Network pharmacology and molecular docking reveal the mechanism of resveratrol in oral squamous cell carcinoma treatment / 口腔疾病防治

Objective@#To explore the molecular mechanism of resveratrol (RES) in the treatment of oral squamous cell carcinoma (OSCC) through the use of biological information methods such as network pharmacology and molecular docking and to provide a theoretical reference for the clinical application of RES in the treatment of OSCC.@*Methods@#The Swiss Target Prediction(http://www.swisstargetprediction.ch), SEA (http://sea.bkslab.org)database, and Pharm mapper database(http://lilab-ecust.cn) were used to retrieve RES-related targets, and the DISGENET (www.disgenet.org), OMIM (https://omim.org) and GeneCards (https://www.genecards.org) databases were used to screen OSCC disease targets. The intersection of drugs and disease targets was determined, and Cytoscape 3.7.2 software was used to construct a "drug-diseasetarget pathway" network. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was used to construct a target protein interaction network, and the DAVID database was used for enrichment analysis of key proteins. Finally, molecular docking validation of key proteins was performed using AutoDock and PyMOL. The enrichment analysis and molecular docking results were integrated to predict the possible molecular mechanisms of RES treatment in OSCC; western blot was used to determine the effect of resveratrol at different concentrations (50, 100) μmol/L on the expression of Src tyrosine kinase (SRC), epidermal growth factor receptor (EGFR), estrogen receptor gene 1 (ESR1), and phosphatidylinositol 3 kinase/protein kinase B (PI3K/AKT) signaling pathway proteins in OSCC HSC-3 cells.@*Results@#A total of 243 targets of RES drugs and 6 094 targets of OSCC were identified. A total of 116 potential common targets were obtained by intersecting drugs with disease targets. These potential targets mainly participate in biological processes such as in vivo protein self-phosphorylation, peptide tyrosine phosphorylation, transmembrane receptor protein tyrosine kinase signaling pathway, and positive regulation of RNA polymerase Ⅱ promoter transcription, and they interfere with the PI3K/AKT signaling pathway to exert anti-OSCC effects. The docking results of resveratrol with OSCC molecules indicated that key targets, such as EGFR, ESR1, and SRC, have good binding activity. The results of cell-based experiments showed that resveratrol inhibited the protein expression of SRC, EGFR, ESR1, p-PI3K, and p-AKT in HSC-3 cells in a dose-dependent manner.@*Conclusion@#RES can inhibit the expression of its targets EGFR, ESR1, SRC, p-PI3K, and p-AKT in OSCC cells.

Caries prevention mechanism of the Xinjiang Mori Cortex based on network pharmacology and its effect on the main cariogenic bacteria / 口腔疾病防治

Objective@#To investigate the potential caries prevention mechanism of the Xinjiang Mori cortex and to analyze its effect on the main cariogenic bacteria.@*Methods@#The active components of the Xinjiang Mori cortex and the main targets were predicted and screened using the TCMSP database. The GeneCards, DisGENET and TTD databases were used to obtain caries-related targets. The common targets were derived, and core genes were screened. The enrichment analysis was performed using the DAVID data platform. Molecular docking was performed using AutoDock software. In in vitro antibacterial experiments, first, the 50% minimum inhibitory concentration (MIC50) and the minimum bactericidal concentration (MBC) of the Xinjiang Mori Cortex extract against Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus were determined and the growth curves were measured. The effects of the Xinjiang Mori Cortex extract on acid production, polysaccharide production and adhesion ability of Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus in the planktonic state were determined. The 50% minimum biofilm inhibition concentration (MBIC50) and 50% minimum biofilm reduction concentration (MBRC50) were determined by crystal violet staining, and biofilm morphology was visualized using scanning electron microscopy (SEM).@*Results@#The main active components of the Xinjiang Mori cortex included quercetin, kaempferol, and β-sitosterol. Tumor necrosis factor (TNF), interleukin-6 (IL-6), and interleukin-1beta (IL-1β) could be the most important targets of the Xinjiang Mori cortex for the prevention of dental caries. The enrichment analysis results showed that Mori cortex extract may have effects on the AGE-RAGE signaling pathway, IL-17 signaling pathway, and TNF signaling pathway. The antibacterial experiment results showed that the MIC50 values of Xinjiang Mori Cortex extract against Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus were 0.5, 0.5 and 0.25 mg/mL, respectively, and the MBCs were 4.0, 2.0 and 1.0 mg/mL, respectively. The inhibitory effect of Xinjiang Mori Cortex extract on the acid production, polysaccharide production and adhesion ability of three major cariogenic bacteria in the planktonic state was stronger than that of the control group, and the differences were statistically significant (P<0.05). The MBIC50 was 1.0, 1.0, and 0.5 mg/mL, and the MBRC50 was 4.0, 4.0, and 2.0 mg/mL. SEM observation showed that the amount of biofilm formation decreased with the drug concentration compared with the control group.@*Conclusion@#Xinjiang Mori cortex extract can prevent caries through quercetin, kaempferol, and β-sitosterol active ingredients, TNF、IL-6、IL-1β key targets and multiple pathways and inhibit the growth, acid production, polysaccharide production, and adhesion ability of three major cariogenic bacteria in the planktonic state and has some inhibitory effect on corticogenic biofilm formation.

