High-throughput transcriptional profiling of perturbations by Panax ginseng saponins and Panax notoginseng saponins using TCM-seq / 药物分析学报

Panax ginseng(PG)and Panax notoginseng(PN)are highly valuable Chinese medicines(CM).Although both CMs have similar active constituents,their clinical applications are clearly different.Over the past decade,RNA sequencing(RNA-seq)analysis has been employed to investigate the molecular mechanisms of extracts or monomers.However,owing to the limited number of samples in standard RNA-seq,few studies have systematically compared the effects of PG and PN spanning multiple conditions at the transcriptomic level.Here,we developed an approach that simultaneously profiles transcriptome changes for multiplexed samples using RNA-seq(TCM-seq),a high-throughput,low-cost workflow to molecularly evaluate CM perturbations.A species-mixing experiment was conducted to illustrate the accuracy of sample multiplexing in TCM-seq.Transcriptomes from repeated samples were used to verify the robustness of TCM-seq.We then focused on the primary active components,Panax notoginseng sa-ponins(PNS)and Panax ginseng saponins(PGS)extracted from PN and PG,respectively.We also char-acterized the transcriptome changes of 10 cell lines,treated with four different doses of PNS and PGS,using TCM-seq to compare the differences in their perturbing effects on genes,functional pathways,gene modules,and molecular networks.The results of transcriptional data analysis showed that the tran-scriptional patterns of various cell lines were significantly distinct.PGS exhibited a stronger regulatory effect on genes involved in cardiovascular disease,whereas PNS resulted in a greater coagulation effect on vascular endothelial cells.This study proposes a paradigm to comprehensively explore the differences in mechanisms of action between CMs based on transcriptome readouts.

Network pharmacology approaches for research of Traditional Chinese Medicines / 中国天然药物

Pharmacodynamics material basis and effective mechanisms are the two main issues to decipher the mechnisms of action of Traditional Chinese medicines (TCMs) for the treatment of diseases. TCMs, in "multi-component, multi-target, multi-pathway" paradigm, show satisfactory clinical results in complex diseases. New ideas and methods are urgently needed to explain the complex interactions between TCMs and diseases. Network pharmacology (NP) provides a novel paradigm to uncover and visualize the underlying interaction networks of TCMs against multifactorial diseases. The development and application of NP has promoted the safety, efficacy, and mechanism investigations of TCMs, which then reinforces the credibility and popularity of TCMs. The current organ-centricity of medicine and the "one disease-one target-one drug" dogma obstruct the understanding of complex diseases and the development of effective drugs. Therefore, more attentions should be paid to shift from "phenotype and symptom" to "endotype and cause" in understanding and redefining current diseases. In the past two decades, with the advent of advanced and intelligent technologies (such as metabolomics, proteomics, transcriptomics, single-cell omics, and artificial intelligence), NP has been improved and deeply implemented, and presented its great value and potential as the next drug-discovery paradigm. NP is developed to cure causal mechanisms instead of treating symptoms. This review briefly summarizes the recent research progress on NP application in TCMs for efficacy research, mechanism elucidation, target prediction, safety evaluation, drug repurposing, and drug design.

Multimodal integrated strategy for the discovery and identification of quality markers in traditional Chinese medicine / 药物分析学报

With the modernization and internationalization of traditional Chinese medicine(TCM),the requirement for quality control has increased.The quality marker(Q-marker)is an important standard in this field and has been implemented with remarkable success in recent years.However,the establishment of Q-markers remains fragmented and the process lacks systematicity,resulting in inconsistent quality control and insufficient correlation with clinical efficacy and safety of TCM.This review introduces four multi-modal integrated approaches that contribute to the discovery of more comprehensive and accurate Q-markers,thus aiding in the establishment of new quality control patterns based on the characteristics and principles of TCM.These include the whole-process quality control strategy,chemical-activity-based screening method,efficacy,safety,and consistent combination strategy,and TCM theory-guided approach.Furthermore,methodologies and representative examples of these strategies are described,and important future directions and questions in this field are also proposed.

