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Gong Q, Jiang R, Ji L, Lin H, Liu M, Tang X, Yang Y, Han W, Chen J, Guo Z, Wang Q, Li Q, Wang X, Jiang T, Xie S, Yang X, Zhou P, Shi Z, Lin X. Establishment of a human organoid-based evaluation system for assessing interspecies infection risk of animal-borne coronaviruses. Emerg Microbes Infect 2024; 13:2327368. [PMID: 38531008 DOI: 10.1080/22221751.2024.2327368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
The COVID-19 pandemic presents a major threat to global public health. Several lines of evidence have shown that the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), along with two other highly pathogenic coronaviruses, SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV) originated from bats. To prevent and control future coronavirus outbreaks, it is necessary to investigate the interspecies infection and pathogenicity risks of animal-related coronaviruses. Currently used infection models, including in vitro cell lines and in vivo animal models, fail to fully mimic the primary infection in human tissues. Here, we employed organoid technology as a promising new model for studying emerging pathogens and their pathogenic mechanisms. We investigated the key host-virus interaction patterns of five human coronaviruses (SARS-CoV-2 original strain, Omicron BA.1, MERS-CoV, HCoV-229E, and HCoV-OC43) in different human respiratory organoids. Five indicators, including cell tropism, invasion preference, replication activity, host response and virus-induced cell death, were developed to establish a comprehensive evaluation system to predict coronavirus interspecies infection and pathogenicity risks. Using this system, we further examined the pathogenicity and interspecies infection risks of three SARS-related coronaviruses (SARSr-CoV), including WIV1 and rRsSHC014S from bats, and MpCoV-GX from pangolins. Moreover, we found that cannabidiol, a non-psychoactive plant extract, exhibits significant inhibitory effects on various coronaviruses in human lung organoid. Cannabidiol significantly enhanced interferon-stimulated gene expression but reduced levels of inflammatory cytokines. In summary, our study established a reliable comprehensive evaluation system to analyse infection and pathogenicity patterns of zoonotic coronaviruses, which could aid in prevention and control of potentially emerging coronavirus diseases.
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Affiliation(s)
- Qianchun Gong
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, People's Republic of China
| | - Rendi Jiang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Lina Ji
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Haofeng Lin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiqin Liu
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaofang Tang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yong Yang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Wei Han
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Jing Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zishuo Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Qi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People's Republic of China
| | - Qian Li
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Tingting Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Shizhe Xie
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Peng Zhou
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People's Republic of China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People's Republic of China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu, People's Republic of China
- School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
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2
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Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 DOI: 10.1371/journal.ppat.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
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Affiliation(s)
- Francesca R Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H J Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
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3
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Peñaranda Figueredo FA, Vicente J, Barquero AA, Bueno CA. Aesculus hippocastanum extract and the main bioactive constituent β-escin as antivirals agents against coronaviruses, including SARS-CoV-2. Sci Rep 2024; 14:6418. [PMID: 38494515 PMCID: PMC10944838 DOI: 10.1038/s41598-024-56759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
Respiratory viruses can cause life-threatening illnesses. The focus of treatment is on supportive therapies and direct antivirals. However, antivirals may cause resistance by exerting selective pressure. Modulating the host response has emerged as a viable therapeutic approach for treating respiratory infections. Additionally, considering the probable future respiratory virus outbreaks emphasizes the need for broad-spectrum therapies to be prepared for the next pandemics. One of the principal bioactive constituents found in the seed extract of Aesculus hippocastanum L. (AH) is β-escin. The clinical therapeutic role of β-escin and AH has been associated with their anti-inflammatory effects. Regarding their mechanism of action, we and others have shown that β-escin and AH affect NF-κB signaling. Furthermore, we have reported the virucidal and broad-spectrum antiviral properties of β-escin and AH against enveloped viruses such as RSV, in vitro and in vivo. In this study, we demonstrate that β-escin and AH have antiviral and virucidal activities against SARS-CoV-2 and CCoV, revealing broad-spectrum antiviral activity against coronaviruses. Likewise, they exhibited NF-κB and cytokine modulating activities in epithelial and macrophage cell lines infected with coronaviruses in vitro. Hence, β-escin and AH are promising broad-spectrum antiviral, immunomodulatory, and virucidal drugs against coronaviruses and respiratory viruses, including SARS-CoV-2.
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Affiliation(s)
- Freddy Armando Peñaranda Figueredo
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, C-1428GBA, Buenos Aires, Argentina
| | - Josefina Vicente
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, C-1428GBA, Buenos Aires, Argentina
| | - Andrea Alejandra Barquero
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, C-1428GBA, Buenos Aires, Argentina
| | - Carlos Alberto Bueno
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, C-1428GBA, Buenos Aires, Argentina.
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Suzuki S, Kuroda M, Aoki K, Kawaji K, Hiramatsu Y, Sasano M, Nishiyama A, Murayama K, Kodama EN, Oishi S, Hayashi H. Helix-based screening with structure prediction using artificial intelligence has potential for the rapid development of peptide inhibitors targeting class I viral fusion. RSC Chem Biol 2024; 5:131-140. [PMID: 38333196 PMCID: PMC10849125 DOI: 10.1039/d3cb00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/04/2023] [Indexed: 02/10/2024] Open
Abstract
The rapid development of drugs against emerging and re-emerging viruses is required to prevent future pandemics. However, inhibitors usually take a long time to optimize. Here, to improve the optimization step, we used two heptad repeats (HR) in the spike protein (S protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a model and established a screening system for peptide-based inhibitors containing an α-helix region (SPICA). SPICA can be used to identify critical amino acid regions and evaluate the inhibitory effects of peptides as decoys. We further employed an artificial intelligence structure-prediction system (AlphaFold2) for the rapid analysis of structure-activity relationships. Here, we identified that critical amino acid regions, DVDLGD (amino acids 1163-1168 in the S protein), IQKEIDRLNE (1179-1188), and NLNESLIDL (1192-1200), played a pivotal role in SARS-CoV-2 fusion. Peptides containing these critical amino acid regions efficiently blocked viral replication. We also demonstrated that AlphaFold2 could successfully predict structures similar to the reported crystal and cryo-electron microscopy structures of the post-fusion form of the SARS-CoV-2 S protein. Notably, the predicted structures of the HR1 region and the peptide-based fusion inhibitors corresponded well with the antiviral effects of each fusion inhibitor. Thus, the combination of SPICA and AlphaFold2 is a powerful tool to design viral fusion inhibitors using only the amino-acid sequence of the fusion protein.
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Affiliation(s)
- Satoshi Suzuki
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Mio Kuroda
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
| | - Keisuke Aoki
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Kumi Kawaji
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Yoshiki Hiramatsu
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Mina Sasano
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Akie Nishiyama
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Eiichi N Kodama
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
- Department of Infectious Disease, Graduate School of Medicine and Tohoku Medical Megabank Organization, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
| | - Shinya Oishi
- Laboratory of Medicinal Chemistry, Kyoto Pharmaceutical University 1, Misasagi-Shichono-cho, Yamashina-ku Kyoto 607-8412 Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Hironori Hayashi
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University 2-1, Seiryo-machi, Aoba-ku Sendai Miyagi 980-8575 Japan
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5
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Doijen J, Heo I, Temmerman K, Vermeulen P, Diels A, Jaensch S, Burcin M, Van den Broeck N, Raeymaekers V, Peremans J, Konings K, Clement M, Peeters D, Van Loock M, Koul A, Buyck C, Van Gool M, Van Damme E. A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects. Antiviral Res 2024; 222:105789. [PMID: 38158129 DOI: 10.1016/j.antiviral.2023.105789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.
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Affiliation(s)
- Jordi Doijen
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Inha Heo
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Koen Temmerman
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Peter Vermeulen
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Annick Diels
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Steffen Jaensch
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Mark Burcin
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | - Joren Peremans
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Katrien Konings
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Maxime Clement
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Danielle Peeters
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Marnix Van Loock
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Anil Koul
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Christophe Buyck
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michiel Van Gool
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ellen Van Damme
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
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Funk LM, Poschmann G, Rabe von Pappenheim F, Chari A, Stegmann KM, Dickmanns A, Wensien M, Eulig N, Paknia E, Heyne G, Penka E, Pearson AR, Berndt C, Fritz T, Bazzi S, Uranga J, Mata RA, Dobbelstein M, Hilgenfeld R, Curth U, Tittmann K. Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Nat Commun 2024; 15:411. [PMID: 38195625 PMCID: PMC10776599 DOI: 10.1038/s41467-023-44621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.
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Affiliation(s)
- Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Marie Wensien
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Nora Eulig
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elham Paknia
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gabi Heyne
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elke Penka
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Hamburg Centre for Ultrafast Imaging, Hamburg University, HARBOR, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Tobias Fritz
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute for Biochemistry, Lübeck University, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research, Hamburg - Lübeck-Borstel-Riems Site, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany.
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany.
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7
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Gallucci L, Bazire J, Davidson AD, Shytaj IL. Broad-spectrum antiviral activity of two structurally analogous CYP3A inhibitors against pathogenic human coronaviruses in vitro. Antiviral Res 2024; 221:105766. [PMID: 38042417 DOI: 10.1016/j.antiviral.2023.105766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023]
Abstract
Coronaviruses pose a permanent risk of outbreaks, with three highly pathogenic species and strains (SARS-CoV, MERS-CoV, SARS-CoV-2) having emerged in the last twenty years. Limited antiviral therapies are currently available and their efficacy in randomized clinical trials enrolling SARS-CoV-2 patients has not been consistent, highlighting the need for more potent treatments. We previously showed that cobicistat, a clinically approved inhibitor of Cytochrome P450-3A (CYP3A), has direct antiviral activity against early circulating SARS-CoV-2 strains in vitro and in Syrian hamsters. Cobicistat is a derivative of ritonavir, which is co-administered as pharmacoenhancer with the SARS-CoV-2 protease inhibitor nirmatrelvir, to inhibit its metabolization by CPY3A and preserve its antiviral efficacy. Here, we used automated image analysis for a screening and parallel comparison of the anti-coronavirus effects of cobicistat and ritonavir. Our data show that both drugs display antiviral activity at low micromolar concentrations against multiple SARS-CoV-2 variants in vitro, including epidemiologically relevant Omicron subvariants. Despite their close structural similarity, we found that cobicistat is more potent than ritonavir, as shown by significantly lower EC50 values in monotherapy and higher levels of viral suppression when used in combination with nirmatrelvir. Finally, we show that the antiviral activity of both cobicistat and ritonavir is maintained against other human coronaviruses, including HCoV-229E and the highly pathogenic MERS-CoV. Overall, our results demonstrate that cobicistat has more potent anti-coronavirus activity than ritonavir and suggest that dose adjustments could pave the way to the use of both drugs as broad-spectrum antivirals against highly pathogenic human coronaviruses.
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Affiliation(s)
- Lara Gallucci
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - James Bazire
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
| | - Iart Luca Shytaj
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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8
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Fu Y, Yu B, Wang Q, Lu Z, Zhang H, Zhang D, Luo F, Liu R, Wang L, Chu Y. Oxidative stress-initiated one-carbon metabolism drives the generation of interleukin-10-producing B cells to resolve pneumonia. Cell Mol Immunol 2024; 21:19-32. [PMID: 38082147 PMCID: PMC10757717 DOI: 10.1038/s41423-023-01109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/07/2023] [Indexed: 01/01/2024] Open
Abstract
The metabolic reprogramming underlying the generation of regulatory B cells during infectious diseases remains unknown. Using a Pseudomonas aeruginosa-induced pneumonia model, we reported that IL-10-producing B cells (IL-10+ B cells) play a key role in spontaneously resolving infection-mediated inflammation. Accumulated cytosolic reactive oxygen species (ROS) during inflammation were shown to drive IL-10+ B-cell generation by remodeling one-carbon metabolism. Depletion of the enzyme serine hydroxymethyltransferase 1 (Shmt1) led to inadequate one-carbon metabolism and decreased IL-10+ B-cell production. Furthermore, increased one-carbon flux elevated the levels of the methyl donor S-adenosylmethionine (SAM), altering histone H3 lysine 4 methylation (H3K4me) at the Il10 gene to promote chromatin accessibility and upregulate Il10 expression in B cells. Therefore, the one-carbon metabolism-associated compound ethacrynic acid (EA) was screened and found to potentially treat infectious pneumonia by boosting IL-10+ B-cell generation. Overall, these findings reveal that ROS serve as modulators to resolve inflammation by reprogramming one-carbon metabolism pathways in B cells.
