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

Journal: Frontiers in immunology
Published Date:

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.

Authors

  • Anna Niarakis
    Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.
  • Marek Ostaszewski
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Alexander Mazein
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Inna Kuperstein
    Institut Curie, P.S.L. Research University, Paris, France.
  • Martina Kutmon
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Marc E Gillespie
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Akira Funahashi
    Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.
  • Marcio Luis Acencio
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Ahmed Hemedan
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Michael Aichem
    Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
  • Karsten Klein
    Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
  • Tobias Czauderna
    Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany.
  • Felicia Burtscher
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Takahiro G Yamada
    Department of Biosciences and Informatics, Keio University, Kanagawa, Japan.
  • Yusuke Hiki
    Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan.
  • Noriko F Hiroi
    Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan.
  • Finterly Hu
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Nhung Pham
    Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands.
  • Friederike Ehrhart
    Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Egon L Willighagen
    Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Alberto Valdeolivas
    Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
  • Aurelien Dugourd
    Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
  • Francesco Messina
    Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases' Lazzaro Spallanzani' - IRCCS, Rome, Italy.
  • Marina Esteban-Medina
    Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Maria Peña-Chilet
    Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Kinza Rian
    Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Sylvain Soliman
    Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
  • Sara Sadat Aghamiri
    Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Bhanwar Lal Puniya
    Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Aurélien Naldi
    Lifeware Group, Inria, Saclay-île de France, Palaiseau, France.
  • Tomáš Helikar
    Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
  • Vidisha Singh
    Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France.
  • Marco Fariñas Fernández
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Viviam Bermudez
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Eirini Tsirvouli
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Arnau Montagud
    Barcelona Supercomputing Center (BSC.), Barcelona, Spain.
  • Vincent Noël
    Institut Curie, P.S.L. Research University, Paris, France.
  • Miguel Ponce-de-Leon
    Barcelona Supercomputing Center (BSC.), Barcelona, Spain.
  • Dieter Maier
    Labvantage-Biomax GmbH, Planegg, Germany.
  • Angela Bauch
    Labvantage-Biomax GmbH, Planegg, Germany.
  • Benjamin M Gyori
    Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States.
  • John A Bachman
    Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States.
  • Augustin Luna
    Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States.
  • Janet Piñero
    Medbioinformatics Solutions SL, Barcelona, Spain.
  • Laura I Furlong
    Medbioinformatics Solutions SL, Barcelona, Spain.
  • Irina Balaur
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Adrien Rougny
    Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan.
  • Yohan Jarosz
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Rupert W Overall
    Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
  • Robert Phair
    Integrative Bioinformatics, Inc., Mountain View, CA, United States.
  • Livia Perfetto
    Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy.
  • Lisa Matthews
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.
  • Devasahayam Arokia Balaya Rex
    Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Derlakatte, Mangalore, India.
  • Marija Orlic-Milacic
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Luis Cristobal Monraz Gomez
    Institut Curie, P.S.L. Research University, Paris, France.
  • Bertrand De Meulder
    Association E.I.S.B.M, Brignais, France.
  • Jean Marie Ravel
    Institut Curie, P.S.L. Research University, Paris, France.
  • Bijay Jassal
    Ontario Institute for Cancer Research, Toronto, ON, Canada.
  • Venkata Satagopam
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Guanming Wu
    Oregon Health Sciences University, Portland, OR, United States.
  • Martin Golebiewski
    Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
  • Piotr Gawron
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
  • Laurence Calzone
    Institut Curie, P.S.L. Research University, Paris, France.
  • Jacques S Beckmann
    University of Lausanne, Lausanne, Switzerland.
  • Chris T Evelo
    Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.
  • Peter D'Eustachio
    Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States.
  • Falk Schreiber
    Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.
  • Julio Saez-Rodriguez
    Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany.
  • Joaquin Dopazo
    Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain.
  • Martin Kuiper
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Alfonso Valencia
    Barcelona Supercomputing Center (BSC.), Barcelona, Spain.
  • Olaf Wolkenhauer
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany.
  • Hiroaki Kitano
    Systems Biology Institute, Tokyo, Japan.
  • Emmanuel Barillot
    Institut Curie, P.S.L. Research University, Paris, France.
  • Charles Auffray
    Association E.I.S.B.M, Brignais, France.
  • Rudi Balling
    Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany.
  • Reinhard Schneider
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.