Molecular Simulation Of The Binding And Unbinding Mechanism Between Triple Reuptake Inhibitors And Human Monoamine Transporters

In recent years,an increasing numbers of multi-target drugs have been developed to treat multifactorial diseases,such as psychiatric disorders,cancer,cardiovascular disease and so on.Compared with single-target drugs,molecules acting on multiple targets have advantages of higher therapeutic effect,better patient compliance and improved safety.Triple reuptake inhibitors(TRIs),as a new class of promising antidepressants,which simultaneously bind to the central sites of human monoamine transporters(hMATs)and inhibit the reuptake of dopamine,norepinephrine and serotonin.However,it is a great challenge to design potent TRIs with fine-tuned binding profiles,due to a high degree of structural homology of the binding sites of these transporters.In this thesis,molecular modeling/simulation methods including homology modeling,molecular docking,molecular dynamics(MD)simulation,binding free energy calculation and protein-interaction fingerprint analysis were first applied to explore the binding mode and selectivity of TRIs to the central sites of hMATs.Then steered molecular dynamics(SMD)was employed to investigate the unbinding pathways of TRIs from hMATs.The potential mean of force(PMF)and conformational changes of the TRIs dissociated from hMATs were characterized.The organization of this thesis is as follows.1.The study on the binding mode of TRIs and hMATs.By selecting three novel series of TRIs with the diversity of substituent groups and the robust antidepressant-like activity as molecular probes,this chapter systematically predicted the binding mode of TRIs in three hMATs.Firstly,molecular docking have been used to predict the initial protein-ligand complex poses.Then,MD was carried out for sampling the conformations of binding complexes to get equilibrated states.The reliability of the predicted binding modes can be judged by comparing the calculated binding free energies with experimental values.As a results,17 residues in h DAT(F76,A77,D79,S149,V152,G153,Y156,F320,S321,G323,F326,V328,S422,A423,G426,M427 and I484),18 residues in h NET(F72,A73,D75,A145,V148,G149,Y152,F317,S318,L319,G320,F323,V325,S419,S420,G423,M424 and V449)and 17 residues in h SERT(Y95,A96,D98,A169,I172,A173,Y176,F335,S336,L337,G338,F341,V343,S438,T439,G442 and L443)have been identified to play a key role in the common mode of TRIs binding to hMATs.2.The study on the subtype selectivity of TRIs to hMATs.Based on the binding mode of three TRIs in hMATs,the selectivity of TRIs binding in h DAT,h NET and h SERT was further studied by per-residue free energy decomposition analysis and protein-ligand interaction fingerprints analysis.The results suggest that the TRIs’ s selectivity was mainly derived from warm spots and these warm spots were located in TM3,TM6,TM8 and TM10.For h DAT simulated systems,eight “warm spots”(F320,F326,V328,A423,M427,V430,A480 and I484)were identified as important features to control the TRIs binding selectivity and enhancing the interaction of ligands with residues F320,F326,A423,M427 and A480 might improve the ligands selectivity.For h NET simulated systems,four “warm spots”(F323,V325,S420 and M424)had a great impact on molecular selectivity.The enhanced interaction of ligands with residues F323,V325 and S420 may strengthen the ligands selectivity for h NET;For h SERT simulated systems,six “warm spots”(A173,F341,V343,T439,L443 and V501)had a pronounced effect on the inhibitors selectivity.The enhanced interaction of ligands with the six residues may increase the ligands selectivity for h SERT.3.The study on the molecular mechanism of TRIs unbinding from hMATs.Steered molecular dynamics(SMD)was chosen for investigate the unbinding pathways and potential mean force of TRIs from hMATs central binding pocket.The results show that TRIs can dissociate through a major unbinding pathway(TM1b,TM3,TM6 a,TM10,EL2,EL4,EL5 and EL6)in hMATs protein,which reveals several residues in h DAT(D79,Y156,F76,D476,P387,R85,S321 and H547),h NET(D75,W80,D473,R81,Y151,F317 and D546)and h SERT(D98,Y176,F335,S336,E493,E494,T233,E299,R104,Y232,P403 and I179)mainly affect the ligand unbinding.In conclusion,computational simulation was used to investigate the thermodynamic and kinetic properties of three TRIs to hMATs.The results provide useful information for understanding the molecular mechanism of TRIs-hMATs binding and unbinding at the atomic level,which are important in structure based antidepressant drugs design.