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Barh D, Aljabali AA, Tambuwala MM, Tiwari S, Serrano-Aroca Á, Alzahrani KJ, Silva Andrade B, Azevedo V, Ganguly NK, Lundstrom K. Predicting COVID-19-Comorbidity Pathway Crosstalk-Based Targets and Drugs: Towards Personalized COVID-19 Management. Biomedicines 2021; 9:556. [PMID: 34067609 PMCID: PMC8156524 DOI: 10.3390/biomedicines9050556] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
It is well established that pre-existing comorbid conditions such as hypertension, diabetes, obesity, cardiovascular diseases (CVDs), chronic kidney diseases (CKDs), cancers, and chronic obstructive pulmonary disease (COPD) are associated with increased severity and fatality of COVID-19. The increased death from COVID-19 is due to the unavailability of a gold standard therapeutic and, more importantly, the lack of understanding of how the comorbid conditions and COVID-19 interact at the molecular level, so that personalized management strategies can be adopted. Here, using multi-omics data sets and bioinformatics strategy, we identified the pathway crosstalk between COVID-19 and diabetes, hypertension, CVDs, CKDs, and cancers. Further, shared pathways and hub gene-based targets for COVID-19 and its associated specific and combination of comorbid conditions are also predicted towards developing personalized management strategies. The approved drugs for most of these identified targets are also provided towards drug repurposing. Literature supports the involvement of our identified shared pathways in pathogenesis of COVID-19 and development of the specific comorbid condition of interest. Similarly, shared pathways- and hub gene-based targets are also found to have potential implementations in managing COVID-19 patients. However, the identified targets and drugs need further careful evaluation for their repurposing towards personalized treatment of COVID-19 cases having pre-existing specific comorbid conditions we have considered in this analysis. The method applied here may also be helpful in identifying common pathway components and targets in other disease-disease interactions too.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Alaa A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK;
| | - Sandeep Tiwari
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia;
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié 45206-190, Brazil;
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Nirmal Kumar Ganguly
- National Institute of Immunology, Aruna Asaf Ali Marg, Jawaharlal Nehru University, New Delhi 110067, India;
- Institute of Liver and Biliary Science, New Delhi 110070, India
- Policy Center for Biomedical Research, Translational Health Science & Technology Institute, Faridabad 121001, India
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52
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He DD, Zhang XK, Zhu XY, Huang FF, Wang Z, Tu JC. Network pharmacology and RNA-sequencing reveal the molecular mechanism of Xuebijing injection on COVID-19-induced cardiac dysfunction. Comput Biol Med 2021; 131:104293. [PMID: 33662681 PMCID: PMC7899014 DOI: 10.1016/j.compbiomed.2021.104293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Up to 20%-30% of patients hospitalized with COVID-19 have evidence of cardiac dysfunction. Xuebijing injection is a compound injection containing five traditional Chinese medicine ingredients, which can protect cells from SARS-CoV-2-induced cell death and improve cardiac function. However, the specific protective mechanism of Xuebijing injection on COVID-19-induced cardiac dysfunction remains unclear. METHODS The therapeutic effect of Xuebijing injection on COVID-19 was validated by the TCM Anti COVID-19 (TCMATCOV) platform. RNA-sequencing (RNA-seq) data from GSE150392 was used to find differentially expressed genes (DEGs) from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) infected with SARS-CoV-2. Data from GSE151879 was used to verify the expression of Angiotensin I Converting Enzyme 2 (ACE2) and central hub genes in both human embryonic-stem-cell-derived cardiomyocytes (hESC-CMs) and adult human CMs with SARS-CoV-2 infection. RESULTS A total of 97 proteins were identified as the therapeutic targets of Xuebijing injection for COVID-19. There were 22 DEGs in SARS-CoV-2 infected hiPSC-CMs overlapped with the 97 therapeutic targets, which might be the therapeutic targets of Xuebijing injection on COVID-19-induced cardiac dysfunction. Based on the bioinformatics analysis, 7 genes (CCL2, CXCL8, FOS, IFNB1, IL-1A, IL-1B, SERPINE1) were identified as central hub genes and enriched in pathways including cytokines, inflammation, cell senescence and oxidative stress. ACE2, the receptor of SARS-CoV-2, and the 7 central hub genes were differentially expressed in at least two kinds of SARS-CoV-2 infected CMs. Besides, FOS and quercetin exhibited the tightest binding by molecular docking analysis. CONCLUSION Our study indicated the underlying protective effect of Xuebijing injection on COVID-19, especially on COVID19-induced cardiac dysfunction, which provided the theoretical basis for exploring the potential protective mechanism of Xuebijing injection on COVID19-induced cardiac dysfunction.
