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Deng W, Hu X, Tian X, Zhang Y, Shang W, Zhang L, Shang L. Peptidomimetic Analogues Act as Effective Inhibitors against SARS-CoV-2 by Blocking the Function of Cathepsin L. J Med Chem 2024. [PMID: 39292661 DOI: 10.1021/acs.jmedchem.4c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Cathepsin L (CatL) is a promising antiviral drug target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an important protease for cleaving the SARS-CoV-2 spike protein and enhancing viral entry to cells. We identified a tripeptide aldehyde candidate, D1-1, which exhibited inhibitory effects against SARS-CoV-2 in Vero E6 cells. The protease screening analysis and protein pull-down assays demonstrated the direct binding of D1-1 to CatL. Guided by molecular docking, we synthesized 72 analogues. Upon analyzing the structure-activity relationships of these inhibitors, the D6 series was developed. Among them, D6-3 functioned as the most potent CatL inhibitor (IC50 = 0.27 nM, EC50 = 0.26 μM). D6-3 effectively blocked the CatL function and substantially hindered the entry of the SARS-CoV-2 pseudovirus to cells. Our work presented novel compounds for targeting and inhibiting CatL, offering valuable insights into the development of SARS-CoV-2 antivirals.
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Affiliation(s)
- Weilong Deng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Xiao Hu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Xiaoman Tian
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Yuanyuan Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Weijuan Shang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Leike Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Luqing Shang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
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2
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Class J, Simons LM, Lorenzo-Redondo R, Achi JG, Cooper L, Dangi T, Penaloza-MacMaster P, Ozer EA, Lutz SE, Rong L, Hultquist JF, Richner JM. Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification. Nat Microbiol 2024; 9:2383-2394. [PMID: 39179693 DOI: 10.1038/s41564-024-01786-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 07/18/2024] [Indexed: 08/26/2024]
Abstract
Severe coronavirus disease 2019 and post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are associated with neurological complications that may be linked to direct infection of the central nervous system (CNS), but the selective pressures ruling neuroinvasion are poorly defined. Here we assessed SARS-CoV-2 evolution in the lung versus CNS of infected mice. Higher levels of viral divergence were observed in the CNS than the lung after intranasal challenge with a high frequency of mutations in the spike furin cleavage site (FCS). Deletion of the FCS significantly attenuated virulence after intranasal challenge, with lower viral titres and decreased morbidity compared with the wild-type virus. Intracranial inoculation of the FCS-deleted virus, however, was sufficient to restore virulence. After intracranial inoculation, both viruses established infection in the lung, but dissemination from the CNS to the lung required the intact FCS. Cumulatively, these data suggest a critical role for the FCS in determining SARS-CoV-2 tropism and compartmentalization.
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Affiliation(s)
- Jacob Class
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Tanushree Dangi
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sarah E Lutz
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Justin M Richner
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA.
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3
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Zhang J, Xie Y, Wang X, Kang Y, Wang C, Xie Q, Dong X, Tian Y, Huang D. The single-cell atlas of the epididymis in mice reveals the changes in epididymis function before and after sexual maturity. Front Cell Dev Biol 2024; 12:1440914. [PMID: 39161591 PMCID: PMC11330779 DOI: 10.3389/fcell.2024.1440914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Introduction: The epididymis is important for sperm transport, maturation, and storage. Methods: The head and tail of the epididymis of 5-week-old and 10-week-old C57 BL/6J male mice were used for single-cell sequencing. Results: 10 cell types including main, basal, and narrow/clear cells are identified. Next, we performed cell subgroup analysis, functional enrichment analysis, and differentiation potential prediction on principal cells, clear cells, and basal cells. Our study indicates that the principal cells are significantly involved in sperm maturation, as well as in antiviral and anti-tumor immune responses. Clear cells are likely to play a crucial role in safeguarding sperm and maintaining epididymal pH levels. Basal cells are implicated in the regulation of inflammatory and stress responses. The composition and functions of the various cell types within the epididymis undergo significant changes before and after sexual maturity. Furthermore, pseudo-temporal analysis elucidates the protective and supportive roles of epididymal cells in sperm maturation during sexual maturation. Discussion: This study offers a theoretical framework and forecasts for the investigation of epididymal sperm maturation and epididymal immunity.
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Affiliation(s)
- Jiaxin Zhang
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye Xie
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyan Wang
- Reproductive Center, Qingdao Women and Children’s Hospital, Qingdao Women and Children’s Hospital Affiliated to Qingdao University, Qingdao, China
| | - Yafei Kang
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuxiong Wang
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinying Xie
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyi Dong
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yonghong Tian
- Department of Reproductive Endocrinology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Donghui Huang
- Institute of Reproduction Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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4
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Padín JF, Pérez-Ortiz JM, Redondo-Calvo FJ. Aprotinin (I): Understanding the Role of Host Proteases in COVID-19 and the Importance of Pharmacologically Regulating Their Function. Int J Mol Sci 2024; 25:7553. [PMID: 39062796 PMCID: PMC11277036 DOI: 10.3390/ijms25147553] [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: 05/27/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Proteases are produced and released in the mucosal cells of the respiratory tract and have important physiological functions, for example, maintaining airway humidification to allow proper gas exchange. The infectious mechanism of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), takes advantage of host proteases in two ways: to change the spatial conformation of the spike (S) protein via endoproteolysis (e.g., transmembrane serine protease type 2 (TMPRSS2)) and as a target to anchor to epithelial cells (e.g., angiotensin-converting enzyme 2 (ACE2)). This infectious process leads to an imbalance in the mucosa between the release and action of proteases versus regulation by anti-proteases, which contributes to the exacerbation of the inflammatory and prothrombotic response in COVID-19. In this article, we describe the most important proteases that are affected in COVID-19, and how their overactivation affects the three main physiological systems in which they participate: the complement system and the kinin-kallikrein system (KKS), which both form part of the contact system of innate immunity, and the renin-angiotensin-aldosterone system (RAAS). We aim to elucidate the pathophysiological bases of COVID-19 in the context of the imbalance between the action of proteases and anti-proteases to understand the mechanism of aprotinin action (a panprotease inhibitor). In a second-part review, titled "Aprotinin (II): Inhalational Administration for the Treatment of COVID-19 and Other Viral Conditions", we explain in depth the pharmacodynamics, pharmacokinetics, toxicity, and use of aprotinin as an antiviral drug.
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Affiliation(s)
- Juan Fernando Padín
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain;
| | - José Manuel Pérez-Ortiz
- Facultad HM de Ciencias de la Salud, Universidad Camilo José Cela, 28692 Madrid, Spain
- Instituto de Investigación Sanitaria HM Hospitales, 28015 Madrid, Spain
| | - Francisco Javier Redondo-Calvo
- Department of Medical Sciences, School of Medicine at Ciudad Real, University of Castilla-La Mancha, 13971 Ciudad Real, Spain;
- Department of Anaesthesiology and Critical Care Medicine, University General Hospital, 13005 Ciudad Real, Spain
- Translational Research Unit, University General Hospital and Research Institute of Castilla-La Mancha (IDISCAM), 13005 Ciudad Real, Spain
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5
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Breidenbach J, Voget R, Si Y, Hingst A, Claff T, Sylvester K, Wolf V, Krasniqi V, Useini A, Sträter N, Ogura Y, Kawaguchi A, Müller CE, Gütschow M. Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV-2 Main Protease Inhibitors as Antiviral Drugs. J Med Chem 2024; 67:8757-8790. [PMID: 38753594 DOI: 10.1021/acs.jmedchem.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Given the crucial role of the main protease (Mpro) in the replication cycle of SARS-CoV-2, this viral cysteine protease constitutes a high-profile drug target. We investigated peptidomimetic azapeptide nitriles as auspicious, irreversibly acting inhibitors of Mpro. Our systematic approach combined an Mpro active-site scanning by combinatorially assembled azanitriles with structure-based design. Encouraged by the bioactive conformation of open-chain inhibitors, we conceptualized the novel chemotype of macrocyclic azanitriles whose binding mode was elucidated by cocrystallization. This strategy provided a favorable entropic contribution to target binding and resulted in the development of the extraordinarily potent Mpro inhibitor 84 with an IC50 value of 3.23 nM and a second-order rate constant of inactivation, kinac/Ki, of 448,000 M-1s-1. The open-chain Mpro inhibitor 58, along with the macrocyclic compounds 83 and 84, a broad-spectrum anticoronaviral agent, demonstrated the highest antiviral activity with EC50 values in the single-digit micromolar range. Our findings are expected to promote the future development of peptidomimetic Mpro inhibitors as anti-SARS-CoV-2 agents.
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Affiliation(s)
- Julian Breidenbach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Rabea Voget
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Yaoyao Si
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Alexandra Hingst
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Katharina Sylvester
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Valentina Wolf
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Vesa Krasniqi
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Abibe Useini
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Yukino Ogura
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Ibaraki, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, 305-8575 Tsukuba, Ibaraki, Japan
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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6
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Klöhn M, Burkard T, Janzen J, Haase JA, Gömer A, Fu R, Ssebyatika G, Nocke MK, Brown RJP, Krey T, Dao Thi VL, Kinast V, Brüggemann Y, Todt D, Steinmann E. Targeting cellular cathepsins inhibits hepatitis E virus entry. Hepatology 2024:01515467-990000000-00876. [PMID: 38728662 DOI: 10.1097/hep.0000000000000912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND AND AIMS HEV is estimated to be responsible for 70,000 deaths annually, yet therapy options remain limited. In the pursuit of effective antiviral therapies, targeting viral entry holds promise and has proven effective for other viruses. However, the precise mechanisms and host factors required during HEV entry remain unclear. Cellular proteases have emerged as host factors required for viral surface protein activation and productive cell entry by many viruses. Hence, we investigated the functional requirement and therapeutic potential of cellular protease during HEV infection. APPROACH AND RESULTS Using our established HEV cell culture model and subgenomic HEV replicons, we found that blocking lysosomal cathepsins (CTS) with small molecule inhibitors impedes HEV infection without affecting replication. Most importantly, the pan-cathepsin inhibitor K11777 suppressed HEV infections with an EC 50 of ~0.02 nM. Inhibition by K11777, devoid of notable toxicity in hepatoma cells, was also observed in HepaRG and primary human hepatocytes. Furthermore, through time-of-addition and RNAscope experiments, we confirmed that HEV entry is blocked by inhibition of cathepsins. Cathepsin L (CTSL) knockout cells were less permissive to HEV, suggesting that CTSL is critical for HEV infection. Finally, we observed cleavage of the glycosylated ORF2 protein and virus particles by recombinant CTSL. CONCLUSIONS In summary, our study highlights the pivotal role of lysosomal cathepsins, especially CTSL, in the HEV entry process. The profound anti-HEV efficacy of the pan-cathepsin inhibitor K11777, especially with its notable safety profile in primary cells, further underscores its potential as a therapeutic candidate.
