SuperToxic: a comprehensive database of toxic compounds

Abstract

Within our everyday life, we are confronted with a variety of toxic substances of natural or artificial origin. Toxins are already used, e.g. in medicine, but there is still an increasing number of toxic compounds, representing a tremendous potential to extract new substances. Since predictive toxicology gains in importance, the careful and extensive investigation of known toxins is the basis to assess the properties of unknown substances. In order to achieve this aim, we have collected toxic compounds from literature and web sources in the database SuperToxic. The current version of this database compiles about 60,000 compounds and their structures. These molecules are classified according to their toxicity, based on more than 2 million measurements. The SuperToxic database provides a variety of search options like name, CASRN, molecular weight and measured values of toxicity. With the aid of implemented similarity searches, information about possible biological interactions can be gained. Furthermore, connections to the Protein Data Bank, UniProt and the KEGG database are available, to allow the identification of targets and those pathways, the searched compounds are involved in. This database is available online at: http://bioinformatics.charite.de/supertoxic.

Figure 1.

Flow chart of queries and search results in SuperToxic. (I) Search option of the web interface. (A) Search for toxic compounds via name, CASRN or NSC number and pathway. (B) Structure search: upload a MOL file, enter SMILES or InChI code or dray the structure, e.g. of a potential drug candidate (Hit1). Based on this query structure a similarity or substructure search can be performed. (C) Search for toxic compounds via properties, like molecular weight, number of atoms or rings, H-bond donors or acceptors, LogP or the toxicity value. (II) Result table of a similarity search (Hit1 a query structure), showing a summary for each compound. (A) A detailed view shows all properties. (B) All toxicity values for a compound. (C) Supplier information. (D) Link to KEGG pathways.