{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Pdf":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.pdf"],"Svg":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.svg"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004-biopax2.owl","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004-biopax3.owl"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004_url.xml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004_urn.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.xpp","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.vcml","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.sci","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.png","https://www.ebi.ac.uk/biomodels/model/download/MODEL1409240004?filename=MODEL1409240004.m"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Rafael Najmanovich"],"curationStatus":["Non-curated"],"modellingApproach":["metabolic network"],"levelVersion":["L2V3"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL1409240004"],"publication_pubmed":["25315994"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Larocque2014 Metabolic reconstruction of Clostridium difficile pathogenic strain 630 (iMLTC806cdf)"],"publication_year":["2014"],"submissionId":["MODEL1409240004"],"modelFlag":["Non Kinetic"],"publication_authors":["Mathieu Larocque, Thierry Chénard, Rafael Najmanovich"],"first_author":["Mathieu Larocque"],"publication":["25315994,\n Background
Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infections present high relapse rates and new hyper-virulent and multi-resistant strains are emerging, making the study of this nosocomial pathogen necessary to find novel therapeutic targets.Results
We present iMLTC806cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC806cdf contains 806 genes, 703 metabolites and 769 metabolic, 117 exchange and 145 transport reactions. iMLTC806cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 89.2% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs (the closest organism for which such data exists). We predict the existence of 76 essential genes and 39 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 29 of these potential therapeutic targets, we find 125 inhibitors of homologous proteins including approved drugs with the potential for drug repositioning, that when validated experimentally could serve as starting points in the development of new antibiotics.Conclusions
We created a highly curated metabolic network model of C. difficile strain 630 and used it to predict essential genes as potential new therapeutic targets in the fight against Clostridium difficile infections.. null, 8.\n Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada. mathieu.larocque2@usherbrooke.ca."],"submitter_mail":["rafael.najmanovich@usherbrooke.ca"],"submitter_affiliation":["University of Sherbrooke"],"pubmed_abstract":["Background
Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infections present high relapse rates and new hyper-virulent and multi-resistant strains are emerging, making the study of this nosocomial pathogen necessary to find novel therapeutic targets.Results
We present iMLTC806cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC806cdf contains 806 genes, 703 metabolites and 769 metabolic, 117 exchange and 145 transport reactions. iMLTC806cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 89.2% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs (the closest organism for which such data exists). We predict the existence of 76 essential genes and 39 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 29 of these potential therapeutic targets, we find 125 inhibitors of homologous proteins including approved drugs with the potential for drug repositioning, that when validated experimentally could serve as starting points in the development of new antibiotics.Conclusions
