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Leibel SL, McVicar RN, Murad R, Kwong EM, Clark AE, Alvarado A, Grimmig BA, Nuryyev R, Young RE, Lee JC, Peng W, Zhu YP, Griffis E, Nowell CJ, James B, Alarcon S, Malhotra A, Gearing LJ, Hertzog PJ, Galapate CM, Galenkamp KMO, Commisso C, Smith DM, Sun X, Carlin AF, Sidman RL, Croker BA, Snyder EY. A therapy for suppressing canonical and noncanonical SARS-CoV-2 viral entry and an intrinsic intrapulmonary inflammatory response. Proc Natl Acad Sci U S A 2024; 121:e2408109121. [PMID: 39028694 PMCID: PMC11287264 DOI: 10.1073/pnas.2408109121] [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: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 07/21/2024] Open
Abstract
The prevalence of "long COVID" is just one of the conundrums highlighting how little we know about the lung's response to viral infection, particularly to syndromecoronavirus-2 (SARS-CoV-2), for which the lung is the point of entry. We used an in vitro human lung system to enable a prospective, unbiased, sequential single-cell level analysis of pulmonary cell responses to infection by multiple SARS-CoV-2 strains. Starting with human induced pluripotent stem cells and emulating lung organogenesis, we generated and infected three-dimensional, multi-cell-type-containing lung organoids (LOs) and gained several unexpected insights. First, SARS-CoV-2 tropism is much broader than previously believed: Many lung cell types are infectable, if not through a canonical receptor-mediated route (e.g., via Angiotensin-converting encyme 2(ACE2)) then via a noncanonical "backdoor" route (via macropinocytosis, a form of endocytosis). Food and Drug Administration (FDA)-approved endocytosis blockers can abrogate such entry, suggesting adjunctive therapies. Regardless of the route of entry, the virus triggers a lung-autonomous, pulmonary epithelial cell-intrinsic, innate immune response involving interferons and cytokine/chemokine production in the absence of hematopoietic derivatives. The virus can spread rapidly throughout human LOs resulting in mitochondrial apoptosis mediated by the prosurvival protein Bcl-xL. This host cytopathic response to the virus may help explain persistent inflammatory signatures in a dysfunctional pulmonary environment of long COVID. The host response to the virus is, in significant part, dependent on pulmonary Surfactant Protein-B, which plays an unanticipated role in signal transduction, viral resistance, dampening of systemic inflammatory cytokine production, and minimizing apoptosis. Exogenous surfactant, in fact, can be broadly therapeutic.
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Affiliation(s)
- Sandra L. Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
| | - Rachael N. McVicar
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Elizabeth M. Kwong
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Alex E. Clark
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Asuka Alvarado
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Bethany A. Grimmig
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Ruslan Nuryyev
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Randee E. Young
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Jamie C. Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Weiqi Peng
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Yanfang P. Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Eric Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA92093
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, VIC3052, Australia
| | - Brian James
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Suzie Alarcon
- La Jolla Institute for Immunology, La Jolla, CA92037
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA92093
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC3168, Australia
- Department of Molecular and Translational Sciences, Monash University Clayton, Clayton, VIC3168, Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC3168, Australia
- Department of Molecular and Translational Sciences, Monash University Clayton, Clayton, VIC3168, Australia
| | - Cheska M. Galapate
- Sanford Burnham Prebys Medical Discovery Institute Cell & Molecular Biology of Cancer, La Jolla, CA92037
| | - Koen M. O. Galenkamp
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Cosimo Commisso
- Sanford Burnham Prebys Medical Discovery Institute Cell & Molecular Biology of Cancer, La Jolla, CA92037
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Aaron F. Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Richard L. Sidman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Evan Y. Snyder
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
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Zhou W, You B, Zheng Y, Si S, Li Y, Zhang J. Expression, purification, and biological activity evaluation of cathepsin L in mammalian cells. Biosci Biotechnol Biochem 2024; 88:405-411. [PMID: 38271604 DOI: 10.1093/bbb/zbae005] [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: 10/17/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024]
Abstract
Cathepsin L (CTSL) could cleave and activate SARS-CoV-2 Spike protein to promote viral entry, making it a hopeful therapeutic target for COVID-19 prevention and treatment. So CTSL inhibitors are considered to be a promising strategy to SARS-CoV-2 infection. CTSL has previously been expressed in inclusion body in Escherichia coli. In order to prepare CTSL with high purity and activity in soluble active form, we transformed HEK-293T cells with a recombinant mammalian expression plasmid. CTSL was purified to a purity about 95%, found to migrate at approximately 43 kDa and exhibited substrate specificity against Z-Phe-Arg-AMC with specific activity of no less than 85 081 U/mg, characteristic of active CTSL. Although eukaryotic purified CTSL is commercially available, our study for the first time reported the details of the expression, purification, and characterization of active, recombinant CTSL in eukaryocyte system, which laid an experimental foundation for the establishment of high-throughput screening model for anti-coronavirus drugs targeting CTSL.