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Affiliation(s)
- Ding-Dong He
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China
| | - Xiao-Kang Zhang
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China
| | - Xin-Yu Zhu
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China
| | - Fang-Fang Huang
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China
| | - Zi Wang
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China
| | - Jian-Cheng Tu
- Department & Program of Clinical Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430071, PR China.
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Padhi S, Sanjukta S, Chourasia R, Labala RK, Singh SP, Rai AK. A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study. Front Mol Biosci 2021; 8:636647. [PMID: 33869283 PMCID: PMC8044374 DOI: 10.3389/fmolb.2021.636647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
Fermented soybean products are traditionally consumed and popular in many Asian countries and the northeastern part of India. To search for potential agents for the interruption of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike glycoprotein 1 (S1) and human angiotensin-converting enzyme 2 (ACE2) receptor interactions, the in silico antiviral prospective of peptides identified from the proteome of kinema was investigated. Soybean was fermented using Bacillus licheniformis KN1G, Bacillus amyloliquefaciens KN2G and two different strains of Bacillus subtilis (KN2B and KN2M). The peptides were screened in silico for possible antiviral activity using two different web servers (AVPpred and meta-iAVP), and binding interactions of selected 44 peptides were further explored against the receptor-binding domain (RBD) of the S1 protein (PDB ID: 6M0J) by molecular docking using ZDOCK. The results showed that a peptide ALPEEVIQHTFNLKSQ (P13) belonging to B. licheniformis KN1G fermented kinema was able to make contacts with the binding motif of RBD by blocking specific residues designated as critical (GLN493, ASN501) in the binding of human angiotensin-converting enzyme 2 (ACE2) cell receptor. The selected peptide was also observed to have a significant affinity towards human toll like receptor 4 (TLR4)/Myeloid Differentiation factor 2 (MD2) (PDB ID: 3FXI) complex known for its essential role in cytokine storm. The energy properties of the docked complexes were analyzed through the Generalized Born model and Solvent Accessibility method (MM/GBSA) using HawkDock server. The results showed peptidyl amino acids GLU5, GLN8, PHE11, and LEU13 contributed most to P13-RBD binding. Similarly, ARG90, PHE121, LEU61, PHE126, and ILE94 were appeared to be significant in P13-TLR4/MD2 complex. The findings of the study suggest that the peptides from fermented soy prepared using B. licheniformis KN1G have better potential to be used as antiviral agents. The specific peptide ALPEEVIQHTFNLKSQ could be synthesized and used in combination with experimental studies to validate its effect on SARS-CoV-2-hACE2 interaction and modulation of TLR4 activity. Subsequently, the protein hydrolysate comprising these peptides could be used as prophylaxis against viral diseases, including COVID-19.
