Discovery Of DJ-1 Inhibitor By Virtual Screening And Structure Optimization And Studies Of Target Selectivity Mechanisms Of Anti-cancer Inhibitors By Molecular Modeling

DJ-1 is very important and essential for the body verified by various experiments.Because of the possession of cysteines in the structure,it makes this protein be sensitive to the oxidative stress(ROS).It has been validated that the dysfunction of DJ-1 is associated with some desease,including Parkinson's disease,Alzheimer's disease,Type II diabetes,cancers and so on.In the past decades,more and more drugs which are aimed at different kinase targets have been approved by FDA and commercial used.Nevertheless,it also reveals some problems.In the process of treatment,kinase inhibitor will lead to the gene mutation and further make the drug losing the therapeutic effect.Hence,if we could inhibit the dimerization of DJ-1 and decrease its expression in tumor cells,it will inhibit the proliferation of the tumor.However,it hasn't been reported a compound targeting at DJ-1.CADD is an important tool,and it has been applied in the field of drug discovery widely.Ligand-based Drug Design(LBDD)is mainly including quantitative structure activity relationship(QSAR)and pharmacophore models.On the other hand,the receptor-based rational drug design mainly includs homology modeling,molecular docking,virtual screen,and molecular dynamics simulation.Based on these combined computational techniques,it will shorten the time of drugs' development effectively.In the part 1 of this thesis,based on the molecular docking and MD simulation,we discover the potential binding pocket of DJ-1 and some crucial interactions.Then,we take advantage of this potential binding pocket and virtual screening based on SYBYL-X 1.3 package.Meanwhile,we also take into account the five rules of Libinski.Finally,we get 23 compounds and purchase them from commercial.The results of Western Blot reveals that compound A-1 shows preferable activity of inhibiting the dimerization of DJ-1.Moreover,we also test the activity of inhibiting proliferation of multiple tumor cells,and the results demonstrate that some compounds reveal good activity against tumor cells in vivo.Based on the results of biological activity,the molecular docking and structuralcomparison was performed to illustrate the mechanism of compound design and optimization.In the part 2 of this thesis,based on the results in part 1,we carried out bioisosterism and analogues design to enhance the activity of compounds inhibiting DJ-1 dimerization and cancer cells proliferation.We synthesis 72 N-amide-hydrazide derivatives.The biological activity test reveals that some compounds show better activity of inhibiting multiple tumor cells proliferation than compound A-1.For example,compound B-1 shows better activity of inhibition the DJ-1 dimerization not only in protein but also in cellular level.Additionally,B-1 also reveals higher inhibition the proliferation of tumor cells than compound A-1.On the other hand,increasing the flexibility of molecular will also enhance the activity of inhibition the tumor cells proliferation.In comparison with compound A-1,compound B-65 shows lower cLogP value and better inhibiting tumor cells proliferation activity.Initial structure-activity relationship reveals that the naphthalene nucleus and hydroxyl in the structure is very important for the biological activity.The hydrogens in the hydrazide is also important.The molecular docking reveals that increasing the ?-? interaction with His 126 of DJ-1 will enhance the activity of the inhibition DJ-1 dimerization.These results will be helpful for the structure modification.The part 3 of this thesis refers to the design of peptidomimetic drug.Based on the active conformation of compound A-1,we design and synthesis the 49 6,5-lactam derivatives.The biological activity test demonstrats that these compounds possess general inhibitory activity to tumor cells.Furthermore,the compound C-48 could have some kinetics reaction with DJ-1.These results will guide the compounds design and optimization.c-Met and ALK are very popular medicinal targets for the treatment of cancer.Selective inhibitor of c-Met or ALK will decrease the side-effects and expand the usable range of drug.In part 4 of this thesis,we performe molecular simulation by applying molecular docking,molecular dynamic simulation,binding free energy calculation,andMESP charges analysis to illustrate the binding mode of selective inhibitors to c-Met and ALK.The calculation results reveal that the ?-? interaction with residue Phe36 of c-Met and the H-bond interaction with residue Asp 169 are crucial for the activity and selectivity.In the meantime,the electrostatic interaction with the resiudes Met97 and Asp101 are essential for the selectivity and activity to ALK.Moreover,as for ALK-mutant L1996M,the electrostatic interaction with Asp101 and Met94 are important for the activity.These important information supply the theoretical foundation for inhibitors design and structure optimization.FGFR is also a popular medicinal target for cancer threapy.It has been reported that the proliferation of tumor cells will be inhibited when the expression of FGFR is decreased.FGFR has four isoforms and possesses high homology.Therefore,if we could discover the selective FGFR1 inhibitors,it will decrease the unnecessary side-effects and further expand the usable range.In the part 5 of this thesis,we perform the molecular simulation by taking advantage of binding site comparison,molecular docking,molecular dynamics simulation(MD),free binding energy calculation,and MESP charges analysis to research the corresponding selective inhibitors binding conformation with FGFRI and FGFR4.The calculation results illustrate that the H-bond interaction with Asp641 and the hydrophobic interaction with Phe642 are essential for the activity and selectivity to FGFR1.Additionally,the H-bond interaction with the backbone of the residue Ala564 makes the ligand insert into the binding pocket with right orientation.In the meantime,the hydrophobic interaction with so-called 'gate-keeper' Va1561 and the Tyr563 also play an active role in binding with FGFR1.The predicted molecular information will guide the FGFR1 selective inhibitors design and further structure optimization.