Neuroprotective effects of Ginkgo biloba dropping pills in Parkinson's disease / 药物分析学报

Parkinson's disease(PD)is the second most common neurodegenerative disease in the world;however,it lacks effective and safe treatments.Ginkgo biloba dropping pill(GBDP),a unique Chinese G.biloba leaf extract preparation,exhibits antioxidant and neuroprotective effects and has a potential as an alternative therapy for PD.Thus,the aims of this study were to evaluate the effects of GBDP in in vitro and in vivo PD models and to compare the chemical constituents and pharmacological activities of GBDP and the G.biloba extract EGb 761.Using liquid chromatography tandem-mass spectrometry,46 GBDP constitu-ents were identified.Principal component analysis identified differences in the chemical profiles of GBDP and EGb 761.A quantitative analysis of 12 constituents showed that GBDP had higher levels of several flavonoids and terpene trilactones than EGb 761,whereas EGb 761 had higher levels of organic acids.Moreover,we found that GBDP prevented 6-hydroxydopamine-induced dopaminergic neuron loss in zebrafish and improved cognitive impairment and neuronal damage in methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced PD mice.Although similar effects were observed after EGb 761 treatment,the neuroprotective effects were greater after GBDP treatment on several endpoints.In addition,in vitro results suggested that the Akt/GSK3β pathway may be involved in the neuroprotective effects of GBDP.These findings demonstrated that GBDP have potential neuroprotective effects in the treatment of PD.

An ultra-robust fingerprinting method for quality assessment of traditional Chinese medicine using multiple reaction monitoring mass spectrometry / 药物分析学报

Chromatographic fingerprinting has been perceived as an essential tool for assessing quality and chemical equivalence of traditional Chinese medicine.However,this pattern-oriented approach still has some weak points in terms of chemical coverage and robustness.In this work,we proposed a multiple reaction monitoring(MRM)-based fingerprinting method in which approximately 100 constituents were simultaneously detected for quality assessment.The derivative MRM approach was employed to rapidly design MRM transitions independent of chemical standards,based on which the large-scale finger-printing method was efficiently established.This approach was exemplified on QiShenYiQi Pill(QSYQ),a traditional Chinese medicine-derived drug product,and its robustness was systematically evaluated by four indices:clustering analysis by principal component analysis,similarity analysis by the congruence coefficient,the number of separated peaks,and the peak area proportion of separated peaks.Compared with conventional ultraviolet-based fingerprints,the MRM fingerprints provided not only better discriminatory capacity for the tested normal/abnormal QSYQ samples,but also higher robustness under different chromatographic conditions(i.e.,flow rate,apparent pH,column temperature,and column).The result also showed for such large-scale fingerprints including a large number of peaks,the angle cosine measure after min-max normalization was more suitable for setting a decision criterion than the unnormalized algorithm.This proof-of-concept application gives evidence that combining MRM tech-nique with proper similarity analysis metrices can provide a highly sensitive,robust and comprehensive analytical approach for quality assessment of traditional Chinese medicine.

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

For multicellular organisms, cell-cell communication is essential to numerous biological processes. Drawing upon the latest development of single-cell RNA-sequencing (scRNA-seq), high-resolution transcriptomic data have deepened our understanding of cellular phenotype heterogeneity and composition of complex tissues, which enables systematic cell-cell communication studies at a single-cell level. We first summarize a common workflow of cell-cell communication study using scRNA-seq data, which often includes data preparation, construction of communication networks, and result validation. Two common strategies taken to uncover cell-cell communications are reviewed, e.g., physically vicinal structure-based and ligand-receptor interaction-based one. To conclude, challenges and current applications of cell-cell communication studies at a single-cell resolution are discussed in details and future perspectives are proposed.

Therapeutic index in liver metastasis-bearing mice by sequential treatment with Newcastle disease virus 7793 strain and 5-FU / 实用医学杂志

Objective The anti-tumor effect by sequential treatment with Newcastle disease virus (NDV) strain 7793 and 5-FU in liver-metastases mice model was evaluated and immune-active response stimulated by sequential therapy was investigated. Methods Liver metastasis mice model was established by intra-peritoneal injection. The model mice were randomly divided into 3 groups, being given PBS (0.1 mL/d,10 d), NDV7793 [512 HU/(kg·d),5 d] and NDV7793[512 HU/(kg·d),5 d] + fluorouracil [5-FU,10 mg/(kg·d),5 d]. The effect on survival time,body weight,liver weight change and the formation of liver metastasis in tumor-bearing mice model were detected after different treatments in evaluating the regression of mice liver metastasis by sequential therapy. The detection of thymus index and IFN-γ concentrations in liver tissue of tumor-bearing mice model may indicate the stimulation of immune-active response by sequential therapy. Results The mean survival time of tumor-bearing mice treated with NDV7793 and 5-Fu sequentially was 32 d , which was significantly higher than those of tumor-bearing mice treated with NDV7793(30 d) or PBS injections (17 d), respectively (P 0.05), and the liver weight was lighter than PBS (P < 0.05); Compared with NDV treatment, the decreased thymus index and increased amount of the effector IFN γ were observed in tumor-bearing mice treated with NDV 7793 and 5-FU sequentially (P <0.05). Conclusions The sequential therapy with Newcastle disease virus 7793 strain and 5-FU was observed to co-exert a significant suppressive effect in liver metastases of colon cancer cells in tumor-bearing mice model. Compared with NDV treatment , the survival time of mice model and the induction of antitumor effector molecules were significantly improved after sequential therapy.

