Investigation of protein-protein and protein-ligand interactions in IRE1-JNK pathway by molecular dynamic simulation method

The IRE1-JNK pathway is the strongest signaling pathway to respond to ER stress in the cell. Due to excessive ER stress in some conditions such as hypoxia, cell death occurs by initiating the apoptotic mechanism via this pathway. In cardiovascular diseases, cells may be exposed to excessive ER stress. Therefore, cells and tissue loss may occur due to apoptosis. The interaction of statins, ACE inhibitors, anti-arrhythmic drugs and flavonoids that effective in cardiovascular diseases with IRE1, ASK1 and JNK1 on the IRE1-JNK pathway is not fully known. In addition, binding of BİP-IRE1LD complex that is most important initiating or stopping factor of the IRE1-JNK pathway is known, but the molecular mechanism of the binding is not fully elucidated. In our study, the interactions of IRE1, ASK1 and JNK1 with the small molecule drugs and flavonoids were investigated by "molecular docking", "molecular dynamics simulation" and "free energy calculations" to determine whether these drugs and flavonoids could play a role or not in the inhibition of the IRE1-JNK pathway in cardiovascular diseases. In addition, molecular dynamic simulation and free energy calculations were performed to elucidate the conformational dynamics of BİP and molecular mechanism of BİP-IRE1LD binding interaction. In the coarse-grained model and cubic orientations, Molecular dynamic simulations were carried out to determine possible BİP-IRE1LD binding patterns. In our study, short term bending of highly flexible SBDα subdomain and returning to the old state was observed that there was a minima on the free energy surface of BİP. Whether correctly predicted the binding pattern of the four different protein complexes that are Ddi1 ubiquitin-like (UBL) domain-ubiquitin complex (2MWS), ubiquitin-USP2 complex (2HD5), fab fragment (1MIM) of chimeric SDZ CHI621 and Sil1-BIP complexes (3QML) known with their binding conformation by coarse-grained cubic orientation approach were statistically measured with F-value and accuracy (ACC) and calculated as 0,88. AUROC value was determined as 0.94. When the possible binding patterns of the BİP-IRELD interaction were investigated by the coarse-grained cubic orientation approach, the disordered domain of the IRE1LD IV. region was bound to the BİP-NBDIIβ open form with a higher free energy difference in comparison with closed form, in addition BİP-SBDα sub-domain played a direct role to the binding of IRE1LD. In the study of the interaction of small molecule drugs and Flavonoids that are effective in cardiovascular diseases with IRE1, ASK1 and JNK1, it was obsorved that Statins could be the most effective molecules in the inhibition of phosphorylation of these proteins. Furthermore, free energy calculations by umbrella sampling were shown that Norizalpine, Chrysin, Luteolin from flavonoids and Atorvastatin, Pitavastatin from Statins could be strong candidate molecules in the inhibition of IRE1-JNK pathway with high potential of mean force. The BİP-IRE1LD binding pattern determined by these studies will shed light on BİP and IRE1LD-targeted therapeutic studies. It may be useful to write algorithms for rapid and easy use of coarse-grained cubic orientation approach to determination of high flexible protein-protein interactions. In the light of the data that we have obtained from result of small molecule interactions with the IRE1-JNK pathway, the molecules to be derived from Statins could be thought effective in preventing severe ER stress induced apoptosis. The numerical calculations reported in this paper were partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).