Structural Prerequisites for Pim-1 Kinase Inhibition and the Identification of a Pyrazolyl-Methylene-Indolinone Hit

Abstract

Introduction Pim-1 is a serine/threonine kinase of the pan-Pim family (Pim-1, −2, and −3), whose overexpression is associated with various cancers. Its distinctive hinge-region architecture provides opportunities for selective inhibitor development, with several inhibitors reported as clinical candidates. Understanding structure–activity relationships is essential for distinguishing biologically active compounds from high-scoring docking hits, a major challenge in structure-based drug discovery. Methods A virtual screening workflow comprising Glide docking and Induced Fit Docking (IFD) was applied to approximately 900,000 commercially available compounds. Six structurally diverse compounds were selected for in vitro Pim-1 inhibitory activity evaluation. Molecular dynamics (MD) simulations and quantum mechanical (QM) calculations were subsequently performed to investigate the structural determinants of inhibitory activity. Results Among the tested compounds, compound 6, representing a previously unreported pyrazolyl-methylene-indolinone scaffold for Pim-1 inhibition, was identified as a Pim-1 inhibitory hit with an IC50 value of 5.77 µM. QM calculations revealed differences in the energetic accessibility of coplanar geometries between the active and inactive compounds, providing a structural explanation for the discrepancy between docking predictions and experimental activity. Moreover, MD simulations of Pim-1 in complex with compound 6 revealed the formation of dual polar interactions between its pyrazole ring and catalytic-region residues K67 and E89. Discussion These findings provide insight into the structural and conformational requirements for productive Pim-1 inhibition and highlight the value of integrating docking, MD simulations, and QM calculations during the search for novel inhibitors. The identified hit represents a previously unreported scaffold for Pim-1 inhibition that may provide a starting point for future optimization.