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Marinho MDS, Ferreira GM, Grosche VR, Nicolau-Junior N, Campos TDL, Santos IA, Jardim ACG. Evolutionary Profile of Mayaro Virus in the Americas: An Update into Genome Variability. Viruses 2024; 16:809. [PMID: 38793690 PMCID: PMC11126029 DOI: 10.3390/v16050809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024] Open
Abstract
The Mayaro virus (MAYV) is an arbovirus with emerging potential, though with a limited understanding of its epidemiology and evolution due to the lack of studies and surveillance. Here, we investigated 71 MAYV genome sequences from the Americas available at GenBank and characterized the phylogenetic relationship among virus strains. A phylogenetic analysis showed that sequences were grouped according to the genotypes L, D, and N. Genotype D sequences were closely related to sequences collected in adjacent years and from their respective countries, suggesting that isolates may have originated from circulating lineages. The coalescent analysis demonstrated similar results, indicating the continuous circulation of the virus between countries as well. An unidentified sequence from the USA was grouped with genotype D, suggesting the insertion of this genotype in the country. Furthermore, the recombination analysis detected homologous and three heterologous hybrids which presented an insertion into the nsP3 protein. Amino acid substitutions among sequences indicated selective pressure sites, suggesting viral adaptability. This also impacted the binding affinity between the E1-E2 protein complex and the Mxra8 receptor, associated with MAYV entry into human cells. These results provide information for a better understanding of genotypes circulating in the Americas.
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Affiliation(s)
- Mikaela dos Santos Marinho
- Institute of Biomedical Sciences, ICBIM, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia 38405-319, MG, Brazil; (M.d.S.M.); (G.M.F.); (V.R.G.)
| | - Giulia Magalhães Ferreira
- Institute of Biomedical Sciences, ICBIM, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia 38405-319, MG, Brazil; (M.d.S.M.); (G.M.F.); (V.R.G.)
| | - Victória Riquena Grosche
- Institute of Biomedical Sciences, ICBIM, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia 38405-319, MG, Brazil; (M.d.S.M.); (G.M.F.); (V.R.G.)
- Institute of Biosciences, Humanities and Exact Sciences (Ibilce), São Paulo State University (Unesp), Campus São José do Rio Preto, São José do Rio Preto 15054-000, SP, Brazil
| | - Nilson Nicolau-Junior
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia 38405-319, MG, Brazil;
| | - Túlio de Lima Campos
- Aggeu Magalhães Institute (Fiocruz), Bioinformatics Core Facility, Recife 50740-465, PE, Brazil;
| | - Igor Andrade Santos
- Institute of Biomedical Sciences, ICBIM, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia 38405-319, MG, Brazil; (M.d.S.M.); (G.M.F.); (V.R.G.)
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Sciences, ICBIM, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia 38405-319, MG, Brazil; (M.d.S.M.); (G.M.F.); (V.R.G.)
- Institute of Biosciences, Humanities and Exact Sciences (Ibilce), São Paulo State University (Unesp), Campus São José do Rio Preto, São José do Rio Preto 15054-000, SP, Brazil
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2
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Barreras P, Pamies D, Hartung T, Pardo CA. Human brain microphysiological systems in the study of neuroinfectious disorders. Exp Neurol 2023; 365:114409. [PMID: 37061175 PMCID: PMC10205672 DOI: 10.1016/j.expneurol.2023.114409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
Microphysiological systems (MPS) are 2D or 3D multicellular constructs able to mimic tissue microenvironments. The latest models encompass a range of techniques, including co-culturing of various cell types, utilization of scaffolds and extracellular matrix materials, perfusion systems, 3D culture methods, 3D bioprinting, organ-on-a-chip technology, and examination of tissue structures. Several human brain 3D cultures or brain MPS (BMPS) have emerged in the last decade. These organoids or spheroids are 3D culture systems derived from induced pluripotent cells or embryonic stem cells that contain neuronal and glial populations and recapitulate structural and physiological aspects of the human brain. BMPS have been introduced recently in the study and modeling of neuroinfectious diseases and have proven to be useful in establishing neurotropism of viral infections, cell-pathogen interactions needed for infection, assessing cytopathological effects, genomic and proteomic profiles, and screening therapeutic compounds. Here we review the different methodologies of organoids used in neuroinfectious diseases including spheroids, guided and unguided protocols as well as microglia and blood-brain barrier containing models, their specific applications, and limitations. The review provides an overview of the models existing for specific infections including Zika, Dengue, JC virus, Japanese encephalitis, measles, herpes, SARS-CoV2, and influenza viruses among others, and provide useful concepts in the modeling of disease and antiviral agent screening.
