[Screening of bioactive components endowing hawthorn with turbidity-eliminating and lipid-lowering functions and development of quality control method of hawthorn].

Hawthorn has the efficacy of eliminating turbidity and lowering the blood lipid level, and it is used for treating hyperlipidemia in clinic. However, the bioactive components of hawthorn are still unclear. In this study, the spectrum-effect relationship was employed to screen the bioactive components of hawthorn in the treatment of hyperlipidemia, and then the bioactive components screened out were verified in vivo. Furthermore, the quality control method for hawthorn was developed based on liquid chromatography-mass spectrometry(LC-MS). The hyperlipidemia model of rats was built, and different polar fractions of hawthorn extracts and their combinations were administrated by gavage. The effects of different hawthorn extract fractions on the total cholesterol(TC), triglycerides(TG), and low-density lipoprotein-cholesterol(LDL-C) in the serum of model rats were studied. The orthogonal projections to latent structures(OPLS) algorithm was used to establish the spectrum-effect relationship model between the 24 chemical components of hawthorn and the pharmacodynamic indexes, and the bioactive components were screened out and verified in vivo. Finally, 10 chemical components of hawthorn, including citric acid and quinic acid, were selected to establish the method for evaluating hawthorn quality based on LC-MS. The results showed that different polar fractions of hawthorn extracts and their combinations regulated the TG, TC, and LDL-C levels in the serum of the model rats. The bioactive components of hawthorn screened by the OPLS model were vitexin-4″-O-glucoside, vitexin-2″-O-rhamnoside, rutin, citric acid, malic acid, and quinic acid. The 10 chemical components of hawthorn, i.e., citric acid, quinic acid, rutin, gallic acid, vitexin-4″-O-glucoside, vitexin-2″-O-rhamnoside, malic acid, vanillic acid, neochlorogenic acid, and fumaric acid were determined, with the average content of 38, 11, 0.018, 0.009 5, 0.037, 0.017, 8.1, 0.009 5, 0.073, and 0.98 mg·g~(-1), respectively. This study provided a scientific basis for elucidating the material basis of hawthorn in treating hyperlipidemia and developed a content determination method for evaluating the quality of hawthorn.

[Application of partial least squares algorithm to explore bioactive components of crude and stir-baked hawthorn for invigorating spleen and promoting digestion].

This study was aimed at identifying the bioactive components of the crude and stir-baked hawthorn for invigorating spleen and promoting digestion, respectively, to clarify the processing mechanism of hawthorn by applying the partial least squares(PLS) algorithm to build the spectrum-effect relationship model. Firstly, different polar fractions of crude and stir-baked hawthorn aqueous extracts and combinations of different fractions were prepared, respectively. Then, the contents of 24 chemical components were determined by ultra-high performance liquid chromatography-mass spectrometry. The effects of different polar fractions of crude hawthorn and stir-baked hawthorn aqueous extracts and combinations of different fractions were evaluated by measuring the gastric emptying rate and small intestinal propulsion rate. Finally, the PLS algorithm was used to establish the spectrum-effect relationship model. The results showed that there were significant differences in the contents of 24 chemical components for different polar fractions of crude and stir-baked hawthorn aqueous extracts and combinations of different fractions, and the gastric emptying rate and small intestinal propulsion rate of model rats were improved by administration of different polar fractions of crude and stir-baked hawthorn aqueous extracts and combinations of different fractions. The bioactive components of crude hawthorn identified by PLS models were vitexin-4″-O-glucoside, vitexin-2″-O-rhamnoside, neochlorogenic acid, rutin, gallic acid, vanillic acid, citric acid, malic acid, quinic acid and fumaric acid, while neochlorogenic acid, cryptochlorogenic acid, rutin, gallic acid, vanillic acid, citric acid, quinic acid and fumaric acid were the bioactive components of stir-baked hawthorn. This study provided data support and scientific basis for identifying the bioactive components of crude and stir-baked hawthorn, and clarifying the processing mechanism of hawthorn.

