Machine learning-guided identification and simulation-based validation of potent JAK3 inhibitors for cancer therapy

Janus kinase 3 (JAK3) is a hematopoietic-specific kinase implicated in cytokine signaling and immune dysregulation and has recently been associated with cancer progression. However, selective and potent JAK3 inhibitors remain underdeveloped. In this study, we established a machine learning (ML)-based pipeline to identify novel JAK3 inhibitors with anti-cancer potential. A curated ChEMBL dataset of JAK3 inhibitors was used to train multiple ML classifiers, with the Random Forest model achieving the highest performance (AUC = 0.80, F1-score = 0.92). This model was applied to virtually screen 25,084 ChEMBL compounds, yielding 400 high-confidence candidates (prediction score > 0.9). Docking analysis identified ten top binders (binding affinity ≤ -8.5 kcal/mol), of which three CHEMBL49087, CHEMBL4117527, and CHEMBL50064 exhibited optimal ADMET profiles. These compounds underwent 200 ns molecular dynamics simulations, showing low RMSD (0.10-0.20 nm), stable binding conformations, and preserved protein compactness. MM/GBSA calculations revealed that CHEMBL4117527 displayed the strongest binding free energy (-29.5 kcal/mol), surpassing even the co-crystallized ligand (-17.7 kcal/mol). Our integrative approach combining machine learning, docking, pharmacokinetics, molecular dynamics, and free energy analysis presents a robust computational strategy for JAK3 inhibitor discovery. These findings support CHEMBL4117527 as promising candidates for further experimental evaluation in cancer therapeutics.