Research On The Relationship Of "Nature-Structure" Based On Information Of Literature And Chemical Biology

The research comes up with "nature-structural relationship" based on "nature-effect-substance relationship" by mining the information of literature and biological chemistry.Objectives:Under the guidance of "nature-structural relationship",this study tried to explore representation system of ingredients’ elements related with nature of TCM and expected to reveal the meaning of nature of TCM by scientific methods.Methods:The research used methods of bibliometrics,information mining,visualization means of biological chemistry,correlation analysis and molecular docking to mine the information of nature-structural,and the results of information mining were proved by SPR(Surface Plasmon Resonance)and molecular docking.Results:As a result,we have made the following research findings:Firstly,by using the methods of literature retrieval,text information mining and bibliometrics,through the search,induction,collation,analysis,summary and text mining of ancient literature records and literature in the past 20 years,it is found that the research on the theory of nature of TCM mainly focused on the micro material basis(such as small molecular compounds,proteins,polysaccharides and their related physical properties and contents),effects(like biothermal effect,antibacterial activity,enzyme activity,delayed luminescence of Scenedesmus,immunoblotting,metabolomics,etc.)and the internal law of nature system of TCM in the field of bioinformatics by using computer.By using bibliometric research method,it is further found that the research of nature focused on the research of nature-effective-substances,including the effect of processing of traditional Chinese medicine on the nature and material of Chinese medicine.Based on previous studies,the research concept of "nature-structure relationship" of TCM was proposed based on the ternary theory of "nature-effect-substance",which provides theoretical and methodological guidance for this studySecondly,23033 components of traditional Chinese medicine from 2444 kinds of traditional Chinese medicine were standardized and classified according to the prediction of bioavailability and the properties of traditional Chinese medicine.Finally,6736 small molecular compounds(3539 from cold Chinese medicine and 3197 from hot Chinese Medicine)were screened.The "nature structure relationship" of traditional Chinese medicine components was studied based on chemical and biological information mining.It was found that there is a significant "nature-structure" distribution law between cold and heat,among which the dominant skeleton of the components from cold nature traditional Chinese medicine is 2-phenylchromone,the dominant skeleton of the hot nature traditional Chinese medicine is α-pyranone.The molecular descriptors of compounds from cold traditional Chinese medicine,like atomic atoms,molecular flexibility,molecular complex,rings and ClogP,are higher than those of compounds from hot nature herbals,while the molecular descriptors of compounds from hot nature herbal are dominant in rotatable bonds,etc.Through the analysis of the target with correlation score greater than 0.9,it was found that the dominant target of flavonoid specific binding was 5-LO(arachidonate 5-lipoxygenase),and through further study of gene annotation analysis,we found that the cold and hot nature related targets in the moto system,signal transmission,heart and blood circulation show opposite phenomena,and there are also some differences in life cycle,energy metabolism,immune system between cold and hot nature.Thirdly,based on the above results,the binding effect and the mode of action between flavonoids and 5-LO target were verified and analyzed.11 compounds that can bind to 5-LO were selected by molecular interaction technology.The interaction between the compounds and proteins was studied by molecular docking technology.The results showed that among the 2-phenylchromone compounds with dominant skeleton,the compounds from cold nature traditional Chinese medicine have better affinity.It was found that the interaction between the compounds and the target amino acids was mainly focused on the formation of hydrogen bond,and there was a correlation between the amount of bond formation and the components of traditional Chinese medicine with different cold and hot nature.It was concluded that the effect of flavonoid compounds derived from traditional Chinese medicine with different cold and hot nature could be related to the amount and location of the substitution base of the compounds,compared with compounds that derived from traditional Chinese medicine with hot nature,compounds derived from cold nature traditional Chinese medicine,have more-OH substitution,which makes the electron cloud density of the basic dominant skeleton change,thus causing the difference of cold and hot effect.Conclusion:The results of the study reveal the material basis and mechanism of the comprehensive interpretation of cold and hot nature of traditional Chinese medicine at the molecular structure level,which constructed the theoretical research system of nature of TCM.The results also provided a new way of thinking and method for study of nature theory of TCM,and guide clinical application of nature theory and new drug research and development.