Markush Structure Usability in Patent and Combinatorial Chemistry: New Approaches and Software Tools
Markush structures are widely used in combinatorial libraries and patents. However, the flexibility and complexity of Markush structures make them difficult to create, index, visualize, search, and enumerate. Recent improvement of various ChemAxon applications to toggle this problem will be introduced in this presentation. With ChemAxon’s Marvin toolkit, Markush structures can be hand drawn, or automatically generated from a library of specific chemical structures, or imported from Thomson Reuters proprietary patent data. A hierarchical diagram of the Markush structures can be interactively displayed using “Markush Viewer”. ChemAxon’s Markush enumeration plug-in allows full, partial, or random enumeration of the Markush structures, with the option to enumerate homology group, and post-enumeration property filtering. Because of the vast chemical space, enumeration of the full Markush structure can be impractical. ChemAxon’s Markush search algorithm can search the Markush structure without enumeration, so it is extremely fast even in a vast chemical space. The search can be done with single or multiple structure queries. Advanced search features include Markush variation in the query, substitution count restriction and broad translation of homology groups. The search result is intuitive to understand with relevant R-group fragment colored. The “Markush Reduction” feature allows construction of the relevant R-group fragments for easy comparison with the query, and irrelevant R-group fragments toggled on/off for easy analysis of the chemical space.