Inhibition Interaction And Delivery Mechanisms Of Janus Kinase Inhibitor On Theoretical Calculation

The Janus kinase/signal transducer and activator of transcription(JAK/STAT)signaling pathway was discovered when investigating candidate genes of the interferon pathway,which was a stress response pathway and was involved in cell proliferation,differentiation,migration and other important biological processes.The JAK/STAT signaling pathway is essential in the regulation of hematopoiesis,immune development,breast development,lactation and lipogenesis.Previous work has demonstrated that delayed or aberrant functioning of the JAK/STAT pathway results in a number of physiological and pathological consequences resulting in inflammatory and tumorigenic disease states.Therefore,the therapy targeting JAK-STAT signaling pathway is the hotspot in current research.There are two main approaches aimed at the treatment of this pathway:(i)Suppressors of cytokine signaling(SOCS)act as negative feedback regulators of JAK-STAT signaling pathway,playing an antibody to specifically bind to the SH2 domain of STAT molecules.When JAKs is activated by cytokines,SOCS can directly bind to phosphorylated JAKs and receptors to shut down the pathway and generate a classical feedback loop.(ii)JAK kinases include JAK1,JAK2,JAK3 and TYK2 were the important targets for the treatment of these diseases,whose inhibitors were associated with diseases of the blood system,tumors,rheumatoid arthritis and psoriasis.However,most studies of JAKs inhibitors are carried out in vitro or in animals,and fewer theoretical studies focus on it,and thus the inhibition mechanism is not clear.In this work,molecular dynamic(MD)simulations were used to study the interaction and delivery mechanism of these inhibitors for JAKs.The main results of the thesis are summarized as follows:(1)SOCS act as negative feedback regulators of the Janus kinase/signal transducer(JAK-STAT)signaling pathway by inhibiting the activity of JAK kinase.To get more insight into the inhibition mechanism of SOCS1 for JAK1 at the atomic level,the binding mode,binding free energy,and desorption mechanism of JAK1-SOCS1 complex and six mutant systems are identified by using extensive molecular dynamics combined with constant pulling velocity(PCV)method.The electrostatic interaction was identified to play main driving force of the interaction between JAK1 and SOCS1,which mainly came from the electrostatic interaction of side chains of polar residues.The binding free energies of six mutants obviously reduced because of vanished of main interactions by the side chains variation.Meanwhile,thesalt bridges are very important in JAK1 and SOCS1 binding or cleavage process.The work provides a comprehensive understanding of SOCS1 and JAK1 thermodynamically and dynamically,which is probably meaningful for the future in-depth studies in designing peptide inhibitors on basis of SOCS1.(2)PF-06651600,as a potent selective JAK3 inhibitor,is highly efficacious at inhibiting ?-c cytokine signaling.Molecular mechanics molecular dynamics(MM MD)method was used to study the interaction and delivery mechanism of PF-06651600 towards to JAK3.The results showed that the binding free energy of complex was-35.63 kcal/mol.The Leu89 ?Leu91 and Cys909 play a significant role in binding of PF-06651600 and JAK3.There are two ordered water molecules stabilized substrate in the active site by forming hydrogen bonds.Moreover,the delivery process also shows two main reasons for PF-0651600 stabilizing in the binding pocket:(i)Hydrogen bonds form by Glu903,Leu905 and Cys909 exist all the time,and thus PF-06651600 binds to the pocket stably.(ii)PF-06651600 is a covalent inhibitor of JAK3,which easily forms strong interactions with Cys909 in its unreacted state;therefore,it is difficult to escape from cavity of JAK3 with the rising energy barrier.(3)The activity of a series of Tetrahydropyrans-JAK1 inhibitors were studied by 3D-QSAR,and the interaction mechanism between four different active JAK1-inhibitor compounds was analyzed by molecular dynamics simulation.The studies revealed that molecule 28 was most closely bound to JAK1,and Leu881,Val889,Glu957,Phe958,Leu959,Gly962,Asn1008,Leu1010 and Gly1020 played crucial roles in binding JAK1-inhibitor complex;In addition,energy decomposition calculations showed that van der Waals,electrostatic and non-polar interactions were favorable in the binding of JAK1-inhibitor complex,and van der Waals interaction were the main driving force for the stability of the complex.Combining four different binding modes of JAK1 kinase receptor and ligands,we found that the main difference in the activity of the compounds was whether the key hydrophobic amino acids such as Leu881,Val889,Phe958 and Leu1010 were bound to the ligand,which was important for the stability of small molecule inhibitor at the active site.