Computational fragment-based design of Wee1 kinase inhibitors with tricyclic core scaffolds

Abstract

Wee1 is cell cycle protein comprising a kinase domain and is a validated cancer target. We have designed molecules with variable tricyclic core scaffolds [6-6-5] system and extended them based on the chemical space available in the active site of Wee1 kinase using de novo drug design. The core scaffolds and linking fragments were extracted from pharmacophore-based virtual screening of ZINC and PubChem databases and Ludi library. These molecules bind the hinge region of kinase active site and form hydrogen bonds as confirmed from molecular docking, molecular dynamics simulations, and MM_PBSA calculations. When compared with reference inhibitors, AZD1775 and PHA-848125, the de novo designed molecules also show good docking scores and stability, retained non-covalent interactions, and high binding free energies contributed from active site residues.