Cyclo-(Phe-Tyr) as a novel cyclic dipeptide compound alleviates ischemic/reperfusion brain injury via JUNB/JNK/NF-κB and SOX5/PI3K/AKT pathways.

Ischemic/reperfusion (IR) can cause adverse reactions including apoptosis, oxidative stress, and inflammation, but the existing therapeutic strategies have been limited. Moreover, the regulation of microglia plays an important role in brain injury after reperfusion. Hence, it is imperative to find new and effective drugs for modulating microglia to treat IR brain injury. Cyclic peptide compound cyclo-(Phe-Tyr) (Sparganin C, SC) is a compound isolated from Sparganii Rhizoma. However, the protective effects of SC on the central nervous system are rather unclear. In an attempt to elucidate the protective effects and mechanism of SC on cerebral damage induced by the IR, we used a middle cerebral artery occlusion reperfusion (MCAO/R) model in rats and discovered that SC significantly decreased the size of cerebral infarcts, improved neurological scores, and blocked inflammatory and oxidative factor release. Using RNA-Seq and metabolomics association analyses, SC was shown to have a protective impact through the JUNB and SOX5-related pathways. Metabolomic analysis revealed twenty-eight differentially expressed biomarkers. In addition, the detection of SC content in brain tissue using LC/MS revealed that SC had blood-brain barrier penetration. To investigate the mechanism, we established an in vitro BV2 cell oxygen-glucose deprivation/reperfusion (OGD/R) model and used siRNA as well as an inhibitor. The protective effects of SC were dependent on the JUNB and SOX5 to inhibit inflammation and apoptosis in microglia. Our findings revealed for the first that SC against IR injury by reducing inflammation and apoptosis while simultaneously acting as potential therapeutic lead compound for ischemic stroke.

Combining ultra-high-performance liquid chromatography quadruple exactive orbitrap mass spectrometry with chemometrics to identify and verify the blood-activating components of hawthorn.

Hawthorn, one of the widely-used Chinese herbal medicines, has been used to treat blood stasis syndrome in the clinic, but its blood-activating components are unclear. This study combined the ultra-high-performance liquid chromatography-quadruple exactive-orbitrap mass spectrometry with chemometrics to identify the blood-activating components of hawthorn. Different polar fractions of hawthorn aqueous extracts were extracted and mixed to prepare 14 samples. The contents of 25 chemical components for 14 samples were determined by the proposed quantitative method which was validated in terms of linearity, precision, stability, repeatability, and recovery, while the blood-activating effect was evaluated by measuring the whole blood viscosity, plasma viscosity, and plasma fibrinogen levels. Then the partial least squares model was established on the spectrum-effect relationship. The result showed that vitexin-2″-O-rhamnoside, rutin, citric acid, malic acid, gallic acid, and fumaric acid could reduce the whole blood viscosity, plasma viscosity, and plasma fibrinogen levels in blood stasis model rats, and these components were the blood-activating components of hawthorn. This study provided a scientific basis for clarifying the blood-activating components of hawthorn, and the spectrum-effect approach proved to be an effective approach to discovering the bioactive components of Chinese herbal medicines.

Developing the liquid chromatography-mass spectrometry method for simultaneously quantifying five components in rat serums after oral administration of hawthorn aqueous extracts and its application to a pharmacokinetic study.

