Exploration in the Mechanism of Action of Licorice by Network Pharmacology.

Licorice is a popular sweetener and a thirst quencher in many food products particularly in Europe and the Middle East and also one of the oldest and most frequently used herbs in traditional Chinese medicine. As a wide application of food additive, it is necessary to clarify bioactive chemical ingredients and the mechanism of action of licorice. In this study, a network pharmacology approach that integrated drug-likeness evaluation, structural similarity analysis, target identification, network analysis, and KEGG pathway analysis was established to elucidate the potential molecular mechanism of licorice. First, we collected and evaluated structural information of 282 compounds in licorice and found 181 compounds that met oral drug rules. Then, structural similarity analysis with known ligands of targets in the ChEMBL database (similarity threshold = 0.8) was applied to the initial target identification, which found 63 compounds in licorice had 86 multi-targets. Further, molecular docking was performed to study their binding modes and interactions, which screened out 49 targets. Finally, 17 enriched KEGG pathways (p < 0.01) of licorice were obtained, exhibiting a variety of biological activities. Overall, this study provided a feasible and accurate approach to explore the safe and effective application of licorice as a food additive and herb medicine.

Discovery of molecular mechanism of a clinical herbal formula upregulating serum HDL-c levels in treatment of metabolic syndrome by in vivo and computational studies.

Decreased HDL cholesterol (HDL-c) is considered as an independent risk factor of cardiovascular disease in metabolic syndrome (Mets). Wendan decoction (WDD), a famous clinical traditional Chinese medicine formula in Mets in China, which can obviously up-regulate serum HDL-c levels in Mets. However, till now, the molecular mechanism of up-regulation still remained unclear. In this study, an integrated approach that combined serum ABCA1 in vivo assay, QSAR modeling and molecular docking was developed to explore the molecular mechanism and chemical substance basis of WDD upregulating HDL-c levels. Compared with Mets model group, serum ABCA1 and HDL-c levels intervened by two different doses of WDD for two weeks were significantly up-regulated. Then, kohonen and LDA were applied to develop QSAR models for ABCA1 up-regulators based flavonoids. The derived QSAR model produced the overall accuracy of 100%, a very powerful tool for screening ABCA1 up-regulators. The QSAR model prediction revealed 67 flavonoids in WDD were ABCA1 up-regulators. Finally, they were subjected to the molecular docking to understand their roles in up-regulating ABCA1 expression, which led to discovery of 23 ABCA1 up-regulators targeting LXR beta. Overall, QSAR modeling and docking studies well accounted for the observed in vivo activities of ABCA1 affected by WDD.

Identfication of Potent LXRß-Selective Agonists without LXRα Activation by In Silico Approaches.

Activating Liver X receptors (LXRs) represents a promising therapeutic option for dyslipidemia. However, activating LXRα may cause undesired lipogenic effects. Discovery of highly LXRß-selective agonists without LXRα activation were indispensable for dyslipidemia. In this study, in silico approaches were applied to develop highly potent LXRß-selective agonists based on a series of newly reported 3-(4-(2-propylphenoxy)butyl)imidazolidine-2,4-dione-based LXRα/ß dual agonists. Initially, Kohonen and stepwise multiple linear regression SW-MLR were performed to construct models for LXRß agonists and LXRα agonists based on the structural characteristics of LXRα/ß dual agonists, respectively. The obtained LXRß agonist model gave a good predictive ability (R²train = 0.837, R²test = 0.843, Q²LOO = 0.715), and the LXRα agonist model produced even better predictive ability (R²train = 0.968, R²test = 0.914, Q²LOO = 0.895). Also, the two QSAR models were independent and can well distinguish LXRß and LXRα activity. Then, compounds in the ZINC database met the lower limit of structural similarity of 0.7, compared to the 3-(4-(2-propylphenoxy)butyl)imidazolidine-2,4-dione scaffold subjected to our QSAR models, which resulted in the discovery of ZINC55084484 with an LXRß prediction value of pEC50 equal to 7.343 and LXRα prediction value of pEC50 equal to -1.901. Consequently, nine newly designed compounds were proposed as highly LXRß-selective agonists based on ZINC55084484 and molecular docking, of which LXRß prediction values almost exceeded 8 and LXRα prediction values were below 0.

Systematic Understanding of Mechanisms of a Chinese Herbal Formula in Treatment of Metabolic Syndrome by an Integrated Pharmacology Approach.

