151
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Tanaka S, Nelson G, Olson CA, Buzko O, Higashide W, Shin A, Gonzalez M, Taft J, Patel R, Buta S, Richardson A, Bogunovic D, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. Sci Rep 2021; 11:12740. [PMID: 34140558 PMCID: PMC8211782 DOI: 10.1038/s41598-021-91809-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
The SARS-CoV-2 variants replacing the first wave strain pose an increased threat by their potential ability to escape pre-existing humoral protection. An angiotensin converting enzyme 2 (ACE2) decoy that competes with endogenous ACE2 for binding of the SARS-CoV-2 spike receptor binding domain (S RBD) and inhibits infection may offer a therapeutic option with sustained efficacy against variants. Here, we used Molecular Dynamics (MD) simulation to predict ACE2 sequence substitutions that might increase its affinity for S RBD and screened candidate ACE2 decoys in vitro. The lead ACE2(T27Y/H34A)-IgG1FC fusion protein with enhanced S RBD affinity shows greater live SARS-CoV-2 virus neutralization capability than wild type ACE2. MD simulation was used to predict the effects of S RBD variant mutations on decoy affinity that was then confirmed by testing of an ACE2 Triple Decoy that included an additional enzyme activity-deactivating H374N substitution against mutated S RBD. The ACE2 Triple Decoy maintains high affinity for mutated S RBD, displays enhanced affinity for S RBD N501Y or L452R, and has the highest affinity for S RBD with both E484K and N501Y mutations, making it a viable therapeutic option for the prevention or treatment of SARS-CoV-2 infection with a high likelihood of efficacy against variants.
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Affiliation(s)
- Shiho Tanaka
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA.
| | - Gard Nelson
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - C Anders Olson
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Oleksandr Buzko
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Wendy Higashide
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Annie Shin
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Marcos Gonzalez
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Justin Taft
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
| | - Roosheel Patel
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
| | - Sofija Buta
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
| | - Ashley Richardson
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
| | - Dusan Bogunovic
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Place, New York, NY, 10029-5674, USA
| | - Patricia Spilman
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
| | - Kayvan Niazi
- ImmunityBio, Inc., 9920 Jefferson Blvd., Culver City, CA, 90232, USA
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152
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Beeckmans S, Van Driessche E. Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study. Front Mol Biosci 2021; 8:671923. [PMID: 34109214 PMCID: PMC8181738 DOI: 10.3389/fmolb.2021.671923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 01/18/2023] Open
Abstract
Since early 2020, the world suffers from a new beta-coronavirus, called SARS-CoV-2, that has devastating effects globally due to its associated disease, Covid-19. Until today, Covid-19, which not only causes life-threatening lung infections but also impairs various other organs and tissues, has killed hundreds of thousands of people and caused irreparable damage to many others. Since the very onset of the pandemic, huge efforts were made worldwide to fully understand this virus and numerous studies were, and still are, published. Many of these deal with structural analyses of the viral spike glycoprotein and with vaccine development, antibodies and antiviral molecules or immunomodulators that are assumed to become essential tools in the struggle against the virus. This paper summarizes knowledge on the properties of the four structural proteins (spike protein S, membrane protein M, envelope protein E and nucleocapsid protein N) of the SARS-CoV-2 virus and its relatives, SARS-CoV and MERS-CoV, that emerged few years earlier. Moreover, attention is paid to ways to analyze such proteins using freely available bioinformatic tools and, more importantly, to bring these proteins alive by looking at them on a computer/laptop screen with the easy-to-use but highly performant and interactive molecular graphics program DeepView. It is hoped that this paper will stimulate non-bioinformaticians and non-specialists in structural biology to scrutinize these and other macromolecules and as such will contribute to establishing procedures to fight these and maybe other forthcoming viruses.
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Affiliation(s)
- Sonia Beeckmans
- Research Unit Protein Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
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153
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Hirsch C, Valk SJ, Piechotta V, Chai KL, Estcourt LJ, Monsef I, Salomon S, Tomlinson E, Popp M, Wood EM, So-Osman C, Roberts DJ, McQuilten Z, Skoetz N, Kreuzberger N. SARS-CoV-2-neutralising monoclonal antibodies to prevent COVID-19. Hippokratia 2021. [DOI: 10.1002/14651858.cd014945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Caroline Hirsch
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
| | - Sarah J Valk
- Jon J van Rood Center for Clinical Transfusion Research; Sanquin/Leiden University Medical Center; Leiden Netherlands
| | - Vanessa Piechotta
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
| | - Khai Li Chai
- Transfusion Research Unit, School of Public Health and Preventive Medicine; Monash University; Melbourne Australia
| | - Lise J Estcourt
- Haematology/Transfusion Medicine; NHS Blood and Transplant; Oxford UK
| | - Ina Monsef
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
| | - Susanne Salomon
- Laboratory of Experimental Immunology, Institute of Virology; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
| | - Eve Tomlinson
- Cochrane Gynaecological, Neuro-oncology and Orphan Cancers; 1st Floor Education Centre, Royal United Hospital; Bath UK
| | - Maria Popp
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine; University Hospital Wuerzburg; Wuerzburg Germany
| | - Erica M Wood
- Transfusion Research Unit, School of Public Health and Preventive Medicine; Monash University; Melbourne Australia
| | | | - David J Roberts
- Systematic Review Initiative; NHS Blood and Transplant; Oxford UK
| | - Zoe McQuilten
- Transfusion Research Unit, School of Public Health and Preventive Medicine; Monash University; Melbourne Australia
| | - Nicole Skoetz
- Cochrane Cancer, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
| | - Nina Kreuzberger
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf; Faculty of Medicine and University Hospital Cologne, University of Cologne; Cologne Germany
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154
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Zhang X, Han P, Wang H, Xu Y, Li F, Li M, Fan L, Zhang H, Dai Q, Lin H, Qi X, Liang J, Wang X, Yang X. Engineering mesenchymal stromal cells with neutralizing and anti-inflammatory capability against SARS-CoV-2 infection. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:754-764. [PMID: 34007862 PMCID: PMC8118700 DOI: 10.1016/j.omtm.2021.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
The emergence of the novel human severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to the pandemic of coronavirus disease 2019 (COVID-19), which has markedly affected global health and the economy. Both uncontrolled viral replication and a proinflammatory cytokine storm can cause severe tissue damage in patients with COVID-19. SARS-CoV-2 utilizes angiotensin-converting enzyme 2 (ACE2) as its entry receptor. In this study, we generated ACE2 extracellular domain-Fc and single-chain variable fragment-interleukin 6 (IL-6) single-chain variable fragment against IL-6 receptor (scFv-IL6R)-Fc fusion proteins to differentially neutralize viruses and ameliorate the cytokine storm. The human ACE2 (hACE2)1-740-Fc fusion protein showed a potent inhibitory effect on pseudo-typed SARS-CoV-2 entry and a good safety profile in mice. In addition, scFv-IL6R-Fc strongly blocked IL-6 signal activation. We also established a mesenchymal stromal cell (MSC)-based hACE21-740-Fc and scFv-IL6R-Fc delivery system, which could serve as a potential therapy strategy for urgent clinical needs of patients with COVID-19.