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Affiliation(s)
- Wenwen Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Baoqing You
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yifan Zheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Zhao S, Jiang M, Qing H, Ni J. Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets. Br J Pharmacol 2023; 180:2455-2481. [PMID: 37403614 DOI: 10.1111/bph.16187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.
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Affiliation(s)
- Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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Zulkifli ND, Zulkifle N. Insight from sirtuins interactome: topological prominence and multifaceted roles of SIRT1 in modulating immunity, aging and cancer. Genomics Inform 2023; 21:e23. [PMID: 37557919 PMCID: PMC10326532 DOI: 10.5808/gi.23003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 07/08/2023] Open
Abstract
The mammalian sirtuin family, consisting of SIRT1-SIRT7, plays a vital role in various biological processes, including cancer, diabetes, neurodegeneration, cardiovascular disease, cellular metabolism, and cellular homeostasis maintenance. Due to their involvement in these biological processes, modulating sirtuin activity seems promising to impact immune- and aging-related diseases, as well as cancer pathways. However, more understanding is required regarding the safety and efficacy of sirtuin-targeted therapies due to the complex regulatory mechanisms that govern their activity, particularly in the context of multiple targets. In this study, the interaction landscape of the sirtuin family was analyzed using a systems biology approach. A sirtuin protein-protein interaction network was built using the Cytoscape platform and analyzed using the NetworkAnalyzer and stringApp plugins. The result revealed the sirtuin family's association with numerous proteins that play diverse roles, suggesting a complex interplay between sirtuins and other proteins. Based on network topological and functional analysis, SIRT1 was identified as the most prominent among sirtuin family members, demonstrating that 25 of its protein partners are involved in cancer, 22 in innate immune response, and 29 in aging, with some being linked to a combination of two or more pathways. This study lays the foundation for the development of novel therapies that can target sirtuins with precision and efficacy. By illustrating the various interactions among the proteins in the sirtuin family, we have revealed the multifaceted roles of SIRT1 and provided a framework for their possible roles to be precisely understood, manipulated, and translated into therapeutics in the future.
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Affiliation(s)
- Nur Diyana Zulkifli
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Nurulisa Zulkifle
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
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5
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DiGuilio KM, Rybakovsky E, Baek Y, Valenzano MC, Mullin JM. The multiphasic TNF-α-induced compromise of Calu-3 airway epithelial barrier function. Exp Lung Res 2023; 49:72-85. [PMID: 37000123 DOI: 10.1080/01902148.2023.2193637] [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: 09/09/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Purpose: Airway epithelial barrier leak and the involvement of proinflammatory cytokines play a key role in a variety of diseases. This study evaluates barrier compromise by the inflammatory mediator Tumor Necrosis Factor-α (TNF-α) in the human airway epithelial Calu-3 model. Methods: We examined the effects of TNF-α on barrier function in Calu-3 cell layers using Transepithelial Electrical Resistance (TER) and transepithelial diffusion of radiolabeled probe molecules. Western immunoblot analyses of tight junctional (TJ) proteins in detergent soluble fractions were performed. Results: TNF-α dramatically reduced TER and increased paracellular permeability of both 14C-D-mannitol and the larger 5 kDa probe, 14C-inulin. A time course of the effects shows two separate actions on barrier function. An initial compromise of barrier function occurs 2-4 hours after TNF-α exposure, followed by complete recovery of barrier function by 24 hrs. Beginning 48 hrs. post-exposure, a second more sustained barrier compromise ensues, in which leakiness persists through 144 hrs. There were no changes in TJ proteins observed at 3 hrs. post exposure, but significant increases in claudins-2, -3, -4, and -5, as well as a decrease in occludin were seen at 72 hrs. post TNF-α exposure. Both the 2-4 hr. and the 72 hr. TNF-α induced leaks are shown to be mediated by the ERK signaling pathway. Conclusion: TNF-α induced a multiphasic transepithelial leak in Calu-3 cell layers that was shown to be ERK mediated, as well as involve changes in the TJ complex. The micronutrients, retinoic acid and calcitriol, were effective at reducing this barrier compromise caused by TNF-α. The significance of these results for airway disease and for COVID-19 specifically are discussed.