Metabolic syndrome (MS) is becoming a worldwide health problem. Wendan decoction (WDD)-a famous traditional Chinese medicine formula-has been extensively employed to relieve syndromes related to MS in clinical practice in China. However, its pharmacological mechanisms still remain vague. In this study, a comprehensive approach that integrated chemomics, principal component analysis, molecular docking simulation, and network analysis was established to elucidate the multi-component and multi-target mechanism of action of WDD in treatment of MS. The compounds in WDD were found to possess chemical diversity, complexity and drug-likeness compared to MS drugs. Six nuclear receptors were obtained to have strong binding affinity with 217 compounds of five herbs in WDD. The importance roles of targets and herbs were also identified due to network parameters. Five compounds from Radix Glycyrrhizae Preparata can hit all six targets, which can assist in screening new MS drugs. The pathway network analysis demonstrated that the main pharmacological effects of WDD might lie in maintaining lipid and glucose metabolisms and anticancer activities as well as immunomodulatory and hepatoprotective effects. This study provided a comprehensive system approach for understanding the multi-component, multi-target and multi-pathway mechanisms of WDD during the treatment of MS.

Structural Investigation for Optimization of Anthranilic Acid Derivatives as Partial FXR Agonists by in Silico Approaches.

In this paper, a three level in silico approach was applied to investigate some important structural and physicochemical aspects of a series of anthranilic acid derivatives (AAD) newly identified as potent partial farnesoid X receptor (FXR) agonists. Initially, both two and three-dimensional quantitative structure activity relationship (2D- and 3D-QSAR) studies were performed based on such AAD by a stepwise technology combined with multiple linear regression and comparative molecular field analysis. The obtained 2D-QSAR model gave a high predictive ability (R²(train) = 0.935, R²(test) = 0.902, Q²(LOO) = 0.899). It also uncovered that number of rotatable single bonds (b_rotN), relative negative partial charges (RPC(-)), oprea's lead-like (opr_leadlike), subdivided van der Waal's surface area (SlogP_VSA2) and accessible surface area (ASA) were important features in defining activity. Additionally, the derived3D-QSAR model presented a higher predictive ability (R²(train) = 0.944, R²(test) = 0.892, Q²(LOO) = 0.802). Meanwhile, the derived contour maps from the 3D-QSAR model revealed the significant structural features (steric and electronic effects) required for improving FXR agonist activity. Finally, nine newly designed AAD with higher predicted EC50 values than the known template compound were docked into the FXR active site. The excellent molecular binding patterns of these molecules also suggested that they can be robust and potent partial FXR agonists in agreement with the QSAR results. Overall, these derived models may help to identify and design novel AAD with better FXR agonist activity.

Multi-Layer Identification of Highly-Potent ABCA1 Up-Regulators Targeting LXRß Using Multiple QSAR Modeling, Structural Similarity Analysis, and Molecular Docking.

In this study, in silico approaches, including multiple QSAR modeling, structural similarity analysis, and molecular docking, were applied to develop QSAR classification models as a fast screening tool for identifying highly-potent ABCA1 up-regulators targeting LXRß based on a series of new flavonoids. Initially, four modeling approaches, including linear discriminant analysis, support vector machine, radial basis function neural network, and classification and regression trees, were applied to construct different QSAR classification models. The statistics results indicated that these four kinds of QSAR models were powerful tools for screening highly potent ABCA1 up-regulators. Then, a consensus QSAR model was developed by combining the predictions from these four models. To discover new ABCA1 up-regulators at maximum accuracy, the compounds in the ZINC database that fulfilled the requirement of structural similarity of 0.7 compared to known potent ABCA1 up-regulator were subjected to the consensus QSAR model, which led to the discovery of 50 compounds. Finally, they were docked into the LXRß binding site to understand their role in up-regulating ABCA1 expression. The excellent binding modes and docking scores of 10 hit compounds suggested they were highly-potent ABCA1 up-regulators targeting LXRß. Overall, this study provided an effective strategy to discover highly potent ABCA1 up-regulators.

2D and 3D QSAR models for identifying diphenylpyridylethanamine based inhibitors against cholesteryl ester transfer protein.

Cholesteryl ester transfer protein (CETP) inhibitors hold promise as new agents against coronary heart disease. Molecular modeling techniques such as 2D-QSAR and 3D-QSAR analysis were applied to establish models to distinguish potent and weak CETP inhibitors. 2D and 3D QSAR models-based a series of diphenylpyridylethanamine (DPPE) derivatives (newly identified as CETP inhibitors) were then performed to elucidate structural and physicochemical requirements for higher CETP inhibitory activity. The linear and spline 2D-QSAR models were developed through multiple linear regression (MLR) and support vector machine (SVM) methods. The best 2D-QSAR model obtained by SVM gave a high predictive ability (R(2)train=0.929, R(2)test=0.826, Q(2)LOO=0.780). Also, the 2D-QSAR models uncovered that SlogP_VSA0, E_sol and Vsurf_DW23 were important features in defining activity. In addition, the best 3D-QSAR model presented higher predictive ability (R(2)train=0.958, R(2)test=0.852, Q(2)LOO=0.734) based on comparative molecular field analysis (CoMFA). Meanwhile, the derived contour maps from 3D-QSAR model revealed the significant structural features (steric and electronic effects) required for improving CETP inhibitory activity. Consequently, twelve newly designed DPPE derivatives were proposed to be robust and potent CETP inhibitors. Overall, these derived models may help to design novel DPPE derivatives with better CETP inhibitory activity.