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Affiliation(s)
- Xiaoqing Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Han
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haiyong Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqin Xu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fanlin Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Min Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lilv Fan
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huihui Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Dai
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Lin
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyue Qi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Liang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Wang
- Shanghai Longyao Biotechnology Limited, Shanghai 201203, China
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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155
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Heinzelman P, Romero PA. Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein. PLoS One 2021; 16:e0251585. [PMID: 33979391 PMCID: PMC8115845 DOI: 10.1371/journal.pone.0251585] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/29/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how human ACE2 genetic variants differ in their recognition by SARS-CoV-2 can facilitate the leveraging of ACE2 as an axis for treating and preventing COVID-19. In this work, we experimentally interrogate thousands of ACE2 mutants to identify over one hundred human single-nucleotide variants (SNVs) that are likely to have altered recognition by the virus, and make the complementary discovery that ACE2 residues distant from the spike interface influence the ACE2-spike interaction. These findings illuminate new links between ACE2 sequence and spike recognition, and could find substantial utility in further fundamental research that augments epidemiological analyses and clinical trial design in the contexts of both existing strains of SARS-CoV-2 and novel variants that may arise in the future.
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Affiliation(s)
- Pete Heinzelman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Philip A. Romero
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemical & Biological Engineering, University of Wisconsin—Madison, Madison, WI, United States of America
- * E-mail:
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156
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Paci E, Ross JF. Computational methods to predict the mutational landscape of the spike protein. Biophys J 2021; 120:2763-2765. [PMID: 34237251 PMCID: PMC8261306 DOI: 10.1016/j.bpj.2021.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emanuele Paci
- Astbury Centre and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
| | - James F Ross
- Astbury Centre and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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157
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D'Onofrio N, Scisciola L, Sardu C, Trotta MC, De Feo M, Maiello C, Mascolo P, De Micco F, Turriziani F, Municinò E, Monetti P, Lombardi A, Napolitano MG, Marino FZ, Ronchi A, Grimaldi V, Hermenean A, Rizzo MR, Barbieri M, Franco R, Campobasso CP, Napoli C, Municinò M, Paolisso G, Balestrieri ML, Marfella R. Glycated ACE2 receptor in diabetes: open door for SARS-COV-2 entry in cardiomyocyte. Cardiovasc Diabetol 2021; 20:99. [PMID: 33962629 PMCID: PMC8104461 DOI: 10.1186/s12933-021-01286-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
Rationale About 50% of hospitalized coronavirus disease 2019 (COVID-19) patients with diabetes mellitus (DM) developed myocardial damage. The mechanisms of direct SARS-CoV-2 cardiomyocyte infection include viral invasion via ACE2-Spike glycoprotein-binding. In DM patients, the impact of glycation of ACE2 on cardiomyocyte invasion by SARS-CoV-2 can be of high importance. Objective To evaluate the presence of SARS-CoV-2 in cardiomyocytes from heart autopsy of DM cases compared to Non-DM; to investigate the role of DM in SARS-COV-2 entry in cardiomyocytes. Methods and results We evaluated consecutive autopsy cases, deceased for COVID-19, from Italy between Apr 30, 2020 and Jan 18, 2021. We evaluated SARS-CoV-2 in cardiomyocytes, expression of ACE2 (total and glycosylated form), and transmembrane protease serine protease-2 (TMPRSS2) protein. In order to study the role of diabetes on cardiomyocyte alterations, independently of COVID-19, we investigated ACE2, glycosylated ACE2, and TMPRSS2 proteins in cardiomyocytes from DM and Non-DM explanted-hearts. Finally, to investigate the effects of DM on ACE2 protein modification, an in vitro glycation study of recombinant human ACE2 (hACE2) was performed to evaluate the effects on binding to SARS-CoV-2 Spike protein. The authors included cardiac tissue from 97 autopsies. DM was diagnosed in 37 patients (38%). Fourth-seven out of 97 autopsies (48%) had SARS-CoV-2 RNA in cardiomyocytes. Thirty out of 37 DM autopsy cases (81%) and 17 out of 60 Non-DM autopsy cases (28%) had SARS-CoV-2 RNA in cardiomyocytes. Total ACE2, glycosylated ACE2, and TMPRSS2 protein expressions were higher in cardiomyocytes from autopsied and explanted hearts of DM than Non-DM. In vitro exposure of monomeric hACE2 to 120 mM glucose for 12 days led to non-enzymatic glycation of four lysine residues in the neck domain affecting the protein oligomerization. Conclusions The upregulation of ACE2 expression (total and glycosylated forms) in DM cardiomyocytes, along with non-enzymatic glycation, could increase the susceptibility to COVID-19 infection in DM patients by favouring the cellular entry of SARS-CoV2. Supplementary Information The online version contains supplementary material available at 10.1186/s12933-021-01286-7.
