1
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Sertbas M, Ulgen KO. Uncovering the Effect of SARS-CoV-2 on Liver Metabolism via Genome-Scale Metabolic Modeling for Reprogramming and Therapeutic Strategies. ACS OMEGA 2024; 9:15535-15546. [PMID: 38585079 PMCID: PMC10993323 DOI: 10.1021/acsomega.4c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024]
Abstract
Genome-scale metabolic models (GEMs) are promising computational tools that contribute to elucidating host-virus interactions at the system level and developing therapeutic strategies against viral infection. In this study, the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on liver metabolism was investigated using integrated GEMs of human hepatocytes and SARS-CoV-2. They were generated for uninfected and infected hepatocytes using transcriptome data. Reporter metabolite analysis resulted in significant transcriptional changes around several metabolites involved in xenobiotics, drugs, arachidonic acid, and leukotriene metabolisms due to SARS-CoV-2 infection. Flux balance analysis and minimization of metabolic adjustment approaches unraveled possible virus-induced hepatocellular reprogramming in fatty acid, glycerophospholipid, sphingolipid cholesterol, and folate metabolisms, bile acid biosynthesis, and carnitine shuttle among others. Reaction knockout analysis provided critical reactions in glycolysis, oxidative phosphorylation, purine metabolism, and reactive oxygen species detoxification subsystems. Computational analysis also showed that administration of dopamine, glucosamine, D-xylose, cysteine, and (R)-3-hydroxybutanoate contributes to alleviating viral infection. In essence, the reconstructed host-virus GEM helps us understand metabolic programming and develop therapeutic strategies to battle SARS-CoV-2.
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Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
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2
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Cherif A, Basharat Z, Yaseen M, Bhat MA, Uddin I, Ziedan NI, Mabood F, Sadfi-Zouaoui N, Messaoudi A. Identification of Disalicyloyl Curcumin as a Potential DNA Polymerase Inhibitor for Marek's Disease Herpesvirus: A Computational Study Using Virtual Screening and Molecular Dynamics Simulations. Molecules 2023; 28:6576. [PMID: 37764352 PMCID: PMC10537106 DOI: 10.3390/molecules28186576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Marek's disease virus (MDV) is a highly contagious and persistent virus that causes T-lymphoma in chickens, posing a significant threat to the poultry industry despite the availability of vaccines. The emergence of new virulent strains has further intensified the challenge of designing effective antiviral drugs for MDV. In this study, our main objective was to identify novel antiviral phytochemicals through in silico analysis. We employed Alphafold to construct a three-dimensional (3D) structure of the MDV DNA polymerase, a crucial enzyme involved in viral replication. To ensure the accuracy of the structural model, we validated it using tools available at the SAVES server. Subsequently, a diverse dataset containing thousands of compounds, primarily derived from plant sources, was subjected to molecular docking with the MDV DNA polymerase model, utilizing AutoDock software V 4.2. Through comprehensive analysis of the docking results, we identified Disalicyloyl curcumin as a promising drug candidate that exhibited remarkable binding affinity, with a minimum energy of -12.66 Kcal/mol, specifically targeting the DNA polymerase enzyme. To further assess its potential, we performed molecular dynamics simulations, which confirmed the stability of Disalicyloyl curcumin within the MDV system. Experimental validation of its inhibitory activity in vitro can provide substantial support for its effectiveness. The outcomes of our study hold significant implications for the poultry industry, as the discovery of efficient antiviral phytochemicals against MDV could substantially mitigate the economic losses associated with this devastating disease.
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Affiliation(s)
- Aziza Cherif
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (A.C.); (N.S.-Z.)
| | | | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Swat 19130, Pakistan; (I.U.); (F.M.)
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Imad Uddin
- Institute of Chemical Sciences, University of Swat, Swat 19130, Pakistan; (I.U.); (F.M.)
| | - Noha I. Ziedan
- Department of Physical Mathematical and Engineering Science, University of Chester, Chester CH2 4NU, UK;
| | - Fazal Mabood
- Institute of Chemical Sciences, University of Swat, Swat 19130, Pakistan; (I.U.); (F.M.)
| | - Najla Sadfi-Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (A.C.); (N.S.-Z.)
| | - Abdelmonaem Messaoudi
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, Tunis 2092, Tunisia; (A.C.); (N.S.-Z.)
