1
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Yu F, Liu X, Ou H, Li X, Liu R, Lv X, Xiao S, Hu M, Liang T, Chen T, Wei X, Zhang Z, Liu S, Liu H, Zhu Y, Liu G, Tu T, Li P, Zhang H, Pan T, Ma X. The histamine receptor H1 acts as an alternative receptor for SARS-CoV-2. mBio 2024:e0108824. [PMID: 38953634 DOI: 10.1128/mbio.01088-24] [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: 04/09/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
Numerous host factors, in addition to human angiotensin-converting enzyme 2 (hACE2), have been identified as coreceptors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), demonstrating broad viral tropism and diversified druggable potential. We and others have found that antihistamine drugs, particularly histamine receptor H1 (HRH1) antagonists, potently inhibit SARS-CoV-2 infection. In this study, we provided compelling evidence that HRH1 acts as an alternative receptor for SARS-CoV-2 by directly binding to the viral spike protein. HRH1 also synergistically enhanced hACE2-dependent viral entry by interacting with hACE2. Antihistamine drugs effectively prevent viral infection by competitively binding to HRH1, thereby disrupting the interaction between the spike protein and its receptor. Multiple inhibition assays revealed that antihistamine drugs broadly inhibited the infection of various SARS-CoV-2 mutants with an average IC50 of 2.4 µM. The prophylactic function of these drugs was further confirmed by authentic SARS-CoV-2 infection assays and humanized mouse challenge experiments, demonstrating the therapeutic potential of antihistamine drugs for combating coronavirus disease 19.IMPORTANCEIn addition to human angiotensin-converting enzyme 2, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can utilize alternative cofactors to facilitate viral entry. In this study, we discovered that histamine receptor H1 (HRH1) not only functions as an independent receptor for SARS-CoV-2 but also synergistically enhances ACE2-dependent viral entry by directly interacting with ACE2. Further studies have demonstrated that HRH1 facilitates the entry of SARS-CoV-2 by directly binding to the N-terminal domain of the spike protein. Conversely, antihistamine drugs, primarily HRH1 antagonists, can competitively bind to HRH1 and thereby prevent viral entry. These findings revealed that the administration of repurposable antihistamine drugs could be a therapeutic intervention to combat coronavirus disease 19.
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Affiliation(s)
- Fei Yu
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqing Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hailan Ou
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xinyu Li
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Ruxin Liu
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xi Lv
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shiqi Xiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Meilin Hu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- Department of Breast Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Taizhen Liang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuepeng Wei
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Zhenglai Zhang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Sen Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Han Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Yiqiang Zhu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Guangyan Liu
- Department of Pathogen Biology, Shenyang Medical College, Shenyang, Liaoning, China
| | - Tianyong Tu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Peiwen Li
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Pan
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiancai Ma
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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2
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Abla N, Almond LM, Bonner JJ, Richardson N, Wells TNC, Möhrle JJ. PBPK-led assessment of antimalarial drugs as candidates for Covid-19: Simulating concentrations at the site of action to inform repurposing strategies. Clin Transl Sci 2024; 17:e13865. [PMID: 39020517 PMCID: PMC11254780 DOI: 10.1111/cts.13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 07/19/2024] Open
Abstract
The urgent need for safe, efficacious, and accessible drug treatments to treat coronavirus disease 2019 (COVID-19) prompted a global effort to evaluate drug repurposing opportunities. Pyronaridine and amodiaquine are both components of approved antimalarials with in vitro activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In vitro activity does not always translate to clinical efficacy across a therapeutic dose range. This study applied available, verified, physiologically based pharmacokinetic (PBPK) models for pyronaridine, amodiaquine, and its active metabolite N-desethylamodiaquine (DEAQ) to predict drug concentrations in lung tissue relative to plasma or blood in the default healthy virtual population. Lung exposures were compared to published data across the reported range of in vitro EC50 values against SARS-CoV-2. In the multicompartment permeability-limited PBPK model, the predicted total Cmax in lung mass for pyronaridine was 34.2 μM on Day 3, 30.5-fold greater than in blood (1.12 μM) and for amodiaquine was 0.530 μM, 8.83-fold greater than in plasma (0.060 μM). In the perfusion-limited PBPK model, the DEAQ predicted total Cmax on Day 3 in lung mass (30.2 μM) was 21.4-fold greater than for plasma (1.41 μM). Based on the available in vitro data, predicted drug concentrations in lung tissue for pyronaridine and DEAQ, but not amodiaquine, appeared sufficient to inhibit SARS-CoV-2 replication. Simulations indicated standard dosing regimens of pyronaridine-artesunate and artesunate-amodiaquine have potential to treat COVID-19. These findings informed repurposing strategies to select the most relevant compounds for clinical investigation in COVID-19. Clinical data for model verification may become available from ongoing clinical studies.
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Affiliation(s)
- Nada Abla
- MMV Medicines for Malaria VentureGenevaSwitzerland
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3
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Guarnieri JW, Haltom JA, Albrecht YES, Lie T, Olali AZ, Widjaja GA, Ranshing SS, Angelin A, Murdock D, Wallace DC. SARS-CoV-2 mitochondrial metabolic and epigenomic reprogramming in COVID-19. Pharmacol Res 2024; 204:107170. [PMID: 38614374 DOI: 10.1016/j.phrs.2024.107170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
To determine the effects of SARS-CoV-2 infection on cellular metabolism, we conducted an exhaustive survey of the cellular metabolic pathways modulated by SARS-CoV-2 infection and confirmed their importance for SARS-CoV-2 propagation by cataloging the effects of specific pathway inhibitors. This revealed that SARS-CoV-2 strongly inhibits mitochondrial oxidative phosphorylation (OXPHOS) resulting in increased mitochondrial reactive oxygen species (mROS) production. The elevated mROS stabilizes HIF-1α which redirects carbon molecules from mitochondrial oxidation through glycolysis and the pentose phosphate pathway (PPP) to provide substrates for viral biogenesis. mROS also induces the release of mitochondrial DNA (mtDNA) which activates innate immunity. The restructuring of cellular energy metabolism is mediated in part by SARS-CoV-2 Orf8 and Orf10 whose expression restructures nuclear DNA (nDNA) and mtDNA OXPHOS gene expression. These viral proteins likely alter the epigenome, either by directly altering histone modifications or by modulating mitochondrial metabolite substrates of epigenome modification enzymes, potentially silencing OXPHOS gene expression and contributing to long-COVID.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeffrey A Haltom
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yentli E Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arnold Z Olali
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sujata S Ranshing
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Deborah Murdock
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Hernández-Mitre MP, Morpeth SC, Venkatesh B, Hills TE, Davis J, Mahar RK, McPhee G, Jones M, Totterdell J, Tong SYC, Roberts JA. TMPRSS2 inhibitors for the treatment of COVID-19 in adults: a systematic review and meta-analysis of randomized clinical trials of nafamostat and camostat mesylate. Clin Microbiol Infect 2024; 30:743-754. [PMID: 38331253 DOI: 10.1016/j.cmi.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Synthetic serine protease inhibitors block the cellular enzyme transmembrane protease serine 2, thus preventing SARS-CoV-2 cell entry. There are two relevant drugs in this class, namely, nafamostat (intravenous formulation) and camostat (oral formulation). OBJECTIVE To determine whether transmembrane protease serine 2 inhibition with nafamostat or camostat is associated with a reduced risk of 30-day all-cause mortality in adults with COVID-19. DATA SOURCES Scientific databases and clinical trial registry platforms. STUDY ELIGIBILITY CRITERIA, INTERVENTIONS, AND PARTICIPANTS Preprints or published randomized clinical trials (RCTs) of nafamostat or camostat vs. usual care or placebo in adults requiring treatment for COVID-19. METHODS OF DATA SYNTHESIS AND RISK-OF-BIAS ASSESSMENT The primary outcome of the meta-analysis was 30-day all-cause mortality. Secondary outcomes included time to recovery, adverse events, and serious adverse events. Risk of bias (RoB) was assessed using the revised Cochrane RoB 2 tool for individually randomized trials. Meta-analysis was conducted in the R package meta (v7.0-0) using inverse variance and random effects. Protocol registration number was INPLASY202320120. RESULTS Twelve RCTs were included. Overall, the number of available patients was small (nafamostat = 387; camostat = 1061), the number of enrolled patients meeting the primary outcome was low (nafamostat = 12; camostat = 13), and heterogeneity was high. In hospitalized adults, we did not identify differences in 30-day all-cause mortality (risk ratio [95% CI]: 0.58 [0.19, 1.80], p 0.34; I2 = 0%; n = 6) and time to recovery (mean difference [95% CI]: 0.08 days [-0.74, 0.89], p 0.86; n = 2) between nafamostat vs. usual care; and for 30-day all-cause mortality (risk ratio [95% CI]: 0.99 [0.31, 3.18], p 0.99; n = 2) between camostat vs. placebo. CONCLUSION The RCT evidence is inconclusive to determine whether there is a mortality reduction and safety with either nafamostat or camostat for the treatment of adults with COVID-19. There were high RoB, small sample size, and high heterogeneity between RCTs.
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Affiliation(s)
| | - Susan C Morpeth
- Departments of Microbiology and Infectious Diseases, Middlemore Hospital, Te Whatu Ora Counties Manukau, New Zealand; Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Balasubramanian Venkatesh
- Intensive Care, Princess Alexandra Hospital, The University of Queensland, Brisbane, Queensland, Australia; Intensive Care, Wesley Hospital, Brisbane, Queensland, Australia; The George Institute for Global Health, UNSW Sydney, New South Wales, Australia
| | - Thomas E Hills
- Departments of Immunology and Infectious Diseases, Auckland District Health Board, Auckland, New Zealand; Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Joshua Davis
- Infection Research Program, Hunter Medical Research Institute, Univerity of Newcastle, Newcastle, New South Wales, Australia
| | - Robert K Mahar
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Grace McPhee
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark Jones
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - James Totterdell
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jason A Roberts
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Queensland, Australia; Departments of Intensive Care Medicine and Pharmacy, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France; Herston Infectious Diseases Institute (HeIDI), Metro North Health, Herston, Queensland, Australia.
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5
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Lui WY, Ong CP, Cheung PHH, Ye ZW, Chan CP, To KKW, Yuen KS, Jin DY. Nsp1 facilitates SARS-CoV-2 replication through calcineurin-NFAT signaling. mBio 2024; 15:e0039224. [PMID: 38411085 PMCID: PMC11005343 DOI: 10.1128/mbio.00392-24] [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: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, has been intensely studied in search of effective antiviral treatments. The immunosuppressant cyclosporine A (CsA) has been suggested to be a pan-coronavirus inhibitor, yet its underlying mechanism remained largely unknown. Here, we found that non-structural protein 1 (Nsp1) of SARS-CoV-2 usurped CsA-suppressed nuclear factor of activated T cells (NFAT) signaling to drive the expression of cellular DEAD-box helicase 5 (DDX5), which facilitates viral replication. Nsp1 interacted with calcineurin A (CnA) to displace the regulatory protein regulator of calcineurin 3 (RCAN3) of CnA for NFAT activation. The influence of NFAT activation on SARS-CoV-2 replication was also validated by using the Nsp1-deficient mutant virus. Calcineurin inhibitors, such as CsA and VIVIT, inhibited SARS-CoV-2 replication and exhibited synergistic antiviral effects when used in combination with nirmatrelvir. Our study delineated the molecular mechanism of CsA-mediated inhibition of SARS-CoV-2 replication and the anti-SARS-CoV-2 action of calcineurin inhibitors. IMPORTANCE Cyclosporine A (CsA), commonly used to inhibit immune responses, is also known to have anti-SARS-CoV-2 activity, but its mode of action remains elusive. Here, we provide a model to explain how CsA antagonizes SARS-CoV-2 through three critical proteins: DDX5, NFAT1, and Nsp1. DDX5 is a cellular facilitator of SARS-CoV-2 replication, and NFAT1 controls the production of DDX5. Nsp1 is a viral protein absent from the mature viral particle and capable of activating the function of NFAT1 and DDX5. CsA and similar agents suppress Nsp1, NFAT1, and DDX5 to exert their anti-SARS-CoV-2 activity either alone or in combination with Paxlovid.
