Theoretical Studies Of Substrate Delivery Mechanisms For Several Proteins And Related Drug Design

Protein,as an important organic macromolecule,plays an important role in life activities.With the deepening of research in the field of life science,more and more protein gene sequences have been resolved.Life sciences,which mainly explore proteomics and functional genomics,enter a new chapter.With the evolution of computing ability and theoretical method,molecular dynamics,a new guidance tool developed from physics,mathematics and chemistry,plays an important role in the mechanism study of protein-substrate interaction,substrate transfer and so on.It can detect transient conformational changes of proteins from a dynamic perspective to explain and predict the experiment.At the same time,the molecular dynamic simulations can explore the biological mechanism at the atomic level in the drug design based on the conformational fit concept,which can also verify the pharmacodynamics model to guide modification of drugs combined with computer aided drug design tools such as homology modeling and molecular docking.In this thesis,molecular dynamic simulations combined with variety techniques are used to study the mechanism of substrate release process for hotspot proteins.Moreover,the related inhibitors are designed on basis of 3D-QSAR method.The main research contents are as follows:1:Histone lysine-specific demethylase 1（LSD1）is a typical histone-specific demethylase,which is significance to explore histone methylation modification.Phenylcyclopropylamine inhibitor is a highly effective and specific LSD1 inhibitor.In order to obtain the interaction mechanism between LSD1 and phenylcyclopropylamine inhibitors,extensive molecular dynamic simulations are used to calculate the binding modes,binding free energy,residue contribution and thermodynamic properties for the substrate release on basis of a series of phenylcyclopropylamine compounds.Then the 3D-QSAR technique is used to establish the CoMFA and CoMSIA models of phenylcyclopropylamine.22 potential inhibitor molecules are designed according to the structure-activity relationship and 3 better compounds are screened for further verification.Results obtained by molecular dynamic simulations combined with MM/GBSA showed that the molecular we designed has potential application,and revealed that the possible active modification sites of phenylcyclopropylamine.This work provides a theoretical basis for the design of LSD1 inhibitors in the future.2:O-GlcNAc glycosyltransferase（OGT）,an important glycosyltransferase in vivo,which plays an important role in many cellular physiological processes.Understanding its mechanism is helpful to detect the glycosylation process.UDP as a product of the catalytic reaction,the study of its release process is not only benefit to comprehend the whole catalytic process,but also useful to the prediction of the UDP-GlcNAc and UDP/UDP-GlcNAc based inhibitors delivery processes.Herein,by using extensive MM/GBSA,RAMD MD,SMD,MM MD simulations combined with umbrella sampling technology,the binding mode and binding free energy of OGT–UDP complex as well as the UDP release process are obtained.The potential UDP release channels and key residues in the process are analyzed and verified,the thermodynamic properties and corresponding mechanisms are determined and discussed.This work is not only meaningful for comprehending the ligand transported mechanism in OGT enzymatic process,but also helpful for the inhibitor design based on UDP or UDP-GlcNAc.3:O-GlcNAc glycosylation is a ubiquitous post-translational modification of proteins in multicellular animals and plant cells,which participates in many complex cellular activities.OGT is a key enzyme for the glycosylation;however,there is no mature technology to explain how it specifically recognizes target proteins in experiment.In order to explore the recognition mechanism of OGT for the target protein,the TPR structure of the OGT and the adaptor protein GABA_A were selected as the research object.Combined molecular docking and classical molecular dynamic simulations,the possible binding modes and binding free energies of OGT_TPR-GABA_A are obtained,and the contribution of key residues for the favorable binding modes were analyzed by using energy decomposition,which lays the foundation for the subsequent future study of the target protein recognition mechanism by OGT-GABA_A complex.