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Affiliation(s)
- Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Sudhir P. Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit K. Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
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Peter AE, Sandeep BV, Rao BG, Kalpana VL. Nanotechnology to the Rescue: Treatment Perspective for the Immune Dysregulation Observed in COVID-19. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.644023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The study of the use of nanotechnology for drug delivery has been extensive. Nanomedical approaches for therapeutics; drug delivery in particular is superior to conventional methods in that it allows for controlled targeted delivery and release, higher stability, extended circulation time, minimal side-effects, and improved pharmacokinetic clearance (of the drug) form the body, to name a few. The magnitude of COVID-19, the current ongoing pandemic has been severe; it has caused widespread the loss of human life. In individuals with severe COVID-19, immune dysregulation and a rampant state of hyperinflammation is observed. This kind of an immunopathological response is detrimental and results in rapid disease progression, development of secondary infections, sepsis and can be fatal. Several studies have pin-pointed the reason for this immune dysregulation; deviations in the signaling pathways involved in the mediation and control of immune responses. In severe COVID-19 patients, many signaling cascades including JAK/STAT, NF-κB, MAPK/ERK, TGF beta, VEGF, and Notch signaling were found to be either upregulated or inactivated. Targeting these aberrant signaling pathways in conjunction with antiviral therapy will effectuate mitigation of the hyperinflammation, hypercytokinemia, and promote faster recovery. The science of the use of nanocarriers as delivery agents to modulate these signaling pathways is not new; it has already been explored for other inflammatory diseases and in particular, cancer therapy. Numerous studies have evaluated the efficacy and potential of nanomedical approaches to modulate these signaling pathways and have been met with positive results. A treatment regime, that includes nanotherapeutics and antiviral therapies will prove effective and holds great promise for the successful treatment of COVID-19. In this article, we review different nanomedical approaches already studied for targeting aberrant signaling pathways, the host immune response to SARS-CoV-2, immunopathology and the dysregulated signaling pathways observed in severe COVID-19 and the current treatment methods in use for targeting signaling cascades in COVID-19. We then conclude by suggesting that the use of nanomedical drug delivery systems for targeting signaling pathways can be extended to effectively target the aberrant signaling pathways in COVID-19 for best treatment results.
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Esposito P, Cipriani L, Verzola D, Grignano MA, De Amici M, Testa G, Grosjean F, Russo E, Garibotto G, Rampino T, Viazzi F. Effects of Different Dialysis Strategies on Inflammatory Cytokine Profile in Maintenance Hemodialysis Patients with COVID-19: A Randomized Trial. J Clin Med 2021; 10:jcm10071383. [PMID: 33808205 PMCID: PMC8037035 DOI: 10.3390/jcm10071383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 02/06/2023] Open
Abstract
Uncontrolled inflammation plays a relevant role in the pathogenesis of coronavirus disease-19 (COVID-19). Here, we studied the time trend of inflammatory markers in a population of hemodialysis (HD) patients affected by COVID-19, undergoing two different dialysis approaches. In a prospective study, thirty-one maintenance HD patients with COVID-19 were randomized to expanded HD (HDx), performed using a medium cut-off membrane, or standard treatment using a protein-leaking dialyzer (PLD). Circulating levels of interleukin-6 (IL-6), interleukin-8 (IL-8), interleukin-10 (IL-10), soluble TLR4 (sTLR4), and interferon-gamma (IFN-γ), were collected at diagnosis, and one and two weeks after. Compared with 14 non-infected HD patients, COVID-19 patients showed lymphopenia and higher ferritin and lactate dehydrogenase levels. Moreover, COVID-19 patients had higher levels of IL-10 (15.2 (12.5) vs. 1.2 (1.4) pg/mL, p = 0.02). Twenty-nine patients were randomized to HDx (n = 15) or PLD (n = 14). After a single treatment, IL-8 showed a significant reduction in both groups, whereas IL-10 decreased only in HDx. All over the study, there were no significant modifications in circulating cytokine levels between the two groups, except for a parallel increase of IL-8 and IL-10 at one week control in the HDx group. No correlations were found between cytokine levels and clinical outcomes. In maintenance HD patients, COVID-19 is not related to a sustained inflammatory response. Therefore, modulation of inflammation seems not to be a suitable therapeutic target in this specific population.
