{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL2404260001?filename=HpM485.xml"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Sepideh Mofidifar"],"curationStatus":["Non-curated"],"modellingApproach":["constraint-based model"],"levelVersion":["L3V1"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL2404260001"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["A genome scale metabolic model for Helicobacter pylori26695"],"publication_year":["2024"],"submissionId":["MODEL2404260001"],"publication_authors":["Sepideh Mofidifar, Abbas Yadegar, Mohammad Hossein Karimi-Jafari"],"first_author":["Sepideh Mofidifar"],"publication":["10.1111/hel.13074,\n Background
Helicobacter pylori is considered a true human pathogen for which rising drug resistance constitutes a drastic concern globally. The present study aimed to reconstruct a genome-scale metabolic model (GSMM) to decipher the metabolic capability of H. pylori strains in response to clarithromycin and rifampicin along with identification of novel drug targets.Materials and methods
The iIT341 model of H. pylori was updated based on genome annotation data, and biochemical knowledge from literature and databases. Context-specific models were generated by integrating the transcriptomic data of clarithromycin and rifampicin resistance into the model. Flux balance analysis was employed for identifying essential genes in each strain, which were further prioritized upon being nonhomologs to humans, virulence factor analysis, druggability, and broad-spectrum analysis. Additionally, metabolic differences between sensitive and resistant strains were also investigated based on flux variability analysis and pathway enrichment analysis of transcriptomic data.Results
The reconstructed GSMM was named as HpM485 model. Pathway enrichment and flux variability analyses demonstrated reduced activity in the ribosomal pathway in both clarithromycin- and rifampicin-resistant strains. Also, a significant decrease was detected in the activity of metabolic pathways of clarithromycin-resistant strain. Moreover, 23 and 16 essential genes were exclusively detected in clarithromycin- and rifampicin-resistant strains, respectively. Based on prioritization analysis, cyclopropane fatty acid synthase and phosphoenolpyruvate synthase were identified as putative drug targets in clarithromycin- and rifampicin-resistant strains, respectively.Conclusions
