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Diakou KI, Mitsis T, Pierouli K, Papakonstantinou E, Bongcam-Rudloff E, Wayengera M, Vlachakis D. Ebola Virus Disease and Current Therapeutic Strategies: A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1339:131-137. [PMID: 35023100 DOI: 10.1007/978-3-030-78787-5_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Ebola virus disease is a severe hemorrhagic fever that affects humans and other primates. Ebola virus, the causative agent of the disease, is transmitted to humans from wild animals and is highly contagious and aggressive with an estimated fatality rate to be around 50%. Since 1976, 11 outbreaks of Ebola virus disease have been reported in total, affecting mostly sub-Saharan Africa, while the most recent ongoing outbreak in the Democratic Republic of the Congo has more than 3000 reported cases and 72 deaths. Although an effective vaccine against Ebola virus disease has become available, no targeted treatment with proven efficacy upon infection is developed. Herein, we review the epidemiology of Ebola virus and the current situation in terms of prevention, diagnosis, and treatment of the disease.
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Affiliation(s)
- Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics Science, University of Agricultural Sciences, Uppsala, Sweden
| | - Misaki Wayengera
- Department of Pathology, Unit of Genetics & Genomics, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Dimitrios Vlachakis
- DarkDNA Group, Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece. .,Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece. .,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London, UK.
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Vlachakis D, Papakonstantinou E, Mitsis T, Pierouli K, Diakou I, Chrousos G, Bacopoulou F. Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic. Food Chem Toxicol 2020; 146:111805. [PMID: 33038452 PMCID: PMC7543766 DOI: 10.1016/j.fct.2020.111805] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
The novel coronavirus SARS-CoV-2 has emerged as a severe threat against public health and global economies. COVID-19, the disease caused by this virus, is highly contagious and has led to an ongoing pandemic. SARS-CoV-2 affects, mainly, the respiratory system, with most severe cases primarily showcasing acute respiratory distress syndrome. Currently, no targeted therapy exists, and since the number of infections and death toll keeps rising, it has become a necessity to study possible therapeutic targets. Antiviral drugs can target various stages of the viral infection, and in the case of SARS-CoV-2, both structural and non-structural proteins have been proposed as potential drug targets. This review focuses on the most researched SARS-CoV-2 proteins, their structure, function, and possible therapeutic approaches.
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Affiliation(s)
- Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece; University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece; Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London WC2R 2LS, UK
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - George Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece.
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Kavianpour M, Saleh M, Verdi J. The role of mesenchymal stromal cells in immune modulation of COVID-19: focus on cytokine storm. Stem Cell Res Ther 2020; 11:404. [PMID: 32948252 PMCID: PMC7499002 DOI: 10.1186/s13287-020-01849-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/30/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic is quickly spreading all over the world. This virus, which is called SARS-CoV-2, has infected tens of thousands of people. Based on symptoms, the pathogenesis of acute respiratory illness is responsible for highly homogenous coronaviruses as well as other pathogens. Evidence suggests that high inflammation rates, oxidation, and overwhelming immune response probably contribute to pathology of COVID-19. COVID-19 causes cytokine storm, which subsequently leads to acute respiratory distress syndrome (ARDS), often ending up in the death of patients. Mesenchymal stem cells (MSCs) are multipotential stem cells that are recognized via self-renewal capacity, generation of clonal populations, and multilineage differentiation. MSCs are present in nearly all tissues of the body, playing an essential role in repair and generation of tissues. Furthermore, MSCs have broad immunoregulatory properties through the interaction of immune cells in both innate and adaptive immune systems, leading to immunosuppression of many effector activities. MSCs can reduce the cytokine storm produced by coronavirus infection. In a number of studies, the administration of these cells has been beneficial for COVID-19 patients. Also, MSCs may be able to improve pulmonary fibrosis and lung function. In this review, we will review the newest research findings regarding MSC-based immunomodulation in patients with COVID-19.