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Affiliation(s)
- Pasquale Esposito
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
- IRCCS Ospedale Policlinico San Martino, Clinica Nefrologica, Dialisi, Trapianto, 16132 Genova, Italy
- Correspondence:
| | - Leda Cipriani
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
| | - Daniela Verzola
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
| | - Maria Antonietta Grignano
- Unit of Nephrology, Dialysis and Transplantation, Fondazione IRCCS Policlinico San Matteo, and University of Pavia, 27100 Pavia, Italy; (M.A.G.); (F.G.); (T.R.)
| | - Mara De Amici
- Laboratory of Immuno-Allergology of Clinical Chemistry and Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Giorgia Testa
- Pediatrics Clinic, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy;
| | - Fabrizio Grosjean
- Unit of Nephrology, Dialysis and Transplantation, Fondazione IRCCS Policlinico San Matteo, and University of Pavia, 27100 Pavia, Italy; (M.A.G.); (F.G.); (T.R.)
| | - Elisa Russo
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
| | - Giacomo Garibotto
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
| | - Teresa Rampino
- Unit of Nephrology, Dialysis and Transplantation, Fondazione IRCCS Policlinico San Matteo, and University of Pavia, 27100 Pavia, Italy; (M.A.G.); (F.G.); (T.R.)
| | - Francesca Viazzi
- Department of Internal Medicine, University of Genova, 16132 Genova, Italy; (L.C.); (D.V.); (E.R.); (G.G.); (F.V.)
- IRCCS Ospedale Policlinico San Martino, Clinica Nefrologica, Dialisi, Trapianto, 16132 Genova, Italy
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Quitadamo PA, Comegna L, Cristalli P. Anti-Infective, Anti-Inflammatory, and Immunomodulatory Properties of Breast Milk Factors for the Protection of Infants in the Pandemic From COVID-19. Front Public Health 2021; 8:589736. [PMID: 33738273 PMCID: PMC7960784 DOI: 10.3389/fpubh.2020.589736] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
COVID-19 pandemic since the end of 2019 spreads worldwide, counting millions of victims. The viral invasion, systemic inflammation, and consequent organ failure are the gravest features of coronavirus disease 2019 (COVID-19), and they are associated with a high mortality rate. The aim of this study is to evaluate the role of breast milk in the COVID-19 pandemic, analyzing its antiviral, anti-inflammatory, and immunoregulatory effects due to its bioactive components, so numerous and important for the protection of infants. The study tried to demonstrate that all the components of human milk are capable of performing functions on all the pathogenic events recognized and described in COVID-19 disease. Those human milk factors are well-tolerated and practically free of side effects, so breast milk should become a research topic to discover therapies even in this epidemic. In the first part, the mechanisms of protection and defense of the breast milk elements will be delineated; in the second section, it will describe the human milk effects in viral infections and it will be hypothesized how the known mechanisms could act in COVID infection.
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Affiliation(s)
- Pasqua Anna Quitadamo
- NICU “Casa Sollievo della Sofferenza” Foundation, Scientific Research and Care Institute, San Giovanni Rotondo, Italy
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Zhang R, Hristovski D, Schutte D, Kastrin A, Fiszman M, Kilicoglu H. Drug repurposing for COVID-19 via knowledge graph completion. J Biomed Inform 2021; 115:103696. [PMID: 33571675 PMCID: PMC7869625 DOI: 10.1016/j.jbi.2021.103696] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. METHODS We propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from PubMed and other COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative and accurate subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant. We used this subset to construct a knowledge graph, and applied five state-of-the-art, neural knowledge graph completion algorithms (i.e., TransE, RotatE, DistMult, ComplEx, and STELP) to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. RESULTS Accuracy classifier based on PubMedBERT achieved the best performance (F1 = 0.854) in identifying accurate semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1 = 0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as others that have not yet been studied. Discovery patterns enabled identification of additional candidate drugs and generation of plausible hypotheses regarding the links between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (i.e., paclitaxel, SB 203580, alpha 2-antiplasmin, metoclopramide, and oxymatrine) and the mechanistic explanations for their potential use are further discussed. CONCLUSION We showed that a LBD approach can be feasible not only for discovering drug candidates for COVID-19, but also for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions. Source code and data are available at https://github.com/kilicogluh/lbd-covid.
