVID-19 pandemic highlighted the clear risk that zoonotic viruses pose to global health and economies. The scientific community responded by developing several efficacious vaccines which were expedited by the global need for vaccines. The emergence of SARS-CoV-2 breakthrough infections highlights the need for additional vaccine modalities to provide stronger, long-lived protective immunity. Here we report the design and preclinical testing of small extracellular vesicles (sEVs) as a multi-subunit vaccine. Cell lines were engineered to produce sEVs containing either the SARS-CoV-2 Spike receptor-binding domain, or an antigenic region from SARS-CoV-2 Nucleocapsid, or both in combination, and we tested their ability to evoke immune responses in vitro and in vivo. B cells incubated with bioengineered sEVs were potent activators of antigen-specific T cell clones. Mice immunised with sEVs containing both sRBD and Nucleocapsid antigens generated sRBD-specific IgGs, nucleocapsid-specific IgGs, which neutralised SARS-CoV-2 infection. sEV-based vaccines allow multiple antigens to be delivered simultaneously resulting in potent, broad immunity, and provide a quick, cheap, and reliable method to test vaccine candidates.
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Affiliation(s)
- Hannah K. Jackson
- Department of PathologyUniversity of CambridgeCambridgeUK
- Exosis, Inc. Palm BeachPalm BeachFloridaUSA
| | - Heather M. Long
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | | | | | - Tracey A. Haigh
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | - Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID)University of CambridgeCambridgeUK
- Department of MedicineUniversity of CambridgeCambridgeUK
| | - Jin S. Lee
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID)University of CambridgeCambridgeUK
- Department of MedicineUniversity of CambridgeCambridgeUK
- NHS Blood and TransplantCambridgeUK
| | | | | | - Mathew Lo
- Exosis, Inc. Palm BeachPalm BeachFloridaUSA
| | - Graham S. Taylor
- Institute of Immunology and ImmunotherapyUniversity of BirminghamBirminghamUK
| | | | - James R. Edgar
- Department of PathologyUniversity of CambridgeCambridgeUK
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7
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Mazzaracchio V, Rios Maciel M, Porto Santos T, Toda-Peters K, Shen AQ. Duplex Electrochemical Microfluidic Sensor for COVID-19 Antibody Detection: Natural versus Vaccine-Induced Humoral Response. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207731. [PMID: 36916701 DOI: 10.1002/smll.202207731] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/03/2023] [Indexed: 06/18/2023]
Abstract
The rapid transmission and resilience of coronavirus disease 2019 (COVID-19) have led to urgent demands in monitoring humoral response for effective vaccine development, thus a multiplex co-detection platform to discriminate infection-induced from vaccine-induced antibodies is needed. Here a duplex electrochemical immunosensor for co-detection of anti-nucleocapsid IgG (N-IgG) and anti-spike IgG (S-IgG) is developed by using a two-working electrode system, via an indirect immunoassay, with antibody quantification obtained by differential pulse voltammetry. The screen-printed electrodes (SPEs) are modified by carbon black and electrodeposited gold nanoflowers for maximized surface areas, enabling the construction of an immunological chain for S-IgG and N-IgG electrochemical detection with enhanced performance. Using an optimized immunoassay protocol, a wide linear range between 30-750 and 20-1000 ng mL-1 , and a limit of detection of 28 and 15 ng mL-1 are achieved to detect N-IgG and S-IgG simultaneously in serum samples. This duplex immunosensor is then integrated in a microfluidic device to obtain significantly reduced detection time (≤ 7 min) while maintaining its analytical performance. The duplex microfluidic immunosensor can be easily expanded into multiplex format to achieve high throughput screening for the sero-surveillance of COVID-19 and other infectious diseases.