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Affiliation(s)
- Nunzia D'Onofrio
- Department of Precision Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Lucia Scisciola
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Celestino Sardu
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy.
| | - Maria Consiglia Trotta
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marisa De Feo
- Department of Cardio-Thoracic Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ciro Maiello
- Unit of Cardiac Surgery and Transplants, AORN Ospedali dei Colli-Monaldi Hospital, 80131, Naples, Italy
| | - Pasquale Mascolo
- Department of Experimental Medicine Forensic Pathology Service, University of Campania L. Vanvitelli, Naples, Italy
| | - Francesco De Micco
- Department of Experimental Medicine Forensic Pathology Service, University of Campania L. Vanvitelli, Naples, Italy
| | - Fabrizio Turriziani
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Emilia Municinò
- Department of Forensic, Evaluative and Necroscopic Medicine, ASL Napoli 2 NORD, Naples, Italy
| | - Pasquale Monetti
- Department of Forensic, Evaluative and Necroscopic Medicine, ASL Napoli 2 NORD, Naples, Italy
| | - Antonio Lombardi
- Department of Forensic, Evaluative and Necroscopic Medicine, ASL Napoli 2 NORD, Naples, Italy
| | | | - Federica Zito Marino
- Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Andrea Ronchi
- Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Vincenzo Grimaldi
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Anca Hermenean
- Institute of Life Science, Vasile Goldis Western University, Arad, Romania
| | - Maria Rosaria Rizzo
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Michelangela Barbieri
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Renato Franco
- Department of Mental and Physical Health and Preventive Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Carlo Pietro Campobasso
- Department of Experimental Medicine Forensic Pathology Service, University of Campania L. Vanvitelli, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy
| | - Maurizio Municinò
- Department of Forensic, Evaluative and Necroscopic Medicine, ASL Napoli 2 NORD, Naples, Italy
| | - Giuseppe Paolisso
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy.,Mediterranea Cardiocentro, Naples, Italy
| | | | - Raffaele Marfella
- Department of Advanced Medical and Surgical Sciences, University of Campania L. Vanvitelli, Piazza Miraglia, 2, 80138, Naples, Italy.,Mediterranea Cardiocentro, Naples, Italy
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158
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Abubakar MB, Usman D, El-Saber Batiha G, Cruz-Martins N, Malami I, Ibrahim KG, Abubakar B, Bello MB, Muhammad A, Gan SH, Dabai AI, Alblihed M, Ghosh A, Badr RH, Thangadurai D, Imam MU. Natural Products Modulating Angiotensin Converting Enzyme 2 (ACE2) as Potential COVID-19 Therapies. Front Pharmacol 2021; 12:629935. [PMID: 34012391 PMCID: PMC8126690 DOI: 10.3389/fphar.2021.629935] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/08/2021] [Indexed: 01/08/2023] Open
Abstract
The 2019 coronavirus disease (COVID-19) is a potentially fatal multisystemic infection caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Currently, viable therapeutic options that are cost effective, safe and readily available are desired, but lacking. Nevertheless, the pandemic is noticeably of lesser burden in African and Asian regions, where the use of traditional herbs predominates, with such relationship warranting a closer look at ethnomedicine. From a molecular viewpoint, the interaction of SARS-CoV-2 with angiotensin converting enzyme 2 (ACE2) is the crucial first phase of COVID-19 pathogenesis. Here, we review plants with medicinal properties which may be implicated in mitigation of viral invasion either via direct or indirect modulation of ACE2 activity to ameliorate COVID-19. Selected ethnomedicinal plants containing bioactive compounds which may prevent and mitigate the fusion and entry of the SARS-CoV-2 by modulating ACE2-associated up and downstream events are highlighted. Through further experimentation, these plants could be supported for ethnobotanical use and the phytomedicinal ligands could be potentially developed into single or combined preventive therapeutics for COVID-19. This will benefit researchers actively looking for solutions from plant bioresources and help lessen the burden of COVID-19 across the globe.
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Affiliation(s)
- Murtala Bello Abubakar
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Dawoud Usman
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna Sate, Nigeria
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Aliyu Ibrahim Dabai
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - M Alblihed
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Reem H. Badr
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
| | | | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
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159
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Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
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160
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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161
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Frappier V, Keating AE. Data-driven computational protein design. Curr Opin Struct Biol 2021; 69:63-69. [PMID: 33910104 DOI: 10.1016/j.sbi.2021.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/28/2023]
Abstract
Computational protein design can generate proteins not found in nature that adopt desired structures and perform novel functions. Although proteins could, in theory, be designed with ab initio methods, practical success has come from using large amounts of data that describe the sequences, structures, and functions of existing proteins and their variants. We present recent creative uses of multiple-sequence alignments, protein structures, and high-throughput functional assays in computational protein design. Approaches range from enhancing structure-based design with experimental data to building regression models to training deep neural nets that generate novel sequences. Looking ahead, deep learning will be increasingly important for maximizing the value of data for protein design.
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Affiliation(s)
- Vincent Frappier
- Generate Biomedicines, 26 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Amy E Keating
- MIT Departments of Biology and Biological Engineering, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.