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Affiliation(s)
- Ying Fu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Baichao Yu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Wang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhou Lu
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Shanghai, China
| | - Hushan Zhang
- Zhaotong Health Vocational College, Zhaotong, Yunnan, China
| | - Dan Zhang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feifei Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ronghua Liu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Luman Wang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- Shanghai Fifth People's Hospital, Fudan University, Shanghai, China.
| | - Yiwei Chu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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9
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Lu D, Han Y, Xu R, Qin M, Shi J, Zhang C, Zhang J, Ye F, Luo Z, Wang Y, Wang C, Wang C. Evaluation of the efficacy, safety and influencing factors of concomitant and sequential administration of viral respiratory infectious disease vaccines: a systematic review and meta-analysis. Front Immunol 2023; 14:1259399. [PMID: 38179050 PMCID: PMC10764558 DOI: 10.3389/fimmu.2023.1259399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Background There is no clear conclusion on the immunogenicity and adverse events of concomitant administration the viral respiratory infectious disease vaccines. We aimed to evaluate the impact of concomitant administering viral respiratory infectious disease vaccines on efficiencies, safety and influencing factors. Methods This meta-analysis included studies from PubMed, Embase, Cochrane Central Register of Clinical Trials, Web of Science, WHO COVID-19 Research, and ClinicalTrials.gov databases. Randomized controlled trials of the adult participants concomitant administered with viral respiratory infectious disease vaccine and other vaccines were included. The main outcomes were the seroconversion rate and seroprotection rate of each vaccine. Used the Mantel-Haenszel fixed effects method as the main analysis to estimate the pooled RRs and the corresponding 95% confidence intervals. The risk of bias for each trial was assessed using the Cochrane Handbook for Systematic Reviews of Interventions, while evidence certainty was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation system. Results A total of 21 studies comprising 14060 participants with two types of vaccines were retained for the meta-analysis. Concomitant immunization reduced the geometric mean titer (RR: 0.858, 95% CI: (0.785 to 0.939)) and the geometric mean fold rise (0.754 (0.629 to 0.902)) in the SARS-COV-2 vaccine group but increased the seroconversion rate (1.033 (1.0002 to 1.067)) in the seasonal influenza vaccine group. Concomitant administration were influenced by the type of vaccine, adjuvant content, booster immunization, and age and gender of the recipient. Conclusion This meta-analysis suggested that the short-term protection and safety of concomitant administered were effective. Appropriate adjuvants, health promotion and counselling and booster vaccines could improve the efficiency and safety of Concomitant vaccination. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022343709.
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Affiliation(s)
- Dafeng Lu
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- Department of Infectious Disease Prevention and Control, Quzhou Center for Disease Prevention and Control, Quzhou, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifang Han
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Ruowei Xu
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Mingke Qin
- Department of Occupational Health, Third Military Medical University, Chongqing, China
| | - Jianwei Shi
- Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Caihong Zhang
- School of Public Health, Bengbu Medical College, Bengbu, China
| | - Jinhai Zhang
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Fuqiang Ye
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Zhenghan Luo
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Yuhe Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunfang Wang
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chunhui Wang
- Department of Infectious Disease Prevention and Control, Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
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10
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Lv Y, Xiang Q, Jiang X, Zhang B, Wu J, Cao H. Effectiveness of inspector mechanism for the emergency infection prevention and control in the SARS-CoV-2 epidemic period: a self-control real-word study. BMC Infect Dis 2023; 23:858. [PMID: 38057717 DOI: 10.1186/s12879-023-08682-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/07/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND To ensure emergency infection prevention and control (IPC) can be fully supervised and monitored in coronavirus disease (COVID-19) epidemic period, a three-level inspector mechanism called "Internal self-check, Departmental cross-check, and Verification of outstanding key and difficult issues" was established in southwest China. The present study aimed to explore the effectiveness of inspector mechanism for the emergency IPC. METHODS A self-control real-world study was conducted during COVID-19 epidemic period from 2020 to 2022. An innovative designed mobile phone application was used to realize paperless information transmission and data management. Data were compared between inspection levels using SPSS 19.0 software. RESULTS A total of 2,800,132 supervision records were collected, including 149,137 comprehensive epidemic IPC projects, 1,410,093 personal protective equipment (PPE) use, 1,223,595 wearing and removing process of PPE and 17,307 ultraviolet light-detectable fluorescent (UV/F) surface marker. During the study period, the inspectors and subjects explored many optimized IPC measures. The compliance rate of check items has exceeded 98%, and internal self-check has a statistically significant higher rate than departmental cross-check (99.95% versus 98.74%, χ2 = 26111.479, P < 0.001). Compare with the failure rate in internal self check, the failure rate of PPE usage and wearing/removing process was statistically higher in departmental cross-check (χ2 = 1957.987, P < 0.001, χ2 = 465.610, P < 0.001, respectively). The overall clearance rate of UV/F surface markers is 87.88%, but there is no statistically significant difference over the three years of the present study (F = 2.902, P = 0.071). CONCLUSIONS Inspector mechanism for the emergency IPC completed an incredible inspection workload and offered creative assistance to combat the COVID-19 outbreak. These methods and accumulated experiences should be helpful for us to strengthen IPC for future epidemic.
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Affiliation(s)
- Yu Lv
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Qian Xiang
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Xiaoyan Jiang
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China
| | - Bo Zhang
- Development Department, Chengdu Yiou Technology Co. LTD, Chengdu, 610000, Sichuan, P. R. China
| | - Jiayu Wu
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China.
| | - Hongrong Cao
- Healthcare-Associated Infection Control Center, Sichuan Provincial People's Hospital, school of medicine, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, P. R. China.
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11
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Vickos U, Camasta M, Grandi N, Scognamiglio S, Schindler T, Belizaire MRD, Lango-Yaya E, Koyaweda GW, Senzongo O, Pounguinza S, Estimé KKJF, N’yetobouko S, Gadia CLB, Feiganazoui DA, Le Faou A, Orsini M, Perno CF, Zinzula L, Rafaï CD. COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome. Viruses 2023; 15:2309. [PMID: 38140550 PMCID: PMC10748234 DOI: 10.3390/v15122309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.
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Affiliation(s)
- Ulrich Vickos
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
- Department of Medicine, Infectious and Tropical Diseases, Sino-Central African Amitié Hospital, Bangui 94045, Central African Republic
| | - Marianna Camasta
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Sante Scognamiglio
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland;
- Department of Medical Parasitology and Infection Biology, University of Basel, 4051 Basel, Switzerland
| | | | - Ernest Lango-Yaya
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Giscard Wilfried Koyaweda
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Oscar Senzongo
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Simon Pounguinza
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Kaleb Kandou Jephté Francis Estimé
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Stephanie N’yetobouko
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Christelle Luce Bobossi Gadia
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Dominos-Alfred Feiganazoui
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Alain Le Faou
- EA 3452 CITHEFOR, Campus Brabois Santé, 54500 Vandœuvre-lès-Nancy, France;
- Faculty of Medicine, Maieutic and Health Sciences, University of Lorraine, Pole Brabois Santé, 54500 Nancy, France
| | - Massimiliano Orsini
- General and Experimental Microbiology, Laboratory of Microbial Ecology and Genomics of Microorganisms, Experimental Zooprophylactic Institute of the Venezie (IZSVe), 35020 Legnaro, Italy;
| | - Carlo Federico Perno
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
| | - Luca Zinzula
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Clotaire Donatien Rafaï
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
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12
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Pan X, Hounye AH, Zhao Y, Cao C, Wang J, Abidi MV, Hou M, Xiong L, Chai X. A Digital Mask-Voiceprint System for Postpandemic Surveillance and Tracing Based on the STRONG Strategy. J Med Internet Res 2023; 25:e44795. [PMID: 37856760 PMCID: PMC10660213 DOI: 10.2196/44795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 09/28/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023] Open
Abstract
Lockdowns and border closures due to COVID-19 imposed mental, social, and financial hardships in many societies. Living with the virus and resuming normal life are increasingly being advocated due to decreasing virus severity and widespread vaccine coverage. However, current trends indicate a continued absence of effective contingency plans to stop the next more virulent variant of the pandemic. The COVID-19-related mask waste crisis has also caused serious environmental problems and virus spreads. It is timely and important to consider how to precisely implement surveillance for the dynamic clearance of COVID-19 and how to efficiently manage discarded masks to minimize disease transmission and environmental hazards. In this viewpoint, we sought to address this issue by proposing an appropriate strategy for intelligent surveillance of infected cases and centralized management of mask waste. Such an intelligent strategy against COVID-19, consisting of wearable mask sample collectors (masklect) and voiceprints and based on the STRONG (Spatiotemporal Reporting Over Network and GPS) strategy, could enable the resumption of social activities and economic recovery and ensure a safe public health environment sustainably.
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Affiliation(s)
- Xiaogao Pan
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, China
- Emergency Medicine and Difficult Diseases Institute, Central South University, Changsha, China
| | | | - Yuqi Zhao
- Department of Gastroenterology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Cong Cao
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Jiaoju Wang
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Mimi Venunye Abidi
- General Surgery Department, Second Xiangya Hospital, Central South University, Changsha, China
| | - Muzhou Hou
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Li Xiong
- General Surgery Department, Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiangping Chai
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, China
- Emergency Medicine and Difficult Diseases Institute, Central South University, Changsha, China
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13
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Guthrie CM, Tan X, Meeker AC, Self AE, Liu L, Cheng Y. Engineering a dual vaccine against COVID-19 and tuberculosis. Front Cell Infect Microbiol 2023; 13:1273019. [PMID: 37965265 PMCID: PMC10641007 DOI: 10.3389/fcimb.2023.1273019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2 virus, has been one of the top public health threats across the world over the past three years. Mycobacterium bovis BCG is currently the only licensed vaccine for tuberculosis, one of the deadliest infectious diseases in the world, that is caused by Mycobacterium tuberculosis. In the past decades, recombinant M.bovis BCG has been studied as a novel vaccine vector for other infectious diseases in humans besides tuberculosis, such as viral infections. In the current study, we generated a recombinant M. bovis BCG strain AspikeRBD that expresses a fusion protein consisting of M. tb Ag85A protein and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein using synthetic biology technique. Our results show that the recombinant M. bovis BCG strain successfully expressed this fusion protein. Interestingly, the recombinant M. bovis BCG strain AspikeRBD significantly induced SARS-CoV-2 spike-specific T cell activation and IgG production in mice when compared to the parental M.bovis BCG strain, and was more potent than the recombinant M.bovis BCG strain expressing SARS-CoV-2 spike RBD alone. As expected, the recombinant M. bovis BCG strain AspikeRBD activated an increased number of M. tb Ag85A-specific IFNγ-releasing T cells and enhanced IgG production in mice when compared to the parental M.bovis BCG strain or the BCG strain expressing SARS-CoV-2 spike RBD alone. Taken together, our results indicate a potential application of the recombinant M. bovis BCG strain AspikeRBD as a novel dual vaccine against SARS-CoV-2 and M. tb in humans.