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Affiliation(s)
- Vincenzo Mazzaracchio
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
- Department of Chemical Science and Technologies, University of Rome "Tor Vergata,", Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Mauricio Rios Maciel
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - Tatiana Porto Santos
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - Kazumi Toda-Peters
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
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8
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Bao HL, Tu G, Yue Q, Liu P, Zheng HL, Yao XJ. Design and synthesis of isatin derivatives as effective SARS-CoV-2 3CL protease inhibitors. Chem Biol Drug Des 2023; 102:857-869. [PMID: 37563791 DOI: 10.1111/cbdd.14296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
SARS-CoV-2 chymotrypsin-like cysteine protease (3CLpro ) is one of the most widely developed drug targets for COVID-19. This study aimed to design and synthesize isatin derivatives to target SARS-CoV-2 3CLpro in a covalent binding manner. Through the process, a potent 3CLpro inhibitor (5g) was discovered with an IC50 value of 0.43 ± 0.17 μM. To understand the binding affinity and specificity of 5g as a candidate inhibitor of SARS-CoV-2 3CLpro , several assays were conducted, including FRET enzyme activity assays, thermodynamic-based and kinetic-based validation of inhibitor-target interactions, and cell-based FlipGFP assays. The interaction mechanism between 3CLpro -5g was characterized by docking. Overall, these findings suggest that 5g is a new potent SARS-CoV-2 3CLpro inhibitor for the treatment of COVID-19.
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Affiliation(s)
- Hong-Lei Bao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Gao Tu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Qiu Yue
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Pei Liu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Hui-Li Zheng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Xiao-Jun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
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9
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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10
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Yam-Puc JC, Hosseini Z, Horner EC, Gerber PP, Beristain-Covarrubias N, Hughes R, Lulla A, Rust M, Boston R, Ali M, Fischer K, Simmons-Rosello E, O'Reilly M, Robson H, Booth LH, Kahanawita L, Correa-Noguera A, Favara D, Ceron-Gutierrez L, Keller B, Craxton A, Anderson GSF, Sun XM, Elmer A, Saunders C, Bermperi A, Jose S, Kingston N, Mulroney TE, Piñon LPG, Chapman MA, Grigoriadou S, MacFarlane M, Willis AE, Patil KR, Spencer S, Staples E, Warnatz K, Buckland MS, Hollfelder F, Hyvönen M, Döffinger R, Parkinson C, Lear S, Matheson NJ, Thaventhiran JED. Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade. Nat Commun 2023; 14:3292. [PMID: 37369658 PMCID: PMC10299999 DOI: 10.1038/s41467-023-38810-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from different conditions are similar and how they impact the longitudinal level of the COVID-19 vaccine response. Single-cell RNA sequencing indicates that ABCs with distinct aetiologies have common transcriptional profiles and can be categorised according to their expression of immune genes, such as the autoimmune regulator (AIRE). Furthermore, higher baseline ABC frequency correlates with decreased levels of antigen-specific memory B cells and reduced neutralising capacity against SARS-CoV-2. ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes, which could contribute to diminish vaccine responses either directly, or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may, therefore, serve as a biomarker identifying individuals at risk of suboptimal responses to vaccination.
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Affiliation(s)
- Juan Carlos Yam-Puc
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK.
| | - Zhaleh Hosseini
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Robert Hughes
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria Rust
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Rebecca Boston
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Magda Ali
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Katrin Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Edward Simmons-Rosello
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Martin O'Reilly
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Harry Robson
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Lucy H Booth
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Lakmini Kahanawita
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Andrea Correa-Noguera
- Department of Oncology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - David Favara
- Department of Oncology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrew Craxton
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Georgina S F Anderson
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Xiao-Ming Sun
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | - Areti Bermperi
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Sherly Jose
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Thomas E Mulroney
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Lucia P G Piñon
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Michael A Chapman
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | | | - Marion MacFarlane
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Anne E Willis
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Sarah Spencer
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
| | - Emily Staples
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Matthew S Buckland
- Department of Clinical Immunology, Barts Health, London, UK
- UCL GOSH Institute of Child Health Division of Infection and Immunity, Section of Cellular and Molecular Immunology, London, UK
| | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rainer Döffinger
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Christine Parkinson
- Department of Oncology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Sara Lear
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - James E D Thaventhiran
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK.
