ArticlePloS one2018
Genome scale metabolic models as tools for drug design and personalized medicine.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 50 citations in OpenAlex.
- A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction.Communications biology · 2026Article
- hiPSCGEM01: A Genome-Scale Metabolic Model for Fibroblast-Derived Human iPSCs.Bioengineering (Basel, Switzerland) · 2025Article
- Screening of Potential Drug Targets Based on the Genome-Scale Metabolic Network Model ofCurrent issues in molecular biology · 2025Article
- Unveiling new features of the human pathogenComputational and structural biotechnology journal · 2025Article
- A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.NPJ systems biology and applications · 2024Article
- Genome-Scale Metabolic Models in Fungal Pathogens: Past, Present, and Future.International journal of molecular sciences · 2024Review
- Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome.Nature communications · 2023Article
- Multi-Omics Analysis Revealed Increased De Novo Synthesis of Serine and Lower Activity of the Methionine Cycle in Breast Cancer Cell Lines.Molecules (Basel, Switzerland) · 2023Article
- YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis.Nucleic acids research · 2023Article
- Genetically personalised organ-specific metabolic models in health and disease.Nature communications · 2022Article
- Reconstructed Genome-Scale Metabolic Model Characterizes Adaptive Metabolic Flux Changes in Peripheral Blood Mononuclear Cells in Severe COVID-19 Patients.International journal of molecular sciences · 2022Article
- Genome-scale metabolic network models: from first-generation to next-generation.Applied microbiology and biotechnology · 2022Review
- Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling.iScience · 2022Article
- Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Review
- Agent Clustering Strategy Based on Metabolic Flux Distribution and Transcriptome Expression for Novel Drug Development.Biomedicines · 2021Article
- Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis.mSystems · 2021Article
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID-19.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work we aim to show how Genome Scale Metabolic Models (GSMMs) can be used as tools for drug design. By comparing the chemical structures of human metabolites (obtained using their KEGG indexes) and the compounds contained in the DrugBank database, we have observed that compounds showing Tanimoto scores higher than 0.9 with a metabolite, are 29.5 times more likely to bind the enzymes metabolizing the considered metabolite, than ligands chosen randomly. By using RNA-seq data to constrain a human GSMM it is possible to obtain an estimation of its distribution of metabolic fluxes and to quantify the effects of restraining the rate of chosen metabolic reactions (for example using a drug that inhibits the enzymes catalyzing the mentioned reactions). This method allowed us to predict the differential effects of lipoamide analogs on the proliferation of MCF7 (a breast cancer cell line) and ASM (airway smooth muscle) cells respectively. These differential effects were confirmed experimentally, which provides a proof of concept of how human GSMMs could be used to find therapeutic windows against cancer. By using RNA-seq data of 34 different cancer cell lines and 26 healthy tissues, we assessed the putative anticancer effects of the compounds in DrugBank which are structurally similar to human metabolites. Among other results it was predicted that the mevalonate pathway might constitute a good therapeutic window against cancer proliferation, due to the fact that most cancer cell lines do not express the cholesterol transporter NPC1L1 and the lipoprotein lipase LPL, which makes them rely on the mevalonate pathway to obtain cholesterol.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.