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Affiliation(s)
- Carlyn Monèt Guthrie
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Xuejuan Tan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Amber Cherry Meeker
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Ashton Elisabeth Self
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Yong Cheng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, United States
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14
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Mgbere O, Iloanusi S, Yunusa I, Iloanusi NJR, Gohil S, Essien EJ. Intersection of Perceived COVID-19 Risk, Preparedness, and Preventive Health Behaviors: Latent Class Segmentation Analysis. Online J Public Health Inform 2023; 15:e50967. [PMID: 38046563 PMCID: PMC10689050 DOI: 10.2196/50967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/13/2023] [Accepted: 09/07/2023] [Indexed: 12/05/2023] Open
Abstract
Background COVID-19 risk perception is a factor that influences the pandemic spread. Understanding the potential behavioral responses to COVID-19, including preparedness and adoption of preventive measures, can inform interventions to curtail its spread. Objective We assessed self-perceived and latent class analysis (LCA)-based risks of COVID-19 and their associations with preparedness, misconception, information gap, and preventive practices among residents of a densely populated city in Nigeria. Methods We used data from a cross-sectional survey conducted among residents (N=140) of Onitsha, Nigeria, in March 2020, before the government-mandated lockdown. Using an iterative expectation-maximization algorithm, we applied LCA to systematically segment participants into the most likely distinct risk clusters. Furthermore, we used bivariate and multivariable logistic regression models to determine the associations among knowledge, attitude, preventive practice, perceived preparedness, misconception, COVID-19 information gap, and self-perceived and LCA-based COVID-19 risks. Results Most participants (85/140, 60.7%) had good knowledge and did not perceive themselves as at risk of contracting COVID-19. Three-quarters of the participants (102/137, 74.6%; P<.001) experienced COVID-19-related information gaps, while 62.9% (88/140; P=.04) of the participants had some misconceptions about the disease. Conversely, most participants (93/140, 66.4%; P<.001) indicated that they were prepared for the COVID-19 pandemic. The majority of the participants (94/138, 68.1%; P<.001) self-perceived that they were not at risk of contracting COVID-19 compared to 31.9% (44/138) who professed to be at risk of contracting COVID-19. Using the LCA, we identified 3 distinct risk clusters (P<.001), namely, prudent or low-risk takers, skeptics or high-risk takers, and carefree or very high-risk takers with prevalence rates (probabilities of cluster membership that represent the prevalence rate [γc]) of 47.5% (95% CI 40%-55%), 16.2% (95% CI 11.4%-20.9%), and 36.4% (95% CI 28.8%-43.9%), respectively. We recorded a significantly negative agreement between self-perceived risk and LCA-based segmentation of COVID-19 risk (κ=-0.218, SD 0.067; P=.01). Knowledge, attitude, and perceived need for COVID-19 information were significant predictors of COVID-19 preventive practices among the Onitsha city residents. Conclusions The clustering patterns highlight the impact of modifiable risk behaviors on COVID-19 preventive practices, which can provide strong empirical support for health prevention policies. Consequently, clusters with individuals at high risk of contracting COVID-19 would benefit from multicomponent interventions delivered in diverse settings to improve the population-based response to the pandemic.
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Affiliation(s)
- Osaro Mgbere
- Institute of Community Health University of Houston College of Pharmacy Houston, TX United States
- Department of Pharmaceutical Health Outcomes and Policy University of Houston College of Pharmacy Houston, TX United States
- Public Health Science and Surveillance Division Houston Health Department Houston, TX United States
| | - Sorochi Iloanusi
- Department of Pharmaceutical Health Outcomes and Policy University of Houston College of Pharmacy Houston, TX United States
| | - Ismaeel Yunusa
- Department of Clinical Pharmacy and Outcomes Sciences University of South Carolina College of Pharmacy Columbia, SC United States
| | | | - Shrey Gohil
- Department of Pharmaceutical Health Outcomes and Policy University of Houston College of Pharmacy Houston, TX United States
| | - Ekere James Essien
- Institute of Community Health University of Houston College of Pharmacy Houston, TX United States
- Department of Pharmaceutical Health Outcomes and Policy University of Houston College of Pharmacy Houston, TX United States
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15
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Boniardi I, Corona A, Basquin J, Basquin C, Milia J, Nagy I, Tramontano E, Zinzula L. Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function. Virus Res 2023; 336:199221. [PMID: 37704176 PMCID: PMC10514558 DOI: 10.1016/j.virusres.2023.199221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.
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Affiliation(s)
- Irene Boniardi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - István Nagy
- Center of Research and Development, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy.
| | - Luca Zinzula
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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16
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Kopplin N, Garcia A, Reczek A, Wilkinson K, Yekkaluri S, Murphy CC, Tiro J, Muthukumar AR, Masica A, Singal AG. Post-acute sequelae of COVID-19 and longitudinal antibody levels in a community-based cohort. PLoS One 2023; 18:e0291259. [PMID: 37682916 PMCID: PMC10490864 DOI: 10.1371/journal.pone.0291259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) infection invokes variable immune responses and poses a risk of post-acute sequelae SARS-CoV-2 infection (PASC) symptoms; however, most data on natural history are derived from patients with severe infection. Further data are needed among patients with mild infection, who comprise most cases. METHODS The Dallas Fort-Worth (DFW) COVID-19 Prevalence Study included 21,597 community-dwelling adults (ages 18-89) who underwent COVID-19 PCR and anti-nucleocapsid antibody testing between July 2020 and March 2021. We invited participants with positive COVID-19 results (cases) and a subset with negative results (controls), matched on age, sex, race/ethnicity, and ZIP code, to complete a follow-up questionnaire for PASC symptoms and repeat anti-nucleocapsid testing, and anti-spike antibody testing between July and December 2021. RESULTS Of 3,917 adults invited to participate, 2260 (57.7%) completed the questionnaire- 1150 cases and 1110 controls. Persistent symptoms were reported in 21.1% of cases, with the most common being shortness of breath, fatigue, and loss of taste or smell. Among 292 cases with asymptomatic infection, >15% reported new fatigue and 8-10% reported new loss of taste/smell, myalgias, or headache. Median anti-nucleocapsid levels in cases decreased from 3.5U to 0.7U over a median follow-up of 8.6 months. Anti-spike antibody levels at 6-7 months post-vaccination in cases were similar to that of controls. CONCLUSIONS More than 1 in 5 patients with COVID-19 infection, including those with mild infection, reported persistent symptoms during follow-up. Both nucleocapsid and spike protein antibody levels decreased within six months following a COVID-19 infection and vaccination.
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Affiliation(s)
- Noa Kopplin
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Angie Garcia
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Annika Reczek
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Kate Wilkinson
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Sruthi Yekkaluri
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Caitlin C. Murphy
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Jasmin Tiro
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Alagar R. Muthukumar
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Andrew Masica
- Texas Health Resources, Fort Worth, TX, United States of America
| | - Amit G. Singal
- University of Texas Southwestern Medical Center, Dallas, TX, United States of America
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17
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Grazia Martina M, Giammarino F, Vicenti I, Groaz E, Rozenski J, Incerti M, Sannio F, Docquier JD, Zazzi M, Radi M. Nucleoside Derivatives of 2,6-Diaminopurine Antivirals: Base-Modified Nucleosides with Broad-Spectrum Antimicrobial Properties. ChemMedChem 2023; 18:e202300200. [PMID: 37221137 DOI: 10.1002/cmdc.202300200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 05/25/2023]
Abstract
The plethora of viral outbreaks experienced in the last decade, together with the widespread distribution of many re-emerging and newly emerging viruses, emphasize the urgent need for novel broad-spectrum antivirals as tools for early intervention in case of future epidemics. Non-natural nucleosides have been at the forefront for the treatment of infectious diseases for many years and still represent one of the most successful classes of antiviral molecules on the market. In the attempt to explore the biologically relevant chemical space of this class of antimicrobials, we describe herein the development of novel base-modified nucleosides by converting previously identified 2,6-diaminopurine antivirals into the corresponding D/L ribonucleosides, acyclic nucleosides and prodrug derivatives. A phenotypic screening against viruses belonging to different families (Flaviviridae, Coronaviridae, Retroviridae) and against a panel of Gram-positive and Gram-negative bacteria, allowed to identify a few interesting molecules with broad-spectrum antimicrobial activities.
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Affiliation(s)
- Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Federica Giammarino
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100, Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100, Siena, Italy
| | - Elisabetta Groaz
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000, Leuven, Belgium
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Jef Rozenski
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Matteo Incerti
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100, Siena, Italy
| | - Jean Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100, Siena, Italy
- Laboratoire de Bactériologie Moléculaire, Centre d'Ingénierie des Protéines, University of Liège, Allée du 6 Août, 4000, Liège, Belgium
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, 53100, Siena, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
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18
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Li J, Fong DYT, Lok KYW, Wong JYH, Man Ho M, Choi EPH, Pandian V, Davidson PM, Duan W, Tarrant M, Lee JJ, Lin CC, Akingbade O, Alabdulwahhab KM, Ahmad MS, Alboraie M, Alzahrani MA, Bilimale AS, Boonpatcharanon S, Byiringiro S, Hasan MKC, Schettini LC, Corzo W, De Leon JM, De Leon AS, Deek H, Efficace F, El Nayal MA, El-Raey F, Ensaldo-Carrasco E, Escotorin P, Fadodun OA, Fawole IO, Goh YSS, Irawan D, Khan NE, Koirala B, Krishna A, Kwok C, Le TT, Leal DG, Lezana-Fernández MÁ, Manirambona E, Mantoani LC, Meneses-González F, Mohamed IE, Mukeshimana M, Nguyen CTM, Nguyen HTT, Nguyen KT, Nguyen ST, Nurumal MS, Nzabonimana A, Omer NAMA, Ogungbe O, Poon ACY, Reséndiz-Rodriguez A, Puang-Ngern B, Sagun CG, Shaik RA, Shankar NG, Sommer K, Toro E, Tran HTH, Urgel EL, Uwiringiyimana E, Vanichbuncha T, Youssef N. Global impacts of COVID-19 on lifestyles and health and preparation preferences: An international survey of 30 countries. J Glob Health 2023; 13:06031. [PMID: 37565394 PMCID: PMC10416140 DOI: 10.7189/jogh.13.06031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
Background The health area being greatest impacted by coronavirus disease 2019 (COVID-19) and residents' perspective to better prepare for future pandemic remain unknown. We aimed to assess and make cross-country and cross-region comparisons of the global impacts of COVID-19 and preparation preferences of pandemic. Methods We recruited adults in 30 countries covering all World Health Organization (WHO) regions from July 2020 to August 2021. 5 Likert-point scales were used to measure their perceived change in 32 aspects due to COVID-19 (-2 = substantially reduced to 2 = substantially increased) and perceived importance of 13 preparations (1 = not important to 5 = extremely important). Samples were stratified by age and gender in the corresponding countries. Multidimensional preference analysis displays disparities between 30 countries, WHO regions, economic development levels, and COVID-19 severity levels. Results 16 512 adults participated, with 10 351 females. Among 32 aspects of impact, the most affected were having a meal at home (mean (m) = 0.84, standard error (SE) = 0.01), cooking at home (m = 0.78, SE = 0.01), social activities (m = -0.68, SE = 0.01), duration of screen time (m = 0.67, SE = 0.01), and duration of sitting (m = 0.59, SE = 0.01). Alcohol (m = -0.36, SE = 0.01) and tobacco (m = -0.38, SE = 0.01) consumption declined moderately. Among 13 preparations, respondents rated medicine delivery (m = 3.50, SE = 0.01), getting prescribed medicine in a hospital visit / follow-up in a community pharmacy (m = 3.37, SE = 0.01), and online shopping (m = 3.33, SE = 0.02) as the most important. The multidimensional preference analysis showed the European Region, Region of the Americas, Western Pacific Region and countries with a high-income level or medium to high COVID-19 severity were more adversely impacted on sitting and screen time duration and social activities, whereas other regions and countries experienced more cooking and eating at home. Countries with a high-income level or medium to high COVID-19 severity reported higher perceived mental burden and emotional distress. Except for low- and lower-middle-income countries, medicine delivery was always prioritised. Conclusions Global increasing sitting and screen time and limiting social activities deserve as much attention as mental health. Besides, the pandemic has ushered in a notable enhancement in lifestyle of home cooking and eating, while simultaneously reducing the consumption of tobacco and alcohol. A health care system and technological infrastructure that facilitate medicine delivery, medicine prescription, and online shopping are priorities for coping with future pandemics.