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.
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11
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van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED. Accelerated waning of the humoral response to COVID-19 vaccines in obesity. Nat Med 2023; 29:1146-1154. [PMID: 37169862 PMCID: PMC10202802 DOI: 10.1038/s41591-023-02343-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023]
Abstract
Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m2) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m2). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.
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Affiliation(s)
- Agatha A van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Utkarsh Agrawal
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Sarah Spencer
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Bensi Vergese
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Isobel D Ramsay
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack A Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Iain M Hay
- Babraham Institute, Babraham Research Campus, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sam Thompson
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Lucy H Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Chris Robertson
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Colin McCowan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Steven Kerr
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Maria A Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Alex Ferreira
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Soraya Ebrahimi
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacopo Scotucci
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Adrian J Park
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Francesco Rubino
- Department of Diabetes, King's College London and King's College Hospital NHS Foundation Trust, London, UK
| | - Abigail A Lamikanra
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lise Estcourt
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - David J Roberts
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rainer Doffinger
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Aziz Sheikh
- Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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12
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Brevini T, Maes M, Webb GJ, John BV, Fuchs CD, Buescher G, Wang L, Griffiths C, Brown ML, Scott WE, Pereyra-Gerber P, Gelson WTH, Brown S, Dillon S, Muraro D, Sharp J, Neary M, Box H, Tatham L, Stewart J, Curley P, Pertinez H, Forrest S, Mlcochova P, Varankar SS, Darvish-Damavandi M, Mulcahy VL, Kuc RE, Williams TL, Heslop JA, Rossetti D, Tysoe OC, Galanakis V, Vila-Gonzalez M, Crozier TWM, Bargehr J, Sinha S, Upponi SS, Fear C, Swift L, Saeb-Parsy K, Davies SE, Wester A, Hagström H, Melum E, Clements D, Humphreys P, Herriott J, Kijak E, Cox H, Bramwell C, Valentijn A, Illingworth CJR, Dahman B, Bastaich DR, Ferreira RD, Marjot T, Barnes E, Moon AM, Barritt AS, Gupta RK, Baker S, Davenport AP, Corbett G, Gorgoulis VG, Buczacki SJA, Lee JH, Matheson NJ, Trauner M, Fisher AJ, Gibbs P, Butler AJ, Watson CJE, Mells GF, Dougan G, Owen A, Lohse AW, Vallier L, Sampaziotis F. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2. Nature 2023; 615:134-142. [PMID: 36470304 PMCID: PMC9977684 DOI: 10.1038/s41586-022-05594-0] [Citation(s) in RCA: 130] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Preventing SARS-CoV-2 infection by modulating viral host receptors, such as angiotensin-converting enzyme 2 (ACE2)1, could represent a new chemoprophylactic approach for COVID-19 that complements vaccination2,3. However, the mechanisms that control the expression of ACE2 remain unclear. Here we show that the farnesoid X receptor (FXR) is a direct regulator of ACE2 transcription in several tissues affected by COVID-19, including the gastrointestinal and respiratory systems. We then use the over-the-counter compound z-guggulsterone and the off-patent drug ursodeoxycholic acid (UDCA) to reduce FXR signalling and downregulate ACE2 in human lung, cholangiocyte and intestinal organoids and in the corresponding tissues in mice and hamsters. We show that the UDCA-mediated downregulation of ACE2 reduces susceptibility to SARS-CoV-2 infection in vitro, in vivo and in human lungs and livers perfused ex situ. Furthermore, we reveal that UDCA reduces the expression of ACE2 in the nasal epithelium in humans. Finally, we identify a correlation between UDCA treatment and positive clinical outcomes after SARS-CoV-2 infection using retrospective registry data, and confirm these findings in an independent validation cohort of recipients of liver transplants. In conclusion, we show that FXR has a role in controlling ACE2 expression and provide evidence that modulation of this pathway could be beneficial for reducing SARS-CoV-2 infection, paving the way for future clinical trials.
