Network pharmacology-based identification of the key mechanism of Qinghuo Rougan Formula acting on uveitis

Integrated Approaches Revealed the Therapeutic Mechanisms of Zuojin Pill Against Gastric Mucosa Injury in a Rat Model with Chronic Atrophic Gastritis

Background

The Zuojin Pill (ZJP) is widely used for treating chronic atrophic gastritis (CAG) in clinical practice, effectively ameliorating symptoms such as vomiting, pain, and abdominal distension in patients. However, the underlying mechanisms of ZJP in treating CAG has not been fully elucidated.

Purpose

This study aimed to clarify the characteristic function of ZJP in the treatment of CAG and its potential mechanism.

Methods

The CAG model was established by alternant administrations of ammonia solution and sodium deoxycholate, as well as an irregular diet. Therapeutic effects of ZJP on body weight, serum biochemical indexes and general condition were analyzed. HE staining and AB-PAS staining were analyzed to characterize the mucosal injury and the thickness of gastric mucosa. Furthermore, network pharmacology and molecular docking were used to predict the regulatory mechanism and main active components of ZJP in CAG treatment. RT-PCR, immunohistochemistry, immunofluorescence and Western blotting were used to measure the expression levels of apoptosis-related proteins, gastric mucosal barrier-associated proteins and PI3K/Akt signaling pathway proteins.

Results

The results demonstrated that ZJP significantly improved the general state of CAG rats, alleviated weight loss and gastric histological damage and reduced the serum biochemical indicators. Network pharmacology and molecular docking found that ZJP in treating CAG by inhibiting inflammation, suppressing apoptosis, and protecting the gastric mucosal barrier via the PI3K/Akt signaling pathway. Further experiments confirmed that ZJP obviously modulated the expression of key proteins involved in gastric mucosal cell apoptosis, such as Bax, Bad, Apaf-1, cleaved-caspase-3, cleaved-caspase-9, Cytochrome C, Bcl-2, and Bcl-xl. Moreover, ZJP significantly reversed the protein expression of Occludin, ZO-1, Claudin-4 and E-cadherin.

Conclusion

Our study revealed that ZJP treats CAG by inhibiting the PI3K/Akt signaling pathway. This research provided a scientific basis for the rational use of ZJP in clinical practice.

Monochasma savatieri Franch. protects against acute lung injury via α7nAChR-TLR4/NF-κB p65 signaling pathway based on integrated pharmacology analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Acute lung injury (ALI) is a life-threatening condition with high morbidity and mortality, underscoring the urgent need for novel treatments. Monochasma savatieri Franch. (LRC) is commonly used clinically to treat wind-heat cold, bronchitis, acute pneumonia and acute gastroenteritis. However, its role in the treatment of ALI and its mechanism of action are still unclear.

AIM OF THE STUDY

This study aimed to demonstrate the pharmacological effects and underlying mechanisms of LRC extract, and provide important therapeutic strategies and theoretical basis for ALI.

MATERIALS AND METHODS

In this study, a research paradigm of integrated pharmacology combining histopathological analysis, network pharmacology, metabolomics, and biochemical assays was used to elucidate the mechanisms underlaying the effects of LRC extract on LPS-induced ALI in BALB/c mice.

RESULTS

The research findings demonstrated that LRC extract significantly alleviated pathological damage in lung tissues and inhibited apoptosis in alveolar epithelial cells, and the main active components were luteolin, isoacteoside, and aucubin. Lung tissue metabolomic and immunohistochemical methods confirmed that LRC extract could restore metabolic disorders in ALI mice by correcting energy metabolism imbalance, activating cholinergic anti-inflammatory pathway (CAP), and inhibiting TLR4/NF-κB signaling pathway.

CONCLUSIONS

This study showed that LRC extract inhibited the occurrence and development of ALI inflammation by promoting the synthesis of antioxidant metabolites, balancing energy metabolism, activating CAP and suppressing the α7nAChR-TLR4/NF-κB p65 signaling pathway. In addition, our study provided an innovative research model for exploring the effective ingredients and mechanisms of traditional Chinese medicine. To the best of our knowledge, this is the first report describing the protective effects of LRC extract in LPS-induced ALI mice.