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Affiliation(s)
- Jiaying Li
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Daniel Yee Tak Fong
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Kris Yuet Wan Lok
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Janet Yuen Ha Wong
- School of Nursing and Health Studies, Hong Kong Metropolitan University, Hong Kong SAR, China
| | - Mandy Man Ho
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Edmond Pui Hang Choi
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Vinciya Pandian
- School of Nursing, Johns Hopkins University, Baltimore, Maryland, USA
| | - Patricia M Davidson
- Vice-Chancellor and Principal, University of Wollongong, Wollongong, Australia
| | - Wenjie Duan
- Department of Social Work, East China University of Science and Technology, Shanghai, China
| | - Marie Tarrant
- School of Nursing, The University of British Columbia, Kelowna British Columbia, Canada
| | - Jung Jae Lee
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Chia-Chin Lin
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Oluwadamilare Akingbade
- The Nethersole School of Nursing, The Chinese University of Hong Kong, Hong Kong
- Institute of Nursing Research, Osogbo, Osun State, Nigeria
| | | | - Mohammad Shakil Ahmad
- Department of Family & Community Medicine, College of Medicine, Majmaah University, Majmaah, Saudi Arabia
| | - Mohamed Alboraie
- Department of Internal Medicine, Al-Azhar University, Cairo, Egypt
| | - Meshari A Alzahrani
- Department of Urology, College of Medicine, Majmaah University, Al Majmaah, Saudi Arabia
| | - Anil S Bilimale
- School of Public Health, JSS Medical College, JSS AHER, Mysuru, India
| | | | - Samuel Byiringiro
- School of Nursing, Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | - Hiba Deek
- Nursing Department, Faculty of Health Science, Beirut Arab University, Lebanon
| | - Fabio Efficace
- Italian Group for Adult Hematologic Diseases (GIMEMA), Data Center and Health Outcomes Research Unit, Rome, Italy
| | | | - Fathiya El-Raey
- Department of hepatogastroenterology and infectious diseases, Damietta faculty of medicine, Al-Azher University, Egypt
| | | | - Pilar Escotorin
- Laboratory of Applied Prosocial Research, Department of Basic, Developmental and Educational Psychology, Autonomous University of Barcelona, Spain
| | | | | | - Yong-Shian Shawn Goh
- Alice Lee Centre for Nursing Studies, National University of Singapore, Singapore
| | - Devi Irawan
- School of Nursing, Wijaya Husada Health Institute, Bogor, Indonesia
| | | | - Binu Koirala
- School of Nursing, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Cannas Kwok
- School of Nursing, Paramedicine and Health Care Science, Charles Sturt University, New South Wales, Australia
| | | | | | | | - Emery Manirambona
- College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Leandro Cruz Mantoani
- Laboratory of Research in Respiratory Physiotherapy (LFIP), Department of Physiotherapy, State University of Londrina (UEL) – Londrina, Brazil
| | | | - Iman Elmahdi Mohamed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Benghazi University, Libya
| | - Madeleine Mukeshimana
- School of Nursing and Midwifery, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | | | | | | | | | - Mohd Said Nurumal
- Kulliyyah of Nursing, International Islamic University, Kuantan, Malaysia
| | - Aimable Nzabonimana
- Center for Language Enhancement, College of Arts and Social Sciences, University of Rwanda, Huye, Rwanda
| | | | | | | | | | | | - Ceryl G Sagun
- School of Nursing, Centro Escolar University, Manila, Philippines
| | - Riyaz Ahmed Shaik
- Department of Family & Community Medicine, College of Medicine, Majmaah University, Majmaah, Saudi Arabia
| | - Nikhil Gauri Shankar
- Mental Health and Learning division, Wrexham Maelor Hospital, Wrexham, United Kingdom
| | - Kathrin Sommer
- Italian Group for Adult Hematologic Diseases (GIMEMA), Data Center and Health Outcomes Research Unit, Rome, Italy
| | - Edgardo Toro
- Pontificia Universidad Católica de Valparaíso, School of Social Work, Valparaíso, Chile
| | | | - Elvira L Urgel
- School of Nursing, Centro Escolar University, Manila, Philippines
| | | | - Tita Vanichbuncha
- Department of Statistics, Chulalongkorn Business School, Bangkok, Thailand
| | - Naglaa Youssef
- Medical-surgical Nursing Department, Faculty of Nursing, Cairo University, Egypt
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19
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Liu J, Pang S, Wang M, Yu H, Ma P, Dong T, Zheng Z, Jiao Y, Zhang Y, Liu A. An ultrasensitive ELISA to assay femtomolar level SARS-CoV-2 antigen based on specific peptide and tyramine signal amplification. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 387:133746. [PMID: 37020533 PMCID: PMC10050199 DOI: 10.1016/j.snb.2023.133746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 05/21/2023]
Abstract
The SARS-CoV-2 spreading rapidly has aroused catastrophic public healthcare issues and economy crisis worldwide. It plays predominant role to rapidly and accurately diagnose the virus for effective prevention and treatment. As an abundant transmembrane protein, spike protein (SP) is one of the most valuable antigenic biomarkers for diagnosis of COVID-19. Herein a phage expression of WNLDLSQWLPPM peptide specific to SARS-CoV-2 SP was screened. Molecular docking revealed that the isolated peptide binds to major antigenic epitope locating at S2 subunit with hydrogen bonding. Taking the specific peptide as antigen sensing probe and tyramine signal amplification (TSA), an ultrasensitive "peptide-antigen-antibody" ELISA (p-ELISA) was explored, by which the limit of detection (LOD) was 14 fM and 2.8 fM SARS-CoV-2 SP antigen for first TSA and secondary TSA, respectively. Compared with the LOD by the p-ELISA by direct mode, the sensitivity with 2nd TSA enhanced 100 times. Further, the proposed p-ELISA method can detect SARS-CoV-2 pseudoviruses down to 10 and 3 TCID50/mL spiked in healthy nasal swab sample with 1st TSA and 2nd TSA, separately. Thus, the proposed p-ELISA method with TSA is expected to be a promising ultrasensitive tool for rapidly detecting SARS-CoV-2 antigen to help control the infectious disease.
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Affiliation(s)
- Junchong Liu
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Zongmei Zheng
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Yiming Jiao
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Yaru Zhang
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, and College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
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20
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Tsuji M, Nair MS, Masuda K, Castagna C, Chong Z, Darling TL, Seehra K, Hwang Y, Ribeiro ÁL, Ferreira GM, Corredor L, Coelho-Dos-Reis JGA, Tsuji Y, Mori M, Boon ACM, Diamond MS, Huang Y, Ho DD. An immunostimulatory glycolipid that blocks SARS-CoV-2, RSV, and influenza infections in vivo. Nat Commun 2023; 14:3959. [PMID: 37402814 DOI: 10.1038/s41467-023-39738-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Prophylactic vaccines for SARS-CoV-2 have lowered the incidence of severe COVID-19, but emergence of viral variants that are antigenically distinct from the vaccine strains are of concern and additional, broadly acting preventive approaches are desirable. Here, we report on a glycolipid termed 7DW8-5 that exploits the host innate immune system to enable rapid control of viral infections in vivo. This glycolipid binds to CD1d on antigen-presenting cells and thereby stimulates NKT cells to release a cascade of cytokines and chemokines. The intranasal administration of 7DW8-5 prior to virus exposure significantly blocked infection by three different authentic variants of SARS-CoV-2, as well as by respiratory syncytial virus and influenza virus, in mice or hamsters. We also found that this protective antiviral effect is both host-directed and mechanism-specific, requiring both the CD1d molecule and interferon-[Formula: see text]. A chemical compound like 7DW8-5 that is easy to administer and cheap to manufacture may be useful not only in slowing the spread of COVID-19 but also in responding to future pandemics long before vaccines or drugs are developed.
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Affiliation(s)
- Moriya Tsuji
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Kazuya Masuda
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Candace Castagna
- Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tamarand L Darling
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kuljeet Seehra
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Youngmin Hwang
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Ágata Lopes Ribeiro
- Basic and Applied Virology Laboratory, Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Geovane Marques Ferreira
- Basic and Applied Virology Laboratory, Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laura Corredor
- Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Yukiko Tsuji
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Munemasa Mori
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.
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21
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Yang Y, Guo L, Lu H. Emerging infectious diseases never end: The fight continues. Biosci Trends 2023:2023.01104. [PMID: 37331800 DOI: 10.5582/bst.2023.01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Emerging infectious diseases have accompanied the development of human society while causing great harm to humans, and SARS-CoV-2 was only one in the long list of microbial threats. Many viruses have existed in their natural reservoirs for a very long time, and the spillover of viruses from natural hosts to humans via interspecies transmission serves as the main source of emerging infectious diseases. Widely existing viruses capable of utilizing human receptors to infect human cells in animals signal the possible outbreak of another viral infection in the near future. Extensive and close collaborative surveillance across nations, more effective wildlife trade legislation, and robust investment into applied and basic research will help to combat the possible pandemics of new emerging infectious diseases in the future.
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Affiliation(s)
- Yang Yang
- National Clinical Research Center for Infectious Diseases, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, China
| | - Liping Guo
- National Clinical Research Center for Infectious Diseases, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, China
| | - Hongzhou Lu
- National Clinical Research Center for Infectious Diseases, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated with the Southern University of Science and Technology, Shenzhen, China
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22
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Oka N, Shimada K, Ishii A, Kobayashi N, Kondo K. SARS-CoV-2 S1 protein causes brain inflammation by reducing intracerebral acetylcholine production. iScience 2023; 26:106954. [PMID: 37275532 PMCID: PMC10208654 DOI: 10.1016/j.isci.2023.106954] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/21/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Neurological complications that occur in SARS-CoV-2 infection, such as olfactory dysfunction, brain inflammation, malaise, and depressive symptoms, are thought to contribute to long COVID. However, in autopsies of patients who have died from COVID-19, there is normally no direct evidence that central nervous system damage is due to proliferation of SARS-CoV-2. For this reason, many aspects of the pathogenesis mechanisms of such symptoms remain unknown. Expressing SARS-CoV-2 S1 protein in the nasal cavity of mice was associated with increased apoptosis of the olfactory system and decreased intracerebral acetylcholine production. The decrease in acetylcholine production was associated with brain inflammation, malaise, depressive clinical signs, and decreased expression of the cytokine degrading factor ZFP36. Administering the cholinesterase inhibitor donepezil to the mice improved brain inflammation, malaise and depressive clinical signs. These findings could contribute to the elucidation of the pathogenesis mechanisms of neurological complications associated with COVID-19 and long COVID.