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Affiliation(s)
- Paula Barreras
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - David Pamies
- Department of Biomedical Science, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology, Basel, Switzerland
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA; CAAT-Europe, University of Konstanz, Germany
| | - Carlos A Pardo
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA.
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3
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Rivas J, Dubois A, Blanquer A, Gérardy M, Ziegler U, Groschup MH, Grobet L, Garigliany MM. Tendon-Derived Mesenchymal Stem Cells (TDSCs) as an In Vitro Model for Virological Studies in Wild Birds. Viruses 2023; 15:1455. [PMID: 37515142 PMCID: PMC10383174 DOI: 10.3390/v15071455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The use of wild animals in research is complicated due to the capture and housing conditions, as well as to legal aspects, making it difficult to develop in vivo and in vitro models for the study of pathologies that affect these species. Here we validate an in vitro model of tendon-derived mesenchymal cells (TDSC) from Eurasian blackbird (Turdus merula) cadaveric samples. Through the expression of surface markers and the ability to differentiate into multiple lineages, the nature of the cells was confirmed. We then evaluated Mesenchymal Stem Cells (MSCs) as an infection model for the Usutu Flavivirus. To this aim, blackbird TDSCs were compared to Vero E6 cells, commonly used in Flavivirus studies. Both cells showed permissiveness to USUV infection as confirmed by immunocytochemistry. Moreover, TDSCs exhibited replication kinetics similar to, although slightly lower than, Vero E6, confirming these cells as a pertinent study model for the study of the pathogenesis of USUV. In this work, we isolated and characterized tendon-derived mesenchymal stem cells, which represent an interesting and convenient in vitro model for the study of wildlife species in laboratories.
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Affiliation(s)
- José Rivas
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Pathology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (J.R.); (A.B.); (M.G.)
| | - Axel Dubois
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Embryology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (A.D.); (L.G.)
| | - Aude Blanquer
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Pathology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (J.R.); (A.B.); (M.G.)
| | - Mazarine Gérardy
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Pathology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (J.R.); (A.B.); (M.G.)
| | - Ute Ziegler
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany; (U.Z.); (M.H.G.)
| | - Martin H. Groschup
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany; (U.Z.); (M.H.G.)
| | - Luc Grobet
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Embryology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (A.D.); (L.G.)
| | - Mutien-Marie Garigliany
- Fundamental and Applied Research for Animals & Health (FARAH), Laboratory of Pathology, Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium; (J.R.); (A.B.); (M.G.)
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4
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van Bree JW, Visser I, Duyvestyn JM, Aguilar-Bretones M, Marshall EM, van Hemert MJ, Pijlman GP, van Nierop GP, Kikkert M, Rockx BH, Miesen P, Fros JJ. Novel approaches for the rapid development of rationally designed arbovirus vaccines. One Health 2023; 16:100565. [PMID: 37363258 PMCID: PMC10288159 DOI: 10.1016/j.onehlt.2023.100565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Vector-borne diseases, including those transmitted by mosquitoes, account for more than 17% of infectious diseases worldwide. This number is expected to rise with an increased spread of vector mosquitoes and viruses due to climate change and man-made alterations to ecosystems. Among the most common, medically relevant mosquito-borne infections are those caused by arthropod-borne viruses (arboviruses), especially members of the genera Flavivirus and Alphavirus. Arbovirus infections can cause severe disease in humans, livestock and wildlife. Severe consequences from infections include congenital malformations as well as arthritogenic, haemorrhagic or neuroinvasive disease. Inactivated or live-attenuated vaccines (LAVs) are available for a small number of arboviruses; however there are no licensed vaccines for the majority of these infections. Here we discuss recent developments in pan-arbovirus LAV approaches, from site-directed attenuation strategies targeting conserved determinants of virulence to universal strategies that utilize genome-wide re-coding of viral genomes. In addition to these approaches, we discuss novel strategies targeting mosquito saliva proteins that play an important role in virus transmission and pathogenesis in vertebrate hosts. For rapid pre-clinical evaluations of novel arbovirus vaccine candidates, representative in vitro and in vivo experimental systems are required to assess the desired specific immune responses. Here we discuss promising models to study attenuation of neuroinvasion, neurovirulence and virus transmission, as well as antibody induction and potential for cross-reactivity. Investigating broadly applicable vaccination strategies to target the direct interface of the vertebrate host, the mosquito vector and the viral pathogen is a prime example of a One Health strategy to tackle human and animal diseases.