- Higher Institute of Biotechnology of Beja, Jendouba University, Habib Bourguiba Street, Beja 9000, Tunisia
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3
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Roshni J, Sivakumar M, Bahammam FA, Bhandi S, Patil S, Kamath M, Abusharha A, Ahmed SSSJ. New Ways to Protect the Host from SARS-CoV-2? Lung Microbiome Metabolites Inhibit STAT3 and Modulate the Immunological Network. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:237-244. [PMID: 37140561 DOI: 10.1089/omi.2023.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
COVID-19 caused by the SARS-CoV-2 infection is a systemic disease that affects multiple organs, biological pathways, and cell types. A systems biology approach would benefit the study of COVID-19 in the pandemic as well as the endemic state. Notably, patients with COVID-19 have dysbiosis of lung microbiota whose functional relevance to the host is largely unknown. We carried out a systems biology investigation of the impact of lung microbiome-derived metabolites on host immune system during COVID-19. RNAseq was performed to identify the host-specific pro- and anti-inflammatory differentially expressed genes (DEGs) in bronchial epithelium and alveolar cells during SARS-CoV-2 infection. The overlapping DEGs were harnessed to construct an immune network while their key transcriptional regulator was deciphered. We identified 68 overlapping genes from both cell types to construct the immune network, and Signal Transducer and Activator of Transcription 3 (STAT3) was found to regulate the majority of the network proteins. Furthermore, thymidine diphosphate produced from the lung microbiome had the highest affinity with STAT3 (-6.349 kcal/mol) than the known STAT3 inhibitors (n = 410), with an affinity ranging from -5.39 to 1.31 kcal/mol. In addition, the molecular dynamic studies showed distinguishable changes in the behavior of the STAT3 complex when compared with free STAT3. Overall, our results provide new observations on the importance of lung microbiome metabolites that regulate the host immune system in patients with COVID-19, and may open up new avenues for preventive medicine and therapeutics innovation.
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Affiliation(s)
- Jency Roshni
- Drug Discovery and Multi-omics Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Mahema Sivakumar
- Drug Discovery and Multi-omics Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Faris Ahmed Bahammam
- Fellow Rhinology and Facial Plastics, Imperial College London, London, United Kingdom
| | - Shilpa Bhandi
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, Utah, USA
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, Utah, USA
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Manjunath Kamath
- Centre for Advance Studies, Sathyabama Institute of Science and Technology, Tamil Nadu, Chennai, India
| | - Ali Abusharha
- Department of Optometry, Applied Medical Sciences College, King Saud University, Riyadh, Saudi Arabia
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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4
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Malinowska JK, Żuradzki T. Reductionist methodology and the ambiguity of the categories of race and ethnicity in biomedical research: an exploratory study of recent evidence. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2023; 26:55-68. [PMID: 36352325 PMCID: PMC9646278 DOI: 10.1007/s11019-022-10122-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual "messiness" (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics.
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Affiliation(s)
- Joanna K. Malinowska
- Faculty of Philosophy, Adam Mickiewicz University, Ul. Szamarzewskiego 89C, 60-568 Poznań, Poland
| | - Tomasz Żuradzki
- Institute of Philosophy & Interdisciplinary Centre for Ethics, Jagiellonian University, Ul. Grodzka 52, 31-044 Kraków, Poland
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5
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Artificial intelligence assessment of the potential of tocilizumab along with corticosteroids therapy for the management of COVID-19 evoked acute respiratory distress syndrome. PLoS One 2023; 18:e0280677. [PMID: 36791125 PMCID: PMC9931125 DOI: 10.1371/journal.pone.0280677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS), associated with high mortality rate, affects up to 67% of hospitalized COVID-19 patients. Early evidence indicated that the pathogenesis of COVID-19 evoked ARDS is, at least partially, mediated by hyperinflammatory cytokine storm in which interleukin 6 (IL-6) plays an essential role. The corticosteroid dexamethasone is an effective treatment for severe COVID-19 related ARDS. However, trials of other immunomodulatory therapies, including anti-IL6 agents such as tocilizumab and sarilumab, have shown limited evidence of benefit as monotherapy. But recently published large trials have reported added benefit of tocilizumab in combination with dexamethasone in severe COVID-19 related ARDS. In silico tools can be useful to shed light on the mechanisms evoked by SARS-CoV-2 infection and of the potential therapeutic approaches. Therapeutic performance mapping system (TPMS), based on systems biology and artificial intelligence, integrate available biological, pharmacological and medical knowledge to create mathematical models of the disease. This technology was used to identify the pharmacological mechanism of dexamethasone, with or without tocilizumab, in the management of COVID-19 evoked ARDS. The results showed that while dexamethasone would be addressing a wider range of pathological processes with low intensity, tocilizumab might provide a more direct and intense effect upon the cytokine storm. Based on this in silico study, we conclude that the use of tocilizumab alongside dexamethasone is predicted to induce a synergistic effect in dampening inflammation and subsequent pathological processes, supporting the beneficial effect of the combined therapy in critically ill patients. Future research will allow identifying the ideal subpopulation of patients that would benefit better from this combined treatment.
