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Research Article
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Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19

View ORCID ProfileBridget P Bannerman  Correspondence email, View ORCID ProfileJorge Júlvez, View ORCID ProfileAlexandru Oarga, Tom L Blundell, Pablo Moreno, View ORCID ProfileR Andres Floto  Correspondence email
Bridget P Bannerman
1Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
5The Center for Research and Interdisciplinarity, Paris, France
Roles: Conceptualization, Data curation, Software, Formal analysis, Investigation, Methodology, Writing—original draft, review, and editing
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  • ORCID record for Bridget P Bannerman
  • For correspondence: bpc28@cam.ac.uk
Jorge Júlvez
3Department of Computer Science and Systems Engineering, University of Zaragoza, Zaragoza, Spain
Roles: Data curation, Software, Formal analysis, Investigation, Writing—original draft, review, and editing
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  • ORCID record for Jorge Júlvez
Alexandru Oarga
3Department of Computer Science and Systems Engineering, University of Zaragoza, Zaragoza, Spain
Roles: Data curation, Software, Formal analysis, Writing—original draft, review, and editing
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  • ORCID record for Alexandru Oarga
Tom L Blundell
2Department of Biochemistry, University of Cambridge, Cambridge, UK
Roles: Formal analysis, Writing—review and editing
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Pablo Moreno
4EMBL-EBI, European Bioinformatics Institute, Hinxton, UK
Roles: Data curation, Formal analysis, Investigation, Writing—review and editing
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R Andres Floto
1Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
Roles: Formal analysis, Investigation, Writing—review and editing
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  • ORCID record for R Andres Floto
  • For correspondence: arf27@cam.ac.uk
Published 5 August 2021. DOI: 10.26508/lsa.202000954
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  • Figure 1.
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    Figure 1. The mechanism of replication of SARS-CoV-2 in the human cell.
  • Figure 2.
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    Figure 2. SARS-CoV-2 viral genome and host-dependent metabolic pathways.
  • Figure 3.
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    Figure 3. PPi-pathway intersection node—Nsp9.

    (A) Methionine degradation. (B) Methionine salvage cycle. (C) Cysteine biosynthesis.

  • Figure 4.
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    Figure 4. PPi-pathway intersection node—Nsp8.
  • Figure 5.
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    Figure 5. PPi-pathway intersection node—Nsp2.

    (A) Fatty acid oxidation. (B) Stearate biosynthesis. (C) Vitamin D3 biosynthesis.

  • Figure 6.
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    Figure 6. PPi-pathway intersection node—Nsp4.
  • Figure 7.
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    Figure 7. Pi-pathway intersection nodes - Nsp7 and Orf8a in carbohydrate and fatty acid metabolism.

    (A) PPi-pathway intersection node—Nsp7. (B) PPi-Pathway intersection node—Orf8a. (C) PPi-pathway intersection node—Nsp7 and Orf8a.

  • Figure 8.
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    Figure 8. Development of an integrated model of the Human Airway Epithelial cell and SARS-CoV-2.

Tables

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    Table 1.

    List of bottleneck and essential enzymes on the PPi-pathway intersection nodes.

    ClassPathwaySub-pathwayHuman geneSars geneMacrophageEpithelial cell
    BiosynthesisAmino acidsL-selenocysteine biosynthesisSEPSECSNsp8YN
    BiosynthesisAmino acidsCysteine, and methionineMAT2BNsp9YY
    BiosynthesisFatty acidsFatty acid and long fatty acid biosynthesisSLC27A2Nsp2YY
    BiosynthesisFatty acidsFatty acid and long fatty acid biosynthesisACSL3Nsp7YN
    BiosynthesisFatty acidsStearate biosynthesisSLC27A2Nsp2YY
    BiosynthesisFatty acidsStearate biosynthesisACSL3Nsp7YY
    BiosynthesisCarbohydrate biosynthesisGlycan and oligosaccharide biosynthesisALG11Nsp4YY
    BiosynthesisCarbohydrate biosynthesisGlycanHS2ST1Orf8aYY
    BiosynthesisCarbohydrate biosynthesisGlycanMOGSNsp7YY
    BiosynthesisCarbohydrate biosynthesisGlycan and oligosaccharide biosynthesisALG5ORF3aYY
    BiosynthesisCarbohydrate biosynthesisGlycan, oligosaccharide, and glycosaminoglycan biosynthesisCHPFORF8aYY
    BiosynthesisCarbohydrate biosynthesisGlycan, oligosaccharide, and glycosaminoglycan biosynthesisHS6ST2ORF8aYY
    BiosynthesisCofactorsVitamin D3 biosynthesisPORNsp2YY
    BiosynthesisCofactorsVitamin K epoxide cycleGGCXMain proteaseNY
    BiosynthesisHormonesC20 prostanoid biosynthesisPTGES2Nsp7YY
    BiosynthesistRNA chargingtRNA chargingTARS2Main proteaseYY
    DegradationAmino acidsL-lysine degradationAASSMain proteaseNY
    DegradationAmino acidsL-tryptophan degradationPORNsp2YY
    DegradationAmino acidsL-methionine degradationMAT2BMain proteaseYY
    DegradationFatty acidsCeramide and sphingolipid recyclingSLC27A2Nsp2YY
    DegradationFatty acidsCeramide and sphingolipid recyclingPORNsp2YY
    DegradationFatty acidsCeramide and sphingolipid recyclingACSL3Nsp7YY
    DegradationFatty acidsPhospholipasesPLD3ORF8aYY
    DegradationAmine degradationDopamine degradationCOMTNsp7YY
    DegradationHormonesHemeHMOX1ORF3aYY
    DegradationHormonesmelatoninPORNsp2YY
    DegradationHormonesAdrenalinCOMTNsp2YY
    DegradationHormonesL-dopa degradationCOMTNsp2YY

Supplementary Materials

  • Figures
  • Tables
  • Supplemental Data 1.

    MEMOTE results of the integrated human airway epithelial model and SARS-CoV-2 (iHsaEC21_SARS-CoV-2).[LSA-2020-00954_Supplemental_Data_1.zip]

  • Table S1 List of essential reactions in the Macrophage model (iAB-AMØ-1410).

  • Table S2 List of essential reactions in the Human Airway epithelial model (iHsaEC21).

  • Table S3 List of bottleneck reactions in the Macrophage model (iAB-AMØ-1410).

  • Table S4 List of bottleneck reactions in the Human Airway epithelial model (iHsaEC21).

  • Supplemental Data 2.

    MEMOTE results of the integrated macrophage model (iAB_AMO1410_SARS-CoV-2) and SARS-CoV-2.[LSA-2020-00954_Supplemental_Data_2.zip]

  • Supplemental Data 3.

    MEMOTE results of the draft human airway epithelial model by Wang et al (2012).[LSA-2020-00954_Supplemental_Data_3.zip]

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Integrated human/SARS-CoV-2 metabolic model
Bridget P Bannerman, Jorge Júlvez, Alexandru Oarga, Tom L Blundell, Pablo Moreno, R Andres Floto
Life Science Alliance Aug 2021, 4 (10) e202000954; DOI: 10.26508/lsa.202000954

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Integrated human/SARS-CoV-2 metabolic model
Bridget P Bannerman, Jorge Júlvez, Alexandru Oarga, Tom L Blundell, Pablo Moreno, R Andres Floto
Life Science Alliance Aug 2021, 4 (10) e202000954; DOI: 10.26508/lsa.202000954
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Volume 4, No. 10
October 2021
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