Evaluate the carotid artery stiffness of acquired immune deficiency syndrome patients by ultrasound quantitive artery stiffness technique / 中华医学超声杂志（电子版）

Objetive To evaluate the carotid artery stiffness of acquired immune deficiency syndrome (AIDS) and analyze the mechanism and influence factors. Methods Fifty cases of AIDS patients and Fifty healthy people were enrolled in this study according to the principles of randomize and control. Quantitive inter-media thickness (QIMT) and quantitive artery stiffness (QAS) technique were employed to evaluate the inter-media thickness (IMT) and stiffness of right carotid artery. The parameters included IMT, compliance coefficent (CC), stiffness β (β), and pulse wave velocity (PWV). Unpaired t test was used to compare the parameters between two groups, and Pearson correlation analysis was used for linear correlation analysis. Results There were no statistically difference of carotid artery IMT between two groups [(0.569±0.095) mm vs (0.512±0.114) mm, P>0.05]. There was statistically difference of stiffness parameters (CC,β, PWV) between two groups [(0.59±0.21) mm2/kPa vs (1.04±0.41) mm2/kPa, 13.01±6.10 vs 8.14±1.37, (8.70±1.65) m/s vs (6.81±1.37) m/s, all P0.05 ). There was no statistically signification association between IMT, CC,β, PWV and CD4+, CD8+T cell count (r was 0.000, 0.012,-0.093,-0.097, 0.096, 0.012, 0.056, 0.024, all P>0.05). Conclusion The carotid artery stiffness of AIDS patients is reduced. HIV may play a role in the development of artery stiffness in AIDS patients.

The Significance of Changes in Sex Hormones after Lamivudine Antiviral Treatment for Hepatitis B in Male Patients with Compensated Cirrhosis / 天津医药

Objective To investigate the changes of sex hormones after lamivudine antiviral treatment in male hepa-titis B patients with compensated cirrhosis, and the significance of changes thereof. Methods Forty-six male patients with compensated cirrhosis were included in patient group. The patient group was given lamivudine antiviral treatment for 24 weeks. The sex hormone levels were compared between before and after treatment. Patients were divided into two groups (complete response group and incomplete response group) according to their response to the treatment. The sex hormone lev-els were compared between these two groups. Results (1)The level of PRL was significantly decreased, and the levels of T and E2 were significantly increased after lamivudine antiviral treatment in patient group.(2)There were significant differenc-es in levels of PRL, T and E2 between complete response group and incomplete response group. Conclusion (1)The lami-vudine antiviral treatment can improve the dysfunction of sex hormones.(2)There was a relationship between the changes of sex hormones and the responses of antiviral treatment.

Inhibitory effects of astragaloside IV on cytochrome P450 enzyme of rat liver microsomes / 中国中药杂志

<p><b>OBJECTIVE</b>To provide a scientific basis for the drug-combination and aim to examine whether astragaloside IV has the impact on the cytochrome P450 enzymes.</p><p><b>METHOD</b>Tolbutamide, chlorzoxazone, coumarin, nifedipine, and phenacetin were as probe substrates of rat CYP2C9, CYP2E1, CYP2A6, CYP3A4, and CYP1A2, and were incubated in rat liver microsomes with astragaloside IV. Triplicate samples were run to generate IC50 value by incubating P450 probe substrates in the presence of five concentrations of astragaloside IV in the incubation mixture. The K(i) values were determined by fitting the probe substrate at various inhibitor concentrations to the equations for competitive inhibition, noncompetitive inhibition, noncompetitive inhibition, and mixed-type inhibition.</p><p><b>RESULT</b>IC50 and K(i) values were estimated, and the types of inhibition were determined. Among the five probe substrates, astragaloside IV might not significantly affect CYP2E1, CYP2A6 and CYP1A2-mediated metabolism in rats, but was a competitive inhibitor of CYP2C9 (IC50 35.40 micromol x L(-1), K(i) 42.88 micromol x L(-1)), and was a uncompetitive inhibitor of CYP3A4 (IC50 88.24 micromol x L(-1), K(i) 33.31 micromol x L(-1)).</p><p><b>CONCLUSION</b>These results suggested that astragaloside IV inhibited CYP2C9 and CYP3A4, which provided useful information for safe and effective use of astragaloside IV.</p>