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Affiliation(s)
- Joyce W.M. van Bree
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
| | - Imke Visser
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jo M. Duyvestyn
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Eleanor M. Marshall
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Martijn J. van Hemert
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Barry H.G. Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Jelke J. Fros
- Laboratory of Virology, Wageningen University & Research, Wageningen, the Netherlands
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5
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Jiang H, Zhang Y, Wu Y, Cheng J, Feng S, Wang J, Wang X, Cheng M. Identification of Montelukast as flavivirus NS2B-NS3 protease inhibitor by inverse virtual screening and experimental validation. Biochem Biophys Res Commun 2022; 606:87-93. [PMID: 35339757 DOI: 10.1016/j.bbrc.2022.03.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/13/2022] [Indexed: 11/02/2022]
Abstract
Flavivirus, such as Dengue Virus (DENV) and Zika virus (ZIKV), infects millions of people and cause the death of thousands of people every year. Despite many efforts, there is no approved anti-flaviviral treatment available. In particular, some antiflavivirus compounds were investigated the cellular activities of DENV and ZIKV, but lacking the exploration of specific target enzyme, thereby resulting in the hindrance of structure-based drug design. One example is Montlukast, which was found to inhibit the replicon replication in DENV and ZIKV infected cells, with EC50 values as 1.03 μM (DENV) and 1.14 μM (ZIKV), while the underlying mechanism remains unclear. In our study, the inhibitory mechanisms of Montelukast against the replicon replication of DENV and ZIKV infected cells were studied by using in silico approaches including inverse virtual screening (IVS), molecular dynamics (MD) simulations and binding free energy calculation, and validated through in vitro protease assay, confirming Montelukast could bind to NS2B-NS3 proteases of DENV and ZIKV as a competitive inhibitor (IC50 for DENV: 25.65 μM, for ZIKV: 15.57 μM). Moreover, Montelukast has no potential off-target effect on NS2B-NS3 protease from thrombin and trypsin inhibitory assay. Overall, Montelukast may be used as a potential candidate to block NS2B-NS3 protease as well as lead for structural modification.
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Affiliation(s)
- Hailun Jiang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yaoliang Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yuming Wu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jiawei Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Shasha Feng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Xuejun Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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6
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Schroeder B, Demirel P, Fischer C, Masri E, Kallis S, Redl L, Rudolf T, Bergemann S, Arkona C, Nitsche C, Bartenschlager R, Rademann J. Nanoparticular Inhibitors of Flavivirus Proteases from Zika, West Nile and Dengue Virus Are Cell-Permeable Antivirals. ACS Med Chem Lett 2021; 12:1955-1961. [PMID: 34917260 DOI: 10.1021/acsmedchemlett.1c00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/16/2021] [Indexed: 11/28/2022] Open
Abstract
Viral proteases have been established as drug targets in several viral diseases including human immunodeficiency virus and hepatitis C virus infections due to the essential role of these enzymes in virus replication. In contrast, no antiviral therapy is available to date against flaviviral infections including those by Zika virus (ZIKV), West Nile virus (WNV), or dengue virus (DENV). Numerous potent inhibitors of flaviviral proteases have been reported; however, a huge gap remains between the in vitro and intracellular activities, possibly due to low cellular uptake of the charged compounds. Here, we present an alternative, nanoparticular approach to antivirals. Conjugation of peptidomimetic inhibitors and cell-penetrating peptides to dextran yielded chemically defined nanoparticles that were potent inhibitors of flaviviral proteases. Peptide-dextran conjugates inhibited viral replication and infection in cells at nontoxic, low micromolar or even nanomolar concentrations. Thus, nanoparticular antivirals might be alternative starting points for the development of broad-spectrum antiflaviviral drugs.