Hawthorn, one of the widely-used traditional Chinese medicines, has been used to treat dyspepsia, hyperlipidemia, and cardiovascular disease in the clinic. Our previous study revealed that gallic acid, neochlorogenic acid, cryptochlorogenic acid, vitexin, and quercetin were active components of hawthorn. In this study, a simple, precise, and reliable liquid chromatography-mass spectrometry method was developed for the simultaneous quantification of five components in rat serums. The separation was achieved on the Hypersil GOLD C18 column, and the mobile phases consisted of 0.1% acetic acid water and methanol at a flow rate of 0.3 mL/min. The mass spectrometry data acquisition was performed on Q-Extractive-Orbitrap mass spectrometry with an electrospray ionization source in negative ion mode. The proposed liquid chromatography-mass spectrometry method was validated in terms of linearity, intra- and inter-precision, accuracy, recoveries, matrix effects, and stability. Then this newly proposed liquid chromatography-mass spectrometry method was successfully applied to a pharmacokinetic study on rats after oral administration of hawthorn aqueous extracts. This study provided relevant information on the pharmacokinetics of active components of hawthorn and explained the underlying mechanism of their bioactivity.

Therapeutic effects of different polar fractions of hawthorn extract on blood stasis model rats revealed by liquid chromatography-mass spectrometry metabolomics.

Hawthorn, a commonly used traditional Chinese medicine, has been suggested to have therapeutic effects on cardiovascular disease. However, effective fractions of hawthorn extract in the treatment of cardiovascular disease, together with possible therapeutic mechanisms, remain unclear. This study aimed to investigate the effects of four different polar fractions of hawthorn extract on blood stasis model rats, and explore the possible metabolic mechanisms by using a liquid chromatography-mass spectrometry metabolomics approach. Evaluation of hemorheology and fibrinogen showed that n-butanol and ethyl acetate fractions of hawthorn extract had significant therapeutic effects on blood stasis model rats. Furthermore, metabolomics analysis showed that n-butanol and ethyl acetate fractions of hawthorn extract could reverse imbalanced biomarkers in plasma and urine of blood stasis model rats. Additionally, metabolic pathway analysis revealed that plasma biomarkers were responsible for several important pathways, including d-glutamine and d-glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, alanine, aspartate, and glutamate metabolism, sphingolipid metabolism, and arginine biosynthesis. Meanwhile, urine biomarkers were responsible for some important pathways, including phenylalanine metabolism, tyrosine metabolism, and lysine degradation. This study demonstrated that n-butanol and ethyl acetate fractions of hawthorn extract had significant therapeutic effects on blood stasis model rats, and the underlying mechanisms involved multiple metabolic pathways.

LC-MS based plasma metabolomics study of the intervention effect of different polar parts of Hawthorn on hyperlipidemia rats.

Hawthorn, a well-known traditional Chinese medicine is used for the treatment of dyspepsia syndrome, cardiovascular disease, and hyperlipidemia. Hawthorn has complex composition. However, the effective fraction and mechanisms of action in alleviating hyperlipidemia are unknown. Therefore, the aim of this study was to evaluate the effects of four different polar components of hawthorn on hyperlipidemia rats, and to explore underlying mechanisms of action through liquid chromatography-mass spectrometry based plasma metabolomics. Hyperlipidemia rat model was established by feeding rats using a high-fat diet. High-fat model rats were then treated with four polar components of hawthorn for 14 consecutive days. Plasma samples were collected and subjected to biochemical and metabolomics analysis. Biochemical analysis showed that hawthorn n-butanol and ethyl acetate extracts had the highest efficacy on hyperlipidemia rats. Water fraction showed a partial effect, whereas petroleum ether extract was not effective against hyperlipidemia rats. Furthermore, liquid chromatography-mass spectrometry metabolomics analysis showed that the most effective fraction of hawthorn reversed the metabolic disorder in plasma of hyperlipidemia rats. Metabolomics analysis showed that hawthorn exerts its activity by modulating lipid metabolism, energy metabolism, oxidative stress, and amino acid metabolism.

LC-MS-based plasma metabolomics study of the intervention effect of different polar parts of hawthorn on gastrointestinal motility disorder rats.