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Affiliation(s)
- Rui Zhang
- Institute for Health Informatics and Department of Pharmaceutical Care & Health Systems, University of Minnesota, MN, USA.
| | - Dimitar Hristovski
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Dalton Schutte
- Institute for Health Informatics and Department of Pharmaceutical Care & Health Systems, University of Minnesota, MN, USA
| | - Andrej Kastrin
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marcelo Fiszman
- NITES - Núcleo de Inovação e Tecnologia Em Saúde, Pontifical Catholic University of Rio de Janeiro, Brazil
| | - Halil Kilicoglu
- School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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Zhang J, Li Q, Cruz Cosme RS, Gerzanich V, Tang Q, Simard JM, Zhao RY. Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. mBio 2021; 13:e0016922. [PMID: 35164548 PMCID: PMC8844912 DOI: 10.1128/mbio.00169-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Therapeutic inhibition of critical viral functions is important for curtailing coronavirus disease 2019 (COVID-19). We sought to identify antiviral targets through the genome-wide characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins that are crucial for viral pathogenesis and that cause harmful cytopathogenic effects. All 29 viral proteins were tested in a fission yeast cell-based system using inducible gene expression. Twelve proteins, including eight nonstructural proteins (NSP1, NSP3, NSP4, NSP5, NSP6, NSP13, NSP14, and NSP15) and four accessory proteins (ORF3a, ORF6, ORF7a, and ORF7b), were identified that altered cellular proliferation and integrity and induced cell death. Cell death correlated with the activation of cellular oxidative stress. Of the 12 proteins, ORF3a was chosen for further study in mammalian cells because it plays an important role in viral pathogenesis and its activities are linked to lung tissue damage and a cytokine storm. In human pulmonary and kidney epithelial cells, ORF3a induced cellular oxidative stress associated with apoptosis and necrosis and caused activation of proinflammatory response with production of the cytokines tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and IFN-β1, possibly through the activation of nuclear factor kappa B (NF-κB). To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, ΔG188. Compared with wild-type ORF3a, the ΔG188 variant yielded more robust activation of cellular oxidative stress, cell death, and innate immune response. Since cellular oxidative stress and inflammation contribute to cell death and tissue damage linked to the severity of COVID-19, our findings suggest that ORF3a is a promising, novel therapeutic target against COVID-19. IMPORTANCE The ongoing COVID-19 pandemic caused by SARS-CoV-2 has claimed over 5.5 million lives with more than 300 million people infected worldwide. While vaccines are effective, the emergence of new viral variants could jeopardize vaccine protection. Treatment of COVID-19 by antiviral drugs provides an alternative to battle against the disease. The goal of this study was to identify viral therapeutic targets that can be used in antiviral drug discovery. Utilizing a genome-wide functional analysis in a fission yeast cell-based system, we identified 12 viral candidates, including ORF3a, which cause cellular oxidative stress, inflammation, apoptosis, and necrosis that contribute to cytopathogenicity and COVID-19. Our findings indicate that antiviral agents targeting ORF3a could have a great impact on COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qi Li
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth S. Cruz Cosme
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Volodymyr Gerzanich
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Surgical Care Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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Interaction of TLR4 and TLR8 in the Innate Immune Response against Mycobacterium Tuberculosis. Int J Mol Sci 2021; 22:ijms22041560. [PMID: 33557133 PMCID: PMC7913854 DOI: 10.3390/ijms22041560] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