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Affiliation(s)
- Teresa Brevini
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gwilym J Webb
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Binu V John
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | - Claudia D Fuchs
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Gustav Buescher
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lu Wang
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Chelsea Griffiths
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marnie L Brown
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - William E Scott
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - William T H Gelson
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Scott Dillon
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Jo Sharp
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Megan Neary
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Helen Box
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lee Tatham
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - James Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paul Curley
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Henry Pertinez
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | | | - Mahnaz Darvish-Damavandi
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Rhoda E Kuc
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Thomas L Williams
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - James A Heslop
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Olivia C Tysoe
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | | | - Thomas W M Crozier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Johannes Bargehr
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Sanjay Sinha
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Sara S Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Corrina Fear
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Lisa Swift
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Susan E Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Axel Wester
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Hagström
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Hybrid Technology Hub Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Jo Herriott
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edyta Kijak
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Helen Cox
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anthony Valentijn
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Bassam Dahman
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Dustin R Bastaich
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Raphaella D Ferreira
- Division of Gastroenterology and Hepatology, University of Miami and Miami VA Health System, Miami, FL, USA
| | - Thomas Marjot
- Oxford Liver Unit, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford Liver Unit, Translational Gastroenterology Unit, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford, UK
| | - Andrew M Moon
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
| | - Alfred S Barritt
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Gareth Corbett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vassilis G Gorgoulis
- Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Simon J A Buczacki
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, USA
- NHS Blood and Transplant, Cambridge, UK
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andrew J Fisher
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Gibbs
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Andrew J Butler
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christopher J E Watson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Roy Calne Transplant Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, and the NIHR Blood and Transplant Research Unit (BTRU) at the University of Cambridge in collaboration with Newcastle University and in partnership with NHS Blood and Transplant (NHSBT), Cambridge, UK
| | - George F Mells
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Owen
- Centre of Excellence in Long-acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ansgar W Lohse
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
- Berlin Institute of Health (BIH), BIH Centre for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Fotios Sampaziotis
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
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13
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Shilts J, Crozier TWM, Teixeira-Silva A, Gabaev I, Gerber PP, Greenwood EJD, Watson SJ, Ortmann BM, Gawden-Bone CM, Pauzaite T, Hoffmann M, Nathan JA, Pöhlmann S, Matheson NJ, Lehner PJ, Wright GJ. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. PLoS Biol 2023; 21:e3001959. [PMID: 36735681 PMCID: PMC9897555 DOI: 10.1371/journal.pbio.3001959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
The interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to Coronavirus Disease 2019 (COVID-19). The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary angiotensin-converting enzyme 2 (ACE2) receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was functionally restricted to SARS-CoV-2 by accessibility. We localized the interaction to the C-terminus of the S1 domain and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Levels of LRRC15 were greatly elevated by inflammatory signals in the lungs of COVID-19 patients. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence that it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Thomas W. M. Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Pehuén Pereyra Gerber
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Edward J. D. Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Samuel James Watson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Brian M. Ortmann
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Christian M. Gawden-Bone
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Tekle Pauzaite
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - James A. Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - Nicholas J. Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Paul J. Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
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14
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Arakawa M, Yoshida A, Okamura S, Ebina H, Morita E. A highly sensitive NanoLuc-based protease biosensor for detecting apoptosis and SARS-CoV-2 infection. Sci Rep 2023; 13:1753. [PMID: 36720982 PMCID: PMC9887574 DOI: 10.1038/s41598-023-28984-4] [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: 08/26/2022] [Accepted: 01/27/2023] [Indexed: 02/02/2023] Open
Abstract
Proteases play critical roles in various biological processes, including apoptosis and viral infection. Several protease biosensors have been developed; however, obtaining a reliable signal from a very low level of endogenous protease activity remains a challenge. In this study, we developed a highly sensitive protease biosensor, named FlipNanoLuc, based on the Oplophorus gracilirostris NanoLuc luciferase. The flipped β-strand was restored by protease activation and cleavage, resulting in the reconstitution of luciferase and enzymatic activity. By making several modifications, such as introducing NanoBiT technology and CL1-PEST1 degradation tag, the FlipNanoLuc-based protease biosensor system achieved more than 500-fold luminescence increase in the corresponding protease-overexpressing cells. We demonstrated that the FlipNanoLuc-based caspase sensor can be utilized for the detection of staurosporine-induced apoptosis with sixfold increase in luminescence. Furthermore, we also demonstrated that the FlipNanoLuc-based coronavirus 3CL-protease sensor can be used to detect human coronavirus OC43 with tenfold increase in luminescence and severe acute respiratory syndrome-coronavirus-2 infections with 20-fold increase in luminescence by introducing the stem-loop 1 sequence to prevent the virus inducing global translational shutdown.
