Traditional Chinese Medicine Database Research Articles

Network Pharmacology and Absolute Bacterial Quantification-Combined Approach to Explore the Mechanism of Tianqi Pingchan Granule Against 6-OHDA-Induced Parkinson's Disease in Rats.

Parkinson’s disease (PD) is the second most common neurodegenerative disease. Tianqi Pingchan Granule (TPG) is a clinically effective formula of traditional Chinese medicine to treat PD. However, the therapeutic effect and underlying mechanisms of TPG in PD remain unclear. Based on network pharmacology, the corresponding targets of TPG were identified using the Traditional Chinese Medicine Database and Analysis Platform Database. Differentially expressed genes in PD were obtained from the Therapeutic Target Database, Online Mendelian Inheritance in Man, GeneCards, and DrugBank databases. The protein-protein interaction (PPI) networks of intersected targets were constructed using the STRING database and visualized using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, and the pathways directly related to the pathogenesis of PD were integrated manually. Furthermore, in vivo studies were carried out based on network pharmacology. The gut microbiota, peripheral inflammatory cytokines, and glia-mediated neuroinflammation in substantia nigra were evaluated. A total of 99 target genes were intersected between targets of TPG and deferentially expressed genes in PD. The PPI network analysis indicated the proinflammatory cytokine as essential targets. GO and KEGG analyses indicated that inflammatory response and its related signaling pathways were closely associated with TPG-mediated PD treatment. In vivo studies revealed that class Negativicutes and order Selenomonadales decreased, whereas class Mollicutes, order Enterobacteriales, and Mycoplasmatales increased in fecal samples of PD rats via 16S rRNA sequence analysis. Furthermore, the function prediction methods purposely revealed that TPG therapy may be involved in flavonoid biosynthesis, which have anti-inflammatory properties. In addition, in vivo studies revealed that TPG exposure was found to not only attenuate the production of peripheral inflammatory cytokines but also inhibit the activation of microglia and astrocytes in substantia nigra of PD rats. Through network pharmacology and in vivo experiment-combined approach, the mechanisms of TPG in the treatment of PD were revealed, and the role of TPG in the regulation of gut microbiota and inflammatory response was confirmed.

An exploratory study on the mechanism of Huangqi Guizhi Wuwu Decoction in the treatment of neuropathic pain.

Huangqi Guizhi Wuwu Decoction (HGWD) has a definite effect on neuropathic pain (NP), whereas the specific mechanism has not been elucidated. The components and targets in HGWD were collected and identified through System Pharmacology Database (Traditional Chinese Medicine Database and Analysis Platform). Genecards and Online Mendelian Inheritance in Mandatabases were used to search for NP-related genes. The Venn diagram was drawn to get the intersection target. Cytoscape 3.8.0 software was used to construct the compound-disease-target-pathway networks. STRINGdatabase was applied to analyze protein-protein interactionof potential targets. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were used to identify the function of genes related to NP. Finally, molecular docking was performed to visualize the binding mode and affinity between proteins and active ingredients. According to the intersection target of the Venn diagram, the network graph is constructed by Cytoscape and the results show the five compounds, β-sitosterol, (+)-catechin, quercetin, Stigmasterol, kaempferol, and 15 genes (CASP3, FOS, GSK3B, HSP90AA1, IKBKB, IL6, MAPK8, RELA, ICAM1, SELE, ELK1, HSPB1, PRKACA, PRKCA, RAF1) were highly correlated with NP. KEGG and GO of 15 genes results that TNF, IL-17 and MAPK signaling pathway were Significantly related to the pathological mechanism of NP. Molecular docking showed that core genes in this network were IL-6 (TNF andIL-17 signaling pathways), ICAM1 (TNF signaling pathway), and CASP3 (three signal pathways). This study found that the five active compounds, threecore genes, and threesignaling pathwaysmay be the key to the treatment of NP by HGWD.

Utilizing Network Pharmacology and Molecular Docking Integrated Surface Plasmon Resonance Technology to Investigate the Potential Targets and Mechanisms of Tripterygium wilfordii against Pulmonary Artery Hypertension

