The challenges related to in-depth analysis of patent molecular spaces in support of drug discovery projects

Size: px

Start display at page:

Download "The challenges related to in-depth analysis of patent molecular spaces in support of drug discovery projects"

Nelson Johns
6 years ago
Views:

1 The challenges related to in-depth analysis of patent molecular spaces in support of drug discovery projects Zhengwei Peng 09/26/2014, 2014 ChemAxon UGM, Boston 1

2 Outline Quick introduction Need for in-depth analysis of patent molecular space Current state, major challenges, and the desired future state Potential implications for the wider community Pharma scientists Pharma patent attorneys Patent offices Patent content providers A pipe dream 2

3 Claimed chemical space by a chemical patent Exemplified Molecules Broadest Claim Encode into computersearchable format(s) The size of a patent Markush claim space could be large ( ). However commercial solutions do exist to encode Markush claims into searchable form(s) and perform structure searches (SSS and Exact) against these vast virtual compound spaces. 3

4 A sample patent Markush claim core R1 R2 R4 R3 R5 CAS & TR are the two dominant Markush content providers analysts are required to encode published chemical patents Time, $$ cost of subscription for customers 4

5 The importance of in-depth patent analysis Viagra Levitra The need for a good defense The power of a good analysis 5

6 Major questions asked by project chemists Is my lead compound patentable, and do we have freedom to operate? This requires comprehensive prior art search (CAS/TR Databases) Patent attorneys provide the analysis and opinion on patentability and FTO What is the competitive landscape in this area (disease, protein target, and compound)? literature and patent searches done by project members & expert searchers I want an in-depth analysis on patents or patent applications pertinent to my project exemplified molecules assay data associated with SAR patent Markush claim(s) I want an in-depth analysis of the strength of my draft patent application Does the draft Markush claim cover all the exemplified molecules? Did I provide sufficient information to cover all embodiments of the invention? 6

7 The current state, challenges, and the desired future states Search expert Expert Search tool Markush patent content Patent attorney Encoding & publish ~ monthly (time & $) Search & browse tool Internal patent store Selective download & encoding anytime needed New patents and patent applications Time delay by the content provider No direct access to expert search tool for project chemists 7

8 Tools and workflow to enable project teams to perform in-depth analysis of patent Markush Patent files (xml/pdf) Doc 2 Str extraction Curation GUI tool Internal patent store Search & browse tool Selective patents relevant to a discovery project ( per project) Auto structure recognition & extraction Manual review & edit to ensure high quality Search Enumerate Compare Markush patent content API 8

9 An early prototype by ChemAxon D2S: Chemical terms inside patent doc are recognized and converted to live molecular structures Molecular structures can be dragged and dropped to construct the searchable patent Markush object 9

Implications for the wider community Win-Win: 1) Patent preparation stage Tool potentially useful for patent attorney to prepare and prosecute patent applications.

stage Higher efficiency & lower cost Benefit society in general Markush search & analysis tool 3) Patent publication stage 10 Patent attorney Objections heard so

10 Implications for the wider community Win-Win: 1) Patent preparation stage Tool potentially useful for patent attorney to prepare and prosecute patent applications. Faster/cheaper content publication (good for content providers as well as content users) Curation GUI tool 4) Content Timely data access by scientists distribution stage Higher efficiency & lower cost Benefit society in general Markush search & analysis tool 3) Patent publication stage 10 Patent attorney Objections heard so far: Naïve, a pipe dream The need for obfuscation is always here.. Migrating from legacy formats to the new one is hard & costly.... Patent Office 2) Patent approval stage

11 Summary To better serve drug discovery projects, in-depth analysis of patent molecular spaces in a timely manner is highly desirable to understand the implication of newly published external patents and patent applications on the project assist the project chemist to understand the scope of the published art to help identify productive areas ChemAxon s suite of tools (D2S, Chem-Curator, Patent Markush Search Platform, etc.) are well positioned as the potential solution for the wider community a newer & better (?) search engine one can license content neutral once adopted by the wider community as a standard, it has the potential to solve a long standing challenge and yield significant benefit to the drug discovery community. Pharma companies have an active role in shaping the future 11

12 Acknowledgements ChemAxon collaborators Tim Dudgeon, David Deng, Doug Drake, and Arpad Figyelmesi Merck colleagues Chris Brofft and Wendy Cornell (MRL-IT) Kenrick Vidale (Legal-IP Group) Michael Altman and Nicolas Zorn (MRL-SC) Chris Waller, Frank Brown, and Emma Parmee (Management sponsorship and support) 12

13 Supplemental material Backup slides 13

14 References Lynch et al., (1996) The Sheffield Generic Structures Project: a retrospective review. J. Chem. Inf. Comput. Sci., 36, The MARPAT patent Markush searching system of CAS: Ebe et a;., (1991) The Chemical Abstracts Service generic chemical (Markush) structure storage and retrieval capabilities. J. Chem. Inf. Comput. Sci. 31, (CAS web link: ) The Merged Markush Service (MMS) of Thomson Reuters: Benichou et al. (1997) Handling genericity in chemical structures using the Markush DARC software. J. Chem. Inf. Comput. Sci. 37, The ChemAxon Markush search technology enables structure searches (SSS and Exact) into vast patent Markush spaces: ChemAxon Instant J-Chem interfaces with the MMS search service form Thomson-Reuters. This provides a more interactive and user-friendly GUI to the existing STN search user interface offered by Thomson Reuters. TR Markush patent content was converted to ChemAxon readable format automatically => 80% concordance in search results between two search engines. ChemProspector ( a project funded by the German government to build software to automatically extract the core and R Groups from chemical patents and store them in a searchable database. Conclusion: it is very hard to automatically construct highquality Markush space definition based on the diverse ways patent claim sections were crafted. 14

15 References Also SciFinder now interfaces with the CAS MARPAT search service. Barnard et al.,(2009) Towards in-house searching of Markush structures from patents. World Patent Inf. 31, Downs & Barnard, (2011) Chemical patents information systems, Wiley Interdiscip. Rev.: Comput. Sci. 1, Cosgrove et al. from Astra Zeneca, (2012) A System for Encoding and Searching Markush Structures, J. Chem. Inf. Model, 52,

Find and analyse the most relevant patents for your research

Derwent Innovation Find and analyse the most relevant patents for your research Powering the innovation lifecycle from idea to commercialisation The pace of technology change is unprecedented with new