Mechanism of Tumor T Cell Exhaustion from Perspective of ''Sanjiao-Yingwei'' Qi Transformation Malfunction / 中国实验方剂学杂志

In order to promote the innovative application of Sanjiao theory and Yingwei theory， this paper tries to apply the ''Sanjiao-Yingwei'' Qi transformation theory to the treatment of tumor diseases， integrating it with T cell exhaustion mechanism to elaborate on its scientific connotation and using network pharmacology and bioinformatics to elucidate the correlation between the anti-tumor mechanism of ''Sanjiao-Yingwei'' Qi transformation and T cell exhaustion. The ''Sanjiao-Yingwei'' Qi transformation function is closely related to the immunometabolic ability of the human body， and the ''Sanjiao-Yingwei'' Qi transformation system constitutes the immunometabolic exchange system within and outside the cellular environment. Cancer toxicity is generated by the fuzzy Sanjiao Qi， and the long-term fuzzy Sanjiao Qi is the primary factor leading to T cell exhaustion， which is related to the long-term activation of T cell receptors by the high tumor antigen load in the tumor microenvironment. Qi transformation malfunction of the Sanjiao produces phlegm and collects stasis， which contributes to T cell exhaustion and is correlated with nutrient deprivation， lipid accumulation， and high lactate levels in the immunosuppressed tumor microenvironment， as well as with the release of transforming growth factor-β and upregulated expression of programmed death receptor-1 by tumor-associated fibroblasts and platelets in the tumor microenvironment. Ying and Wei damage due to Sanjiao Qi transformation malfunction is similar to the abnormal manifestations such as progressive loss of exhausted T cell effector function and disturbance of cellular energy metabolism. Guizhi decoction， Shengming decoction， and Wendan decoction can correct T cell exhaustion and exert anti-tumor effects through multi-target and multi-pathways by regulating ''Sanjiao-Yingwei'' Qi transformation， and hypoxia inducible factor-1α （HIF-1α） may be one of the main pathways to correct T cell exhaustion. It was found that HIF-1α may be one of the important prognostic indicators in common tumors by bioinformatics. The use of the ''Sanjiao-Yingwei'' Qi transformation method may play an important part in improving the prognosis of tumor patients in clinical practice.

Mechanism of Astragaloside Ⅳ on db/db Mice with Type 2 Diabetes Mellitus and Non-alcoholic Fatty Liver Disease Based on AMPK Signaling Pathway / 中国实验方剂学杂志

ObjectiveTo study the mechanism of astragaloside Ⅳ （AS Ⅳ） on db/db mice with type 2 diabetes mellitus （T2DM） and non-alcoholic fatty liver disease （NAFLD） based on network pharmacology and experimental validation. MethodA total of 24 db/db mice were randomly divided into four groups： model group， metformin group， and low-dose and high-dose AS Ⅳ groups. Six C57 mice were used as the blank group. The low-dose and high-dose AS Ⅳ groups were given AS Ⅳ of 0.015 and 0.030 g·kg-1 by gavage， and the metformin group was given 0.067 g·kg-1 by gavage. The blank and model groups were given equal volumes of distilled water by gavage. After intragastric administration， fasting blood glucose （FBG） was detected， and an oral glucose tolerance test was performed. Serum lipid level and liver histopathology were detected. The target and enrichment pathway of AS Ⅳ for treating T2DM and NAFLD were predicted by network pharmacology， and the main enrichment pathway was verified by molecular biology techniques. The protein expressions of AMPK， p-AMPK， sterol regulatory element-binding protein-1 （SREBP-1）， and fatty acid synthetase （FAS） in liver tissue were detected by Western blot. ResultCompared with the blank group， the levels of body mass， liver weight coefficient， fasting blood glucose， serum total cholesterol， triglyceride， and low-density lipoprotein cholesterol in mice treated with AS Ⅳ were decreased （P<0.05， P<0.01）. The pathology of liver tissue showed significant improvement in lipid accumulation， and imaging results showed that the degree of fatty liver was reduced after AS Ⅳ therapy. Network pharmacological prediction results showed that vascular endothelial growth factor α （VEGFA）， galactoagglutinin 3 （LGALS3）， serine/threonine kinase B2 （Akt2）， RHO-associated coiled-coil protein kinase 1 （ROCK1）， serine/threonine kinase B1 （Akt1）， signaling and transcriptional activator protein （STAT3）， and messtimal epidermal transformation factor （MET） were key targets in "drug-disease" network. The results from the Kyoto encyclopedia of genes and genomes （KEGG） enrichment showed that the AMP-dependent protein kinase （AMPK） signaling pathway was strongly associated with T2DM and NAFLD. Western blot results showed that compared with the blank group， the expression levels of p-AMPK/AMPK in the model group were significantly down-regulated， while those of SREBP-1 and FAS proteins were significantly up-regulated （P<0.01）. Compared with the model group， the expression levels of p-AMPK/AMPK in the metformin group and high-dose AS Ⅳ group were significantly up-regulated， while those of SREBP-1 and FAS proteins were significantly down-regulated （P<0.05， P<0.01）. ConclusionAS Ⅳ regulates the expression of lipid proteins by activating the AMPK signaling pathway， thereby improving lipid metabolism.

Determination and Mechanism Prediction of Potential Active Ingredients in Erdongtang Based on UHPLC-QqQ-MS and Network Pharmacology / 中国实验方剂学杂志

