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A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.
Schultz, Bruce; Zaliani, Andrea; Ebeling, Christian; Reinshagen, Jeanette; Bojkova, Denisa; Lage-Rupprecht, Vanessa; Karki, Reagon; Lukassen, Sören; Gadiya, Yojana; Ravindra, Neal G; Das, Sayoni; Baksi, Shounak; Domingo-Fernández, Daniel; Lentzen, Manuel; Strivens, Mark; Raschka, Tamara; Cinatl, Jindrich; DeLong, Lauren Nicole; Gribbon, Phil; Geisslinger, Gerd; Ciesek, Sandra; van Dijk, David; Gardner, Steve; Kodamullil, Alpha Tom; Fröhlich, Holger; Peitsch, Manuel; Jacobs, Marc; Hoeng, Julia; Eils, Roland; Claussen, Carsten; Hofmann-Apitius, Martin.
  • Schultz B; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Zaliani A; ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany.
  • Ebeling C; Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany.
  • Reinshagen J; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Bojkova D; ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany.
  • Lage-Rupprecht V; Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany.
  • Karki R; Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany.
  • Lukassen S; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Gadiya Y; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Ravindra NG; Center for Digital Health, Berlin Institute of Health (BIH), Charité Universitätsmedizin Berlin, Berlin, Germany.
  • Das S; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Baksi S; Center for Biomedical Data Science, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA.
  • Domingo-Fernández D; Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK.
  • Lentzen M; Causality BioModels Pvt Ltd., Kinfra Hi-Tech Park, Kerala Technology Innovation Zone- KTIZ, Kalamassery, Cochin, 683503, India.
  • Strivens M; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Raschka T; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Cinatl J; Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK.
  • DeLong LN; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Gribbon P; Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany.
  • Geisslinger G; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
  • Ciesek S; ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany.
  • van Dijk D; Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany.
  • Gardner S; Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany.
  • Kodamullil AT; Pharmazentrum Frankfurt/ZAFES, Institut Für Klinische Pharmakologie, Klinikum Der Goethe-Universität Frankfurt, 60590, Frankfurt am Main, Germany.
  • Fröhlich H; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany.
  • Peitsch M; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany.
  • Jacobs M; Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany.
  • Hoeng J; DZIF, German Centre for Infection Research, External Partner Site, 60596, Frankfurt am Main, Germany.
  • Eils R; Center for Biomedical Data Science, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA.
  • Claussen C; Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK.
  • Hofmann-Apitius M; Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
Sci Rep ; 11(1): 11049, 2021 05 26.
Article in English | MEDLINE | ID: covidwho-1246386
ABSTRACT
The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific community's massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2/COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Drug Repositioning / SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Prognostic study / Systematic review/Meta Analysis Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-90296-2

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Drug Repositioning / SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Prognostic study / Systematic review/Meta Analysis Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-90296-2