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162
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Glasgow J, Glasgow A, Kortemme T, Wells JA. Reply to Liu et al.: Specific mutations matter in specificity and catalysis in ACE2. Proc Natl Acad Sci U S A 2021; 118:e2024450118. [PMID: 33833059 PMCID: PMC8053976 DOI: 10.1073/pnas.2024450118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Anum Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
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163
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His345 mutant of angiotensin-converting enzyme 2 (ACE2) remains enzymatically active against angiotensin II. Proc Natl Acad Sci U S A 2021; 118:2023648118. [PMID: 33833058 PMCID: PMC8053926 DOI: 10.1073/pnas.2023648118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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164
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Jia H, Neptune E, Cui H. Targeting ACE2 for COVID-19 Therapy: Opportunities and Challenges. Am J Respir Cell Mol Biol 2021; 64:416-425. [PMID: 33296619 PMCID: PMC8008810 DOI: 10.1165/rcmb.2020-0322ps] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic is sweeping the globe. Even with a number of effective vaccines being approved and available to the public, new cases and escalating mortality are climbing every day. ACE2 (angiotensin-converting enzyme 2) is the primary receptor for the COVID-19 causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and its complexation with spike proteins plays a crucial role in viral entry into host cells and the subsequent infection. Blocking this binding event or reducing the accessibility of the virus to the ACE2 receptor, represents an alternative strategy to prevent COVID-19. In addition, the biological significance of ACE2 in modulating the innate immune system and tissue repair cascades and anchors its therapeutic potential for treating the infected patients. In this viewpoint article, we review the current efforts of exploiting ACE2 as a therapeutic target to address this dire medical need. We also provide a holistic view of the pros and cons of each treatment strategy. We highlight the fundamental and translational challenges in moving these research endeavors to clinical applications.
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Affiliation(s)
- Hongpeng Jia
- Division of Pediatric Surgery, Department of Surgery
| | - Enid Neptune
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, and
- Institute for Nano Biotechnology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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165
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Oz M, Lorke DE. Multifunctional angiotensin converting enzyme 2, the SARS-CoV-2 entry receptor, and critical appraisal of its role in acute lung injury. Biomed Pharmacother 2021; 136:111193. [PMID: 33461019 PMCID: PMC7836742 DOI: 10.1016/j.biopha.2020.111193] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/11/2022] Open
Abstract
The recent emergence of coronavirus disease-2019 (COVID-19) as a pandemic affecting millions of individuals has raised great concern throughout the world, and the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was identified as the causative agent for COVID-19. The multifunctional protein angiotensin converting enzyme 2 (ACE2) is accepted as its primary target for entry into host cells. In its enzymatic function, ACE2, like its homologue ACE, regulates the renin-angiotensin system (RAS) critical for cardiovascular and renal homeostasis in mammals. Unlike ACE, however, ACE2 drives an alternative RAS pathway by degrading Ang-II and thus operates to balance RAS homeostasis in the context of hypertension, heart failure, and cardiovascular as well as renal complications of diabetes. Outside the RAS, ACE2 hydrolyzes key peptides, such as amyloid-β, apelin, and [des-Arg9]-bradykinin. In addition to its enzymatic functions, ACE2 is found to regulate intestinal amino acid homeostasis and the gut microbiome. Although the non-enzymatic function of ACE2 as the entry receptor for SARS-CoV-2 has been well established, the contribution of enzymatic functions of ACE2 to the pathogenesis of COVID-19-related lung injury has been a matter of debate. A complete understanding of this central enzyme may begin to explain the various symptoms and pathologies seen in SARS-CoV-2 infected individuals, and may aid in the development of novel treatments for COVID-19.
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Affiliation(s)
- Murat Oz
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Kuwait University, Safat 13110, Kuwait.
| | - Dietrich Ernst Lorke
- Department of Anatomy and Cellular Biology, Khalifa University, Abu Dhabi, United Arab Emirates; Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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166
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Kiseleva AA, Troisi EM, Hensley SE, Kohli RM, Epstein JA. SARS-CoV-2 spike protein binding selectively accelerates substrate-specific catalytic activity of ACE2. J Biochem 2021; 170:299-306. [PMID: 33774672 PMCID: PMC8083718 DOI: 10.1093/jb/mvab041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has given rise to the devastating global pandemic. In most cases, SARS-CoV-2 infection results in the development of viral pneumonia and acute respiratory distress syndrome, known as ‘coronavirus disease 2019’ or COVID-19. Intriguingly, besides the respiratory tract, COVID-19 affects other organs and systems of the human body. COVID-19 patients with pre-existing cardiovascular disease have a higher risk of death, and SARS-CoV-2 infection itself may cause myocardial inflammation and injury. One possible explanation of such phenomena is the fact that SARS-CoV-2 utilizes angiotensin-converting enzyme 2 (ACE2) as the receptor required for viral entry. ACE2 is expressed in the cells of many organs, including the heart. ACE2 functions as a carboxypeptidase that can cleave several endogenous substrates, including angiotensin II, thus regulating blood pressure and vascular tone. It remains largely unknown if the SARS-CoV-2 infection alters the enzymatic properties of ACE2, thereby contributing to cardiovascular complications in patients with COVID-19. Here, we demonstrate that ACE2 cleavage of des-Arg9-bradykinin substrate analogue is markedly accelerated, while cleavage of angiotensin II analogue is minimally affected by the binding of spike protein. These findings may have implications for a better understanding of COVID-19 pathogenesis.