Protective effects of triptolide against oxidative stress in retinal pigment epithelium cells via the PI3K/AKT/Nrf2 pathway: a network pharmacological method and experimental validation

PURPOSE

Among aging adults, age-related macular degeneration (AMD), is a prevalent cause of blindness. Nevertheless, its progression may be halted by antioxidation in retinal pigment epithelium (RPE). The primary effective constituent of Tripterygium wilfordii Hook. F., triptolide (TP), has demonstrated anti-inflammatory, antiproliferative, and antioxidant properties. The mechanics of the protective effect of triptolide against the oxidative damage in retinal pigment epithelial (RPE) were assessed in this study.

METHODS

ARPE-19 cells were pretreated with TP, and then exposed to sodium iodate (SI). First, cell viability was assessed using CCK-8. Subsequently, we measured indicators for cell oxidation including reactive oxygen species (ROS), catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA). Then, we used network pharmacological analysis and molecular docking to explore the signaling pathway of TP. Last, we used western blot, ELISA, and immunofluorescence assays to clarify the potential mechanistic pathways.

RESULTS

The network pharmacology data suggested that TP may inhibit AMD by regulating the PI3K/Akt signaling pathway. Experimental results showed that the potential mechanism is that it regulates the PI3K/Akt pathway and promotes Nrf2 phosphorylation and activation, thereby raising the level of antioxidant factors (HO-1, NQO1) and reducing the generation of ROS, which inhibit oxidative damage.

CONCLUSION

Our findings suggested that the effect of TP on SI-exposed RPE cells principally relies on the regulation of oxidative stress through the PI3K/Akt/Nrf2 signaling pathway.

Mechanism underlying the effect of Pulsatilla decoction in hepatocellular carcinoma treatment: a network pharmacology and in vitro analysis

BACKGROUND

Currently, hepatocellular carcinoma (HCC) is associated with a poor prognosis. Moreover, there exist limited strategies for treating HCC. Pulsatilla decoction (PD), a traditional Chinese medicine formula, has been used to treat inflammatory bowel disease and several cancer types. Accordingly, we explored the mechanism of PD in HCC treatment via network pharmacology and in vitro experiments.

METHODS

Online databases were searched for gene data, active components, and potential target genes associated with HCC development. Subsequently, bioinformatics analysis was performed using protein-protein interaction and Network Construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) to screen for potential anticancer components and therapeutic targets of PD. Finally, the effect of PD on HCC was further verified by in vitro experiments.

RESULTS

Network pharmacological analysis revealed that 65 compounds and 180 possible target genes were associated with the effect of PD on HCC. These included PI3K, AKT, NF-κB, FOS, and NFKBIA. KEGG analysis demonstrated that PD exerted its effect on HCC mainly via the PI3K-AKT, IL-17, and TNF signaling pathways. Cell viability and cell cycle experiments revealed that PD could significantly inhibit cancer cell proliferation and kill HCC cells by inducing apoptosis. Furthermore, western blotting confirmed that apoptosis was mediated primarily via the PI3K-AKT, IL-17, and TNF signaling pathways.

CONCLUSION

To the best of our knowledge, this is the first study to elucidate the molecular mechanism and potential targets of PD in the treatment of HCC using network pharmacology.

Identification of the key mechanisms of action of Si-Ni-San in uveitis using bioinformatics and network pharmacology

BACKGROUND

Uveitis is an eye disease with a high rate of blindness, whose pathogenesis is not completely understood. Si-Ni-San (SNS) has been used as a traditional medicine to treat uveitis in China. However, its mechanism of action remains unclear. This study explored the potential mechanisms of SNS in the treatment of uveitis through network pharmacology and bioinformatics.

METHODS

Using R language and Perl software, the active components and predicted targets of SNS, as well as the related gene targets of uveitis, were mined through the Traditional Chinese Medicine Systems Pharmacology, Therapeutic Target, Gene Expression Omnibus, GeneCards, and DrugBank databases. The network diagram of active components and intersection targets was constructed using Cytoscape software and the String database. The CytoNCA plug-in was used to conduct topological analysis on the network diagram and screen out the core compounds and key targets. The genes were analyzed for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment. Chemoffice, Pymol, AutoDock, and Vina were used to analyze the molecular docking of key targets and core compounds of diseases through the PubChem database.