ObjectiveTo establish an ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry（UHPLC-QqQ-MS） for determination of the active ingredients in Erdongtang， and to predict the targets and pathways of anti-insulin resistance action of this formula. MethodThe analysis was performed on an ACQUITY UPLC BEH C18 column（2.1 mm×100 mm， 1.7 μm） with the mobile phase of 0.1% formic acid aqueous solution（A）-acetonitrile（B） for gradient elution（0-3 min， 90%-87%A； 3-6 min， 87%-86%A； 6-9 min， 86%-83%A； 9-11 min， 83%-75%A； 11-18 min， 75%-70%A； 18-19 min， 70%-52%A； 19-22 min， 52%A； 22-25 min， 52%-5%A； 25-27 min， 5%-90%A； 27-30 min， 90%A）. The contents of active ingredients in Erdongtang was detected by electrospray ionization（ESI） and multiple reaction monitoring（MRM） mode under positive and negative ion modes. On this basis， network pharmacology was applied to predict the targets and pathways of Erdongtang exerting anti-insulin resistance effect. ResultThe 20 active ingredients in Erdongtang showed good linear relationships within a certain mass concentration range， and the precision， stability， repeatability and recovery rate were good. The results of determination showed that the ingredients with high content in 15 batches of samples were baicalein（1 259.39-1 635.78 mg·L-1）， baicalin（1 078.37-1 411.52 mg·L-1）， the ingredients with medium content were mangiferin（148.59-217.04 mg·L-1）， timosaponin BⅡ（245.10-604.89 mg·L-1）， quercetin-3-O-glucuronide（89.30-423.26 mg·L-1）， rutin（46.91-1 553.61 mg·L-1）， glycyrrhizic acid（55.97-391.47 mg·L-1）， neomangiferin（37.45-127.03 mg·L-1）， nuciferine（0.89-63.48 mg·L-1）， hyperoside（6.96-136.78 mg·L-1）， liquiritin（30.89-122.78 mg·L-1）， liquiritigenin（26.64-110.67 mg·L-1）， protodioscin（58.57-284.26 mg·L-1）， the ingredients with low content were wogonin（7.16-20.74 mg·L-1）， pseudoprotodioscin（5.49-22.96 mg·L-1）， ginsenoside Rb1（7.31-23.87 mg·L-1）， ginsenoside Rg1（10.78-28.33 mg·L-1）， ginsenoside Re（7.78-24.76 mg·L-1）， ophiopogonin D（2.08-4.29 mg·L-1）， methylophiopogonanone A（0.74-1.67 mg·L-1）. The results of network pharmacology indicated that the mechanism of anti-insulin resistance exerted by Erdongtang might be related to the phosphatidylinositol 3-kinase/protein kinase B（PI3K/Akt） signaling pathway. ConclusionThe established UHPLC-QqQ-MS has the advantages of simple sample processing， strong exclusivity and high sensitivity， and can simultaneously determine the contents of the main ingredients from seven herbs in Erdongtang， which can lay the foundation for the development of Erdongtang compound preparations. The results of the network pharmacology can provide a reference for the mechanism study of Erdongtang in the treatment of type 2 diabetes mellitus.

Mechanism of Qizhenziyin mixture in the treatment of hypogonadism based on network pharmacology analysis and molecular docking / 药学实践杂志

Objective To investigate the mechanism of Qizhenziyin mixture in the treatment of hypogonadism by using the network pharmacology approach. Methods The active components of Qizhenziyin mixture were obtained by searching TCMSP ，TCMID and HIT databases.The related targets of candidate compounds were obtained by searching STITCH databases. The potential targets of Qizhenziyin mixture in the treatment of hypogonadism were obtained by mapping the disease genes of hypogonadism with Genecards and DisGeNet databases. The protein interaction platform database (STRING) was used to construct the interaction relationship between action targets. The target protein interaction （PPI） network was constructed by introducing Cytoscape software. The mechanism of Qizhenziyin mixture in the treatment of hypogonadism was explained through the enrichment analysis of GO, KEGG and molecular docking technology. Results A total of 148 drug-disease chemical compounds, 96 drug-disease intersection targets, 1085 disease targets were obtained；the components for treating diseases are: quercetin，kaempferol, luteolin, etc; enrichment analysis of GO revealed 1792 biological processes （BP）, 31 cellular components (CC) and 79 molecular functions (MF)；the results of KEGG pathway enrichment analysis indicated such as FOXO signaling pathway, prostate cancer, AGE-RAGE signaling pathway in diabetic complications, HIF-1 signaling pathway, etc.The results of molecular docking showed that kaempferol and LEP had the best and stable binding energy. Conclusion The active components of Qizhenziyin mixture may play a role of the treatment of hypogonadism by improving insulin resistance and the expression of testosterone synthetase of Leydig cells.

Analysis of Antidepressant Quality Markers of Bupleuri Radix Before and After Vinegar-processing Based on UPLC-Q-TOF-MS and Network Pharmacology / 中国实验方剂学杂志

ObjectiveTo analyze the antidepressant quality markers（Q-Marker） of Bupleuri Radix（BP） before and after vinegar-processing by ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry（UPLC-Q-TOF-MS）， multivariate statistical analysis and network pharmacology. MethodUPLC-Q-TOF-MS was used to analyze the chemical basis of raw and vinegar-processed products of BP， and principal component analysis（PCA） orthogonal partial least squares-discriminant analysis（OPLS-DA） were used to identify the differential components in BP that changed significantly before and after vinegar-processing， which were regarded as candidate quality markers（Q-Marker）. Then the disease-drug-component-target network related to antidepressant effect of BP was constructed by network pharmacology， and the antidepressant Q-Marker of raw and vinegar-processed products of BP was determined. Rats were randomly divided into blank group， model group， fluoxetine group（2.67 mg·kg-1） and total saponin group（0.72 mg·kg-1）， except the blank group， rats in the other groups were subjected to chronic unpredictable mild stress（CUMS）. Three weeks after the start of modeling， rats in each administration group were given the corresponding dose of drugs once a day for 4 weeks， and rats in the blank and model groups were given normal saline with dose of 10 mL·kg-1. At 1 day before modeling， 21 days and 28 days after administration， body mass weighing， sucrose preference test and open field test were performed on each group . After 28 days of administration， real-time fluorescence quantitative polymerase chain reaction（Real-time PCR） was used to detect the mRNA expression levels of phosphatidylinositol 3-kinase（PI3K）， protein kinase B（Akt）， mammalian target of rapamycin（mTOR）， glycogen synthase kinase-3β（GSK-3β）， forkhead box transcription factor O3a（FoxO3a） and β-catenin in hippocampal tissues of rats in each group， while protein expression levels of PI3K， Akt， mTOR and FoxO3a in hippocampal tissues of rats in each group were detected by Western blot. ResultThere were 19 components in BP showed significant changes before and after vinegar-processing， and 9 components such as saikosaponin A， saikosaponin B1， saikosaponin B2， saikosaponin C and saikosaponin D were identified as potential Q-Marker through S-plot differential marker screening. Combined with the disease-drug-component-target network， saikosaponin A， saikosaponin B1， saikosaponin B2 and saikosaponin D were identified as antidepressant Q-Marker of raw and vinegar-processed products of BP. According to the results of pharmacodynamic tests， after 28 d of administration， compared with the blank group， the body mass， sucrose preference index and open field total score of rats in model group， fluoxetine group and total saponin group decreased significantly（P<0.01）. Compared with the model group， the body mass， sucrose preference index and open field total score in total saponin group increased significantly（P<0.01）. Compared with the blank group， mRNA expression levels of PI3K， Akt， mTOR and β-catenin in hippocampus of rats in the model group decreased significantly（P<0.05）， while mRNA expression levels of GSK-3β and FoxO3a increased significantly（P<0.05）. Compared with the model group， mRNA expression levels of PI3K， Akt， mTOR and β-catenin in hippocampus of rats in the total saponin group were increased significantly（P<0.05）， while mRNA expression levels of GSK-3β and FoxO3a decreased significantly（P<0.05）. Compared with the blank group， the protein expression levels of Akt and mTOR in hippocampus of the model group decreased significantly（P<0.01）， while the protein expression levels of PI3K and FoxO3a increased significantly（P<0.01）. Compared with the model group， the expression level of Akt in hippocampus of the total saponin group increased significantly（P<0.01）， the mTOR expression level was increased but not statistically significant， while the protein expression levels of PI3K and FoxO3a decreased significantly（P<0.01）. ConclusionThe chemical constituents of BP changed greatly after vinegar-processing， and the antidepressant Q-Marker of raw and vinegar-processed products of BP was determined by chemical basis， pharmacodynamics， network pharmacology and signaling pathway， which provided a reference for further research on quality control， pharmacodynamic substance basis and processing mechanism of BP.