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Affiliation(s)
- Mara Klöhn
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Burkard
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Juliana Janzen
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Jil A Haase
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - André Gömer
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Rebecca Fu
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg, Germany
| | - George Ssebyatika
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
| | - Maximilian K Nocke
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Richard J P Brown
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Krey
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Viet Loan Dao Thi
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Volker Kinast
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Yannick Brüggemann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- German Centre for Infection Research (DZIF), External Partner Site, Bochum, Germany
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7
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Pečar Fonović U, Kos J, Mitrović A. Compensational role between cathepsins. Biochimie 2024:S0300-9084(24)00085-3. [PMID: 38663456 DOI: 10.1016/j.biochi.2024.04.010] [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: 01/23/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Cathepsins, a family of lysosomal peptidases, play a crucial role in maintaining cellular homeostasis by regulating protein turnover and degradation as well as many specific regulatory actions that are important for proper cell function and human health. Alterations in the activity and expression of cathepsins have been observed in many diseases such as cancer, inflammation, neurodegenerative disorders, bone remodelling-related conditions and others. These changes are not exclusively harmful, but rather appear to be a compensatory response on the lack of one cathepsin in order to maintain tissue integrity. The upregulation of specific cathepsins in response to the inhibition or dysfunction of other cathepsins suggests a fine-tuned system of proteolytic balance and understanding the compensatory role of cathepsins may improve therapeutic potential of cathepsin's inhibitors. Selectively targeting one cathepsin or modulating their activity could offer new treatment strategies for a number of diseases. This review emphasises the need for comprehensive research into cathepsin biology in the context of disease. The identification of the specific cathepsins involved in compensatory responses, the elucidation of the underlying molecular mechanisms and the development of targeted interventions could lead to innovative therapeutic approaches.
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Affiliation(s)
- Urša Pečar Fonović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Ana Mitrović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
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8
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Minami S, Kotaki T, Sakai Y, Okamura S, Torii S, Ono C, Motooka D, Hamajima R, Nouda R, Nurdin JA, Yamasaki M, Kanai Y, Ebina H, Maeda Y, Okamoto T, Tachibana T, Matsuura Y, Kobayashi T. Vero cell-adapted SARS-CoV-2 strain shows increased viral growth through furin-mediated efficient spike cleavage. Microbiol Spectr 2024; 12:e0285923. [PMID: 38415690 PMCID: PMC10986611 DOI: 10.1128/spectrum.02859-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes several host proteases to cleave the spike (S) protein to enter host cells. SARS-CoV-2 S protein is cleaved into S1 and S2 subunits by furin, which is closely involved in the pathogenicity of SARS-CoV-2. However, the effects of the modulated protease cleavage activity due to S protein mutations on viral replication and pathogenesis remain unclear. Herein, we serially passaged two SARS-CoV-2 strains in Vero cells and characterized the cell-adapted SARS-CoV-2 strains in vitro and in vivo. The adapted strains showed high viral growth, effective S1/S2 cleavage of the S protein, and low pathogenicity compared with the wild-type strain. Furthermore, the viral growth and S1/S2 cleavage were enhanced by the combination of the Δ68-76 and H655Y mutations using recombinant SARS-CoV-2 strains generated by the circular polymerase extension reaction. The recombinant SARS-CoV-2 strain, which contained the mutation of the adapted strain, showed increased susceptibility to the furin inhibitor, suggesting that the adapted SARS-CoV-2 strain utilized furin more effectively than the wild-type strain. Pathogenicity was attenuated by infection with effectively cleaved recombinant SARS-CoV-2 strains, suggesting that the excessive cleavage of the S proteins decreases virulence. Finally, the high-growth-adapted SARS-CoV-2 strain could be used as the seed for a low-cost inactivated vaccine; immunization with this vaccine can effectively protect the host from SARS-CoV-2 variants. Our findings provide novel insights into the growth and pathogenicity of SARS-CoV-2 in the evolution of cell-cell transmission. IMPORTANCE The efficacy of the S protein cleavage generally differs among the SARS-CoV-2 variants, resulting in distinct viral characteristics. The relationship between a mutation and the entry of SARS-CoV-2 into host cells remains unclear. In this study, we analyzed the sequence of high-growth Vero cell-adapted SARS-CoV-2 and factors determining the enhancement of the growth of the adapted virus and confirmed the characteristics of the adapted strain by analyzing the recombinant SARS-CoV-2 strain. We successfully identified mutations Δ68-76 and H655Y, which enhance viral growth and the S protein cleavage by furin. Using recombinant viruses enabled us to conduct a virus challenge experiment in vivo. The pathogenicity of SARS-CoV-2 introduced with the mutations Δ68-76, H655Y, P812L, and Q853L was attenuated in hamsters, indicating the possibility of the attenuation of excessive cleaved SARS-CoV-2. These findings provide novel insights into the infectivity and pathogenesis of SARS-CoV-2 strains, thereby significantly contributing to the field of virology.
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Affiliation(s)
- Shohei Minami
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yusuke Sakai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinya Okamura
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Rina Hamajima
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryotaro Nouda
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jeffery A. Nurdin
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Moeko Yamasaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hirotaka Ebina
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
| | - Yusuke Maeda
- Laboratory of Viral Dynamism Research, Research Institute for Microbial Diseases Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-creation Studies, Research Institute for Microbial Diseases Osaka University, Osaka, Japan
| | - Taro Tachibana
- Cell Engineering Corporation, Osaka, Japan
- Department of Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
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9
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Rodriguez Galvan JJ, de Vries M, Belblidia S, Fisher A, Prescott RA, Crosse KM, Mangel WF, Duerr R, Dittmann M. In-silico docking platform with serine protease inhibitor (SERPIN) structures identifies host cysteine protease targets with significance for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.11.18.517133. [PMID: 36415456 PMCID: PMC9681043 DOI: 10.1101/2022.11.18.517133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Serine Protease Inhibitors (SERPINs) regulate protease activity in various physiological processes such as inflammation, cancer metastasis, angiogenesis, and neurodegenerative diseases. However, their potential in combating viral infections, where proteases are also crucial, remains underexplored. This is due to our limited understanding of SERPIN expression during viral-induced inflammation and of the SERPINs' full spectrum of target proteases. Here, we demonstrate widespread expression of human SERPINs in response to respiratory virus infections, both in vitro and in vivo , alongside classical antiviral effectors. Through comprehensive in-silico docking with full-length SERPIN and protease 3D structures, we confirm known inhibitors of specific proteases; more importantly, the results predict novel SERPIN-protease interactions. Experimentally, we validate the direct inhibition of key proteases essential for viral life cycles, including the SERPIN PAI-1's capability to inhibit select cysteine proteases such as cathepsin L, and the serine protease TMPRSS2. Consequently, PAI-1 suppresses spike maturation and multi-cycle SARS-CoV-2 replication. Our findings challenge conventional notions of SERPIN selectivity, underscore the power of in-silico docking for SERPIN target discovery, and offer potential therapeutic interventions targeting host proteolytic pathways to combat viruses with urgent unmet therapeutic needs. SIGNIFICANCE Serine protease inhibitors (SERPINs) play crucial roles in various physiological processes, including viral infections. However, our comprehension of the full array of proteases targeted by the SERPIN family has traditionally been limited, hindering a comprehensive understanding of their regulatory potential. We developed an in-silico docking platform to identify new SERPIN target proteases expressed in the respiratory tract, a critical viral entry portal. The platform confirmed known and predicted new targets for every SERPIN examined, shedding light on previously unrecognized patterns in SERPIN selectivity. Notably, both key proteases for SARS-CoV-2 maturation were among the newly predicted targets, which we validated experimentally. This underscores the platform's potential in uncovering targets with significance in viral infections, paving the way to define the full potential of the SERPIN family in infectious disease and beyond.
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10
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Flury P, Breidenbach J, Krüger N, Voget R, Schäkel L, Si Y, Krasniqi V, Calistri S, Olfert M, Sylvester K, Rocha C, Ditzinger R, Rasch A, Pöhlmann S, Kronenberger T, Poso A, Rox K, Laufer SA, Müller CE, Gütschow M, Pillaiyar T. Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity. ACS Pharmacol Transl Sci 2024; 7:493-514. [PMID: 38357286 PMCID: PMC10863444 DOI: 10.1021/acsptsci.3c00313] [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: 11/10/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024]
Abstract
Cathepsins (Cats) are proteases that mediate the successful entry of SARS-CoV-2 into host cells. We designed and synthesized a tailored series of 21 peptidomimetics and evaluated their inhibitory activity against human cathepsins L, B, and S. Structural diversity was realized by combinations of different C-terminal warhead functions and N-terminal capping groups, while a central Leu-Phe fragment was maintained. Several compounds were identified as promising cathepsin L and S inhibitors with Ki values in the low nanomolar to subnanomolar range, for example, the peptide aldehydes 9a and 9b (9a, 2.67 nM, CatL; 0.455 nM, CatS; 9b, 1.76 nM, CatL; 0.512 nM, CatS). The compounds' inhibitory activity against the main protease of SARS-CoV-2 (Mpro) was additionally investigated. Based on the results at CatL, CatS, and Mpro, selected inhibitors were subjected to investigations of their antiviral activity in cell-based assays. In particular, the peptide nitrile 11e exhibited promising antiviral activity with an EC50 value of 38.4 nM in Calu-3 cells without showing cytotoxicity. High metabolic stability and favorable pharmacokinetic properties make 11e suitable for further preclinical development.
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Affiliation(s)
- Philipp Flury
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Julian Breidenbach
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Rabea Voget
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Laura Schäkel
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Yaoyao Si
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Vesa Krasniqi
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Sara Calistri
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Matthias Olfert
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Katharina Sylvester
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Raphael Ditzinger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Alexander Rasch
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Thales Kronenberger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
- Excellence
Cluster “Controlling Microbes to Fight Infections” (CMFI), Tübingen 72076, Germany
| | - Antti Poso
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), Braunschweig 38124, Germany
- Partner
Site Hannover-Braunschweig, German Center
for Infection Research (DZIF), Braunschweig 38124, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Michael Gütschow
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Thanigaimalai Pillaiyar
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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11
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Gheitasi H, Sabbaghian M, Shekarchi AA, Mirmazhary AA, Poortahmasebi V. Exosome-mediated regulation of inflammatory pathway during respiratory viral disease. Virol J 2024; 21:30. [PMID: 38273382 PMCID: PMC10811852 DOI: 10.1186/s12985-024-02297-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
Viruses have developed many mechanisms by which they can stimulate or inhibit inflammation and cause various diseases, including viral respiratory diseases that kill many people every year. One of the mechanisms that viruses use to induce or inhibit inflammation is exosomes. Exosomes are small membrane nanovesicles (30-150 nm) released from cells that contain proteins, DNA, and coding and non-coding RNA species. They are a group of extracellular vesicles that cells can take up to produce and mediate communication. Intercellular effect exosomes can deliver a broad confine of biological molecules, containing nucleic acids, proteins, and lipids, to the target cell, where they can convey therapeutic or pathogenic consequences through the modulation of inflammation and immune processes. Recent research has shown that exosomes can deliver entire virus genomes or virions to distant target cells, then the delivered viruses can escape the immune system and infect cells. Adenoviruses, orthomyxoviruses, paramyxoviruses, respiratory syncytial viruses, picornaviruses, coronaviruses, and rhinoviruses are mostly related to respiratory diseases. In this article, we will first discuss the current knowledge of exosomes. We will learn about the relationship between exosomes and viral infections, and We mention the inflammations caused by viruses in the airways, the role of exosomes in them, and finally, we examine the relationship between the viruses as mentioned earlier, and the regulation of inflammatory pathways that play a role in causing the disease.
