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Perovic V, Glisic S, Veljkovic M, Paessler S, Veljkovic V. In Silico Exploration of CD200 as a Therapeutic Target for COVID-19. Microorganisms 2024; 12:1185. [PMID: 38930566 PMCID: PMC11205781 DOI: 10.3390/microorganisms12061185] [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: 05/20/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
SARS-CoV-2, the pathogen causing COVID-19, continues to pose a significant threat to public health and has had major economic implications. Developing safe and effective vaccines and therapies offers a path forward for overcoming the COVID-19 pandemic. The presented study, performed by using the informational spectrum method (ISM), representing an electronic biology-based tool for analysis of protein-protein interactions, identified the highly conserved region of spike protein (SP) from SARS-CoV-2 virus, which is essential for recognition and targeting between the virus and its protein interactors on the target cells. This domain is suggested as a promising target for the drug therapy and vaccines, which could be effective against all currently circulating variants of SARS-CoV-2 viruses. The analysis of the virus/host interaction, performed by the ISM, also revealed OX-2 membrane glycoprotein (CD200) as a possible interactor of SP, which could serve as a novel therapeutic target for COVID-19 disease.
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Affiliation(s)
- Vladimir Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia;
| | - Sanja Glisic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia;
| | - Milena Veljkovic
- Department of Clinical Laboratory Medicine, Hospital for Cerebrovascular Diseases Sveti Sava, 11000 Belgrade, Serbia
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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Perovic V, Glisic S, Veljkovic M, Paessler S, Veljkovic V. Novel Entropy-Based Phylogenetic Algorithm: A New Approach for Classifying SARS-CoV-2 Variants. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1463. [PMID: 37895584 PMCID: PMC10606860 DOI: 10.3390/e25101463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is known for its genetic diversity. Virus variants of concern (VOCs) as well as variants of interest (VOIs) are classified by the World Health Organization (WHO) according to their potential risk to global health. This study seeks to enhance the identification and classification of such variants by developing a novel bioinformatics criterion centered on the virus's spike protein (SP1), a key player in host cell entry, immune response, and a mutational hotspot. To achieve this, we pioneered a unique phylogenetic algorithm which calculates EIIP-entropy as a distance measure based on the distribution of the electron-ion interaction potential (EIIP) of amino acids in SP1. This method offers a comprehensive, scalable, and rapid approach to analyze large genomic data sets and predict the impact of specific mutations. This innovative approach provides a robust tool for classifying emergent SARS-CoV-2 variants into potential VOCs or VOIs. It could significantly augment surveillance efforts and understanding of variant characteristics, while also offering potential applicability to the analysis and classification of other emerging viral pathogens and enhancing global readiness against emerging and re-emerging viral pathogens.
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Affiliation(s)
| | - Sanja Glisic
- Biomed Protection, Galveston, TX 77550, USA (M.V.)
| | | | - Slobodan Paessler
- Galveston National Laboratory, Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA;
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3
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Byerly CD, Mitra S, Patterson LL, Pittner NA, Velayutham TS, Paessler S, Veljkovic V, McBride JW. Ehrlichia SLiM ligand mimetic activates Hedgehog signaling to engage a BCL-2 anti-apoptotic cellular program. PLoS Pathog 2022; 18:e1010345. [PMID: 35576232 PMCID: PMC9135340 DOI: 10.1371/journal.ppat.1010345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Ehrlichia chaffeensis (E. chaffeensis) has evolved eukaryotic ligand mimicry to repurpose multiple cellular signaling pathways for immune evasion. In this investigation, we demonstrate that TRP120 has a novel repetitive short linear motif (SLiM) that activates the evolutionarily conserved Hedgehog (Hh) signaling pathway to inhibit apoptosis. In silico analysis revealed that TRP120 has sequence and functional similarity with Hh ligands and a candidate Hh ligand SLiM was identified. siRNA knockdown of Hh signaling and transcriptional components significantly reduced infection. Co-immunoprecipitation and surface plasmon resonance demonstrated that rTRP120-TR interacted directly with Hh receptor Patched-2 (PTCH2). E. chaffeensis infection resulted in early upregulation of Hh transcription factor GLI-1 and regulation of Hh target genes. Moreover, soluble recombinant TRP120 (rTRP120) activated Hh and induced gene expression consistent with the eukaryotic Hh ligand. The TRP120-Hh-SLiM (NPEVLIKD) induced nuclear translocation of GLI-1 in THP-1 cells and primary human monocytes and induced a rapid and expansive activation of Hh pathway target genes. Furthermore, Hh activation was blocked by an α-TRP120-Hh-SLiM antibody. TRP120-Hh-SLiM significantly increased levels of Hh target, anti-apoptotic protein B-cell lymphoma 2 (BCL-2), and siRNA knockdown of BCL-2 dramatically inhibited infection. Blocking Hh signaling with the inhibitor Vismodegib, induced a pro-apoptotic cellular program defined by decreased mitochondria membrane potential, significant reductions in BCL-2, activation of caspase 3 and 9, and increased apoptotic cells. This study reveals a novel E. chaffeensis SLiM ligand mimetic that activates Hh signaling to maintain E. chaffeensis infection by engaging a BCL-2 anti-apoptotic cellular program.
