The document discusses some of the unintended consequences of including patent-extracted and deuterated drug compounds in PubChem, including increased complexity and confusion for users. Specifically, it notes that the same marketed drug like Rosuvastatin is represented by over 15 compound IDs in PubChem due to different deuterated forms extracted from patents. This "multiplexing" of compound IDs can mess up search results and integration with other databases. While filtering out such compounds may be ideal, it is difficult to distinguish experimental from hypothetical structures in patents. Better flags or clustering of related compounds could help address the issues.
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Deuterated drugs in PubChem
1. The Unforseen Consequences of Opportunistic Deuterated Drug Claims, Patent Extraction Feeds and the PubChem Chemistry Rules When data integration gets fuzzy Chris Southan ChrisDS Consulting, Göteborg, Sweden BioIT World, Hannover, Oct 2010
7. Patent Filings on Deuterated Drugs “ Protia's patents appear to be a blunderbuss approach, with a mass of US filings 237 published to date but only 11 PCT applications. None of these provide exemplification or any biological description. Concert has 39 PCTs and 26 US applications published, Auspex 57 PCTS and 39 US applications” (Comment from “In the Pipeline” blog, June 2009)
Rank by Mw 6 have same Mw 481 Three were esters eg tert-Butyl rosuvastatin; AC-3415; CID11478210
Same Connectivity cannonical smiles or core layer InChI CID date 2009-05-08 TP Deposit Date: 2009-05-04 DG Deposit Date: 2009-08-04 Other Ids 6 have same Mw 481 Three were esters eg tert-Butyl rosuvastatin; AC-3415; CID11478210
6 have same Mw 481 Three were esters eg tert-Butyl rosuvastatin; AC-3415; CID11478210
Same Connectivity cannonical smiles or core layer InChI CID date 2009-05-08 TP Deposit Date: 2009-05-04 DG Deposit Date: 2009-08-04 Other Ids 6 have same Mw 481 Three were esters eg tert-Butyl rosuvastatin; AC-3415; CID11478210
Rank by Mw 6 have same Mw 481 Three were esters eg tert-Butyl rosuvastatin; AC-3415; CID11478210