Network Pharmacology in Research on Efficacy of Traditional Chinese Medicine and Compound Prescriptions / 中国实验方剂学杂志

The efficacy of traditional Chinese medicine （TCM） and compound prescriptions is confirmed based on practical experience. It is a highly generalized expression of the clinical characteristics and scope of prescriptions and a unique expression of the medical effects of TCM. Network pharmacology， as a cross-disciplinary field based on the theory of systems biology and multi-level analysis of biological systems， has become a common virtual screening tool in TCM research and gradually developed with the progress in big data and artificial intelligence. In the context of modern medicine， the efficacy of TCM compound prescriptions has a vague concept and lacks scientific evidence. Elucidating the connotation of TCM efficacy and guiding TCM theoretical research has become one of the hotspots and difficulties in TCM research. This article explores the feasibility of using network pharmacology for the research on the efficacy of TCM compound prescriptions and investigates whether the research results can represent part of the efficacy of prescriptions. Furthermore， the research platforms and algorithms in this field are summarized. The research ideas and existing problems in this field are proposed from the aspects of efficacy concept embodiment， target screening， result verification， efficacy network building， and homogenization avoiding of network pharmacology research results. Finally， the future development directions are prospected. This article is expected to provide a reference for exploring the modern biological basis of the efficacy of TCM and compound prescriptions and for the clinical application and theoretical research of TCM.

Network pharmacology and molecular docking study of the active ingredients in Saptasaram kashayam for the treatment of Polycystic ovary syndrome-Supplemenntary data

Polycystic Ovary Syndrome (PCOS) is one of the most prevalent endocrine disorder in women of reproductive age characterized by hyperandrogenism (HA). Current treatment options for PCOS are either with adverse effects or ineffective. Saptasaram kashayam (SK), an ayurvedic formulation is often been a safe traditional alternative medicine to improve the PCOS symptoms as well as its pathological development. However, its principle phytoconstituents or underlying mechanisms have not been investigated. In order to achieve this, the current study systematically utilized computational tools, network pharmacology approaches and molecular docking studies. All identified phytoconstituents of SK were screened by QikProp ADME prediction and 47 were selected based on oral bioavailability and drug likeliness scores. Their 3D structures were submitted to three online target fishing webservers PharmMapper, ChemMapper and Swiss Target Prediction which produced 1084 biological targets for SK comprehensively. 350 known PCOS therapeutic targets were retreived as common targets from three different interrogative disease centric bioinformatic platforms DisGeNET, OMIM and GeneCards. Intersection of 1084 biological targets of SK and 350 PCOS therapeutic targets produced, 88 potential therapeutic targets of SK against PCOS. STRING PPI and Compound-Target-Pathway networks were constructed and analysed using Cytoscape software. GO & KEGG pathway enrichment analysis was performed using DAVID database. 15 PCOS therapeutic target proteins were short listed from network analysis report- PIK3CA, PDPK1, AKT1, PIK3R1, STAT3, MAPK1, MAPK3, EGFR, AR, ESR1, ESR2, SHGB, NOS3, F2 & CREBBP. Targets that were likely to be inhibited/modulated by SK for treatment of PCOS were docked against the screened phytoconstituents and their respective standard inhibitors using GLIDE-SP of Schrodinger suite, Maestro version- 13.0. Results showed that Quercetin, Catechin, Boeravinone J, Genistein, Protocatechuic Acid, Gentisic Acid, Xanthoarnol, Luteolin, Boeravinone F, Tyrosine, Kaempferol, Dalbergioidin, etc exhibited good binding affinities when compared to standard drugs and might be responsible for synergistic/additive protective effect of SK against PCOS. Meanwhile PI3K-Akt signaling pathway, Prolactin signaling pathway, AGE-RAG diabetic complications, HIF-1 signaling pathway and Estrogen signaling pathway were found to be involving the hub genes of interest and in this way, they might be intervened during treatment of PCOS by SK. Present study succeeded in identifying the drug like principle phytoconstituents, probable PCOS therapeutic targets and the underlying molecular mechanism of SK apart from providing reliable evidence for therapeutic potential of SK against PCOS. However further validation by in vitro and in vivo investigations is necessary.