The interaction and crosstalk of Toll-like receptors (TLRs) is an established pathway in which the innate immune system recognises and fights pathogens. In a single nucleotide polymorphisms (SNP) analysis of an Indian cohort, we found evidence for both TLR4-399T and TRL8-1A conveying increased susceptibility towards tuberculosis (TB) in an interdependent manner, even though there is no established TLR4 ligand present in Mycobacterium tuberculosis (Mtb), which is the causative pathogen of TB. Docking studies revealed that TLR4 and TLR8 can build a heterodimer, allowing interaction with TLR8 ligands. The conformational change of TLR4-399T might impair this interaction. With immunoprecipitation and mass spectrometry, we precipitated TLR4 with TLR8-targeted antibodies, indicating heterodimerisation. Confocal microscopy confirmed a high co-localisation frequency of TLR4 and TLR8 that further increased upon TLR8 stimulation. The heterodimerisation of TLR4 and TLR8 led to an induction of IL12p40, NF-κB, and IRF3. TLR4-399T in interaction with TLR8 induced an increased NF-κB response as compared to TLR4-399C, which was potentially caused by an alteration of subsequent immunological pathways involving type I IFNs. In summary, we present evidence that the heterodimerisation of TLR4 and TLR8 at the endosome is involved in Mtb recognition via TLR8 ligands, such as microbial RNA, which induces a Th1 response. These findings may lead to novel targets for therapeutic interventions and vaccine development regarding TB.
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Aboudounya MM, Heads RJ. COVID-19 and Toll-Like Receptor 4 (TLR4): SARS-CoV-2 May Bind and Activate TLR4 to Increase ACE2 Expression, Facilitating Entry and Causing Hyperinflammation. Mediators Inflamm 2021; 2021:8874339. [PMID: 33505220 PMCID: PMC7811571 DOI: 10.1155/2021/8874339] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
Causes of mortality from COVID-19 include respiratory failure, heart failure, and sepsis/multiorgan failure. TLR4 is an innate immune receptor on the cell surface that recognizes pathogen-associated molecular patterns (PAMPs) including viral proteins and triggers the production of type I interferons and proinflammatory cytokines to combat infection. It is expressed on both immune cells and tissue-resident cells. ACE2, the reported entry receptor for SARS-CoV-2, is only present on ~1-2% of the cells in the lungs or has a low pulmonary expression, and recently, the spike protein has been proposed to have the strongest protein-protein interaction with TLR4. Here, we review and connect evidence for SARS-CoV-1 and SARS-CoV-2 having direct and indirect binding to TLR4, together with other viral precedents, which when combined shed light on the COVID-19 pathophysiological puzzle. We propose a model in which the SARS-CoV-2 spike glycoprotein binds TLR4 and activates TLR4 signalling to increase cell surface expression of ACE2 facilitating entry. SARS-CoV-2 also destroys the type II alveolar cells that secrete pulmonary surfactants, which normally decrease the air/tissue surface tension and block TLR4 in the lungs thus promoting ARDS and inflammation. Furthermore, SARS-CoV-2-induced myocarditis and multiple-organ injury may be due to TLR4 activation, aberrant TLR4 signalling, and hyperinflammation in COVID-19 patients. Therefore, TLR4 contributes significantly to the pathogenesis of SARS-CoV-2, and its overactivation causes a prolonged or excessive innate immune response. TLR4 appears to be a promising therapeutic target in COVID-19, and since TLR4 antagonists have been previously trialled in sepsis and in other antiviral contexts, we propose the clinical trial testing of TLR4 antagonists in the treatment of severe COVID-19. Also, ongoing clinical trials of pulmonary surfactants in COVID-19 hold promise since they also block TLR4.