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Affiliation(s)
- Naomi Oka
- Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Kazuya Shimada
- Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Azusa Ishii
- Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Nobuyuki Kobayashi
- Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Kazuhiro Kondo
- Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
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23
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Luo H, Chen J, Jiang Q, Yu Y, Yang M, Luo Y, Wang X. Comprehensive DNA methylation profiling of COVID-19 and hepatocellular carcinoma to identify common pathogenesis and potential therapeutic targets. Clin Epigenetics 2023; 15:100. [PMID: 37309005 DOI: 10.1186/s13148-023-01515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND & AIMS The effects of SARS-CoV-2 infection can be more complex and severe in patients with hepatocellular carcinoma (HCC) as compared to other cancers. This is due to several factors, including pre-existing conditions such as viral hepatitis and cirrhosis, which are commonly associated with HCC. METHODS We conducted an analysis of epigenomics in SARS-CoV-2 infection and HCC patients, and identified common pathogenic mechanisms using weighted gene co-expression network analysis (WGCNA) and other analyses. Hub genes were identified and analyzed using LASSO regression. Additionally, drug candidates and their binding modes to key macromolecular targets of COVID-19 were identified using molecular docking. RESULTS The epigenomic analysis of the relationship between SARS-CoV-2 infection and HCC patients revealed that the co-pathogenesis was closely linked to immune response, particularly T cell differentiation, regulation of T cell activation and monocyte differentiation. Further analysis indicated that CD4+ T cells and monocytes play essential roles in the immunoreaction triggered by both conditions. The expression levels of hub genes MYLK2, FAM83D, STC2, CCDC112, EPHX4 and MMP1 were strongly correlated with SARS-CoV-2 infection and the prognosis of HCC patients. In our study, mefloquine and thioridazine were identified as potential therapeutic agents for COVID-19 in combined with HCC. CONCLUSIONS In this research, we conducted an epigenomics analysis to identify common pathogenetic processes between SARS-CoV-2 infection and HCC patients, providing new insights into the pathogenesis and treatment of HCC patients infected with SARS-CoV-2.
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Affiliation(s)
- Huiyan Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jixin Chen
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiyin Jiang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yifan Yu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Miaolun Yang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuehua Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiongwen Wang
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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24
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Chakraborty C, Bhattacharya M, Saha A, Alshammari A, Alharbi M, Saikumar G, Pal S, Dhama K, Lee SS. Revealing the structural and molecular interaction landscape of the favipiravir-RTP and SARS-CoV-2 RdRp complex through integrative bioinformatics: Insights for developing potent drugs targeting SARS-CoV-2 and other viruses. J Infect Public Health 2023; 16:1048-1056. [PMID: 37196368 DOI: 10.1016/j.jiph.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which was approved for the treatment of influenza viruses, including drug-resistant influenza. Despite the limited information on its molecular activity, clinical trials have attempted to determine the effectiveness of favipiravir in patients with mild to moderate COVID-19. Here, we report the structural and molecular interaction landscape of the macromolecular complex of favipiravir-RTP and SARS-CoV-2 RdRp with the RNA chain. METHODS Integrative bioinformatics was used to reveal the structural and molecular interaction landscapes of two macromolecular complexes retrieved from RCSB PDB. RESULTS We analyzed the interactive residues, H-bonds, and interaction interfaces to evaluate the structural and molecular interaction landscapes of the two macromolecular complexes. We found seven and six H-bonds in the first and second interaction landscapes, respectively. The maximum bond length is 3.79 Å. In the hydrophobic interactions, five residues (Asp618, Asp760, Thr687, Asp623, and Val557) were associated with the first complex and two residues (Lys73 and Tyr217) were associated with the second complex. The mobilities, collective motion, and B-factor of the two macromolecular complexes were analyzed. Finally, we developed different models, including trees, clusters, and heat maps of antiviral molecules, to evaluate the therapeutic status of favipiravir as an antiviral drug. CONCLUSIONS The results revealed the structural and molecular interaction landscape of the binding mode of favipiravir with the nsp7-nsp8-nsp12-RNA SARS-CoV-2 RdRp complex. Our findings can help future researchers in understanding the mechanism underlying viral action and guide the design of nucleotide analogs that mimic favipiravir and exhibit greater potency as antiviral drugs against SARS-CoV-2 and other infectious viruses. Thus, our work can help in preparing for future epidemics and pandemics.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - G Saikumar
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Soumen Pal
- School of Mechanical Engineering, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
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25
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Yen FS, Wang SI, Lin SY, Cheng-Chung Wei J. Metformin use before COVID-19 vaccination and the risks of COVID-19 incidence, medical utilization, and all-cause mortality in patients with type 2 diabetes mellitus. Diabetes Res Clin Pract 2023; 200:110692. [PMID: 37156428 PMCID: PMC10163786 DOI: 10.1016/j.diabres.2023.110692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/14/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
AIMS We designed this study to determine whether metformin use before COVID-19 vaccination influences the risk of COVID-19 infection, medical utilization, and mortality. METHODS We used the US collaborative network of TriNetX to identify 123,709 patients with type 2 diabetes mellitus fully vaccinated against COVID-19 between January 1, 2020, and November 22, 2022. The study selected 20,894 pairs of metformin users and nonusers by propensity score matching. The Kaplan-Meier method and Cox proportional hazards models were used to compare the risks of COVID-19 infection, medical utilization, and mortality between the study and control groups. RESULTS No significant difference was noted between metformin users and nonusers in the risk of COVID-19 incidence (aHR =1.02, 95% CI=0.94-1.10). Compared to the control cohort, the metformin cohort exhibited a significantly lower risk of hospitalization (aHR=0.85, 95% CI=0.81-0.89), critical care services (aHR=0.81, 95% CI=0.70-0.94), mechanical ventilation (aHR=0.75, 95% CI=0.60-0.95), and mortality (aHR=0.75, 95% CI=0.63-0.89). The subgroup analyses and sensitivity analysis showed similar results. CONCLUSION The present study showed that metformin use before COVID-19 vaccination could not reduce COVID-19 incidence; however, it was associated with significantly lower risks of hospitalization, intensive care service, mechanical ventilation, and mortality in fully vaccinated type 2 diabetes mellitus patients.
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Affiliation(s)
- Fu-Shun Yen
- Dr. Yen's Clinic, No. 15, Shanying Road, Gueishan District, Taoyuan 33354, Taiwan.
| | - Shiow-Ing Wang
- Center for Health Data Science, Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., South District, Taichung 40201, Taiwan; Institute of Medicine, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., South District, Taichung 40201, Taiwan.
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Sect. 4, Taichung 40705, Taiwan; Department of Medicine, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec.2, Linong Street, Taipei 11221, Taiwan.
| | - James Cheng-Chung Wei
- Institute of Medicine, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., South District, Taichung 40201, Taiwan; Department of Allergy, Immunology & Rheumatology, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., South District, Taichung City 40201, Taiwan; Graduate Institute of Integrated Medicine, China Medical University, No. 91, Hsueh-Shih Road, Taichung 40402, Taiwan.
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26
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Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape. iScience 2023; 26:106282. [PMID: 36910327 PMCID: PMC9968663 DOI: 10.1016/j.isci.2023.106282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.
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27
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Vicente J, Benedetti M, Martelliti P, Vázquez L, Gentilini MV, Peñaranda Figueredo FA, Nabaes Jodar MS, Viegas M, Barquero AA, Bueno CA. The Flavonoid Cyanidin Shows Immunomodulatory and Broad-Spectrum Antiviral Properties, Including SARS-CoV-2. Viruses 2023; 15:v15040989. [PMID: 37112969 PMCID: PMC10143848 DOI: 10.3390/v15040989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
New antiviral treatments are needed to deal with the unpredictable emergence of viruses. Furthermore, vaccines and antivirals are only available for just a few viral infections, and antiviral drug resistance is an increasing concern. Cyanidin (a natural product also called A18), a key flavonoid that is present in red berries and other fruits, attenuates the development of several diseases, through its anti-inflammatory effects. Regarding its mechanism of action, A18 was identified as an IL-17A inhibitor, resulting in the attenuation of IL-17A signaling and associated diseases in mice. Importantly, A18 also inhibits the NF-κB signaling pathway in different cell types and conditions in vitro and in vivo. In this study, we report that A18 restricts RSV, HSV-1, canine coronavirus, and SARS-CoV-2 multiplication, indicating a broad-spectrum antiviral activity. We also found that A18 can control cytokine and NF-κB induction in RSV-infected cells independently of its antiviral activity. Furthermore, in mice infected with RSV, A18 not only significantly reduces viral titers in the lungs, but also diminishes lung injury. Thus, these results provide evidence that A18 could be used as a broad-spectrum antiviral and may contribute to the development of novel therapeutic targets to control these viral infections and pathogenesis.
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Affiliation(s)
- Josefina Vicente
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Martina Benedetti
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Paula Martelliti
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Luciana Vázquez
- Unidad Operativa Centro de Contención Biológica (UOCCB), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Buenos Aires 1282, Argentina
| | - María Virginia Gentilini
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB)-CONICET, Buenos Aires 1093, Argentina
| | - Freddy Armando Peñaranda Figueredo
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Mercedes Soledad Nabaes Jodar
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1425, Argentina
- Laboratorio de Virología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires 1417, Argentina
| | - Mariana Viegas
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1425, Argentina
- Laboratorio de Virología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires 1417, Argentina
| | - Andrea Alejandra Barquero
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Carlos Alberto Bueno
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires 1428, Argentina
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28
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Li Y, Wang K, Sun H, Wu S, Wang H, Shi Y, Li X, Yan H, Yang G, Wu M, Li Y, Ding X, Si S, Jiang J, Du Y, Li Y, Hong B. Omicsynin B4 potently blocks coronavirus infection by inhibiting host proteases cathepsin L and TMPRSS2. Antiviral Res 2023; 214:105606. [PMID: 37076089 PMCID: PMC10110284 DOI: 10.1016/j.antiviral.2023.105606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/21/2023]
Abstract
The emergence of SARS-CoV-2 variants represents a major threat to public health and requires identification of novel therapeutic agents to address the unmet medical needs. Small molecules impeding viral entry through inhibition of spike protein priming proteases could have potent antiviral effects against SARS-CoV-2 infection. Omicsynin B4, a pseudo-tetrapeptides identified from Streptomyces sp. 1647, has potent antiviral activity against influenza A viruses in our previous study. Here, we found omicsynin B4 exhibited broad-spectrum anti-coronavirus activity against HCoV-229E, HCoV-OC43 and SARS-CoV-2 prototype and its variants in multiple cell lines. Further investigations revealed omicsynin B4 blocked the viral entry and might be related to the inhibition of host proteases. SARS-CoV-2 spike protein mediated pseudovirus assay supported the inhibitory activity on viral entry of omicsynin B4 with a more potent inhibition of Omicron variant, especially when overexpression of human TMPRSS2. Moreover, omicsynin B4 exhibited superior inhibitory activity in the sub-nanomolar range against CTSL, and a sub-micromolar inhibition against TMPRSS2 in biochemical assays. The molecular docking analysis confirmed that omicsynin B4 fits well in the substrate binding sites and forms a covalent bond to Cys25 and Ser441 in CTSL and TMPRSS2, respectively. In conclusion, we found that omicsynin B4 may serve as a natural protease inhibitor for CTSL and TMPRSS2, blocking various coronavirus S protein-driven entry into cells. These results further highlight the potential of omicsynin B4 as an attractive candidate as a broad-spectrum anti-coronavirus agent that could rapidly respond to emerging variants of SARS-CoV-2.
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Affiliation(s)
- Yihua Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kun Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongmin Sun
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuo Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Huiqiang Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xingxing Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Haiyan Yan
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Mengyuan Wu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiaotian Ding
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuyi Si
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jiandong Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yu Du
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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29
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Sahun M, Privat-Maldonado A, Lin A, De Roeck N, Van der Heyden L, Hillen M, Michiels J, Steenackers G, Smits E, Ariën KK, Jorens PG, Delputte P, Bogaerts A. Inactivation of SARS-CoV-2 and Other Enveloped and Non-Enveloped Viruses with Non-Thermal Plasma for Hospital Disinfection. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:5206-5215. [PMID: 37034498 PMCID: PMC10068876 DOI: 10.1021/acssuschemeng.2c07622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/10/2023] [Indexed: 06/19/2023]
Abstract
As recently highlighted by the SARS-CoV-2 pandemic, viruses have become an increasing burden for health, global economy, and environment. The control of transmission by contact with contaminated materials represents a major challenge, particularly in hospital environments. However, the current disinfection methods in hospital settings suffer from numerous drawbacks. As a result, several medical supplies that cannot be properly disinfected are not reused, leading to severe shortages and increasing amounts of waste, thus prompting the search for alternative solutions. In this work, we report that non-thermal plasma (NTP) can effectively inactivate SARS-CoV-2 from non-porous and porous materials commonly found in healthcare facilities. We demonstrated that 5 min treatment with a dielectric barrier discharge NTP can inactivate 100% of SARS-CoV-2 (Wuhan and Omicron strains) from plastic material. Using porcine respiratory coronavirus (surrogate for SARS-CoV-2) and coxsackievirus B3 (highly resistant non-enveloped virus), we tested the NTP virucidal activity on hospital materials and obtained complete inactivation after 5 and 10 min, respectively. We hypothesize that the produced reactive species and local acidification contribute to the overall virucidal effect of NTP. Our results demonstrate the potential of dielectric barrier discharge NTPs for the rapid, efficient, and low-cost disinfection of healthcare materials.