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Affiliation(s)
| | | | - Yoongyeong Baek
- Department of Chemistry, Drexel University, Philadelphia, PA, USA
| | | | - James M Mullin
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
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6
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Rivera RG, Regidor PJS, Ruamero Jr EC, Allanigue EJV, Salinas MV. A network pharmacology and molecular docking approach in the exploratory investigation of the biological mechanisms of lagundi (Vitex negundo L.) compounds against COVID-19. Genomics Inform 2023; 21:e4. [PMID: 37037462 PMCID: PMC10085743 DOI: 10.5808/gi.22060] [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: 09/22/2022] [Revised: 12/27/2022] [Accepted: 02/08/2023] [Indexed: 04/03/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available, treatment of the disease is primarily supportive and symptomatic. Several research have suggested the potential of herbal medicines as an adjunctive treatment for the disease. A popular herbal medicine approved in the Philippines for the treatment of acute respiratory disease is Vitex negundo L. In fact, the Department of Science and Technology of the Philippines has funded a clinical trial to establish its potential as an adjunctive treatment for COVID-19. Here, we utilized network pharmacology and molecular docking in determining pivotal targets of Vitex negundo compounds against COVID-19. The results showed that significant targets of Vitex negundo compounds in COVID-19 are CSB, SERPINE1, and PLG which code for cathepsin B, plasminogen activator inhibitor-1, and plasminogen, respectively. Molecular docking revealed that α-terpinyl acetate and geranyl acetate have good binding affinity in cathepsin B; 6,7,4-trimethoxyflavanone, 5,6,7,8,3',4',5'-heptamethoxyflavone, artemetin, demethylnobiletin, gardenin A, geranyl acetate in plasminogen; and 7,8,4-trimethoxyflavanone in plasminogen activator inhibitor-1. While the results are promising, these are bound to the limitations of computational methods and further experimentation are needed to completely establish the molecular mechanisms of Vitex negundo against COVID-19.
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Affiliation(s)
- Robertson G. Rivera
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Patrick Junard S. Regidor
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Edwin C. Ruamero Jr
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Eric John V. Allanigue
- Department of Pharmacology and Toxicology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Melanie V. Salinas
- Safety and Medical Affairs Department, Clinchoice Inc., Fort Washington, PA 19034, USA
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Avdonin PP, Rybakova EY, Trufanov SK, Avdonin PV. SARS-CoV-2 Receptors and Their Involvement in Cell Infection. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2023; 17:1-11. [PMID: 37008884 PMCID: PMC10050803 DOI: 10.1134/s1990747822060034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 03/30/2023]
Abstract
The new coronavirus infection (COVID-19) pandemic caused by SARS-CoV-2 has many times surpassed the epidemics caused by SARS-CoV and MERS-CoV. The reason for this was the presence of sites in the protein sequence of SARS-CoV-2 that provide interaction with a broader range of receptor proteins on the host cell surface. In this review, we consider both already known receptors common to SARS-CoV and SARS-CoV-2 and new receptors specific to SARS-CoV-2.
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Affiliation(s)
- P. P. Avdonin
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - E. Yu. Rybakova
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - S. K. Trufanov
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - P. V. Avdonin
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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Hasankhani A, Bahrami A, Tavakoli-Far B, Iranshahi S, Ghaemi F, Akbarizadeh MR, Amin AH, Abedi Kiasari B, Mohammadzadeh Shabestari A. The role of peroxisome proliferator-activated receptors in the modulation of hyperinflammation induced by SARS-CoV-2 infection: A perspective for COVID-19 therapy. Front Immunol 2023; 14:1127358. [PMID: 36875108 PMCID: PMC9981974 DOI: 10.3389/fimmu.2023.1127358] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a severe respiratory disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that affects the lower and upper respiratory tract in humans. SARS-CoV-2 infection is associated with the induction of a cascade of uncontrolled inflammatory responses in the host, ultimately leading to hyperinflammation or cytokine storm. Indeed, cytokine storm is a hallmark of SARS-CoV-2 immunopathogenesis, directly related to the severity of the disease and mortality in COVID-19 patients. Considering the lack of any definitive treatment for COVID-19, targeting key inflammatory factors to regulate the inflammatory response in COVID-19 patients could be a fundamental step to developing effective therapeutic strategies against SARS-CoV-2 infection. Currently, in addition to well-defined metabolic actions, especially lipid metabolism and glucose utilization, there is growing evidence of a central role of the ligand-dependent nuclear receptors and peroxisome proliferator-activated receptors (PPARs) including PPARα, PPARβ/δ, and PPARγ in the control of inflammatory signals in various human inflammatory diseases. This makes them attractive targets for developing therapeutic approaches to control/suppress the hyperinflammatory response in patients with severe COVID-19. In this review, we (1) investigate the anti-inflammatory mechanisms mediated by PPARs and their ligands during SARS-CoV-2 infection, and (2) on the basis of the recent literature, highlight the importance of PPAR subtypes for the development of promising therapeutic approaches against the cytokine storm in severe COVID-19 patients.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Bahareh Tavakoli-Far