Network pharmacology and molecular docking study of the active ingredients in Saptasaram kashayam for the treatment of Polycystic ovary syndrome

Polycystic Ovary Syndrome (PCOS) is one of the most prevalent endocrine disorder in women of reproductive age characterized by hyperandrogenism (HA). Current treatment options for PCOS are either with adverse effects or ineffective. Saptasaram kashayam (SK), an ayurvedic formulation is often been a safe traditional alternative medicine to improve the PCOS symptoms as well as its pathological development. However, its principle phytoconstituents or underlying mechanisms have not been investigated. In order to achieve this, the current study systematically utilized computational tools, network pharmacology approaches and molecular docking studies. All identified phytoconstituents of SK were screened by QikProp ADME prediction and 47 were selected based on oral bioavailability and drug likeliness scores. Their 3D structures were submitted to three online target fishing webservers PharmMapper, ChemMapper and Swiss Target Prediction which produced 1084 biological targets for SK comprehensively. 350 known PCOS therapeutic targets were retreived as common targets from three different interrogative disease centric bioinformatic platforms DisGeNET, OMIM and GeneCards. Intersection of 1084 biological targets of SK and 350 PCOS therapeutic targets produced, 88 potential therapeutic targets of SK against PCOS. STRING PPI and Compound-Target-Pathway networks were constructed and analysed using Cytoscape software. GO & KEGG pathway enrichment analysis was performed using DAVID database. 15 PCOS therapeutic target proteins were short listed from network analysis report- PIK3CA, PDPK1, AKT1, PIK3R1, STAT3, MAPK1, MAPK3, EGFR, AR, ESR1, ESR2, SHGB, NOS3, F2 & CREBBP. Targets that were likely to be inhibited/modulated by SK for treatment of PCOS were docked against the screened phytoconstituents and their respective standard inhibitors using GLIDE-SP of Schrodinger suite, Maestro version- 13.0. Results showed that Quercetin, Catechin, Boeravinone J, Genistein, Protocatechuic Acid, Gentisic Acid, Xanthoarnol, Luteolin, Boeravinone F, Tyrosine, Kaempferol, Dalbergioidin, etc exhibited good binding affinities when compared to standard drugs and might be responsible for synergistic/additive protective effect of SK against PCOS. Meanwhile PI3K-Akt signaling pathway, Prolactin signaling pathway, AGE-RAG diabetic complications, HIF-1 signaling pathway and Estrogen signaling pathway were found to be involving the hub genes of interest and in this way, they might be intervened during treatment of PCOS by SK. Present study succeeded in identifying the drug like principle phytoconstituents, probable PCOS therapeutic targets and the underlying molecular mechanism of SK apart from providing reliable evidence for therapeutic potential of SK against PCOS. However further validation by in vitro and in vivo investigations is necessary.

Mechanism of Calculus Bovis treating keratitis based on network pharmacology / 中华实验眼科杂志

Objective:To investigate the complex Calculus Bovis-target-keratitis network and to explore the molecular mechanism of Calculus Bovis treating keratitis through network pharmacology. Methods:Genes related to keratitis were searched in the online DisGeNET database and the protein-protein interaction (PPI) network of keratitis-associated proteins was constructed.The components isolated and identified in Calculus Bovis were collected through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP, https: //tcmsp-e.com/tcmsp.php), Chemistry Database by Shanghai Institute of Organic Chemistry of CAS (http: //www.organchem.csdb.cn), and published literature.The canonical SMILES information of the collected components was exported, which were submitted to the SwissTargetPrediction platform to predict potential targets of the components.The active component-predicted target network of Calculus Bovis was constructed and merged with the PPI network of keratitis-associated proteins to build the active component-potential target network of Calculus Bovis and systemically investigate the potential targets and signal pathways of Calculus Bovis in treatment of keratitis.The component-target-pathway network was established to analyze the mechanism of Calculus Bovis treating keratitis. Results:Thirty-nine components isolated and identified in Calculus Bovis were searched and 65 target genes related to keratitis were screened.Of the 28 potential targets involved in Calculus Bovis treating keratitis, there were 7 direct targets, including tumor necrosis factor, caspase 1, Toll-like receptor 9, C-X-C motif chemokine ligand 8, interleukin-6, mitogen-activated protein kinase 8, neurotrophic receptor tyrosine kinase 1.The 28 potential targets were annotated to 12 entries for biological process, 18 for cellular components and 13 for molecular function.In the Kyoto encyclopedia of genes and genomes pathway enrichment analysis, 10 signal pathways were identified as enriched categories, which were mainly related to human cytomegalovirus infection, amoebiasis, antifolate resistance, PI3K-Akt signaling pathway, rheumatoid arthritis, apoptosis, cytokine-cytokine receptor interaction, malaria, non-alcoholic fatty liver disease, interleukin-17 signaling pathway. Conclusions:Calculus Bovis may play an adjuvant therapeutic effect on keratitis through anti-inflammatory, antibacterial, antiviral, immune regulation, inflammatory regulation and other functions.

Study on the mechanism of Kangmin Zhisou Granules in the treatment of bronchial asthma based on network pharmacology and animal experiments / 国际中医中药杂志

