Tools for Analyzing Exemplified and Markush Structures in Chemical Patents

September 2011 Author: ()

Medicinal chemists rely on patent intelligence at three distinct junctures of a research project: inception of an idea, ongoing competitive intelligence during project development, and preparation of the patent application. Typically, a medicinal chemist collaborates with expert information scientists and patent attorneys to evaluate competitor’s intellectual property in order to assess where drug design efforts should be focused. The availability of comprehensive databases of exemplified and Markush structures make it feasible for medicinal chemists to carryout preliminary IP analyses on their own. The search capabilities of these databases generally are limited to substructure and similarity comparisons and few tools exist to fully evaluate and visualize the chemical space disclosed within a patent. To address the need for better IP analysis tools, Pfizer has developed a suite of patent analysis tools and made these available to medicinal chemists throughout the research organization. In addition to performing substructure, similarity and exact match searching against databases of exemplified structures from
patents, two of these tools compare structures based on an overlay of their reduced graph representations to facilitate analysis and visualization of the chemical fragments within a set of exemplified structures, and rank order a set of patents by structural relevance to one or more query molecules. Lastly, a Markush tool has been developed to facilitate analysis of the detailed chemical space disclosed within a patent. Using this tool, medicinal chemists can perform substructure and exact match searches against Markush structures from patents of interest and enumerate representative structures from the search hits.

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