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In 2012, after the first IBM deposition, few would have predicted that PubChem compounds that included patent-extracted structures would exceed 20 million within three years (i.e. 30% of the total). The current major open patent chemistry submitters (in size order) are NextMove, SCRIPDB, Thomson Pharma, IBM and SureChEMBL. This “big bang” has a range of utilities and implications. Firstly, pharmaceutical companies must now integrate their exploitation of both public and commercial patent chemistry because capture is divergent. Secondly, the academic community and small companies can now patent-mine extensively without commercial sources. Thirdly, first-filings of most lead series and clinical candidates can now be tracked. Fourthly, drug targets in ChEMBL can be intersected with Structure Activity Relationship (SAR) data sets from patents, some of which are now target-mapped in other databases (doi:10.1016/j.ddtec.2014.12.001). However, while this patent chemistry “big bang” is generally welcomed by database users, there are significant caveats. In particular, both automated and manual extraction bring in a variety of artefacts that add confounding structural “noise”. These include a) permutations of mixtures and chiral exemplifications, b) virtual structures (including isotopic analogues of approved drugs), c) an emerging trend of vendor “patent picking” for non-stocked compounds, d) 85% of public patent chemistry has no biological data links and c) extractions from documents do not directly indicate IP status. These problems and some partial solutions will be discussed.

The open patent chemistry “big bang”: Implications, opportunities and caveats

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