ArticlePLoS computational biology2009
A mapping of drug space from the viewpoint of small molecule metabolism.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- A Computational Approach Using Bioinformatics to Screening Drug Targets forEvidence-based complementary and alternative medicine : eCAM · 2018Article
- Second harmonic generation correlation spectroscopy for characterizing translationally diffusing protein nanocrystals.Acta crystallographica. Section D, Structural biology · 2016Article
- Proteome-wide drug screening using mass spectrometric imaging of bead-arrays.Scientific reports · 2016Article
- Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach.Journal of chemical information and modeling · 2015Article
- Curation and analysis of multitargeting agents for polypharmacological modeling.Journal of chemical information and modeling · 2014Article
- Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery.Antibiotics (Basel, Switzerland) · 2014Review
- Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens.PLoS neglected tropical diseases · 2014Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.Journal of chemical information and modeling · 2013Article
- Polypharmacology: drug discovery for the future.Expert review of clinical pharmacology · 2013Review
- Combining cheminformatics methods and pathway analysis to identify molecules with whole-cell activity against Mycobacterium tuberculosis.Pharmaceutical research · 2012Article
- Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).PloS one · 2012Article
- Toward mechanistic classification of enzyme functions.Current opinion in chemical biology · 2011Review
- Navigating the human metabolome for biomarker identification and design of pharmaceutical molecules.Journal of biomedicine & biotechnology · 2011Article
- A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs.Metabolomics : Official journal of the Metabolomic SocietyArticle
- A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports.Journal of the American Medical Informatics Association : JAMIAArticle
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Small molecule drugs target many core metabolic enzymes in humans and pathogens, often mimicking endogenous ligands. The effects may be therapeutic or toxic, but are frequently unexpected. A large-scale mapping of the intersection between drugs and metabolism is needed to better guide drug discovery. To map the intersection between drugs and metabolism, we have grouped drugs and metabolites by their associated targets and enzymes using ligand-based set signatures created to quantify their degree of similarity in chemical space. The results reveal the chemical space that has been explored for metabolic targets, where successful drugs have been found, and what novel territory remains. To aid other researchers in their drug discovery efforts, we have created an online resource of interactive maps linking drugs to metabolism. These maps predict the "effect space" comprising likely target enzymes for each of the 246 MDDR drug classes in humans. The online resource also provides species-specific interactive drug-metabolism maps for each of the 385 model organisms and pathogens in the BioCyc database collection. Chemical similarity links between drugs and metabolites predict potential toxicity, suggest routes of metabolism, and reveal drug polypharmacology. The metabolic maps enable interactive navigation of the vast biological data on potential metabolic drug targets and the drug chemistry currently available to prosecute those targets. Thus, this work provides a large-scale approach to ligand-based prediction of drug action in small molecule metabolism.
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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.