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Affiliation(s)
- Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-Cho, Hirosaki-Shi, Aomori, 036-8561, Japan.,Division of Biomolecular Function, Bioresources Science, United Graduate School of Agricultural Sciences, Iwate University, Morioka, 020-0066, Japan
| | - Akiho Yoshida
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Shinya Okamura
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Hirotaka Ebina
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.,Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.,The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-Cho, Hirosaki-Shi, Aomori, 036-8561, Japan. .,Division of Biomolecular Function, Bioresources Science, United Graduate School of Agricultural Sciences, Iwate University, Morioka, 020-0066, Japan.
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15
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Choi JH. Proteolytic Biosensors with Functional Nanomaterials: Current Approaches and Future Challenges. BIOSENSORS 2023; 13:171. [PMID: 36831937 PMCID: PMC9953628 DOI: 10.3390/bios13020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Proteolytic enzymes are one of the important biomarkers that enable the early diagnosis of several diseases, such as cancers. A specific proteolytic enzyme selectively degrades a certain sequence of a polypeptide. Therefore, a particular proteolytic enzyme can be selectively quantified by changing detectable signals causing degradation of the peptide chain. In addition, by combining polypeptides with various functional nanomaterials, proteolytic enzymes can be measured more sensitively and rapidly. In this paper, proteolytic enzymes that can be measured using a polypeptide degradation method are reviewed and recently studied functional nanomaterials-based proteolytic biosensors are discussed. We anticipate that the proteolytic nanobiosensors addressed in this review will provide valuable information on physiological changes from a cellular level for individual and early diagnosis.
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Affiliation(s)
- Jin-Ha Choi
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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16
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Touizer E, Alrubayyi A, Ford R, Hussain N, Gerber PP, Shum HL, Rees-Spear C, Muir L, Gea-Mallorquí E, Kopycinski J, Jankovic D, Jeffery-Smith A, Pinder CL, Fox TA, Williams I, Mullender C, Maan I, Waters L, Johnson M, Madge S, Youle M, Barber TJ, Burns F, Kinloch S, Rowland-Jones S, Gilson R, Matheson NJ, Morris E, Peppa D, McCoy LE. Attenuated humoral responses in HIV after SARS-CoV-2 vaccination linked to B cell defects and altered immune profiles. iScience 2023; 26:105862. [PMID: 36590902 PMCID: PMC9788849 DOI: 10.1016/j.isci.2022.105862] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We assessed a cohort of people living with human immunodeficiency virus (PLWH) (n = 110) and HIV negative controls (n = 64) after 1, 2 or 3 SARS-CoV-2 vaccine doses. At all timepoints, PLWH had significantly lower neutralizing antibody (nAb) titers than HIV-negative controls. We also observed a delayed development of neutralization in PLWH that was underpinned by a reduced frequency of spike-specific memory B cells (MBCs). Improved neutralization breadth was seen against the Omicron variant (BA.1) after the third vaccine dose in PLWH but lower nAb responses persisted and were associated with global MBC dysfunction. In contrast, SARS-CoV-2 vaccination induced robust T cell responses that cross-recognized variants in PLWH. Strikingly, individuals with low or absent neutralization had detectable functional T cell responses. These PLWH had reduced numbers of circulating T follicular helper cells and an enriched population of CXCR3+CD127+CD8+T cells after two doses of SARS-CoV-2 vaccination.