Objective:To deeply explore the potential mechanism of Kangmin Zhisou Granules in the treatment of bronchial asthma through network pharmacology method; To verify it with animal experiments.Methods:The active components and corresponding target information of Kangmin Zhisou Granules were screened with the help of BATMAN-TCM database, and the related disease targets of bronchial asthma were obtained through GeneCards and OMIM databases. The drug targets and bronchial asthma targets were intersected and imported String database was used to establish PPI network. Cytoscape 3.9.1 software was used to draw the network diagram of "Chinese materia medica-active components-intersection targets" and the core targets were screened. GO and KEGG enrichment analysis was performed on the core targets using DAVID database. A mouse model of asthma induced by ovalbumin was prepared. After the intervention of Kangmin Zhisou Granules, the pathological changes of mouse lung tissue were observed, and the contents of serum TNF-α, IL-6, IL-1 β were detected by ELISA.Results:Totally 240 active components and 1 364 potential targets were obtained from Kangmin Zhisou Granules. Tumor necrosis factor (TNF), interleukin-6 (IL-6), protein kinase B (AKT1), albumin (ALB), interleukin 1-beta (IL-1β) and other 11 core targets were obtained after screening. The results of GO enrichment analysis showed that the treatment of bronchial asthma by Kangmin Zhisou Granules mainly involved the positive regulation of protein phosphorylation, the regulation of inflammatory response, lipopolysaccharide response and other biological processes, as well as TNF, activated protein kinase (MAPK), interleukin-17 (IL-17) and other signaling pathways. Animal experiments confirmed that Kangmin Zhisou Granules could reduce the expression levels of TNF-α, IL-6 and IL-1β in serum ( P<0.05), and reduce the infiltration of inflammatory cells in the lung tissue of mice, thereby relieving asthma symptoms. Conclusion:Kangmin Zhisou Granules may exert anti-inflammatory effects by acting on TNF-α, IL-6, IL-1β and other targets to alleviate asthma symptoms.

Study on network pharmacology of Polygalae Radix- Acori Tatarinowii Rhizoma medicinal pair for depression and Alzheimer disease with the same treatment / 国际中医中药杂志

Objective:To explore the molecular mechanism of Polygalae Radix - Acori Tatarinowii Rhizoma medicinal pair for depression and Alzheimer disease (AD) with the same treatment through network pharmacology. Methods:Effective components of Polygalae Radix - Acori Tatarinowii Rhizoma medicinal pair were retrieved from TCMSP, TCMID and ETCM databases. The disease targets of depression and AD were retrieved from GeneCards, TTD and CTD databases. Targets of action of drugs on active components were predicted through SwissTargetPrediction, and then the intersection targets of medicinal pair and the diseases were taken. Cytoscape 3.6.1 was used to construct the interaction network of Polygalae Radix - Acori Tatarinowii Rhizoma medicinal pair on "component-common target-disease". The enrichment analysis of GO function and KEGG pathway was carried out with the help of Metascape platform, and molecular docking verification was carried out. Results:Through searching the databases and literature, 78 compounds in Polygalae Radix - Acori Tatarinowii Rhizoma medicinal pair were obtained, corresponding to 41 targets of different diseases with the same treatment. The GO function was mainly concentrated in response to lipopolysaccharide and cellular response to nitrogen compound. The KEGG pathway was mainly concentrated in lipid and atherosclerosis, calcium signaling pathway, serotonergic synapse, insulin resistance and so on. The core targets were PTGS2, ESR2, etc. Molecular docking showed that most of the core components could form stable conformation with the core targets. Conclusions:Polygalae Radix - Acori Tatarinowii Rhizoma medicinal pair has the characteristics of multi-component, multi-target and multi-pathway in the same treatment of depression and AD. Through their core components of senegenin, 1-carbobutoxy-β-carboline, 6-hydroxy-1,2,3,7-tetramethoxyxanthone, kaempferol and etc., the pair can act on PTGS2 and other targets, regulate lipid and atherosclerosis, calcium signaling pathway, serotonergic synapse, insulin resistance and so on, and play a therapeutic role in depression and Alzheimer's disease with the same treatment.

Study on mechanism of Yangxue Qingnao Granule for the treatment of vascular dementia disease based on network pharmacology and bioinformatics / 国际中医中药杂志

Objective:To explore the possible mechanism of Yangxue Qingnao Granule for the treatment of vascular dementia (VaD) based on network pharmacology and bioinformatics.Methods:The active components and potential targets of Yangxue Qingnao Granule in the treatment of VaD were obtained from TCMSP database, BATMAN-TCM database, GEO database and OMIM database, etc. The heatmap was visualized by using the pheatmap packages in R. Cytoscape 3.8.2 software and the CytoNCA plugin were utilized to build a network of "Chinese materia medica-active component-potential target". CytoNCA plug-in was used to analyze PPI network topology. Metascape was used for GO and KEGG pathway enrichment analyses. Finally, AutoDock Vina 1.5.6 software was applied to construct molecular docking between the active components and potential core targets. Resuls A total of 135 active components of Yangxue Qingnao Granule were screened and 186 potential targets of Yangxue Qingnao Granule against VaD were obtained. GO function enrichment analysis found protein kinase binding, transcription factor binding and other biological functions. KEGG pathway enrichment analysis identified PI3K-Akt signaling pathway, AGE-RAGE signaling pathway, TNF signaling pathway, etc. Molecular docking showed that the main active components of Yangxue Qingnao Granule had good binding activity with the potential targets. Conclusion:Yangxue Qingnao Granule has the characteristics of multi-targets and multi- pathways in the treatment of VaD. It may play a therapeutic role in VaD by inhibiting neuronal apoptosis and reducing inflammatory response.

Network pharmacological mechanism and experimental validation of Yinjiushu in the treatment of non-alcoholic fatty liver disease based on the homology of medicine and food / 国际中医中药杂志

