Molecular Dynamics Simulations On JAK2 Kinase And SMO Receptor And Drug Design

With the development of interdisciplinary and computer-related technology,the use of computational methods to extract,deal with and analyze the mass of biochemical information becomes the inevitable development of disciplines.In this paper,the mechanism of JAK2 kinase and SMO receptor to the corresponding inhibitors were studied by molecular docking and molecular dynamics simulation.The novel promising inhibitors were further developed and designed rationally.The main contents include:Chapter 1: the concept and methods of computer-aided drug design were briefed with highlighting the importance of computational techniques in drug development.In addition,based on the computer-aided drug design methods,we mainly introduced the molecular basis of the two drug targets JAK2 kinase and SMO receptor.Chapter 2: The selective inhibition for JAK2 over the other JAK family kinases(JAK1,JAK3 and TYK2)has shared an immense challenge due to high conservatism.The highly JAK2 selective mechanism of the thienopyridine derivative 19 was identified at the molecular level,based on insights into the inhibitory effects of compound 19 on four JAK kinases.The results clearly indicated that the nonpolar contribution and the H-bond network in the hinge region played a critical selective role in stabilizing ligand JAK2,and the residues Glu930,Leu932 and Gly935 in JAK2 kinase were the key differences compared to the equivalence residues of JAK1,JAK3 and TYK2,which were further verified by simulating four complexes of JAK kinases with another highly selective thienopyridine JAK2 inhibitor 22.Finally,several novel molecules were designed according to above findings and further verified by the same comprehensive modeling protocol.The obtained results not only demonstrated the rationality of our models and analyses,but also suggested that the designed molecules with higher JAK2 selectivity and bioactivity potential would provide an update of JAK2 inhibitors.Chapter 3: A number of type I JAK2 inhibitors binding to the active conformation have emerged so far,while the type II JAK2 inhibitors binding also to the allosteric site adjacent to the ATP-binding pocket in the inactive conformation,have been less studied.The individual mechanisms and the differences of the type I and type II inhibitors binding into DFG-in and DFG-out JAK2 were characterized.Comparison between the type I thienopyridine inhibitors suggest that the binding affinities are mainly determined by hydrogen bonds with residues E930 and L932 and strong hydrophobic contributions with V863,Y931 and R980 in the ATP-binding pocket.For type II JAK2 inhibitors BBT594 and CHZ868,not only do their type I heads bind in a similar mode in the ATP-binding site,but also the type II tail and the linker can be anchored by hydrogen bonds with E898 and D994 and lead to substantial hydrophobic contributions with residues L902,L893 and F995 in the unique allosteric site.In addition,new type II JAK2 inhibitors are reasonably designed and further evaluated by a comprehensive modeling study.The expected interactions in the ATP-binding and allosteric pocket indicate that the structural and energetic insights into JAK2 inhibitors can facilitate the process of more promising type II JAK2 inhibitors.Chapter 4: The smoothened(SMO)receptor,an essential signal transducer in the Hedgehog pathway,was targeted with antagonists to suppress the tumor.The D473 H SMO mutation confer resistance on drug LDE-225 rather than LEQ-506.The binding modes of them against the wild type and mutant SMO receptors were identified to insights into the resistant and non-resistant factors,based on the comprehensive computational protocol involving molecular docking,molecular dynamic simulations,free energy calculation and decomposition.The results reveal that the D473 H mutation disrupts the salt bridges network with residues R400 and Q477 and results in the TM6 conformation inward.A comparison of LDE-225 and LEQ-506 indicates that the volume of the binding cavity decreases seriously in the mutant complex with the resistant drug LDE-225.The adverse interaction ascribes to the mutant residue H473 with the greater polarity around the nonpolar phenmethyl of LDE-225.Owing to the absence of the salt bridges,residues R400 and Q477 make weak contributions to LDE-225.However,the D473 H mutation along with TM6 conformational change has no effect on non-resistant drug LEQ-506.The elaborate insights into structural and energetic mechanism of drug resistance will provide an effective strategy to design rationally more promising SMO receptor antagonists.