Background Pulmonary artery hypertension (PAH) is a rare, life-limiting cardiopulmonary disorder characterized by the progressive and remodeling of pulmonary vasculature. Although the development of the technology brings us many approaches for the treatment of PAH, the effect of treatment is unsatisfactory. Tripterygium wilfordii (TW), as a traditional Chinese medicine (TCM), has been widely used in anti-inflammation, anticancer, and other fields. However, the potential of TW in treating PAH is currently unclear. Methods Active ingredients and their corresponding genes were harvested from the Traditional Chinese Medicine Database and Analysis Platform (TCMSP), CTD, and STITCH. Meanwhile, genes associated with PAH were adopted from OMIM and GeneCards databases. Through Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses, potential targeting KEGG pathways and functions were further collected. Then, STRING was used to generate the protein-protein interaction (PPI) network. The “ingredients-targets-pathway” network was built by Cystoscope. Finally, the binding between active ingredients of TW and corresponding targets of PAH was identified via molecular docking technology and surface plasmon resonance (SPR) experiments. Results The network pharmacology analysis revealed 36 active ingredients in TW and 150 potential targets related to the treatment of PAH with TW. Moreover, GO enrichment analysis showed that the key function in molecular function (MF) was related to enzyme binding, the key function in biological process (BP) was related to cellular response to organic substance, and the key function in cellular component (CC) was related to KEGG enrichment analysis and found that it was closely related to the IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and apoptosis. At last, molecular docking results revealed that the main active ingredients of TW had a strong binding ability with the PAH target protein. In addition, the SPR experiment revealed that kaempferol was combined with the CASP3 protein rather than PARP1, while triptolide was combined with PARP1 rather than the CASP3 protein. Conclusion TW may have therapeutic effects on PAH through multitargets and multimethods, which provide a scientific basis for further elaborating the mechanism of Tripterygium wilfordii in the treatment of PAH.

Virtual screening based on pharmacophore model for developing novel HPPD inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for herbicide design. A multilayered virtual screening workflow was constructed by combining two pharmacophore models based on ligand and crystal complexes, molecular docking, molecular dynamics (MD), and biological activity determination to identify novel small-molecule inhibitors of HPPD. About 110, 000 compounds of Bailingwei and traditional Chinese medicine databases were screened. Of these, 333 were analyzed through docking experiments. Five compounds were selected by analyzing the binding pattern of inhibitors with amino acid residues in the active pocket. All five compounds could produce stable coordination with cobalt ion, and form favorable π-π interactions. MD simulation demonstrated that Phe381 and Phe424 made large contributions to the strength of binding. The enzyme activity experiment verified that compound-139 displayed excellent potency against AtHPPD (IC50 = 0.742 μM), however, compound-5222 had inhibitory effect on human HPPD (IC50 = 6 nM). Compound-139 exhibited herbicidal activity to some extent on different gramineous weeds. This work provided a strong insight into the design and development of novel HPPD inhibitor using in silico techniques.

Anticolon Cancer Targets and Molecular Mechanisms of Tao-He-Cheng-Qi Formula.

Background Tao-He-Cheng-Qi Formula (THCQF) is a traditional Chinese medicine that has been proven to have antitumor effects. The aim of this study was to elucidate the molecular targets and mechanisms of THCQF against colon cancer and construct a prognostic model based on network pharmacology, bioinformatics analysis, and in vitro experiments. Methods Potential THCQF compounds and targets were retrieved from the Traditional Chinese Medicine Systems Pharmacology and Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine databases. Differentially expressed genes for colon cancer were screened in The Cancer Genome Atlas and Gene Expression Omnibus databases. The anticolon cancer mechanisms of THCQF were explored using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Molecular docking simulations and molecular dynamics analysis were used to evaluate the binding between target proteins and active compounds. Finally, the identified compounds were used to treat colon cancer cells from the HCT116 cell line, and expression of mRNA and protein after relevant posttreatment were tested using real-time polymerase chain reaction and western blotting. Results A total of 27 anticolon cancer targets of THCQF were selected, among which four genes (CCNB1, CCNA2, IL1A, and MMP3) were shown to effectively predict patient outcomes in a prognostic colon cancer model. GO and KEGG enrichment analyses indicated that the activity against colon cancer of THCQF was associated with the interleukin (IL)-4 and IL-3 signaling pathways. Two compounds in THCQF, aloe emodin (AE) and quercetin (QR), were shown to efficiently bind to cyclin B1, the protein encoded by CCNB1. Finally, incubation of HCT116 cells with AE and QR significantly decreased CCNB1 mRNA expression and cyclin B1 levels. Conclusions Taken together, the results indicate that AE and QR are the pivotal active compounds of THCQF, and CCNB1 is the main molecular target through which THCQF exerts its anticolon cancer effects. The study findings provide insight for studies investigating the anticancer effects of other traditional Chinese medicines.

