Molecular Dynamics Study Of Tryptophan And Its Derivatives To Inhibit ?-amyloid Aggregation

Purpose:Alzheimer's disease(AD)is one of many neurodegenerative diseases that affects the most people.The neurotoxicity caused by the accumulation of?-amyloid(A?)in the brain is confirmed to cause AD Key factors.Although researchers have long been committed to the study of A?aggregation and its inhibition,effective therapeutic drugs have not been developed so far.There is an urgent need to find treatment methods that are non-toxic and side-effects and are not limited to the blood-brain barrier.Exercise can promote fat mobilization and induce the human body's essential amino acid Tryptophan(Trp)to efficiently cross the blood-brain barrier.The amino acid level also strengthens the synthesis of the human body's important neurotransmitter Serotonin(Serotonin,Ser)and the hormone Melatonin(Melatonin,Mel).Experimental studies have found that tryptophan can inhibit the aggregation process of A?,destroy mature A?fibers,and reduce the neurotoxicity of A?fibers,and serotonin and melatonin have also been shown to inhibit the fibrosis process of A?,but the specific mechanism by which these molecules exert their inhibitory effects is still unclear.This study uses molecular dynamics simulations,replica exchange molecular dynamics simulations and other methods to explore the molecular mechanism of tryptophan and its metabolites(serotonin and melatonin)to inhibit/destroy A?oligomers and A?fibrils,which can provides an explanation perspective on the influence of exercise on the A?fibrosis process and a certain theoretical support for elucidating the influence of exercise on the pathological process of AD,and also provides a structural basis and theoretical reference for the design of drug replacement therapy such as exercise intervention.Methods:In order to investigate the detailed mechanism of Trp and metabolites(Ser and Mel)affecting the A?aggregation process,this study used all-atom replica exchange molecular dynamics simulation to explore the inhibitory mechanism of Trp,Ser and Mel on A?oligomer aggregation.Moreover,this study using all-atom molecular dynamics simulation to study the mechanism of these small molecules dissociating A?fibrils.All the all-atom molecular dynamics simulations in this study were performed using GROMACS software.GAFF force field was used to process the relevant parameters of Trp and Ser and Mel.The formal molecular dynamics simulation used AMBER99SB-ILDN force field.In addition,the data processing and analysis involved in this research are also carried out using GROMACS.At the same time,self-compiled scripts and programs and some third-party programs are used as supplementary tools for data analysis.Results:Elucidating the molecular mechanism of tryptophan and metabolites affecting the A?aggregation process will help provide an explanation for the delay of the pathological process of AD by exercise.This study comprehensively used molecular dynamics and replica exchange molecular dynamics simulation methods to explore the detailed mechanism of tryptophan and metabolites that inhibit A?aggregation,which is difficult to characterize in existing experiments.The main results of the research are as follows:(1)The addition of Trp effectively inhibits the formation of?-sheet structure in the secondary structure,especially in the N-terminal region 2AEF4,the central hydrophobic region 17LVF19 and the C-terminal region 34LMVGGVV40.At the same time,Trp also promotes the corresponding regions of the generation of coil and helix structure.Trp can weaken the interaction between the amino acid pairs in the A?₄₂dimer,and the weakening of the inter-chain interaction is more significant,with regard to the solution accessible surface area,inter-chain contact area,inter-chain contact number and inter-chain binding free energy yielded the same result.This study identified the main binding sites of Trp in A?₄₂dimers,including F4,Y10,F19,F20,I31,I32 and 34LMVGGV39.The results of studies on the interaction between Trp and A?₄₂fibrils show that the addition of Trp significantly reduces the structural stability of the N-terminal of A?₄₂fibrils and destroys the?-sheet structure of the N-terminal of A?42 fibrils.The RMSF calculation results show that Trp is enhanced the flexibility of the N-terminal region.Trp can destroy the stability of peptide chains,reduce main chain hydrogen bonds,destroy the hydrophobic interaction of the local hydrophobic core HC1,and weaken the stability of K28 and A42 to form intra-chain and inter-chain salt bridges.The main binding sites of Trp and A?₄₂fibrils include F4,H6,Y10,H13,H14 and L34.(2)Ser can affect the secondary structure of A?