Dyspepsia, one of the most prevalent diseases of the digestive tract that impacts the quality of patient life, is mainly caused by gastrointestinal motility disorder. Hawthorn is a commonly used traditional Chinese medicine for treating dyspepsia, and has been proven to improve gastrointestinal motility. Herein, a rat model of gastrointestinal motility disorder was established by subcutaneous injection with atropine. The modeled rats were treated with four polar parts (T1-4 in descending polarity, corresponding to water, n-butanol, ethyl acetate and petroleum ether extracts, respectively) of hawthorn. Through metabolomics analysis, a total of 20 significantly metabolites were identified with significant changes in their abundance levels and these metabolites were related to many metabolic pathways such as amino acid metabolism and primary bile acid biosynthesis. The results showed that T3 had the best therapeutic effect of promoting gastrointestinal motility. Other parts showed no obvious therapeutic effect, demonstrating that the effective components of hawthorn may be compounds of medium polarity. T3 might achieve good therapeutic effects owing to the gastrointestinal motility promotion activity, and by rectifying the disturbed metabolic pathways in the gastrointestinal motility disorder model.

A NMR-Based Metabonomics Approach to Determine Protective Effect of a Combination of Multiple Components Derived from Naodesheng on Ischemic Stroke Rats.

Naodesheng (NDS) is a widely used traditional Chinese medicine (TCM) prescription for the treatment of ischemic stroke. A combination of 10 components is derived from NDS. They are: Notoginsenoside R1, ginsenoside Rg1, ginsenoside b1, ginsenoside Rd, hydroxysafflor yellow A, senkyunolide I, puerarin, daidzein, vitexin, and ferulic acid. This study aimed to investigate the protective effect of the ten-component combination derived from NDS (TCNDS) on ischemic stroke rats with a middle cerebral artery occlusion (MCAO) model by integrating an NMR-based metabonomics approach with biochemical assessment. Our results showed that TCNDS could improve neurobehavioral function, decrease the cerebral infarct area, and ameliorate pathological features in MCAO model rats. In addition, TCNDS was found to decrease plasma lactate dehydrogenase (LDH) and malondialdehyde (MDA) production and increase plasma superoxide dismutase (SOD) production. Furthermore, 1H-NMR metabonomic analysis indicated that TCNDS could regulate the disturbed metabolites in the plasma, urine, and brain tissue of MCAO rats, and the possible mechanisms were involved oxidative stress, energy metabolism, lipid metabolism, amino acid metabolism, and inflammation. Correlation analysis were then performed to further confirm the metabolites involved in oxidative stress. Correlation analysis showed that six plasma metabolites had high correlations with plasma LDH, MDA, and SOD. This study provides evidence that an NMR-based metabonomics approach integrated with biochemical assessment can help to better understand the underlying mechanisms as well as the holistic effect of multiple compounds from TCM.

[System modeling on Chinese herbal medicine process based on multi-block partial least squares].

The system model of Chinese herbal medicine process is the basis for improving the precision of pharmaceutical process and ensuring the stable transmission of quality between different sections of the process. By taking the wet granulation-tableting process as the research object and using the Panax notoginsengs sapions (PNS) as a model drug, multi-block partial least squares method (MBPLS) was used in this article to build the system model of Chinese herbal medicine process, analyze the mass transmission rules in the process and improve the understanding on pharmaceutical process system of Chinese medicine. According to the process flow, the quality attributes of raw materials, granules and tablets collected in the process were divided into different data blocks, and the MBPLS method was used to establish system model. The R²Y and Q²Y of MBPLS model were 89.1% and 65.5%, respectively, indicating that the performance of the MBPLS model was good. By analyzing the parameters of MBPLS model, it was determined that the physical quality attributes of PNS raw materials and quality attributes of PNS granules were the key factors to affect the quality of PNS tablets. The particle size, bulk density and tapped density of PNS raw materials were the critical quality attributes which caused the quality variations of PNS granules and PNS tablets. MBPLS can quantify the contributions of each unit to the product quality by dividing the quality attributes into different units. It was helpful to analyze the interactions between the process units of Chinese herbal medicine and it could be applied to build system model of other Chinese herbal preparations processes.