Objective:To the molecular mechanism of Yinjiushu in the treatment of non-alcoholic fatty liver disease (NAFLD) by network pharmacology based on the theory of homology of medicine and food; To conduct experimental verification.Methods:The active components and targets of the Yinjiushu were screened through the TCMSP platform. Cytoscape 3.7.2 was used to construct the "Chinese materia medica-component-target" network of Yinjiushu. The potential targets of NAFLD were obtained by using TTD, GeneCards database and DisGeNET database, and the intersection targets of Yinjiushu and NAFLD were obtained by mapping targets with Venn diagram. The high confidence interaction relationship of intersection targets was obtained in STRING database, and the core targets of Yinjiushu in treating NAFLD were screened out. GO function and KEGG pathway enrichment of common targets were analyzed by David database, and the above results were further verified by animal experiments. The rats were divided into blank group, model group, Western medicine group and Yinjiushu high-, medium- and low-dosage groups according to random number table method, with 8 rats in each group. Except the blank group, rats in other groups were fed with high-fat diet to prepare NAFLD model. Each group was given corresponding drugs for intervention. The rats were weighed regularly. The serum contents of GPT, GOT, TC, TG, IL-6, TNF-α, MPO of rats were detected by ELISA. The liver index was calculated. The degree of fatty degeneration of hepatocytes was observed by HE. The expressions of CAT, NOS3, SOD, PI3K, p-Akt, Akt protein were detected by Western blot.Results:A total of 8 418 NAFLD-related targets, 118 kinds of active components from Yinjiushu, and 137 targets acting on NAFLD were screened. The core targets included IL-6, TNF, VEGFA, TP53, JUN, CAT, NOS3, SOD, etc. 20 related signaling pathways were screened from KEGG enrichment pathway, among which PI3K/Akt pathway, calcium ion pathway, cAMP pathway and TNF pathway may play key roles in the treatment. Yinjiushu was closely related to inflammatory reaction, oxidative stress, angiogenesis, autophagy, cell proliferation, differentiation, metabolism, apoptosis, etc., or it could treat NAFLD by promoting cell apoptosis, inhibiting cell proliferation, inhibiting cell migration, etc. The animal experiment proved that Yinjiushu could reduce the body weight, wet liver weight and liver-body ratio of NAFLD rats, reduce some liver function and blood lipid indexes (GPT, GOT, TG, TC), down-regulate serum IL-6, TNF-α and MPO, up-regulate the expression of CAT, NOS3 and SOD in hepatocytes, and activate the expression of PI3K/Akt key protein.Conclusion:Yinjiushu can play a role in treating NAFLD by inhibiting the release of inflammatory mediators, improving lipid metabolism disorder of hepatocytes, repairing oxidative stress injury and promoting the recovery of liver function.

Discussion on the mechanism of Coptidis Rhizoma- Puerariae Lobamle Radix on diabetic retinopathy and diabetic nephropathy "different diseases with the same treatment" based on network pharmacology and molecular docking / 国际中医中药杂志

Objective:To explore the mechanism of Coptidis Rhizoma- Puerariae Lobamle Radix on the treatment of diabetic retinopathy (DR) and diabetic nephropathy (DN) by means of network pharmacology. Methods:The TCMSP and UniProt databases were used to retrieve the active components and targets of Coptidis Rhizoma and Puerariae Lobamle Radix. GeneCards and OMIM databases were used to search for DR and DN genes, and the online tool Venny was used to obtain intersection targets. Cytoscape 3.8.2 software was used to construct a network diagram of "components-targets", and the STRING platform was used to construct a protein interaction (PPI) network. GO function and KEGG pathway enrichment analysis were carried out through the DAVID annotation database. Molecular docking verification was performed. Results:A total of 18 active components and 74 disease-drug intersection targets were screened out from Coptidis Rhizoma- Puerariae Lobamle Radix. GO functional enrichment analysis showed that intersection targets were mainly concentrated in biological processes such as inflammation and apoptosis, involving cellular components such as extracellular space, plasma membrane, and cytoplasm, and was related to molecular functions such as protein binding, ATP binding, and enzyme binding. Enrichment analysis of KEGG revealed that the intersection target may be related to TNF signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway, etc. The results of molecular docking showed that the core component had a good binding energy with the core targets. Conclusion:Coptidis Rhizoma-Puerariae Lobamle Radix may regulate TNF signal pathway, Toll-like receptor signal pathway and PI3K/Akt signal pathway through TNF, IL6, TP53 and other targets, and play a role in inhibiting cell apoptosis, oxidative stress and reducing inflammation.

Discussion on the mechanism of Yanghe Decoction in treating chronic osteomyelitis based on network pharmacology and molecular docking / 国际中医中药杂志

Objective:To study the active components and their potential mechanism of Yanghe Decoction for the treatment of chronic osteomyelitis (CO) via the methods of network pharmacology and molecular docking.Methods:Active components and action targets of Yanghe Decoction were screened from TCMSP, BATMAN-TCM and relevant literature. GeneCards, OMIM, DisGeNET, and PharmGKB databases were used to predict the targets for the CO. Cytoscape 3.8.0 software and STRING database were used to build the networks of "Chinese materia medica-active components-potential targets" and "protein-protein interaction", and according to topological parameters in the network, the core active components as well as Hub genes were screened. MCODE plug was used to accomplish clustering analysis of protein modules in PPI network. Then, intersection targets were enriched and analyzed by GO and KEGG in KOBAS database. Finally, molecular docking was carried out with the help of Autodock tool platform to predict the binding ability between the main active components and key targets.Results:A total of 120 active components of Yanghe Decoction and 402 targets were obtained; 1 464 CO-related targets were screened, and there were 103 intersection target genes of Yanghe Decoction-CO, 110 active components related to intersection targets, which mainly contained some flavonoids and Phytosterols, such as quercetin, Kaempferol, and Beta-Sitosterol. There were 9 Hub genes, including TNF, IL6, AKT1, etc., and 4 protein modules which involved the regulation of immune inflammatory response, vascular microcirculation, bone development, and formation, material synthesis and metabolism and other physiological processes. 193 signaling pathways and 1 552 GO results were acquired in KOBAS database. Molecular docking results showed that the active compounds had good binding activity with key targets based on the minimum binding energy of less than - 5 kcal/mol.Conclusion:The mechanism in the treatment of CO with Yanghe Decoction is a complex process of multiple components, multiple targets, and multiple pathways. It mainly regulates targets such as TNF, IL-6, CXCL8, VEGFA, and AKT1 through pathways such as TNF signaling pathway, IL-17 signaling pathway, and Toll-like receptors, participating in local inflammatory reactions, microcirculation, and bone cell metabolism in chronic osteomyelitis, and interfering with the immune escape mechanism of pathogenic bacteria.