₄₂dimer and inhibit the formation of beta structure in the 26SNKGAII32 region.By analyzing the results of residue-residue interaction,solution accessibility surface area,inter-chain contact area,contact number,and binding free energy,it can be seen that the addition of Ser significantly affects the overall and local inter-chain interaction of A?₄₂dimer.This study identified Ser and A?₄₂dimer binding to 4FRH6,Y10,13HHQKLVFF20,K28,I31,I32 and 34LMV36.In the analysis of the interaction between Ser and A?42fibrils,it is found that Ser can weaken the structural stability of A?42 fibrils,and has a more obvious effect on the N-terminal and C-terminal regions.In addition,the addition of Ser also largely destroyed the intra-chain and inter-chain salt bridges between K28-A42.Combining the calculation results of the number of contacts,the number of hydrogen bonds and the?-?stacking form,it can be seen that Ser can weaken the hydrophobic interaction in HC1,destroy the N-terminal?-sheet structure,and weaken the structural stability of the fibril.(3)The results of C?-RMSD of A?₄₂fibrils show that Ser can increase C?-RMSD stronger than Ser_pro.The calculation results of the gyration radius show that the protonated Ser_procan increase the gyration radius of the fibril to a certain extent.The results of the study on the influence of Ser/Ser_proon the number of contacts and binding energy between chains show that both Ser and Ser_procan reduce the number of contacts and weaken the binding energy between chains,and Ser_prohas a relatively strong effect.The analysis results of amino acids interaction show that although Ser/Ser_procan destroy the hydrophobic interaction between amino acids in HC1 and the K28-A42 salt bridge interaction,the destruction effect of Ser is stronger than Ser_pro.This study identified that aromatic interactions mainly drive the binding between Ser and binding sites F4,H6,Y10,H13,Q15 and L34,while aromatic interactions,hydrophobic interactions and electrostatic interactions together drive Ser_probinding to the binding sites D1,F4,R5,H6,D7,Y10,H13,Q15,F20,E22,D23and L34.However,although Ser_prohas a wider binding site and forms a?-?stacking with more aromatic amino acids,the binding strength between Ser and the binding site is stronger and the?-?stacking formed with the N-terminal of the fibril is more abundant,which enables Ser to destroy the stable structure of A?₄₂fibrils to a greater extent and depolymerize the formed A?₄₂fibrils.(4)The binding sites of Mel on A?₄₂dimer are almost all over the entire sequence.Mel weakens the possibility of beta structure formation in the N-terminal region and the central hydrophobic region,and inhibits further fibrillation of A?₄₂oligomers.Mel can reduce the mutual contact between the amino acid pairs in the chain and the amino acid pairs in the chain of the A?₄₂dimer,especially the influence on the chain interaction is more significant.The calculation results of the accessible surface area of the dimer solution,the contact area and number between the two peptide chains,and the binding free energy also show that Mel can weaken the interchain interaction between adjacent peptide chains.The results of the study on the interaction between Mel and A?₄₂fibrils show that Mel can increase the C?-RMSD of A?42 fibrils,reduce the?-sheet structure content of fibrils,and weaken the interchain stability of A?₄₂fibrils.At the same time,it reduces the contact of amino acids in the hydrophobic core and destroys the inter-chain and intra-chain salt bridges between K28 and A42.In addition,this study also identified Mel can be widely bound to the outer and inner surfaces of A?₄₂fibrils.(5)Trp and Trp?Ser both increase the C?-RMSD of A?₄₂fibrils,but although Trp?Ser increases the C?-RMSD of the A?₄₂fibril structure at the N-terminal and C-terminals,Trp can still increase the C?-RMSD of the N-terminal and destroys the overall stability of A?₄₂fibrils to a greater extent.The results of RMSF,main chain hydrogen bond and Rg also showed that Trp changed the overall protein configuration from a compact structure to a loose structure to a greater extent.However,Trp?Ser weakens the interaction between chains stronger than Trp.The analysis of the secondary structure shows that both Trp and Trp?Ser can significantly reduce the probability of the formation of?-sheet at the N-terminal of the fibril.The analysis results of the stability of the hydrophobic core showed that Trp and Trp?Ser destroyed the stable structures of the N-terminal and C-terminal of the fibril more obviously,and Trp?Ser destroyed the K28-A42 salt bridge to a greater extent.This study also identified that in the A?₄₂?protofibril+Trp and A?