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Affiliation(s)
- Anna A Kiseleva
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth M Troisi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jonathan A Epstein
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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167
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Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection. Nat Biotechnol 2021; 39:928-935. [PMID: 33767397 DOI: 10.1038/s41587-021-00878-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
Current serology tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies mainly take the form of enzyme-linked immunosorbent assays, chemiluminescent microparticle immunoassays or lateral flow assays, which are either laborious, expensive or lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost, solution-based assay to detect antibodies in serum, plasma, whole blood and to a lesser extent saliva, using rationally designed split luciferase antibody biosensors. This new assay, which generates quantitative results in 30 min, substantially reduces the complexity and improves the scalability of coronavirus disease 2019 (COVID-19) antibody tests. This assay is well-suited for point-of-care, broad population testing, and applications in low-resource settings, for monitoring host humoral responses to vaccination or viral infection.
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168
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Diagnostic Value of IgM and IgG Detection in COVID-19 Diagnosis by the Mobile Laboratory B-LiFE: A Massive Testing Strategy in the Piedmont Region. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073372. [PMID: 33805139 PMCID: PMC8036500 DOI: 10.3390/ijerph18073372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/23/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infectious disease caused by the novel coronavirus (SARS-CoV-2) identified in 2019. The COVID-19 outbreak continues to have devastating consequences for human lives and the global economy. The B-LiFe mobile laboratory in Piedmont, Italy, was deployed for the surveillance of COVID-19 cases by large-scale testing of first responders. The objective was to assess the seroconversion among the regional civil protection (CP), police, health care professionals, and volunteers. The secondary objective was to detect asymptomatic individuals within this cohort in the light of age, sex, and residence. In this paper, we report the results of serological testing performed by the B-LiFe mobile laboratory deployed from 10 June to 23 July 2020. The tests included whole blood finger-prick and serum sampling for detection of SARS-CoV-2 spike receptor-binding domain (S-RBD) antibodies. The prevalence of SARS-CoV-2 antibodies was approximately 5% (294/6013). The results of the finger-prick tests and serum sample analyses showed moderate agreement (kappa = 0.77). Furthermore, the detection rates of serum antibodies to the SARS-CoV-2 nucleocapsid protein (NP) and S-RBD among the seroconverted individuals were positively correlated (kappa = 0.60), at least at the IgG level. Seroprevalence studies based on serological testing for the S-RBD protein or SARS-CoV-2 NP antibodies are not sufficient for diagnosis but might help in screening the population to be vaccinated and in determining the duration of seroconversion.
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169
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Freitas FC, Ferreira PHB, Favaro DC, Oliveira RJD. Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides. J Chem Inf Model 2021; 61:1226-1243. [PMID: 33619962 PMCID: PMC7931628 DOI: 10.1021/acs.jcim.0c01320] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 01/07/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the host cellular receptor that locks onto the surface spike protein of the 2002 SARS coronavirus (SARS-CoV-1) and of the novel, highly transmissible and deadly 2019 SARS-CoV-2, responsible for the COVID-19 pandemic. One strategy to avoid the virus infection is to design peptides by extracting the human ACE2 peptidase domain α1-helix, which would bind to the coronavirus surface protein, preventing the virus entry into the host cells. The natural α1-helix peptide has a stronger affinity to SARS-CoV-2 than to SARS-CoV-1. Another peptide was designed by joining α1 with the second portion of ACE2 that is far in the peptidase sequence yet grafted in the spike protein interface with ACE2. Previous studies have shown that, among several α1-based peptides, the hybrid peptidic scaffold is the one with the highest/strongest affinity for SARS-CoV-1, which is comparable to the full-length ACE2 affinity. In this work, binding and folding dynamics of the natural and designed ACE2-based peptides were simulated by the well-known coarse-grained structure-based model, with the computed thermodynamic quantities correlating with the experimental binding affinity data. Furthermore, theoretical kinetic analysis of native contact formation revealed the distinction between these processes in the presence of the different binding partners SARS-CoV-1 and SARS-CoV-2 spike domains. Additionally, our results indicate the existence of a two-state folding mechanism for the designed peptide en route to bind to the spike proteins, in contrast to a downhill mechanism for the natural α1-helix peptides. The presented low-cost simulation protocol demonstrated its efficiency in evaluating binding affinities and identifying the mechanisms involved in the neutralization of spike-ACE2 interaction by designed peptides. Finally, the protocol can be used as a computer-based screening of more potent designed peptides by experimentalists searching for new therapeutics against COVID-19.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
| | - Paulo Henrique Borges Ferreira
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
| | - Denize Cristina Favaro
- Departamento de Química Orgânica,
Instituto de Química, Universidade Estadual de
Campinas, São Paulo, SP 13083-970, Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
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170
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Hassler L, Wysocki J, Gelarden I, Tomatsidou A, Gula H, Nicoleascu V, Randall G, Henkin J, Yeldandi A, Batlle D. A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33758841 DOI: 10.1101/2021.03.12.435191] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) uses full-length angiotensin converting enzyme 2 (ACE2), which is membrane bound, as its initial cell contact receptor preceding viral entry. Here we report a human soluble ACE2 variant fused with a 5kD albumin binding domain (ABD) and bridged via a dimerization motif hinge-like 4-cysteine dodecapeptide, which we term ACE2 1-618-DDC-ABD. This protein is enzymatically active, has increased duration of action in vivo conferred by the ABD-tag, and displays 20-30-fold higher binding affinity to the SARS-CoV-2 receptor binding domain than its des-DDC monomeric form (ACE2 1-618-ABD) due to DDC-linked dimerization. ACE2 1-618-DDC-ABD was administered for 3 consecutive days to transgenic k18-hACE2 mice, a model that develops lethal SARS-CoV-2 infection, to evaluate the preclinical preventative/ therapeutic value for COVID-19. Mice treated with ACE2 1-618-DDC-ABD developed a mild to moderate disease for the first few days assessed by a clinical score and modest weight loss. The untreated control animals, by contrast, became severely ill and had to be sacrificed by day 6/7 and lung histology revealed extensive pulmonary alveolar hemorrhage and mononuclear infiltrates. At 6 days, mortality was totally prevented in the treated group, lung histopathology was improved and viral titers markedly reduced. This demonstrates for the first time in vivo the preventative/ therapeutic potential of a novel soluble ACE2 protein in a preclinical animal model.
