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  • Open Access

Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules

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  • 1Email author
Journal of Cheminformatics20135 (Suppl 1) :O12

  • Published:


  • Chinese Medicine
  • Traditional Chinese Medicine
  • Property Space
  • Drug Molecule
  • Fundamental Importance
Understanding the metabolic fate of small organic molecules is of fundamental importance to the successful design and development of drugs, nutritional supplements, cosmetics and agrochemicals [1, 2]. In the current study we investigated how the products of metabolism differ from their parent molecules by analysing a large dataset of experimentally determined metabolic transformations (Figure 1). This dataset was split into three specific chemical domains representing approved drug molecules, human metabolites and molecules from traditional Chinese medicines to allow individual analysis. We also quantified the impact of individual Phase I and Phase II metabolic reactions on calculated chemical descriptors using MetaPrint2D [3] and suggest new approaches to utilise metabolism for the design of drugs and cosmetics. The last section of this study investigates the properties of metabolites found in the bile, faeces and urine and analyses their commonalities and differences.
Figure 1
Figure 1

Four important questions pertinent to the design and development of new molecules with favourable ADME properties addressed in this work. d, approved drugs; h, human metabolites; t, molecules from traditional Chinese medicines; MW, molecular weight.

Authors’ Affiliations

Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
TNO Research Group Quality & Safety, P.O. Box 360, 3700 AJ Zeist, The Netherlands
Leiden/Amsterdam Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands
Unilever R&D, 3133 AT Vlaardingen, The Netherlands


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  3. Adams SE: Molecular similarity and xenobiotic metabolism. Ph.D. Thesis, Unilever Centre for Molecular Sciences Informatics, Department of Chemistry. 2010, University of CambridgeGoogle Scholar


© Kirchmair et al.; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.