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Affiliation(s)
- Emma Touizer
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Aljawharah Alrubayyi
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rosemarie Ford
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Noshin Hussain
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hiu-Long Shum
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Chloe Rees-Spear
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Luke Muir
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | | | - Jakub Kopycinski
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dylan Jankovic
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Anna Jeffery-Smith
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Christopher L. Pinder
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Thomas A. Fox
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Ian Williams
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, London, UK
| | - Claire Mullender
- Institute for Global Health, University College London, London, UK
| | - Irfaan Maan
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, London, UK
- Institute for Global Health, University College London, London, UK
| | - Laura Waters
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, London, UK
| | - Margaret Johnson
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sara Madge
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Michael Youle
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Tristan J. Barber
- Institute for Global Health, University College London, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Fiona Burns
- Institute for Global Health, University College London, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sabine Kinloch
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | | | - Richard Gilson
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, London, UK
- Institute for Global Health, University College London, London, UK
| | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Emma Morris
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Dimitra Peppa
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust, London, UK
| | - Laura E. McCoy
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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17
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Gerber PP, Donde MJ, Matheson NJ, Taylor AI. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun 2022; 13:6716. [PMID: 36385143 PMCID: PMC9668987 DOI: 10.1038/s41467-022-34339-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The unprecedented emergence and spread of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, underscores the need for diagnostic and therapeutic technologies that can be rapidly tailored to novel threats. Here, we show that site-specific RNA endonuclease XNAzymes - artificial catalysts composed of single-stranded synthetic xeno-nucleic acid oligonucleotides (in this case 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid) - may be designed, synthesised and screened within days, enabling the discovery of a range of enzymes targeting SARS-CoV-2 ORF1ab, ORF7b, spike- and nucleocapsid-encoding RNA. Three of these are further engineered to self-assemble into a catalytic nanostructure with enhanced biostability. This XNA nanostructure is capable of cleaving genomic SARS-CoV-2 RNA under physiological conditions, and when transfected into cells inhibits infection with authentic SARS-CoV-2 virus by RNA knockdown. These results demonstrate the potential of XNAzymes to provide a platform for the rapid generation of antiviral reagents.
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Affiliation(s)
- Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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18
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Touizer E, Alrubbayi A, Ford R, Hussain N, Gerber PP, Shum HL, Rees-Spear C, Muir L, Gea-Mallorquí E, Kopycinski J, Jankovic D, Pinder C, Fox TA, Williams I, Mullender C, Maan I, Waters L, Johnson M, Madge S, Youle M, Barber T, Burns F, Kinloch S, Rowland-Jones S, Gilson R, Matheson NJ, Morris E, Peppa D, McCoy LE. Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.11.516111. [PMID: 36380764 PMCID: PMC9665338 DOI: 10.1101/2022.11.11.516111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
People living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can have residual immune dysfunction and often display poorer responses to vaccination. We assessed in a cohort of PLWH (n=110) and HIV negative controls (n=64) the humoral and spike-specific B-cell responses following 1, 2 or 3 SARS-CoV-2 vaccine doses. PLWH had significantly lower neutralizing antibody (nAb) titers than HIV-negative controls at all studied timepoints. Moreover, their neutralization breadth was reduced with fewer individuals developing a neutralizing response against the Omicron variant (BA.1) relative to controls. We also observed a delayed development of neutralization in PLWH that was underpinned by a reduced frequency of spike-specific memory B cells (MBCs) and pronounced B cell dysfunction. Improved neutralization breadth was seen after the third vaccine dose in PLWH but lower nAb responses persisted and were associated with global, but not spike-specific, MBC dysfunction. In contrast to the inferior antibody responses, SARS-CoV-2 vaccination induced robust T cell responses that cross-recognized variants in PLWH. Strikingly, a subset of PLWH with low or absent neutralization had detectable functional T cell responses. These individuals had reduced numbers of circulating T follicular helper cells and an enriched population of CXCR3 + CD127 + CD8 + T cells after two doses of SARS-CoV-2 vaccination, which may compensate for sub-optimal serological responses in the event of infection. Therefore, normalisation of B cell homeostasis could improve serological responses to vaccines in PLWH and evaluating T cell immunity could provide a more comprehensive immune status profile in these individuals and others with B cell imbalances.