RESULTS

JUN, RELA, and MAPK may play important roles in the treatment of uveitis by SNS. Kyoto encyclopedia of genes and genomes pathway enrichment analysis showed that core genes were mainly concentrated in MAPK, toll-like receptor, tumor necrosis factor, and nucleotide oligomerization domain-like receptor signaling pathways. In addition, molecular docking results showed that the bioactive compounds (kaempferol, luteolin, naringin, and quercetin) exhibited good binding ability to JUN, RELA, and MAPK.

CONCLUSION

Based on these findings, SNS exhibits multi-component and multi-target synergistic action in the treatment of uveitis, and its mechanism may be related to anti-inflammatory and immune regulation.

Investigation on the potential adverse outcome pathway of the sensitive endpoint for nephrotoxicity induced by gardenia yellow based on an integrated strategy using bioinformatics analysis and in vitro testing validation

To explore the potential the adverse outcome pathway of Gardenia Yellow (GY)-induced sensitive endpoint for nephrotoxicity, an integrated strategy was applied in the present study. Using bioinformatic analysis, based on the constructed Protein-protein interaction networks, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on the core target network were performed to illustrate the potential gene targets and signal pathways. Then, the most enriched pathway was validated with Cell counting kit-8 assays and Western blot analysis in embryonic kidney epithelial 293 cell models. According to the findings, GY may interact with 321 targets related to the endpoint. The five targets on the top ranking in the PPI network were STAT3, SRC, HRAS, AKT1, EP300. Among them, PI3K/Akt was the most enriched pathway. In vitro testing showed that GY exerted a proliferative effect on the cell variability in a dose-dependent manner. GY at concentration of 1000 μg/ml and stimulation for 30 min can significantly enhance the expression of phosphorylated Akt. Thus, after the quantitative weight of evidence evaluation, Akt phosphorylation induced PI3K/Akt activation was speculated as a molecular initiating event leading to a proliferative and inflammatory response in renal tubular epithelial cells.

Mechanism of salidroside against coronary artery disease by network pharmacology analysis

BACKGROUND

Rosenroot (Rhodiola rosea) is a traditional Chinese herbal medicine. It has been used to treat patients with coronary artery disease (CAD). Salidroside is the main active constituent of rosenroot. This study was designed to explore the mechanism of salidroside in treating CAD and its role in angiogenesis in CAD systematically.

METHODS

In this study, potential targets related to salidroside and CAD were obtained from public databases. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) and CellMarker enrichment analyses were performed. The binding of salidroside to angiogenesis-related targets was assessed by PyMOL and Ligplot. Furthermore, the effects of salidroside on collateral circulation were evaluated by correlation analysis of these angiogenesis-related targets with the coronary flow index (CFI), and the influence of salidroside on human umbilical vein endothelial cell (HUVEC) proliferation and migration was assessed.

RESULTS

Eighty-three targets intersected between targets of salidroside and CAD. GO and KEGG analyses indicated that salidroside mainly treated CAD through angiogenesis and anti-inflammatory action. There were 12 angiogenesis-related targets of salidroside in coronary heart disease, among which FGF1 (r = 0.237, P = 2.597E-3), KDR (r = 0.172, P = 3.007E-2) and HIF1A (r = -0.211, P = 7.437E-3) were correlated with the coronary flow index (CFI), and salidroside docked well with them. Finally, cell experiments confirmed that salidroside promoted the proliferation and migration of HUVECs.

CONCLUSIONS

This study revealed the potential molecular mechanism of salidroside on angiogenesis in CAD and provided new ideas for the clinical application of salidroside in the treatment of CAD.

Deciphering the underlying wound healing mechanisms of Streptocaulon juventas (Lour.) Merr. by integrating network pharmacology, transcriptomics, and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Streptocaulon juventas (Lour.) Merr. (SJ), a traditional Chinese folk medicine, has been widely used for the treatment of dysentery and traumatic injuries since ancient times. However, the mechanisms underlying its wound healing activity remain unclear.

AIM OF THE STUDY

The aim of this study was to evaluate the wound healing activity of SJ and clarify the underlying molecular mechanisms.

