W3_Unwanted_substructures

Compounds can contain unwanted substructures that may cause mutagenic, reactive, or other unfavorable pharmacokinetic effects or that may lead to non-specific interactions with assays (PAINS). Knowledge on unwanted substructures in a dataset can be integrated in cheminformatics pipelines to either perform an additional filtering step before screening or - more often - to set alert flags to compounds being potentially problematic (for manual inspection by medicinal chemists). In this workflow, the following steps are presented:

1.Filter out PAINS
2.Filter out unwanted substructures by Brenk et al.
3.Highlight unwanted substructures

Author:
Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory Landrum, and Andrea Volkamer

External resources

• Pan Assay Interference Compounds (PAINS): Baell et al. (2010)
• Brenk list of unwanted/toxic substructures: Brenk et al.(2008)