High-throughput inhibitor screening and molecular dynamics simulation studies against Human JAK2

Purpose: To investigate the lead molecule for inhibition of JAK2 using high-throughput screening and molecular dynamics simulation.Methods: The MCULE database was used to screen 5 million ligands in a structure-based mode. The ligand hits were ranked according to VINA scores. Further filtration was achieved by approaches like MCULE-Toxicity Checker, Zero-RO5-Violation-Check, synthetic accessibility and overall pharmacokinetic features. Stability of the JAK2-inhibitor-complex was confirmed by molecular dynamics simulation of 120 ns, which used the AMBER14 force field in YASARA Structure-21.8.27. W.64.Results: The top molecule, 4-pyrimidinamine, 2,6-dimethyl-5-(2,4,5-trimethylpyrido (2,3-d) pyrimidin-7- yl), demonstrated strong binding with JAK2 involving 17 amino acid residues, 16 of which overlapped with the reference (PDB: 3JY9). It successfully passed all screening tests. The RMSD-time plot indicated that equilibrium was reached around 20 ns. Throughout the simulation from 20 to 120 ns, thebackbone RMSD fluctuations remained within a narrow range of 1.0 – 1.7 Å.Conclusion: The ligand, 4-pyrimidinamine, 2,6-dimethyl-5-(2,4,5-trimethylpyrido (2,3-d) pyrimidin-7-yl), meets the ADMET criteria. Also, an extended 120 ns Molecular Dynamics Simulation confirms the feasibility of the 'JAK2-Top ligand' complex. This ligand is a promising lead for designing inhibitors against JAK2 and should be further evaluated in future laboratory experiments.