Quality assessment of crude and processed Arecae semen based on colorimeter and HPLC combined with chemometrics methods.

Raw Arecae Semen, the seed of Areca catechu L., as well as Arecae Semen Tostum and Arecae semen carbonisata are traditionally processed by stir-baking for subsequent use in a variety of clinical applications. These three Arecae semen types, important Chinese herbal drugs, have been used in China and other Asian countries for thousands of years. In this study, the sensory technologies of a colorimeter and sensitive validated high-performance liquid chromatography with diode array detection were employed to discriminate raw Arecae semen and its processed drugs. The color parameters of the samples were determined by a colorimeter instrument CR-410. Moreover, the fingerprints of the four alkaloids of arecaidine, guvacine, arecoline and guvacoline were surveyed by high-performance liquid chromatography. Subsequently, Student's t test, the analysis of variance, fingerprint similarity analysis, hierarchical cluster analysis, principal component analysis, factor analysis and Pearson's correlation test were performed for final data analysis. The results obtained demonstrated a significant color change characteristic for components in raw Arecae semen and its processed drugs. Crude and processed Arecae semen could be determined based on colorimetry and high-performance liquid chromatography with a diode array detector coupled with chemometrics methods for a comprehensive quality evaluation.

LC-high-resolution-MS/MS analysis of chemical compounds in rat plasma after oral administration of Nao-Mai-Tong and its individual herbs.

Nao-Mai-Tong (NMT), a Chinese herbal formula, is used for treating ischemia cerebral apoplexy. To discover the components of NMT with potential in vivo bioactivity and investigate the differences between NMT and its single herb components, this study rigorously compared plasma samples collected from rats dosed with NMT and single-herb extracts at different times through LC-high resolution-MS/MS and data processing (Metworks). The plasma of the NMT group contained a total of 66 identified compounds (25 prototypes and 41 metabolites), including anthraquinones, triterpenoid saponins, isoflavones and phthalides. Additionally, glucuronidation, sulfation and cysteine conjugation were the major reactions through which the compounds in NMT were metabolized. The comparison of the groups revealed two metabolites that were only detected in the plasma from the NMT-dosed group, whereas seven prototype ingredients (chrysophanol-8-O-glucoside, ginsenoside Rf, Rg2, Rh1, F1, F2 and chikusetsusaponin IVa) and 12 metabolites (two novel triterpenoid saponins) were only discovered in the plasma samples from the single-herb-dosed groups. Moreover, the trends in the chemical compounds detected presented marked differences between NMT-dosed rat plasma and plasma samples from the single-herb-dosed groups. The above data indicate that prescription compatibility affects the assimilation and elimination of ingredients and provides useful information for further pharmacokinetic studies.

[Study on the Identification of Gypsum Fibrosum with FTIR].

To establish a new identification method of Gypsum Fibrosum with FTIR and analyze different kinds of the sulfate mineral medicine with clustering method. With the use of FTIR, identify different kinds of sulfate mineral medicine, such as gypsum fibrosum, gypsum ustum and natrii sulfas , in addition, clustering method and first derivative spectra are used to analyze the intrinsic relationship in these kinds of sulfate mineral medicine. What's more, 24 batches of Gypsum Fibrosum samples which from different production are analyzed with FTIR; then the spectrum control fingerprint with pattern is established with common peaks; at last the similarity between the simple spectrum fingerprint and the spectrum control fingerprint is calculated with angle cosine value and correlation coefficient. There are distinctions about the wave number, the peak position, the spike and the peak intensity in the infrared spectroscopy and first derivative spectra. Therefore, the sulfate mineral medicine is divided into two main regions with the based on these clusters: put the gypsum fibrosum and gypsum ustum in the same class, the natrii sulfas in the other class. Between 400 and 4 000 cm-1, the experiment showed that 24 batches of samples were more than 0.980 0. Provide a new, rapid and specificity method for identification and standard of gypsum fibrosum and build a successful cluster analysis about the sulfate mineral medicine.