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Affiliation(s)
- Maxime Sahun
- Plasma
Lab for Applications in Sustainability and Medicine—Antwerp
(PLASMANT), Department of Chemistry, University
of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Angela Privat-Maldonado
- Plasma
Lab for Applications in Sustainability and Medicine—Antwerp
(PLASMANT), Department of Chemistry, University
of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
- Center
for Oncological Research (CORE), Integrated Personalized & Precision
Oncology Network (IPPON), University of
Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Abraham Lin
- Plasma
Lab for Applications in Sustainability and Medicine—Antwerp
(PLASMANT), Department of Chemistry, University
of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
- Center
for Oncological Research (CORE), Integrated Personalized & Precision
Oncology Network (IPPON), University of
Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Naomi De Roeck
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical,
Biomedical and Veterinary Sciences, University
of Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Lisa Van der Heyden
- Plasma
Lab for Applications in Sustainability and Medicine—Antwerp
(PLASMANT), Department of Chemistry, University
of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
- Center
for Oncological Research (CORE), Integrated Personalized & Precision
Oncology Network (IPPON), University of
Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Michaël Hillen
- Industrial
Vision Lab (InViLab), Department of Electromechanical Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Johan Michiels
- Virology
Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium
| | - Gunther Steenackers
- Industrial
Vision Lab (InViLab), Department of Electromechanical Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Evelien Smits
- Center
for Oncological Research (CORE), Integrated Personalized & Precision
Oncology Network (IPPON), University of
Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Kevin K. Ariën
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical,
Biomedical and Veterinary Sciences, University
of Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
- Virology
Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000 Antwerp, Belgium
| | - Philippe G. Jorens
- Department
of Intensive Care Medicine, Antwerp University
Hospital, Wilrijkstraat
10, 2650 Antwerp, Belgium
- Laboratory
of Experimental Medicine and Pediatrics (LEMP), University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Peter Delputte
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical,
Biomedical and Veterinary Sciences, University
of Antwerp, Universiteitsplein
1, 2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Plasma
Lab for Applications in Sustainability and Medicine—Antwerp
(PLASMANT), Department of Chemistry, University
of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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30
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Targeting RNA G-quadruplex with repurposed drugs blocks SARS-CoV-2 entry. PLoS Pathog 2023; 19:e1011131. [PMID: 36701392 PMCID: PMC9904497 DOI: 10.1371/journal.ppat.1011131] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/07/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants of concern, the complexity of infection, and the functional redundancy of host factors, underscore an urgent need for broad-spectrum antivirals against the continuous COVID-19 pandemic, with drug repurposing as a viable therapeutic strategy. Here we report the potential of RNA G-quadruplex (RG4)-targeting therapeutic strategy for SARS-CoV-2 entry. Combining bioinformatics, biochemical and biophysical approaches, we characterize the existence of RG4s in several SARS-CoV-2 host factors. In silico screening followed by experimental validation identify Topotecan (TPT) and Berbamine (BBM), two clinical approved drugs, as RG4-stabilizing agents with repurposing potential for COVID-19. Both TPT and BBM can reduce the protein level of RG4-containing host factors, including ACE2, AXL, FURIN, and TMPRSS2. Intriguingly, TPT and BBM block SARS-CoV-2 pseudovirus entry into target cells in vitro and murine tissues in vivo. These findings emphasize the significance of RG4 in SARS-CoV-2 pathogenesis and provide a potential broad-spectrum antiviral strategy for COVID-19 prevention and treatment.
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31
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Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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32
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Wu D, Mitchell J, Lambert JH. Global systemic risk and resilience for novel coronavirus with evolving perspectives. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2023; 43:5-7. [PMID: 36792528 DOI: 10.1111/risa.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Affiliation(s)
- Desheng Wu
- University of Chinese Academy of Sciences, Beijing, China
| | - Jade Mitchell
- Department of Biosystems Engineering, Michigan State University, East Lansing, Michigan, USA
| | - James H Lambert
- Department of Systems & Information Engineering, and Department of Civil & Environmental Engineering, University of Virginia, Charlottesville, Virginia, USA
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33
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Wang N, Li E, Deng H, Yue L, Zhou L, Su R, He B, Lai C, Li G, Gao Y, Zhou W, Gao Y. Inosine: A broad-spectrum anti-inflammatory against SARS-CoV-2 infection-induced acute lung injury via suppressing TBK1 phosphorylation. J Pharm Anal 2023; 13:11-23. [PMID: 36313960 PMCID: PMC9595505 DOI: 10.1016/j.jpha.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 02/02/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storms constitute the primary cause of coronavirus disease 19 (COVID-19) progression, severity, criticality, and death. Glucocorticoid and anti-cytokine therapies are frequently administered to treat COVID-19, but have limited clinical efficacy in severe and critical cases. Nevertheless, the weaknesses of these treatment modalities have prompted the development of anti-inflammatory therapy against this infection. We found that the broad-spectrum anti-inflammatory agent inosine downregulated proinflammatory interleukin (IL)-6, upregulated anti-inflammatory IL-10, and ameliorated acute inflammatory lung injury caused by multiple infectious agents. Inosine significantly improved survival in mice infected with SARS-CoV-2. It indirectly impeded TANK-binding kinase 1 (TBK1) phosphorylation by binding stimulator of interferon genes (STING) and glycogen synthase kinase-3β (GSK3β), inhibited the activation and nuclear translocation of the downstream transcription factors interferon regulatory factor (IRF3) and nuclear factor kappa B (NF-κB), and downregulated IL-6 in the sera and lung tissues of mice infected with lipopolysaccharide (LPS), H1N1, or SARS-CoV-2. Thus, inosine administration is feasible for clinical anti-inflammatory therapy against severe and critical COVID-19. Moreover, targeting TBK1 is a promising strategy for inhibiting cytokine storms and mitigating acute inflammatory lung injury induced by SARS-CoV-2 and other infectious agents.
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Affiliation(s)
- Ningning Wang
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Huifang Deng
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Lanxin Yue
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Lei Zhou
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Rina Su
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130022, China
| | - Baokun He
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Chengcai Lai
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Gaofu Li
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
- Corresponding author.
| | - Wei Zhou
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
- Corresponding author.
| | - Yue Gao
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Corresponding author. Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
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34
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Caravez JC, Iyer KS, Kavthe RD, Kincaid JRA, Lipshutz BH. A 1-Pot Synthesis of the SARS-CoV-2 M pro Inhibitor Nirmatrelvir, the Key Ingredient in Paxlovid. Org Lett 2022; 24:9049-9053. [DOI: 10.1021/acs.orglett.2c03683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan C. Caravez
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Karthik S. Iyer
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Rahul D. Kavthe
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joseph R. A. Kincaid
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Bruce H. Lipshutz
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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35
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Kincaid JRA, Caravez JC, Iyer KS, Kavthe RD, Fleck N, Aue DH, Lipshutz BH. A sustainable synthesis of the SARS-CoV-2 M pro inhibitor nirmatrelvir, the active ingredient in Paxlovid. Commun Chem 2022; 5:156. [PMID: 36465589 PMCID: PMC9685088 DOI: 10.1038/s42004-022-00758-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
Pfizer's drug for the treatment of patients infected with COVID-19, Paxlovid, contains most notably nirmatrelvir, along with ritonavir. Worldwide demand is projected to be in the hundreds of metric tons per year, to be produced by several generic drug manufacturers. Here we show a 7-step, 3-pot synthesis of the antiviral nirmatrelvir, arriving at the targeted drug in 70% overall yield. Critical amide bond-forming steps utilize new green technology that completely avoids traditional peptide coupling reagents, as well as epimerization of stereocenters. Likewise, dehydration of a primary amide to the corresponding nitrile is performed and avoids use of the Burgess reagent and chlorinated solvents. DFT calculations for various conformers of nirmatrelvir predict that two rotamers about the tertiary amide would be present with an unusually high rotational barrier. Direct comparisons with the original literature procedures highlight both the anticipated decrease in cost and environmental footprint associated with this route, potentially expanding the availability of this important drug worldwide.
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Affiliation(s)
- Joseph R. A. Kincaid
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Juan C. Caravez
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Karthik S. Iyer
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Rahul D. Kavthe
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Nico Fleck
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Donald H. Aue
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Bruce H. Lipshutz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
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36
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Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. CELL INSIGHT 2022; 2:100068. [PMID: 37192911 PMCID: PMC9670597 DOI: 10.1016/j.cellin.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
The proteins and RNAs of viruses extensively interact with host proteins after infection. We collected and reanalyzed all available datasets of protein-protein and RNA-protein interactions related to SARS-CoV-2. We investigated the reproducibility of those interactions and made strict filters to identify highly confident interactions. We systematically analyzed the interaction network and identified preferred subcellular localizations of viral proteins, some of which such as ORF8 in ER and ORF7A/B in ER membrane were validated using dual fluorescence imaging. Moreover, we showed that viral proteins frequently interact with host machinery related to protein processing in ER and vesicle-associated processes. Integrating the protein- and RNA-interactomes, we found that SARS-CoV-2 RNA and its N protein closely interacted with stress granules including 40 core factors, of which we specifically validated G3BP1, IGF2BP1, and MOV10 using RIP and Co-IP assays. Combining CRISPR screening results, we further identified 86 antiviral and 62 proviral factors and associated drugs. Using network diffusion, we found additional 44 interacting proteins including two proviral factors previously validated. Furthermore, we showed that this atlas could be applied to identify the complications associated with COVID-19. All data are available in the AIMaP database (https://mvip.whu.edu.cn/aimap/) for users to easily explore the interaction map.
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Lazarus JV, Romero D, Kopka CJ, Karim SA, Abu-Raddad LJ, Almeida G, Baptista-Leite R, Barocas JA, Barreto ML, Bar-Yam Y, Bassat Q, Batista C, Bazilian M, Chiou ST, Del Rio C, Dore GJ, Gao GF, Gostin LO, Hellard M, Jimenez JL, Kang G, Lee N, Matičič M, McKee M, Nsanzimana S, Oliu-Barton M, Pradelski B, Pyzik O, Rabin K, Raina S, Rashid SF, Rathe M, Saenz R, Singh S, Trock-Hempler M, Villapol S, Yap P, Binagwaho A, Kamarulzaman A, El-Mohandes A. A multinational Delphi consensus to end the COVID-19 public health threat. Nature 2022; 611:332-345. [PMID: 36329272 PMCID: PMC9646517 DOI: 10.1038/s41586-022-05398-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Despite notable scientific and medical advances, broader political, socioeconomic and behavioural factors continue to undercut the response to the COVID-19 pandemic1,2. Here we convened, as part of this Delphi study, a diverse, multidisciplinary panel of 386 academic, health, non-governmental organization, government and other experts in COVID-19 response from 112 countries and territories to recommend specific actions to end this persistent global threat to public health. The panel developed a set of 41 consensus statements and 57 recommendations to governments, health systems, industry and other key stakeholders across six domains: communication; health systems; vaccination; prevention; treatment and care; and inequities. In the wake of nearly three years of fragmented global and national responses, it is instructive to note that three of the highest-ranked recommendations call for the adoption of whole-of-society and whole-of-government approaches1, while maintaining proven prevention measures using a vaccines-plus approach2 that employs a range of public health and financial support measures to complement vaccination. Other recommendations with at least 99% combined agreement advise governments and other stakeholders to improve communication, rebuild public trust and engage communities3 in the management of pandemic responses. The findings of the study, which have been further endorsed by 184 organizations globally, include points of unanimous agreement, as well as six recommendations with >5% disagreement, that provide health and social policy actions to address inadequacies in the pandemic response and help to bring this public health threat to an end.