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Affiliation(s)
- Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Ali Mirmazhary
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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12
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Saha A, Pushpa, Moitra S, Basak D, Brahma S, Mondal D, Molla SH, Samadder A, Nandi S. Targeting Cysteine Proteases and their Inhibitors to Combat Trypanosomiasis. Curr Med Chem 2024; 31:2135-2169. [PMID: 37340748 DOI: 10.2174/0929867330666230619160509] [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: 01/22/2023] [Revised: 04/21/2023] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Trypanosomiasis, caused by protozoan parasites of the Trypanosoma genus, remains a significant health burden in several regions of the world. Cysteine proteases play a crucial role in the pathogenesis of Trypanosoma parasites and have emerged as potential therapeutic targets for the development of novel antiparasitic drugs. INTRODUCTION This review article aims to provide a comprehensive overview of the role of cysteine proteases in trypanosomiasis and their potential as therapeutic targets. We discuss the biological significance of cysteine proteases in Trypanosoma parasites and their involvement in essential processes, such as host immune evasion, cell invasion, and nutrient acquisition. METHODS A comprehensive literature search was conducted to identify relevant studies and research articles on the role of cysteine proteases and their inhibitors in trypanosomiasis. The selected studies were critically analyzed to extract key findings and provide a comprehensive overview of the topic. RESULTS Cysteine proteases, such as cruzipain, TbCatB and TbCatL, have been identified as promising therapeutic targets due to their essential roles in Trypanosoma pathogenesis. Several small molecule inhibitors and peptidomimetics have been developed to target these proteases and have shown promising activity in preclinical studies. CONCLUSION Targeting cysteine proteases and their inhibitors holds great potential for the development of novel antiparasitic drugs against trypanosomiasis. The identification of potent and selective cysteine protease inhibitors could significantly contribute to the combat against trypanosomiasis and improve the prospects for the treatment of this neglected tropical disease.
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Affiliation(s)
- Aloke Saha
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Pushpa
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Susmita Moitra
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Deblina Basak
- Endocrinology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sayandeep Brahma
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Dipu Mondal
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sabir Hossen Molla
- Parasitology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Global Institute of Pharmaceutical Education and Research (Affiliated to Veer Madho Singh Bhandari Uttarakhand Technical University), Kashipur, 244713, India
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13
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Pennisi R, Gentile D, Rescifina A, Napoli E, Trischitta P, Piperno A, Sciortino MT. An Integrated In Silico and In Vitro Approach for the Identification of Natural Products Active against SARS-CoV-2. Biomolecules 2023; 14:43. [PMID: 38254643 PMCID: PMC10813393 DOI: 10.3390/biom14010043] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has provoked a global health crisis due to the absence of a specific therapeutic agent. 3CLpro (also known as the main protease or Mpro) and PLpro are chymotrypsin-like proteases encoded by the SARS-CoV-2 genome, and play essential roles during the virus lifecycle. Therefore, they are recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2 infection. Thus, this work aims to collectively present potential natural 3CLpro and PLpro inhibitors by in silico simulations and in vitro entry pseudotype-entry models. We screened luteolin-7-O-glucuronide (L7OG), cynarin (CY), folic acid (FA), and rosmarinic acid (RA) molecules against PLpro and 3CLpro through a luminogenic substrate assay. We only reported moderate inhibitory activity on the recombinant 3CLpro and PLpro by L7OG and FA. Afterward, the entry inhibitory activity of L7OG and FA was tested in cell lines transduced with the two different SARS-CoV-2 pseudotypes harboring alpha (α) and omicron (o) spike (S) protein. The results showed that both compounds have a consistent inhibitory activity on the entry for both variants. However, L7OG showed a greater degree of entry inhibition against α-SARS-CoV-2. Molecular modeling studies were used to determine the inhibitory mechanism of the candidate molecules by focusing on their interactions with residues recognized by the protease active site and receptor-binding domain (RBD) of spike SARS-CoV-2. This work allowed us to identify the binding sites of FA and L7OG within the RBD domain in the alpha and omicron variants, demonstrating how FA is active in both variants. We have confidence that future in vivo studies testing the safety and effectiveness of these natural compounds are warranted, given that they are effective against a variant of concerns.
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Affiliation(s)
- Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V.le A. Doria 6, 95125 Catania, Italy;
| | - Edoardo Napoli
- Istituto di Chimica Biomolecolare—Consiglio Nazionale delle Ricerche, 95126 Catania, Italy;
| | - Paola Trischitta
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
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14
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Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Pappone F, Grillo A, Nakashio M, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Inaba T, Tanino Y, Nukui Y, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions. ACS Infect Dis 2023; 9:2226-2251. [PMID: 37850869 PMCID: PMC10644350 DOI: 10.1021/acsinfecdis.3c00312] [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: 07/03/2023] [Indexed: 10/19/2023]
Abstract
The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Molecular Science and Nanosystems, Ca’
Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Eriko Ohgitani
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Hayata Imamura
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Pappone
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Alfio Grillo
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Maiko Nakashio
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Masaharu Shin-Ya
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Toshiro Yamamoto
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Tohru Inaba
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Tanino
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Nukui
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Kazu Okuma
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Osam Mazda
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
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15
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Fernández-de-la-Pradilla A, Royo S, Schirmeister T, Barthels F, Świderek K, González FV, Moliner V. Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L. ACS Catal 2023; 13:13354-13368. [PMID: 37881790 PMCID: PMC10594577 DOI: 10.1021/acscatal.3c02748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/12/2023] [Indexed: 10/27/2023]
Abstract
Cathepsin L (CatL) is a lysosomal cysteine protease whose activity has been related to several human pathologies. However, although preclinical trials using CatL inhibitors were promising, clinical trials have been unsuccessful up to now. We are presenting a study of two designed dipeptidyl keto Michael acceptor potential inhibitors of CatL with either a keto vinyl ester or a keto vinyl sulfone (KVS) warhead. The compounds were synthesized and experimentally assayed in vitro, and their inhibition molecular mechanism was explored based on molecular dynamics simulations at the density functional theory/molecular mechanics level. The results confirm that both compounds inhibit CatL in the nanomolar range and show a time-dependent inhibition. Interestingly, despite both presenting almost equivalent equilibrium constants for the reversible formation of the noncovalent enzyme/inhibitor complex, differences are observed in the chemical step corresponding to the enzyme-inhibitor covalent bond formation, results that are mirrored by the computer simulations. Theoretically determined kinetic and thermodynamic results, which are in very good agreement with the experiments, afford a detailed explanation of the relevance of the different structural features of both compounds having a significant impact on enzyme inhibition. The unprecedented binding interactions of both inhibitors in the P1' site of CatL represent valuable information for the design of inhibitors. In particular, the peptidyl KVS can be used as a starting lead compound in the development of drugs with medical applications for the treatment of cancerous pathologies since sulfone warheads have previously shown promising cell stability compared to other functions such as carboxylic esters. Future improvements can be guided by the atomistic description of the enzyme-inhibitor interactions established along the inhibition reaction derived from computer simulations.
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Affiliation(s)
| | - Santiago Royo
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Katarzyna Świderek
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Florenci V. González
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
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16
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Zhao S, Jiang M, Qing H, Ni J. Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets. Br J Pharmacol 2023; 180:2455-2481. [PMID: 37403614 DOI: 10.1111/bph.16187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.
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Affiliation(s)
- Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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17
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Szabo D, Ostorhazi E, Stercz B, Makra N, Penzes K, Kristof K, Antal I, Rethelyi JM, Zsigmond RI, Birtalan E, Merkely B, Tamas L. Specific nasopharyngeal Corynebacterium strains serve as gatekeepers against SARS-CoV-2 infection. GeroScience 2023; 45:2927-2938. [PMID: 37338780 PMCID: PMC10643471 DOI: 10.1007/s11357-023-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
The SARS-CoV-2 virus is still causing a worldwide problem. The virus settles primarily on the nasal mucosa, and the infection and its course depend on individual susceptibility. Our aim was to investigate the nasopharynx composition's role in the individual susceptibility. During the first phase of SARS-CoV-2 pandemic, nasopharyngeal microbiome samples of close contact unvaccinated patients were investigated by 16S rRNA analysis and by culturing. The whole genome of cultured Corynebacteria was sequenced. The relative expression of ACE2, TMPRSS2, and cathepsin L on Caco-2 cells and the strength of S1-ACE2 binding were determined in the presence of Corynebacteria. From 55 close contacts exposed to identical SARS-CoV-2 exposure, 26 patients became infected and 29 remained uninfected. The nasopharyngeal microbiome analysis showed significantly higher abundance of Corynebacteria in uninfected group. Corynebacterium accolens could be cultivated only from uninfected individuals and Corynebacterium propinquum from both infected and uninfected. Corynebacteria from uninfected patient significantly reduced the ACE2 and cathepsin L expression. C. accolens significantly reduced the TMPRSS2 expression compared to other Corynebacteria. Furthermore, Corynebacterium spp. weakened the binding of the S1-ACE2. Most C. accolens isolates harbored the TAG lipase LipS1 gene. Based on these results, the presence of Corynebacterium spp. in the nasopharyngeal microbiota, especially C. accolens strains, could reduce the individual susceptibility to SARS-CoV-2 infection by several mechanisms: by downregulation the ACE2, the TMPRSS2 receptors, and cathepsin L in the host; through the inhibition of S1-ACE2 binding; and lipase production. These results suggest the use of C. accolens strains as probiotics in the nasopharynx in the future.
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Affiliation(s)
- Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary.
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary.
| | - Eszter Ostorhazi
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Balazs Stercz
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Nora Makra
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Kinga Penzes
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Katalin Kristof
- Institute of Laboratory Medicine, Clinical Microbiology Laboratory, Semmelweis University, Budapest, Hungary
| | - Istvan Antal
- Department of Pharmaceutics, Semmelweis University, Budapest, Hungary
| | - Janos M Rethelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Reka I Zsigmond
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Ede Birtalan
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
| | - Bela Merkely
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Laszlo Tamas
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
- Department of Voice, Speech and Swallowing Therapy, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
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18
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El-Fakharany EM, El-Gendi H, El-Maradny YA, Abu-Serie MM, Abdel-Wahhab KG, Shabana ME, Ashry M. Inhibitory effect of lactoferrin-coated zinc nanoparticles on SARS-CoV-2 replication and entry along with improvement of lung fibrosis induced in adult male albino rats. Int J Biol Macromol 2023; 245:125552. [PMID: 37356684 PMCID: PMC10290166 DOI: 10.1016/j.ijbiomac.2023.125552] [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: 04/11/2023] [Revised: 06/12/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Severe acute respiratory syndrome 2019-new coronavirus (SARS-CoV-2) is a major global challenge caused by a pandemic disease, named 'COVID-19' with no effective and selective therapy available so far. COVID-19-associated mortality is directly related to the inability to suppress the viral infection and the uncontrolled inflammatory response. So, we investigated the antiviral efficiency of the nanofabricated and well-characterized lactoferrin-coated zinc nanoparticles (Lf-Zn-NPs) on SARS-CoV-2 replication and entry into host cells. Lf-Zn-NPs showed potent inhibition of the entry of SARS-CoV-2 into the host cells by inhibition of ACE2, the SARS-CoV-2 receptor. This inhibitory activity of Lf-Zn-NPs to target the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor offers potent protection against COVID-19 outbreaks. Moreover, the administration of Lf-Zn-NPs markedly improved lung fibrosis disorders, as supported by histopathological findings and monitored by the significant reduction in the values of CRP, LDH, ferritin, and D-dimer, with a remarkable rise in CD4+, lung SOD, GPx, GSH, and CAT levels. Lf-Zn-NPs revealed therapeutic efficiency against lung fibrosis owing to their anti-inflammatory, antioxidant, and ACE2-inhibiting activities. These findings suggest a promising nanomedicine agent against COVID-19 and its complications, with improved antiviral and immunomodulatory properties as well as a safer mode of action.
