ArticleBMC systems biology2015
PROXIMAL: a method for Prediction of Xenobiotic Metabolism.
Article in BMC systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Transcriptomic Analysis in a Model of Aniridia-Associated Keratopathy for Target Discovery and Evaluation of Duloxetine Therapy.Investigative ophthalmology & visual science · 2026Article
- Enzyme promiscuity in the field of synthetic biology applied to white biotechnology: Opportunities and weaknesses.Biodesign research · 2025Review
- Article
- Computational analysis of the gut microbiota-mediated drug metabolism.Computational and structural biotechnology journal · 2025Article
- Exploring Potential Bifunctional Peptides with Anti-tyrosinase and Antioxidant Activities fromCombinatorial chemistry & high throughput screening · 2025Article
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- Pickaxe: a Python library for the prediction of novel metabolic reactions.BMC bioinformatics · 2023Article
- Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.Bioinformatics (Oxford, England) · 2023Article
- Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA.BMC bioinformatics · 2021Article
- Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification.Bioinformatics (Oxford, England) · 2021Article
- Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.Metabolic engineering communications · 2021Article
- Learning graph representations of biochemical networks and its application to enzymatic link prediction.Bioinformatics (Oxford, England) · 2021Article
- Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks.Computational and structural biotechnology journal · 2021Review
- Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites.Journal of chemical information and modeling · 2020Article
- Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics.Metabolites · 2020Article
- System Prediction and Validation of TCM for Chronic Myeloid Leukemia Treatment from the Perspective of Low-Toxicity Chemotherapy: A StilbeneEvidence-based complementary and alternative medicine : eCAM · 2020Article
- Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data.Microbial cell factories · 2019Article
- Computational methods and tools to predict cytochrome P450 metabolism for drug discovery.Chemical biology & drug design · 2019Review
- Network pharmacological mechanisms of Vernonia anthelmintica (L.) in the treatment of vitiligo: Isorhamnetin induction of melanogenesis via up-regulation of melanin-biosynthetic genes.BMC systems biology · 2017Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundContamination of the environment with bioactive chemicals has emerged as a potential public health risk. These substances that may cause distress or disease in humans can be found in air, water and food supplies. An open question is whether these chemicals transform into potentially more active or toxic derivatives via xenobiotic metabolizing enzymes expressed in the body. We present a new prediction tool, which we call PROXIMAL (Prediction of Xenobiotic Metabolism) for identifying possible transformation products of xenobiotic chemicals in the liver. Using reaction data from DrugBank and KEGG, PROXIMAL builds look-up tables that catalog the sites and types of structural modifications performed by Phase I and Phase II enzymes. Given a compound of interest, PROXIMAL searches for substructures that match the sites cataloged in the look-up tables, applies the corresponding modifications to generate a panel of possible transformation products, and ranks the products based on the activity and abundance of the enzymes involved.
resultsPROXIMAL generates transformations that are specific for the chemical of interest by analyzing the chemical's substructures. We evaluate the accuracy of PROXIMAL's predictions through case studies on two environmental chemicals with suspected endocrine disrupting activity, bisphenol A (BPA) and 4-chlorobiphenyl (PCB3). Comparisons with published reports confirm 5 out of 7 and 17 out of 26 of the predicted derivatives for BPA and PCB3, respectively. We also compare biotransformation predictions generated by PROXIMAL with those generated by METEOR and Metaprint2D-react, two other prediction tools.
conclusionsPROXIMAL can predict transformations of chemicals that contain substructures recognizable by human liver enzymes. It also has the ability to rank the predicted metabolites based on the activity and abundance of enzymes involved in xenobiotic transformation.
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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.