Discussion on the mechanism of Guizhi Fuling Pills in the treatment of atherosclerosis based on network pharmacology and molecular docking technology / 国际中医中药杂志

Objective:To explore the active components, targets and mechanism of Guizhi Fuling Pills in the treatment of atherosclerosis (AS) based on network pharmacology and molecular docking technology.Methods:The active components and potential target information of Guizhi Fuling Pills in the treatment of AS was obtained using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), SwissTargetPrediction database and Genecards database. The target protein interaction network was constructed by using STRING database. The DAVID database was used to perform the Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment on potential targets. AutoDockVina and PyMOL software were used to verify the molecular docking of the main active components and key targets of Guizhi Fuling Pills.Results:A total of 74 active components, 239 potential targets and 4 710 AS-related disease targets were screened, and 182 intersection targets were obtained. A total of 484 biological process items, 132 molecular function items and 74 cellular component items were obtained by GO functional enrichment analysis, and 116 signal pathways were screened by KEGG enrichment analysis. The results of molecular docking suggested that the active components of Guizhi Fuling Pills have good binding activity to the key intersection targets.Conclusion:The active components of Guizhi Fuling Pills, such as sitosterol and paeoniflorin, mainly treat AS by regulating estrogen signal pathway and inflammatory signal pathway through TNF, VEGFA and other targets.

Mechanism of Ginseng Radix et Rhizoma-Notoginseng Radix et Rhizoma-Chuanxiong Rhizoma medicinal pair in delaying heart aging based on animal experiments and computer verification / 国际中医中药杂志

Objective:To explore the mechanism of Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma medicinal pair in delaying heart aging based on animal experiments, network pharmacology and molecular docking. Methods:Mice were divided into control group, aging group, metformin group and TCM group according to random number table method. All the groups were injected subcutaneously by D-galactose except the control group to build the subacute aging model. Two weeks later, the metformin group was given metformin suspension (150 mg/kg), the TCM group was given Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma lyophilized powder solution (650 mg/kg), and the control group and aging group were given an equivalent volume of ultrapure water by gastric gavage, once a day, six times a week, for 10 weeks. The level of heart TERT mRNA was detected by PCR; the expression of heart p53 was observed by immunohistochemical staining; the morphology of heart tissue was observed by HE staining. TCMSP and SwissTargetPrediciton databases were used to retrieve the active components and targets of Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma medicinal pair; TTD, OMIM, Gene, HAGR, DisGeNET and other data platforms were used to screen the targets of heart aging; after the drug and disease targets were intersected, the active components of them were collected; STRING database, Cytoscape 3.8.0 software, etc. were used to make PPI of the intersection targets, and screen out the key targets; FunRich was used to perform enrichment analysis of cellular components, molecular functions, biological processes, and biological signal pathways for key targets; Schr?dinger Maestro software was used to do the molecular docking of the screened active components and key targets, and docking results were visualized via PyMOL 2.1 software. Results:Experiment results showed that Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma could significantly ameliorate the damage of aging heart tissues, elevate TERT mRNA level, while significantly reducing the positive expression of p53. A total of 32 active components from the medicinal pair were screened, corresponding to 637 target genes. There were 263 targets for heart aging, and 67 intersection targets of drug active component targets and heart aging targets. 31 key targets were obtained after screening. Enrichment analysis showed that molecular functions were related to transcription factor activity and protein-tyrosine kinase activity. Biological processes involved signal transduction and cell communication. Signaling pathways mainly involved PDGFR-beta, PI3K-Akt, S1P1, Glypican, TRAIL, and Glypican 1. The molecular docking results showed that kaempferol, suchilactone, and ginsenoside Rg5_qt in the medicinal pair had a strong binding ability to p53. Conclusion:Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma may achieve the effect of delaying heart aging by inhibiting p53 expression, providing a foundation for further research on mechanism of invigorating qi and activating blood circulation drugs to delay heart aging.

Discussion on the anti-tumor metastasis mechanism of Notoginseng Radix et Rhizoma based on internet pharmacology / 国际中医中药杂志

Objective:To analyze and explore the possible mechanism of anti-tumor metastasis of Notoginseng Radix et Rhizoma using Internet pharmacology. Methods:The active components and targets of Notoginseng Radix et Rhizoma were screened by retrieving Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP). GeneCards database was used to screen the anti-tumor metastasis-related targets, and compounds and disease targets were under mapping analysis. Key targets of Notoginseng Radix et Rhizoma for anti-tumor metastasis were screened through Venn map. With the help of Cytoscape 3.7.2 software, a compound-disease network diagram was constructed. String platform was used to build a PPI network. Bioconductor was used to enrich the target genes for KEGG signaling pathway and GO biological process analysis. Results:Totally 119 active components were selected from Notoginseng Radix et Rhizoma. There were 8 eligible active components, corresponding to 162 related targets, 121 targets related to anti-tumor metastasis, and 30 key targets screened by PPI network, including AKT1, MAPK1, JUN, RELA, IL6, etc. GO enrichment analysis mainly involved biological processes such as cytokine receptor binding, heme binding, RNA polymerase Ⅱ transcription factor binding, ubiquitin protein ligase binding, and steroid hormone receptor activity. 149 signal pathways related to Notoginseng Radix et Rhizoma anti-tumor metastasis were obtained by KEGG enrichment analysis, mainly involving multiple signal pathways, such as AGE-RAGE and PI3K-Akt, and hepatitis B, Kaposi's sarcoma-associated herpes virus infection, human cytomegalovirus infection and other viral infections and various tumors. Conclusion:Notoginseng Radix et Rhizoma can pass multiple active components, such as ginsenoside f2, ginsenoside rh2 β-, sitosterol, stigmasterol and quercetin, and multiple targets, such as AKT1, MAPK1, JUN, RELA and IL6, acting on multiple pathways such as PI3K-Akt, thereby playing the role of anti-tumor metastasis.