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Affiliation(s)
- Wai-Yin Lui
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chon Phin Ong
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | | | - Zi-Wei Ye
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kelvin Kai-Wang To
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- School of Nursing, Tung Wah College, Kowloon, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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6
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Zhang J, Kennedy A, de Melo Jorge DM, Xing L, Reid W, Bui S, Joppich J, Rose M, Ercan S, Tang Q, Tai AW, Wang Y. SARS-CoV-2 remodels the Golgi apparatus to facilitate viral assembly and secretion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.03.04.483074. [PMID: 35291301 PMCID: PMC8923104 DOI: 10.1101/2022.03.04.483074] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2, an enveloped RNA virus. Despite extensive investigation, the molecular mechanisms for its assembly and secretion remain largely elusive. Here, we show that SARS-CoV-2 infection induces global alterations of the host endomembrane system, including dramatic Golgi fragmentation. SARS-CoV-2 virions are enriched in the fragmented Golgi. Disrupting Golgi function with small molecules strongly inhibits viral infection. Significantly, SARS-CoV-2 infection down-regulates GRASP55 but up-regulates TGN46 protein levels. Surprisingly, GRASP55 expression reduces both viral secretion and spike number on each virion, while GRASP55 depletion displays opposite effects. In contrast, TGN46 depletion only inhibits viral secretion without affecting spike incorporation into virions. TGN46 depletion and GRASP55 expression additively inhibit viral secretion, indicating that they act at different stages. Taken together, we show that SARS-CoV-2 alters Golgi structure and function to control viral assembly and secretion, highlighting the Golgi as a potential therapeutic target for blocking SARS-CoV-2 infection.
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7
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González-Paz L, Lossada C, Hurtado-León ML, Vera-Villalobos J, Paz JL, Marrero-Ponce Y, Martinez-Rios F, Alvarado Y. Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data. ACS OMEGA 2024; 9:8923-8939. [PMID: 38434903 PMCID: PMC10905729 DOI: 10.1021/acsomega.3c06968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/20/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Recent reports have suggested that the susceptibility of cells to SARS-CoV-2 infection can be influenced by various proteins that potentially act as receptors for the virus. To investigate this further, we conducted simulations of viral dynamics using different cellular systems (Vero E6, HeLa, HEK293, and CaLu3) in the presence and absence of drugs (anthelmintic, ARBs, anticoagulant, serine protease inhibitor, antimalarials, and NSAID) that have been shown to impact cellular recognition by the spike protein based on experimental data. Our simulations revealed that the susceptibility of the simulated cell systems to SARS-CoV-2 infection was similar across all tested systems. Notably, CaLu3 cells exhibited the highest susceptibility to SARS-CoV-2 infection, potentially due to the presence of receptors other than ACE2, which may account for a significant portion of the observed susceptibility. Throughout the study, all tested compounds showed thermodynamically favorable and stable binding to the spike protein. Among the tested compounds, the anticoagulant nafamostat demonstrated the most favorable characteristics in terms of thermodynamics, kinetics, theoretical antiviral activity, and potential safety (toxicity) in relation to SARS-CoV-2 spike protein-mediated infections in the tested cell lines. This study provides mathematical and bioinformatic models that can aid in the identification of optimal cell lines for compound evaluation and detection, particularly in studies focused on repurposed drugs and their mechanisms of action. It is important to note that these observations should be experimentally validated, and this research is expected to inspire future quantitative experiments.
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Affiliation(s)
- Lenin González-Paz
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC). Departamento de Biología. Laboratorio
de Genética y Biología Molecular (LGBM),Universidad del Zulia (LUZ),Maracaibo 4001, República Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad
de Ciencias Naturales y Matemáticas, Departamento de Química
y Ciencias Ambientales, Laboratorio de Análisis Químico
Instrumental (LAQUINS), Escuela Superior
Politécnica del Litoral, Guayaquil EC090112, Ecuador
| | - José L. Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos. Cercado de Lima, Lima 15081, Perú
| | - Yovani Marrero-Ponce
- Grupo
de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias
de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades
Médicas; e Instituto de Simulación Computacional (ISC-USFQ),
Diego de Robles y vía Interoceánica, Universidad San Francisco de Quito (USFQ), Quito, Pichincha 170157, Ecuador
| | - Felix Martinez-Rios
- Universidad
Panamericana. Facultad de Ingeniería. Augusto Rodin 498, Ciudad de México 03920, México
| | - Ysaías.
J. Alvarado
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE),Instituto
Venezolano de Investigaciones Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana
de Venezuela
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8
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Kim SK, Suebka S, Gin A, Nguyen PD, Tang Y, Su J, Goddard WA. Methotrexate Inhibits the Binding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor Binding Domain to the Host-Cell Angiotensin-Converting Enzyme-2 (ACE-2) Receptor. ACS Pharmacol Transl Sci 2024; 7:348-362. [PMID: 38357278 PMCID: PMC10863433 DOI: 10.1021/acsptsci.3c00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 02/16/2024]
Abstract
As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus mutates, finding effective drugs becomes more challenging. In this study, we use ultrasensitive frequency locked microtoroid optical resonators in combination with in silico screening to search for COVID-19 drugs that can stop the virus from attaching to the human angiotensin-converting enzyme 2 (hACE2) receptor in the lungs. We found 29 promising candidates that could block the binding site and selected four of them that were likely to bind very strongly. We tested three of these candidates using frequency locked optical whispering evanescent resonator (FLOWER), a label-free sensing method based on microtoroid resonators. FLOWER has previously been used for sensing single macromolecules. Here we show, for the first time, that FLOWER can provide accurate binding affinities and sense the inhibition effect of small molecule drug candidates without labels, which can be prohibitive in drug discovery. One of the candidates, methotrexate, showed binding to the spike protein 1.8 million times greater than that to the receptor binding domain (RBD) binding to hACE2, making it difficult for the virus to enter cells. We tested methotrexate against different variants of the SARS-CoV-2 virus and found that it is effective against all four of the tested variants. People taking methotrexate for other conditions have also shown protection against the original SARS-CoV-2 virus. Normally, it is assumed that methotrexate inhibits the replication and release of the virus. However, our findings suggest that it may also block the virus from entering cells. These studies additionally demonstrate the possibility of extracting candidate ligands from large databases, followed by direct receptor-ligand binding experiments on the best candidates using microtoroid resonators, thus creating a workflow that enables the rapid discovery of new drug candidates for a variety of applications.
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Affiliation(s)
- Soo-Kyung Kim
- Materials
and Process Simulation Center, California
Institute of Technology, Pasadena, California 91125, United States
| | - Sartanee Suebka
- Wyant
College of Optical Sciences, The University
of Arizona, Tucson, Arizona 85721, United States
| | - Adley Gin
- Wyant
College of Optical Sciences, The University
of Arizona, Tucson, Arizona 85721, United States
- Department
of Biomedical Engineering, The University
of Arizona, Tucson, Arizona 85721, United States
| | - Phuong-Diem Nguyen
- Department
of Biomedical Engineering, The University
of Arizona, Tucson, Arizona 85721, United States
| | - Yisha Tang
- Department
of Biomedical Engineering, The University
of Arizona, Tucson, Arizona 85721, United States
| | - Judith Su
- Wyant
College of Optical Sciences, The University
of Arizona, Tucson, Arizona 85721, United States
| | - William A. Goddard
- Materials
and Process Simulation Center, California
Institute of Technology, Pasadena, California 91125, United States
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9
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Bond ACS, Crocker MA, Wilczek MP, DuShane JK, Sandberg AL, Bennett LJ, Leclerc NR, Maginnis MS. High-throughput drug screen identifies calcium and calmodulin inhibitors that reduce JCPyV infection. Antiviral Res 2024; 222:105817. [PMID: 38246207 PMCID: PMC10922812 DOI: 10.1016/j.antiviral.2024.105817] [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: 11/18/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
JC polyomavirus (JCPyV) is a nonenveloped, double-stranded DNA virus that infects the majority of the population. Immunocompetent individuals harbor infection in their kidneys, while severe immunosuppression can result in JCPyV spread to the brain, causing the neurodegenerative disease progressive multifocal leukoencephalopathy (PML). Due to a lack of approved therapies to treat JCPyV and PML, the disease results in rapid deterioration, and is often fatal. In order to identify potential antiviral treatments for JCPyV, a high-throughput, large-scale drug screen was performed using the National Institutes of Health Clinical Collection (NCC). Drugs from the NCC were tested for inhibitory effects on JCPyV infection, and drugs from various classes that reduced JCPyV infection were identified, including receptor agonists and antagonists, calcium signaling modulators, and enzyme inhibitors. Given the role of calcium signaling in viral infection including Merkel cell polyomavirus and simian virus 40 polyomavirus (SV40), calcium signaling inhibitors were further explored for the capacity to impact JCPyV infection. Calcium and calmodulin inhibitors trifluoperazine (TFP), W-7, tetrandrine, and nifedipine reduced JCPyV infection, and TFP specifically reduced viral internalization. Additionally, TFP and W-7 reduced infection by BK polyomavirus, SV40, and SARS-CoV-2. These results highlight specific inhibitors, some FDA-approved, for the possible treatment and prevention of JCPyV and several other viruses, and further illuminate the calcium and calmodulin pathway as a potential target for antiviral drug development.
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Affiliation(s)
- Avery C S Bond
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Mason A Crocker
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Michael P Wilczek
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Jeanne K DuShane
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Amanda L Sandberg
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Lucas J Bennett
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Nicholas R Leclerc
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA
| | - Melissa S Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, 04469, USA; Graduate School of Biomedical Science and Engineering, Orono, ME, 04469, USA.
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10
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Doijen J, Heo I, Temmerman K, Vermeulen P, Diels A, Jaensch S, Burcin M, Van den Broeck N, Raeymaekers V, Peremans J, Konings K, Clement M, Peeters D, Van Loock M, Koul A, Buyck C, Van Gool M, Van Damme E. A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects. Antiviral Res 2024; 222:105789. [PMID: 38158129 DOI: 10.1016/j.antiviral.2023.105789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.
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Affiliation(s)
- Jordi Doijen
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Inha Heo
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Koen Temmerman
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Peter Vermeulen
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Annick Diels
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Steffen Jaensch
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Mark Burcin
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | - Joren Peremans
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Katrien Konings
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Maxime Clement
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Danielle Peeters
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Marnix Van Loock
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Anil Koul
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Christophe Buyck
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michiel Van Gool
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ellen Van Damme
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
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11
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Feijoo-Coronel ML, Mendes B, Ramírez D, Peña-Varas C, de los Monteros-Silva NQE, Proaño-Bolaños C, de Oliveira LC, Lívio DF, da Silva JA, da Silva JMSF, Pereira MGAG, Rodrigues MQRB, Teixeira MM, Granjeiro PA, Patel K, Vaiyapuri S, Almeida JR. Antibacterial and Antiviral Properties of Chenopodin-Derived Synthetic Peptides. Antibiotics (Basel) 2024; 13:78. [PMID: 38247637 PMCID: PMC10812719 DOI: 10.3390/antibiotics13010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Antimicrobial peptides have been developed based on plant-derived molecular scaffolds for the treatment of infectious diseases. Chenopodin is an abundant seed storage protein in quinoa, an Andean plant with high nutritional and therapeutic properties. Here, we used computer- and physicochemical-based strategies and designed four peptides derived from the primary structure of Chenopodin. Two peptides reproduce natural fragments of 14 amino acids from Chenopodin, named Chen1 and Chen2, and two engineered peptides of the same length were designed based on the Chen1 sequence. The two amino acids of Chen1 containing amide side chains were replaced by arginine (ChenR) or tryptophan (ChenW) to generate engineered cationic and hydrophobic peptides. The evaluation of these 14-mer peptides on Staphylococcus aureus and Escherichia coli showed that Chen1 does not have antibacterial activity up to 512 µM against these strains, while other peptides exhibited antibacterial effects at lower concentrations. The chemical substitutions of glutamine and asparagine by amino acids with cationic or aromatic side chains significantly favoured their antibacterial effects. These peptides did not show significant hemolytic activity. The fluorescence microscopy analysis highlighted the membranolytic nature of Chenopodin-derived peptides. Using molecular dynamic simulations, we found that a pore is formed when multiple peptides are assembled in the membrane. Whereas, some of them form secondary structures when interacting with the membrane, allowing water translocations during the simulations. Finally, Chen2 and ChenR significantly reduced SARS-CoV-2 infection. These findings demonstrate that Chenopodin is a highly useful template for the design, engineering, and manufacturing of non-toxic, antibacterial, and antiviral peptides.
