Study On The Interaction Between Small Molecular Structural Analogs And Trypsin Based On A Variety Of Spectroscopy And Molecular Docking Techniques

Protein is the most basic structural and functional substance that constitutes an organism.It is of great significance to study the changes in protein conformation and function.Various small molecular compounds,whether drugs or poisons,have more or less effects on proteins after uptaken into the human body,thereby affecting the body’s metabolism and other functions.Therefore,the research on the interaction between small molecule compounds and proteins has become a research hotspot in many fields such as life sciences,medicinal chemistry and pharmaceutical analysis.The study of its mechanism of action can provide valuable information for screening drugs and obtaining small molecule drug candidates that specifically bind to corresponding proteins.In this research,oxazoles,phenanthridines,and benzimidazole-quinoxaline compounds were studied using multi-spectral analysis methods and molecular simulation docking technology to investigate the mechanism of interaction of these three types of compounds with trypsin.Besides,radicicol was also analyzed to explore the mechanism of its interaction with human serum protein,catalase,pepsin and trypsin.The article is mainly divided into the following parts:Chapter 1:An overview of the structure and function of proteins,as well as the methods and contents of studying the interactions between protein and small molecules.Chapter 2:The study of the interaction mechanism of 9 oxazole compounds with trypsin using a variety of spectroscopic methods and molecular docking technology.The results indicats that these compounds can cause the fluorescence quenching of trypsin,and the number of binding sites is approximately 1.The ranking of the binding ability of these nine compounds is:2f>2a>2b>2d>2c>2e>2g>2h>2i.Structural analysis shows that steric hindrance can affect the binding ability between compounds and protein,and the combination of protein with para-substituted small molecule compounds shows stronger binding ability.According to the Forster energy transfer theory,the binding distance is less than 7 nm,indicating that there is non-radiative energy transfer during the interaction between oxazole compounds and trypsin.Synchronous and three-dimensional fluorescence data prove that these compounds have a certain influence on the conformation of the protein.The molecular docking data show that the main force in the interaction process is van der Waals force,and the minor force is hydrogen bonds,which is consistent with the experimental results.Chapter 3:We used a variety of spectroscopic methods and molecular docking techniques to study the interaction of phenanthridine compounds with trypsin.Using Autodock vina software,three compounds with better binding were selected from 10 phenanthridine compounds.Based on this result,we further explored the interaction mechanism through spectroscopy.Through analyzing the fluorescence data,we concluded that the action mechanism of phenanthridine compound and trypsin is a static quenching mechanism.The thermodynamic data and the molecular docking results reveal that the forces of the three phenanthridine compounds and trypsin are mainly hydrogen bonds and van der Waals forces.The binding constant indicates that the binding ability of the three compounds in order is:3b>3a>3c.The structure analysis of the compound shows that the electron withdrawing ability of the functional group can inhibit the binding of the compound and the protein.The circular dichroism data demonstates that the β-sheet content of the protein was reduced,confirming the effect of phenanthridine compounds on the secondary structure of trypsin.The experimental data of protein activity showed that phenanthridine compounds had inhibitory effect on protein,and the inhibitory degree of 3b was greater.Chapter 4:The interaction between 5 kinds of benzimidazole-quinoxaline compounds and trypsin is studied.Through combining the thermodynamic and molecular docking data,we found out that the interaction force types of 4b,4c and 4d are mainly hydrophobic forces,and the interaction force type of 4a and 4e is mainly van der Waals force.Among the five compounds,4d has the strongest ability to bind trypsin.Based on the structure of the compound,we hypothesize that the methoxy group on the benzene ring may enhance the binding of the compound to the protein.Synchronous and three-dimensional data results show that these 5 compounds all have effects on the conformation of trypsin.Chapter 5:The interaction between radicicol and four proteins(human serum protein,trypsin,catalase,and pepsin)are studied respectively,and their mechanism of action is also analyzed using spectroscopy and molecular docking technology.The mechanism of action of radicicol and the four proteins is static quenching mechanism.Among them,human serum protein has the strongest binding ability with radicicol,and the protein activity experiment proves that radicicol has an inhibitory effect on trypsin,catalase,pepsin.Radicicol reduces the α-helix content of human serum protein and catalase,and it also decreases the β-sheet content of trypsin and pepsin.These results match the experimental data results.