Combined multi-omics and network pharmacology approach reveals the role of Tripterygium Wilfordii Hook F in treating HIV immunological non-responders

BackgroundThe HIV-1 infected immunological non-responders (INRs) are characterized by poor immune reconstitution after long-term treatment. Tripterygium Wilfordii Hook F (TwHF) pill is a traditional Chinese patent drug with extensive immunosuppressive effects and has been clinically proven efficacy in treating INRs. PurposeThe therapeutic mechanism of TwHF pills in the treatment of INRs was investigated by the combined multi-omics analysis on clinical samples and network pharmacology approach. MethodsClinically, the peripheral blood mononuclear cells (PBMC) samples of TwHF-treated INRs from different time points were collected to conduct the transcriptomic and proteomic profiling. Key effector pathways of TwHF were enriched and analyzed by the ingenuity pathway analysis (IPA). Computationally, the TwHF-related compounds were obtained from traditional Chinese medicine databases, and literature search and structural prediction were performed to identify TwHF-related targets. Integrated with the INR-related targets, the 'TwHF-compounds-targets-INR' network was constructed to analyze core effector targets by centrality measurement. Experimentally, the effects of TwHF compounds on the T cells activation and expression of identified targets were evaluated with in vitro cell culture. Results33 INRs were included and treated with TwHF pills for 17 (IQR, 12–24) months. These patients experienced rapid growth in the CD4+ T cell counts and decreased T cell activation. The multi-omics analysis showed that the interferon (IFN)-signaling pathway was significantly inhibited after taking TwHF pills. The network pharmacology predicted the central role of the signal transducer and activator of transcription 1 (STAT1) in the 'TwHF-compounds-targets-INR' network. Further bioinformatic analysis predicted STAT1 would regulate over 58.8% of identified down-regulated genes. Cell experiments validated that triptolide (TPL) would serve as the major bioactivity compound of TwHF pills to inhibit the immune cell activation, the production of IFN-γ, the expression of downstream IFN-stimulated genes, and the phosphorylation of STAT1. ConclusionOur research is the first to systemic verify the mechanisms of TwHF in treating INRs. The IFN signaling pathway and the STAT1 would be the major effector targets of TwHF pills in treating INRs. The TPL would be the major bioactive compound to inhibit the IFN response and the phosphorylation of STAT1. Our observations suggest the basis for further application of TPL analogous in treating INRs.

Network Pharmacology-Based Prediction and Verification of the Potential Targets of Pinoresinol Diglucoside for OA Treatment.

Objective This study aimed to explore the effects and related mechanisms of pinoresinol diglucoside (PDG) on osteoarthritis (OA) via a combination of pharmacology and animal experiments. Methods Traditional Chinese Medicine Database and Analysis Platform (TCMSP) Drugbank, Online Mendelian Inheritance in Man, and GeneCards databases were used to predict the putative targets of PGD against OA. A protein protein interaction (PPI) network was constructed in STING database to analyze the interaction network of these targets. Enrichment analysis was performed with DAVID database. The OA model was built by anterior cruciate ligament transection and then injected with PDG for 5 weeks. Hematoxylin and eosin (HE) staining and safranin-fixed green staining were used to evaluate the pathological change. ELISA was applied to measure the serum levels of interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α). Immunohistochemistry was employed to detect the protein levels of kinase B (AKT), BAX, Bcl2, matrix metalloproteinase-1 (MMP-1), tissue inhibitor of metalloproteinases 1 (TIMP-1), and phosphatidylinositol 3 kinase (PI3K) in knee cartilage tissues. Results Seventy-one key targets were identified, including AKT1, epidermal growth factor receptor, SRC, estrogen receptor 1 (ESR1), and MMP9. Enrichment analysis revealed a series of pathway related to cancer, PI3K-Akt signaling pathway, and proteoglycans in cancer. Animal experiments showed that PDG alleviated the abnormal histomorphological changes of OA; suppressed TIPM, serum IL-1β, IL-6, and TNF-α levels, and PI3K and AKT activation; and increased MMP-1 expression and Bcl2/Bax ratio. Conclusion PDG has a cartilage-protecting effect associated with PI3K/AKT signaling pathway in rabbit with OA and therefore might serve as a potential agent for the treatment of this disease.