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Affiliation(s)
- Marcia L. Feijoo-Coronel
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Bruno Mendes
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Carlos Peña-Varas
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | | | - Carolina Proaño-Bolaños
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Leonardo Camilo de Oliveira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Diego Fernandes Lívio
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Antônio da Silva
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Maurício S. F. da Silva
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marília Gabriella A. G. Pereira
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marina Q. R. B. Rodrigues
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
- Departamento de Engenharia de Biossistemas, Campus Dom Bosco, Federal University of São João Del-Rei, Praça Dom Helvécio, 74, Fábricas, São João del-Rei 36301-160, Brazil
| | - Mauro M. Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Paulo Afonso Granjeiro
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - Ketan Patel
- School of Biological Sciences, University of Reading, Reading RG6 6UB, UK
| | | | - José R. Almeida
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
- School of Pharmacy, University of Reading, Reading RG6 6UB, UK
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12
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Baker J, Ombredane H, Daly L, Knowles I, Rapeport G, Ito K. Pan-antiviral effects of a PIKfyve inhibitor on respiratory virus infection in human nasal epithelium and mice. Antimicrob Agents Chemother 2024; 68:e0105023. [PMID: 38063402 PMCID: PMC10777833 DOI: 10.1128/aac.01050-23] [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: 08/11/2023] [Accepted: 11/06/2023] [Indexed: 01/11/2024] Open
Abstract
Endocytosis, or internalization through endosomes, is a major cell entry mechanism used by respiratory viruses. Phosphoinositide 5-kinase (PIKfyve) is a critical enzyme for the synthesis of phosphatidylinositol (3, 5)biphosphate (PtdIns (3, 5)P2) and has been implicated in virus trafficking via the endocytic pathway. In fact, antiviral effects of PIKfyve inhibitors against SARS-CoV-2 and Ebola have been reported, but there is little evidence regarding other respiratory viruses. In this study, we demonstrated the antiviral effects of PIKfyve inhibitors on influenza virus and respiratory syncytial virus in vitro and in vivo. PIKfyve inhibitors Apilimod mesylate (AM) and YM201636 concentration-dependently inhibited several influenza strains in an MDCK cell-cytopathic assay. AM also reduced the viral load and cytokine release, while improving the cell integrity of human nasal air-liquid interface cultured epithelium infected with influenza PR8. In PR8-infected mice, AM (2 mg/mL), when intranasally treated, exhibited a significant reduction of viral load and inflammation and inhibited weight loss caused by influenza infection, with effects being similar to oral oseltamivir (10 mg/kg). In addition, AM demonstrated antiviral effects in RSV A2-infected human nasal epithelium in vitro and mouse in vivo, with an equivalent effect to that of ribavirin. AM also showed antiviral effects against human rhinovirus and seasonal coronavirus in vitro. Thus, PIKfyve is found to be involved in influenza and RSV infection, and PIKfyve inhibitor is a promising molecule for a pan-viral approach against respiratory viruses.
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Affiliation(s)
- Jonathan Baker
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Hugo Ombredane
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Leah Daly
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | | | - Garth Rapeport
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Kazuhiro Ito
- National Heart and Lung Institute, Imperial College, London, United Kingdom
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13
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Razzaq A, Disoma C, Zhou Y, Tao S, Chen Z, Liu S, Zheng R, Zhang Y, Liao Y, Chen X, Liu S, Dong Z, Xu L, Deng X, Li S, Xia Z. Targeting epidermal growth factor receptor signalling pathway: A promising therapeutic option for COVID-19. Rev Med Virol 2024; 34:e2500. [PMID: 38126937 DOI: 10.1002/rmv.2500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/20/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously producing new variants, necessitating effective therapeutics. Patients are not only confronted by the immediate symptoms of infection but also by the long-term health issues linked to long COVID-19. Activation of epidermal growth factor receptor (EGFR) signalling during SARS-CoV-2 infection promotes virus propagation, mucus hyperproduction, and pulmonary fibrosis, and suppresses the host's antiviral response. Over the long term, EGFR activation in COVID-19, particularly in COVID-19-induced pulmonary fibrosis, may be linked to the development of lung cancer. In this review, we have summarised the significance of EGFR signalling in the context of SARS-CoV-2 infection. We also discussed the targeting of EGFR signalling as a promising strategy for COVID-19 treatment and highlighted erlotinib as a superior option among EGFR inhibitors. Erlotinib effectively blocks EGFR and AAK1, thereby preventing SARS-CoV-2 replication, reducing mucus hyperproduction, TNF-α expression, and enhancing the host's antiviral response. Nevertheless, to evaluate the antiviral efficacy of erlotinib, relevant clinical trials involving an appropriate patient population should be designed.
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Affiliation(s)
- Aroona Razzaq
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Cyrollah Disoma
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Department of Biology, College of Natural Sciences and Mathematics, Mindanao State University, Marawi City, Philippines
| | - Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Siyi Tao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Sixu Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Rong Zheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yongxing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yujie Liao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Xuan Chen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Sijie Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Zijun Dong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liangtao Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Science, Central South University, Changsha, China
| | - Shanni Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Centre for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
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14
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Bess A, Berglind F, Mukhopadhyay S, Brylinski M, Alvin C, Fattah F, Wasan KM. Identification of oral therapeutics using an AI platform against the virus responsible for COVID-19, SARS-CoV-2. Front Pharmacol 2023; 14:1297924. [PMID: 38186640 PMCID: PMC10770831 DOI: 10.3389/fphar.2023.1297924] [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: 09/29/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose: This study introduces a sophisticated computational pipeline, eVir, designed for the discovery of antiviral drugs based on their interactions within the human protein network. There is a pressing need for cost-effective therapeutics for infectious diseases (e.g., COVID-19), particularly in resource-limited countries. Therefore, our team devised an Artificial Intelligence (AI) system to explore repurposing opportunities for currently used oral therapies. The eVir system operates by identifying pharmaceutical compounds that mirror the effects of antiviral peptides (AVPs)-fragments of human proteins known to interfere with fundamental phases of the viral life cycle: entry, fusion, and replication. eVir extrapolates the probable antiviral efficacy of a given compound by analyzing its established and predicted impacts on the human protein-protein interaction network. This innovative approach provides a promising platform for drug repurposing against SARS-CoV-2 or any virus for which peptide data is available. Methods: The eVir AI software pipeline processes drug-protein and protein-protein interaction networks generated from open-source datasets. eVir uses Node2Vec, a graph embedding technique, to understand the nuanced connections among drugs and proteins. The embeddings are input a Siamese Network (SNet) and MLPs, each tailored for the specific mechanisms of entry, fusion, and replication, to evaluate the similarity between drugs and AVPs. Scores generated from the SNet and MLPs undergo a Platt probability calibration and are combined into a unified score that gauges the potential antiviral efficacy of a drug. This integrated approach seeks to boost drug identification confidence, offering a potential solution for detecting therapeutic candidates with pronounced antiviral potency. Once identified a number of compounds were tested for efficacy and toxicity in lung carcinoma cells (Calu-3) infected with SARS-CoV-2. A lead compound was further identified to determine its efficacy and toxicity in K18-hACE2 mice infected with SARS-CoV-2. Computational Predictions: The SNet confidently differentiated between similar and dissimilar drug pairs with an accuracy of 97.28% and AUC of 99.47%. Key compounds identified through these networks included Zinc, Mebendazole, Levomenol, Gefitinib, Niclosamide, and Imatinib. Notably, Mebendazole and Zinc showcased the highest similarity scores, while Imatinib, Levemenol, and Gefitinib also ranked within the top 20, suggesting their significant pharmacological potentials. Further examination of protein binding analysis using explainable AI focused on reverse engineering the causality of the networks. Protein interaction scores for Mebendazole and Imatinib revealed their effects on notable proteins such as CDPK1, VEGF2, ABL1, and several tyrosine protein kinases. Laboratory Studies: This study determined that Mebendazole, Gefitinib, Topotecan and to some extent Carfilzomib showed conventional drug-response curves, with IC50 values near or below that of Remdesivir with excellent confidence all above R2>0.91, and no cytotoxicity at the IC50 concentration in Calu-3 cells. Cyclosporine A showed antiviral activity, but also unconventional drug-response curves and low R2 which are explained by the non-dose dependent toxicity of the compound. Additionally, Niclosamide demonstrated a conventional drug-response curve with high confidence; however, its inherent cytotoxicity may be a confounding element that misrepresents true antiviral efficacy, by reflecting cellular damage rather than a genuine antiviral action. Remdesivir was used as a control compound and was evaluated in parallel with the submitted test article and had conventional drug-response curves validating the overall results of the assay. Mebendazole was identified from the cell studies to have efficacy at non-toxic concentrations and were further evaluated in mice infected with SARS-CoV-2. Mebendazole administered to K18-hACE2 mice infected with SARS-CoV-2, resulted in a 44.2% reduction in lung viral load compared to non-treated placebo control respectively. There were no significant differences in body weight and all clinical chemistry determinations evaluated (i.e., kidney and liver enzymes) between the different treatment groups. Conclusion: This research underscores the potential of repurposing existing compounds for treating COVID-19. Our preliminary findings underscore the therapeutic promise of several compounds, notably Mebendazole, in both in vitro and in vivo settings against SARS-CoV-2. Several of the drugs explored, especially Mebendazole, are off-label medication; their cost-effectiveness position them as economical therapies against SARS-CoV-2.
