How To Conduct A Markush Chemical Structure Search?

Chemical structure search is an essential aspect in chemical research and the pharmaceutical industry for performing elaborate, efficient, and exact searches. Chemical structure search allows the searchers to filter out relevant patents with precision. Chemical search requires an exact search or spatial arrangement of the alkyl group as this information is vital to determine biological effects.

In pharmaceutical and chemical industry domains, conducting structure searches requires a distinct skill in the know-how of Markush structures and their interpretation thereof, particularly chemical compounds whose IUPAC names/CAS numbers/common names are not disclosed. Most of the patents, especially compound-focused, are typically drafted in Markush language. Therefore, for a disclosed structure, basic scaffold, variation in functional moieties in Markush structures becomes pivotal for a researcher to develop a structure search strategy to retrieve the most relevant patents and scientific publications.

It becomes important for a pharmaceutical company to boost its R&D efforts, handle patent litigation, monitor competition, and strengthen its intellectual property rights.

How to perform an efficient chemical patent search?

1. A detailed review of the structure disclosed — Investigating the disclosed structure to identify the common scaffold and other R groups defined generically or specifically.
2. Drawing query structure — Preparing an appropriate query structure around the common scaffold identified and G group definition to capture the R groups or other variables/attributes. A researcher should pay due attention in defining:
• Class Atom Match Level
• Limited Unlimited Count
• Point of Attachment etc.
3. Conducting searches — Performing Markush structure search using the query structure on Registry, Marat, and DWPI files via STN. Following types of searches are conducted based on specific requirements.

• Substructure (SSS) — It allows the query to retrieve Markush structures that match it exactly and those that have substitution at any available positions.
• Closed substructure (CSS) — Blocks all positions in the query from further substitution unless otherwise specified. CSS is much more restrictive than SSS.

Note: A sample structure search is performed, and few hit structures are evaluated to ascertain the prepared query structure’s accuracy and do the modification if required.

4. Analysis and interpretation of results — Analysis of results considering the following:

a. A structural elucidation given common scaffold/variables/attributes

b. Identify hit structure in case the structure is too generic, e.g., R-A-B-C-D-E-R1

c. Applying genus — species concept during interpretation

5. Presentation of results — Research presents results as follows depending upon the level of analysis required.

• Quick — A list of relevant references is provided without any structural/variable/attributes mapping around the common scaffold structure.
• Moderate — For the identified relevant references, the definition of R-groups, variables/attributes are provided to elucidate the chemical structure of interest.
• Extensive — Actual structures that map to the structure of interest are prepared in view of disclosed Markush structures in the identified relevant references.

Ingenious e-Brain Solutions provides comprehensive and time-bound chemical structure search services in the pharmaceutical space across various IP projects (patentability search, FTO, invalidation/opposition search, and landscape studies).