MATERIALS AND METHODS

The wound healing activity of an ethanol extract of SJ (ESJ) was confirmed in rat full-thickness wound models. UPLC-Q-TOF-MS/MS was used to analyze the composition of ESJ. Potential molecular targets and signaling pathways involved in the wound healing activity of ESJ were predicted using network pharmacology and transcriptomic analyses. In addition, the L929 cells were used to evaluate the in vitro wound healing activity of ESJ and to verify the predicted pathways.

RESULTS

In rat wound models, ESJ significantly accelerated wound healing and promoted hydroxyproline production in wounds. Network pharmacology and transcriptomic analyses results revealed that ESJ might promote wound healing by activating the AKT and MAPK pathways. In L929 cells, ESJ significantly promoted cell proliferation, migration, and expression of collagen I and α-SMA. Additionally, ESJ treatment increased the phosphorylation of AKT, mTOR, ERK, and p38 in a time- and dose-dependent manner.

CONCLUSIONS

ESJ significantly promoted wound healing in vivo and in vitro. AKT-mTOR and ERK-p38 signaling pathways were involved in the wound healing activity of ESJ.

Molecular docking, network pharmacology and experimental verification to explore the mechanism of Wulongzhiyangwan in the treatment of pruritus

Wulongzhiyangwan (WLZYW) is a Chinese prescription medicine for the treatment of pruritus, but its mechanism has not been clarified. The purpose of this study was to explore the mechanism of WLZYW in pruritus through network pharmacology analysis and experimental validation. The active components and corresponding targets of WLZYW were obtained from the Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database. Pruritus-related targets were obtained from the GeneCards, TTD (Therapeutic Target Database), and DrugBank databases. The key compounds, core targets, main biological processes and signaling pathways related to WLZYW were identified by constructing and analyzing related networks. The binding affinity between WLZYW components and core targets was validated by AutoDock Vina software. In this study, RBL-2H3 cells were used to construct a degranulation model to simulate histamine-dependent pruritus. 10 chemical constituents, 235 targets and 3606 pruritus-related targets of WLZYW were obtained. Subsequently, 26 core targets were identified through analysis, VEGFA and AKT1 were the main candidates. A pathway enrichment analysis showed that overlapping targets were significantly enriched in the PI3K/AKT signaling pathway. A molecular docking analysis revealed tight binding of VEGF to three core compounds, kaempferol, luteolin and quercetin. Experiments showed that WZLYW inhibited mast cell degranulation, regulated VEGFa mRNA and protein expression levels by inhibiting PI3K/AKT and ERK1/2 signaling pathway activation. The mechanism of WZLYW in pruritus may be regulating VEGFa expression. Network pharmacology assays suggested that WLZYW downregulates VEGFa expression by regulating the PI3K/AKT and ERK1/2 signaling pathways in pruritis treatment.

Network pharmacology-based analysis and experimental in vitro validation on the mechanism of Paeonia lactiflora Pall. in the treatment for type I allergy

Background

The incidence of allergic reaction is increasing year by year, but the specific mechanism is still unclear. Paeonia lactiflora Pall.(PLP) is a traditional Chinese medicine with various pharmacological effects such as anti-tumor, anti-inflammatory, and immune regulation. Previous studies have shown that PLP has potential anti-allergic activity. However, there is still no comprehensive analysis of the targeted effects and exact molecular mechanisms of the anti-allergic components of PLP. This study aimed to reveal the mechanism of PLP. in the treatment of type I allergy by combining network pharmacological methods and experimental verification.

Methods

First, we used the traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform to screen the main components and targets of PLP, and then used databases such as GeneCards to retrieve target information related to ‘allergy’. Protein–protein interaction (PPI) analysis obtained the core target genes in the intersection target, and then imported the intersection target into the David database for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis. Furthermore, the therapeutic effect of paeoniflorin, the main component of PLP, on IgE-induced type I allergy was evaluated in vitro.

Results

GO analysis obtained the main biological processes, cell components and molecular functions involved in the target genes. KEGG analysis screened out MAPK1, MAPK10, MAPK14 and TNF that have a strong correlation with PLP anti-type I allergy, and showed that PLP may pass through signal pathways such as IgE/FcεR I, PI3K/Akt and MAPK to regulate type I allergy. RT-qPCR and Western Blot results confirmed that paeoniflorin can inhibit the expression of key genes and down-regulate the phosphorylation level of proteins in these signal pathways. It further proved the reliability of the results of network pharmacology research.