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Affiliation(s)
- Mohamed M. Aboudounya
- Department of Cardiology, The Rayne Institute, St Thomas' Hospital, British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, UK
| | - Richard J. Heads
- Department of Cardiology, The Rayne Institute, St Thomas' Hospital, British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, UK
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Matteucci C, Minutolo A, Balestrieri E, Petrone V, Fanelli M, Malagnino V, Ianetta M, Giovinazzo A, Barreca F, Di Cesare S, De Marco P, Miele MT, Toschi N, Mastino A, Sinibaldi Vallebona P, Bernardini S, Rogliani P, Sarmati L, Andreoni M, Grelli S, Garaci E. Thymosin Alpha 1 Mitigates Cytokine Storm in Blood Cells From Coronavirus Disease 2019 Patients. Open Forum Infect Dis 2020; 8:ofaa588. [PMID: 33506065 PMCID: PMC7798699 DOI: 10.1093/ofid/ofaa588] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is characterized by immune-mediated lung injury and complex alterations of the immune system, such as lymphopenia and cytokine storm, that have been associated with adverse outcomes underlining a fundamental role of host response in severe acute respiratory syndrome coronavirus 2 infection and the pathogenesis of the disease. Thymosin alpha 1 (Tα1) is one of the molecules used in the management of COVID-19, because it is known to restore the homeostasis of the immune system during infections and cancer. Methods In this study, we captured the interconnected biological processes regulated by Tα1 in CD8+ T cells under inflammatory conditions. Results Genes associated with cytokine signaling and production were upregulated in blood cells from patients with COVID-19, and the ex vivo treatment with Tα1-mitigated cytokine expression, and inhibited lymphocyte activation in a CD8+ T-cell subset specifically. Conclusion These data suggest the potential role of Tα1 in modulating the immune response homeostasis and the cytokine storm in vivo.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Marialaura Fanelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Marco Ianetta
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | | | - Filippo Barreca
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Silvia Di Cesare
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Diseases, Academic Department of Pediatrics, Bambino Gesù Childrens' Hospital-Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - Patrizia De Marco
- Respiratory Medicine Unit, University Hospital Policlinico Tor Vergata, Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Athinoula A. Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Mastino
- Institute of Translational Pharmacology, National Research Council, Rome, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Paola Sinibaldi Vallebona
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Respiratory Medicine Unit, University Hospital Policlinico Tor Vergata, Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Infectious Diseases Clinic, Policlinic of Tor Vergata, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Virology Unit, Policlinic of Tor Vergata, Rome, Italy
| | - Enrico Garaci
- University San Raffaele, Rome, Italy.,IRCCS San Raffaele Pisana, Rome, Italy
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Dezfuli NK, Adcock IM, Montazami N, Mortaz E, Velayati A. Update on Immunology of COVID-19 Disease and Potential Strategy for Controlling. TANAFFOS 2020; 19:274-290. [PMID: 33959165 PMCID: PMC8088154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/12/2020] [Indexed: 11/02/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel form of the coronavirus that caused severe acute respiratory syndrome (SARS). SARS-CoV-2 raised in China and has broadcast to 261 countries globally. SARS-CoV-2 a member of β-coronavirus family and has an almost matching genome sequence to a bat coronavirus, pointing to the bat as the natural host before it was transmitted to humans. SARS-CoV-2 uses the same receptor, angiotensin-converting enzyme 2 (ACE2) as that used by SARS-CoV and principally infects the respiratory tract. The clinical symptoms of COVID-19 patients include fever, cough and fatigue whilst small populations of patients have gastrointestinal symptoms. The old people and people with underlying metabolic and cardiovascular diseases are more affected to infection and have worse outcomes. These may be associated with acute respiratory distress syndrome (ARDS) and a cytokine storm. In this review, we discuss the pathogenesis and clinical characteristics of disease and the pharmacologic approaches that may control COVID-19.
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Affiliation(s)
- Neda K. Dezfuli
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Ian M Adcock
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Nooshin Montazami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Esmaeil Mortaz
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aliakbar Velayati
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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