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Affiliation(s)
- Barbara Schroeder
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Peter Demirel
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Christina Fischer
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Enaam Masri
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Stephanie Kallis
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120 Heidelberg, Germany
| | - Lisa Redl
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Thomas Rudolf
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Silke Bergemann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Christoph Arkona
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120 Heidelberg, Germany
| | - Jörg Rademann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2 + 4, 14195 Berlin, Germany
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7
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Chetta M, Tarsitano M, Vicari L, Saracino A, Bukvic N. In Silico Analysis of Possible Interaction between Host Genomic Transcription Factors (TFs) and Zika Virus (ZikaSPH2015) Strain with Combinatorial Gene Regulation; Virus Versus Host-The Game Reloaded. Pathogens 2021; 10:pathogens10010069. [PMID: 33466592 PMCID: PMC7828653 DOI: 10.3390/pathogens10010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
In silico analysis is a promising approach for understanding biological events in complex diseases. Herein we report on the innovative computational workflow allowed to highlight new direct interactions between human transcription factors (TFs) and an entire genome of virus ZikaSPH2015 strain in order to identify the occurrence of specific motifs on a genomic Zika Virus sequence that is able to bind and, therefore, sequester host’s TFs. The analysis pipeline was performed using different bioinformatics tools available online (free of charge). According to obtained results of this in silico analysis, it is possible to hypothesize that these TFs binding motifs might be able to explain the complex and heterogeneous phenotype presentation in Zika-virus-affected fetuses/newborns, as well as the less severe condition in adults. Moreover, the proposed in silico protocol identified thirty-three different TFs identical to the distribution of TFBSs (Transcription Factor Binding Sites) on ZikaSPH2015 strain, potentially able to influence genes and pathways with biological functions confirming that this approach could find potential answers on disease pathogenesis.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
- Correspondence:
| | - Marina Tarsitano
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Laura Vicari
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Annalisa Saracino
- Clinica di Malattie Infettive, Dipartimento di Scienze Biomediche ed Oncologia Umana, Università degli Studi “Aldo Moro” di Bari, 70124 Bari, Italy;
| | - Nenad Bukvic
- Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
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8
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Goh GKM, Dunker AK, Foster JA, Uversky VN. A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder. J Proteome Res 2020; 19:4355-4363. [PMID: 33006287 PMCID: PMC7640981 DOI: 10.1021/acs.jproteome.0c00672] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Indexed: 12/29/2022]
Abstract
A model that predicts levels of coronavirus (CoV) respiratory and fecal-oral transmission potentials based on the shell disorder has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nucleocapsid, N, and membrane, M, proteins of the inner and outer viral shells, respectively. Using primarily the PID of N, SARS-CoV-2 is grouped as having intermediate levels of both respiratory and fecal-oral transmission potentials. Related studies, using similar methodologies, have found strong positive correlations between virulence and inner shell disorder among numerous viruses, including Nipah, Ebola, and Dengue viruses. There is some evidence that this is also true for SARS-CoV-2 and SARS-CoV, which have N PIDs of 48% and 50%, and case-fatality rates of 0.5-5% and 10.9%, respectively. The underlying relationship between virulence and respiratory potentials has to do with the viral loads of vital organs and body fluids, respectively. Viruses can spread by respiratory means only if the viral loads in saliva and mucus exceed certain minima. Similarly, a patient is likelier to die when the viral load overwhelms vital organs. Greater disorder in inner shell proteins has been known to play important roles in the rapid replication of viruses by enhancing the efficiency pertaining to protein-protein/DNA/RNA/lipid bindings. This paper suggests a novel strategy in attenuating viruses involving comparison of disorder patterns of inner shells (N) of related viruses to identify residues and regions that could be ideal for mutation. The M protein of SARS-CoV-2 has one of the lowest M PID values (6%) in its family, and therefore, this virus has one of the hardest outer shells, which makes it resistant to antimicrobial enzymes in body fluid. While this is likely responsible for its greater contagiousness, the risks of creating an attenuated virus with a more disordered M are discussed.