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6
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Yu W, Bai Y, Raha A, Su Z, Geng F. Integrative In Silico Investigation Reveals the Host-Virus Interactions in Repurposed Drugs Against SARS-CoV-2. FRONTIERS IN BIOINFORMATICS 2022; 1:763540. [PMID: 36303774 PMCID: PMC9580895 DOI: 10.3389/fbinf.2021.763540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
The ongoing COVID-19 outbreak have posed a significant threat to public health worldwide. Recently Toll-like receptor (TLR) has been proposed to be the drug target of SARS-CoV-2 treatment, the specificity and efficacy of such treatments remain unknown. In the present study we performed the investigation of repurposed drugs via a framework comprising of Search Tool for Interacting Chemicals (STITCH), Kyoto Encyclopedia of Genes and Genomes (KEGG), molecular docking, and virus-host-drug interactome mapping. Chloroquine (CQ) and hydroxychloroquine (HCQ) were utilized as probes to explore the interaction network that is linked to SARS-CoV-2. 47 drug targets were shown to be overlapped with SARS-CoV-2 network and were enriched in TLR signaling pathway. Molecular docking analysis and molecular dynamics simulation determined the direct binding affinity of TLR9 to CQ and HCQ. Furthermore, we established SARS-CoV-2-human-drug protein interaction map and identified the axis of TLR9-ERC1-Nsp13 and TLR9-RIPK1-Nsp12. Therefore, the elucidation of the interactions of SARS-CoV-2 with TLR9 axis will not only provide pivotal insights into SARS-CoV-2 infection and pathogenesis but also improve the treatment against COVID-19.
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Affiliation(s)
- Wenhui Yu
- Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Yuxin Bai
- Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Arjun Raha
- Department of Mechanical Engineering, McMaster University, Hamilton, ON, Canada
| | - Zhi Su
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON, Canada
| | - Fei Geng
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON, Canada
- *Correspondence: Fei Geng,
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7
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Campos-Ferreira D, Visani V, Córdula C, Nascimento G, Montenegro L, Schindler H, Cavalcanti I. COVID-19 challenges: From SARS-CoV-2 infection to effective point-of-care diagnosis by electrochemical biosensing platforms. Biochem Eng J 2021; 176:108200. [PMID: 34522158 PMCID: PMC8428033 DOI: 10.1016/j.bej.2021.108200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022]
Abstract
In January 2020, the World Health Organization (WHO) identified a new zoonotic virus, SARS-CoV-2, responsible for causing the COVID-19 (coronavirus disease 2019). Since then, there has been a collaborative trend between the scientific community and industry. Multidisciplinary research networks try to understand the whole SARS-CoV-2 pathophysiology and its relationship with the different grades of severity presented by COVID-19. The scientific community has gathered all the data in the quickly developed vaccines that offer a protective effect for all variants of the virus and promote new diagnostic alternatives able to have a high standard of efficiency, added to shorter response analysis time and portability. The industry enters in the context of accelerating the path taken by science until obtaining the final product. In this review, we show the principal diagnostic methods developed during the COVID-19 pandemic. However, when we observe the diagnostic tools section of an efficient infection outbreak containment report and the features required for such tools, we could observe a highlight of electrochemical biosensing platforms. Such devices present a high standard of analytical performance, are low-cost tools, easy to handle and interpret, and can be used in the most remote and low-resource regions. Therefore, probably, they are the ideal point-of-care diagnostic tools for pandemic scenarios.