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Affiliation(s)
- Jeffrey V Lazarus
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.
- Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA.
| | - Diana Romero
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
| | | | - Salim Abdool Karim
- University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Program of Research in South Africa (CAPRISA), Durban, South Africa
| | - Laith J Abu-Raddad
- Weill Cornell Medicine, Cornell University, Ithaca, NY, USA
- Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
| | | | - Ricardo Baptista-Leite
- UNITE Global Parliamentarians Network, Lisbon, Portugal
- Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute of Health Sciences (CIIS), Catholic University of Portugal, Lisbon, Portugal
| | | | - Mauricio L Barreto
- Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- University of Bahia, Salvador, Brazil
| | - Yaneer Bar-Yam
- New England Complex Systems Institute, Cambridge, MA, USA
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Manhiça Health Research Center (CISM), Maputo, Mozambique
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Biomedical Research Consortium in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Carolina Batista
- Doctors Without Borders (MSF), Geneva, Switzerland
- Baraka Impact Finance, Geneva, Switzerland
| | | | - Shu-Ti Chiou
- National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Gregory J Dore
- University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - George F Gao
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lawrence O Gostin
- The O'Neill Institute for National and Global Health Law, Georgetown University, Washington, DC, USA
| | | | - Jose L Jimenez
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, USA
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Mojca Matičič
- Clinic for Infectious Diseases and Febrile Illnesses, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martin McKee
- The London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Bary Pradelski
- French National Centre for Scientific Research (CNRS), Grenoble, France
| | | | - Kenneth Rabin
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
| | - Sunil Raina
- Dr. Rajendra Prasad Government Medical College, Himachal Pradesh, India
| | - Sabina Faiz Rashid
- James P. Grant School of Public Health, BRAC University, Dhaka, Bangladesh
| | | | - Rocio Saenz
- University of Costa Rica, San José, Costa Rica
| | - Sudhvir Singh
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | | | - Sonia Villapol
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Peiling Yap
- International Digital Health & AI Research Collaborative (I-DAIR), Geneva, Switzerland
| | | | | | - Ayman El-Mohandes
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
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38
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Loike JD, Flaum RT. CRISPR Technology: A Jewish Legal Perspective. Rambam Maimonides Med J 2022; 13:RMMJ.10487. [PMID: 36394501 PMCID: PMC9622389 DOI: 10.5041/rmmj.10487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) gene editing is an innovative and potentially game-changing biotechnology that can potentially reverse DNA mutations in a tissue-specific manner. In addition, CRISPR is being targeted for xenotransplantation, for increasing human longevity, in animal breeding, and in plant science. However, there are many ethical challenges that emerge from CRISPR technology. This article discusses several positions that relate to these ethical challenges from a Jewish legal perspective. In addition, we present several other applications of CRISPR technology that lack a defined Jewish legal precedent and require rabbinical scholars to address and resolve them in the future.
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Affiliation(s)
- John D. Loike
- Interim Director of Bioethics, School of Health Sciences and Practice, New York Medical College—Associated with Touro University, Valhalla, NY, USA
- Professor of Biology, Touro University, New York, NY, USA
- To whom correspondence should be addressed. E-mail:
| | - Rabbi Tzvi Flaum
- Associate Professor, Judaic Studies, Mashgiach Ruchani, Lander College for Women (Touro College), New York, NY, USA
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39
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Maio N, Cherry S, Schultz DC, Hurst BL, Linehan WM, Rouault TA. TEMPOL inhibits SARS-CoV-2 replication and development of lung disease in the Syrian hamster model. iScience 2022; 25:105074. [PMID: 36093377 PMCID: PMC9444323 DOI: 10.1016/j.isci.2022.105074] [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: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/31/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide outbreak, known as coronavirus disease 2019 (COVID-19). Alongside vaccines, antiviral therapeutics is an important part of the healthcare response to COVID-19. We previously reported that TEMPOL, a small molecule stable nitroxide, inactivated the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by causing the oxidative degradation of its iron-sulfur cofactors. Here, we demonstrate that TEMPOL is effective in vivo in inhibiting viral replication in the Syrian hamster model. The inhibitory effect of TEMPOL on SARS-CoV-2 replication was observed in animals when the drug was administered 2 h before infection in a high-risk exposure model. These data support the potential application of TEMPOL as a highly efficacious antiviral against SARS-CoV-2 infection in humans. TEMPOL’s IC90 in human lung epithelial Calu-3 cells is 2.89 μM and CC50 > 10 mM TEMPOL has potent antiviral activity against highly pathogenic SARS- and MERS-Co-Vs TEMPOL inhibits SARS-CoV-2 replication and lung pathology in the Syrian hamster Fe-S cofactor insertion can be targeted to interfere with coronavirus replication
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Chemogenomic Discovery Program. University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, High-throughput Screening Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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40
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What the COVID-19 pandemic revealed about intellectual property. Nat Biotechnol 2022; 40:1428-1430. [DOI: 10.1038/s41587-022-01485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Wells K, Flynn R. Managing host-parasite interactions in humans and wildlife in times of global change. Parasitol Res 2022; 121:3063-3071. [PMID: 36066742 PMCID: PMC9446624 DOI: 10.1007/s00436-022-07649-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Global change in the Anthropocene has modified the environment of almost any species on earth, be it through climate change, habitat modifications, pollution, human intervention in the form of mass drug administration (MDA), or vaccination. This can have far-reaching consequences on all organisational levels of life, including eco-physiological stress at the cell and organism level, individual fitness and behaviour, population viability, species interactions and biodiversity. Host-parasite interactions often require highly adapted strategies by the parasite to survive and reproduce within the host environment and ensure efficient transmission among hosts. Yet, our understanding of the system-level outcomes of the intricate interplay of within host survival and among host parasite spread is in its infancy. We shed light on how global change affects host-parasite interactions at different organisational levels and address challenges and opportunities to work towards better-informed management of parasite control. We argue that global change affects host-parasite interactions in wildlife inhabiting natural environments rather differently than in humans and invasive species that benefit from anthropogenic environments as habitat and more deliberate rather than erratic exposure to therapeutic drugs and other control efforts.
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Affiliation(s)
- Konstans Wells
- Department of Biosciences, Swansea University, Swansea, SA28PP, UK.
| | - Robin Flynn
- Graduate Studies Office, South East Technological University, Cork Road Campus, Waterford, X91 K0EK, Ireland
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42
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Wu S, Zhang L, Wang W. Screened α-Helix Peptide Inhibitor toward SARS-CoV-2 by Blocking a Prion-like Domain in the Receptor Binding Domain. Anal Chem 2022; 94:11464-11469. [PMID: 35816660 PMCID: PMC9305731 DOI: 10.1021/acs.analchem.2c02223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
A new peptide inhibitor was designed and optimized from an α-helix-rich peptide library specifically toward the critical prion-like domain (PLD) of SARS-CoV-2. It compactly blocked the S1 protein and potently neutralized the pseudovirus which shows promising potential for prophylactic and treatment of COVID-19.
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Affiliation(s)
- Shang Wu
- Key Laboratory of Medical Molecule Science and
Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory
of Cluster Science of Ministry of Education, Beijing Key Laboratory of
Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical
Engineering, Institute of Engineering Medicine, Beijing Institute of
Technology, Beijing 100081, PR China
| | - Limin Zhang
- Key Laboratory of Medical Molecule Science and
Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory
of Cluster Science of Ministry of Education, Beijing Key Laboratory of
Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical
Engineering, Institute of Engineering Medicine, Beijing Institute of
Technology, Beijing 100081, PR China
| | - Weizhi Wang
- Key Laboratory of Medical Molecule Science and
Pharmaceutics Engineering, Ministry of Industry and Information Technology, Key Laboratory
of Cluster Science of Ministry of Education, Beijing Key Laboratory of
Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical
Engineering, Institute of Engineering Medicine, Beijing Institute of
Technology, Beijing 100081, PR China
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43
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Filip R, Gheorghita Puscaselu R, Anchidin-Norocel L, Dimian M, Savage WK. Global Challenges to Public Health Care Systems during the COVID-19 Pandemic: A Review of Pandemic Measures and Problems. J Pers Med 2022; 12:1295. [PMID: 36013244 PMCID: PMC9409667 DOI: 10.3390/jpm12081295] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/21/2022] [Accepted: 08/05/2022] [Indexed: 12/15/2022] Open
Abstract
Beginning in December 2019, the world faced a critical new public health stressor with the emergence of SARS-CoV-2. Its spread was extraordinarily rapid, and in a matter of weeks countries across the world were affected, notably in their ability to manage health care needs. While many sectors of public structures were impacted by the pandemic, it particularly highlighted shortcomings in medical care infrastructures around the world that underscored the need to reorganize medical systems, as they were vastly unprepared and ill-equipped to manage a pandemic and simultaneously provide general and specialized medical care. This paper presents modalities in approaches to the pandemic by various countries, and the triaged reorganization of medical sections not considered first-line in the pandemic that was in many cases transformed into wards for treating COVID-19 cases. As new viruses and structural variants emerge, it is important to find solutions to streamline medical care in hospitals, which includes the expansion of digital network medicine (i.e., telemedicine and mobile health apps) for patients to continue to receive appropriate care without risking exposure to contagions. Mobile health app development continues to evolve with specialized diagnostics capabilities via external attachments that can provide rapid information sharing between patients and care providers while eliminating the need for office visits. Telemedicine, still in the early stages of adoption, especially in the developing world, can ensure access to medical information and contact with care providers, with the potential to release emergency rooms from excessive cases, and offer multidisciplinary access for patients and care providers that can also be a means to avoid contact during a pandemic. As this pandemic illustrated, an overhaul to streamline health care is essential, and a move towards greater use of mobile health and telemedicine will greatly benefit public health to control the spread of new variants and future outbreaks.
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Affiliation(s)
- Roxana Filip
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
- BK Laboratory, SuceavaCounty Emergency Hospital, 720224 Suceava, Romania
| | - Roxana Gheorghita Puscaselu
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies, and Distributed Systems for Fabrication and Control, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Liliana Anchidin-Norocel
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies, and Distributed Systems for Fabrication and Control, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
- Department of Computers, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Wesley K. Savage
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies, and Distributed Systems for Fabrication and Control, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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44
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Time-of-Day Variation in SARS-CoV-2 RNA Levels during the Second Wave of COVID-19. Viruses 2022; 14:v14081728. [PMID: 36016350 PMCID: PMC9413669 DOI: 10.3390/v14081728] [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: 06/16/2022] [Revised: 07/25/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Circadian rhythms influence and coordinate an organism's response to its environment and to invading pathogens. We studied the diurnal variation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasal/throat swabs collected in late 2020 to spring 2021 in a population immunologically naïve to SARS-CoV-2 and prior to widespread vaccination. SARS-CoV-2 diagnostic PCR data from 1698 participants showed a significantly higher viral load in samples obtained in the afternoon, in males, and in hospitalised patients when linear mixed modelling was applied. This study illustrates the importance of recording sample collection times when measuring viral replication parameters in clinical and research studies.