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Affiliation(s)
- Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA- City), New Borg El-Arab City 21934, Alexandria, Egypt.
| | - Hamada El-Gendi
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt.
| | - Yousra A El-Maradny
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA- City), New Borg El-Arab City 21934, Alexandria, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), Alamein 51718, Egypt
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab 21934, Alexandria, Egypt
| | | | | | - Mahmoud Ashry
- Zoology Department, Faculty of Science, Al-Azhar University, Assuit, Egypt
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19
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Milan Bonotto R, Mitrović A, Sosič I, Martinez-Orellana P, Dattola F, Gobec S, Kos J, Marcello A. Cathepsin inhibitors nitroxoline and its derivatives inhibit SARS-CoV-2 infection. Antiviral Res 2023:105655. [PMID: 37355023 PMCID: PMC10287183 DOI: 10.1016/j.antiviral.2023.105655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The severity of the SARS-CoV-2 pandemic and the recurring (re)emergence of viruses prompted the development of new therapeutic approaches that target viral and host factors crucial for viral infection. Among them, host peptidases cathepsins B and L have been described as essential enzymes during SARS-CoV-2 entry. In this study, we evaluated the effect of potent selective cathepsin inhibitors as antiviral agents. We demonstrated that selective cathepsin B inhibitors, such as the antimicrobial agent nitroxoline and its derivatives, impair SARS-CoV-2 infection in vitro. Antiviral activity observed at early stage of virus entry was cell-type dependent and correlated well with the intracellular content and enzymatic function of cathepsins B or L. Furthermore, tested inhibitors were effective against the ancestral SARS-CoV-2 D614 as well as against the more recent BA.1_4 (Omicron). Taken together, our results highlight the important role of host cysteine cathepsin B in SARS-CoV-2 virus entry and show that cathepsin-specific inhibitors, such as nitroxoline and its derivatives, could be used to treat COVID-19. Finally, these results also suggest that nitroxoline has potential to be further explored as repurposed drug in antiviral therapy.
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Affiliation(s)
- Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Pamela Martinez-Orellana
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Federica Dattola
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy.
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20
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Zabiegala A, Kim Y, Chang KO. Roles of host proteases in the entry of SARS-CoV-2. ANIMAL DISEASES 2023; 3:12. [PMID: 37128508 PMCID: PMC10125864 DOI: 10.1186/s44149-023-00075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023] Open
Abstract
The spike protein (S) of SARS-CoV-2 is responsible for viral attachment and entry, thus a major factor for host susceptibility, tissue tropism, virulence and pathogenicity. The S is divided with S1 and S2 region, and the S1 contains the receptor-binding domain (RBD), while the S2 contains the hydrophobic fusion domain for the entry into the host cell. Numerous host proteases have been implicated in the activation of SARS-CoV-2 S through various cleavage sites. In this article, we review host proteases including furin, trypsin, transmembrane protease serine 2 (TMPRSS2) and cathepsins in the activation of SARS-CoV-2 S. Many betacoronaviruses including SARS-CoV-2 have polybasic residues at the S1/S2 site which is subjected to the cleavage by furin. The S1/S2 cleavage facilitates more assessable RBD to the receptor ACE2, and the binding triggers further conformational changes and exposure of the S2' site to proteases such as type II transmembrane serine proteases (TTPRs) including TMPRSS2. In the presence of TMPRSS2 on the target cells, SARS-CoV-2 can utilize a direct entry route by fusion of the viral envelope to the cellular membrane. In the absence of TMPRSS2, SARS-CoV-2 enter target cells via endosomes where multiple cathepsins cleave the S for the successful entry. Additional host proteases involved in the cleavage of the S were discussed. This article also includes roles of 3C-like protease inhibitors which have inhibitory activity against cathepsin L in the entry of SARS-CoV-2, and discussed the dual roles of such inhibitors in virus replication.
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Affiliation(s)
- Alexandria Zabiegala
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506 USA
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21
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Xie Z, Zhao M, Yan C, Kong W, Lan F, Zhao S, Yang Q, Bai Z, Qing H, Ni J. Cathepsin B in programmed cell death machinery: mechanisms of execution and regulatory pathways. Cell Death Dis 2023; 14:255. [PMID: 37031185 PMCID: PMC10082344 DOI: 10.1038/s41419-023-05786-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Cathepsin B (CatB), a cysteine protease, is primarily localized within subcellular endosomal and lysosomal compartments. It is involved in the turnover of intracellular and extracellular proteins. Interest is growing in CatB due to its diverse roles in physiological and pathological processes. In functional defective tissues, programmed cell death (PCD) is one of the regulable fundamental mechanisms mediated by CatB, including apoptosis, pyroptosis, ferroptosis, necroptosis, and autophagic cell death. However, CatB-mediated PCD is responsible for disease progression under pathological conditions. In this review, we provide an overview of the critical roles and regulatory pathways of CatB in different types of PCD, and discuss the possibility of CatB as an attractive target in multiple diseases. We also summarize current gaps in the understanding of the involvement of CatB in PCD to highlight future avenues for research.
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Affiliation(s)
- Zhen Xie
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China
| | - Mengyuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China
| | - Chengxiang Yan
- Research Center for Resource Peptide Drugs, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Wei Kong
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China
| | - Fei Lan
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China
| | - Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China
| | - Qinghu Yang
- Research Center for Resource Peptide Drugs, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Zhantao Bai
- Research Center for Resource Peptide Drugs, Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China.
- Yan'an Key Laboratory for Neural Immuno-Tumor and Stem Cell and Engineering and Technological Research Center for Natural Peptide Drugs, Yan'an, 716000, China.
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China.
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, 100081, Beijing, China.
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22
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Mok CK, Ng YL, Ahidjo BA, Aw ZQ, Chen H, Wong YH, Lee RCH, Loe MWC, Liu J, Tan KS, Kaur P, Wang DY, Hao E, Hou X, Tan YW, Deng J, Chu JJH. Evaluation of In Vitro and In Vivo Antiviral Activities of Vitamin D for SARS-CoV-2 and Variants. Pharmaceutics 2023; 15:pharmaceutics15030925. [PMID: 36986786 PMCID: PMC10058714 DOI: 10.3390/pharmaceutics15030925] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
The COVID-19 pandemic has brought about unprecedented medical and healthcare challenges worldwide. With the continual emergence and spread of new COVID-19 variants, four drug compound libraries were interrogated for their antiviral activities against SARS-CoV-2. Here, we show that the drug screen has resulted in 121 promising anti-SARS-CoV-2 compounds, of which seven were further shortlisted for hit validation: citicoline, pravastatin sodium, tenofovir alafenamide, imatinib mesylate, calcitriol, dexlansoprazole, and prochlorperazine dimaleate. In particular, the active form of vitamin D, calcitriol, exhibits strong potency against SARS-CoV-2 on cell-based assays and is shown to work by modulating the vitamin D receptor pathway to increase antimicrobial peptide cathelicidin expression. However, the weight, survival rate, physiological conditions, histological scoring, and virus titre between SARS-CoV-2 infected K18-hACE2 mice pre-treated or post-treated with calcitriol were negligible, indicating that the differential effects of calcitriol may be due to differences in vitamin D metabolism in mice and warrants future investigation using other animal models.
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Affiliation(s)
- Chee-Keng Mok
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yan Ling Ng
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Bintou Ahmadou Ahidjo
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Zhen Qin Aw
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Huixin Chen
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Yi Hao Wong
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Marcus Wing Choy Loe
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Jing Liu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kai Sen Tan
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Parveen Kaur
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Erwei Hao
- Guangxi Key Laboratory of Efficacy Study on Chinese Materia Medica, Guangxi University of Chinese Medicine, Nanning 530200, China
- Guangxi Collaborative Innovation Center for Research on Functional Ingredients of Agricultural Residues, Guangxi University of Chinese Medicine, Nanning 530200, China
- China-ASEAN Joint Laboratory for International Cooperation in Traditional Medicine Research, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Xiaotao Hou
- Guangxi Key Laboratory of Efficacy Study on Chinese Materia Medica, Guangxi University of Chinese Medicine, Nanning 530200, China
- Guangxi Collaborative Innovation Center for Research on Functional Ingredients of Agricultural Residues, Guangxi University of Chinese Medicine, Nanning 530200, China
- China-ASEAN Joint Laboratory for International Cooperation in Traditional Medicine Research, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yong Wah Tan
- Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Jiagang Deng
- Guangxi Key Laboratory of Efficacy Study on Chinese Materia Medica, Guangxi University of Chinese Medicine, Nanning 530200, China
- Guangxi Collaborative Innovation Center for Research on Functional Ingredients of Agricultural Residues, Guangxi University of Chinese Medicine, Nanning 530200, China
- China-ASEAN Joint Laboratory for International Cooperation in Traditional Medicine Research, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Justin Jang Hann Chu
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Disease Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Correspondence: ; Tel.: +65-65163278
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23
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Structure-based lead optimization of peptide-based vinyl methyl ketones as SARS-CoV-2 main protease inhibitors. Eur J Med Chem 2023; 247:115021. [PMID: 36549112 PMCID: PMC9751013 DOI: 10.1016/j.ejmech.2022.115021] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Despite several major achievements in the development of vaccines and antivirals, the fight against SARS-CoV-2 and the health problems accompanying COVID-19 are still ongoing. SARS-CoV-2 main protease (Mpro), an essential viral cysteine protease, is a crucial target for the development of antiviral agents. A virtual screening analysis of in-house cysteine protease inhibitors against SARS-CoV-2 Mpro allowed us to identify two hits (i.e., 1 and 2) bearing a methyl vinyl ketone warhead. Starting from these compounds, we herein report the development of Michael acceptors targeting SARS-CoV-2 Mpro, which differ from each other for the warhead and for the amino acids at the P2 site. The most promising vinyl methyl ketone-containing analogs showed sub-micromolar activity against the viral protease. SPR38, SPR39, and SPR41 were fully characterized, and additional inhibitory properties towards hCatL, which plays a key role in the virus entry into host cells, were observed. SPR39 and SPR41 exhibited single-digit micromolar EC50 values in a SARS-CoV-2 infection model in cell culture.