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Affiliation(s)
- D. Campos-Ferreira
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Corresponding author
| | - V. Visani
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil
| | - C. Córdula
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil
| | - G.A. Nascimento
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Centro Acadêmico do Agreste - CAA/UFPE, Av. Marielle Franco, s/n - Km 59 - Bairro Nova Caruaru, CEP: 55.014-900 Caruaru, PE, Brazil
| | - L.M.L. Montenegro
- Fundação Oswaldo Cruz (Fiocruz), Centro de Pesquisas Instituto Aggeu Magalhães (IAM), Av. Professor Moraes Rego s/n, CEP: 50670-901 Recife, PE, Brazil
| | - H.C. Schindler
- Fundação Oswaldo Cruz (Fiocruz), Centro de Pesquisas Instituto Aggeu Magalhães (IAM), Av. Professor Moraes Rego s/n, CEP: 50670-901 Recife, PE, Brazil
| | - I.M.F. Cavalcanti
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Centro Acadêmico de Vitória – CAV/UFPE, R. Alto do Reservatório, CEP: 55 612-440 Vitória de Santo Antão, PE, Brazil
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8
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Hu S, Jiang S, Qi X, Bai R, Ye XY, Xie T. Races of small molecule clinical trials for the treatment of COVID-19: An up-to-date comprehensive review. Drug Dev Res 2021; 83:16-54. [PMID: 34762760 PMCID: PMC8653368 DOI: 10.1002/ddr.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
The coronavirus disease‐19 (COVID‐19) pandemic has become a global threat since its first outbreak at the end of 2019. Several review articles have been published recently, focusing on the aspects of target biology, drug repurposing, and mechanisms of action (MOAs) for potential treatment. This review gathers all small molecules currently in active clinical trials, categorizes them into six sub‐classes, and summarizes their clinical progress. The aim is to provide the researchers from both pharmaceutical industries and academic institutes with the handful information and dataset to accelerate their research programs in searching effective small molecule therapy for treatment of COVID‐19.
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Affiliation(s)
- Suwen Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China.,Hangzhou Huadong Medicine Group, Pharmaceutical Research Institute Co. Ltd., Hangzhou, China.,Department of Chemistry and Biochemistry Los Angeles, University of California, Los Angeles, California, USA
| | - Songwei Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Xiang Qi
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
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9
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Villar M, Urra JM, Rodríguez-Del-Río FJ, Artigas-Jerónimo S, Jiménez-Collados N, Ferreras-Colino E, Contreras M, de Mera IGF, Estrada-Peña A, Gortázar C, de la Fuente J. Characterization by Quantitative Serum Proteomics of Immune-Related Prognostic Biomarkers for COVID-19 Symptomatology. Front Immunol 2021; 12:730710. [PMID: 34566994 PMCID: PMC8457011 DOI: 10.3389/fimmu.2021.730710] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 challenges the understanding of factors affecting disease progression and severity. The identification of prognostic biomarkers and physiological processes associated with disease symptoms is relevant for the development of new diagnostic and therapeutic interventions to contribute to the control of this pandemic. To address this challenge, in this study, we used a quantitative proteomics together with multiple data analysis algorithms to characterize serum protein profiles in five cohorts from healthy to SARS-CoV-2-infected recovered (hospital discharge), nonsevere (hospitalized), and severe [at the intensive care unit (ICU)] cases with increasing systemic inflammation in comparison with healthy individuals sampled prior to the COVID-19 pandemic. The results showed significantly dysregulated proteins and associated biological processes and disorders associated to COVID-19. These results corroborated previous findings in COVID-19 studies and highlighted how the representation of dysregulated serum proteins and associated BPs increases with COVID-19 disease symptomatology from asymptomatic to severe cases. The analysis was then focused on novel disease processes and biomarkers that were correlated with disease symptomatology. To contribute to translational medicine, results corroborated the predictive value of selected immune-related biomarkers for disease recovery [Selenoprotein P (SELENOP) and Serum paraoxonase/arylesterase 1 (PON1)], severity [Carboxypeptidase B2 (CBP2)], and symptomatology [Pregnancy zone protein (PZP)] using protein-specific ELISA tests. Our results contributed to the characterization of SARS-CoV-2–host molecular interactions with potential contributions to the monitoring and control of this pandemic by using immune-related biomarkers associated with disease symptomatology.
