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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.
Niarakis, Anna; Ostaszewski, Marek; Mazein, Alexander; Kuperstein, Inna; Kutmon, Martina; Gillespie, Marc E; Funahashi, Akira; Acencio, Marcio Luis; Hemedan, Ahmed; Aichem, Michael; Klein, Karsten; Czauderna, Tobias; Burtscher, Felicia; Yamada, Takahiro G; Hiki, Yusuke; Hiroi, Noriko F; Hu, Finterly; Pham, Nhung; Ehrhart, Friederike; Willighagen, Egon L; Valdeolivas, Alberto; Dugourd, Aurelien; Messina, Francesco; Esteban-Medina, Marina; Peña-Chilet, Maria; Rian, Kinza; Soliman, Sylvain; Aghamiri, Sara Sadat; Puniya, Bhanwar Lal; Naldi, Aurélien; Helikar, Tomás; Singh, Vidisha; Fernández, Marco Fariñas; Bermudez, Viviam; Tsirvouli, Eirini; Montagud, Arnau; Noël, Vincent; Ponce-de-Leon, Miguel; Maier, Dieter; Bauch, Angela; Gyori, Benjamin M; Bachman, John A; Luna, Augustin; Piñero, Janet; Furlong, Laura I; Balaur, Irina; Rougny, Adrien; Jarosz, Yohan; Overall, Rupert W; Phair, Robert.
Affiliation
  • Niarakis A; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.
  • Ostaszewski M; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
  • Mazein A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Kuperstein I; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Kutmon M; Institut Curie, P.S.L. Research University, Paris, France.
  • Gillespie ME; INSERM, Paris, France.
  • Funahashi A; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.
  • Acencio ML; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Hemedan A; Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Aichem M; St. John's University, Queens, NY, United States.
  • Klein K; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.
  • Czauderna T; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Burtscher F; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Yamada TG; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
  • Hiki Y; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
  • Hiroi NF; Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany.
  • Hu F; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Pham N; Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.
  • Ehrhart F; Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan.
  • Willighagen EL; Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan.
  • Valdeolivas A; Keio University School of Medicine, Tokyo, Japan.
  • Dugourd A; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Messina F; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Esteban-Medina M; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Peña-Chilet M; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Rian K; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Soliman S; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Aghamiri SS; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
  • Puniya BL; Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
  • Naldi A; Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases' Lazzaro Spallanzani' - IRCCS, Rome, Italy.
  • Helikar T; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Singh V; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.
  • Fernández MF; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Bermudez V; Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain.
  • Tsirvouli E; Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain.
  • Montagud A; Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Noël V; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
  • Ponce-de-Leon M; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Maier D; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Bauch A; Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
  • Gyori BM; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Bachman JA; Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.
  • Luna A; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Piñero J; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Furlong LI; Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Balaur I; Barcelona Supercomputing Center (BSC.), Barcelona, Spain.
  • Rougny A; Institut Curie, P.S.L. Research University, Paris, France.
  • Jarosz Y; INSERM, Paris, France.
  • Overall RW; MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.
  • Phair R; Barcelona Supercomputing Center (BSC.), Barcelona, Spain.
Front Immunol ; 14: 1282859, 2023.
Article in En | MEDLINE | ID: mdl-38414974
ABSTRACT

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.
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Full text: 1 Database: MEDLINE Main subject: COVID-19 Limits: Humans Language: En Journal: Front Immunol Year: 2023 Type: Article Affiliation country: France
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Full text: 1 Database: MEDLINE Main subject: COVID-19 Limits: Humans Language: En Journal: Front Immunol Year: 2023 Type: Article Affiliation country: France