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Affiliation(s)
- Caitlan D. Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Shubhajit Mitra
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - LaNisha L. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nicholas A. Pittner
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Thangam S. Velayutham
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Biomed Protection, LLC, Galveston, Texas, United States of America
| | - Veljko Veljkovic
- Biomed Protection, LLC, Galveston, Texas, United States of America
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
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4
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Rogan MR, Patterson LL, Byerly CD, Luo T, Paessler S, Veljkovic V, Quade B, McBride JW. Ehrlichia chaffeensis TRP120 Is a Wnt Ligand Mimetic That Interacts with Wnt Receptors and Contains a Novel Repetitive Short Linear Motif That Activates Wnt Signaling. mSphere 2021; 6:6/2/e00216-21. [PMID: 33883266 PMCID: PMC8546699 DOI: 10.1128/msphere.00216-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ehrlichia chaffeensis expresses the TRP120 multifunctional effector, which is known to play a role in phagocytic entry, on the surface of infectious dense-cored ehrlichiae, but a cognate host receptor has not been identified. We recently reported that E. chaffeensis activates canonical Wnt signaling in monocytes to promote bacterial uptake and intracellular survival and that TRP120 was involved in this activation event. To identify the specific mechanism of pathway activation, we hypothesized that TRP120 is a Wnt signaling ligand mimetic that initiates Wnt pathway activity through direct interaction with the Wnt pathway Frizzled family of receptors. In this study, we used confocal immunofluorescence microscopy to demonstrate very strong colocalization between E. chaffeensis and Fzd2, 4, 5, 7, and 9 as well as coreceptor LRP5 at 1 to 3 h postinfection. Direct binding between TRP120 and multiple Fzd receptors was further confirmed by enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR). Interfering RNA knockdown of Wnt receptors, coreceptors, and signaling pathway components significantly reduced E. chaffeensis infection, demonstrating that complex and redundant interactions are involved in Wnt pathway exploitation. We utilized in silico approaches to identify a repetitive short linear motif (SLiM) in TRP120 that is homologous to Wnt ligands and used mutant SLiM peptides and an α-TRP120-Wnt-SLiM antibody to demonstrate that the TRP120 Wnt SLiM activates the canonical Wnt pathway and promotes E. chaffeensis infection. This study reports the first example of bacterial mimicry of Wnt pathway ligands and highlights a pathogenic mechanism with potential for targeting by antimicrobial therapeutics.IMPORTANCE Upon infecting mammalian hosts, Ehrlichia chaffeensis establishes a replicative niche in microbe-eating immune system cells where it expertly orchestrates infection and spread. One of the ways Ehrlichia survives within these phagocytes is by activating evolutionarily conserved signaling pathways including the Wnt pathway; however, the molecular details of pathway hijacking have not been defined. This study is significant because it identifies an ehrlichial protein that directly interacts with components of the Wnt receptor complex, influencing pathway activity and promoting infection. Consequentially, Ehrlichia serves as a unique tool to investigate the intricacies of how pathogens repurpose human immune cell signaling and provides an opportunity to better understand many cellular processes in health and disease. Furthermore, understanding how this bacterium utilizes its small genome to survive within cells that evolved to destroy pathogens will facilitate the development of antibacterial therapeutics that could target Ehrlichia as well as other intracellular agents of human disease.
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Affiliation(s)
- Madison R Rogan
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - LaNisha L Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Caitlan D Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tian Luo
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- BiomedProtection, LLC, Galveston, Texas, USA
| | | | - Bethany Quade
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jere W McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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5
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Abstract
A safe and effective vaccine is urgently needed to bring the current SARS-CoV-2 pandemic under control. The spike protein (SP) of SARS-CoV-2 represents the principal target for most vaccines currently under development. This protein is highly conserved indicating that vaccine based on this antigen will be efficient against all currently circulating SARS-CoV-2 strains. The present analysis of SP suggests that mutation D614G could significantly decrease the effectiveness of the COVID-19 vaccine through modulation of the interaction between SARS-CoV-2 and its principal receptor ACE2.