[Application of drug-target prediction technology in network pharmacology of traditional Chinese medicine].

In recent years, network pharmacology has been developed rapidly, and especially, the concept of ″network target″ has brought a new era in the field of traditional Chinese medicine (TCM). The integrity and systematicness emphasized in network pharmacology comply with the characteristics of holistic view and treatment in Chinese medicine. It can provide deeper insights into the underlying mechanisms of TCM theories, including the illustration on action mechanism of Chinese medicine, selection of pharmacodynamic materials and the combination principles of various Chinese herbs, etc. Therefore, this theory is more suitable for TCM academic characteristics and practical conditions. The key problem in network pharmacology is how to efficiently and quickly identify the interactions between large amounts of drugs and target proteins. As an efficient and high throughput way, drug-target prediction technology can reduce costs, quickly predict the component targets, and provide foundation for the application of TCM network pharmacology. In view of the large amount of compounds and target databases, different prediction methods and technologies have been developed, and used to predict the drug-target interactions. Many virtual screening technologies have been successfully applied to network pharmacology. Based on different prediction principles, drug-target prediction technology can be generally divided into four types： ligand-based prediction, receptor-based prediction, machine learning and combined prediction. In this paper, we are going to review the prediction methods of drug-target interactions and give acomprehensive elaboration of their application in network pharmacology of TCM, hoping to provide beneficial references for various Chinese medicine researchers.

[Network Pharmacological Studies of Puerariae Radix in Improving Insulin Resistance].

Objective: To investigate the active components and potential mechanism of Puerariae Radix in improving insulin resistance by using network pharmacological method. Methods: Key target proteins related with insulin resistance were selected based on molecular docking technology, and then took the selected components with 31 target proteins of four pathways for docking. Meanwhile, component-target proteins network was established to network analysis by software Cytoscape 3. 2. 1. Results: 19 compounds had close interactions with four pathways such as AMPK. There were 13 compositions can verify through literature, which revealing that active ingredients and potential molecular mechanism of Puerariae Radix in improving insulin resistance, preliminarily. Conclusion: The network pharmacological method is helpful to explore the possible active components in Puerariae Radix and elucidate the mechanism.

[Intervention effects of Jiaotai pills on PCPA-induced insomnia in rats].

To elucidate the intervention effects of Jiaotai pills(JTP) on p-chlorophenylalanine (PCPA)-induced insomnia in rats and its underlying mechanism, the insomnia model was established by single intraperitoneal injection with PCPA in rats. The locomotor activity of rats was observed, and the levels of nerve growth factor(NGF) in hypothalamus, hippocampus, prefrontal cortex and serum of rats were determined by using ELISA. Moreover, a proton nuclear magnetic resonance(¹H-NMR)-based metabonomic approach was developed to profile insomnia-related metabolites in rat serum and hippocampus and analyze the intervention effects of JTP on changes in underlying biomarkers related to locomotor activity, NGF and insomnia. According to the results, JTP could significantly suppress the locomotor activity of insomnia rats, and increase the NGF levels in hypothalamus, hippocampus, prefrontal cortex and serum of rats with insomnia. The disturbed metabolic state associated with PCPA-induced insomnia in rat serum and hippocampus could be intervened by JTP. Meanwhile, six and five potential biomarkers related to insomnia in rat serum and hippocampus were reversed by administration of JTP. In conclusion, the current study demonstrated that JTP had protective effects against PCPA-induced insomnia in rats, which was probably correlated with regulation of NGF level and metabolism of amino acids, lipids and choline.

Two new triterpenoids from the resin of Styrax tonkinensis.