Conclusion

The results of this study will provide a basis for revealing the multi-dimensional regulatory mechanism of PLP for the treatment of type I allergy and the development of new drugs.

The therapeutic role of Jingchuan tablet on ischaemic cerebral stroke via the HIF-1α/EPO/VEGFA signalling pathway

CONTEXT

Jingchuan tablet (JCT) is a Chinese medicine prescription for treating ischaemic cerebral stroke (ICS). However, its relevant mechanisms remain unclear.

OBJECTIVE

To unravel the intrinsic mechanisms of JCT anti-ICS.

MATERIALS AND METHODS

'Hongjingtian', 'chuanxiong', 'yanhusuo', 'bingpian', 'cerebral infarction', 'cerebral ischemia' or 'stroke' were used as keywords, and then components, targets and underlying mechanisms of JCT anti-ICS were analysed in TCMSP, TTD, DrugBank, STRING and Metascape databases up to June 2020. Male Sprague-Dawley rats under permanent middle cerebral artery occlusion (pMCAO) model, randomly assigned as: model, sham, nimodipine (0.012 g/kg/d) and JCT (0.78, 1.56 and 3.12 g/kg/d) groups, received oral gavage administration for a week. Therapeutic effects were evaluated by detecting the proportion of cerebral infarction, neuronal apoptosis and neurological deficits. Bioactive components were detected by HPLC-MS. Molecular biology and computational docking were used to verify the underlying mechanisms.

RESULTS

Eighty-one components, 166 targets and HIF-1α/EPO/VEGFA pathway contributed to the anti-ICS effect of JCT. JCT treatment effectively reduced the proportion of cerebral infarction (33.13%), apoptosis rate (14.80%) and neurobehavioural score (2.00). JCT increased the protein levels of HIF-1α (0.84), EPO (0.64) and VEGFA (0.69), respectively (p < 0.05). Gallic acid, salidroside, chlorogenic acid, ethyl gallate, ferulic acid and tetrahydropalmatine detected by HPLC-MS showed good interaction and binding with HIF-1α/EPO/VEGFA.

CONCLUSIONS

Our study demonstrated the mechanisms of JCT anti-ICS associated with the activation of the HIF-1α/EPO/VEGFA pathway, which provided a pharmacological basis for expanding the clinical application and some scientific ideas for further research into the material basis JCT anti-ICS.

Decoding the Key Functional Combined Components Group and Uncovering the Molecular Mechanism of Longdan Xiegan Decoction in Treating Uveitis

Objective

Longdan Xiegan Decoction (LXD) is a famous herbal formula in China. It has been proved that LXD has been shown to have a significant inhibitory effect on suppresses the inflammatory cells associated with uveitis. However, the key functional combination of component groups and their possible mechanisms remain unclear.

Methods

The community detecting model of the network, the functional response space, and reverse prediction model were utilized to decode the key components group (KCG) and possible mechanism of LXD in treating uveitis. Finally, MTT assay, NO assay and ELISA assay were applied to verify the effectiveness of KCG and the accuracy of our strategy.

Results

In the components-targets-pathogenic genes-disease (CTP) network, a combination of Huffman coding and random walk algorithm was used and eight foundational acting communities (FACs) were discovered with important functional significance. Verification has shown that FACs can represent the corresponding C-T network for treating uveitis. A novel node importance calculation method was designed to construct the functional response space and pick out 349 effective proteins. A total of 54 components were screened and defined as KCG. The pathway enrichment results showed that KCG and their targets enriched signal pathways of IL-17, Toll-like receptor, and T cell receptor played an important role in the pathogenesis of uveitis. Furthermore, experimental verification results showed that important KCG quercetin and sitosterol markedly inhibited the production of nitric oxide and significantly regulated the level of TNF-α and IFN-γ in Lipopolysaccharide-induced RAW264.7 cells.

Discussion

In this research, we decoded the potential mechanism of the multi-components-genes-pathways of LXD’s pharmacological action mode against uveitis based on an integrated pharmacology approach. The results provided a new perspective for the future studies of the anti-uveitis mechanism of traditional Chinese medicine.

Mechanism of Shishiwei Wendan Decoction in the Prevention and Treatment of Lung Adenocarcinoma Using Network Pharmacology and Molecular Docking

Objective

This study used network pharmacology and molecular docking technology to elucidate the mechanism of action of Shishiwei Wendan Decoction against lung adenocarcinoma.