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6
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Veljkovic V, Vergara-Alert J, Segalés J, Paessler S. Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target. F1000Res 2020; 9:52. [PMID: 32419926 DOI: 10.12688/f1000research.22149.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/07/2023] Open
Abstract
A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.
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Affiliation(s)
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, 08193 Bellaterra, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Veljkovic V, Vergara-Alert J, Segalés J, Paessler S. Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target. F1000Res 2020; 9:52. [PMID: 32419926 PMCID: PMC7202090 DOI: 10.12688/f1000research.22149.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed
in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.
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Affiliation(s)
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, 08193 Bellaterra, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77555, USA
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8
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Veljkovic V, Vergara-Alert J, Segalés J, Paessler S. Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target. F1000Res 2020; 9:52. [PMID: 32419926 DOI: 10.12688/f1000research.22149.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2020] [Indexed: 01/13/2023] Open
Abstract
A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.
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Affiliation(s)
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, 08193 Bellaterra, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Veljkovic V, Vergara-Alert J, Segalés J, Paessler S. Use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus 2019-nCoV: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target. F1000Res 2020; 9:52. [PMID: 32419926 DOI: 10.12688/f1000research.22149.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
A novel coronavirus recently identified in Wuhan, China (SARS-CoV-2) has expanded the number of highly pathogenic coronaviruses affecting humans. The SARS-CoV-2 represents a potential epidemic or pandemic threat, which requires a quick response for preparedness against this infection. The present report uses the informational spectrum methodology to identify the possible origin and natural host of the new virus, as well as putative therapeutic and vaccine targets. The performed in silico analysis indicates that the newly emerging SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS)-CoV and, to a lesser degree, Middle East respiratory syndrome (MERS)-CoV. Moreover, the well-known SARS-CoV receptor (ACE2) might be a putative receptor for the novel virus as well. Actin protein was also suggested as a host factor that participates in cell entry and pathogenesis of SARS-CoV-2; therefore, drugs modulating biological activity of this protein (e.g. ibuprofen) were suggested as potential candidates for treatment of this viral infection. Additional results indicated that civets and poultry are potential candidates for the natural reservoir of the SARS-CoV-2, and that domain 288-330 of S1 protein from the SARS-CoV-2 represents promising therapeutic and/or vaccine target.
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Affiliation(s)
| | - Júlia Vergara-Alert
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, 08193 Bellaterra, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Abstract
High throughput techniques such as RNA-seq or microarray analysis have proven to be invaluable for the characterizing of global transcriptional gene activity changes due to external stimuli or diseases. Differential gene expression analysis (DGEA) is the first step in the course of data interpretation, typically producing lists of dozens to thousands of differentially expressed genes. To further guide the interpretation of these lists, different pathway analysis approaches have been developed. These tools typically rely on the classification of genes into sets of genes, such as pathways, based on the interactions between the genes and their function in a common biological process. Regardless of technical differences, these methods do not properly account for cross talk between different pathways and most of the methods rely on binary separation into differentially expressed gene and unaffected genes based on an arbitrarily set
p-value cut-off. To overcome this limitation, we developed a novel approach to identify concertedly modulated sub-graphs in the global cell signaling network, based on the DGEA results of all genes tested. To this end, expression patterns of genes are integrated according to the topology of their interactions and allow potentially to read the flow of information and identify the effectors. The described software, named Modulated Sub-graph Finder (MSF) is freely available at
https://github.com/Modulated-Subgraph-Finder/MSF.
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Affiliation(s)
- Mariam R Farman
- Institute for Theoretical Chemistry,Theoretical Biochemistry Group,, University of Vienna, Vienna, 1090, Austria
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry,Theoretical Biochemistry Group,, University of Vienna, Vienna, 1090, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry,Theoretical Biochemistry Group,, University of Vienna, Vienna, 1090, Austria.,Department of Chromosome Biology, Max F. Perutz Laboratories,, University of Vienna, Vienna, 1030, Austria
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Abstract
Zika virus (ZIKV) causes mostly asymptomatic infection or mild febrile illness. However, with an increasing number of patients, various clinical features such as microcephaly, Guillain-Barré syndrome and thrombocytopenia have also been reported. To determine which host factors are related to pathogenesis, the E protein of ZIKV was analyzed with the Informational Spectrum Method, which identifies common information encoded by primary structures of the virus and the respective host protein. The data showed that the ZIKV E protein and the complement component C1q cross-spectra are characterized by a single dominant peak at the frequency F = 0.338, suggesting similar biological properties. Indeed, C1q-specific antibodies were detected in sera obtained from mice and monkeys infected with ZIKV. As C1q has been known to be involved not only in immunity, but also in synaptic organization and different autoimmune diseases, a ZIKV-induced anti-C1q antibody response may contribute to the neurological complications. These findings might also be exploited for the design of safe and efficacious vaccines in the future.