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45
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Seephetdee C, Bhukhai K, Buasri N, Leelukkanaveera P, Lerdwattanasombat P, Manopwisedjaroen S, Phueakphud N, Kuhaudomlarp S, Olmedillas E, Saphire EO, Thitithanyanont A, Hongeng S, Wongtrakoongate P. A circular mRNA vaccine prototype producing VFLIP-X spike confers a broad neutralization of SARS-CoV-2 variants by mouse sera. Antiviral Res 2022; 204:105370. [PMID: 35772601 PMCID: PMC9235288 DOI: 10.1016/j.antiviral.2022.105370] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
Next-generation COVID-19 vaccines are critical due to the ongoing evolution of SARS-CoV-2 virus and rapid waning duration of the neutralizing antibody response against current vaccines. The mRNA vaccines mRNA-1273 and BNT162b2 were developed using linear transcripts encoding the prefusion-stabilized trimers (S-2P) of the wildtype spike, which have shown a reduced neutralizing activity against the variants of concern B.1.617.2 and B.1.1.529. Recently, a new version of spike trimer, termed VFLIP (five (V) prolines, Flexibly-Linked, Inter-Protomer disulfide) was developed. Based on the original amino acid sequence of the wildtype spike, VFLIP was genetically engineered by using five proline substitutions, a flexible cleavage site amino acid linker, and an inter-protomer disulfide bond. It has been suggested to possess native-like glycosylation, and greater pre-fusion trimeric stability as opposed to S-2P. Here, we report that the spike protein VFLIP-X, containing six rationally substituted amino acids to reflect emerging variants (K417N, L452R, T478K, E484K, N501Y and D614G), offers a promising candidate for a next-generation SARS-CoV-2 vaccine. Mice immunized by a circular mRNA (circRNA) vaccine prototype producing VFLIP-X had detectable neutralizing antibody titers for up to 7 weeks post-boost against SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs). In addition, a balance in TH1 and TH2 responses was achieved by immunization with VFLIP-X. Our results indicate that the VFLIP-X delivered by circRNA induces humoral and cellular immune responses, as well as broad neutralizing activity against SARS-CoV-2 variants.
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Affiliation(s)
- Chotiwat Seephetdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Nattawut Buasri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Puttipatch Leelukkanaveera
- International Program of Bioinnovation, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Pat Lerdwattanasombat
- International Program of Biomedical Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | | | - Nut Phueakphud
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Sakonwan Kuhaudomlarp
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | | | | | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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46
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Volkov V. System analysis of the fast global coronavirus disease 2019 (COVID-19) spread. Can we avoid future pandemics under global climate change? Commun Integr Biol 2022; 15:150-157. [PMID: 35656201 PMCID: PMC9154790 DOI: 10.1080/19420889.2022.2082735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The recent fast global spread of COVID-19 caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) questions why and how the disease managed to be so effective against existing health protection measures. These measures, developed by many countries over centuries and strengthened over the last decades, proved to be ineffective against COVID-19. The sharp increase in human longevity and current transport systems in economically developing countries with the background of persisting cultural frameworks and stable local pools of high bacterial and viral mutations generated the wide gap between the established health protection systems and the new emerging diseases. SARS-CoV-2 targets human populations over the world with long incubation periods, often without symptoms, and serious outcomes. Hence, novel strategies are necessary to meet the demands of developing economic and social environments. Moreover, the ongoing climate change adds extra challenges while altering the existing system of interactions in biological populations and in human society. Climate change may lead to new sources of viral and microbial mutations, new ways of zoonotic disease transmission and to huge social and economic transformations in many countries. The present short Opinion applies a system approach linking biomedical, climate change, social and economic aspects and, accordingly, discusses the measures and more efficient means to avoid future pandemics.
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Affiliation(s)
- Vadim Volkov
- Research Institute of Russian Academy of Sciences, K.A. Timiriazev Institute of Plant Physiology RAS, Moscow, Russia
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47
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Amanatidou E, Gkiouliava A, Pella E, Serafidi M, Tsilingiris D, Vallianou NG, Karampela I, Dalamaga M. Breakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges. Metabol Open 2022; 14:100180. [PMID: 35313532 PMCID: PMC8928742 DOI: 10.1016/j.metop.2022.100180] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 12/19/2022] Open
Abstract
Vaccination programs against SARS-CoV-2 constitute the mainstay of public health interventions against the global COVID-19 pandemic. Currently available vaccines have shown 90% or better rates of protection against severe disease and mortality. Barely a year after vaccines became available, the Omicron variant and its unprecedented speed of transmission has posed a new challenge. Overall, Omicron presents increased immune escape, transmissibility, and decreased pathogenicity. Vaccines do not offer a full protection against SARS-CoV-2 acquisition, since "breakthrough" infections may occur in fully vaccinated individuals, who may in turn spread the virus to others. Breakthrough infections may be causally related to the viral profile (viral variant and load, incubation period, transmissibility, pathogenicity, immune evasion), immunity characteristics (mucosal versus systemic immunity, duration of immunity, etc.), host determinants (age, comorbidities, immune status, immunosuppressive drugs) and vaccination properties (platform, antigen dose, dose number, dose interval, route of administration). Determining the rate of breakthrough infections may be challenging and necessitates the conduction of population-based studies regarding vaccine effectiveness as well as neutralizing antibody testing, a surrogate of immune protection. In this review, we analyze the causes of breakthrough infections, their clinical consequences (severity of infection and transmission), methods of determining their incidence as well as challenges and perspectives. Long COVID as well as multi-inflammatory syndrome in adolescents may be significantly reduced in breakthrough infections. The need for universal pancoranavirus vaccines that would aim at protecting against a plethora of SARS-CoV-2 variants as well as emerging variants is discussed. Finally, novel vaccine strategies, such as nasal vaccines, may confer robust mucosal and systemic protection, reducing efficiently transmission.
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Affiliation(s)
- Evropi Amanatidou
- Laboratory of Biomathematics, School of Medicine, University of Thessaly, Larissa, Greece
| | - Anna Gkiouliava
- Laboratory of Biomathematics, School of Medicine, University of Thessaly, Larissa, Greece
| | - Eva Pella
- Laboratory of Biomathematics, School of Medicine, University of Thessaly, Larissa, Greece
| | - Maria Serafidi
- Laboratory of Biomathematics, School of Medicine, University of Thessaly, Larissa, Greece
| | - Dimitrios Tsilingiris
- First Department of Propaedeutic Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Laiko General Hospital, Athens, Greece
| | - Natalia G. Vallianou
- First Department of Internal Medicine, Evangelismos General Hospital, Athens, Greece
| | - Irene Karampela
- Second Department of Critical Care, Attikon General University Hospital, Medical School, National and Kapodistrian University of Athens, Chaidari, Athens, Greece
| | - Maria Dalamaga
- Department of Biological Chemistry, School of Medicine, National and Kapodistrian University of Athens, Greece
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48
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Watkins RR. Using Precision Medicine for the Diagnosis and Treatment of Viral Pneumonia. Adv Ther 2022; 39:3061-3071. [PMID: 35596912 PMCID: PMC9123616 DOI: 10.1007/s12325-022-02180-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/04/2022] [Indexed: 01/06/2023]
Abstract
The COVID-19 pandemic has drawn considerable attention to viral pneumonia from clinicians, public health authorities, and the general public. With dozens of viruses able to cause pneumonia in humans, differentiating viral from bacterial pneumonia can be very challenging in clinical practice using traditional diagnostic methods. Precision medicine is a medical model in which decisions, practices, interventions, and therapies are adapted to the individual patient on the basis of their predicted response or risk of disease. Precision medicine approaches hold promise as a way to improve outcomes for patients with viral pneumonia. This review describes the latest advances in the use of precision medicine for diagnosing and treating viral pneumonia in adults and discusses areas where further research is warranted.
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Affiliation(s)
- Richard R Watkins
- Department of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.
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49
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Sigel A, Sigel H, Sigel RKO. Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations. Molecules 2022; 27:2625. [PMID: 35565975 PMCID: PMC9103026 DOI: 10.3390/molecules27092625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Considering that practically all reactions that involve nucleotides also involve metal ions, it is evident that the coordination chemistry of nucleotides and their derivatives is an essential corner stone of biological inorganic chemistry. Nucleotides are either directly or indirectly involved in all processes occurring in Nature. It is therefore no surprise that the constituents of nucleotides have been chemically altered-that is, at the nucleobase residue, the sugar moiety, and also at the phosphate group, often with the aim of discovering medically useful compounds. Among such derivatives are acyclic nucleoside phosphonates (ANPs), where the sugar moiety has been replaced by an aliphatic chain (often also containing an ether oxygen atom) and the phosphate group has been replaced by a phosphonate carrying a carbon-phosphorus bond to make the compounds less hydrolysis-sensitive. Several of these ANPs show antiviral activity, and some of them are nowadays used as drugs. The antiviral activity results from the incorporation of the ANPs into the growing nucleic acid chain-i.e., polymerases accept the ANPs as substrates, leading to chain termination because of the missing 3'-hydroxyl group. We have tried in this review to describe the coordination chemistry (mainly) of the adenine nucleotides AMP and ATP and whenever possible to compare it with that of the dianion of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2- = adenine(N9)-CH2-CH2-O-CH2-PO32) [or its diphosphate (PMEApp4-)] as a representative of the ANPs. Why is PMEApp4- a better substrate for polymerases than ATP4-? There are three reasons: (i) PMEA2- with its anti-like conformation (like AMP2-) fits well into the active site of the enzyme. (ii) The phosphonate group has an enhanced metal ion affinity because of its increased basicity. (iii) The ether oxygen forms a 5-membered chelate with the neighboring phosphonate and favors thus coordination at the Pα group. Research on ANPs containing a purine residue revealed that the kind and position of the substituent at C2 or C6 has a significant influence on the biological activity. For example, the shift of the (C6)NH2 group in PMEA to the C2 position leads to 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer with only a moderate antiviral activity. Removal of (C6)NH2 favors N7 coordination, e.g., of Cu2+, whereas the ether O atom binding of Cu2+ in PMEA facilitates N3 coordination via adjacent 5- and 7-membered chelates, giving rise to a Cu(PMEA)cl/O/N3 isomer. If the metal ions (M2+) are M(α,β)-M(γ)-coordinated at a triphosphate chain, transphosphorylation occurs (kinases, etc.), whereas metal ion binding in a M(α)-M(β,γ)-type fashion is relevant for polymerases. It may be noted that with diphosphorylated PMEA, (PMEApp4-), the M(α)-M(β,γ) binding is favored because of the formation of the 5-membered chelate involving the ether O atom (see above). The self-association tendency of purines leads to the formation of dimeric [M2(ATP)]2(OH)- stacks, which occur in low concentration and where one half of the molecule undergoes the dephosphorylation reaction and the other half stabilizes the structure-i.e., acts as the "enzyme" by bridging the two ATPs. In accord herewith, one may enhance the reaction rate by adding AMP2- to the [Cu2(ATP)]2(OH)- solution, as this leads to the formation of mixed stacked Cu3(ATP)(AMP)(OH)- species, in which AMP2- takes over the structuring role, while the other "half" of the molecule undergoes dephosphorylation. It may be added that Cu3(ATP)(PMEA) or better Cu3(ATP)(PMEA)(OH)- is even a more reactive species than Cu3(ATP)(AMP)(OH)-. - The matrix-assisted self-association and its significance for cell organelles with high ATP concentrations is summarized and discussed, as is, e.g., the effect of tryptophanate (Trp-), which leads to the formation of intramolecular stacks in M(ATP)(Trp)3- complexes (formation degree about 75%). Furthermore, it is well-known that in the active-site cavities of enzymes the dielectric constant, compared with bulk water, is reduced; therefore, we have summarized and discussed the effect of a change in solvent polarity on the stability and structure of binary and ternary complexes: Opposite effects on charged O sites and neutral N sites are observed, and this leads to interesting insights.
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Affiliation(s)
- Astrid Sigel
- Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland;
| | - Helmut Sigel
- Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland;
| | - Roland K. O. Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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