We present a robust and reliable metabolic model of H. pylori. This model can predict novel drug targets to combat drug resistance and explore the metabolic capability of H. pylori in various conditions.. 2, 29.\n Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran."],"submitter_mail":["s.mofidifar@gmail.com"],"publication_doi":["10.1111/hel.13074"],"submitter_affiliation":["Institute of Biochemistry and Biophysics,University of Tehran"],"additional_accession":[]},"is_claimable":false,"name":"A genome scale metabolic model for Helicobacter pylori26695","description":"No 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N","META:CPD-12575","META:FMNH2","META:CPD-2961","META:DIHYDROPTERIN-CH2OH-PP","META:2-PG","META:FORMAMIDE","META:D-GLT","META:10-FORMYL-THF","META:4-HYDROXY-L-PROLINE","META:L-CYSTATHIONINE","META:GLUTAMATE-1-SEMIALDEHYDE","META:HOMO-SER","META:GLUCOSAMINE-1P","META:O-PHOSPHO-L-HOMOSERINE","META:2-KETO-ISOVALERATE","META:N-ACETYL-D-GLUCOSAMINE-1-P","META:5-METHYLTHIOADENOSINE","META:5-AMINO-LEVULINATE","META:CPD-560","META:5-10-METHENYL-THF","META:GLYCEROL-3P","META:G3P","META:L-GLUTAMATE_GAMMA-SEMIALDEHYDE","META:3-P-HYDROXYPYRUVATE","META:ISOCHORISMATE","META:L-DELTA1-PYRROLINE_5-CARBOXYLATE","META:CARBOXYPHENYLAMINO-DEOXYRIBULOSE-P","META:D-6-P-GLUCONO-DELTA-LACTONE","META:DEAMIDO-NAD","META:GDP-MANNOSE","META:2-ACETO-LACTATE","META:CPD-12335","META:D-ALPHABETA-D-HEPTOSE-7-PHOSPHATE","META:CPD-13357","META:2-ACETO-2-HYDROXY-BUTYRATE","META:1-KETO-2-METHYLVALERATE","META:R-3-Hydroxypalmitoyl-ACPs","META:GALACTOSE-1P","META:CDP","META:UDP-GALACTOSE","META:R-3-hydroxystearoyl-ACPs","META:GLC-1-P","META:XANTHOSINE-5-PHOSPHATE","META:DUDP","META:DPG","META:CPD-19753","META:KDO","META:B-DMAN-OCT-2:6_1:A_2:KETO_3:D","META:UDP-N-ACETYL-D-GLUCOSAMINE","META:CMP-KDO","META:UDP","META:KDO-8P","META:FARNESYL-PP","META:GLUTATHIONE","META:DCDP","META:CYS-GLY","META:2K-4CH3-PENTANOATE","META:CPD0-1283","META:NICOTINATE_NUCLEOTIDE","META:QUINOLINATE","META:SHIKIMATE","META:MANNOSE-1P","META:SHIKIMATE-5P","META:MANNOSE-6P","META:CPD-15979","META:4-hydroxybenzoate","META:CPD-6972","META:3-OCTAPRENYL-4-HYDROXYBENZOATE","META:CPD-1063","META:Red-Thioredoxin","META:THZ","META:Ox-Thioredoxin","META:THZ-P","META:PHENYL-PYRUVATE","META:PORPHOBILINOGEN","META:HYDROXYMETHYLBILANE","META:AMINO-HYDROXYMETHYL-METHYL-PYR-P","META:2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE","META:AMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP","META:OCTAPRENYL-METHOXY-BENZOQUINONE","META:PYRROLINE-HYDROXY-CARBOXYLATE","META:OCTAPRENYL-METHYL-METHOXY-BENZQ","META:CPD-11444","META:PANTOTHENATE","META:COPROPORPHYRINOGEN_I","META:4-P-PANTOTHENATE","META:3-P-SERINE","META:OROTIDINE-5-PHOSPHATE","META:UMP","META:DEOXYGUANOSINE","META:2-OCTAPRENYLPHENOL","META:2-OXOBUTANOATE","META:R-4-PHOSPHOPANTOTHENOYL-L-CYSTEINE","META:INOSINE","META:PANTETHEINE-P","META:DEOXYINOSINE","META:XANTHOSINE","META:THIAMINE-PYROPHOSPHATE","META:X-DRIB-PEN-1:4","META:RIBOFLAVIN","META:SPERMINE","META:DIMETHYL-D-RIBITYL-LUMAZINE","META:O-SUCCINYLBENZOATE","META:KDO-LIPID-IVA","META:RIBOSE-1P","META:N-SUCCINYLLL-2-6-DIAMINOPIMELATE","META:CPD-15318","META:2-OCTAPRENYL-6-HYDROXYPHENOL","META:SUCCINYL-OH-CYCLOHEXADIENE-COOH","META:2-OCTAPRENYL-6-METHOXYPHENOL","META:SO3","META:HSO3","META:H2SO3","META:CPD-9646","META:CPD-10484","META:C5","META:CPD-11419","META:P3I","META:CDP-ETHANOLAMINE","META:GUANOSINE-5DP-3DP","META:D-SEDOHEPTULOSE-7-P","META:N-SUCCINYL-2-AMINO-6-KETOPIMELATE","META:P-HYDROXY-PHENYLPYRUVATE","META:GDP-TP","META:PROTOPORPHYRINOGEN","META:XYLULOSE-5-PHOSPHATE","META:L-CYSTEATE","META:5-P-BETA-D-RIBOSYL-AMINE","META:5-PHOSPHO-RIBOSYL-GLYCINEAMIDE","META:CPD-380","META:THIAMINE-P","META:INDOLE","META:UDP-AA-GLUTAMATE","META:CPD-597","META:UDP-ACETYL-CARBOXYVINYL-GLUCOSAMINE","META:UDP-D-GLUCOSAMINE","META:C6","META:CPD0-1456","META:UDP-N-ACETYLMURAMATE","UNDECAPRENYL-DIPHOSPHATE","META:UROPORPHYRINOGEN-III","META:COPROPORPHYRINOGEN_III","META:LIPID-IV-A","META:KDO2-LIPID-IVA","META:PROPIONYL-COA","META:PROPIONATE","META:PROPIONYL-P","META:HMP","META:NICOTINAMIDE_RIBOSE","META:NIACINAMIDE","META:CPD-8259","META:NIACINE","CPD-12454","Enoylglutaryl-ACP-methyl-esters","Pimeloyl-ACP-methyl-esters","META:GLUCONATE","META:Fructofuranose","CPD-8122","CPD-582","CPD-4","PRECURSOR-Z","META:GLYCERALD","META:L-RIBULOSE","META:L-RIBULOSE-5-P","META:L-FUCULOSE","CPD-10012","META:L-1-LYSOPHOSPHATIDATE","META:2-AMINOBENZOYL-COA","META:CPD-15907","META:FORMALDEHYDE","META:L-XYLULOSE","CPD-13043","META:L-XYLULOSE-5-P","META:7-CYANO-7-DEAZAGUANINE","CPD0-1699","7-AMINOMETHYL-7-DEAZAGUANINE","META:CPD-12175","META:D-RIBULOSE","META:CPD-12179","META:CPD-15403","META:N-METHYLHYDANTOIN","META:DCMP","META:CH33ADO","META:CPD-9164","META:6-PYRUVOYL-5678-TETRAHYDROPTERIN","META:TRIMETHYLAMINE","META:TRIMETHYLAMINE-N-O","META:TRIMENTHLAMINE-N-O","META:CD+2","META:SACCHAROPINE","META:SEPO3","META:D-ALLULOSE-6-PHOSPHATE","META:1-AMINO-PROPAN-2-ONE-3-PHOSPHATE","META:PYRIDOXINE-5P","META:4-PHOSPHONOOXY-THREONINE","META:CPD-653","META:CPD-15629","META:D-Allopyranose","META:CPD0-2472","META:D-ALLOSE-6-PHOSPHATE","META:apo-ACP","META:AMINO-OXOBUT","META:AMINO-ACETONE","META:L-ALLO-THREONINE","MTA:CPD-488","META:OXIDIZED-GLUTATHIONE","META:TRANS-RXN0-240","META:TRANS-RXN0-476","META:PHOSPHOLIPASE-A2-RXN","META:CITSYN-RXN","META:CITRATE-RE-SYNTHASE-RXN","META:RXN-14905","META:RXN-14325","META:ACSERLY-RXN","META:SAMDECARB-RXN","META:DEOXYADENYLATE-KINASE-RXN","META