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171
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Meganck RM, Baric RS. Developing therapeutic approaches for twenty-first-century emerging infectious viral diseases. Nat Med 2021; 27:401-410. [PMID: 33723456 DOI: 10.1038/s41591-021-01282-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
The twenty-first century has already recorded more than ten major epidemic or pandemic virus emergence events, including the ongoing and devastating coronavirus disease 2019 (COVID-19) pandemic. As viral disease emergence is expected to accelerate, these data dictate a need for proactive approaches to develop broadly active family-specific and cross-family therapeutics for use in future disease outbreaks. Emphasis should focus not only on the development of broad-spectrum small-molecule and antibody direct-acting antivirals, but also on host-factor therapeutics, including repurposing previously approved or in-pipeline drugs. Another new class of therapeutics with great antiviral therapeutic potential is RNA-based therapeutics. Rather than only focusing on known risks, dedicated efforts must be made toward pre-emptive research focused on outbreak-prone virus families, ultimately offering a strategy to shorten the gap between outbreak and response. Emphasis should also focus on orally available drugs for outpatient use, if possible, and on identifying combination therapies that combat viral and immune-mediated pathologies, extend the effectiveness of therapeutic windows and reduce drug resistance. While such an undertaking will require new vision, dedicated funding and private, federal and academic partnerships, this approach offers hope that global populations need never experience future pandemics such as COVID-19.
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Affiliation(s)
- Rita M Meganck
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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172
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Uthaya Kumar A, Kadiresen K, Gan WC, Ling APK. Current updates and research on plant-based vaccines for coronavirus disease 2019. Clin Exp Vaccine Res 2021; 10:13-23. [PMID: 33628750 PMCID: PMC7892944 DOI: 10.7774/cevr.2021.10.1.13] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/18/2022] Open
Abstract
The primary outbreak of severe acute respiratory syndrome coronavirus 2, causing pneumonia-like symptoms in patients named coronavirus disease 2019 (COVID-19) had evolved into a global pandemic. COVID-19 has surpassed Middle East respiratory syndrome and severe acute respiratory syndrome in terms of rate and scale causing more than one million deaths. Development of an effective vaccine to fight against the spread of COVID-19 is the main goal of many countries around the world and plant-based vaccines are one of the available methods in vaccine developments. Plant-based vaccine has gained its reputation among researchers for its known effective manufacturing process and cost effectiveness. Many companies around the world are participating in the race to develop an effective vaccine by using the plant system. This review discusses different approaches used as well as highlights the challenges faced by various companies and research groups in developing the plant-based COVID-19 vaccine.
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Affiliation(s)
- Asqwin Uthaya Kumar
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Kirthikah Kadiresen
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Wen Cong Gan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Anna Pick Kiong Ling
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
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173
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Bonadio A, Shifman JM. Computational design and experimental optimization of protein binders with prospects for biomedical applications. Protein Eng Des Sel 2021; 34:gzab020. [PMID: 34436606 PMCID: PMC8388154 DOI: 10.1093/protein/gzab020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 11/12/2022] Open
Abstract
Protein-based binders have become increasingly more attractive candidates for drug and imaging agent development. Such binders could be evolved from a number of different scaffolds, including antibodies, natural protein effectors and unrelated small protein domains of different geometries. While both computational and experimental approaches could be utilized for protein binder engineering, in this review we focus on various computational approaches for protein binder design and demonstrate how experimental selection could be applied to subsequently optimize computationally-designed molecules. Recent studies report a number of designed protein binders with pM affinities and high specificities for their targets. These binders usually characterized with high stability, solubility, and low production cost. Such attractive molecules are bound to become more common in various biotechnological and biomedical applications in the near future.
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Affiliation(s)
- Alessandro Bonadio
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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174
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. SCIENCE ADVANCES 2021; 7:eabf1738. [PMID: 33597251 PMCID: PMC7888922 DOI: 10.1126/sciadv.abf1738] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/31/2020] [Indexed: 05/04/2023]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, because of close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find that an engineered decoy receptor, sACE22v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild-type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild-type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign, IL 61821, USA
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA.
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175
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Cruz-Teran C, Tiruthani K, McSweeney M, Ma A, Pickles R, Lai SK. Challenges and opportunities for antiviral monoclonal antibodies as COVID-19 therapy. Adv Drug Deliv Rev 2021; 169:100-117. [PMID: 33309815 PMCID: PMC7833882 DOI: 10.1016/j.addr.2020.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 01/08/2023]
Abstract
To address the COVID-19 pandemic, there has been an unprecedented global effort to advance potent neutralizing mAbs against SARS-CoV-2 as therapeutics. However, historical efforts to advance antiviral monoclonal antibodies (mAbs) for the treatment of other respiratory infections have been met with categorical failures in the clinic. By investigating the mechanism by which SARS-CoV-2 and similar viruses spread within the lung, along with available biodistribution data for systemically injected mAb, we highlight the challenges faced by current antiviral mAbs for COVID-19. We summarize some of the leading mAbs currently in development, and present the evidence supporting inhaled delivery of antiviral mAb as an early intervention against COVID-19 that could prevent important pulmonary morbidities associated with the infection.