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Affiliation(s)
- Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain.,Biochemistry Section, Faculty of Science and Chemical Technologies, and Regional Centre for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
| | - José Miguel Urra
- Immunology, Hospital General Universitario de Ciudad Real, Ciudad Real, Spain.,Medicine School, Universidad de Castilla la Mancha, Ciudad Real, Spain
| | | | - Sara Artigas-Jerónimo
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | | | - Elisa Ferreras-Colino
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Marinela Contreras
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, University of Murcia, Murcia, Spain
| | | | - Agustín Estrada-Peña
- Department of Animal Pathology, Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
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10
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Rashidi S, Tuteja R, Mansouri R, Ali-Hassanzadeh M, Shafiei R, Ghani E, Karimazar M, Nguewa P, Manzano-Román R. The main post-translational modifications and related regulatory pathways in the malaria parasite Plasmodium falciparum: An update. J Proteomics 2021; 245:104279. [PMID: 34089893 DOI: 10.1016/j.jprot.2021.104279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022]
Abstract
There are important challenges when investigating individual post-translational modifications (PTMs) or protein interaction network and delineating if PTMs or their changes and cross-talks are involved during infection, disease initiation or as a result of disease progression. Proteomics and in silico approaches now offer the possibility to complement each other to further understand the regulatory involvement of these modifications in parasites and infection biology. Accordingly, the current review highlights key expressed or altered proteins and PTMs are invisible switches that turn on and off the function of most of the proteins. PTMs include phosphorylation, glycosylation, ubiquitylation, palmitoylation, myristoylation, prenylation, acetylation, methylation, and epigenetic PTMs in P. falciparum which have been recently identified. But also other low-abundant or overlooked PTMs that might be important for the parasite's survival, infectivity, antigenicity, immunomodulation and pathogenesis. We here emphasize the PTMs as regulatory pathways playing major roles in the biology, pathogenicity, metabolic pathways, survival, host-parasite interactions and the life cycle of P. falciparum. Further validations and functional characterizations of such proteins might confirm the discovery of therapeutic targets and might most likely provide valuable data for the treatment of P. falciparum, the main cause of severe malaria in human.
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Affiliation(s)
- Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Renu Tuteja
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Reza Mansouri
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Mohammad Ali-Hassanzadeh
- Department of Immunology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Reza Shafiei
- Vector-borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Esmaeel Ghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammadreza Karimazar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Paul Nguewa
- University of Navarra, ISTUN Instituto de Salud Tropical, Department of Microbiology and Parasitology, IdiSNA (Navarra Institute for Health Research), c/Irunlarrea 1, 31008 Pamplona, Spain.
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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Rouka E, Gourgoulianis KI, Zarogiannis SG. In silico investigation of the viroporin E as a vaccine target against SARS-CoV-2. Am J Physiol Lung Cell Mol Physiol 2021; 320:L1057-L1063. [PMID: 33822639 PMCID: PMC8203416 DOI: 10.1152/ajplung.00443.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Viroporins, integral viral membrane ion channel proteins, interact with host-cell proteins deregulating physiological processes and activating inflammasomes. Severity of COVID-19 might be associated with hyperinflammation, thus we aimed at the complete immunoinformatic analysis of the SARS-CoV-2 viroporin E, P0DTC4. We also identified the human proteins interacting with P0DTC4 and the enriched molecular functions of the corresponding genes. The complete sequence of P0DTC4 in FASTA format was processed in 10 databases relative to secondary and tertiary protein structure analyses and prediction of optimal vaccine epitopes. Three more databases were accessed for the retrieval and the molecular functional characterization of the P0DTC4 human interactors. The immunoinformatics analysis resulted in the identification of 4 discontinuous B-cell epitopes along with 1 linear B-cell epitope and 11 T-cell epitopes which were found to be antigenic, immunogenic, nonallergen, nontoxin, and unable to induce autoimmunity thus fulfilling prerequisites for vaccine design. The functional enrichment analysis showed that the predicted host interactors of P0DTC4 target the cellular acetylation network. Two of the identified host-cell proteins – BRD2 and BRD4 – have been shown to be promising targets for antiviral therapy. Thus, our findings have implications for COVID-19 therapy and indicate that viroporin E could serve as a promising vaccine target against SARS-CoV-2. Validation experiments are required to complement these in silico results.
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Affiliation(s)
- Erasmia Rouka
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, Greece.,Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, Greece
| | - Sotirios G Zarogiannis
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, Greece.,Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, Greece
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