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
- Department of Physiology and Pharmacology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Setare Iranshahi
- School of Pharmacy, Shahid Beheshty University of Medical Sciences, Tehran, Iran
| | - Farnaz Ghaemi
- Department of Biochemistry, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Majid Reza Akbarizadeh
- Department of Pediatric, School of Medicine, Amir al momenin Hospital, Zabol University of Medical Sciences, Zabol, Iran
| | - Ali H. Amin
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Bahman Abedi Kiasari
- Virology Department, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Alireza Mohammadzadeh Shabestari
- Department of Dental Surgery, Mashhad University of Medical Sciences, Mashhad, Iran
- Khorasan Covid-19 Scientific Committee, Mashhad, Iran
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Mathkor DM, Faidah H, Jalal NA, Qashqari FSI, Haque S, Bantun F. In silico identification of microRNAs targeting the PPARα/γ: promising therapeutics for SARS-CoV‑2 infection. Biotechnol Genet Eng Rev 2023:1-12. [PMID: 36708330 DOI: 10.1080/02648725.2022.2163867] [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: 08/06/2022] [Accepted: 12/26/2022] [Indexed: 01/29/2023]
Abstract
The SARS-CoV-2 lifecycle is dependent on the host metabolism machinery. It upregulates the PPARα and PPARγ genes in lipid metabolism, which supports the essential viral replication complex including lipid rafts and palmitoylation of viral protein. The use of PPAR ligands in SARS-CoV-2 infection may have positive effects by preventing cytokine storm and the ensuing inflammatory cascade. The inhibition of PPARα and PPARγ genes may alter the metabolism and may disrupt the lifecycle of SARS-CoV-2 and COVID-19 progression. In the present work, we have identified possible miRNAs targeting PPARα and PPARγ in search of modulators of PPARα and PPARγ genes expression. The identified miRNAs could possibly be viewed as new therapeutic targets against COVID-19 infection.
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Affiliation(s)
- Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Fadi S I Qashqari
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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10
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Leibel SL, McVicar RN, Murad R, Kwong EM, Clark AE, Alvarado A, Grimmig BA, Nuryyev R, Young RE, Lee JC, Peng W, Zhu YP, Griffis E, Nowell CJ, Liu K, James B, Alarcon S, Malhotra A, Gearing LJ, Hertzog PJ, Galapate CM, Galenkamp KM, Commisso C, Smith DM, Sun X, Carlin AF, Croker BA, Snyder EY. The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525578. [PMID: 36747824 PMCID: PMC9900938 DOI: 10.1101/2023.01.26.525578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.
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11
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Khatoon F, Haque S, Hashem A, Mahmoud A, Tashkandi H, Mathkor D, Harakeh S, Alghamdi B, Kumar V. Network-based approach for targeting human kinases commonly associated with amyotrophic lateral sclerosis and cancer. Front Mol Neurosci 2022; 15:1023286. [PMID: 36590916 PMCID: PMC9802580 DOI: 10.3389/fnmol.2022.1023286] [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: 08/19/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Background Amyotrophic Lateral Sclerosis (ALS) is a rare progressive and chronic motor neuron degenerative disease for which at present no cure is available. In recent years, multiple genes encode kinases and other causative agents for ALS have been identified. Kinases are enzymes that show pleiotropic nature and regulate different signal transduction processes and pathways. The dysregulation of kinase activity results in dramatic changes in processes and causes many other human diseases including cancers. Methods In this study, we have adopted a network-based system biology approach to investigate the kinase-based molecular interplay between ALS and other human disorders. A list of 62 ALS-associated-kinases was first identified and then we identified the disease associated with them by scanning multiple disease-gene interaction databases to understand the link between the ALS-associated kinases and other disorders. Results An interaction network with 36 kinases and 381 different disorders associated with them was prepared, which represents the complexity and the comorbidity associated with the kinases. Further, we have identified 5 miRNAs targeting the majority of the kinases in the disease-causing network. The gene ontology and pathways enrichment analysis of those miRNAs were performed to understand their biological and molecular functions along with to identify the important pathways. We also identified 3 drug molecules that can perturb the disease-causing network by drug repurposing. Conclusion This network-based study presented hereby contributes to a better knowledge of the molecular underpinning of comorbidities associated with the kinases associated with the ALS disease and provides the potential therapeutic targets to disrupt the highly complex disease-causing network.