Mechanism of Ba Zhen Tang Delaying Skin Photoaging Based on Network Pharmacology and Molecular Docking

PurposeTo study the efficacy of Ba Zhen Tang in delaying skin photoaging and its potential mechanism based on network pharmacology and molecular docking.MethodsFirst, we screened the active components and targets of Ba Zhen Tang by Traditional Chinese Medicine Database and Analysis Platform (TCMSP) and The Universal Protein Resource (UniProt). The target genes of skin photoaging were obtained from GeneCards and GeneMap database. Then, we analyzed the protein–protein interaction (PPI) by STRING database. The network map was constructed by Cytoscape. Finally, we performed Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis by Metascape database. The molecular docking via Autodock Vina and Pymol. Furthermore, skin photoaging cellular models were established, and the effects of Ba Zhen Tang on ameliorating skin photoaging were investigated.ResultsA total of 160 active ingredients in Ba Zhen Tang and 60 targets of Ba Zhen Tang for delaying skin photoaging were identified. By GO enrichment analysis, 1153 biological process entries, 45 cellular component entries and 89 molecular functional entries were obtained. A total of 155 signal pathways were obtained by KEGG analysis. Ba Zhen Tang is related to MAPK signaling pathway, TNF signaling pathway and AGE-RAGE signaling pathway in diabetic complications, etc., which directly affect the key nodes of photoaging. The molecular docking results showed that there was a certain affinity between the main compounds (kaempferol, quercetin, β-sitosterol, naringenin) and core target genes (PTGS2, CASP3, MAPK1, MAPK3, TP53). Ba Zhen Tang-treated mouse serum inhibited the senescence and p16INK4a expression of human immortalized keratinocyte (HaCaT) cells irradiated by ultraviolet-B (UVB).ConclusionOur study elucidated the potential pharmacological mechanism of Ba Zhen Tang in the treatment of photoaging through multiple targets and pathways. The therapeutic effects of Ba Zhen Tang on skin photoaging were validated in cellular models.

English

Numerous studies have shown that the rhizosphere allelochemicals closely related to the formation of replant problems in Pseudostellaria heterophylla. In this study, ultra-high performance liquid chromatography-quadrupole time-of-flight mass technology was employed to screen the specific compounds in rhizosphere soil induced the formation of replant disease. Simultaneously, the compounds in cultured seedling of P. heterophylla and corresponding medium were identified using the identical methods to obtain compounds that had not been transformed or degraded by soil microbes. As a result, 176 specific molecules were identified in the rhizosphere soil, 1,011 in the rhizosphere tissue culture medium and 1,447 in plant tissue cultures were obtained by matching to the Traditional Chinese Medicine database. Further analysis found that 21 potential allelochemicals might be directly secreted from P. heterophylla plants, which had not been transformed or degraded in theory. Of which, 13 compounds possessed the allelopathic characteristics based on structural analysis that have been identified in other plants. Simultaneously, eight compounds were only present in the rhizosphere tissue culture medium and plant tissue cultures also were found to possess the allelopathic properties. This study provides an important reference for further screening and identification of specific allelochemicals that related closely to the formation of replant problems in P. heterophylla. © 2022 Friends Science Publishers

Pharmacological systemic analysis of gardenia fructus against non-alcoholic fatty liver disease and validation of animal models.

[Purpose]We aimed to investigate the systemic pharmacological analysis of gardenia fructus (GF) and the proof of concepts. We examined the antioxidant and anti-inflammatory effects in high-fat (HF) diet mice.[Methods]The active compounds of GF and the target genes were identified using the Traditional Chinese Medicine Database and Analysis Platform (oral bioavailability ≥ 30%, Caco-2 permeability ≥ -0.4, and drug-likeness ≥ 0.18). The rats were divided into four groups: untreated group, HF group, HF and metformin (17 mg/kg) treated group, and HF and treated with GF (28 mg/kg) for 8 weeks group. Hepatic lesion changes and markers were analyzed using hematoxylin and eosin staining and immunohistochemistry assay.[Results]In the systemic analysis, we identified 14 active compounds including A, B, and C. From these 14 compounds, 242 biological target genes were identified. The top 10 Gene Ontology were analyzed using GO-biological process analysis: removal of superoxide radicals, regulation of endothelial cell apoptotic process, and cellular response to lipopolysaccharide. GF extracts in high-fat diet-induced non-alcoholic fatty liver disease (NAFLD) mice models significantly regulated hepatic lesion markers, such as mTOR, 8-Hydroxy-2'-deoxyguanosine as well as oxidative stress activities, TGF-β, and phosphorylation of ERK1/2.[Conclusion]These results suggest that GF, as an exercise supplement, can alleviate NAFLD disease or fatty liver inflammation. Further studies are required to verify the synergistic effect of GF treatment combined with exercise, which is known to alleviate NAFLD and fatty liver inflammation.

Identification of Key Drug Targets and Molecular Mechanisms of Curcumae Rhizoma Acting on HBV-Related HCC: Weighted Correlation Network and Network Pharmacological Analyses.

