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Scaffold-Based Drug Discovery
The pre-clinical lead candidates in complex with the protein targets and their structural knowledge are extensively employed at an early stage of drug discovery program in Arrien Pharmaceuticals before lead optimization and full-scale medicinal chemistry efforts. Combining our Fragment-Field Drug Design (FFDD) based lead discovery strategies, we also take the advantage of implementing and using scaffolds (>150 - <350 MW) as starting points particularly in the target space of the same protein family where the greater efficiency with which potency can be achieved through the synthesis of fewer compounds.

In order to facilitate the identification of novel scaffolds we have created an in-house scaffold-library size between >150-<350 MW with the application of Custom filters along with MedChem Tractability, Scaffold Efficiency, Lead-Like, Drug-Like and Similarity Index filters from all the available vendor libraries provided the final set of ~40,000 unique compounds collectively referred to as Custom Scaffold Library (CSL) which fulfils the greater extent the Ro3 and Ro5. The CSL successfully implemented into our entire pipeline provided novel lead-like scaffolds considered for lead optimization and candidate selection process.

Our scaffold-based inhibitor design process typically involves the definition of binding site geometry; a query scaffold site describes the binding site residues, interaction fields, shape and electrostatics, distance between the anchor/attachment points & query scaffolds and connecting point dihedral angle terms employed for finding novel scaffolds and scaffold hopping for scaffold optimization.
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