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Affiliation(s)
- Fatima Khatoon
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, Uttar Pradesh, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Anwar Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmad Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Hanaa Tashkandi
- Department of General Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Darin Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Badra Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vijay Kumar
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Kumar,
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12
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Castrejón-Jiménez NS, García-Pérez BE, Reyes-Rodríguez NE, Vega-Sánchez V, Martínez-Juárez VM, Hernández-González JC. Challenges in the Detection of SARS-CoV-2: Evolution of the Lateral Flow Immunoassay as a Valuable Tool for Viral Diagnosis. BIOSENSORS 2022; 12:bios12090728. [PMID: 36140114 PMCID: PMC9496238 DOI: 10.3390/bios12090728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 is an emerging infectious disease of zoonotic origin that caused the coronavirus disease in late 2019 and triggered a pandemic that has severely affected human health and caused millions of deaths. Early and massive diagnosis of SARS-CoV-2 infected patients is the key to preventing the spread of the virus and controlling the outbreak. Lateral flow immunoassays (LFIA) are the simplest biosensors. These devices are clinical diagnostic tools that can detect various analytes, including viruses and antibodies, with high sensitivity and specificity. This review summarizes the advantages, limitations, and evolution of LFIA during the SARS-CoV-2 pandemic and the challenges of improving these diagnostic devices.
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Affiliation(s)
- Nayeli Shantal Castrejón-Jiménez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Exhacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Mexico
| | - Blanca Estela García-Pérez
- Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, México City 11340, Mexico
| | - Nydia Edith Reyes-Rodríguez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Exhacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Mexico
| | - Vicente Vega-Sánchez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Exhacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Mexico
| | - Víctor Manuel Martínez-Juárez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Exhacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Mexico
| | - Juan Carlos Hernández-González
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km 1 Exhacienda de Aquetzalpa A.P. 32, Tulancingo 43600, Mexico
- Correspondence: ; Tel.: +52-775-756-0308
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13
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The immunology and immunotherapy for COVID-19. Expert Rev Mol Med 2021; 23:e24. [PMID: 34915958 PMCID: PMC8723987 DOI: 10.1017/erm.2021.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and significantly impacts the world economy and daily life. Symptoms of COVID-19 range from asymptomatic to fever, dyspnoea, acute respiratory distress and multiple organ failure. Critical cases often occur in the elderly and patients with pre-existing conditions. By binding to the angiotensin-converting enzyme 2 receptor, SARS-CoV-2 can enter and replicate in the host cell, exerting a cytotoxic effect and causing local and systemic inflammation. Currently, there is no specific treatment for COVID-19, and immunotherapy has consistently attracted attention because of its essential role in boosting host immunity to the virus and reducing overwhelming inflammation. In this review, we summarise the immunopathogenic features of COVID-19 and highlight recent advances in immunotherapy to illuminate ideas for the development of new potential therapies.
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14
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Insights into the SARS-CoV-2-Mediated Alteration in the Stress Granule Protein Regulatory Networks in Humans. Pathogens 2021; 10:pathogens10111459. [PMID: 34832615 PMCID: PMC8624858 DOI: 10.3390/pathogens10111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022] Open
Abstract
The rapidly and constantly evolving coronavirus, SARS-CoV-2, imposes a great threat to human health causing severe lung disease and significant mortality. Cytoplasmic stress granules (SGs) exert anti-viral activities due to their involvement in translation inhibition and innate immune signaling. SARS-CoV-2 sequesters important SG nucleator proteins and impairs SG formation, thus evading the host response for efficient viral replication. However, the significance of SGs in COVID-19 infection remains elusive. In this study, we utilize a protein-protein interaction network approach to systematically dissect the crosstalk of human post-translational regulatory networks governed by SG proteins due to SARS-CoV-2 infection. We uncovered that 116 human SG proteins directly interact with SARS-CoV-2 proteins and are involved in 430 different brain disorders including COVID-19. Further, we performed gene set enrichment analysis to identify the drugs against three important key SG proteins (DYNC1H1, DCTN1, and LMNA) and also looked for potential microRNAs (miRNAs) targeting these proteins. We identified bexarotene as a potential drug molecule and miRNAs, hsa-miR-615-3p, hsa-miR-221-3p, and hsa-miR-124-3p as potential candidates for the treatment of COVID-19 and associated manifestations.
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