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Affiliation(s)
- Emma Touizer
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Aljawharah Alrubbayi
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
- Nuffield Department of Medicine, University of Oxford, UK
| | - Rosemarie Ford
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Noshin Hussain
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, UK
| | - Hiu-Long Shum
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Chloe Rees-Spear
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Luke Muir
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | | | | | - Dylan Jankovic
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Christopher Pinder
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Thomas A Fox
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Ian Williams
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, UK
| | | | - Irfaan Maan
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, UK
- Institute for Global Health, University College London, UK
| | - Laura Waters
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, UK
| | - Margaret Johnson
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | - Sara Madge
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | - Michael Youle
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | - Tristan Barber
- Institute for Global Health, University College London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | - Fiona Burns
- Institute for Global Health, University College London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | - Sabine Kinloch
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
- The Ian Charleson Day Centre, Royal Free Hospital NHS Foundation Trust UK
| | | | - Richard Gilson
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, UK
- Institute for Global Health, University College London, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Emma Morris
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
| | - Dimitra Peppa
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
- Mortimer Market Centre, Department of HIV, Central and North West London NHS Trust, UK
- Institute for Global Health, University College London, UK
| | - Laura E McCoy
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, UK
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19
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Abstract
The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here, we report quantitative reporters for Mpro function in living cells in which protease inhibition by genetic or chemical methods results in robust signal readouts by fluorescence (enhanced green fluorescent protein [eGFP]) or bioluminescence (firefly luciferase). These gain-of-signal systems are scalable to high-throughput platforms for quantitative discrimination between Mpro mutants and/or inhibitor potencies as evidenced by validation of several reported inhibitors. Additional utility is shown by single Mpro amino acid variants and structural information combining to demonstrate that both inhibitor conformational dynamics and amino acid differences are able to influence inhibitor potency. We further show that a recent variant of concern (Omicron) has an unchanged response to a clinically approved drug, nirmatrelvir, whereas proteases from divergent coronavirus species show differential susceptibility. Together, we demonstrate that these gain-of-signal systems serve as robust, facile, and scalable assays for live cell quantification of Mpro inhibition, which will help expedite the development of next-generation antivirals and enable the rapid testing of emerging variants. IMPORTANCE The main protease, Mpro, of SARS-CoV-2 is an essential viral protein required for the earliest steps of infection. It is therefore an attractive target for antiviral drug development. Here, we report the development and implementation of two complementary cell-based systems for quantification of Mpro inhibition by genetic or chemical approaches. The first is fluorescence based (eGFP), and the second is luminescence based (firefly luciferase). Importantly, both systems rely upon gain-of-signal readouts such that stronger inhibitors yield higher fluorescent or luminescent signal. The high versatility and utility of these systems are demonstrated by characterizing Mpro mutants and natural variants, including Omicron, as well as a panel of existing inhibitors. These systems rapidly, safely, and sensitively identify Mpro variants with altered susceptibilities to inhibition, triage-nonspecific, or off-target molecules and validate bona fide inhibitors, with the most potent thus far being the first-in-class drug nirmatrelvir.
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20
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Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. BIOSENSORS 2022; 12:410. [PMID: 35735558 PMCID: PMC9220779 DOI: 10.3390/bios12060410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.
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Affiliation(s)
- Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Jalees ul Hassan
- Department of Wildlife and Ecology, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences-UVAS, Lahore 54000, Pakistan;
| | - Mohsin Rafique
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China;
| | - Mashooq Khan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
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21
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Tan H, Hu Y, Jadhav P, Tan B, Wang J. Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease. J Med Chem 2022; 65:7561-7580. [PMID: 35620927 PMCID: PMC9159073 DOI: 10.1021/acs.jmedchem.2c00303] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PLpro) mediates the cleavage of viral polyprotein and modulates the host's innate immune response upon viral infection, rendering it a promising antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PLpro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PLpro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PLpro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PLpro inhibitors to the clinic.