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Affiliation(s)
- Maria Kavianpour
- Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Cell-Based Therapies Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Saleh
- Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Javad Verdi
- Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review. BIOMED RESEARCH INTERNATIONAL 2015; 2015:183918. [PMID: 25785262 PMCID: PMC4345249 DOI: 10.1155/2015/183918] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/05/2014] [Indexed: 01/08/2023]
Abstract
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.
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Vlachakis D, Fakourelis P, Megalooikonomou V, Makris C, Kossida S. DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit. PeerJ 2015; 3:e725. [PMID: 25648563 PMCID: PMC4304849 DOI: 10.7717/peerj.725] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 12/24/2014] [Indexed: 11/20/2022] Open
Abstract
During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Computer Engineering and Informatics Department, University of Patras, Patras, Greece
| | - Paraskevas Fakourelis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Computer Engineering and Informatics Department, University of Patras, Patras, Greece
| | | | - Christos Makris
- Computer Engineering and Informatics Department, University of Patras, Patras, Greece
| | - Sophia Kossida
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,IMGT, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, Montpellier, France
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Papageorgiou L, Loukatou S, Koumandou VL, Makałowski W, Megalooikonomou V, Vlachakis D, Kossida S. Structural models for the design of novel antiviral agents against Greek Goat Encephalitis. PeerJ 2014; 2:e664. [PMID: 25392762 PMCID: PMC4226726 DOI: 10.7717/peerj.664] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/22/2014] [Indexed: 12/23/2022] Open
Abstract
The Greek Goat Encephalitis virus (GGE) belongs to the Flaviviridae family of the genus Flavivirus. The GGE virus constitutes an important pathogen of livestock that infects the goat’s central nervous system. The viral enzymes of GGE, helicase and RNA-dependent RNA polymerase (RdRP), are ideal targets for inhibitor design, since those enzymes are crucial for the virus’ survival, proliferation and transmission. In an effort to understand the molecular structure underlying the functions of those viral enzymes, the three dimensional structures of GGE NS3 helicase and NS5 RdRP have been modelled. The models were constructed in silico using conventional homology modelling techniques and the known 3D crystal structures of solved proteins from closely related species as templates. The established structural models of the GGE NS3 helicase and NS5 RdRP have been evaluated for their viability using a repertoire of in silico tools. The goal of this study is to present the 3D conformations of the GGE viral enzymes as reliable structural models that could provide the platform for the design of novel anti-GGE agents.
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Affiliation(s)
- Louis Papageorgiou
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece ; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens , Athens , Greece
| | - Styliani Loukatou
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece
| | - Vassiliki Lila Koumandou
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece
| | | | | | - Dimitrios Vlachakis
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece
| | - Sophia Kossida
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens , Athens , Greece
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Vlachakis D, Tsaniras SC, Ioannidou K, Papageorgiou L, Baumann M, Kossida S. A series of Notch3 mutations in CADASIL; insights from 3D molecular modelling and evolutionary analyses. JOURNAL OF MOLECULAR BIOCHEMISTRY 2014; 3:134. [PMID: 31799216 PMCID: PMC6887539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CADASIL disease belongs to the group of rare diseases. It is well established that the Notch3 protein is primarily responsible for the development of CADASIL syndrome. Herein, we attempt to shed light to the actual molecular mechanism underlying CADASIL via insights that we have from preliminary in silico and proteomics studies on the Notch3 protein. At the moment, we are aware of a series of Notch3 point mutations that promote CADASIL. In this direction, we investigate the nature, extent, physicochemical and structural significance of the mutant species in an effort to identify the underlying mechanism of Notch3 role and implications in cell signal transduction. Overall, our in silico study has revealed a rather complex molecular mechanism of Notch3 on the structural level; depending of the nature and position of each mutation, a consensus significant loss of beta-sheet structure is observed throughout all in silico modeled mutant/wild type biological systems.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Katerina Ioannidou
- School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | - Louis Papageorgiou
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Marc Baumann
- Protein Chemistry/Proteomics Unit, Biomedicum Helsinki, Institute of Biomedicine, University of Helsinki, P.O. Box 63, Finland
| | - Sophia Kossida
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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