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Camel Paucar V, Galeano E, Carrer H. Análisis in silico y expresión génica del factor de transcripción TgNAC01 implicado en xilogénesis y estrés abiótico en Tectona grandis. ACTA BIOLÓGICA COLOMBIANA 2017. [DOI: 10.15446/abc.v22n3.62164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El xilema secundario es el componente más abundante de la biomasa vegetal. Por tanto, conocer los genes que regulan su formación ayudaría a diseñar estrategias para el mejoramiento genético de la madera. Así, el objetivo de este trabajo fue realizar el análisis computacional de la estructura primaria y secundaria del factor de transcripción (FT) TgNAC01 de Tectona grandis, además de evaluar su historia evolutiva, dominios conservados y expresión génica en tejidos lignificados de árboles de 12 y 60 años. Para ello, se realizó una evaluación del potencial de interacción ion-electrón (PIIE), mediante el método del espectro de la información (MEI) utilizando la librería SFAPS de R-Project, seguido del modelamiento estructural utilizando el software MODELLER y visualizado mediante PyMol. Además, el análisis de alineamiento de secuencia múltiple y filogenia fue mediante el software Bioedit y MrBayes respectivamente. También se evaluó los niveles de síntesis del FT TgNAC01 mediante qRT-PCR. Como resultados, se evidencio que el FT mantiene una estructura β-hoja antiparalela retorcida, que se compacta contra una α-hélice en la región N-terminal, teniendo así tres dominios α hélice y siete dominios β plegada. Asimismo, mediante el MEI se demostró que tiene alrededor de cinco funciones biológicas y mutaciones sobre los aminoácidos con mayor PIIE, lo que conlleva a evoluciones sobre las redes de regulación genética. Finalmente, el FT TgNAC01 juega un papel fundamental en la organización y desarrollo de las partes que componen la albura, como las células radiales de la zona cambial, los vasos, fibras y los anillos de crecimiento.
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Dash R, Das R, Junaid M, Akash MFC, Islam A, Hosen SZ. In silico-based vaccine design against Ebola virus glycoprotein. Adv Appl Bioinform Chem 2017; 10:11-28. [PMID: 28356762 PMCID: PMC5367765 DOI: 10.2147/aabc.s115859] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Here, protein sequences of all glycoproteins of EBOV were collected and examined via in silico methods to determine the most immunogenic protein. From the identified antigenic protein, the peptide region ranging from 186 to 220 and the sequence HKEGAFFLY from the positions of 154-162 were considered the most potential B-cell and T-cell epitopes, correspondingly. Moreover, this peptide (HKEGAFFLY) interacted with HLA-A*32:15 with the highest binding energy and stability, and also a good conservancy of 83.85% with maximum population coverage. The results imply that the designed epitopes could manifest vigorous enduring defensive immunity against EBOV.
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Affiliation(s)
- Raju Dash
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
| | - Rasel Das
- Nanotechnology and Catalysis Research Center, University of Malaya, Kuala Lumpur, Malaysia
| | - Md Junaid
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | | | - Ashekul Islam
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Sm Zahid Hosen
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
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Veljkovic V, Paessler S. Possible repurposing of seasonal influenza vaccine for prevention of Zika virus infection. F1000Res 2016; 5:190. [PMID: 27158449 PMCID: PMC4857754 DOI: 10.12688/f1000research.8102.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
The
in silico analysis shows that the envelope glycoproteins E of Zika viruses (ZIKV) isolated in Asia, Africa and South and Central America encode highly conserved information determining their interacting profile and immunological properties. Previously it was shown that the same information is encoded in the primary structure of the hemagglutinin subunit 1 (HA1) from pdmH1N1 influenza A virus. This similarity suggests possible repurposing of the seasonal influenza vaccine containing pdmH1N1 component for prevention of the ZIKV infection.
