SureChem - Integrating with public and proprietary data sources (ACS Fall 2012)

Integrating patent chemistry withpublic and private non-patentresearch resources Nicko Goncharoff ACS Fall 2012Andrew Hinton, PhD 19 AugustChristopher Southan, PhD

SureChem Data Collection!Database of automatically mined structure datafrom text and images!!• 20M annotated US, EP, WO full text recordsand Japan patent abstracts! I!• 12M unique chemical structures!• MEDLINE – 19M abstracts (coming Q4)!

ª  Free resource for researchers! ª  Professional search needs!ª  Enables linking to public and ª  Data export, alerts, patent family proprietary content search, chemical relevance ﬁlters…! ª  API or Data Feed access to chemistry & full text! ª  Integrate with internal databases & workﬂows

Chemistry Mining Workﬂow!

Public Patent Chemistry Landscape!

Current Patent Sources In PubChem! 4000000 3.7 M 3500000 3000000Numbers of SIDs 2.3 M 2500000 2000000 1500000 1000000 500000 280 K 10 K 0 EPO(Sling) Chemicalize.org IBM Thomson Thompson Pharma

Patent & Literature Sources in PubChem ! The Big Three Thomson Pharma,! ChEMBL + !patents and literature ! PubMed + Journals! 3,756,283! 918,077! 41% lead-like! 45% lead-like! 3,291,940 281,920 515,745 52,975 129,448 67,437 2,113,169 IBM, pre-‐2000 patents 2,369,481 32% lead-‐like

SureChem to Deposit All Structures* into PubChem - 2012!• 1976 to present• Deposition of structures only• View related patents in SureChemOpen• *Some filtering of common chemistry likely

SureChem and IBM in PubChem   (2 Example Patents)!SureChem Total: 776! IBM Total : 527! US583593, Inhibitors of squalene synthetase and protein farnesyltransferase. Abbott ! 478 298 229 SureChem Total: 832 ! IBM Total: 239! 686 146 93 WO-1994018188-A1 ! 4-hydroxy-benzopyran-2-ones and 4- hydroxy-cycloalkyl[b]pyran-2-ones HIV protease inhibitors, Upjohn!

Identifying Relevant Chemistry - IC50! US-20120035195-A1 BACE2, Hoffman LaRoche

Structures with IC50 Values! US-20120035195-A1PDF SureChemOpen Excel

Search IC50 Structures in PubChem! search

SureChem Unique Contribution! SureChem Pubchem 79 96 (ThomsonPharma , Chemicalize) Stage! No. of Structures! Available from SureChem (SC)! 1848! Pre-Exist in PubChem! 669! Pre-Exist – not from IC50 table! 573! Pre-Exist – from IC50 table! 96 (12 from TP + 84 via chemicalize.org)! Unique-SC with IC50! 79! Unique-SC – beyond IC50 table! 1100!

Identifying Relevant Chemistry! Patent   US-20120035195-A1!http://opentox.informatik.uni- freiburg.de/ches-mapper/!

SureChem Chemical Relevance Filtering!•  Frequency counts of chemicals within patents •  AddiHonal molecular property filtering i.e. Lipinski descriptors !•  Natural Language Processing – based indexing of Exemplified Compounds ! ! Automated indexing of Exemplified Compounds in text!

Conclusion!SureChem deposition into PubChem will –  Significantly expand public patent chemistry scope –  Contribute unique and timely MedChem-relevant data –  Enable open drug discovery and chemical biology –  Advance progress toward a more open, federated chemical information network

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SureChem - Integrating with public and proprietary data sources (ACS Fall 2012)

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