We created a highly curated metabolic network model of C. difficile strain 630 and used it to predict essential genes as potential new therapeutic targets in the fight against Clostridium difficile infections."],"pubmed_title":["A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors."],"pubmed_authors":["Larocque Mathieu M, Chénard Thierry T, Najmanovich Rafael R"],"additional_accession":[]},"is_claimable":false,"name":"Larocque2014 - Metabolic reconstruction of Clostridium difficile pathogenic strain 630 (iMLTC806cdf)","description":"In the current work, we present the first extensively curated metabolic network reconstruction for C. difficile (strain 630) i MLTC806cdf and validate it with experimental data on essential metabolites and carbon sources. We compare i MLTC806cdf to existing networks showing the importance of manual curation and using the network to predict essential genes. The predictions agree with experimental data for B. subtilis (the closest organism for which such data is available). We detect potential cross-reactivity targets for each of these genes using a variety of methods combining systems and structural computational biology and determine that for only 4 out of 76 predicted essential genes, if exiting, the potential human cross-reactivity targets are themselves essential in the human metabolic network reconstruction RECON2. For a number of essential genes, we find potential binding small molecules, including approved drugs such as Ribavirin, which may inhibit the respective gene products. We hope that i MLTC806cdf will find further use in the community and the results here lead to the development of novel antibiotics against C. difficile infections.","dates":{"last_modification":"2021-11-03","publication":"2021-11-03","submission":"2014-09-24"},"accession":"MODEL1409240004","cross_references":{"ec-code":["3.6.3.27","3.6.3.5","3.6.3.20","6.4.1.1","3.6.3.34","3.6.3.33","3.6.3.-","4.2.1.3","3.6.3.8","1.1.1.41","3.6.3.2","3.6.3.12","2.3.3.1","6.3.5.4","6.2.1.5","6.3.1.1","1.2.1.79","4.2.1.2","3.5.1.4","1.1.1.37","1.4.1.2","2.6.1.19","1.2.1.24","2.6.1.1","2.5.1.6","2.6.1.16","2.3.1.31","2.6.1.96","3.2.2.9","5.1.1.3","2.3.1.57","4.3.2.1","3.5.1.1","3.1.3.77","1.4.1.13","2.1.1.13","3.1.3.87","5.3.2.-","3.5.1.2","2.5.1.48","2.5.1.16","2.6.1.2","4.1.1.50","4.4.1.1","2.8.1.7","5.1.1.2","4.2.1.109","4.4.1.11","2.3.1.46","2.5.1.49","6.3.2.8","4.4.1.21","2.7.1.100","2.3.2.2","6.3.2.9","6.3.1.2","5.3.1.23","3.2.2.16","4.4.1.8","5.1.1.1","2.1.1.10","5.1.1.12","6.3.2.4","2.3.1.-","5.4.3.5","1.4.1.12","2.6.1.51","6.3.4.5","1.3.8.1","1.4.1.14","4.1.1.-","4.2.1.55","4.2.1.17","2.3.1.9","4.1.1.12","1.1.1.35","3.5.99.6","3.1.2.20","2.7.1.59","5.1.2.3","2.7.7.23","5.4.2.10","3.6.1.-","2.3.1.157","2.5.1.15","3.5.1.25","5.1.3.14","2.5.1.7","2.7.6.3","1.1.1.158","2.6.1.85","4.1.3.3","6.3.2.17","5.1.3.9","2.7.1.60","4.1.3.38","3.5.1.81","4.1.1.19","3.5.4.16","4.1.2.25","3.5.1.54","5.4.2.8","1.2.1.38","2.7.1.56","3.5.3.11","2.1.3.3","2.7.1.11","3.5.1.16","1.1.1.140","2.7.7.22","2.3.1.35","2.7.1.1","1.2.1.3","2.7.2.8","3.1.3.11","2.3.1.1","2.2.1.2","5.1.1.4","2.7.1.4","4.1.2.13","6.3.4.6","2.6.1.82","4.1.2.17","2.6.1.11","3.5.3.6","2.8.3.-","5.3.3.3","1.2.1.57","5.3.1.5","1.1.1.157","5.3.1.8","2.8.3.8","1.1.1.17","1.1.1.304","1.1.1.14","4.2.1.120","1.1.1.303","1.1.1.61","1.1.1.30","2.7.7.10","1.1.1.1","2.7.7.13","4.2.1.1","5.1.2.4","5.1.3.3","0.0.0.0","4.1.1.70","5.1.3.15","2.3.1.19","2.7.1.144","1.1.1.251","1.1.1.-","2.7.2.7","2.7.7.12","4.1.1.5","1.1.1.42","5.1.3.2","1.8.1.4","2.7.1.107","2.7.1.6","4.1.2.40","5.3.1.26","1.1.1.100","1.1.1.21","4.2.1.58","1.1.1.72","4.2.1.61","1.1.1.2","2.3.1.41","4.2.1.59","1.3.1.9","3.1.2.14","2.4.1.157","6.3.2.10","2.4.1.208","2.3.1.51","2.7.1.30","2.7.8.20","2.6.1.17","2.3.1.117","4.1.1.20","5.4.3.2","1.4.1.11","4.3.1.14","5.4.3.3","2.8.3.9","2.4.2.1","1.1.1.94","2.4.2.19","3.5.1.19","3.6.1.26","2.7.7.1 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