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Affiliation(s)
- Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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22
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Garland GD, Harvey RF, Mulroney TE, Monti M, Fuller S, Haigh R, Gerber PP, Barer MR, Matheson NJ, Willis AE. Development of a colorimetric assay for the detection of SARS-CoV-2 3CLpro activity. Biochem J 2022; 479:901-920. [PMID: 35380004 PMCID: PMC9162461 DOI: 10.1042/bcj20220105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/15/2022]
Abstract
Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes the 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts an in vitro colorimetric gold nanoparticle (AuNP) based protease assay to specifically detect the activity of SARS-CoV-2 3CLpro as a purified recombinant protein and as a cellular protein exogenously expressed in HEK293T human cells. We also demonstrate that the specific sensitivity of the assay for SARS-CoV-2 3CLpro can be improved by use of an optimised peptide substrate and through hybrid dimerisation with inactive 3CLpro mutant monomers. These findings highlight the potential for further development of the AuNP protease assay to detect SARS-CoV-2 3CLpro activity as a novel, accessible and cost-effective diagnostic test for SARS-CoV-2 infection at the point-of-care. Importantly, this versatile assay could also be easily adapted to detect specific protease activity associated with other viruses or diseases conditions.
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Affiliation(s)
- Gavin D. Garland
- MRC Toxicology Unit, Gleeson Building, Tennis Court Rd, Cambridge, U.K
- Correspondence: Gavin D. Garland () or Anne E. Willis ()
| | - Robert F. Harvey
- MRC Toxicology Unit, Gleeson Building, Tennis Court Rd, Cambridge, U.K
| | | | - Mie Monti
- MRC Toxicology Unit, Gleeson Building, Tennis Court Rd, Cambridge, U.K
| | - Stewart Fuller
- Department of Medicine, University of Cambridge, Cambridge, U.K
| | - Richard Haigh
- Department of Respiratory Sciences, Maurice Shock Medical Sciences Building, University Road, Leicester, U.K
| | - Pehuén Pereyra Gerber
- Department of Medicine, University of Cambridge, Cambridge, U.K
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, U.K
| | - Michael R. Barer
- Department of Respiratory Sciences, Maurice Shock Medical Sciences Building, University Road, Leicester, U.K
| | - Nicholas J. Matheson
- Department of Medicine, University of Cambridge, Cambridge, U.K
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, U.K
- NHS Blood and Transplant, Cambridge, U.K
| | - Anne E. Willis
- MRC Toxicology Unit, Gleeson Building, Tennis Court Rd, Cambridge, U.K
- Correspondence: Gavin D. Garland () or Anne E. Willis ()
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23
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Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature 2022; 603:706-714. [PMID: 35104837 PMCID: PMC8942856 DOI: 10.1038/s41586-022-04474-x] [Citation(s) in RCA: 659] [Impact Index Per Article: 329.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/26/2022] [Indexed: 11/08/2022]
Abstract
The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and has multiple mutations in its spike protein2. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.
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Affiliation(s)
- Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Niluka Goonawardane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Saman Fatihi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Surabhi Rathore
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Guido Papa
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | | | - Shigeki Mitsunaga
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Teresa Brevini
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Virology, University of Cambridge, Cambridge, UK
| | | | | | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Jinwook Choi
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Elo Madissoon
- Welcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kerstin B Meyer
- Welcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Rainer Doffinger
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sarah A Teichmann
- Welcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Andrew J Fisher
- Transplant and Regenerative Medicine Laboratory, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Anna de Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Myra Hosmillo
- Department of Virology, University of Cambridge, Cambridge, UK
| | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Leo C James
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Lipi Thukral
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fotios Sampaziotis
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- CREST, Japan Science and Technology Agency, Saitama, Japan.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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