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Affiliation(s)
- Adam Bess
- Department of Computer Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Frej Berglind
- Department of Computer Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Supratik Mukhopadhyay
- Department of Environmental Sciences, Center for Computation & Technology, Coastal Studies Institute, Louisiana State University, Baton Rouge, LA, United States
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Chris Alvin
- Department of Computer Science, Furman University, Greenville, SC, United States
| | - Fanan Fattah
- Department of Urologic Sciences, Faculty of Medicine and the Neglected Global Diseases Initiative, University of British Columbia, Vancouver, BC, Canada
| | - Kishor M. Wasan
- Department of Urologic Sciences, Faculty of Medicine and the Neglected Global Diseases Initiative, University of British Columbia, Vancouver, BC, Canada
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15
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Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544327. [PMID: 37333151 PMCID: PMC10274905 DOI: 10.1101/2023.06.09.544327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
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Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
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16
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Arends EJ, Meziyerh S, Moes DJA, Kamerling SW, van der Kooy S, Ogando NS, Snijder EJ, van Hemert M, Visser LG, Feltkamp MC, Claas EC, Rabelink TJ, van Kooten C, de Vries AP, Teng YO. Voclosporin and the Antiviral Effect Against SARS-CoV-2 in Immunocompromised Kidney Patients. Kidney Int Rep 2023; 8:2654-2664. [PMID: 38106593 PMCID: PMC10719564 DOI: 10.1016/j.ekir.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Immunocompromised kidney patients are at increased risk of prolonged SARS-CoV-2 infection and related complications. Preclinical evidence demonstrates a more potent inhibitory effect of voclosporin on SARS-CoV-2 replication than tacrolimus in vitro. We investigated the potential antiviral effects of voclosporin on SARS-CoV-2 in immunocompromised patients. Methods First, we conducted a prospective, randomized, open-label, proof-of-concept study in 20 kidney transplant recipients (KTRs) on tacrolimus-based immunosuppression who contracted mild to moderate SARS-CoV-2 infection. Patients were randomized to continue tacrolimus or switch to voclosporin. Second, we performed a post hoc analysis on SARS-CoV-2 infections in 216 patients with lupus nephritis (LN) on standard immunosuppression who were randomly exposed to voclosporin or placebo as part of a clinical trial that was conducted during the worldwide COVID-19 pandemic. Results The primary end point was clearance of SARS-CoV-2 viral load and that did not differ between voclosporin-treated KTRs (median 12 days, interquartile range [IQR] 8-28) and tacrolimus-treated KTRs (median 12 days, IQR 4-16) nor was there a difference in clinical recovery. Pharmacokinetic analyses demonstrated that, when voclosporin trough levels were on-target, SARS-CoV-2 viral load dropped significantly more (ΔCt 7.7 [3.4-10.7]) compared to tacrolimus-treated KTRs (ΔCt 2.7 [2.0-4.3]; P = 0.035). In voclosporin-exposed patients with LN, SARS-CoV-2 infection was detected in 6% (7/116) compared to 12% (12/100) in placebo-exposed patients (relative risk [RR] 1.4 [0.97-2.06]). Notably, no voclosporin-exposed patients with LN died from severe SARS-CoV-2 infection compared to 3% (3/100) in placebo-exposed patients (RR 2.2 [1.90-2.54]). Conclusion This proof-of-concept study shows a potential positive risk-benefit profile for voclosporin in immunocompromised patients with SARS-CoV-2 infection. These results warrant further investigations on voclosporin to establish an equipoise between infection and maintenance immunosuppression.
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Affiliation(s)
- Eline J. Arends
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Soufian Meziyerh
- Department of Internal Medicine section Nephrology, Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Dirk Jan A.R. Moes
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia W.A. Kamerling
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandra van der Kooy
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Natacha S. Ogando
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J. Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Leo G. Visser
- Department of Internal Medicine section Infectious diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Mariet C.W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C.J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ton J. Rabelink
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Cees van Kooten
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Aiko P.J. de Vries
- Department of Internal Medicine section Nephrology, Leiden Transplant Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Y.K. Onno Teng
- Department of Internal Medicine section Nephrology, Center of Expertise for Lupus-, Vasculitis and Complement- mediated Systemic Autoimmune Diseases, Leiden University Medical Center, Leiden, the Netherlands
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17
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Chen K, Wang F. Cell-specific genome-scale metabolic modeling of SARS-CoV-2-infected lung to identify antiviral enzymes. FEBS Open Bio 2023; 13:2172-2186. [PMID: 37734920 PMCID: PMC10699103 DOI: 10.1002/2211-5463.13710] [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: 06/21/2023] [Revised: 08/09/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023] Open
Abstract
Computational systems biology plays a key role in the discovery of suitable antiviral targets. We designed a cell-specific, constraint-based modeling technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected lungs. We used the gene sequence of the alpha variant of SARS-CoV-2 to build a viral biomass reaction (VBR). We also used the mass proportion of lipids between the viral biomass and its host cell to estimate the stoichiometric coefficients of viral lipids in the reaction. We then integrated the VBR, the gene expression of the alpha variant of SARS-CoV-2, and the generic human metabolic network Recon3D to reconstruct a cell-specific genome-scale metabolic model. An antiviral target discovery (AVTD) platform was introduced using this model to identify therapeutic drug targets for combating COVID-19. The AVTD platform not only identified antiviral genes for eliminating viral replication but also predicted side effects of treatments. Our computational results revealed that knocking out dihydroorotate dehydrogenase (DHODH) might reduce the synthesis rate of cytidine-5'-triphosphate and uridine-5'-triphosphate, which terminate the viral building blocks of DNA and RNA for SARS-CoV-2 replication. Our results also indicated that DHODH is a promising antiviral target that causes minor side effects, which is consistent with the results of recent reports. Moreover, we discovered that the genes that participate in the de novo biosynthesis of glycerophospholipids and ceramides become unidentifiable if the VBR does not involve the stoichiometry of lipids.
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Affiliation(s)
- Ke‐Lin Chen
- Department of Chemical EngineeringNational Chung Cheng UniversityChiayiTaiwan
| | - Feng‐Sheng Wang
- Department of Chemical EngineeringNational Chung Cheng UniversityChiayiTaiwan
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18
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Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. PLoS Pathog 2023; 19:e1011870. [PMID: 38117830 PMCID: PMC10766180 DOI: 10.1371/journal.ppat.1011870] [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: 06/16/2023] [Revised: 01/04/2024] [Accepted: 11/28/2023] [Indexed: 12/22/2023] Open
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
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Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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19
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Wang X, Chiu W, Klaassen H, Marchand A, Chaltin P, Neyts J, Jochmans D. A Robust Phenotypic High-Throughput Antiviral Assay for the Discovery of Rabies Virus Inhibitors. Viruses 2023; 15:2292. [PMID: 38140533 PMCID: PMC10747594 DOI: 10.3390/v15122292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/24/2023] Open
Abstract
Rabies virus (RABV) causes severe neurological symptoms in mammals. The disease is almost inevitably lethal as soon as clinical symptoms appear. The use of rabies immunoglobulins (RIG) and vaccination in post-exposure prophylaxis (PEP) can provide efficient protection, but many people do not receive this treatment due to its high cost and/or limited availability. Highly potent small molecule antivirals are urgently needed to treat patients once symptoms develop. In this paper, we report on the development of a high-throughput phenotypic antiviral screening assay based on the infection of BHK-21 cells with a fluorescent reporter virus and high content imaging readout. The assay was used to screen a repurposing library of 3681 drugs (all had been studied in phase 1 clinical trials). From this series, salinomycin was found to selectively inhibit viral replication by blocking infection at the entry stage. This shows that a high-throughput assay enables the screening of large compound libraries for the purposes of identifying inhibitors of RABV replication. These can then be optimized through medicinal chemistry efforts and further developed into urgently needed drugs for the treatment of symptomatic rabies.
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Affiliation(s)
- Xinyu Wang
- Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (X.W.); (W.C.)
| | - Winston Chiu
- Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (X.W.); (W.C.)
| | - Hugo Klaassen
- Cistim Leuven vzw, Bioincubator 2, Gaston Geenslaan 2, 3001 Leuven, Belgium; (H.K.); (A.M.); (P.C.)
| | - Arnaud Marchand
- Cistim Leuven vzw, Bioincubator 2, Gaston Geenslaan 2, 3001 Leuven, Belgium; (H.K.); (A.M.); (P.C.)
| | - Patrick Chaltin
- Cistim Leuven vzw, Bioincubator 2, Gaston Geenslaan 2, 3001 Leuven, Belgium; (H.K.); (A.M.); (P.C.)
- Center for Drug Design and Discovery (CD3), KU Leuven R&D, 3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (X.W.); (W.C.)
| | - Dirk Jochmans
- Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49 Box 1043, 3000 Leuven, Belgium; (X.W.); (W.C.)
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20
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Lee JS, Dittmar M, Miller J, Li M, Ayyanathan K, Ferretti M, Hulahan J, Whig K, Etwebi Z, Griesman T, Schultz DC, Cherry S. Evolutionary arms race between SARS-CoV-2 and interferon signaling via dynamic interaction with autophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566859. [PMID: 38014114 PMCID: PMC10680587 DOI: 10.1101/2023.11.13.566859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SARS-CoV-2 emerged, and is evolving to efficiently infect humans worldwide. SARS-CoV-2 evades early innate recognition, interferon signaling activated only in bystander cells. This balance of innate activation and viral evasion has important consequences, but the pathways involved are incompletely understood. Here we find that autophagy genes regulate innate immune signaling, impacting the basal set point of interferons, and thus permissivity to infection. Mechanistically, autophagy genes negatively regulate MAVS, and this low basal level of MAVS is efficiently antagonized by SARS-CoV-2 ORF9b, blocking interferon activation in infected cells. However, upon loss of autophagy increased MAVS overcomes ORF9b-mediated antagonism suppressing infection. This has led to the evolution of SARS-CoV-2 variants to express higher levels of ORF9b, allowing SARS-CoV-2 to replicate under conditions of increased MAVS signaling. Altogether, we find a critical role of autophagy in the regulation of innate immunity and uncover an evolutionary trajectory of SARS-CoV-2 ORF9b to overcome host defenses.
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21
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Jones T, Monakhova N, Guivel-Benhassine F, Lepioshkin A, Bruel T, Lane TR, Schwartz O, Puhl AC, Makarov V, Ekins S. Synthesis and Evaluation of 9-Aminoacridines with SARS-CoV-2 Antiviral Activity. ACS OMEGA 2023; 8:40817-40822. [PMID: 37929131 PMCID: PMC10620940 DOI: 10.1021/acsomega.3c05900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
There have been relatively few small molecules developed with direct activity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two existing antimalarial drugs, pyronaridine and quinacrine, display whole cell activity against SARS-CoV-2 in A549 + ACE2 cells (pretreatment, IC50 = 0.23 and 0.19 μM, respectively) with moderate cytotoxicity (CC50 = 11.53 and 9.24 μM, respectively). Moreover, pyronaridine displays in vitro activity against SARS-CoV-2 PLpro (IC50 = 1.8 μM). Given their existing antiviral activity, these compounds are strong candidates for repurposing against COVID-19 and prompt us to study the structure-activity relationship of the 9-aminoacridine scaffold against SARS-CoV-2 using traditional medicinal chemistry to identify promising new analogs. Our studies identified several novel analogs possessing potent in vitro activity in U2-OS ACE2 GFP 1-10 and 1-11 (IC50 < 1.0 μM) as well as moderate cytotoxicity (CC50 > 4.0 μM). Compounds such as 7g, 9c, and 7e were more active, demonstrating selectivity indices SI > 10, and 9c displayed the strongest activity (IC50 ≤ 0.42 μM, CC50 ≥ 4.41 μM, SI > 10) among them, indicating that it has potential as a new lead molecule in this series against COVID-19.
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Affiliation(s)
- Thane Jones
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Natalia Monakhova
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | | | - Alexander Lepioshkin
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Timothée Bruel
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olivier Schwartz
- Institut
Pasteur, 28 rue du Dr Roux, Paris Cedex 15 75724, France
| | - Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Vadim Makarov
- Federal
Research Centre “Fundamentals of Biotechnology” of the
Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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22
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Jordan R, Ford-Scheimer SL, Alarcon RM, Atala A, Borenstein JT, Brimacombe KR, Cherry S, Clevers H, Davis MI, Funnell SGP, Gehrke L, Griffith LG, Grossman AC, Hartung T, Ingber DE, Kleinstreuer NC, Kuo CJ, Lee EM, Mummery CL, Pickett TE, Ramani S, Rosado-Olivieri EA, Struble EB, Wan Z, Williams MS, Hall MD, Ferrer M, Markossian S. Report of the Assay Guidance Workshop on 3-Dimensional Tissue Models for Antiviral Drug Development. J Infect Dis 2023; 228:S337-S354. [PMID: 37669225 PMCID: PMC10547463 DOI: 10.1093/infdis/jiad334] [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] [Indexed: 09/07/2023] Open
Abstract
The National Center for Advancing Translational Sciences (NCATS) Assay Guidance Manual (AGM) Workshop on 3D Tissue Models for Antiviral Drug Development, held virtually on 7-8 June 2022, provided comprehensive coverage of critical concepts intended to help scientists establish robust, reproducible, and scalable 3D tissue models to study viruses with pandemic potential. This workshop was organized by NCATS, the National Institute of Allergy and Infectious Diseases, and the Bill and Melinda Gates Foundation. During the workshop, scientific experts from academia, industry, and government provided an overview of 3D tissue models' utility and limitations, use of existing 3D tissue models for antiviral drug development, practical advice, best practices, and case studies about the application of available 3D tissue models to infectious disease modeling. This report includes a summary of each workshop session as well as a discussion of perspectives and challenges related to the use of 3D tissues in antiviral drug discovery.
