Pyrazolopyrimidine fused thiazolidinone hybrids as CDK2 inhibitors: insights from pharmacophore modeling, docking, DFT and molecular dynamics simulations

Cancer remains a significant global health challenge, primarily driven by the dysregulation of key cellular pathways, including kinase-mediated signaling. Cyclin-dependent kinases (CDKs), particularly CDK2, play a crucial role in regulating the cell cycle and tumor progression, making them attractive targets for anticancer drug development. Pyrazolopyrimidines, known as bioisosteres of purines, exhibit potent kinase inhibitory activity by selectively targeting ATP-binding sites. The molecular hybridization of pyrazolopyrimidines with thiazolidinones provides a rational strategy for designing novel CDK2 inhibitors with enhanced selectivity and therapeutic potential. In this study, 30 hybrid compounds (PPT1–30) were designed to target CDK2. A ligand-based pharmacophore model was constructed using a training set of six potent CDK2 inhibitors, resulting in a robust model featuring one Aro/Hyd and three Acc/Don pharmacophore features. Virtual screening led to the identification of 13 potential hits from the 30 hybrids. The top 10 compounds underwent further molecular docking analysis, revealing docking scores ranging from −7.2 to −8.2 kcal/mol, with PPT15 demonstrating the highest potency (−8.2 kcal/mol), surpassing the standard CDK2 inhibitor Roscovitine (−8.0 kcal/mol). ADMET analysis of the top 10 compounds showed favorable pharmacokinetic and toxicity profiles, aligning well with drug-like properties. Density Functional Theory (DFT) analysis further confirmed the superior electronic properties of PPT15, with a high energy gap (0.2804 eV), enhancing receptor interactions. Molecular dynamics simulations over 500 ns validated the stability of the CDK2-PPT15 complex, maintaining minimal RMSD (protein: 2.0–3.2 Å, ligand: 2.8–4.8 Å), low RMSF (<1.8 Å protein, <1.5 Å ligand), and strong interactions with key residues such as Leu83, Lys33, Lys89, Ala31, and Val18. MMGBSA analysis revealed a higher binding affinity (−34.794 kcal/mol), stronger Coulombic interactions (−26.2546 kcal/mol), and improved hydrogen bonding (−1.52033 kcal/mol) for PPT15. Post-dynamic simulation analysis of PPT15 at various time frames (200, 400, 600, 800, and 1000 ns) further demonstrated stable interactions with residues Leu83, Asp145, Lys33, and Lys89, ensuring its stability within the binding pocket. These overall key findings revealed that PPT15 is a potent CDK2 inhibitor.