Prioritizing Compounds, Step 2: Analyse Cytotoxicities of the Cramer Class I compounds
Analyse Cytotoxicities of the Cramer Class I compounds
From the previous step we ended up with a list of compounds considered safe according to Cramer rules. However, we would like to have some more information other than just the chemical structures. For example, we would like to know the antimalarial activity of these compounds.
To add such a column, we need to edit the URL by adding an entry denoting the antimalarial activity given in the TCAMS Dataset. All data columns in OpenTox have their unique URL, and in this example, the URL of the data indicating the percentage inhibition of the growth of the P. falciparum strain 3D7 (column “Percentage_Inhibition_3D7” in the TCAMS dataset) is
http://pirin.uni plovdiv.bg:8080/malaria/feature/190
To add this column to our filtered list of compounds considered safe according to Cramer rules (Cramer class I), we simply add a feature_uris[] parameter to the URL of our filtered list:
http://pirin.uni plovdiv.bg:8080/malaria/compound?type=smiles&property=&search=Low+%28Class+I%29&feature_uris[]=http://pirin.uni plovdiv.bg:8080/malaria/feature/190
Copy this address into the web browser. There will be a small number of nonempty entries in the second column (see next Figure).
We’re not only interested in the antimalarial activity, but would also like to take into account the experimentally determined human cytotoxicity. To do so, we add a second data column to our filtered list, now with human cytotoxicity data from the TCAMS dataset (Percentage_inhibition_HEPG2 , http://pirin.uni plovdiv.bg:8080/malaria/feature/179). The combination of the two features – antimalarial activity and human cytotoxicity - will result in the following URL (see next Figure):
http://pirin.uni plovdiv.bg:8080/malaria/compound?type=smiles&property=&search=Low+%28Class+I%29&feature_uris[]=http://pirin.uni plovdiv.bg:8080/malaria/feature/190&feature_uris[]=http://pirin.uni-plovdiv.bg:8080/malaria/feature/179
