Fused pyrido[3,4-D]pyrimidine moiety with phthalazinone ring accelerate dual inhibition of PARP1 and CDK4 in triple-negative breast cancer: a hybrid design with computational investigation through molecular modeling and quantum mechanics.

Context: The PARP inhibitor olaparib is effective in breast cancer patients; however, its efficacy is reduced in triple-negative breast cancer (TNBC) due to mechanisms of drug resistance. Recent studies demonstrate that the CDK4 inhibitor palbociclib can enhance the sensitivity of cancer cells to PARP inhibitors. We designed 43 hybrid compounds by combining the pyrido[3,4-d]pyrimidine moiety from palbociclib with the phthalazinone ring from olaparib. Pharmacokinetic profiling and molecular docking revealed compound 17 as a promising candidate, demonstrating a binding affinity of - 8.42 kcal/mol with PARP1 and - 10.05 kcal/mol with CDK4, in contrast to the native inhibitors. Furthermore, the induced fit docking validated its superiority compared to the native inhibitors. Molecular dynamics simulations over 500 ns confirmed the structural stability of compound 17 with both targets. Moreover, the QM/MM, DFT, TD-DFT, and MEP analyses yielded significant insights into charge transfer and electronic transitions, augmenting our understanding of the electronic and bonding properties of the hybrid compound.

Methods: To facilitate the design of 43 hybrid compounds, ChemSketch was utilized, and QikProp, a module of the Maestro Schrödinger suite (v13.5), was used to make predictions regarding the pharmacokinetic properties of these compounds. We checked the binding affinities using docking methods and the stability of the protein-ligand complex using molecular dynamics simulations with Desmond module in Maestro Schrödinger suite (v13.5). Quantum mechanical analyses at the B3LYP/6-31G** level were conducted to elucidate the DFT/TD-DFT, molecular electrostatic potential, Mulliken charges, chemical descriptors, NBO, and NLO properties.