Computational modeling of the Janus Kinases: investigation of the conformational plasticity and molecular basis for inhibitions

Abstract

The Janus kinases (JAKs) are crucial targets for several disease drug development. JAKs are involved in cell signaling associated with T-cell and B-cell mediated diseases. Although, accounting for the impact of possible structure rearrangements on the binding of different types of kinase inhibitors is complicated by the extensive conformational variability of their catalytic kinase domain (KD). The dynamic KD contains mainly four prominent mobile structural motifs, the phosphate-binding loop (P-loop) and the αC helix; from C-lobe, the Asp-Phe-Gly (DFG) motif, and the activation loop (A-loop). These distinct structural features controlled the JAK activation and deactivation mechanism. However, the exact dynamical features of the JAK induced by posttranslational modification (phosphorylation) and different types of inhibitor-induced structures remain unclear. We performed an extensive, nanosecond to microsecond-long replica molecular dynamics (MD) coupled with enhanced sampling and Gaussian accelerated MD (GaMD) analyses of JAK and their complexes with inhibitors. Results from our simulations show that the single pTyr1034 phosphorylation could stabilize the JAK1/SOCS1 (suppressor of cytokines signaling) complex as well as the flexible A-loop in active JAK1. Our results indicate significant conformational variations upon inhibitor binding in the A-loop and αC helix motions. Our studies also reveal that the DFG-out inactive conformation is characterized by a close A-loop rearrangement, open catalytic cleft of N and C-lobe, the outward movement of the αC helix, and open P-loop states. Moreover, the outward sign of αC helix impacts the hallmark salt bridge formation of Lys882 and Glu898 in an inactive conformation. Furthermore, we compared the active and inactive inhibitor binding poses and free energy by the MM/PBSA approach. The free energy calculations suggested that the binding affinity of AI (type II/ allosteric inhibitors) over CI (ATPcompetitive inhibitors) against JAK2 was due to an increased favorable contribution from the total non-polar interactions and the involvement of the αC helix. Finally, we systematically screened the extensive phytochemicals database and found some prominent future drug candidates for the JAK/STAT pathway. Our study provides the structural and energetic details to develop more promising type I/II JAK inhibitors for treating JAK-related diseases. Keywords: Janus Kinases, JAK/STAT Signaling Pathway, Molecular Modeling, Molecular Docking, Molecular Dynamics Simulations, Gaussian Accelerated Molecular Dynamics Simulations, Binding Free energy Calculations, Conformational Dynamics, Network Analysis, Principal Component Analysis, Computer-aided Drug Design, Auto-immune Disorders, and Cancers.