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Affiliation(s)
- Robert Jordan
- Bill and Melinda Gates Foundation, Seattle, Washington, USA
| | - Stephanie L Ford-Scheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Rodolfo M Alarcon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Mindy I Davis
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Simon G P Funnell
- UK Health Security Agency, Salisbury, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Abigail C Grossman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Thomas Hartung
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Donald E Ingber
- Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, USA
- Boston Children's Hospital, Boston, Massachusetts, USA
| | - Nicole C Kleinstreuer
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle, North Carolina, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Emily M Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Thames E Pickett
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Evi B Struble
- US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Zhengpeng Wan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mark S Williams
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sarine Markossian
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
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23
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Puhl AC, Lane TR, Ekins S. Learning from COVID-19: How drug hunters can prepare for the next pandemic. Drug Discov Today 2023; 28:103723. [PMID: 37482237 PMCID: PMC10994687 DOI: 10.1016/j.drudis.2023.103723] [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: 06/02/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
Over 3 years, the SARS-CoV-2 pandemic killed nearly 7 million people and infected more than 767 million globally. During this time, our very small company was able to contribute to antiviral drug discovery efforts through global collaborations with other researchers, which enabled the identification and repurposing of multiple molecules with activity against SARS-CoV-2 including pyronaridine tetraphosphate, tilorone, quinacrine, vandetanib, lumefantrine, cetylpyridinium chloride, raloxifene, carvedilol, olmutinib, dacomitinib, crizotinib, and bosutinib. We highlight some of the key findings from this experience of using different computational and experimental strategies, and detail some of the challenges and strategies for how we might better prepare for the next pandemic so that potential antiviral treatments are available for future outbreaks.
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Affiliation(s)
- Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
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24
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Chu SW, Wang FS. Fuzzy optimization for identifying antiviral targets for treating SARS-CoV-2 infection in the heart. BMC Bioinformatics 2023; 24:364. [PMID: 37759157 PMCID: PMC10537911 DOI: 10.1186/s12859-023-05487-7] [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: 06/24/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
In this paper, a fuzzy hierarchical optimization framework is proposed for identifying potential antiviral targets for treating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the heart. The proposed framework comprises four objectives for evaluating the elimination of viral biomass growth and the minimization of side effects during treatment. In the application of the framework, Dulbecco's modified eagle medium (DMEM) and Ham's medium were used as uptake nutrients on an antiviral target discovery platform. The prediction results from the framework reveal that most of the antiviral enzymes in the aforementioned media are involved in fatty acid metabolism and amino acid metabolism. However, six enzymes involved in cholesterol biosynthesis in Ham's medium and three enzymes involved in glycolysis in DMEM are unable to eliminate the growth of the SARS-CoV-2 biomass. Three enzymes involved in glycolysis, namely BPGM, GAPDH, and ENO1, in DMEM combine with the supplemental uptake of L-cysteine to increase the cell viability grade and metabolic deviation grade. Moreover, six enzymes involved in cholesterol biosynthesis reduce and fail to reduce viral biomass growth in a culture medium if a cholesterol uptake reaction does not occur and occurs in this medium, respectively.
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Affiliation(s)
- Sz-Wei Chu
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, 621301, Taiwan
| | - Feng-Sheng Wang
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, 621301, Taiwan.
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25
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Ali H, Naseem A, Siddiqui ZI. SARS-CoV-2 Syncytium under the Radar: Molecular Insights of the Spike-Induced Syncytia and Potential Strategies to Limit SARS-CoV-2 Replication. J Clin Med 2023; 12:6079. [PMID: 37763019 PMCID: PMC10531702 DOI: 10.3390/jcm12186079] [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: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 infection induces non-physiological syncytia when its spike fusogenic protein on the surface of the host cells interacts with the ACE2 receptor on adjacent cells. Spike-induced syncytia are beneficial for virus replication, transmission, and immune evasion, and contribute to the progression of COVID-19. In this review, we highlight the properties of viral fusion proteins, mainly the SARS-CoV-2 spike, and the involvement of the host factors in the fusion process. We also highlight the possible use of anti-fusogenic factors as an antiviral for the development of therapeutics against newly emerging SARS-CoV-2 variants and how the fusogenic property of the spike could be exploited for biomedical applications.
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Affiliation(s)
- Hashim Ali
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Zaheenul Islam Siddiqui
- Diabetes and Obesity Research Center, NYU Grossman Long Island School of Medicine, New York, NY 11501, USA
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26
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Dittmar M, Whig K, Miller J, Kamalia B, Suppiah S, Perelygina L, Sullivan KE, Schultz DC, Cherry S. Nucleoside analogs NM107 and AT-527 are antiviral against rubella virus. PNAS NEXUS 2023; 2:pgad256. [PMID: 37674858 PMCID: PMC10479830 DOI: 10.1093/pnasnexus/pgad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 09/08/2023]
Abstract
Rubella is a highly contagious viral infection that usually causes a mild disease in children and adults. However, infection during pregnancy can result in a fetal or newborn death or congenital rubella syndrome (CRS), a constellation of permanent birth defects including cataracts, heart defects, and sensorineural deafness. The live-attenuated rubella vaccine has been highly effective, with the Americas declared free of endemic rubella transmission in 2015. However, rubella remains a significant problem worldwide and the leading cause of vaccine-preventable birth defects globally. Thus, elimination of rubella and CRS is a goal of the World Health Organization. No specific therapeutics are approved for the rubella virus. Therefore, we set out to identify whether existing small molecules may be repurposed for use against rubella virus infection. Thus, we performed a high-throughput screen for small molecules active against rubella virus in human respiratory cells and identified two nucleoside analogs, NM107 and AT-527, with potent antiviral activity. Furthermore, we found that combining these nucleoside analogs with inhibitors of host nucleoside biosynthesis had synergistic antiviral activity. These studies open the door to new potential approaches to treat rubella infections.
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Affiliation(s)
- Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
| | - Kanupriya Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Jesse Miller
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
| | - Brinda Kamalia
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Suganthi Suppiah
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. Atlanta, GA 30329, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. Atlanta, GA 30329, USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, 3450 Hamilton Walk Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, 3620 Hamilton Walk Philadelphia, PA 19104, USA
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27
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Li M, Ayyanathan K, Dittmar M, Miller J, Tapescu I, Lee JS, McGrath ME, Xue Y, Vashee S, Schultz DC, Frieman MB, Cherry S. SARS-CoV-2 ORF6 protein does not antagonize interferon signaling in respiratory epithelial Calu-3 cells during infection. mBio 2023; 14:e0119423. [PMID: 37377442 PMCID: PMC10470815 DOI: 10.1128/mbio.01194-23] [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: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths, posing a substantial threat to global public health. Viruses evolve different strategies to antagonize or evade host immune responses. While ectopic expression of SARS-CoV-2 accessory protein ORF6 blocks interferon (IFN) production and downstream IFN signaling, the role of ORF6 in IFN signaling during bona fide viral infection of respiratory cells is unclear. By comparing wild-type (WT) and ORF6-deleted (ΔORF6) SARS-CoV-2 infection and IFN signaling in respiratory cells, we found that ΔORF6 SARS-CoV-2 replicates more efficiently than WT virus and, thus, stimulates more robust immune signaling. Loss of ORF6 does not alter innate signaling in infected cells: both WT and ΔORF6 virus induce delayed IFN responses only in bystander cells. Moreover, expression of ORF6 in the context of SARS-CoV-2 infection has no effect on Sendai virus-stimulated IFN induction: robust translocation of IRF3 is observed in both SARS-CoV-2 infected and bystander cells. Furthermore, IFN pretreatment potently blocks WT and ΔORF6 virus replication similarly, and both viruses fail to suppress the induction of interferon-stimulated genes (ISGs) upon IFN-β treatment. However, upon treatment with IFN-β, only bystander cells induce STAT1 translocation during infection with WT virus, whereas ΔORF6 virus-infected cells now show translocation. This suggests that under conditions of high IFN activation, ORF6 can attenuate STAT1 activation. These data provide evidence that ORF6 is not sufficient to antagonize IFN production or IFN signaling in SARS-CoV-2-infected respiratory cells but may impact the efficacy of therapeutics that stimulate innate immune pathways. IMPORTANCE Previous studies identified several SARS-CoV-2 proteins, including ORF6, that antagonize host innate immune responses in the context of overexpression of viral proteins in non-respiratory cells. We set out to determine the role of ORF6 in IFN responses during SARS-CoV-2 infection of respiratory cells. Using a deletion strain, we observed no reduction of infection and no difference in evasion of IFN signaling, with responses limited to bystander cells. Moreover, stimulation of Sendai virus-induced IFN production or IFN-β-stimulated ISG expression was comparable between SARS-CoV-2 virus and SARS-CoV-2 lacking ORF6 virus, suggesting that ORF6 is not sufficient to counteract IFN induction or IFN signaling during viral infection.
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Affiliation(s)
- Minghua Li
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kasirajan Ayyanathan
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse Miller
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Iulia Tapescu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jae Seung Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa E. McGrath
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yong Xue
- J Craig Venter Institute, Rockville, Maryland, USA
| | | | - David C. Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew B. Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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28
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Gurukkalot K, Rajendran V. Repurposing Polyether Ionophores as a New-Class of Anti-SARS-Cov-2 Agents as Adjunct Therapy. Curr Microbiol 2023; 80:273. [PMID: 37414909 DOI: 10.1007/s00284-023-03366-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
The emergence of SARS-CoV-2 and its variants have posed a significant threat to humankind in tackling the viral spread. Furthermore, currently repurposed drugs and frontline antiviral agents have failed to cure severe ongoing infections effectively. This insufficiency has fuelled research for potent and safe therapeutic agents to treat COVID-19. Nonetheless, various vaccine candidates have displayed a differential efficacy and need for repetitive dosing. The FDA-approved polyether ionophore veterinary antibiotic for treating coccidiosis has been repurposed for treating SARS-CoV-2 infection (as shown by both in vitro and in vivo studies) and other deadly human viruses. Based on selectivity index values, ionophores display therapeutic effects at sub-nanomolar concentrations and exhibit selective killing ability. They act on different viral targets (structural and non-structural proteins), host-cell components leading to SARS-CoV-2 inhibition, and their activity is further enhanced by Zn2+ supplementation. This review summarizes the anti-SARS-CoV-2 potential and molecular viral targets of selective ionophores like monensin, salinomycin, maduramicin, CP-80,219, nanchangmycin, narasin, X-206 and valinomycin. Ionophore combinations with Zn2+ are a new therapeutic strategy that warrants further investigation for possible human benefits.
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Affiliation(s)
- Keerthana Gurukkalot
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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29
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Tomezsko PJ, Phillipson CW, Walsh ME. Lessons Learned From Limited Overlap of 15 In Vitro COVID-19 Drug Repurposing Screens. Health Secur 2023; 21:249-257. [PMID: 37196212 PMCID: PMC10357111 DOI: 10.1089/hs.2022.0132] [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: 10/03/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
Drug repurposing can quickly and cost-effectively identify medical countermeasures against pathogens with pandemic potential and could be used as a down-selection method for selecting US Food and Drug Administration-approved drugs to test in clinical trials. We compared results from 15 high-throughput in vitro screening efforts that tested approved and clinically evaluated drugs for activity against SARS-CoV-2 replication. From the 15 studies, 304 drugs were identified as displaying the highest level of confidence from the individual screens. Of those 304 drugs, 30 were identified in 2 or more screens, while only 3 drugs (apilimod, tetrandrine, and salinomycin) were identified in 4 screens. The lack of concordance in high-confidence hits and variations in protocols makes it challenging to use the collective data as down-selection criteria for identifying repurposing candidates to move into a clinical trial.
