Skip to main content


Showing posts from March, 2023

Drug warning update: withdrawn drugs and drugs that carry a black box warning

The drug warning information in ChEMBL has been updated for version 32. In particular, the withdrawn drug data has been fully reviewed and, to assist the manual curation process, our rules have been updated, clarified and formally written.  In ChEMBL, a withdrawn drug is an approved drug (ie Phase 4) that has subsequently been withdrawn for toxicity reasons. For example, a drug is assigned as 'withdrawn' if: All doses are withdrawn (and not just the highest dose). The drug is withdrawn for all populations (and not just infants). The drugs is withdrawn for all indications.  Any drug withdrawn for a lack of evidence of efficacy is not included.  Any drug withdrawn for drug-drug interactions is included if it is a safety-related withdrawal. A regulatory body (e.g. EMA, FDA) is the preferred source of information for the withdrawn status. The withdrawn status is mapped to an individual drug form (e.g. a parent (salt-stripped) or salt drug form within a family of compound structures

Natural Product-likeness in ChEMBL

Recently, we included a Natural Product-likeness score for chemical compounds stored in ChEMBL. We made use of an algorithm published by Peter Ertl, Silvio Roggo and Ansgar Schuffenhauer in 2008 .  Whereas the original version of this algorithm used a commercial data set of Natural Product molecules for training the algorithm (the CRC Dictionary of Natural Products) and an in-house library of synthetic molecules as a negative set, we used Greg Landrum's  RDKit implementation  which is based on  ~50,000 natural products collected from various open databases and ~1 million drug-like molecules from ZINC as a "non-Natural Product background". After including the new score into ChEMBL, we were interested to see whether the results look meaningful. We had a handful of simple questions: How is Natural Product-likeness distributed in ChEMBL and how does this compare to Natural Product-likeness for "real" NPs? Can we observe any difference in Natural Product-likeness for