Background Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) has poor prognosis and high mortality rate. Curcumae Rhizoma, a classic Chinese medicinal herb, is often used to treat tumors. Methods Active ingredients of Curcumae Rhizoma were extracted from the Traditional Chinese Medicine Database and Analysis Platform (TCMSP) database, and potential targets were predicted by the TCMSP database and Swiss Target Prediction database. The key drug targets were filtered by intersecting predicted targets, DEGs, and genes in important modules from WGCNA. Besides, the key drug targets were used to construct a network of “herb-active ingredient-target-disease” interactions and subjected to enrichment analysis and protein-protein interaction (PPI) analysis. The hub targets based on PPI analysis was evaluated by the KMplotter database. Results Three active ingredients of Curcumae Rhizoma were collected with OB ≥ 30% and DL ≥ 0.18, including hederagenin, wenjine, and bisdemethoxycurcumin. The key drug targets were mainly enriched in cell cycle checkpoint, DNA integrity checkpoint, and peptidyl-serine modification. Besides, Curcumae Rhizoma treatment of HBV-related HCC mainly involved the p53 signaling pathway and arachidonic acid metabolism. Finally, ESR1 and PTGS2 were identified as hub targets from PPI analysis. ESR1 was found to be correlated with survival in liver cancer patients with hepatitis. Conclusion Based on WGCNA and network pharmacological analysis, our results illustrated that Curcumae Rhizoma might work through regulating multitargets and multipathways in HBV-related HCC.

Unveiling Potential Mechanisms of Spatholobi Caulis against Lung Metastasis of Malignant Tumor by Network Pharmacology and Molecular Docking.

Background Lung metastasis of malignant tumor signifies worse prognosis and immensely deteriorates patients' life quality. Spatholobi Caulis (SC) has been reported to reduce lung metastasis, but the mechanism remains elusive. Methods The active components and corresponding targets of SC were obtained from the Traditional Chinese Medicine Database and Analysis Platform (TCMSP) database and the SwissTargetPrediction database. The disease targets were acquired from DisGeNET and GeneCards databases. Venn map was composed to figure out intersection targets by using R. The PPI network was constructed through STRING and Cytoscape, and MCODE plug-in was used to sift hub targets. Gene Ontology (GO)-Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was carried out by utilizing clusterProfiler package (R3.6.1) with adjusted P value <0.05. Network of SC-active components-intersection targets-KEGG pathway was accomplished with Cytoscape. Molecular docking between hub targets and active components was performed, analyzed, and visualized by AutoDockTools, AutoDock Vina, PLIP Web tool, and PYMOL. Results 24 active components and 123 corresponding targets were screened, and the number of disease targets and intersection targets was 1074 and 47, respectively. RELA, JUN, MAPK1, MAPK14, STAT3, IL-4, ESR1, and TP53 were the 8 hub targets. GO analysis and KEGG analysis elucidated that SC could ameliorate lung metastasis mainly by intervening oxidative stress, AGE-RAGE signaling pathway, and microRNAs in cancer. All 8 hub targets were proven to combine successfully with active components of SC. Conclusion Inflammation is the core factor that integrates all these targets, biological process, and signaling pathways, which indicates that SC prevents or reduces lung metastasis mainly by dispelling inflammation.

LTM-TCM: A comprehensive database for the linking of Traditional Chinese Medicine with modern medicine at molecular and phenotypic levels

Benefiting from the development of network pharmacology, Traditional Chinese Medicine (TCM) shows great potential in modern drug discovery. Recently, more and more TCM-related databases have been established for both academic and industry research, but they are still insufficient in data standardization, integrity, and precision. To better accelerate the TCM research and overcome these shortcomings, we construct a web-based TCM platform, LTM-TCM, which is currently the most comprehensive TCM database that includes the following advantages: (1) High-quality data integration from fourteen TCM authoritative databases, especially with additional manual collected 41,025 clinical treatment records and 213 ancient Chinese medical books. (2) Accurate correction of multi-source TCM interactions (between symptoms, prescriptions, herbs, ingredients and targets) through in-house Biomedical Natural Language Processing (BioNLP) approaches in more than 30 million articles. (3) Diverse cross-field pipelines (e.g., bioactive ingredients screening, targets prediction, and mechanism prediction, etc.) help integrating traditional medicine with modern science in common aspects at both the molecular and phenotypic levels. In summary, LTM-TCM contains 1928 symptoms, 48,126 prescriptions, 9122 plants, 34,967 ingredients, 13,109 targets and 1170,133 interactions among all TCM related components. LTM-TCM has both Chinese and English interfaces, and it is accessible at http://cloud.tasly.com/#/tcm/home.

Data-mining-based of ancient traditional Chinese medicine records from 475 BC to 1949 to potentially treat COVID-19.