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24
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Bauer A, Pachl E, Hellmuth JC, Kneidinger N, Heydarian M, Frankenberger M, Stubbe HC, Ryffel B, Petrera A, Hauck SM, Behr J, Kaiser R, Scherer C, Deng L, Teupser D, Ahmidi N, Muenchhoff M, Schubert B, Hilgendorff A. Proteomics reveals antiviral host response and NETosis during acute COVID-19 in high-risk patients. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166592. [PMID: 36328146 PMCID: PMC9622026 DOI: 10.1016/j.bbadis.2022.166592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
SARS-CoV-2 remains an acute threat to human health, endangering hospital capacities worldwide. Previous studies have aimed at informing pathophysiologic understanding and identification of disease indicators for risk assessment, monitoring, and therapeutic guidance. While findings start to emerge in the general population, observations in high-risk patients with complex pre-existing conditions are limited. We addressed the gap of existing knowledge with regard to a differentiated understanding of disease dynamics in SARS-CoV-2 infection while specifically considering disease stage and severity. We biomedically characterized quantitative proteomics in a hospitalized cohort of COVID-19 patients with mild to severe symptoms suffering from different (co)-morbidities in comparison to both healthy individuals and patients with non-COVID related inflammation. Deep clinical phenotyping enabled the identification of individual disease trajectories in COVID-19 patients. By the use of the individualized disease phase assignment, proteome analysis revealed a severity dependent general type-2-centered host response side-by-side with a disease specific antiviral immune reaction in early disease. The identification of phenomena such as neutrophil extracellular trap (NET) formation and a pro-coagulatory response characterizing severe disease was successfully validated in a second cohort. Together with the regulation of proteins related to SARS-CoV-2-specific symptoms identified by proteome screening, we not only confirmed results from previous studies but provide novel information for biomarker and therapy development.
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Affiliation(s)
- Alina Bauer
- Helmholtz Zentrum München, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Elisabeth Pachl
- Helmholtz Zentrum München, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany,Fraunhofer IKS, Fraunhofer Institute for Cognitive Systems IKS, 80686 Munich, Germany
| | - Johannes C. Hellmuth
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany,German Cancer Consortium (DKTK), Munich, Germany,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Nikolaus Kneidinger
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany,Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Marion Frankenberger
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Hans C. Stubbe
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany,Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Bernhard Ryffel
- Laboratory of Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355 CNRS-University of Orleans and Artimmune, Orléans, France
| | - Agnese Petrera
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Jürgen Behr
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany,Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Rainer Kaiser
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany,Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany,Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Li Deng
- Helmholtz Zentrum München, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany,Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Narges Ahmidi
- Fraunhofer IKS, Fraunhofer Institute for Cognitive Systems IKS, 80686 Munich, Germany
| | - Maximilian Muenchhoff
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Benjamin Schubert
- Helmholtz Zentrum München, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany,Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Anne Hilgendorff
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for Lung Research (DZL), Munich, Germany; Center for Comprehensive Developmental Care (CDeC(LMU)) at the Interdisciplinary Social Pediatric Center (iSPZ), LMU Hospital, Munich, Germany.
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25
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Mziray SR, van Zwetselaar M, Kayuki CC, Mbelele PM, Makubi AN, Magesa AS, Kisonga RM, Sonda TB, Kibiki GS, Githinji G, Heysell SK, Chilongola JO, Mpagama SG. Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania. Front Med (Lausanne) 2023; 9:1034682. [PMID: 36687433 PMCID: PMC9846855 DOI: 10.3389/fmed.2022.1034682] [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: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Background Coronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa. Methods This cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0. Results Twenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2. Conclusion We provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.
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Affiliation(s)
- Shabani Ramadhani Mziray
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kibong’oto Infectious Diseases Hospital, Sanya Juu, Tanzania
| | | | | | | | | | | | | | | | - Gibson S. Kibiki
- The Africa Research Excellence Fund (AREF), London, United Kingdom
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Jaffu O. Chilongola
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
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26
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Moumbock AFA, Tran HTT, Lamy E, Günther S. BC-11 is a covalent TMPRSS2 fragment inhibitor that impedes SARS-CoV-2 host cell entry. Arch Pharm (Weinheim) 2023; 356:e2200371. [PMID: 36316225 PMCID: PMC9874818 DOI: 10.1002/ardp.202200371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Host cell entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is facilitated via priming of its spike glycoprotein by the human transmembrane protease serine 2 (TMPRSS2). Although camostat and nafamostat are two highly potent covalent TMPRSS2 inhibitors, they nevertheless did not hold promise in COVID-19 clinical trials, presumably due to their short plasma half-lives. Herein, we report an integrative chemogenomics approach based on computational modeling and in vitro enzymatic assays, for repurposing serine-targeted covalent inhibitors. This led to the identification of BC-11 as a covalent TMPRSS2 inhibitor displaying a unique selectivity profile for serine proteases, ascribable to its boronic acid warhead. BC-11 showed modest inhibition of SARS-CoV-2 (omicron variant) spike pseudotyped particles in a cell-based entry assay, and a combination of BC-11 and AHN 1-055 (a spike glycoprotein inhibitor) demonstrated better viral entry inhibition than either compound alone. Given its low molecular weight and good activity against TMPRSS2, BC-11 qualifies as a good starting point for further structural optimizations.
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Affiliation(s)
- Aurélien F. A. Moumbock
- Faculty of Chemistry and Pharmacy, Institute of Pharmaceutical SciencesAlbert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Hoai T. T. Tran
- Molecular Preventive Medicine, Faculty of MedicineUniversity Medical Center, Albert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Evelyn Lamy
- Molecular Preventive Medicine, Faculty of MedicineUniversity Medical Center, Albert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Stefan Günther
- Faculty of Chemistry and Pharmacy, Institute of Pharmaceutical SciencesAlbert‐Ludwigs‐Universität FreiburgFreiburgGermany
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27
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Calidonio JM, Hamad-Schifferli K. Biophysical and biochemical insights in the design of immunoassays. Biochim Biophys Acta Gen Subj 2023; 1867:130266. [PMID: 36309294 PMCID: PMC11193098 DOI: 10.1016/j.bbagen.2022.130266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Rapid antigen assays have been attractive for decentralized, point of care diagnostics because of their low cost, robustness, and ease of use. The development of a diagnostic assay for a newly emerging infectious disease needs to take into account the progression of a disease, whether there is human to human transmission, and patient biomarker levels with time, and these all impact the choice of antigen targets and affinity agents. SCOPE OF REVIEW The factors involved in the biophysical design of rapid antigen immunoassays are discussed, focusing on antigen selection and designing for cross-reactivity. State of the art in the biophysical characterization of protein-ligand or antigen-antibody interactions, the different types of affinity agents used in immunoassays, and biochemical conjugation strategies are described. MAJOR CONCLUSIONS Antigen choice is a critical factor in immunoassay diagnostic development, and should account for the properties of the virion, virus, and disease progression. Biophysical and biochemical aspects of immunoassays are critical for performance. GENERAL SIGNIFICANCE This review can serve as an instructive guide to aid in diagnostic development for future emerging diseases.
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Affiliation(s)
| | - Kimberly Hamad-Schifferli
- Dept. of Engineering, University of Massachusetts Boston, Boston, MA, USA; School for the Environment, University of Massachusetts Boston, Boston, MA, USA.
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28
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Guo C, Tsai SJ, Ai Y, Li M, Anaya E, Pekosz A, Cox A, Gould SJ. The D614G mutation redirects SARS-CoV-2 spike to lysosomes and suppresses deleterious traits of the furin cleavage site insertion mutation. SCIENCE ADVANCES 2022; 8:eade5085. [PMID: 36563151 PMCID: PMC9788772 DOI: 10.1126/sciadv.ade5085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) egress occurs by lysosomal exocytosis. We show that the Spike D614G mutation enhances Spike trafficking to lysosomes, drives Spike-mediated reprogramming of lysosomes, and reduces cell surface Spike expression by ~3-fold. D614G is not a human-specific adaptation. Rather, it is an adaptation to the earlier furin cleavage site insertion (FCSI) mutation that occurred at the genesis of SARS-CoV-2. While advantageous to the virus, furin cleavage of spike has deleterious effects on spike structure and function, inhibiting its trafficking to lysosomes and impairing its infectivity by the transmembrane serine protease 2(TMPRSS2)-independent, endolysosomal pathway. D614G restores spike trafficking to lysosomes and enhances the earliest events in SARS-CoV-2 infectivity, while spike mutations that restore SARS-CoV-2's TMPRSS2-independent infectivity restore spike's trafficking to lysosomes. Together, these and other results show that D614G is an intragenic suppressor of deleterious traits linked to the FCSI and lend additional support to the endolysosomal model of SARS-CoV-2 egress and entry.
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Affiliation(s)
- Chenxu Guo
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Shang-Jui Tsai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Yiwei Ai
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Maggie Li
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Eduardo Anaya
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew Pekosz
- Department of Microbiology and Immunology, Johns Hopkins University, School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrea Cox
- Department of Medicine, Department of Microbiology and Immunology, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Stephen J. Gould
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205, USA
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29
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McCann N, Castellino FJ. Cell Entry and Unusual Replication of SARS-CoV-2. Curr Drug Targets 2022; 23:1539-1554. [PMID: 36239725 DOI: 10.2174/1389450124666221014102927] [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: 06/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND SARS-CoV-2 is the causative virus for the CoVID-19 pandemic that has frequently mutated to continue to infect and resist available vaccines. Emerging new variants of the virus have complicated notions of immunity conferred by vaccines versus immunity that results from infection. While we continue to progress from epidemic to endemic as a result of this collective immunity, the pandemic remains a morbid and mortal problem. OBJECTIVE The SARS-CoV-2 virus has a very complex manner of replication. The spike protein, one of the four structural proteins of the encapsulated virus, is central to the ability of the virus to penetrate cells to replicate. The objective of this review is to summarize these complex features of viral replication. METHODS A review of the recent literature was performed on the biology of SARS-CoV-2 infection from published work from PubMed and works reported to preprint servers, e.g., bioRxiv and medRxiv. RESULTS AND CONCLUSION The complex molecular and cellular biology involved in SARS-CoV-2 replication and the origination of >30 proteins from a single open reading frame (ORF) have been summarized, as well as the structural biology of spike protein, a critical factor in the cellular entry of the virus, which is a necessary feature for it to replicate and cause disease.
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Affiliation(s)
- Nathan McCann
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Francis J Castellino
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
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30
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Mondal S, Chen Y, Lockbaum GJ, Sen S, Chaudhuri S, Reyes AC, Lee JM, Kaur AN, Sultana N, Cameron MD, Shaffer SA, Schiffer CA, Fitzgerald KA, Thompson PR. Dual Inhibitors of Main Protease (M Pro) and Cathepsin L as Potent Antivirals against SARS-CoV2. J Am Chem Soc 2022; 144:21035-21045. [PMID: 36356199 PMCID: PMC9662648 DOI: 10.1021/jacs.2c04626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Indexed: 11/12/2022]
Abstract
Given the current impact of SARS-CoV2 and COVID-19 on human health and the global economy, the development of direct acting antivirals is of paramount importance. Main protease (MPro), a cysteine protease that cleaves the viral polyprotein, is essential for viral replication. Therefore, MPro is a novel therapeutic target. We identified two novel MPro inhibitors, D-FFRCMKyne and D-FFCitCMKyne, that covalently modify the active site cysteine (C145) and determined cocrystal structures. Medicinal chemistry efforts led to SM141 and SM142, which adopt a unique binding mode within the MPro active site. Notably, these inhibitors do not inhibit the other cysteine protease, papain-like protease (PLPro), involved in the life cycle of SARS-CoV2. SM141 and SM142 block SARS-CoV2 replication in hACE2 expressing A549 cells with IC50 values of 8.2 and 14.7 nM. Detailed studies indicate that these compounds also inhibit cathepsin L (CatL), which cleaves the viral S protein to promote viral entry into host cells. Detailed biochemical, proteomic, and knockdown studies indicate that the antiviral activity of SM141 and SM142 results from the dual inhibition of MPro and CatL. Notably, intranasal and intraperitoneal administration of SM141 and SM142 lead to reduced viral replication, viral loads in the lung, and enhanced survival in SARS-CoV2 infected K18-ACE2 transgenic mice. In total, these data indicate that SM141 and SM142 represent promising scaffolds on which to develop antiviral drugs against SARS-CoV2.