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Affiliation(s)
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA; Galveston National Laboratory, Institute for Human Infectious and Immunity, Galveston, TX, USA
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15
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Yu F, Wang H, Liu W, Lu L. Grass carp Ctenopharyngodon idella Fibulin-4 as a potential interacting partner for grass carp reovirus outer capsid proteins. FISH & SHELLFISH IMMUNOLOGY 2016; 48:169-174. [PMID: 26626583 DOI: 10.1016/j.fsi.2015.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/21/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
Mammalian EGF containing fibulin-like extracellular matrix protein 2 (Fibulin-4/EFEMP2), an extracellular matrix(ECM) protein and a member of the fibulin family, is involved in elastic fiber formation, connective tissue development and some human diseases. In a yeast-two hybrid screening of host proteins interacting with outer capsid protein of grass carp reovirus (GCRV), a grass carp homologue of Fibulin-4 (designated as GcFibulin-4) is suggested to hold the potential to bind VP7, VP56 and VP55, the outer capsid protein encoded by type I, II, III GCRV, respectively. GcFibulin-4 gene of grass carp was cloned and sequenced from the cDNA library constructed for the yeast two-hybrid screening. Full-length cDNA of GcFibulin-4 contains an open reading frame (ORF) of 1323 bp encoding a putative protein of 440 amino acids. Phylogenetic analysis of GcFibulin-4 indicated that it shared a high homology with zebra fish Fibulin-4 protein. Transcriptional distribution analysis of GcFibulin-4 in various tissues of healthy grass carp showed that GcFibulin-4 was highly expressed in muscle, moderately expressed in the intestine and brain, and slightly expressed in other examined tissues; the expression pattern is consistent with tissue tropism of GCRV resulting in hemorrhage symptom in the corresponding tissues. Our results suggested that Fibulin-4 might enable free GCRV particles, the pathogen for grass carp hemorrhagic disease, to target fish tissues more efficiently by interacting with viral outer capsid proteins.
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Affiliation(s)
- Fei Yu
- National Pathogen Collection Center for Aquatic Animals, Key Laboratory of Aquatic Genetic Resources of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Hao Wang
- National Pathogen Collection Center for Aquatic Animals, Key Laboratory of Aquatic Genetic Resources of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Weisha Liu
- National Pathogen Collection Center for Aquatic Animals, Key Laboratory of Aquatic Genetic Resources of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Key Laboratory of Aquatic Genetic Resources of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China; Aquaculture Collaborative Innovation Center of Hubei Province, PR China.
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16
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Glisic S, Paessler S, Veljkovic N, Perovic VR, Prljic J, Veljkovic V. Improving attrition rates in Ebola virus drug discovery. Expert Opin Drug Discov 2015; 10:1025-32. [DOI: 10.1517/17460441.2015.1062872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Veljkovic V, Goeijenbier M, Glisic S, Veljkovic N, Perovic VR, Sencanski M, Branch DR, Paessler S. In silico analysis suggests repurposing of ibuprofen for prevention and treatment of EBOLA virus disease. F1000Res 2015; 4:104. [PMID: 26167272 PMCID: PMC4482208 DOI: 10.12688/f1000research.6436.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 11/20/2022] Open
Abstract
The large 2014/2015 Ebola virus outbreak in West Africa points out the urgent need to develop new preventive and therapeutic approaches that are effective against Ebola viruses and can be rapidly utilized. Recently, a simple theoretical criterion for the virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection was proposed. Using this method the ‘drug space’ was screened and 267 approved and 382 experimental drugs as candidates for treatment of the Ebola virus disease (EVD) have been selected. Detailed analysis of these drugs revealed the non-steroidal anti-inflammatory drug ibuprofen as an inexpensive, widely accessible and minimally toxic candidate for prevention and treatment of EVD. Furthermore, the molecular mechanism underlying this possible protective effect of ibuprofen against EVD is suggested in this article.
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Affiliation(s)
- Veljko Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mihajla Petrovica 12-14, 11001 Belgrade, Serbia
| | | | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mihajla Petrovica 12-14, 11001 Belgrade, Serbia
| | - Nevena Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mihajla Petrovica 12-14, 11001 Belgrade, Serbia
| | - Vladimir R Perovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mihajla Petrovica 12-14, 11001 Belgrade, Serbia
| | - Milan Sencanski
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mihajla Petrovica 12-14, 11001 Belgrade, Serbia
| | - Donald R Branch
- Canadian Blood Services, Center for Innovation, 67 College Street, Toronto, M5G 2M1, Canada
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
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