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Affiliation(s)
| | - A. Keith Dunker
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - James A. Foster
- Department
of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
- Institute
for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844, United States
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
- Laboratory
of New Methods in Biology, Institute for Biological Instrumentation
of the Russian Academy of Sciences, Federal
Research Center “Pushchino Scientific Center for Biological
Research of the Russian Academy of Sciences”, Pushchino, Moscow region 142290, Russia
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9
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Benzarti E, Garigliany M. In Vitro and In Vivo Models to Study the Zoonotic Mosquito-Borne Usutu Virus. Viruses 2020; 12:E1116. [PMID: 33008141 PMCID: PMC7599730 DOI: 10.3390/v12101116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/15/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022] Open
Abstract
Usutu virus (USUV), a mosquito-borne zoonotic flavivirus discovered in South Africa in 1959, has spread to many European countries over the last 20 years. The virus is currently a major concern for animal health due to its expanding host range and the growing number of avian mass mortality events. Although human infections with USUV are often asymptomatic, they are occasionally accompanied by neurological complications reminiscent of those due to West Nile virus (another flavivirus closely related to USUV). Whilst USUV actually appears less threatening than some other emergent arboviruses, the lessons learned from Chikungunya, Dengue, and Zika viruses during the past few years should not be ignored. Further, it would not be surprising if, with time, USUV disperses further eastwards towards Asia and possibly westwards to the Americas, which may result in more pathogenic USUV strains to humans and/or animals. These observations, inviting the scientific community to be more vigilant about the spread and genetic evolution of USUV, have prompted the use of experimental systems to understand USUV pathogenesis and to boost the development of vaccines and antivirals. This review is the first to provide comprehensive coverage of existing in vitro and in vivo models for USUV infection and to discuss their contribution in advancing data concerning this neurotropic virus. We believe that this paper is a helpful tool for scientists to identify gaps in the knowledge about USUV and to design their future experiments to study the virus.
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Affiliation(s)
| | - Mutien Garigliany
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Sart Tilman B43, B-4000 Liège, Belgium;
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Pach S, Sarter TM, Yousef R, Schaller D, Bergemann S, Arkona C, Rademann J, Nitsche C, Wolber G. Catching a Moving Target: Comparative Modeling of Flaviviral NS2B-NS3 Reveals Small Molecule Zika Protease Inhibitors. ACS Med Chem Lett 2020; 11:514-520. [PMID: 32292558 DOI: 10.1021/acsmedchemlett.9b00629] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
The pivotal role of viral proteases in virus replication has already been successfully exploited in several antiviral drug design campaigns. However, no efficient antivirals are currently available against flaviviral infections. In this study, we present lead-like small molecule inhibitors of the Zika Virus (ZIKV) NS2B-NS3 protease. Since only few nonpeptide competitive ligands are known, we take advantage of the high structural similarity with the West Nile Virus (WNV) NS2B-NS3 protease. A comparative modeling approach involving our in-house software PyRod was employed to systematically analyze the binding sites and develop molecular dynamics-based 3D pharmacophores for virtual screening. The identified compounds were biochemically characterized revealing low micromolar affinity for both ZIKV and WNV proteases. Their lead-like properties together with rationalized binding modes represent valuable starting points for future lead optimization. Since the NS2B-NS3 protease is highly conserved among flaviviruses, these compounds may also drive the development of pan-flaviviral antiviral drugs.
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Affiliation(s)
- Szymon Pach
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - Tim M. Sarter
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Rafe Yousef
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - David Schaller
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - Silke Bergemann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - Jörg Rademann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, Berlin 14195, Germany
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