Traditional Chinese Medicine (TCM) plays a role in preventing and treating COVID‐19 in China. Based on the manifestations and symptoms of COVID‐19, our study used the data mining method to summarize related therapeutic experience left by predecessors who used TCM to treat epidemics in their eras. Initially, we collected abundant medical records with similar manifestations of COVID‐19 in Chinese ancient times. The key words including wen (瘟), yi (疫), li (疠), and zhang (瘴) were searched in ZhongyiZhiku (https://www.zk120.com/) from Warring States Period (475 BC–221 BC) to the Republic of China era (1912–1949) to locate ancient medical records according to inclusion criteria and exclusion criteria. Moreover, COVID‐19‐related manifestations and corresponding medications in those records were categorized. Eventually, Traditional Chinese Medicine Inheritance Support System version 2.5 was used to build a medical record database of TCM treating COVID‐19. Our study collected 263 epidemic medical records comprising COVID‐19 related manifestations and found that Chinese Materia Medica (CMM) combinations excavated from ancient medical records included Ren Shen Bai Du San, Wu Ling San, Xiao Chai Hu Tang, Da Cheng Qi Tang, Da Chai Hu Tang, Ling Gui Zhu Gan Tang, and Qing Wen Bai Du Yin. The recurrent CMMs with a high frequency for treating COVID‐19 manifestations were Scutellariae Radix (Huang Qin), Paeoniae Alba Radix (Bai Shao), Poria (Fu Ling), and Bupleuri Radix (Chai Hu). Our study suggests that TCM might offer new therapeutic strategies for COVID‐19.

Network pharmacology and molecular docking analysis on molecular targets and mechanism prediction of Huanglian Jiedu Decoction in the treatment of COVID-19

ObjectiveTo investigate and predict the molecular targets and mechanism of Huanglian Jiedu Decoction (黄连解毒汤, HLJDD) in the treatment of Corona Virus Disease 2019 (COVID-19) through network pharmacology and molecular docking analysis. MethodsThe chemical constituents and action targets of HLJDD were retrieved on Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), SymMap v2, Encyclopedia of Traditional Chinese Medicine (ETCM), a High-throughput Experiment- and Reference-guided Database of Traditional Chinese Medicine (HERB), and Traditional Chinese Medicine Integrated Database (TCMID). UniProt and GeneCards were used to query the target genes that corresponding to the active compounds, and then a compound-target network was constructed using Cytoscape 3.7.2. Gene Ontology (GO) database was used to annotate GO functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to predict the possible mechanisms of active compounds. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to analysis the tissue enrichment. The main active compounds in HLJDD are molecularly docked with their corresponding related targets. ResultsSeventy-six compounds were screened and 458 corresponding targets in the network were obtained. Gene annotation showed that the targets were involved mainly in 1953 biological processes. 884 signaling pathways was enriched, involving signaling by interleukins, cytokine signaling in immune system, generic transcription pathway, and RNA polymerase II transcription. The targets mainly distributed in the lung, liver, and placenta, involving a variety of immune cells, such as T cells and B cells. The molecular docking results showed that core compounds such as wogonin, berberine, and baicalein had high affinity with tumor necrosis factor (TNF), insulin (INS), and tumor protein 53 (TP53). ConclusionThe active compounds in HLJDD may have a therapeutic effect on COVID-19 through regulating multiple signal pathways by targeting genes such as vascular endothelial growth factor A (VEGFA), INS, interleukin-6 (IL-6), TNF, caspase-3 , TP53, and mitogen-activated protein kinase 3 (MAPK3).

Using Network Pharmacology to Systematically Decipher the Potential Mechanisms of Jisuikang in the Treatment of Spinal Cord Injury.

Objective To identify the potential pharmacological targets of Jisuikang (JSK) for the treatment of spinal cord injury (SCI) using network pharmacology. Methods The bioactive compounds of JSK herbs and their corresponding potential SCI targets were obtained from three traditional Chinese medicine (TCM) databases. SCI-related therapeutic target genes were obtained from the Comparative Toxicogenomics Database and the GeneCards Database. The common target genes between the JSK compounds and SCI-related therapeutic targets were screened using GO/KEGG functional enrichment and protein-protein interaction (PPI) analyses to identify hub genes and their categories of biological function. Gene expression distribution and receiver operating characteristic curve (ROC) analyses were used to identify probable SCI-related target genes. Molecular docking was used to quantify molecular interactions between target genes and the bioactive compounds of JSK. Results A total of 183 JSK bioactive compounds and 197 target genes for the treatment of SCI were screened and assessed. The target genes were enriched primarily in drug metabolism and in inflammation-related biological processes. Ten genes with statistical significance were identified as therapeutic SCI-related target genes of JSK. Molecular docking experiments demonstrated that the proteins of these 10 genes docked with binding energies of less than −5 kcal/mol with the bioactive compounds in JSK. Conclusion This study showed that the anti-SCI effects of JSK may be mediated through numerous bioactive components, multiple gene targets, and inflammation-related pathways and provided potential novel targets for directed therapies for treating SCI. These results provide a foundation for further experimental investigations into treatment options for SCI.