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Affiliation(s)
- Phillip J. Tomezsko
- Phillip J. Tomezsko, PhD, is Technical Staff, Counter WMD Systems Group, MIT Lincoln Laboratory, Lexington, MA
| | | | - Matthew E. Walsh
- Matthew E. Walsh was Associate Technical Staff, Biological and Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA
- Matthew E. Walsh is currently a PhD Student, Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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30
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Cervantes M, Hess T, Morbioli GG, Sengar A, Kasson PM. The ACE2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion. Chem Sci 2023; 14:6997-7004. [PMID: 37389252 PMCID: PMC10306070 DOI: 10.1039/d2sc06967a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
The SARS-CoV-2 coronavirus infects human cells via the ACE2 receptor. Structural evidence suggests that ACE2 may not just serve as an attachment factor but also conformationally activate the SARS-CoV-2 spike protein for membrane fusion. Here, we test that hypothesis directly, using DNA-lipid tethering as a synthetic attachment factor in place of ACE2. We find that SARS-CoV-2 pseudovirus and virus-like particles are capable of membrane fusion without ACE2 if activated with an appropriate protease. Thus, ACE2 is not biochemically required for SARS-CoV-2 membrane fusion. However, addition of soluble ACE2 speeds up the fusion reaction. On a per-spike level, ACE2 appears to promote activation for fusion and then subsequent inactivation if an appropriate protease is not present. Kinetic analysis suggests at least two rate-limiting steps for SARS-CoV-2 membrane fusion, one of which is ACE2 dependent and one of which is not. Since ACE2 serves as a high-affinity attachment factor on human cells, the possibility to replace it with other factors implies a flatter fitness landscape for host adaptation by SARS-CoV-2 and future related coronaviruses.
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Affiliation(s)
- Marcos Cervantes
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Tobin Hess
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Giorgio G Morbioli
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Anjali Sengar
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
| | - Peter M Kasson
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia Charlottesville VA 22908 USA
- Science for Life Laboratory and Department of Molecular and Cellular Biology, Uppsala University Uppsala SE 75123 USA
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31
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Puhl AC, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Oliva G, Ekins S. Discovery of PL pro and M pro Inhibitors for SARS-CoV-2. ACS OMEGA 2023; 8:22603-22612. [PMID: 37387790 PMCID: PMC10275482 DOI: 10.1021/acsomega.3c01110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
There are very few small-molecule antivirals for SARS-CoV-2 that are either currently approved (or emergency authorized) in the US or globally, including remdesivir, molnupiravir, and paxlovid. The increasing number of SARS-CoV-2 variants that have appeared since the outbreak began over three years ago raises the need for continual development of updated vaccines and orally available antivirals in order to fully protect or treat the population. The viral main protease (Mpro) and the papain-like protease (PLpro) are key for viral replication; therefore, they represent valuable targets for antiviral therapy. We herein describe an in vitro screen performed using the 2560 compounds from the Microsource Spectrum library against Mpro and PLpro in an attempt to identify additional small-molecule hits that could be repurposed for SARS-CoV-2. We subsequently identified 2 hits for Mpro and 8 hits for PLpro. One of these hits was the quaternary ammonium compound cetylpyridinium chloride with dual activity (IC50 = 2.72 ± 0.09 μM for PLpro and IC50 = 7.25 ± 0.15 μM for Mpro). A second inhibitor of PLpro was the selective estrogen receptor modulator raloxifene (IC50 = 3.28 ± 0.29 μM for PLpro and IC50 = 42.8 ± 6.7 μM for Mpro). We additionally tested several kinase inhibitors and identified olmutinib (IC50 = 0.54 ± 0.04 μM), bosutinib (IC50 = 4.23 ± 0.28 μM), crizotinib (IC50 = 3.81 ± 0.04 μM), and dacominitinib (IC50 = IC50 3.33 ± 0.06 μM) as PLpro inhibitors for the first time. In some cases, these molecules have also been tested by others for antiviral activity for this virus, or we have used Calu-3 cells infected with SARS-CoV-2. The results suggest that approved drugs can be identified with promising activity against these proteases, and in several cases we or others have validated their antiviral activity. The additional identification of known kinase inhibitors as molecules targeting PLpro may provide new repurposing opportunities or starting points for chemical optimization.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Andre S. Godoy
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Gabriela D. Noske
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Aline M. Nakamura
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Victor O. Gawriljuk
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Rafaela S. Fernandes
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Glaucius Oliva
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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32
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Procario MC, Sexton JZ, Halligan BS, Imperiale MJ. Single-Cell, High-Content Microscopy Analysis of BK Polyomavirus Infection. Microbiol Spectr 2023; 11:e0087323. [PMID: 37154756 PMCID: PMC10269497 DOI: 10.1128/spectrum.00873-23] [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: 02/27/2023] [Accepted: 04/08/2023] [Indexed: 05/10/2023] Open
Abstract
By adulthood, the majority of the population is persistently infected with BK polyomavirus (BKPyV). Only a subset of the population, generally transplant recipients on immunosuppressive drugs, will experience disease from BKPyV, but those who do have few treatment options and, frequently, poor outcomes, because to date there are no effective antivirals to treat or approved vaccines to prevent BKPyV. Most studies of BKPyV have been performed on bulk populations of cells, and the dynamics of infection at single-cell resolution have not been explored. As a result, much of our knowledge is based upon the assumption that all cells within a greater population are behaving the same way with respect to infection. The present study examines BKPyV infection on a single-cell level using high-content microscopy to measure and analyze the viral protein large T antigen (TAg), promyelocytic leukemia protein (PML), DNA, and nuclear morphological features. We observed significant heterogeneity among infected cells, within and across time points. We found that the levels of TAg within individual cells did not necessarily increase with time and that cells with the same TAg levels varied in other ways. Overall, high-content, single-cell microscopy is a novel approach to studying BKPyV that enables experimental insight into the heterogenous nature of the infection. IMPORTANCE BK polyomavirus (BKPyV) is a human pathogen that infects nearly everyone by adulthood and persists throughout a person's life. Only people with significant immune suppression develop disease from the virus, however. Until recently the only practical means of studying many viral infections was to infect a group of cells in the laboratory and measure the outcomes in that group. However, interpreting these bulk population experiments requires the assumption that infection influences all cells within a group similarly. This assumption has not held for multiple viruses tested so far. Our study establishes a novel single-cell microscopy assay for BKPyV infection. Using this assay, we discovered differences among individual infected cells that have not been apparent in bulk population studies. The knowledge gained in this study and the potential for future use demonstrate the power of this assay as a tool for understanding the biology of BKPyV.
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Affiliation(s)
- Megan C. Procario
- Department of Microbiology and Immunology, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
- Center for Drug Repurposing, University of Michigan, Ann Arbor, Michigan, USA
| | - Benjamin S. Halligan
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, Medical School, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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33
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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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34
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Wang RS, Loscalzo J. Repurposing Drugs for the Treatment of COVID-19 and Its Cardiovascular Manifestations. Circ Res 2023; 132:1374-1386. [PMID: 37167362 PMCID: PMC10171294 DOI: 10.1161/circresaha.122.321879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
COVID-19 is an infectious disease caused by SARS-CoV-2 leading to the ongoing global pandemic. Infected patients developed a range of respiratory symptoms, including respiratory failure, as well as other extrapulmonary complications. Multiple comorbidities, including hypertension, diabetes, cardiovascular diseases, and chronic kidney diseases, are associated with the severity and increased mortality of COVID-19. SARS-CoV-2 infection also causes a range of cardiovascular complications, including myocarditis, myocardial injury, heart failure, arrhythmias, acute coronary syndrome, and venous thromboembolism. Although a variety of methods have been developed and many clinical trials have been launched for drug repositioning for COVID-19, treatments that consider cardiovascular manifestations and cardiovascular disease comorbidities specifically are limited. In this review, we summarize recent advances in drug repositioning for COVID-19, including experimental drug repositioning, high-throughput drug screening, omics data-based, and network medicine-based computational drug repositioning, with particular attention on those drug treatments that consider cardiovascular manifestations of COVID-19. We discuss prospective opportunities and potential methods for repurposing drugs to treat cardiovascular complications of COVID-19.
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Affiliation(s)
- Rui-Sheng Wang
- Channing Division of Network Medicine (R.-S.W., J.L.), Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, MA
| | - Joseph Loscalzo
- Channing Division of Network Medicine (R.-S.W., J.L.), Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, MA
- Division of Cardiovascular Medicine (J.L.), Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, MA
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35
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Sengar A, Cervantes M, Bondalapati ST, Hess T, Kasson PM. Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry. J Virol 2023; 97:e0199222. [PMID: 37133381 DOI: 10.1128/jvi.01992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to cell surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here, we used single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We found that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases is used to activate the virus. This suggests that the fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2 in which the subcellular location of entry likely depends on the differential activity of airway, cellsurface, and endosomal proteases, but all support infection. Inhibition of any single host protease may thus reduce infection in some cells but may be less clinically robust. IMPORTANCE SARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we used single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effects. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.
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Affiliation(s)
- Anjali Sengar
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Marcos Cervantes
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Sai T Bondalapati
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Tobin Hess
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
| | - Peter M Kasson
- Department of Molecular Physiology, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, Global Infectious Diseases Institute, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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36
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Chen TH, Chang CJ, Hung PH. Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder. Int J Mol Sci 2023; 24:8034. [PMID: 37175745 PMCID: PMC10179190 DOI: 10.3390/ijms24098034] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can alter the mitochondria responsible for energy production in cells. This alteration leads to mitochondrial dysfunction which, in turn, increases oxidative stress. Ultimately, this results in a loss of mitochondrial integrity and cell death. Moreover, viral proteins can bind to mitochondrial complexes, disrupting mitochondrial function and causing the immune cells to over-react. This over-reaction leads to inflammation and potentially long COVID symptoms. It is important to note that the roles of mitochondrial damage and inflammatory responses caused by SARS-CoV-2 in the development of long COVID are still being elucidated. Targeting mitochondrial function may provide promising new clinical approaches for long-COVID patients; however, further studies are needed to evaluate the safety and efficacy of such approaches.
