Bannerman2020 - Integrated model of the human airway epithelial cell and the SARS-CoV-2 virus

  public model
Model Identifier
MODEL2007210001
Short description
We have developed a new model of the human airway epithelial cell by deriving the cell-specific metabolic reactions identified from (i) a draft automated model by Wang et al. 2017 (ii) gene expression datasets of the human airway epithelial cell (Deprez et al., 2020; Braga et al., 2020). (iii) We obtained additional reactions, gene-to-reaction associations and pathways (that were not in the automated model) from HumanCyc (Trupp et al., 2010) and (iv) performed stochastic and dynamic simulations on the model generated including manual curations from primary literature and Recon3D (Brunk et al., 2018). (v) We added the viral biomass maintenance function into the model, previously developed for the macrophage cell (Renz et al. 2020) to develop the new integrated model of the human airway epithelial cell and the SARS-CoV-2 virus, (iBBEC4660).
Format
SBML (L3V1)
Related Publication
  • Structural and dynamical analysis of integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19
  • Bridget Bannerman, Jorge Julvez, Alexandru Oarga, Pablo Moreno, Tom Blundell, Andres Floto
  • Nature Preprint , 1/ 2021 , DOI: 10.21203/rs.3.rs-46892/v2
  • Multidisciplinary Researcher, University of Cambridge and MRC Laboratory of Molecular Biology
  • The coronavirus disease 2019 (COVID-19) pandemic caused by the new coronavirus (SARS-CoV-2) is currently responsible for over 500 thousand deaths in 216 countries across the world and is affecting over 10 million people. The absence of FDA approved drugs against the new SARS-CoV-2 virus has highlighted an urgent need to design new drugs. We developed an integrated model of the human cell and the SARS-CoV-2 virus to provide insight into the pathogenetic mechanism of the virus and to support current therapeutic strategies. We show the biochemical reactions required for the growth and general maintenance of the human cell, first of all, in its healthy state. We then demonstrate how the entry of the SARS-CoV-2 virus into the human cell causes biochemical and structural changes, leading to a change of cell functions or cell death. We have completed a comparative analysis of our model and other previously generated cell type models and highlight 48 pathways and over 800 reactions hijacked by the virus for its replication and survival. We designed a new tool which predicts 15 unique reactions as drug targets from our models (the integrated human macrophage, human airway epithelial cells and the SARS-CoV-2 virus) and provide a platform for future studies on viral entry inhibition and drug optimisation strategies.
Contributors
Pablo Moreno, Bridget Bannerman, Krishna Kumar Tiwari, Tung Nguyen

Metadata information


Curation status
Non-curated

Modelling approach(es)

Name Description Size Actions

Model files

iHsaEC21.xml Integrated human airway epithelial cell and the SARS-CoV-2 virus 17.36 MB Preview | Download

Additional files

iBBEC4660_amended_v6.xml Integrated human airway epithelial cell and the SARS-CoV-2 virus, initial version 14.78 MB Preview | Download
iBBEC4660.json COBRAPy json export of the model 2.15 MB Preview | Download

  • Model originally submitted by : Bridget Bannerman
  • Submitted: 30-Oct-2020 14:57:40
  • Last Modified: 28-Jun-2021 17:56:47
Revisions
  • Version: 17 public model Download this version
    • Submitted on: 28-Jun-2021 17:56:47
    • Submitted by: Bridget Bannerman
    • With comment: We have updated the meta-data of the revised model, iHsaEC21.xml
  • Version: 16 public model Download this version
    • Submitted on: 24-Jun-2021 09:32:02
    • Submitted by: Bridget Bannerman
    • With comment: I have corrected the Meta-data for the model, iHsaEC21.xml, initially called iBBEC4660
  • Version: 15 public model Download this version
    • Submitted on: 13-Nov-2020 13:36:21
    • Submitted by: Tung Nguyen
    • With comment: Edited model metadata online.
  • Version: 8 public model Download this version
    • Submitted on: 30-Oct-2020 14:57:40
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Edited model metadata online.

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

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