New Approach for Targeted Treatment of Mild COVID-19 by Honeysuckle through Network Pharmacology Analysis.

Objective To investigate the potential pharmacological value of extracts from honeysuckle on patients with mild coronavirus disease 2019 (COVID-19) infection. Methods The active components and targets of honeysuckle were screened by Traditional Chinese Medicine Database and Analysis Platform (TCMSP). SwissADME and pkCSM databases predict pharmacokinetics of ingredients. The Gene Expression Omnibus (GEO) database collected transcriptome data for mild COVID-19. Data quality control, differentially expressed gene (DEG) identification, enrichment analysis, and correlation analysis were implemented by R toolkit. CIBERSORT evaluated the infiltration of 22 immune cells. Results The seven active ingredients of honeysuckle had good oral absorption and medicinal properties. Both the active ingredient targets of honeysuckle and differentially expressed genes of mild COVID-19 were significantly enriched in immune signaling pathways. There were five overlapping immunosignature genes, among which RELA and MAP3K7 expressions were statistically significant (P < 0.05). Finally, immune cell infiltration and correlation analysis showed that RELA, MAP3K7, and natural killer (NK) cell are with highly positive correlation and highly negatively correlated with hematopoietic stem cells. Conclusion Our analysis suggested that honeysuckle extract had a safe and effective protective effect against mild COVID-19 by regulating a complex molecular network. The main mechanism was related to the proportion of infiltration between NK cells and hematopoietic stem cells.

Antidiabetic potential of Catechu via assays for α-glucosidase, α-amylase, and glucose uptake in adipocytes

Ethnopharmacological relevanceCatechu is the dry water extract of barked branches or stems from Senegalia catechu(L. F.)P. J. H. Hurter & Mabb, which is used as a hypoglycemic regulator in recent researches. Potential anti-hyperglycemic components and the putative mechanisms were evaluated in this investigation. Aim of the studyEvaluated the hypoglycemic activity of Catechu via α-glucosidase, α-amylase inhibition assays, and glucose uptake in 3T3-L1 adipocytes. Materials and methodsThe effects of Catechu on α-glucosidase, α-amylase inhibition assays and glucose uptake experiment were tested after the ethanol extract of Catechu (EE) was sequentially partitioned with petroleum ether (PEE), ethyl acetate (EAE), and n-butanol fractions (NBE). Next, HPLC-MS and traditional Chinese medicine (TCM) database were used to detect and analyze the primary active ingredients presented in hypoglycemic fraction. In addition, in silico molecular docking study was used to evaluate the candidates' inhibitory activity against α-glucosidase and α-amylase. ResultsThe results of α-glucosidase and α-amylase inhibition assays indicated that all fractions, with the exception of PEE, presented significant inhibitory effects on α-glucosidase and α-amylase. The inhibitory effect of NBE on α-glucosidase was similar to the positive control (NBE IC50 = 0.3353 ± 0.1215 μg/mL; Acarbose IC50 = 0.1123 ± 0.0023 μg/mL). Furthermore, the inhibitory kinetics of α-glucosidase revealed that all fractions except for PEE belong to uncompetitive type. In silico molecular docking analysis showed that the main compositions of NBE ((−)-epicatechin, cyanidin, and delphinidin) possessed superior binding capacities with α-glucosidase (3WY1 AutoDock score: 4.82 kcal/mol; −5.59 kcal/mol; −5.63 kcal/mol) and α-amylase (4GQR AutoDock score: 4.80 kcal/mol; −5.89 kcal/mol; −4.26 kcal/mol), respectively. The results of glucose uptake experiment indicated that EE, PEE, EAE, and NBE without significant promotion effect on glucose uptake rate of 3T3-L1 adipocytes (P > 0.05). ConclusionThis study revealed that the hypoglycemic effect of Catechu might be related to the inhibitory effects of phenols on digestive enzymes (α-glucosidase and α-amylase), and the possible active phenols were (−)-epicatechin, cyanidin, delphinidin and their derivatives, which provided scientific evidences for Catechu's traditional use to treat T2DM.