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Affiliation(s)
- Santanu Mondal
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Gordon J. Lockbaum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sudeshna Sen
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Sauradip Chaudhuri
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Archie C. Reyes
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jeong Min Lee
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshia N. Kaur
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Nadia Sultana
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Michael D. Cameron
- Department of Molecular Medicine, The Scripps Research Institute,130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott A. Shaffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Paul R. Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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31
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Lemke C, Jílková A, Ferber D, Braune A, On A, Johe P, Zíková A, Schirmeister T, Mareš M, Horn M, Gütschow M. Two Tags in One Probe: Combining Fluorescence- and Biotin-based Detection of the Trypanosomal Cysteine Protease Rhodesain. Chemistry 2022; 28:e202201636. [PMID: 35852812 PMCID: PMC9826439 DOI: 10.1002/chem.202201636] [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: 05/26/2022] [Indexed: 01/11/2023]
Abstract
Rhodesain is the major cysteine protease of the protozoan parasite Trypanosoma brucei and a therapeutic target for sleeping sickness, a fatal neglected tropical disease. We designed, synthesized and characterized a bimodal activity-based probe that binds to and inactivates rhodesain. This probe exhibited an irreversible mode of action and extraordinary potency for the target protease with a kinac /Ki value of 37,000 M-1 s-1 . Two reporter tags, a fluorescent coumarin moiety and a biotin affinity label, were incorporated into the probe and enabled highly sensitive detection of rhodesain in a complex proteome by in-gel fluorescence and on-blot chemiluminescence. Furthermore, the probe was employed for microseparation and quantification of rhodesain and for inhibitor screening using a competition assay. The developed bimodal rhodesain probe represents a new proteomic tool for studying Trypanosoma pathobiochemistry and antitrypanosomal drug discovery.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Adéla Jílková
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Dominic Ferber
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Annett Braune
- Research Group Intestinal MicrobiologyGerman Institute of Human Nutrition Potsdam-RehbrueckeArthur-Scheunert-Allee 114–11614558NuthetalGermany
| | - Anja On
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Alena Zíková
- Biology Centre CASInstitute of ParasitologyUniversity of South BohemiaFaculty of ScienceBranišovská 1160/3137005České BudějoviceCzech Republic
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Michael Mareš
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Martin Horn
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Michael Gütschow
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
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32
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Heinl ES, Lorenz S, Schmidt B, Nasser M Laqtom N, Mazzulli JR, Francelle L, Yu TW, Greenberg B, Storch S, Tegtmeier I, Othmen H, Maurer K, Steinfurth M, Witzgall R, Milenkovic V, Wetzel CH, Reichold M. CLN7/MFSD8 may be an important factor for SARS-CoV-2 cell entry. iScience 2022; 25:105082. [PMID: 36093380 PMCID: PMC9444308 DOI: 10.1016/j.isci.2022.105082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/12/2022] [Accepted: 08/31/2022] [Indexed: 11/12/2022] Open
Abstract
The SARS-CoV-2 virus has triggered a worldwide pandemic. According to the BioGrid database, CLN7 (MFSD8) is thought to interact with several viral proteins. The aim of this work was to investigate a possible involvement of CLN7 in the infection process. Experiments on a CLN7-deficient HEK293T cell line exhibited a 90% reduced viral load compared to wild-type cells. This observation may be linked to the finding that CLN7 ko cells have a significantly reduced GM1 content in their cell membrane. GM1 is found highly enriched in lipid rafts, which are thought to play an important role in SARS-CoV-2 infection. In contrast, overexpression of CLN7 led to an increase in viral load. This study provides evidence that CLN7 is involved in SARS-CoV-2 infection. This makes it a potential pharmacological target for drug development against COVID-19. Furthermore, it provides insights into the physiological function of CLN7 where still only little is known about.
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Affiliation(s)
- Elena-Sofia Heinl
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
| | - Sebastian Lorenz
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany
| | - Nouf Nasser M Laqtom
- Departments of Chemical Engineering and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joseph R. Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Laetitia Francelle
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Timothy W. Yu
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Benjamin Greenberg
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Storch
- Children’s Hospital Biochemistry, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Ines Tegtmeier
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
| | - Helga Othmen
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
- Institute for Molecular and Cellular Anatomy, University Regensburg, 93053 Regensburg, Germany
| | - Katja Maurer
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
| | - Malin Steinfurth
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
| | - Ralph Witzgall
- Institute for Molecular and Cellular Anatomy, University Regensburg, 93053 Regensburg, Germany
| | - Vladimir Milenkovic
- Department of Psychiatry and Psychotherapy, University of Regensburg, 93053 Regensburg, Germany
| | - Christian H. Wetzel
- Department of Psychiatry and Psychotherapy, University of Regensburg, 93053 Regensburg, Germany
| | - Markus Reichold
- Medical Cell Biology, University Regensburg, 93053 Regensburg, Germany
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33
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Delgado CP, Rocha JBT, Orian L, Bortoli M, Nogara PA. In silico studies of M pro and PL pro from SARS-CoV-2 and a new class of cephalosporin drugs containing 1,2,4-thiadiazole. Struct Chem 2022; 33:2205-2220. [PMID: 36106095 PMCID: PMC9463509 DOI: 10.1007/s11224-022-02036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 proteases Mpro and PLpro are important targets for the development of antivirals against COVID-19. The functional group 1,2,4-thiadiazole has been indicated to inhibit cysteinyl proteases, such as papain and cathepsins. Of note, the 1,2,4-thiadiazole moiety is found in a new class of cephalosporin FDA-approved antibiotics: ceftaroline fosamil, ceftobiprole, and ceftobiprole medocaril. Here we investigated the interaction of these new antibiotics and their main metabolites with the SARS-CoV-2 proteases by molecular docking, molecular dynamics (MD), and density functional theory (DFT) calculations. Our results indicated the PLpro enzyme as a better in silico target for the new antibacterial cephalosporins. The results with ceftaroline fosamil and the dephosphorylate metabolite compounds should be tested as potential inhibitor of PLpro, Mpro, and SARS-CoV-2 replication in vitro. In addition, the data here reported can help in the design of new potential drugs against COVID-19 by exploiting the S atom reactivity in the 1,2,4-thiadiazole moiety. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02036-5.
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Affiliation(s)
- Cássia Pereira Delgado
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
| | - João Batista Teixeira Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
| | - Laura Orian
- Dipartimento di Scuenze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padua, Italy
| | - Marco Bortoli
- Institut de Química Computacionali Catàlisi (IQCC), Departament de Química, Facultat de Ciències, Universitat de Girona, C/M. A. Capmany 69, 17003 Girona, Spain
| | - Pablo Andrei Nogara
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS 97105-900 Brazil
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Zhou L, Hou W, Wang Y, Lin X, Hu J, Li J, Liu C, Liu H, Li H. An extracellular matrix biosensing mimetic for evaluating cathepsin as a host target for COVID-19. Anal Chim Acta 2022; 1225:340267. [PMID: 36038228 PMCID: PMC9380907 DOI: 10.1016/j.aca.2022.340267] [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: 07/08/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/25/2022]
Abstract
To combat the new virus currently ravaging the whole world, every possible anti-virus strategy should be explored. As the main strategy of targeting the virus itself is being frustrated by the rapid mutation of the virus, people are seeking an alternative "host targeting" strategy: neutralizing proteins in the human body that cooperate with the virus. The cathepsin family is such a group of promising host targets, the main biological function of which is to digest the extracellular matrix (ECM) to clear a path for virus spreading. To evaluate the potential of cathepsin as a host target, we have constructed a biosensing interface mimicking the ECM, which can detect cathepsin from 3.3 pM to 33 nM with the limit of detection of 1 pM. Based on our quantitative analysis enabled by this biosensing interface, it is clear that patients with background diseases such as chronic inflammation and tumor, tend to have higher cathepsin activity, confirming the potential of cathepsin to serve as a host target for combating COVID-19 virus.
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Affiliation(s)
- Lei Zhou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China; Shandong Keyuan Pharmaceutical Co., Ltd, 250022, China.
| | - Wenmin Hou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China
| | - Ying Wang
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China
| | - Xia Lin
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China
| | - Jianguo Hu
- Department of Food Science and Nutrition, College of Culture and Tourism, University of Jinan, 13#, Shungeng Road, Jinan, 250000, China
| | - Jinlong Li
- Department of Laboratory Medicine, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, PR China
| | - Chen Liu
- Children's Hospital Affiliated to Shandong University Jinan, Jinan Children's Hospital Jinan, 250002, PR China.
| | - Hongkai Liu
- Department of Food Science and Nutrition, College of Culture and Tourism, University of Jinan, 13#, Shungeng Road, Jinan, 250000, China.
| | - Hao Li
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan, Xinzhuang, 250022, China.
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The Key Role of Lysosomal Protease Cathepsins in Viral Infections. Int J Mol Sci 2022; 23:ijms23169089. [PMID: 36012353 PMCID: PMC9409221 DOI: 10.3390/ijms23169089] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Cathepsins encompass a family of lysosomal proteases that mediate protein degradation and turnover. Although mainly localized in the endolysosomal compartment, cathepsins are also found in the cytoplasm, nucleus, and extracellular space, where they are involved in cell signaling, extracellular matrix assembly/disassembly, and protein processing and trafficking through the plasma and nuclear membrane and between intracellular organelles. Ubiquitously expressed in the body, cathepsins play regulatory roles in a wide range of physiological processes including coagulation, hormone secretion, immune responses, and others. A dysregulation of cathepsin expression and/or activity has been associated with many human diseases, including cancer, diabetes, obesity, cardiovascular and inflammatory diseases, kidney dysfunctions, and neurodegenerative disorders, as well as infectious diseases. In viral infections, cathepsins may promote (1) activation of the viral attachment glycoproteins and entry of the virus into target cells; (2) antigen processing and presentation, enabling the virus to replicate in infected cells; (3) up-regulation and processing of heparanase that facilitates the release of viral progeny and the spread of infection; and (4) activation of cell death that may either favor viral clearance or assist viral propagation. In this review, we report the most relevant findings on the molecular mechanisms underlying cathepsin involvement in viral infection physiopathology, and we discuss the potential of cathepsin inhibitors for therapeutical applications in viral infectious diseases.
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Rashid F, Xie Z, Suleman M, Shah A, Khan S, Luo S. Roles and functions of SARS-CoV-2 proteins in host immune evasion. Front Immunol 2022; 13:940756. [PMID: 36003396 PMCID: PMC9394213 DOI: 10.3389/fimmu.2022.940756] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.