₄₂?protofibril+Trp?Ser systems,the binding sites of Trp and Trp?Ser are very similar,almost all located at the N-terminal of the fibril.Conclusions:(1)Trp can inhibit the formation of ordered structures such as A?₄₂dimer?-sheet,so that the protein conformation maintains a more disordered secondary structure under the inhibitory effect of Trp.Trp weakens the interaction between dimer chains and destroys the structural basis of A?₄₂fibrillation,thereby inhibiting the process of A?₄₂abnormal fibrillation.The binding of Trp to the N-terminal of A?₄₂dimer is mainly through?-?stacking and hydrogen bond interaction,while the binding to the C-terminal is mainly through hydrophobic interaction.At the same time,the addition of Trp significantly reduced the structural stability of A?₄₂fibrils,and the most significant impact occurred in the N-terminal region of A?₄₂.Trp formed more hydrogen bonds and abundant?-?accumulation with the N-terminal.It shows that Trp can damage A?₄₂fibrils at the N-terminal of A?₄₂,and then depolymerize the formed fibrils and inhibit the further aggregation of fibrils.(2)Ser effectively inhibited the formation of beta structure in the secondary structure of A?₄₂dimer in the 26SNKGAII32 region.Moreover,Ser greatly weakens the stable structure formed by the inter-chain interaction,thereby preventing the formation of stable aggregates.Electrostatic interaction,hydrophobic interaction and benzene ring interaction are jointly driven,and the hydrogen bond formed with the N-terminal charged amino acid are the main driving force to make Ser more bound to the N-terminal.In addition,Ser can weaken the structural stability of the N-terminal and C-terminal regions of A?₄₂fibrils,and destroy the N-terminal?-sheet structure.This study found that Ser can rely on hydrogen bonding and?-?stacking to combine with the N-terminus of A?₄₂fibrils,making the N-terminus a key area for depolymerization of A?₄₂fibrils.(3)Ser can weaken the stability of A?₄₂fibrils and promote the depolymerization of the stable fibrils that have been formed.Although protonated Ser_procan loosen the protein structure to a certain extent,it has less influence on the overall structure of the protein than Ser.The weaken effect of Ser_proon the inter-chain stability of fibrils is relatively stronger than Ser,indicating that Ser_promainly depolymerizes the formed A?42 fibrils by weakening the inter-chain stability.On the basis of weakening the inter-chain interaction,Ser can also destroy the?-sheet structure of the N-terminal of A?₄₂fibrils by reducing the probability of formation of the N-terminal?-sheet,thereby depolymerizing the A?₄₂fibrils.In addition,the binding of Ser to the binding site mainly relies on aromatic interactions,while the binding of Ser_proto the binding site is mainly driven by aromatic interactions,hydrophobic interactions and electrostatic interactions,which promotes the ability of Ser to be more effective than Ser_proto depolymerize the formed A?₄₂fibrils.(4)Mel can inhibit the further fibrillation of A?₄₂oligomers by weakening the formation probability of beta structure in the N-terminal region and the central hydrophobic region,and weakening the interaction between peptide chains.Mel can bind to almost the entire sequence of A?₄₂dimers through?-?stacking and hydrophobic interactions.The hydrophobic interaction is an important driving force for the binding of Mel to the C-terminal.At the same time,Mel can greatly reduce the structural stability of the N-terminal and C-terminal regions of A?₄₂fibrils.The analysis of the binding mode shows that the main driving force driving Mel to combine with the N-terminal and C-terminal is?-?stacking.The role and hydrophobic interaction,and under the combined influence of these effects,Mel can largely destroy the?-sheet structure of the N-terminal and C-terminal of the fibril.(5)Trp and Trp?Ser destroy the stable structure of fibrils by weakening the overall stability of A?₄₂fibrils and the interaction between chains.Both Trp and Trp?Ser can obviously destroy the stable?-sheet structure at the N-terminal of the fibril,thereby depolymerizing A?₄₂fibril,and the depolymerization effect of Trp?Ser is stronger.Due to the influence on water transport interaction and salt bridge interaction,Trp and Trp?Ser have more obvious damage to the stable structure of the N-terminal and C-terminal of the fibril,respectively.The binding sites of Trp and Trp?Ser are almost the same at the N-terminal of the fibril.Among them,the hydrogen bond interactions with N-terminal charged amino acids and N-terminal aromatic amino acids and?-?stacking together drive the combination of small molecules and fibrils in the two systems.