Structure-Guided Identification of JAK2 Inhibitors: From Similarity to Stability and Specificity

Background/Objectives: Janus kinase 2 (JAK2) is a pivotal signaling protein implicated in various hematological malignancies and inflammatory disorders, making it a compelling target for therapeutic intervention. Methods: In this study, we employed an integrative computational approach combining ligand-based screening, pharmacophore modeling, molecular docking, molecular dynamics (MD) simulations, and MM/PBSA free energy calculations to identify JAK2 inhibitors from the ChEMBL database. A comprehensive virtual screening of over 1,900,000 compounds was conducted using Tanimoto similarity and a validated pharmacophore model, resulting in the identification of 39 structurally promising candidates. Docking analyses prioritized compounds with favorable interaction energies, while MD simulations over 100 ns assessed the dynamic behavior and binding stability of top hits. Results: Four compounds, CHEMBL4169802, CHEMBL4162254, CHEMBL4286867, and CHEMBL2208033, exhibited consistently superior performance, forming stable hydrogen bonds, favorable RMSD profiles (≤0.5 nm), and strong binding interactions, including salt bridges. Notably, the binding free energies revealed ΔG values as low as −29.91 kcal/mol, surpassing that of the reference inhibitor, momelotinib (−24.17 kcal/mol). Conclusions: Among these, CHEMBL4169802 emerged as the most promising candidate due to its synergistic electrostatic and hydrophobic interactions. Collectively, our results highlight these compounds as probable, JAK2-selective inhibitors with strong potential for further biological validation and optimization.