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Affiliation(s)
- Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- *Correspondence: Zhixun Xie,
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
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In Silico Analysis Using SARS-CoV-2 Main Protease and a Set of Phytocompounds to Accelerate the Development of Therapeutic Components against COVID-19. Processes (Basel) 2022. [DOI: 10.3390/pr10071397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2, the virus that caused the widespread COVID-19 pandemic, is homologous to SARS-CoV. It would be ideal to develop antivirals effective against SARS-CoV-2. In this study, we chose one therapeutic target known as the main protease (Mpro) of SARS-CoV-2. A crystal structure (Id: 6LU7) from the protein data bank (PDB) was used to accomplish the screening and docking studies. A set of phytocompounds was used for the docking investigation. The nature of the interaction and the interacting residues indicated the molecular properties that are essential for significant affinity. Six compounds were selected, based on the docking as well as the MM-GBSA score. Pentagalloylglucose, Shephagenin, Isoacteoside, Isoquercitrin, Kappa-Carrageenan, and Dolabellin are the six compounds with the lowest binding energies (−12 to −8 kcal/mol) and show significant interactions with the target Mpro protein. The MMGBSA scores of these compounds are highly promising, and they should be investigated to determine their potential as Mpro inhibitors, beneficial for COVID-19 treatment. In this study, we highlight the crucial role of in silico technologies in the search for novel therapeutic components. Computational biology, combined with structural biology, makes drug discovery studies more rigorous and reliable, and it creates a scenario where researchers can use existing drug components to discover new roles as modulators or inhibitors for various therapeutic targets. This study demonstrated that computational analyses can yield promising findings in the search for potential drug components. This work demonstrated the significance of increasing in silico and wetlab research to generate improved structure-based medicines.
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Dual Inhibition of Vacuolar-ATPase and TMPRSS2 Is Required for Complete Blockade of SARS-CoV-2 Entry into Cells. Antimicrob Agents Chemother 2022; 66:e0043922. [PMID: 35703551 PMCID: PMC9295568 DOI: 10.1128/aac.00439-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
An essential step in the infection life cycle of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the proteolytic activation of the viral spike (S) protein, which enables membrane fusion and entry into the host cell. Two distinct classes of host proteases have been implicated in the S protein activation step: cell-surface serine proteases, such as the cell-surface transmembrane protease, serine 2 (TMPRSS2), and endosomal cathepsins, leading to entry through either the cell-surface route or the endosomal route, respectively. In cells expressing TMPRSS2, inhibiting endosomal proteases using nonspecific cathepsin inhibitors such as E64d or lysosomotropic compounds such as hydroxychloroquine fails to prevent viral entry, suggesting that the endosomal route of entry is unimportant; however, mechanism-based toxicities and poor efficacy of these compounds confound our understanding of the importance of the endosomal route of entry. Here, to identify better pharmacological agents to elucidate the role of the endosomal route of entry, we profiled a panel of molecules identified through a high-throughput screen that inhibit endosomal pH and/or maturation through different mechanisms. Among the three distinct classes of inhibitors, we found that inhibiting vacuolar-ATPase using the macrolide bafilomycin A1 was the only agent able to potently block viral entry without associated cellular toxicity. Using both pseudotyped and authentic virus, we showed that bafilomycin A1 inhibits SARS-CoV-2 infection both in the absence and presence of TMPRSS2. Moreover, synergy was observed upon combining bafilomycin A1 with Camostat, a TMPRSS2 inhibitor, in neutralizing SARS-CoV-2 entry into TMPRSS2-expressing cells. Overall, this study highlights the importance of the endosomal route of entry for SARS-CoV-2 and provides a rationale for the generation of successful intervention strategies against this virus that combine inhibitors of both entry pathways.
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SARS-CoV-2 Spike Furin Cleavage Site and S2' Basic Residues Modulate the Entry Process in a Host Cell-Dependent Manner. J Virol 2022; 96:e0047422. [PMID: 35678602 PMCID: PMC9278140 DOI: 10.1128/jvi.00474-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SARS-CoV-2 spike (S) envelope glycoprotein constitutes the main determinant of virus entry and the target of host immune response, thus being of great interest for antiviral research. It is constituted of S1 and S2 subunits, which are involved in ACE2 receptor binding and fusion between the viral envelope and host cell membrane, respectively. Induction of the fusion process requires S cleavage at the S1-S2 junction and the S2′ site located upstream of the fusion peptide. Interestingly, the SARS-CoV-2 spike harbors a 4-residue insertion at the S1-S2 junction that is absent in its closest relatives and constitutes a polybasic motif recognized by furin-like proteases. In addition, the S2′ site is characterized by the presence of conserved basic residues. Here, we sought to determine the importance of the furin cleavage site (FCS) and the S2′ basic residues for S-mediated entry functions. We determined the impact of mutations introduced at these sites on S processing, fusogenic activity, and its ability to mediate entry in different cellular backgrounds. Strikingly, mutation phenotypes were highly dependent on the host cell background. We confirmed that although the FCS was not absolutely required for virus entry, it contributed to extending the fusogenic potential of S. Cleavage site mutations, as well as inhibition of furin protease activity, affected the cell surface expression of S in a host cell-dependent manner. Finally, inhibition of furin activity differentially affected SARS-CoV-2 virus infectivity in the tested host cells, thereby confirming the host cell-dependent effect of spike processing for the viral life cycle. IMPORTANCE SARS-CoV-2 is responsible for the current global pandemic that has resulted in several million deaths. As the key determinant of virus entry into host cells and the main target of host immune response, the spike glycoprotein constitutes an attractive target for therapeutics development. Entry functions of spike rely on its processing at two sites by host cell proteases. While SARS-CoV-2 spike differs from its closest relatives by the insertion of a basic furin cleavage motif at the first site, it harbors conserved basic residues at the second cleavage site. Characterization of the importance of the basic sequences present at the two cleavage sites revealed that they were influencing spike processing, intracellular localization, induction of fusion, and entry in a host cell-dependent manner. Thus, our results revealed a high heterogeneity in spike sequence requirement for entry functions in the different host cells, in agreement with the high adaptability of the SARS-CoV-2 virus.
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40
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Rani P, Kapoor B, Gulati M, Atanasov AG, Alzahrani Q, Gupta R. Antimicrobial peptides: A plausible approach for COVID-19 treatment. Expert Opin Drug Discov 2022; 17:473-487. [PMID: 35255763 PMCID: PMC8935455 DOI: 10.1080/17460441.2022.2050693] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), which emerged as a major public health threat, has affected >400 million people globally leading to >5 million mortalities to date. Treatments of COVID-19 are still to be developed as the available therapeutic approaches are not able to combat the virus causing the disease (severe acute respiratory syndrome coronavirus-2; SARS-CoV-2) satisfactorily. However, antiviral peptides (AVPs) have demonstrated prophylactic and therapeutic effects against many coronaviruses (CoVs). AREAS COVERED This review critically discusses various types of AVPs evaluated for the treatment of COVID-19 along with their mechanisms of action. Furthermore, the peptides inhibiting the entry of the virus by targeting its binding to angiotensin-converting enzyme 2 (ACE2) or integrins, fusion mechanism as well as activation of proteolytic enzymes (cathepsin L, transmembrane serine protease 2 (TMPRSS2), or furin) are also discussed. EXPERT OPINION Although extensively investigated, successful treatment of COVID-19 is still a challenge due to emergence of virus mutants. Antiviral peptides are anticipated to be blockbuster drugs for the management of this serious infection because of their formulation and therapeutic advantages. Although they may act on different pathways, AVPs having a multi-targeted approach are considered to have the upper hand in the management of this infection.
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Affiliation(s)
- Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Atanas G. Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Magdalenka, Poland
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville, Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
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Ni J, Lan F, Xu Y, Nakanishi H, Li X. Extralysosomal cathepsin B in central nervous system: Mechanisms and therapeutic implications. Brain Pathol 2022; 32:e13071. [PMID: 35411983 PMCID: PMC9425006 DOI: 10.1111/bpa.13071] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
Cathepsin B (CatB) is a typical cysteine lysosomal protease involved in a variety of physiologic and pathological processes. It is expressed in most cell types and is primarily localized within subcellular endosomal and lysosomal compartments. Emerging scientific evidence indicates that lysosomal leaked CatB is involved in mitochondrial stress, inflammasome activation, and nuclear senescence, but without the acidic environment. CatB is also secreted as a myokine, which is involved in muscle‐brain cross talk and neuronal dendritic remodeling. Lysosomal‐leaked and cellular‐secreted CatB functions are dependent on its enzymatic activity at a neutral pH. In the present review, we summarize the available experimental evidence that mechanistically links extralysosomal CatB to physiological and pathological functions in central nervous system, and their potential for use in therapeutic approaches.
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Affiliation(s)
- Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Fei Lan
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yan Xu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hiroshi Nakanishi
- Department of Pharmacology, Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Xue Li
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
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Rhoades R, Solomon S, Johnson C, Teng S. Impact of SARS-CoV-2 on Host Factors Involved in Mental Disorders. Front Microbiol 2022; 13:845559. [PMID: 35444632 PMCID: PMC9014212 DOI: 10.3389/fmicb.2022.845559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates the involvement of the olfactory bulb in COVID-19 disease and provides a route into the central nervous system. However, little is known about how SARS-CoV-2 affects neurological or psychological symptoms. SARS-CoV-2 exploits host receptors that converge on pathways that impact psychological symptoms. This systemic review discusses the ways involved by coronavirus infection and their impact on mental health disorders. We begin by briefly introducing the history of coronaviruses, followed by an overview of the essential proteins to viral entry. Then, we discuss the downstream effects of viral entry on host proteins. Finally, we review the literature on host factors that are known to play critical roles in neuropsychiatric symptoms and mental diseases and discuss how COVID-19 could impact mental health globally. Our review details the host factors and pathways involved in the cellular mechanisms, such as systemic inflammation, that play a significant role in the development of neuropsychological symptoms stemming from COVID-19 infection.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC, United States
| | - Sarah Solomon
- Department of Biology, Howard University, Washington, DC, United States
| | - Christina Johnson
- Department of Biology, Howard University, Washington, DC, United States
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Danziger O, Patel RS, DeGrace EJ, Rosen MR, Rosenberg BR. Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor. PLoS Pathog 2022; 18:e1010464. [PMID: 35421191 PMCID: PMC9041830 DOI: 10.1371/journal.ppat.1010464] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/26/2022] [Accepted: 03/23/2022] [Indexed: 11/19/2022] Open
Abstract
Interferons establish an antiviral state through the induction of hundreds of interferon-stimulated genes (ISGs). The mechanisms and viral specificities for most ISGs remain incompletely understood. To enable high-throughput interrogation of ISG antiviral functions in pooled genetic screens while mitigating potentially confounding effects of endogenous interferon and antiproliferative/proapoptotic ISG activities, we adapted a CRISPR-activation (CRISPRa) system for inducible ISG expression in isogenic cell lines with and without the capacity to respond to interferons. We used this platform to screen for ISGs that restrict SARS-CoV-2. Results included ISGs previously described to restrict SARS-CoV-2 and novel candidate antiviral factors. We validated a subset of these by complementary CRISPRa and cDNA expression experiments. OAS1, a top-ranked hit across multiple screens, exhibited strong antiviral effects against SARS-CoV-2, which required OAS1 catalytic activity. These studies demonstrate a high-throughput approach to assess antiviral functions within the ISG repertoire, exemplified by identification of multiple SARS-CoV-2 restriction factors.