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Affiliation(s)
- Tsung-Hsien Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
| | - Chia-Jung Chang
- Division of Critical Care Medicine, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
| | - Peir-Haur Hung
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
- Department of Life and Health Science, Chia-Nan University of Pharmacy and Science, Tainan 717301, Taiwan
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37
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Durojaye OA, Okoro NO, Odiba AS, Nwanguma BC. MasitinibL shows promise as a drug-like analog of masitinib that elicits comparable SARS-Cov-2 3CLpro inhibition with low kinase preference. Sci Rep 2023; 13:6972. [PMID: 37117213 PMCID: PMC10141821 DOI: 10.1038/s41598-023-33024-2] [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: 02/03/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023] Open
Abstract
SARS-CoV-2 infection has led to several million deaths worldwide and ravaged the economies of many countries. Hence, developing therapeutics against SARS-CoV-2 remains a core priority in the fight against COVID-19. Most of the drugs that have received emergency use authorization for treating SARS-CoV-2 infection exhibit a number of limitations, including side effects and questionable efficacy. This challenge is further compounded by reinfection after vaccination and the high likelihood of mutations, as well as the emergence of viral escape mutants that render SARS-CoV-2 spike glycoprotein-targeting vaccines ineffective. Employing de novo drug synthesis or repurposing to discover broad-spectrum antivirals that target highly conserved pathways within the viral machinery is a focus of current research. In a recent drug repurposing study, masitinib, a clinically safe drug against the human coronavirus OC43 (HCoV-OC43), was identified as an antiviral agent with effective inhibitory activity against the SARS-CoV-2 3CLpro. Masitinib is currently under clinical trial in combination with isoquercetin in hospitalized patients (NCT04622865). Nevertheless, masitinib has kinase-related side effects; hence, the development of masitinib analogs with lower anti-tyrosine kinase activity becomes necessary. In this study, in an attempt to address this limitation, we executed a comprehensive virtual workflow in silico to discover drug-like compounds matching selected pharmacophore features in the SARS-CoV-2 3CLpro-bound state of masitinib. We identified a novel lead compound, "masitinibL", a drug-like analog of masitinib that demonstrated strong inhibitory properties against the SARS-CoV-2 3CLpro. In addition, masitinibL further displayed low selectivity for tyrosine kinases, which strongly suggests that masitinibL is a highly promising therapeutic that is preferable to masitinib.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Department of Chemical Sciences, Coal City University, Emene, Enugu State, Nigeria
| | - Nkwachukwu Oziamara Okoro
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Nigeria
| | - Arome Solomon Odiba
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
| | - Bennett Chima Nwanguma
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
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38
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Liu D, Ndongwe TP, Ji J, Huber AD, Michailidis E, Rice CM, Ralston R, Tedbury PR, Sarafianos SG. Mechanisms of Action of the Host-Targeting Agent Cyclosporin A and Direct-Acting Antiviral Agents against Hepatitis C Virus. Viruses 2023; 15:981. [PMID: 37112961 PMCID: PMC10143304 DOI: 10.3390/v15040981] [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: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Several direct-acting antivirals (DAAs) are available, providing interferon-free strategies for a hepatitis C cure. In contrast to DAAs, host-targeting agents (HTAs) interfere with host cellular factors that are essential in the viral replication cycle; as host genes, they are less likely to rapidly mutate under drug pressure, thus potentially exhibiting a high barrier to resistance, in addition to distinct mechanisms of action. We compared the effects of cyclosporin A (CsA), a HTA that targets cyclophilin A (CypA), to DAAs, including inhibitors of nonstructural protein 5A (NS5A), NS3/4A, and NS5B, in Huh7.5.1 cells. Our data show that CsA suppressed HCV infection as rapidly as the fastest-acting DAAs. CsA and inhibitors of NS5A and NS3/4A, but not of NS5B, suppressed the production and release of infectious HCV particles. Intriguingly, while CsA rapidly suppressed infectious extracellular virus levels, it had no significant effect on the intracellular infectious virus, suggesting that, unlike the DAAs tested here, it may block a post-assembly step in the viral replication cycle. Hence, our findings shed light on the biological processes involved in HCV replication and the role of CypA.
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Affiliation(s)
- Dandan Liu
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Tanya P. Ndongwe
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Juan Ji
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Andrew D. Huber
- CS Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Robert Ralston
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Philip R. Tedbury
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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39
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Han N, Li J, Zhao F, Li Y, Wang J, Dai X, Zeng D, Xiong W, Zeng Z. Isopropoxy Benzene Guanidine Ameliorates Streptococcus suis Infection In Vivo and In Vitro. Int J Mol Sci 2023; 24:ijms24087354. [PMID: 37108521 PMCID: PMC10138962 DOI: 10.3390/ijms24087354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Streptococcus suis, an encapsulated zoonotic pathogen, has been reported to cause a variety of infectious diseases, such as meningitis and streptococcal-toxic-shock-like syndrome. Increasing antimicrobial resistance has triggered the need for new treatments. In the present study, we found that isopropoxy benzene guanidine (IBG) significantly attenuated the effects caused by S. suis infection, in vivo and in vitro, by killing S. suis and reducing S. suis pathogenicity. Further studies showed that IBG disrupted the integrity of S. suis cell membranes and increased the permeability of S. suis cell membranes, leading to an imbalance in proton motive force and the accumulation of intracellular ATP. Meanwhile, IBG antagonized the hemolysis activity of suilysin and decreased the expression of Sly gene. In vivo, IBG improved the viability of S. suis SS3-infected mice by reducing tissue bacterial load. In conclusion, IBG is a promising compound for the treatment of S. suis infections, given its antibacterial and anti-hemolysis activity.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Feifei Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yangyang Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaolan Dai
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Dongping Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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40
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Rizzi M, D'Onghia D, Tonello S, Minisini R, Colangelo D, Bellan M, Castello LM, Gavelli F, Avanzi GC, Pirisi M, Sainaghi PP. COVID-19 Biomarkers at the Crossroad between Patient Stratification and Targeted Therapy: The Role of Validated and Proposed Parameters. Int J Mol Sci 2023; 24:ijms24087099. [PMID: 37108262 PMCID: PMC10138390 DOI: 10.3390/ijms24087099] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Clinical knowledge about SARS-CoV-2 infection mechanisms and COVID-19 pathophysiology have enormously increased during the pandemic. Nevertheless, because of the great heterogeneity of disease manifestations, a precise patient stratification at admission is still difficult, thus rendering a rational allocation of limited medical resources as well as a tailored therapeutic approach challenging. To date, many hematologic biomarkers have been validated to support the early triage of SARS-CoV-2-positive patients and to monitor their disease progression. Among them, some indices have proven to be not only predictive parameters, but also direct or indirect pharmacological targets, thus allowing for a more tailored approach to single-patient symptoms, especially in those with severe progressive disease. While many blood test-derived parameters quickly entered routine clinical practice, other circulating biomarkers have been proposed by several researchers who have investigated their reliability in specific patient cohorts. Despite their usefulness in specific contexts as well as their potential interest as therapeutic targets, such experimental markers have not been implemented in routine clinical practice, mainly due to their higher costs and low availability in general hospital settings. This narrative review will present an overview of the most commonly adopted biomarkers in clinical practice and of the most promising ones emerging from specific population studies. Considering that each of the validated markers reflects a specific aspect of COVID-19 evolution, embedding new highly informative markers into routine clinical testing could help not only in early patient stratification, but also in guiding a timely and tailored method of therapeutic intervention.
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Affiliation(s)
- Manuela Rizzi
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Davide D'Onghia
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Stelvio Tonello
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Rosalba Minisini
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Donato Colangelo
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Mattia Bellan
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Luigi Mario Castello
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Francesco Gavelli
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Gian Carlo Avanzi
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Mario Pirisi
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Pier Paolo Sainaghi
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
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41
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Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform. iScience 2023; 26:105944. [PMID: 36644320 PMCID: PMC9822553 DOI: 10.1016/j.isci.2023.105944] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/07/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a readout for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in numerous cell culture models, independently of cytopathogenic effect formation. Compared to other models, the Caco-2 subline Caco-2-F03 displayed superior performance. It possesses a stable SARS-CoV-2 susceptibility phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (HK2) inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2-F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false-positive hits.
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42
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Abou-Hamdan M, Saleh R, Mani S, Dournaud P, Metifiot M, Blondot ML, Andreola ML, Abdel-Sater F, De Reggi M, Gressens P, Laforge M. Potential antiviral effects of pantethine against SARS-CoV-2. Sci Rep 2023; 13:2237. [PMID: 36754974 PMCID: PMC9906591 DOI: 10.1038/s41598-023-29245-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 interacts with cellular cholesterol during many stages of its replication cycle. Pantethine was reported to reduce total cholesterol levels and fatty acid synthesis and potentially alter different processes that might be involved in the SARS-CoV-2 replication cycle. Here, we explored the potential antiviral effects of pantethine in two in vitro experimental models of SARS-CoV-2 infection, in Vero E6 cells and in Calu-3a cells. Pantethine reduced the infection of cells by SARS-CoV-2 in both preinfection and postinfection treatment regimens. Accordingly, cellular expression of the viral spike and nucleocapsid proteins was substantially reduced, and we observed a significant reduction in viral copy numbers in the supernatant of cells treated with pantethine. In addition, pantethine inhibited the infection-induced increase in TMPRSS2 and HECT E3 ligase expression in infected cells as well as the increase in antiviral interferon-beta response and inflammatory gene expression in Calu-3a cells. Our results demonstrate that pantethine, which is well tolerated in humans, was very effective in controlling SARS-CoV-2 infection and might represent a new therapeutic drug that can be repurposed for the prevention or treatment of COVID-19 and long COVID syndrome.
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Affiliation(s)
- M Abou-Hamdan
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France.,Biology Department, Faculty of Sciences (I), Lebanese University, Beirut, Lebanon
| | - R Saleh
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - S Mani
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - P Dournaud
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - M Metifiot
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - M L Blondot
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - M L Andreola
- Université Bordeaux, CNRS, UMR 5234, Microbiologie Fondamentale et Pathogénicité, 33076, Bordeaux, France
| | - F Abdel-Sater
- Biochemistry Department, Faculty of Sciences (I), Lebanese University, Beirut, Lebanon
| | - M De Reggi
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - P Gressens
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France
| | - M Laforge
- NeuroDiderot, Inserm, Université Paris Cité, 48 Boulevard Sérurier, 75019, Paris, France.
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43
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Chiu W, Schepers J, Francken T, Vangeel L, Abbasi K, Jochmans D, De Jonghe S, Thibaut HJ, Thiel V, Neyts J, Laporte M, Leyssen P. Development of a robust and convenient dual-reporter high-throughput screening assay for SARS-CoV-2 antiviral drug discovery. Antiviral Res 2023; 210:105506. [PMID: 36565756 PMCID: PMC9767876 DOI: 10.1016/j.antiviral.2022.105506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Massive efforts on both vaccine development and antiviral research were launched to combat the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We contributed, amongst others, by the development of a high-throughput screening (HTS) antiviral assay against SARS-CoV-2 using a fully automated, high-containment robot system. Here, we describe the development of this novel, convenient and phenotypic dual-reporter virus-cell-based high-content imaging assay using the A549+hACE2+TMPRSS2_mCherry reporter lung carcinoma cell line and an ancestral SARS-CoV-2_Wuhan_mNeonGreen reporter virus. Briefly, by means of clonal selection, a host cell subclone was selected that (i) efficiently supports replication of the reporter virus with high expression, upon infection, of the NeonGreen fluorescent reporter protein, (ii) that is not affected by virus-induced cytopathogenic effects and, (iii) that expresses a strong fluorescent mCherry signal in the nucleus. The selected clone matched these criteria with an infection rate on average of 75% with limited cell death. The average (R)Z'-factors of the assay plates were all >0.8, which indicates a robust assay suitable for HTS purposes. A selection of reference compounds that inhibits SARS-CoV-2 replication in vitro were used to validate this novel dual-reporter assay and confirms the data reported in the literature. This assay is a convenient and powerful tool for HTS of large compound libraries against SARS-CoV-2.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Gaston Geenslaan 2, 3001, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Manon Laporte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium.
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44
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McNulty J, Babu-Dokuburra C, Scattolon J, Zepeda-Velazquez C, Wesesky MA, Caldwell JK, Zheng W, Milosevic J, Kinchington PR, Bloom DC, Nimgaonkar VL, D'Aiuto L. Truncated ring-A amaryllidaceae alkaloid modulates the host cell integrated stress response, exhibiting antiviral activity to HSV-1 and SARSCoV-2. Sci Rep 2023; 13:1639. [PMID: 36717567 PMCID: PMC9885069 DOI: 10.1038/s41598-023-28691-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
The total synthesis of four novel mono-methoxy and hydroxyl substituted ring-A dihydronarciclasine derivatives enabled identification of the 7-hydroxyl derivative as a potent and selective antiviral agent targeting SARSCoV-2 and HSV-1. The concentration of this small molecule that inhibited HSV-1 infection by 50% (IC50), determined by using induced pluripotent stem cells (iPCS)-derived brain organ organoids generated from two iPCS lines, was estimated to be 0.504 µM and 0.209 µM. No significant reduction in organoid viability was observed at concentrations up to 50 mM. Genomic expression analyses revealed a significant effect on host-cell innate immunity, revealing activation of the integrated stress response via PERK kinase upregulation, phosphorylation of eukaryotic initiation factor 2α (eIF2α) and type I IFN, as factors potentiating multiple host-defense mechanisms against viral infection. Following infection of mouse eyes with HSV-1, treatment with the compound dramatically reduced HSV-1 shedding in vivo.
