Generation of new synthetic scaffolds using framework libraries selected and refined via medicinal chemist synthetic expertise.

With the expansion in the application of library methods in medicinal chemistry and chemical biology there is a growing need for improved technology for the design of novel templates that are well suited for the synthesis of libraries targeted toward specific subsets of protein families. In this report, we delineate an improved stepwise general method that is well suited for this purpose. This process uses virtual framework libraries to identify frameworks that rigidly match specific aspects of a ligand's bioactive conformation. The resulting frameworks can then be ranked and sequentially modified by a combination of computational scripts and human derived expertise, in order to develop rational proposals for new combinatorial templates or new sets of potential ligands.