[Mining rules on determination of four properties based on traditional Chinese medicine functional combination].

OBJECTIVE: It laid the foundation of the large sample data mining for a comprehensive summary concerning four properties theory of traditional Chinese medicine (TCM), and also provided theory clues on determination of four properties for the new resource development of TCM and the clinical use of Chinese medicine. METHOD: Four properties data of 8 980 Chinese medicines from "Chinese herbal medicine (CHM)" and associated function index data were chose as data sets. Then, the IBM SPSS Clementine 14.1 data mining platform and Apriori model were adopted to mining classification-association rules, setting the minimum support threshold of rule antecedent and the minimum confidence threshold as 0.5% and 60%. RESULT: 11 classification-association rules involved in warm, cold and mild natures were found. CONCLUSION: It was discovered that the TCM with functions of "dispelling wind-cold, warming the middle, stopping pain and expelling wind-removing dampness, tonifying kidney yang, unblocking meridians and expelling wind-removing dampness, dispelling cold to stop pain, strengthening sinews-bones and expelling wind-removing dampness" was likely warm-natured, with functions of "tonifying the lung" was likely mild-natured, and with functions of " clearing heat and drying dampness, clearing heat and purging fire, eliminating restlessness" was likely cold-natured.

[Four properties law of nature data of Chinese materia medica in "Chinese herbal medicine (CHM)"].

OBJECTIVE: In order to provide theoretical clues and data support for the use of Chinese medicine clinical drug, experimental study of Chinese materia medica and development of new resources of Chinese materia medica, the four properties as the core, the relationships of property, flavor, channel tropism and toxicity in nature data of Chinese materia medica were analyzed. METHOD: The spearman rank correlation method was employed to analyze 8 356 Chinese drugs with characteristic of four properties from " Chinese Herbal Medicine" based on data level coding. RESULT: It was discovered that four properties showed significant positive correlations with tastes of "pungent and sweet" , channels of "spleen" , "stomach" , "kidney" and "toxicity" , but also showed significant negative correlations with tastes of "bitter" and "light" and six channels such as "large intestine" , "heart", "bladder" , "gallbladder" , "small intestine" and "lung" (in descending order of correlation ) (P <0. 01). CONCLUSION: It was indicated that the more hot the Chinese medicine nature, the more possible it contained "toxicity" , tastes of "pungent" and "sweet" , and the more possible it was belong to channels of "spleen" , "stomach" and "kidney". As well, the more cold the Chinese medicine nature, the more possible it contained tastes of "bitter" and "light", and the more possible it was belong to six channels such as "large intestine", etc.

(S)-Benzyl 3-(4-hy-droxy-phen-yl)-2-(trityl-amino)-propano-ate.

The title compound, C(35)H(31)NO(3), was obtained by the reaction of (S)-benzyl 2-amino-3-(4-hy-droxy-phen-yl)propano-ate and (chloro-methane-tri-yl)tribenzene. The enanti-omer has been assigned by reference to an unchanging chiral centre in the synthetic procedure. In the crystal, mol-ecules are linked into chains running along the a axis by inter-molecular O-H⋯O hydrogen bonds.

[Research and analysis of data source--analysis of the items of medical plants in Xiandai Bencao Gangmu].

Scientific data is the source of innovation in knowledge. In order to change the situation that there is few information in plenty of data and to obtain useful knowledge which has high information content, it is necessary to clean data and ensure data's accuracy and without noise off when database is established initially. High-quality data comes from high-quality data source. But incomplete and incorrect and irregular data exist widely in the data source of Chinese materia medica. The phenomenon of synonyms and homonym is quite serious, and there is no unified description for the name and origin of Chinese materia medica among different data sources. So data processing including data analysis and research is very important in the establishment of Chinese materia medica database. In order to get the most accurate and standard data, this paper analyzed the items of Medical Plants in Xiandai Bencao Gangmu, including classification analysis of medical plants: distribution analysis of different classes and analysis of medical part; analysis of synonyms and homonym; analysis of incorrect data and analysis of advantage and disadvantage of data sources.

[Discussion on optimizing data processing of Chinese materia medica].

Correct data without noise is the basis for obtaining useful information and knowledge. The database system of Chinese materia medica is the application of database technology in the field of Chinese materia medica. Its establishment is based on the analysis, processing and supplementary of much irregular raw data during studying Chinese materia medica information. This paper reviewed several key problems in the data processing of Chinese materia medica based on the information system of Chinese herbal medicine that we are constructing.