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Affiliation(s)
- Carlos Cruz-Teran
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karthik Tiruthani
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Alice Ma
- UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raymond Pickles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel K Lai
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Inhalon Biopharma, Durham, NC 27709, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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176
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The role of chemical biology in the fight against SARS-CoV-2. Biochem J 2021; 478:157-177. [PMID: 33439990 DOI: 10.1042/bcj20200514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023]
Abstract
Since late 2019, biomedical labs all over the world have been struggling to cope with the 'new normal' and to find ways in which they can contribute to the fight against COVID-19. In this unique situation where a biomedical issue dominates people's lives and the news cycle, chemical biology has a great deal to contribute. This review will describe the importance of science at the chemistry/biology interface to both understand and combat the SARS-CoV-2 pandemic.
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177
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Lim SA, Gramespacher JA, Pance K, Rettko NJ, Solomon P, Jin J, Lui I, Elledge SK, Liu J, Bracken CJ, Simmons G, Zhou XX, Leung KK, Wells JA. Bispecific VH/Fab antibodies targeting neutralizing and non-neutralizing Spike epitopes demonstrate enhanced potency against SARS-CoV-2. MAbs 2021; 13:1893426. [PMID: 33666135 PMCID: PMC7939556 DOI: 10.1080/19420862.2021.1893426] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous neutralizing antibodies that target SARS-CoV-2 have been reported, and most directly block binding of the viral Spike receptor-binding domain (RBD) to angiotensin-converting enzyme II (ACE2). Here, we deliberately exploit non-neutralizing RBD antibodies, showing they can dramatically assist in neutralization when linked to neutralizing binders. We identified antigen-binding fragments (Fabs) by phage display that bind RBD, but do not block ACE2 or neutralize virus as IgGs. When these non-neutralizing Fabs were assembled into bispecific VH/Fab IgGs with a neutralizing VH domain, we observed a ~ 25-fold potency improvement in neutralizing SARS-CoV-2 compared to the mono-specific bi-valent VH-Fc alone or the cocktail of the VH-Fc and IgG. This effect was epitope-dependent, reflecting the unique geometry of the bispecific antibody toward Spike. Our results show that a bispecific antibody that combines both neutralizing and non-neutralizing epitopes on Spike-RBD is a promising and rapid engineering strategy to improve the potency of SARS-CoV-2 antibodies.
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MESH Headings
- Antibodies, Bispecific/genetics
- Antibodies, Bispecific/immunology
- Antibodies, Bispecific/therapeutic use
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- COVID-19/genetics
- COVID-19/immunology
- Epitopes/genetics
- Epitopes/immunology
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/immunology
- Immunoglobulin Fab Fragments/therapeutic use
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Drug Treatment
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Affiliation(s)
- Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Josef A. Gramespacher
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Nicholas J. Rettko
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Jing Jin
- Vitalant Research Institute and Department of Laboratory Medicine, University of California San Francisco, University of California San Francisco, California, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Susanna K. Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Jia Liu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Colton J. Bracken
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Graham Simmons
- Vitalant Research Institute and Department of Laboratory Medicine, University of California San Francisco, University of California San Francisco, California, USA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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178
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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179
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Bernard I, Limonta D, Mahal LK, Hobman TC. Endothelium Infection and Dysregulation by SARS-CoV-2: Evidence and Caveats in COVID-19. Viruses 2020; 13:E29. [PMID: 33375371 PMCID: PMC7823949 DOI: 10.3390/v13010029] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 12/25/2020] [Indexed: 02/06/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) poses a persistent threat to global public health. Although primarily a respiratory illness, extrapulmonary manifestations of COVID-19 include gastrointestinal, cardiovascular, renal and neurological diseases. Recent studies suggest that dysfunction of the endothelium during COVID-19 may exacerbate these deleterious events by inciting inflammatory and microvascular thrombotic processes. Although controversial, there is evidence that SARS-CoV-2 may infect endothelial cells by binding to the angiotensin-converting enzyme 2 (ACE2) cellular receptor using the viral Spike protein. In this review, we explore current insights into the relationship between SARS-CoV-2 infection, endothelial dysfunction due to ACE2 downregulation, and deleterious pulmonary and extra-pulmonary immunothrombotic complications in severe COVID-19. We also discuss preclinical and clinical development of therapeutic agents targeting SARS-CoV-2-mediated endothelial dysfunction. Finally, we present evidence of SARS-CoV-2 replication in primary human lung and cardiac microvascular endothelial cells. Accordingly, in striving to understand the parameters that lead to severe disease in COVID-19 patients, it is important to consider how direct infection of endothelial cells by SARS-CoV-2 may contribute to this process.