Methods

By using the world's largest TCM System Pharmacology Database and Analysis Technology Platform (TCMSP) system to conduct in-depth mining analysis and data collection of the main active components of the medicinal components in Shishiwei Wendan Decoction and using the human gene card database (GeneCards), Human Mendelian Inheritance Online System (OMIM), and Human Disease-Related Gene and Mutation Information Database (DisGeNET) to collect the pathogenic targets of lung adenocarcinoma and build a PPI network; for the core drug targets, use GO enrichment analysis and KEGG pathway analysis; use Cytoscape software to build relevant network maps; and use AutoDock to achieve molecular docking.

Results

Shishiwei Wendan Decoction screened 144 active ingredients and 384 drug targets; 7680 lung adenocarcinoma disease targets were obtained, including 380 targets for Shishiwei Wendan Decoction in the treatment of lung adenocarcinoma. GO enrichment analysis demonstrated 2,299 downstream genes, and key target genes were closely related to nutrient levels, membrane rafts, and protein serine/threonine kinase activity; KEGG functional enrichment analysis yielded 179 related pathways, including tumor necrosis factor signaling pathway which is related to the target gene. Molecular docking showed that the core active ingredients and key targets could be well combined.

Conclusion

Through the network pharmacology analysis and molecular docking experiments of Shishiwei Wendan Decoction against lung adenocarcinoma, it is found that Shishiwei Wendan Decoction has multidimensional effects on the treatment of lung adenocarcinoma, and it is the first Shiwei Wendan Decoction to treat lung adenocarcinoma. Decoction in the treatment of lung adenocarcinoma provides biointellectual support and the oretical support.

Sipeimine ameliorates PM2.5-induced lung injury by inhibiting ferroptosis via the PI3K/Akt/Nrf2 pathway: A network pharmacology approach

Fine particulate matter (PM2.5) exposure can cause lung injury and a large number of respiratory diseases. Sipeimine is a steroidal alkaloid isolated from Fritillaria roylei which has been associated with anti-inflammatory, antitussive and antiasthmatic properties. In this study, we explored the potential effects of sipeimine against PM2.5-induced lung injury in Sprague Dawley rats. Sipeimine alleviated lung injury caused by PM2.5 and decreased pulmonary edema, inflammation and the levels of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) in the bronchoalveolar lavage fluid. In addition, sipeimine upregulated the glutathione (GSH) expression and downregulated the expression of 4-hydroxynonenal (4-HNE), tissue iron and malondialdehyde (MDA). The downregulation of proteins involved in ferroptosis, including nuclear factor E2-related factor 2 (Nrf2), glutathione peroxidase 4 (GPX4), heme oxygenase-1 (HO-1) and solute carrier family 7 member 11 (SLC7A11) was reversed by sipeimine. The administration of RSL3, a potent ferroptosis-triggering agent, blocked the effects of sipeimine. Using network pharmacology, we found that the effects of sipeimine were presumably mediated through the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling pathway. A PI3K inhibitor (LY294002) blocked the PI3K/Akt signaling pathway and reversed the effects of sipeimine. Overall, this study suggested that the protective effect of sipeimine against PM2.5-induced lung injury was mainly mediated through the PI3K/Akt pathway, ultimately leading to a reduction in ferroptosis.

Identification of miRNA–mRNA Pairs in the Alzheimer’s Disease Expression Profile and Explore the Effect of miR-26a-5p/PTGS2 on Amyloid-β Induced Neurotoxicity in Alzheimer’s Disease Cell Model