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Affiliation(s)
- Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Roosheel S. Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Emma J. DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mikaela R. Rosen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Mendonça MM, da Cruz KR, Pinheiro DDS, Moraes GCA, Ferreira PM, Ferreira-Neto ML, da Silva ES, Gonçalves RV, Pedrino GR, Fajemiroye JO, Xavier CH. Dysregulation in erythrocyte dynamics caused by SARS-CoV-2 infection: possible role in shuffling the homeostatic puzzle during COVID-19. Hematol Transfus Cell Ther 2022; 44:235-245. [PMID: 35098037 PMCID: PMC8786672 DOI: 10.1016/j.htct.2022.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction The evolving COVID-19 pandemic became a hallmark in human history, not only by changing lifestyles, but also by enriching scientific knowledge on viral infection and its consequences. Objective Although the management of cardiorespiratory changes is pivotal to a favorable prognosis during severe clinical findings, dysregulation of other systems caused by SARS-CoV-2 infection may imbalance erythrocyte dynamics, such as a bidirectional positive feedback loop pathophysiology. Method and Results Recent evidence shows that SARS-CoV-2 is capable of affecting the genetics and dynamics of erythrocytes and this coexists with a non-homeostatic function of cardiovascular, respiratory and renal systems during COVID-19. In hypothesis, SARS-CoV-2-induced systematical alterations of erythrocytes dynamics would constitute a setpoint for COVID-19-related multiple organ failure syndrome and death. Conclusion The present review covers the most frequent erythrocyte-related non-homeostatic findings during COVID-19 capable of providing mechanistic clues of SARS-CoV-2-induced infection and inspiring therapeutic-oriented scientific evidence.
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Affiliation(s)
| | - Kellen Rosa da Cruz
- Instituto de Ciências Biológicas da Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | | | | | - Patricia Maria Ferreira
- Instituto de Ciências Biológicas da Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Marcos Luiz Ferreira-Neto
- Instituto de Ciências Biomédicas da Universidade Federal de Uberlândia (ICBIM UFU), Uberlândia, MG, Brazil
| | | | | | | | - James O Fajemiroye
- Instituto de Ciências Biológicas da Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Carlos Henrique Xavier
- Instituto de Ciências Biológicas da Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil.
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Bugatti A, Filippini F, Bardelli M, Zani A, Chiodelli P, Messali S, Caruso A, Caccuri F. SARS-CoV-2 Infects Human ACE2-Negative Endothelial Cells through an αvβ3 Integrin-Mediated Endocytosis Even in the Presence of Vaccine-Elicited Neutralizing Antibodies. Viruses 2022; 14:v14040705. [PMID: 35458435 PMCID: PMC9032829 DOI: 10.3390/v14040705] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Integrins represent a gateway of entry for many viruses and the Arg-Gly-Asp (RGD) motif is the smallest sequence necessary for proteins to bind integrins. All Severe Acute Respiratory Syndrome Virus type 2 (SARS-CoV-2) lineages own an RGD motif (aa 403–405) in their receptor binding domain (RBD). We recently showed that SARS-CoV-2 gains access into primary human lung microvascular endothelial cells (HL-mECs) lacking Angiotensin-converting enzyme 2 (ACE2) expression through this conserved RGD motif. Following its entry, SARS-CoV-2 remodels cell phenotype and promotes angiogenesis in the absence of productive viral replication. Here, we highlight the αvβ3 integrin as the main molecule responsible for SARS-CoV-2 infection of HL-mECs via a clathrin-dependent endocytosis. Indeed, pretreatment of virus with αvβ3 integrin or pretreatment of cells with a monoclonal antibody against αvβ3 integrin was found to inhibit SARS-CoV-2 entry into HL-mECs. Surprisingly, the anti-Spike antibodies evoked by vaccination were neither able to impair Spike/integrin interaction nor to prevent SARS-CoV-2 entry into HL-mECs. Our data highlight the RGD motif in the Spike protein as a functional constraint aimed to maintain the interaction of the viral envelope with integrins. At the same time, our evidences call for the need of intervention strategies aimed to neutralize the SARS-CoV-2 integrin-mediated infection of ACE2-negative cells in the vaccine era.
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Affiliation(s)
- Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Federica Filippini
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Marta Bardelli
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Paola Chiodelli
- Section of General Pathology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.F.); (M.B.); (A.Z.); (S.M.); (A.C.)
- Correspondence:
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46
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Nocentini A, Capasso C, Supuran CT. Perspectives on the design and discovery of α-ketoamide inhibitors for the treatment of novel coronavirus: where do we stand and where do we go? Expert Opin Drug Discov 2022; 17:547-557. [DOI: 10.1080/17460441.2022.2052847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
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47
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Ashhurst A, Tang AH, Fajtová P, Yoon MC, Aggarwal A, Bedding MJ, Stoye A, Beretta L, Pwee D, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CT, Larance M, Turville S, Gerwick WH, O’Donoghue AJ, Payne RJ. Potent Anti-SARS-CoV-2 Activity by the Natural Product Gallinamide A and Analogues via Inhibition of Cathepsin L. J Med Chem 2022; 65:2956-2970. [PMID: 34730959 PMCID: PMC8577376 DOI: 10.1021/acs.jmedchem.1c01494] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 12/15/2022]
Abstract
Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is a promising drug target for novel antivirals against SARS-CoV-2. The marine natural product gallinamide A and several synthetic analogues were identified as potent inhibitors of cathepsin L with IC50 values in the picomolar range. Lead molecules possessed selectivity over other cathepsins and alternative host proteases involved in viral entry. Gallinamide A directly interacted with cathepsin L in cells and, together with two lead analogues, potently inhibited SARS-CoV-2 infection in vitro, with EC50 values in the nanomolar range. Reduced antiviral activity was observed in cells overexpressing transmembrane protease, serine 2 (TMPRSS2); however, a synergistic improvement in antiviral activity was achieved when combined with a TMPRSS2 inhibitor. These data highlight the potential of cathepsin L as a COVID-19 drug target as well as the likely need to inhibit multiple routes of viral entry to achieve efficacy.
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Affiliation(s)
- Anneliese
S. Ashhurst
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- School
of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW2006, Australia
| | - Arthur H. Tang
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Pavla Fajtová
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Institute
of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, 16610Prague, Czech Republic
| | - Michael C. Yoon
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Anupriya Aggarwal
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - Max J. Bedding
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Alexander Stoye
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
| | - Laura Beretta
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Dustin Pwee
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Aleksandra Drelich
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Danielle Skinner
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Linfeng Li
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - Thomas D. Meek
- Department
of Biochemistry and Biophysics, Texas A&M
University, 301 Old Main
Drive, College Station, Texas77843, United States
| | - James H. McKerrow
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Chien-Te Tseng
- Department
of Microbiology and Immunology, University
of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas77755-1001, United States
| | - Mark Larance
- Charles
Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Stuart Turville
- Kirby
Institute, University of New South Wales, Sydney, NSW2052, Australia
| | - William H. Gerwick
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California92093, United States
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, NSW2006, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, The University of Sydney, Sydney, NSW2006, Australia
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48
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Cao W, Cho CCD, Geng ZZ, Shaabani N, Ma XR, Vatansever EC, Alugubelli YR, Ma Y, Chaki SP, Ellenburg WH, Yang KS, Qiao Y, Allen R, Neuman BW, Ji H, Xu S, Liu WR. Evaluation of SARS-CoV-2 Main Protease Inhibitors Using a Novel Cell-Based Assay. ACS CENTRAL SCIENCE 2022; 8:192-204. [PMID: 35229034 PMCID: PMC8848508 DOI: 10.1021/acscentsci.1c00910] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 05/22/2023]
Abstract
As an essential enzyme of SARS-CoV-2, main protease (MPro) triggers acute toxicity to its human cell host, an effect that can be alleviated by an MPro inhibitor. Using this toxicity alleviation, we developed an effective method that allows a bulk analysis of the cellular potency of MPro inhibitors. This novel assay is advantageous over an antiviral assay in providing precise cellular MPro inhibition information to assess an MPro inhibitor. We used this assay to analyze 30 known MPro inhibitors. Contrary to their strong antiviral effects and up to 10 μM, 11a, calpain inhibitor II, calpain XII, ebselen, bepridil, chloroquine, and hydroxychloroquine showed relatively weak to undetectable cellular MPro inhibition potency implicating their roles in interfering with key steps other than just the MPro catalysis in the SARS-CoV-2 life cycle. Our results also revealed that MPI5, MPI6, MPI7, and MPI8 have high cellular and antiviral potency. As the one with the highest cellular and antiviral potency among all tested compounds, MPI8 has a remarkable cellular MPro inhibition IC50 value of 31 nM that matches closely to its strong antiviral effect with an EC50 value of 30 nM. Therefore, we cautiously suggest exploring MPI8 further for COVID-19 preclinical tests.
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Affiliation(s)
- Wenyue Cao
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Chia-Chuan Dean Cho
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zhi Zachary Geng
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Namir Shaabani
- Sorrento
Therapeutics, Inc., San Diego, California 92121, United States
| | - Xinyu R. Ma
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Erol C. Vatansever
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yugendar R. Alugubelli
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yuying Ma
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Sankar P. Chaki
- Global
Health Research Complex, Division of Research, Texas A&M University, College Station, Texas 77843, United States
| | - William H. Ellenburg
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kai S. Yang
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yuchen Qiao
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Robert Allen
- Sorrento
Therapeutics, Inc., San Diego, California 92121, United States
| | - Benjamin W. Neuman
- Department
of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Henry Ji
- Sorrento
Therapeutics, Inc., San Diego, California 92121, United States
- E-mail:
| | - Shiqing Xu
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- E-mail:
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, Texas 77843, United States
- E-mail:
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49
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Puerta-Guardo H. Editorial: From Pathogenic Infections to Inflammation and Disease - the Tumultuous Road of the 'Cytokine Storm'. Front Cell Infect Microbiol 2022; 11:827151. [PMID: 35083169 PMCID: PMC8785243 DOI: 10.3389/fcimb.2021.827151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Henry Puerta-Guardo
- Collaborative Unit for Entomological Bioassays, Campus of Biological Sciences and Agriculture, Autonomous University of Yucatan, Merida, Mexico.,Virology Laboratory, Center for Research "Dr. Hideyo Noguchi", Autonomous University of Yucatan, Merida, Mexico
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50
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Rasalkar AA, Bhatia S, Katte T, Narayanan P, Vinjamuri S, Shettihalli AK, Kabade S, Manas RN, Kadappa V, Reddy DNS. COVID-19 and its impact on cancer, HIV, and mentally ill patients. LESSONS FROM COVID-19 2022. [PMCID: PMC9347297 DOI: 10.1016/b978-0-323-99878-9.00006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) and its disease, COVID-19 is a global pandemic creating an unprecedented medical as well economic havoc across the world. Despite the wide spread global infection rates, the death rate is low for COVID-19. However, COVID-19 patients with other comorbid conditions face severe health complications irrespective of their gender or age. As the management of COVID-19 patients is taking up health resources, it is getting difficult to treat patients suffering from other dreadful diseases like cancer, HIV, and mental health issues. In this chapter, we discuss the effects of COVID-19 and management of cancer patients of main cancer subtypes (e.g., breast, lung, blood cancers), and patients affected with HIV and mental health issues. Finally, we also add a perspective on Ayurvedic treatment and its efficacy on COVID-19 patients.
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