Integrating QSAR-Machine Learning, Biochemical Assays, and Molecular Dynamics for the Discovery of JAK2 Inhibitors in...

Cervical cancer remains a major global health challenge, where dysregulated JAK2 signaling constitutes a key molecular driver. Nevertheless, selective small-molecule JAK2 inhibitors for HPV-positive cervical cancer are still limited. Here, we integrated biochemical assays, QSAR-machine learning, and molecular dynamics simulations to identify potent JAK2 inhibitors. A series of naphthalene-based derivatives, including hydroxynaphthalenamide and phosphorylated dihydronaphthylamide analogs, were evaluated for cytotoxicity in HeLa cells and JAK2 kinase inhibition. Several compounds exhibited selective cytotoxicity with minimal activity toward normal fibroblasts, among which 2q and 2s showed low-nanomolar JAK2 inhibition and strong apoptosis induction through suppression of the JAK2/STAT3/STAT5 pro-tumorigenic signaling pathway. To accelerate hit identification, a QSAR-machine learning (QSAR-ML) framework was employed to prioritize 13 newly designed derivatives. Among three ensemble boosting models, the Categorical Boosting (CB) model demonstrated the strongest predictive capability, achieving a high R² of 0.955 for the training set and a low RMSE of 0.156 for the test set. This model successfully identified five active candidates with strong prediction-experiment agreement (MAPE = 2.6-14.4%), with D4 and D13 meeting drug-likeness criteria and displaying potent nanomolar JAK2 inhibition. Finally, 1-μs molecular dynamics simulations revealed that hydrophobic contacts and hydrogen bonding cooperatively stabilize these inhibitors within the JAK2 ATP-binding pocket. Collectively, these findings establish a QSAR-ML-guided strategy for accelerating JAK2 inhibitor discovery and highlight naphthalene-based scaffolds as promising leads for targeted cervical cancer therapy.