ArticleFrontiers in pharmacology2015
Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites.
Article in Frontiers in pharmacology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The Gini coefficient as a surrogate for the regulability or homeostasis of metabolite concentrations: focus on ergothioneine.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Enhancement of gemcitabine toxicity and specificity through PI3K/Akt/Nrf2 pathway inhibition in pancreatic cancer.Frontiers in pharmacology · 2026Article
- Systems biology and microbiome innovations for personalized diabetic retinopathy management.NPJ systems biology and applications · 2025Review
- The Biology and Biochemistry of Kynurenic Acid, a Potential Nutraceutical with Multiple Biological Effects.International journal of molecular sciences · 2024Review
- Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems.Metabolites · 2023Review
- Assessing How Chemical Exposures Affect Human Health.LC GC Europe · 2023Article
- Article
- The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes.Molecules (Basel, Switzerland) · 2021Review
- FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space.Molecules (Basel, Switzerland) · 2021Article
- Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products.Marine drugs · 2020Article
- VAE-Sim: A Novel Molecular Similarity Measure Based on a Variational Autoencoder.Molecules (Basel, Switzerland) · 2020Article
- Unique metabolite preferences of the drug transporters OAT1 and OAT3 analyzed by machine learning.The Journal of biological chemistry · 2020Article
- The human endogenous metabolome as a pharmacology baseline for drug discovery.Drug discovery today · 2019Review
- Generation of a Small Library of Natural Products Designed to Cover Chemical Space Inexpensively.Pharmaceutical frontiers · 2019Article
- Identifying diseases-related metabolites using random walk.BMC bioinformatics · 2018Article
- Expression and regulation of drug transporters in vertebrate neutrophils.Scientific reports · 2017Article
- Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?Bioanalysis · 2017Article
- Enhancing Drug Efficacy and Therapeutic Index through Cheminformatics-Based Selection of Small Molecule Binary Weapons That Improve Transporter-Mediated Targeting: A Cytotoxicity System Based on Gemcitabine.Frontiers in pharmacology · 2017Article
- Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures.Journal of cheminformatics · 2017Article
- An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network.The Journal of biological chemistry · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundA recent comparison showed the extensive similarities between the structural properties of metabolites in the reconstructed human metabolic network ("endogenites") and those of successful, marketed drugs ("drugs").
resultsClustering indicated the related but differential population of chemical space by endogenites and drugs. Differences between the drug-endogenite similarities resulting from various encodings and judged by Tanimoto similarity could be related simply to the fraction of the bitstrings set to 1. By extracting drug/endogenite substructures, we develop a novel family of fingerprints, the Drug Endogenite Substructure (DES) encodings, based on the ranked frequency of the various substructures. These provide a natural assessment of drug-endogenite likeness, and may be used as descriptors with which to derive quantitative structure-activity relationships (QSARs).
conclusions"Drug-endogenite likeness" seems to have utility, and leads to a simple, novel and interpretable substructure-based molecular encoding for cheminformatics.
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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.