Network Pharmacology Combined with Molecular Docking and Experimental Verification Reveals the Bioactive Components and Potential Targets of Danlong Dingchuan Decoction against Asthma.

Background Danlong Dingchuan Decoction has a definite effect in the clinical treatment of asthma. This study aimed to explore the material and molecular biological basis of Danlong Dingchuan Decoction in treating asthma through network pharmacology combined with animal experiments. Materials and Methods First, the chemical constituents of Danlong Dingchuan Decoction were screened from the Traditional Chinese Medicine Systematic Pharmacology Analysis Platform (TCMSP) and the Traditional Chinese Medicine and Chemical Composition Database. Literature reports on asthma targets were obtained from the Online Mendelian Inheritance in Man (OMIM), Therapeutic Targets Database (TTD), and other databases. Then, the protein-protein interaction network was constructed according to the matching results of Danlong Dingchuan Decoction and asthma targets. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Finally, the interaction between the active compounds of Danlong Dingchuan Decoction and key targets was simulated using molecular docking. In animal experiments, ovalbumin was used to induce asthma in mice. After treating the mice by oral gavage administration of Danlong Dingchuan Decoction, the expression levels of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were detected in the lung tissue of the mice by enzyme-linked immunosorbent assay kit, whereas TLR4 mRNA expression was detected by quantitative reverse transcription-polymerase chain reaction. Results A total of 247 active compounds and 155 potential targets were obtained. Enrichment analysis showed that quercetin, xanthine, lysine, kaempferol, ß-sitosterol, and four other active compounds were the main components of Danlong Dingchuan Decoction; IL-6, TNF, CXCL8, VEGFA, MAPK3, IL-10, PTGS2, IL-1β, IL-4, and TLR4 were the potential targets for therapy. KEGG analysis showed that the cAMP signaling pathway, cGMP-PKG signaling pathway, NF-κB signaling pathway, and PI3K-Akt signaling pathway might play an important role in treating asthma. Molecular docking analysis showed that quercetin combined well with TNF, CXCL8, and TLR4. Animal experiments showed that Danlong Dingchuan Decoction effectively reduced the expression levels of TNF-α, IL-4, TGF-β1, IL-6, IL-8, and IL-1β in the lung tissue of asthmatic mice and inhibited TLR4 mRNA expression. Conclusions Danlong Dingchuan Decoction may act on key targets (such as IL-6, TNF, CXCL8, VEGFA, and MAPK3) with key active ingredients (such as quercetin, xanthine, lysine, kaempferol, and ß-sitosterol) to reduce the expression levels of IL-4, IL-6, IL-8, and other Th2 cytokines. This may be the mechanism by which Danlong Dingchuan Decoction reduces airway inflammation and treats asthma mediated by Th2 cytokines.

A network pharmacology approach to explore active compounds and pharmacological mechanisms of a patented Chinese herbal medicine in the treatment of endometriosis.

ObjectiveEndometriosis is a common benign disease in women of reproductive age. Qu’s formula (QUF) is a patented Chinese herbal medicine for treating endometriosis that has been proven to be effective in treating and preventing the recurrence of endometriosis. This study is aimed to discover its molecular mechanism and to explore the potential drug targets.MethodsA QUF target and endometriosis-related gene set was identified by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM) databases and five disease-gene databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed, and a protein–protein interaction (PPI) network was established to discover the potential mechanism. MalaCards was searched for targets and signaling pathways related to endometriosis, and the search results were also used to identify the key factors in QUF. Molecular docking was performed to visualize the interactions between the effective molecules and proteins encoded by critical genes. Cell experiments and molecular dynamics (MD) simulations were used to further validate the therapeutic effects of the active compounds in QUF on endometriosis.ResultsA compound-target network with 117 nodes (94 genes and 23 active compounds) and 224 edges was generated. The results of GO and KEGG analyses indicated that QUF could act by regulating the immune response, apoptosis and proliferation, oxidative stress, and angiogenesis. VEGFA, CXCL8, CCL2, IL1B and PTGS2 were selected for molecular docking analysis from two critical subnetworks with high correlation scores in MalaCards, and the active compounds of QUF had binding potential and high affinity for them. The mRNA expression levels of CCL2, IL1B and PTGS2 significantly decreased after treatment with quercetin. MD simulations showed that the combinations of quercetin and these proteins were relatively stable.ConclusionThe network pharmacological strategy integrates molecular docking to unravel the molecular mechanism by which QUF protects against endometriosis. Our findings not only confirm the clinical effectiveness of QUF but also provide a foundation for further experimental study.