Alzheimer’s disease (AD) is a progressive neurodegenerative disease and the most common type of dementia. MicroRNAs (miRNAs) have been extensively studied in many diseases, including AD. To identify the AD-specific differentially expressed miRNAs and mRNAs, we used bioinformatics analysis to study candidate miRNA–mRNA pairs involved in the pathogenesis of AD. These miRNA–mRNAs may serve as promising biomarkers for early diagnosis or targeted therapy of AD patients. In this study, based on the AD mRNA and miRNA expression profile data in Gene Expression Omnibus (GEO), through differential expression analysis, functional annotation and enrichment analysis, weighted gene co-expression network analysis, miRNA–mRNA regulatory network, protein–protein interaction network, receiver operator characteristic and Least absolute shrinkage and selection operator (LASSO) regression and other analysis, we screened the key miRNA–mRNA in the progress of AD: miR-26a-5p/PTGS2. Dual-luciferase and qPCR experiments confirmed that PTGS2 is a direct target gene of miR-26a-5p. The expression of miR-26a-5p in the peripheral blood of AD patients and AD model cells (SH-SY5Y cells treated with Aβ_25–35) was up-regulated, and the expression of PTGS2 was down-regulated. Functional gain -loss experiments confirmed that PTGS2 protects AD model cells from damage by inhibiting proliferation and migration. However, the expression of miR-26a-5p promotes the proliferation of AD model cells. It is further found that PTGS2 is involved in the regulation of miR-26a-5p and can reverse the effect of miR-26a-5p on the proliferation of AD model cells. In addition, through network pharmacology, qPCR and CCK-8, we found that baicalein may affect the progression of AD by regulating the expression of PTGS2. Therefore, PTGS2 can be used as a target for AD research, and miR-26a-5p/PTGS2 can be used as an axis of action to study the pathogenesis of AD.

Network pharmacology analysis and experimental validation to explore the mechanism of Bushao Tiaozhi capsule (BSTZC) on hyperlipidemia

Bushao Tiaozhi Capsule (BSTZC) is a novel drug in China that is used in clinical practice and has significant therapeutic effects on hyperlipidemia (HLP). In our previous study, BSTZC has a good regulatory effect on lipid metabolism of HLP rats. However, its bioactive compounds, potential targets, and underlying mechanism remain largely unclear. We extracted the active ingredients and targets in BSTZC from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and literature mining. Subsequently, core ingredients, potential targets, and signaling pathways were determined through bioinformatics analysis, including constructed Drug-Ingredient-Gene symbols-Disease (D-I-G-D), protein–protein interaction (PPI), the Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, the reliability of the core targets was evaluated using in vivo studies. A total of 36 bioactive ingredients and 209 gene targets were identified in BSTZC. The network analysis revealed that quercetin, kaempferol, wogonin, isorhamnetin, baicalein and luteolin may be the core ingredients. The 26 core targets of BSTZC, including IL-6, TNF, VEGFA, and CASP3, were considered potential therapeutic targets. Furthermore, GO and KEGG analyses indicated that the treatment of HLP by BSTZC might be related to lipopolysaccharide, oxidative stress, inflammatory response and cell proliferation, differentiation and apoptosis. The pathway analysis showed enrichment for different pathways like MAPK signaling pathway, AGE-RAGE signaling pathway in diabetic, IL-17 signaling pathway and TNF signaling pathway. In this study, network pharmacology analysis, and experiment verification were combined, and revealed that BSTZC may regulate key inflammatory markers and apoptosis for ameliorating HLP.

Network Pharmacology-Based Strategy to Identify the Pharmacological Mechanisms of Pulsatilla Decoction against Crohn's Disease

Purpose: To explore pharmacological mechanisms of Pulsatilla decoction (PD) against Crohn's disease (CD) via network pharmacology analysis followed by experimental validation. Methods: Public databases were searched to identify bioactive compounds and related targets of PD as well as related genes in patients with CD. Analyses using the drug-compound-target-disease network, the protein-protein interaction (PPI) network, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to predict the core targets and pathways of PD against CD. Colon tissue resected from patients with CD and tissue samples from a mouse model of CD fibrosis treated with PD were assessed to verify the major targets of PD in CD predicted by network pharmacologic analysis. Results: A search of the targets of bioactive compounds in PD and targets in CD identified 134 intersection targets. The target HSP90AA1, which was common to the drug-compound-target-disease and PPI networks, was used to simulate molecular docking with the corresponding bioactive compound. GO and KEGG enrichment analyses showed that multiple targets in the antifibrotic pathway were enriched and could be experimentally validated in CD patients and in a mouse model of CD fibrosis. Assays of colon tissues from CD patients showed that intestinal fibrosis was greater in stenoses than in nonstenoses, with upregulation of p-AKT, AKT, p-mTOR, mTOR, p-ERK1/2, ERK1/2, p-PKC, and PKC targets. Treatment of CD fibrosis mice with PD reduced the degree of fibrosis, with downregulation of the p-AKT, AKT, p-mTOR, mTOR, p-ERK1/2, ERK1/2, and PKC targets. Conclusion: Network pharmacology analysis was able to predict bioactive compounds in PD and their potential targets in CD. Several of these targets were validated experimentally, providing insight into the pharmacological mechanisms underlying the biological activities of PD in patients with CD.