:ADENPRIBOSYLTRAN-RXN","META:ALANINE-DEHYDROGENASE-RXN","META:ADENYLYLSULFKIN-RXN","META:ALARACECAT-RXN","META:AMPSYN-RXN","META:RXN-14118","META:AICARSYN-RXN","META:ALCOHOL-DEHYDROGENASE-NADP+-RXN","META:RXN-12484","META:ADENYLOSUCCINATE-SYNTHASE-RXN","META:DIAMINOPIMDECARB-RXN","META:ACETYL-COA-CARBOXYLTRANSFER-RXN","META:DIAMINOPIMEPIM-RXN","META:RXN-7957","META:ACETATEKIN-RXN","META:ACP-S-ACETYLTRANSFER-RXN","META:DAPASYN-RXN","META:DIOHBUTANONEPSYN-RXN","META:DAHPSYN-RXN","META:DETHIOBIOTIN-SYN-RXN","META:ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN","META:4OH2OXOGLUTARALDOL-RXN","META:DARAB5PISOM-RXN","META:GMKALT-RXN","META:ACETYL-COA-ACETYLTRANSFER-RXN","META:DIHYDROPICRED-RXN","META:ACETYLHOMOSER-CYS-RXN","Meta:DIHYDRODIPICSYN-RXN","META:DALADALALIG-RXN","META:RXN-12492","META:DCTP-DEAM-RXN","META:RXN-19329","META:DIHYDROFOLATEREDUCT-RXN","META:GLUTAMIN-RXN","META:GLUTAMINASE-ASPARAGIN-ASE-RXN","META:RXN-14728","META:GLUTRACE-RXN","META:ADCLY-RXN","META:DIHYDROFOLATESYNTH-RXN","META:FORMYLTHFDEFORMYL-RXN","META:FORMATETHFLIG-RXN","META:PRTRANS-RXN","META:FUMHYDR-RXN","META:ANTHRANSYN-RXN","META:ADENINE-DEAMINASE-RXN","META:ADENYL-KIN-RXN","META:2.3.1.157-RXN","META:GSAAMINOTRANS-RXN","META:H2NEOPTERINALDOL-RXN","META:1.1.1.8-RXN","META:GLYC3PDEHYDROGBIOSYN-RXN","META:7KAPSYN-RXN","META:RIBOFLAVINSYNREDUC-RXN","META:RXN-969","META:ARGDECARBOX-RXN","META:GLYCEROL-KIN-RXN","META:SPONTPRO-RXN","META:DIHYDROOROT-RXN","META:GLU6PDEHYDROG-RXN","META:GDPMANDEHYDRA-RXN","META:RIBOFLAVINSYNDEAM-RXN","META:RXN0-4342","META:ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN","META:ASPARAGHYD-RXN","META:UTPHEXPURIDYLYLTRANS-RXN","META:ASNSYNA-RXN","META:RXN-11988","META:RXN-11505","META:3-DEHYDROQUINATE-DEHYDRATASE-RXN","META:GLUC1PURIDYLTRANS-RXN","META:ASPDECARBOX-RXN","META:GMP-REDUCT-RXN","META:ASPCARBTRANS-RXN","META:GMP-SYN-GLUT-RXN","META:ASPARTATEKIN-RXN","META:GAPDHSYNEC-RXN","META:GAPOXNPHOSPHN-RXN","META:ASPARTASE-RXN","META:ASPAMINOTRANS-RXN","META:FPPSYN-RXN","META:RXN-13697","META:3-DEHYDROQUINATE-SYNTHASE-RXN","META:GTP-CYCLOHYDRO-I-RXN","META:ATPSYN-RXN","META:GUANPRIBOSYLTRAN-RXN","META:CARBODEHYDRAT-RXN","META:RXN0-5224","META:GPPSYN-RXN","META:325-BISPHOSPHATE-NUCLEOTIDASE-RXN","META:MALSYN-RXN","META:TRANS-RXN-151","META:2.7.7.13-RXN","META:RXN0-884","META:4OHBENZOATE-OCTAPRENYLTRANSFER-RXN","META:MALONYL-COA-ACP-TRANSACYL-RXN","META:RXN-12121","META:CATAL-RXN","META:CARBPSYN-RXN","META:R145-RXN","META:2.7.1.148-RXN","META:THIAZOLSYN3-RXN","META:GLUCOKIN-RXN","META:CHORISMATEMUT-RXN","META:OHMETHYLBILANESYN-RXN","META:CHORISMATE-SYNTHASE-RXN","META:RXN0-302","META:DEPHOSPHOCOAKIN-RXN","META:2.7.7.60-RXN","META:2-DEHYDROPANTOATE-REDUCT-RXN","META:S-ADENMETSYN-RXN","META:RXN-7912","META:DTMPKI-RXN","META:RXN-721","META:URA-PHOSPH-RXN","META:DEOXYURIDINE-PHOSPHORYLASE-RXN","META:HOMOSERDEHYDROG-RXN","META:GLYCOLALD-DEHYDROG-RXN","META:HOMOSERKIN-RXN","META:HYPOXANPRIBOSYLTRAN-RXN","META:FUCPALDOL-RXN","META:RXN0-6258","META:PROTOHEMEFERROCHELAT-RXN","META:3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN","META:METHYLTHIOADENOSINE-NUCLEOSIDASE-RXN","META:METHENYLTHFCYCLOHYDRO-RXN","META:DUTP-PYROP-RXN","META:PGLYCDEHYDROG-RXN","META:3.6.1.19-RXN","META:DXPREDISOM-RXN","META:METHYLENETHFDEHYDROG-NADP-RXN","META:1.5.1.20-RXN","META:GLYOHMETRANS-RXN","META:ISOCHORSYN-RXN","META:GUANYL-KIN-RXN","META:DXS-RXN","META:KDPGALDOL-RXN","META:NAD-KIN-RXN","META:GLUTAMINESYN-RXN","META:NQOR-RXN","META:FMNREDUCT-RXN","META:RXN-12444","META:BRANCHED-CHAINAMINOTRANSFERILEU-RXN","META:PGLUCONDEHYDRAT-RXN","META:FADSYN-RXN","META:NAD-SYNTH-NH3-RXN","META:3.6.3.21-RXN","META:PHOSGLYPHOS-RXN","META:ABC-12-RXN","META:PHOSMANMUT-RXN","META:TRANS-RXN-233","META:4-HYDROXYGLUTAMATE-AMINOTRANSFERASE-RXN","META:IMP-DEHYDROG-RXN","META:H2PTEROATESYNTH-RXN","META:6PGLUCONOLACT-RXN","META:2PGADEHYDRAT-RXN","META:ISPH2-RXN","META:FORMAMIDASE-RXN","META:GLUTDEHYD-RXN","META:GLUTAMATE-DEHYDROGENASE-NADP+-RXN","META:3PGAREARR-RXN","META:RXN-15513","META:DCDPKIN-RXN","META:ACETOLACTREDUCTOISOM-RXN","META:ACETOOHBUTREDUCTOISOM-RXN","META:DADPKIN-RXN","META:NUCLEOSIDE-DIP-KIN-RXN","META:GDPKIN-RXN","Meta:LEUCINE-AMINOTRANSFERASE-RXN","META:BRANCHED-CHAINAMINOTRANSFERLEU-RXN","META:PHOSPHOGLUCMUT-RXN","META:RXN-16999","META:5.4.2.5-RXN","META:2.7.7.1-RXN","META:UDPKIN-RXN","META:NICONUCADENYLYLTRAN-RXN","META:3-OXOACYL-ACP-SYNTH-BASE-RXN","META:QUINOPRIBOTRANS-RXN","META:2.3.1.180-RXN","META:HYDROXYPYRROLINEDEH-RXN","META:SHIKIMATE-KINASE-RXN","META:CDPKIN-RXN","META:O-SUCCHOMOSERLYASE-RXN","META:DTDPKIN-RXN","META:RXN-14471","META:DGDPKIN-RXN","META:DUDPKIN-RXN","META:PHEAMINOTRANS-RXN","META:RXN-10814","META:CPM-KDOSYNTH-RXN","META:KDO-8PPHOSPHAT-RXN","META:RXN-9384","META:KDO-8PSYNTH-RXN","META:RXNI-2","META:PYRIMSYN3-RXN","META:PHOSACETYLTRANS-RXN","META:RXN-8992","META:2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN","META:PANTEPADENYLYLTRAN-RXN","META:PANTOTHENATE-KIN-RXN","META:RXN-14122","META:OROTPDECARB-RXN","META:ADENPHOSPHOR-RXN","META:DEOXYADENPHOSPHOR-RXN","META:INORGPYROPHOSPHAT-RXN","META:BRANCHED-CHAINAMINOTRANSFERVAL-RXN","META:PORPHOBILSYNTH-RXN","META:3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN","META:RXN0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