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Affiliation(s)
- Isabelle Bernard
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Daniel Limonta
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada;
| | - Tom C. Hobman
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Women & Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
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180
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Sahai A, Bhandari R, Koupenova M, Freedman JE, Godwin M, McIntyre T, Chung MK, Iskandar JP, Kamran H, Hariri E, Aggarwal A, Kalra A, Bartholomew JR, McCrae KR, Elbadawi A, Svensson LG, Kapadia S, Cameron SJ. SARS-CoV-2 Receptors are Expressed on Human Platelets and the Effect of Aspirin on Clinical Outcomes in COVID-19 Patients. RESEARCH SQUARE 2020:rs.3.rs-119031. [PMID: 33398263 PMCID: PMC7781327 DOI: 10.21203/rs.3.rs-119031/v1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Coronavirus disease-2019 (COVID-19) caused by SARS-CoV-2 is an ongoing viral pandemic marked by increased risk of thrombotic events. However, the role of platelets in the elevated observed thrombotic risk in COVID-19 and utility of anti-platelet agents in attenuating thrombosis is unknown. We aimed to determine if human platelets express the known SARS-CoV-2 receptor-protease axis on their cell surface and assess whether the anti-platelet effect of aspirin may mitigate risk of myocardial infarction (MI), cerebrovascular accident (CVA), and venous thromboembolism (VTE) in COVID-19. Expression of ACE2 and TMPRSS2 on human platelets were detected by immunoblotting and confirmed by confocal microscopy. We evaluated 22,072 symptomatic patients tested for COVID-19. Propensity-matched analyses were performed to determine if treatment with aspirin or non-steroidal anti-inflammatory drugs (NSAIDs) affected thrombotic outcomes in COVID-19. Neither aspirin nor NSAIDs affected mortality in COVID-19. However, both aspirin and NSAID therapies were associated with increased risk of the combined thrombotic endpoint of (MI), (CVA), and (VTE). Thus, while platelets clearly express ACE2-TMPRSS2 receptor-protease axis for SARS-CoV-2 infection, aspirin does not prevent thrombosis and death in COVID-19. The mechanisms of thrombosis in COVID-19, therefore, appears distinct and the role of platelets as direct mediators of SARS-CoV-2-mediated thrombosis warrants further investigation.
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Affiliation(s)
- Aditya Sahai
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
| | - Rohan Bhandari
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH
| | - Milka Koupenova
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Jane E. Freedman
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Matthew Godwin
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
| | - Thomas McIntyre
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Mina K. Chung
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | | | - Hayaan Kamran
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
| | - Essa Hariri
- Department of Medicine, Cleveland Clinic, Cleveland, OH
| | - Anu Aggarwal
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH
| | - Ankur Kalra
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
| | - John R. Bartholomew
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Keith R. McCrae
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Ayman Elbadawi
- Division of Cardiovascular Medicine, University of Texas Medical Branch, Galveston, TX
| | - Lars G. Svensson
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Samir Kapadia
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Scott J. Cameron
- Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH
- Case Western Reserve University Cleveland Clinic Lerner College of Medicine, Cleveland, OH
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181
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.18.344622. [PMID: 33398275 PMCID: PMC7781310 DOI: 10.1101/2020.10.18.344622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE2 2 .v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign IL 61821
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
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182
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Pomplun S. Targeting the SARS-CoV-2-spike protein: from antibodies to miniproteins and peptides. RSC Med Chem 2020; 12:197-202. [PMID: 34041482 PMCID: PMC8128053 DOI: 10.1039/d0md00385a] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022] Open
Abstract
Coronavirus disease-19, caused by the novel β-coronavirus SARS-CoV-2, has created a global pandemic unseen in a century. Rapid worldwide efforts have enabled the characterization of the virus and its pathogenic mechanism. An early key finding is that SARS-CoV-2 uses spike proteins, the virus' most exposed structures, to bind to human ACE2 receptors and initiate cell invasion. Competitive targeting of the spike protein is a promising strategy to neutralize virus infectivity. This review article summarizes the discovery, binding modes and eventual applications of several classes of (bio)molecules targeting the spike protein: antibodies, nanobodies, soluble ACE2 variants, miniproteins, peptides and small molecules.
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Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology 77 Massachusetts Ave Cambridge MA 02139 USA
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183
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Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biophys J 2020; 120:1072-1084. [PMID: 33189680 PMCID: PMC7661960 DOI: 10.1016/j.bpj.2020.10.036] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection. Here, we perform explicitly solvated, all-atom, molecular dynamics simulations of the glycosylated, full-length, membrane-bound ACE2 receptor in both an apo and spike RBD-bound state to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full-length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer and suggests a mechanical contribution of the host receptor toward the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can potentially be exploited for the rational design of effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Yuzhang Wang
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lucy Fallon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lauren Raguette
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Kellon Belfon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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184
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Diego-Martin B, González B, Vazquez-Vilar M, Selma S, Mateos-Fernández R, Gianoglio S, Fernández-del-Carmen A, Orzáez D. Pilot Production of SARS-CoV-2 Related Proteins in Plants: A Proof of Concept for Rapid Repurposing of Indoor Farms Into Biomanufacturing Facilities. FRONTIERS IN PLANT SCIENCE 2020; 11:612781. [PMID: 33424908 PMCID: PMC7785703 DOI: 10.3389/fpls.2020.612781] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/02/2020] [Indexed: 05/21/2023]
Abstract
The current CoVid-19 crisis is revealing the strengths and the weaknesses of the world's capacity to respond to a global health crisis. A critical weakness has resulted from the excessive centralization of the current biomanufacturing capacities, a matter of great concern, if not a source of nationalistic tensions. On the positive side, scientific data and information have been shared at an unprecedented speed fuelled by the preprint phenomena, and this has considerably strengthened our ability to develop new technology-based solutions. In this work, we explore how, in a context of rapid exchange of scientific information, plant biofactories can serve as a rapid and easily adaptable solution for local manufacturing of bioreagents, more specifically recombinant antibodies. For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. For the design of the antibodies, we took advantage, among other data sources, of the DNA sequence information made rapidly available by other groups in preprint publications. mAbs were engineered as single-chain fragments fused to a human gamma Fc and transiently expressed using a viral vector. In parallel, we also produced the recombinant SARS-CoV-2 N protein and the receptor binding domain (RBD) of the Spike protein in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies, we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Our results indicate that gram amounts of anti-SARS-CoV-2 antibodies could be easily produced in little more than 6 weeks in repurposed greenhouses with little infrastructure requirements using N. benthamiana as production platform. Similar procedures could be easily deployed to produce diagnostic reagents and, eventually, could be adapted for rapid therapeutic responses.
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