Study on the binding mode of a pyrrolotriazin derivative with JAK2 by docking and MD simulation

The pyrrolotriazin derivative 2-(4-(4-((7-(3-(N-methylmethylsulfonamido)phenyl)pyrrolo 2,1-f]1,2,4]triazin-2-yl)amino)phenyl)piperidin-1-yl)acetamide (PPA) is a potential Janus kinase 2 (JAK2) inhibitor. The binding mode between PPA and JAK2 was investigated by using a combined method of docking, molecular dynamics (MD) simulation and binding free-energy calculation. The docking calculations preliminarily indicated that there were two possible binding modes 1 and 2; MD simulations and binding free-energy calculations identified that binding mode 1 was more stable and favourable, with the lower MM-PBSA binding free energy of ?34.00?±?0.17?kcal/mol. Moreover, some valuable binding information is revealed as follows: the inhibitor PPA is suitably located at the ATP-binding site of JAK2 and the hydrophobic interaction plays an essential role. PPA not only interacts with residues Leu855, Val863, Ala880, Tyr931, Leu932 and Leu983 via hydrophobic interaction but also interacts with Ser936 and Asp994 by hydrogen bonds. These two factors are advantageous for PPA to strongly bind to JAK2. These results help to understand the action mechanisms and designing new compounds with a higher affinity to JAK2.