| Enzyme is a kind of protein with catalytic action produced by living cells.Understanding the interaction between enzyme and substrate is helpful to comprehend catalytic mechanism of enzyme,and it is significance for the research of drug development and drug action mechanism.With the continuous enrichment of all kinds of protein databases,some traditional biological experimental methods have been difficult to meet the needs of predicting the structure and function for biological enzymes and drug design.At present,molecular dynamics has developed into an effective tool to study the function of biological systems.The method mainly relies on Newtonian mechanics to simulate the motion of molecular systems,so as to take samples from systems composed of different states of molecular systems.Thus,the configuration integral of the system is calculated,and the thermodynamic and other macroscopic properties of the system are further calculated based on the results of the configuration integral.In this thesis,molecular dynamics simulations combined with various methods and techniques such as MM/GBSA,SMD,RAMD MD,and umbrella sampling are used to study the delivery and interaction mechanism of ligand for several kinds of enzymes.The main contents are as follows:1: Butyrylcholinesterase is a non-specific esterase synthesized by the liver.It plays a key role in acetylcholine hydrolysis in the late stage of Alzheimer’s disease that is a potential therapeutic target for Alzheimer’s disease.Tacrine is a classic pharmacophore that can inhibit both butyrylcholinesterase and acetylcholinesterase.As an effective drug for the treatment of Alzheimer’s disease,tacrine has now become a skeleton molecule for the synthesis of related inhibitors.We use a variety of molecular dynamics simulation methods and techniques to study the binding and transport mechanism of tacrine in BCh E.The key residues influenced the ligand binding and delivery,the important non-covalent interactions,the possible pathway of tacrine release and the corresponding thermodynamic property and mechanism are studied.Moreover,the “gating mechanism” in the delivery process is discovered.This work will provide theoretical support for the inhibitor design based on tacrine as the parent nucleus.2: Acetylcholinesterase plays a key role in biological nerve transmission.It can degrade acetylcholine among cholinergic synapses,so as to stop the excitatory effect of neurotransmitters on postsynaptic membrane,which ensures the normal transmission of nerve signals in vivo.As a highly selective,reversible and competitive acetylcholinesterase inhibitor,galantamine hydrobromide is effective for the treatment of mild to moderate(AD).Here we explored the binding mode and release process of galantamine in ACh E by MM MD method combined with umbrella sampling and other techniques.The key residues that affect the binding of galantamine to ACh E are found,and the possible release channels of galantamine are identified.Moreover,the release mechanism and thermodynamic properties of the ligand from the dominant channel are explored.The protein conformational changes during the release process and the effect of key residues are further analyzed and verified.This work is helpful to understand the action and transportation mechanism of inhibitor with similar skeleton for ACh E.3: Camellia oleifera Abel is a unique industrial tree species in China.Many kinds of Camellia oleifera polysaccharides extracted from Camellia oleifera seeds or shells have been proved to have antioxidant and anti-tumor activities in vivo,and Camellia oleifera polysaccharides can inhibit glucosidase and play a hypoglycemic effect.The polysaccharides of camellia oleracea can be degraded into four kinds of disaccharides and two kinds of trisaccharides.In order to obtain the polysaccharides that most easily acting on glucosidase,based on the possible molecules degraded from polysaccharides of oil tea,six complex models of glucosidase and polysaccharides were established,and their binding free energies and binding modes were obtained.The system with the strongest binding energy of enzyme-disaccharide and enzyme-trisaccharide complex was selected to study the transport mechanism of polysaccharides from glucosidase.The possible transport channels and the thermodynamic properties for the two systems were discussed and compared.The key residues were determined,and the molecular forms of polysaccharides most likely to act on glucosidase were screened.We hope the study will help to further understand the interaction mechanism between polysaccharides and glucosidase,which will provide some theoretical guidance for the design and development of glucosidase inhibitors. |