Prediction of multi-target of Aconiti Lateralis Radix Praeparata and its network pharmacology / 中国中药杂志

<p><b>OBJECTIVE</b>To predict multi-targets by multi-compounds found in Aconiti Lateralis Radix Praeparata and construct the corresponding multi-compound-multi-target network.</p><p><b>METHOD</b>Based on drug-target relationships of FDA approved drugs, a model for predicting targets was established by random forest algorithm. This model was then applied to predict the targets of Aconiti Lateralis Radix Praeparata and construct the multi-compound-multi-target network.</p><p><b>RESULT</b>The predicted targets of 22 compounds of Aconiti Lateralis Radix Praeparata are validated by literature. Each compound in the established network was correlated with 16. 3 targets on average, while each target was correlated with 4. 77 compounds on average, which reflects the "multi-compound and multi-target" characteristic of Chinese medicine.</p><p><b>CONCLUSION</b>The proposed approach can be used to find potential targets of Chinese medicine.</p>

Network pharmacology study on major active compounds of Fufang Danshen formula / 中国中药杂志

<p><b>OBJECTIVE</b>To investigate the correlations between multi-compounds of Fufang Danshen formula and their multi targets and multi diseases.</p><p><b>METHOD</b>Literature knowledge of nine major active compounds from Fufang Danshen formula, including tanshinone II(A), salvianolic acid B, protocatechuic aldehyde, danshensu, cryptotanshinone, notoginsenoside R1, ginsenoside Rg1, ginsenoside Rb1 and borneol were collected from PubMed. Combined with cardiovascular related diseases and genes from OMIM database, the corresponding multi-compound-multi- target-multi-disease network was constructed and visualized by Cytoscape software.</p><p><b>RESULT</b>AND CONCLUSION: Network analysis showed that the 9 compounds could modulate 42 cardiovascular associated genes (e. g. PPARG, ACE, KCNJ11, KCNQ1, ABCC8, et al), which related to 30 cardiovascular associated diseases including non-insulin-dependent diabetes mellitus, hyperinsulinemic hypoglycemia, hypertension, and coronary heart disease. These results suggested new potential indications of Fufang Danshen formula.</p>

Symptom-based traditional Chinese medicine slices relationship network and its network pharmacology study / 中国中药杂志

<p><b>OBJECTIVE</b>To discover and interpret the correlations between traditional Chinese medicine (TCM) slices and their properties such as function, symptom and channel tropism by constructing the relationship network using network pharmacology approaches.</p><p><b>METHOD</b>TCM slices related information was extracted from Chinese Pharmacopeia (2010 edition, volume I) by text mining, and was used to construct the TCM slices-symptom relationship network. The corresponding network analysis was also performed.</p><p><b>RESULT</b>Three thousands and sixteen pair of TCM slice-symptom correlation associated with 646 TCM slices was discovered, and the constructed network unfolded the complex relationships between TCM slices. Further network analysis results indicated that the un-annotated function and channel tropism of TCM slice can be revealed by proposed symptom-based network.</p><p><b>CONCLUSION</b>Network pharmacology approaches can be applied in TCM research to discover and interpret the relationships between TCM slices and their properties.</p>

Network toxicology and its application to traditional Chinese medicine / 中国中药杂志

The concept and framework of network toxicology and network toxicology of traditional Chinese medicine has been proposed in this paper. The related tools and technologies have been briefly introduced, and the prospects for network toxicology of traditional Chinese medicine are forecasted.

Simultaneous characterization of two types of major active components in Kushen by high performance liquid chromatography coupled to multi-stage mass spectrometry / 中国中药杂志

In this study, a high performance liquid chromatography coupled with multi-stage mass spectrometry method was developed for simultaneous characterization of alkaloids and flavonoids, the main active components, in Kushen with diverse physical and chemical properties. Forty-two major constituents, including sixteen Kushen alkaloids and twenty-six Kushen flavonoids were tentatively identified. Additionally, useful and characteristic fragmentation pathways of two types of Kushen alkaloids, namely cytisine-type and sparteine-type, in positive ions mode were proposed and summarized, which would lay a foundation for the rapid identification of the active ingredients in traditional Chinese medicine Kushen.