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Affiliation(s)
- James McNulty
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Chanti Babu-Dokuburra
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Jon Scattolon
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Carlos Zepeda-Velazquez
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Maribeth A Wesesky
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Jill K Caldwell
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Wenxiao Zheng
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Second Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jadranka Milosevic
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
- Captis Diagnostics Inc, Pittsburgh, PA, USA
| | - Paul R Kinchington
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David C Bloom
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Veterans Administration Pittsburgh Healthcare System, 4100 Allequippa St (University Drive C), Pittsburgh, PA, 15240, USA
| | - Leonardo D'Aiuto
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
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45
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Liu J, Wang F, Wang X, Fan S, Li Y, Xu M, Hu H, Liu K, Zheng B, Wang L, Zhang H, Li J, Li W, Zhang W, Hu Z, Cao R, Zhuang X, Wang M, Zhong W. Antiviral effects and tissue exposure of tetrandrine against SARS-CoV-2 infection and COVID-19. MedComm (Beijing) 2023; 4:e206. [PMID: 36699286 PMCID: PMC9851407 DOI: 10.1002/mco2.206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/21/2023] Open
Abstract
Tetrandrine (TET) has been used to treat silicosis in China for decades. The aim of this study was to facilitate rational repurposing of TET against SARS-CoV-2 infection. In this study, we confirmed that TET exhibited antiviral potency against SARS-CoV-2 in the African green monkey kidney (Vero E6), human hepatocarcinoma (Huh7), and human lung adenocarcinoma epithelial (Calu-3) cell lines. TET functioned during the early-entry stage of SARS-CoV-2 and impeded intracellular trafficking of the virus from early endosomes to endolysosomes. An in vivo study that used adenovirus (AdV) 5-human angiotensin-converting enzyme 2 (hACE2)-transduced mice showed that although TET did not reduce pulmonary viral load, it significantly alleviated pathological damage in SARS-CoV-2-infected murine lungs. The systemic preclinical pharmacokinetics were investigated based on in vivo and in vitro models, and the route-dependent biodistribution of TET was explored. TET had a large volume of distribution, which contributed to its high tissue accumulation. Inhaled administration helped TET target the lung and reduced its exposure to other tissues, which mitigated its off-target toxicity. Based on the available human pharmacokinetic data, it appeared feasible to achieve an unbound TET 90% maximal effective concentration (EC90) in human lungs. This study provides insights into the route-dependent pulmonary biodistribution of TET associated with its efficacy.
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Affiliation(s)
- Jia Liu
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Furun Wang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Xi Wang
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Shiyong Fan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Yufeng Li
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Mingyue Xu
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Hengrui Hu
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Ke Liu
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Bohong Zheng
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Lingchao Wang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Huanyu Zhang
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Jiang Li
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Wei Li
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wenpeng Zhang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Zhihong Hu
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Xiaomei Zhuang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Manli Wang
- State Key Laboratory of VirologyWuhan Institute of VirologyCenter for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
- Hubei Jiangxia LaboratoryWuhanChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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Rizzi M, Tonello S, D’Onghia D, Sainaghi PP. Gas6/TAM Axis Involvement in Modulating Inflammation and Fibrosis in COVID-19 Patients. Int J Mol Sci 2023; 24:ijms24020951. [PMID: 36674471 PMCID: PMC9861142 DOI: 10.3390/ijms24020951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Gas6 (growth arrest-specific gene 6) is a widely expressed vitamin K-dependent protein that is involved in many biological processes such as homeostatic regulation, inflammation and repair/fibrotic processes. It is known that it is the main ligand of TAMs, a tyrosine kinase receptor family of three members, namely MerTK, Tyro-3 and Axl, for which it displays the highest affinity. Gas6/TAM axis activation is known to be involved in modulating inflammatory responses as well as fibrotic evolution in many different pathological conditions. Due to the rapidly evolving COVID-19 pandemic, this review will focus on Gas6/TAM axis activation in SARS-CoV-2 infection, where de-regulated inflammatory responses and fibrosis represent a relevant feature of severe disease manifestation. Furthermore, this review will highlight the most recent scientific evidence supporting an unsuspected role of Axl as a SARS-CoV-2 infection driver, and the potential therapeutic advantages of the use of existing Axl inhibitors in COVID-19 management. From a physiological point of view, the Gas6/TAM axis plays a dual role, fostering the tissue repair processes or leading to organ damage and loss of function, depending on the prevalence of its anti-inflammatory or profibrotic properties. This review makes a strong case for further research focusing on the Gas6/TAM axis as a pharmacological target to manage different disease conditions, such as chronic fibrosis or COVID-19.
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47
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SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression. Proc Natl Acad Sci U S A 2023; 120:e2208525120. [PMID: 36574644 PMCID: PMC9910621 DOI: 10.1073/pnas.2208525120] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β2-microglobulin (β2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that down-regulate MHC-I expression to avoid CD8+ T cell recognition. Here, we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, down-regulate MHC-I expression using distinct mechanisms. First, ORF3a, a viroporin, reduces the global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a specific mechanism that allows immune evasion by SARS-CoV-2.
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48
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Chen D, Yun X, Lee D, DiCostanzo JR, Donini O, Shikuma CM, Thompson K, Lehrer AT, Shimoda L, Suk JS. Telmisartan Nanosuspension for Inhaled Therapy of COVID-19 Lung Disease and Other Respiratory Infections. Mol Pharm 2023; 20:750-757. [PMID: 36448927 PMCID: PMC9718101 DOI: 10.1021/acs.molpharmaceut.2c00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
Vaccine hesitancy and the occurrence of elusive variants necessitate further treatment options for coronavirus disease 2019 (COVID-19). Accumulated evidence indicates that clinically used hypertensive drugs, angiotensin receptor blockers (ARBs), may benefit patients by mitigating disease severity and/or viral propagation. However, current clinical formulations administered orally pose systemic safety concerns and likely require a very high dose to achieve the desired therapeutic window in the lung. To address these limitations, we have developed a nanosuspension formulation of an ARB, entirely based on clinically approved materials, for inhaled treatment of COVID-19. We confirmed in vitro that our formulation exhibits physiological stability, inherent drug activity, and inhibitory effect against SARV-CoV-2 replication. Our formulation also demonstrates excellent lung pharmacokinetics and acceptable tolerability in rodents and/or nonhuman primates following direct administration into the lung. Thus, we are currently pursuing clinical development of our formulation for its uses in patients with COVID-19 or other respiratory infections.
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Affiliation(s)
- Daiqin Chen
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xin Yun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daiheon Lee
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | | | | | - Cecilia M. Shikuma
- Department of Medicine, John A. Burns School of Medicine, University of Hawaiʻi at Mānoa, Honolulu, HI 96813, USA
| | - Karen Thompson
- Department of Pathology, John A. Burns School of Medicine, University of Hawaiʻi at Mānoa, Honolulu, HI 96813, USA
| | - Axel T. Lehrer
- Department of Tropical Medicine, Medical Microbiology & Pharmacology, John A. Burns School of Medicine, University of Hawaiʻi at Mānoa, Honolulu, HI 96813, USA
| | - Larissa Shimoda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jung Soo Suk
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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49
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Guarnieri JW, Angelin A, Murdock DG, Schaefer P, Portluri P, Lie T, Huang J, Wallace DC. SARS-COV-2 viroporins activate the NLRP3-inflammasome by the mitochondrial permeability transition pore. Front Immunol 2023; 14:1064293. [PMID: 36891303 PMCID: PMC9986324 DOI: 10.3389/fimmu.2023.1064293] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Background Compared to healthy controls, severe COVID19 patients display increased levels of activated NLRP3-inflammasome (NLRP3-I) and interleukin (IL)-1β. SARS-CoV-2 encodes viroporin proteins E and Orf3a(2-E+2-3a) with homologs to SARS-CoV-1, 1-E+1-3a, which elevate NLRP3-I activation; by an unknown mechanism. Thus, we investigated how 2-E+2-3a activates the NLRP3-I to better understand the pathophysiology of severe COVID-19. Methods We generated a polycistronic expression-vector co-expressing 2-E+2-3a from a single transcript. To elucidate how 2-E+2-3a activates the NLRP3-I, we reconstituted the NLRP3-I in 293T cells and used THP1-derived macrophages to monitor the secretion of mature IL-1β. Mitochondrial physiology was assessed using fluorescent microscopy and plate reader assays, and the release of mitochondrial DNA (mtDNA) was detected from cytosolic-enriched fractions using Real-Time PCR. Results Expression of 2-E+2-3a in 293T cells increased cytosolic Ca++ and elevated mitochondrial Ca++, taken up through the MCUi11-sensitive mitochondrial calcium uniporter. Increased mitochondrial Ca++ stimulated NADH, mitochondrial reactive oxygen species (mROS) production and the release of mtDNA into the cytosol. Expression of 2-E+2-3a in NLRP3-I reconstituted 293T cells and THP1-derived macrophages displayed increased secretion of IL-1β. Increasing mitochondrial antioxidant defenses via treatment with MnTBAP or genetic expression of mCAT abolished 2-E+2-3a elevation of mROS, cytosolic mtDNA levels, and secretion of NLRP3-activated-IL-1β. The 2-E+2-3a-induced release of mtDNA and the secretion of NLRP3-activated-IL-1β were absent in cells lacking mtDNA and blocked in cells treated with the mitochondrial-permeability-pore(mtPTP)-specific inhibitor NIM811. Conclusion Our findings revealed that mROS activates the release of mitochondrial DNA via the NIM811-sensitive mitochondrial-permeability-pore(mtPTP), activating the inflammasome. Hence, interventions targeting mROS and the mtPTP may mitigate the severity of COVID-19 cytokine storms.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick Schaefer
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Prasanth Portluri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Huang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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50
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Pérez-Vargas J, Shapira T, Olmstead AD, Villanueva I, Thompson CAH, Ennis S, Gao G, De Guzman J, Williams DE, Wang M, Chin A, Bautista-Sánchez D, Agafitei O, Levett P, Xie X, Nuzzo G, Freire VF, Quintana-Bulla JI, Bernardi DI, Gubiani JR, Suthiphasilp V, Raksat A, Meesakul P, Polbuppha I, Cheenpracha S, Jaidee W, Kanokmedhakul K, Yenjai C, Chaiyosang B, Teles HL, Manzo E, Fontana A, Leduc R, Boudreault PL, Berlinck RGS, Laphookhieo S, Kanokmedhakul S, Tietjen I, Cherkasov A, Krajden M, Nabi IR, Niikura M, Shi PY, Andersen RJ, Jean F. Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics. Antiviral Res 2023; 209:105484. [PMID: 36503013 PMCID: PMC9729583 DOI: 10.1016/j.antiviral.2022.105484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andrea D Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Meng Wang
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Aaleigha Chin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Diana Bautista-Sánchez
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Vitor F Freire
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Virayu Suthiphasilp
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Achara Raksat
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Pornphimol Meesakul
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Isaraporn Polbuppha
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | | | - Wuttichai Jaidee
- Medicinal Plants Innovation Center of Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kwanjai Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Boonyanoot Chaiyosang
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Helder Lopes Teles
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, CEP 78736-900, Rondonópolis, MT, Brazil
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, 80126, Napoli, Italy
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Surat Laphookhieo
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Somdej Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ian Tietjen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, School of Biomedical Engineering, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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