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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Bioinformatics

Open Access Proceedings

Physicochemical property space distribution among human metabolites, drugs and toxins

Varun Khanna1 and Shoba Ranganathan12*

Author Affiliations

1 Dept. of Chemistry and Biomolecular Sciences & ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia

2 Dept. of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

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BMC Bioinformatics 2009, 10(Suppl 15):S10  doi:10.1186/1471-2105-10-S15-S10

Published: 3 December 2009



The current approach to screen for drug-like molecules is to sieve for molecules with biochemical properties suitable for desirable pharmacokinetics and reduced toxicity, using predominantly biophysical properties of chemical compounds, based on empirical rules such as Lipinski's "rule of five" (Ro5). For over a decade, Ro5 has been applied to combinatorial compounds, drugs and ligands, in the search for suitable lead compounds. Unfortunately, till date, a clear distinction between drugs and non-drugs has not been achieved. The current trend is to seek out drugs which show metabolite-likeness. In identifying similar physicochemical characteristics, compounds have usually been clustered based on some characteristic, to reduce the search space presented by large molecular datasets. This paper examines the similarity of current drug molecules with human metabolites and toxins, using a range of computed molecular descriptors as well as the effect of comparison to clustered data compared to searches against complete datasets.


We have carried out statistical and substructure functional group analyses of three datasets, namely human metabolites, drugs and toxin molecules. The distributions of various molecular descriptors were investigated. Our analyses show that, although the three groups are distinct, present-day drugs are closer to toxin molecules than to metabolites. Furthermore, these distributions are quite similar for both clustered data as well as complete or unclustered datasets.


The property space occupied by metabolites is dissimilar to that of drugs or toxin molecules, with current drugs showing greater similarity to toxins than to metabolites. Additionally, empirical rules like Ro5 can be refined to identify drugs or drug-like molecules that are clearly distinct from toxic compounds and more metabolite-like. The inclusion of human metabolites in this study provides a deeper insight into metabolite/drug/toxin-like properties and will also prove to be valuable in the prediction or optimization of small molecules as ligands for therapeutic applications.