Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Autor:	Niarakis A; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Ostaszewski M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Mazein A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Kuperstein I; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Kutmon M; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands., Gillespie ME; Ontario Institute for Cancer Research, Toronto, ON, Canada.; St. John's University, Queens, NY, United States., Funahashi A; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan., Acencio ML; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Hemedan A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Aichem M; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany., Klein K; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany., Czauderna T; Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany., Burtscher F; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Yamada TG; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan., Hiki Y; Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan., Hiroi NF; Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan.; Keio University School of Medicine, Tokyo, Japan., Hu F; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Pham N; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Ehrhart F; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Willighagen EL; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., Valdeolivas A; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Dugourd A; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Messina F; Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases' Lazzaro Spallanzani' - IRCCS, Rome, Italy., Esteban-Medina M; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain., Peña-Chilet M; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain., Rian K; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain., Soliman S; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Aghamiri SS; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Puniya BL; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Naldi A; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France., Helikar T; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States., Singh V; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France., Fernández MF; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Bermudez V; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Tsirvouli E; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Montagud A; Barcelona Supercomputing Center (BSC.), Barcelona, Spain., Noël V; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Ponce-de-Leon M; Barcelona Supercomputing Center (BSC.), Barcelona, Spain., Maier D; Labvantage-Biomax GmbH, Planegg, Germany., Bauch A; Labvantage-Biomax GmbH, Planegg, Germany., Gyori BM; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States., Bachman JA; Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States., Luna A; Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States.; Department of Systems Biology, Harvard Medical School, Boston, MA, United States., Piñero J; Medbioinformatics Solutions SL, Barcelona, Spain.; Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain., Furlong LI; Medbioinformatics Solutions SL, Barcelona, Spain.; Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain., Balaur I; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Rougny A; Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.; Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan., Jarosz Y; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Overall RW; Institute for Biology, Humboldt University of Berlin, Berlin, Germany., Phair R; Integrative Bioinformatics, Inc., Mountain View, CA, United States., Perfetto L; Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy., Matthews L; Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States., Rex DAB; Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Derlakatte, Mangalore, India., Orlic-Milacic M; Ontario Institute for Cancer Research, Toronto, ON, Canada., Gomez LCM; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., De Meulder B; Association E.I.S.B.M, Brignais, France., Ravel JM; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Jassal B; Ontario Institute for Cancer Research, Toronto, ON, Canada., Satagopam V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany., Wu G; Oregon Health Sciences University, Portland, OR, United States., Golebiewski M; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany., Gawron P; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg., Calzone L; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Beckmann JS; University of Lausanne, Lausanne, Switzerland., Evelo CT; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands., D'Eustachio P; Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States., Schreiber F; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia., Saez-Rodriguez J; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany., Dopazo J; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain.; FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain., Kuiper M; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway., Valencia A; Barcelona Supercomputing Center (BSC.), Barcelona, Spain.; I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain., Wolkenhauer O; Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany.; Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany., Kitano H; Systems Biology Institute, Tokyo, Japan., Barillot E; Institut Curie, P.S.L. Research University, Paris, France.; INSERM, Paris, France.; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France., Auffray C; Association E.I.S.B.M, Brignais, France., Balling R; Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany., Schneider R; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
Jazyk:	angličtina
Zdroj:	Frontiers in immunology [Front Immunol] 2024 Feb 13; Vol. 14, pp. 1282859. Date of Electronic Publication: 2024 Feb 13 (Print Publication: 2023).
DOI:	10.3389/fimmu.2023.1282859
Abstrakt:	Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies. Competing Interests: AN collaborates with SANOFI-AVENTIS R&D via a public–private partnership grant CIFRE contract, n° 2020/0766. DM and AB are employed at Labvantage-Biomax GmbH and will be affected by any effect of this publication on the commercial version of the AILANI software. JB and BG received consulting fees from Two Six Labs, LLC. TH has served as a shareholder and has consulted for Discovery Collective, Inc. RB and RS are founders and shareholders of MEGENO SA and ITTM SA. JS-R reports funding from GSK, Pfizer and Sanofi and fees/honoraria from Travere Therapeutics, Stadapharm, Astex, Owkin, Pfizer and Grunenthal. JP and LF are employees and shareholders of MedBioinformatics Solutions SL. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be constructed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision. (Copyright © 2024 Niarakis, Ostaszewski, Mazein, Kuperstein, Kutmon, Gillespie, Funahashi, Acencio, Hemedan, Aichem, Klein, Czauderna, Burtscher, Yamada, Hiki, Hiroi, Hu, Pham, Ehrhart, Willighagen, Valdeolivas, Dugourd, Messina, Esteban-Medina, Peña-Chilet, Rian, Soliman, Aghamiri, Puniya, Naldi, Helikar, Singh, Fernández, Bermudez, Tsirvouli, Montagud, Noël, Ponce-de-Leon, Maier, Bauch, Gyori, Bachman, Luna, Piñero, Furlong, Balaur, Rougny, Jarosz, Overall, Phair, Perfetto, Matthews, Rex, Orlic-Milacic, Gomez, De Meulder, Ravel, Jassal, Satagopam, Wu, Golebiewski, Gawron, Calzone, Beckmann, Evelo, D’Eustachio, Schreiber, Saez-Rodriguez, Dopazo, Kuiper, Valencia, Wolkenhauer, Kitano, Barillot, Auffray, Balling, Schneider and the COVID-19 Disease Map Community.)
Databáze:	MEDLINE
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