Tools for network pharmacology study: network visualization and network analysis / 中国中药杂志

Network pharmacology has been one of the academic frontiers of traditional Chinese medicine research. In this paper, we generally showed the work flow of network pharmacology research, and introduced concepts of network visualization and network analysis, as well the commonly-used tools, such as Cytoscape.

Sort similarity based on computational method for chemical fingerprinting / 中国中药杂志

The key parts of chemical fingerprinting. However, the performance of the current whole similarity determining method sometimes is inadequate when the chromatograms of different classes are similar. The present study was focused on developing a sort similarity measure determining method for these problems. In this method, chemical fingerprint features are extracted from original chromatograms for classifying the samples. Further, the fluctuations of chemical compositions among the same class samples are evaluated using an inter-class similarity measure. The proposed method was applied to evaluate the quality of Sarcandra glabra samples through their HPLC fingerprints. The results showed that the different parts of this plant, i.e., the aerial and the whole, were clearly classified, and chemical fluctuations of samples with the same sort were well represented.

Serum metabolome analysis reveals effect of panax notoginosides on ischemic rat after acute myocardial infarction / 中国中药杂志

<p><b>OBJECTIVE</b>The effect of panax notoginosides on ischemic rat after acute myocardial infarction by coronary artery ligation was preliminarily investigated using metabonomics approach.</p><p><b>METHOD</b>GC-MS based metabonomics approach was applied to analyse the serum metabolome of normal group, model group and treatment group of rats. Furthermore, PCA and PIS-DA was used to identify the differentially expressed metabolites among the three groups.</p><p><b>RESULT</b>A good fit and prediction results using metabolome data was obtained by PCA and PL-DA. Moreover, 10 metabolites were selected as potential biomarkers for efficacy evaluation of panax notoginosides by t-test and variable importance in the projection.</p><p><b>CONCLUSION</b>Metabonomics provides a whole-organism biological description of pathological or physiological state, and likely can be used as a new approach for efficacy evaluation of traditional Chinese medicine.</p>

Discovering active components from traditional Chinese medicine by component-knockout approach / 中国中药杂志

<p><b>OBJECTIVE</b>A component-knockout approach was established to discover active components from traditional Chinese medicine.</p><p><b>METHOD</b>According to the principle of gene knockout technique, an experiment workflow for component-knockout method was developed, which is distinct from the bio-guided screening method. The differences of therapeutic efficacies between different combinations of individual components were analyzed by some statistical methods including Analysis of Variance (ANOVA), whilst a set of criterias were established to assess active components. By comparing the difference of drug efficacy between the original formulae and the mixture being knockout certain component, the active components can be identified.</p><p><b>RESULT</b>The presented component-knockout method was applied to discover the active components of Shenmai formulae for the synergistic effects on the cyclophosphamide chemotherapy for S180 tumor-bearing mice. The results indicated that panoxadiol, a type of ginsenosides, were the effective components of Shenmai formulae.</p><p><b>CONCLUSION</b>A new method for identifying effective components from Chinese medicinal formulae was developed and successfully applied to discover the active components of Shenmai Formulae, which possesses the synergistic actions towards chemotherapy process.</p>

Prevalence of Avian Influenza Virus Receptor in Human Respiratory Tract / 生物化学与生物物理进展

SAαt2,6 and SAα2,3 linked sialic acid molecules on epithelial cell membrane served as receptors for influenza virus, which axe specifically recognized by human and avian influenza viruses, respectively. The distribution of these two species of sialic acids in human respiratory tract from different anatomical sites and different age groups was investigated. The results showed that SAα2,3Gal species was prevalent in respiratory bronchiole and lung alveolar epithelium, but was infiequent in trachea, bronchus and bronchiole. On the contrary, the SAα2,6Gal species was more common in the trachea and bronchus and to a lesser degree in the alveolar epithelium. When compared the expression levels of SAα2,6Gal and α2,3Gal in the respiratory tract among different age groups, no significant difference was found. In the ex vivo H5N1 virus infection study, alveolus epithelium were found to be more susceptible to avian influenza than trachea and bronchus epithelial cells. These results suggest that the human respiratory tract, to some extent, is permissive for avian influenza viruses. The currently-observed limited human to human transmission of H5N1 virus may be associated with the different abundance of SAα2,3Gal linkages in human upper respiratory tract among individuals.