Development of potential CDK9 inhibitors through pharmacophore-based virtual screening, 3D-QSAR, molecular docking,...

Cyclin-dependent kinase 9 (CDK9) is a transcription-regulating serine/threonine kinase, and its dysregulation drives tumour initiation, thereby establishing CDK9 inhibition as a mechanistically validated and therapeutically attractive strategy for treating diverse malignancies. In this study, a comprehensive computational strategy was utilized to identify novel CDK9 inhibitors. A pharmacophore-based virtual screening was implemented in combination with atom-based 3D-QSAR, molecular docking, binding free energies, in silico ADME, and MD simulation studies. A statistically validated five-point pharmacophore model (ADHRR) was developed and demonstrating strong predictive performance (R² = 0.98, Q² = 0.84). This optimized model was used to screen chemical databases for potential CDK9 inhibitors. Structural insights gained from the resulting hits guided the rational design of indole-based biphenyl amide hybrids (IBA's). Seven analogues (D1-D7) exhibited strong binding affinities comparable to or greater than those of the screened hits and the reference CDK9 inhibitor 23. Additionally, molecular dynamics simulations and DFT analysis confirmed the stability of both D3 and D6 complexes. Subsequent synthesis and biological evaluation against a panel of cancer cell lines identified compounds D3 and D6 as the most potent. Collectively, these results identify D3 and D6 as promising lead candidates for further CDK9-focused medicinal chemistry optimization and mechanistic studies.