Two new triterpenoids, 3ß,6ß-dihydroxy-12-oxo-13Hα-olean-28,19ß-olide (1) and 3-oxo-olean-11,13(18)-dien-28,19ß-olide (2) were isolated from the resin of Styrax tonkinensis (Pier.) Craib. The structures of both triterpenoids were determined by physicochemical and spectroscopic methods. Compound 1 is the second triterpene found with cis-fused C/D ring from the resin, which is rarely observed in oleanane-type triterpenes.

[Effects of Different Pretreatment Methods on the Phenylketonuria Screening Model by FTIR/ATR Spectroscopy].

To establish a phenylketonuria screening model by FTIR/ATR spectroscopy, and to compare the effects of different pretreatment methods, such as baseline correction, smoothing, derivation, Fourier deconvolution, on the model quality. A consensus partial least squares regression method (cPLS) was used to build the quantitative model of phenylalanine in dried blood spots. The effects of different pretreatment methods on the model performance were investigated, using the correlation coefficient (r), root mean square error of prediction (RMSEP), mean relative error (MRE) and predictive accuracy (Acc). The nine-point smoothing coupled with the first differential was found to perform the best. Compared with the model by the original spectra, its r, RMSEP, MRE and Acc were improved from 0. 822 7, 115. 8, 0. 395 and 94. 6 to 0. 889 9, 102. 2, 0. 286 and 100, respectively. With the advantages of fast speed, easy process, no reagents consumption and environmental protection, the present method is expected to become a simple and green technology for rapidly screening the neonatal phenylketonuria in a large population.

[Study on material base of Ligusticum wallichii for treating brain ischemia and its molecular mechanism based on molecular docking].

To explore the effective ingredients and mechanism of Ligusticum wallichii in treating brain ischemia. Four brain ischemia-related target proteins were selected in the joint screening for the 45 component in L. wallichii reported in literatures based on molecular docking by reference to the corresponding drugs in the market. According to the docking results, multiple components in L. wallichii, such as phthalides, were superior to the corresponding drugs in the market, suggesting that they may be the major effective components in L. wallichii for treating brain ischemia. The method can be used to study the material base and molecular mechanism of traditional Chinese medicines.

[Study on action mechanism and material base of compound Danshen dripping pills in treatment of carotid atherosclerosis based on techniques of gene expression profile and molecular fingerprint].

Action mechanism and material base of compound Danshen dripping pills in treatment of carotid atherosclerosis were discussed based on gene expression profile and molecular fingerprint in this paper. First, gene expression profiles of atherosclerotic carotid artery tissues and histologically normal tissues in human body were collected, and were screened using significance analysis of microarray (SAM) to screen out differential gene expressions; then differential genes were analyzed by Gene Ontology (GO) analysis and KEGG pathway analysis; to avoid some genes with non-outstanding differential expression but biologically importance, Gene Set Enrichment Analysis (GSEA) were performed, and 7 chemical ingredients with higher negative enrichment score were obtained by Cmap method, implying that they could reversely regulate the gene expression profiles of pathological tissues; and last, based on the hypotheses that similar structures have similar activities, 336 ingredients of compound Danshen dripping pills were compared with 7 drug molecules in 2D molecular fingerprints method. The results showed that 147 differential genes including 60 up-regulated genes and 87 down regulated genes were screened out by SAM. And in GO analysis, Biological Process ( BP) is mainly concerned with biological adhesion, response to wounding and inflammatory response; Cellular Component (CC) is mainly concerned with extracellular region, extracellular space and plasma membrane; while Molecular Function (MF) is mainly concerned with antigen binding, metalloendopeptidase activity and peptide binding. KEGG pathway analysis is mainly concerned with JAK-STAT, RIG-I like receptor and PPAR signaling pathway. There were 10 compounds, such as hexadecane, with Tanimoto coefficients greater than 0.85, which implied that they may be the active ingredients (AIs) of compound Danshen dripping pills in treatment of carotid atherosclerosis (CAs). The present method can be applied to the research on material base and molecular action mechanism of TCM.