Tsp-1 is involved in DNA stability through Tgf-β1 activation domain in cone photoreceptor 661 W cells

Thrombospondin-1 (Tsp-1), a matricellular protein, could protect retinal neurons from endogenous or exogenous insults; however, its underlying mechanism remains unclear. Thus, this study aimed to investigate Tsp-1-mediated neuron-protection effect in retinal cells. Our data showed that Tsp-1 downregulation would aggravate UV irradiation-induced DNA damage in 661 W cells and cone photoreceptor cells. The increasing levels of poly (ADP ribose) polymer (PAR) and γ-H2AX in Tsp-1-silenced 661 W cells indicate severe DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). By utilizing an error-prone substrate, Tsp-1 silencing significantly increased deleted DNA end joining in 661 W cells with spontaneous DNA damage (SDD). Moreover, Tsp-1 is indirectly involved in DNA stability in 661 W cells as UV treatment caused a significant Tsp-1 decreasing in cytoplasm, but no obvious Tsp-1 alteration in cell nuclear of 661 W cells. Furthermore, our data indicate that Tgf-β1 activation domain in Tsp-1 plays a critical role in DNA stability in 661 W cells through expressing mutated exogenous Tsp-1 and Tgf-β inhibitor, LSKL. Therefore, this study provides new insights into the mechanism of the neuroprotective action positively mediated by Tsp-1, which might be a therapeutic target for the treatment of retinal pathology.

Immunometabolism at the service of traditional Chinese medicine

To enhance therapeutic efficacy and reduce adverse effects, ancient practitioners of traditional Chinese medicine (TCM) prescribe combinations of plant species/animal species and minerals designated "TCM formulae" developed based on TCM theory and clinical experience. TCM formulae have been shown to exert curative effects on complex diseases via immune regulation but the underlying mechanisms remain unknown at present. Considerable progress in the field of immunometabolism, referring to alterations in the intracellular metabolism of immune cells that regulate their function, has been made over the past decade. The core context of immunometabolism is regulation of the allocation of metabolic resources supporting host defense and survival, which provides a critical additional dimension and emerging insights into how the immune system and metabolism influence each other during disease progression. This review summarizes research findings on the significant association between the immune function and metabolic remodeling in health and disease as well as the therapeutic modulatory effects of TCM formulae on immunometabolism. Progressive elucidation of the immunometabolic mechanisms involved during the course of TCM treatment continues to aid in the identification of novel potential targets against pathogenicity. In this report, we have provided a comprehensive overview of the benefits of TCM based on regulation of immunometabolism that are potentially applicable for the treatment of modern diseases.

Decoding the chemical composition and pharmacological mechanisms of Jiedu Tongluo Tiaogan Formula using high-performance liquid chromatography coupled with network pharmacology-based investigation

Type 2 diabetes mellitus (T2DM), a chronic low-grade inflammatory disease with high morbidity and mortality, is a serious threat to public health. Previously we demonstrated that a traditional Chinese medicine formulation, Jiedu Tongluo Tiaogan Formula (JDTL), exerted a favorable hypoglycemic effect due to unknown molecular mechanisms involving interactions among JDTL compounds and various cellular components. This study aimed to explore JDTL mechanisms for alleviating hyperglycemia using an integrated strategy incorporating system pharmacology, bioinformatics analysis, and experimental verification. This strategy entailed initial elucidation of JDTL chemical composition using fingerprint analysis via high performance liquid chromatography (HPLC). Next, functions of putative shared target genes and associated pathways were deduced using GO and KEGG pathway enrichment and molecular docking analyses. Ultimately, targets associated with JTDL anti-T2DM effects were found to be functionally associated with biological functions related to lipopolysaccharide and cytokine receptor binding. These results implicated PI3K-Akt signaling pathway involvement in JDTL anti-T2DM effects, as this pathway had been previously shown to play significant roles in glucose and lipid metabolism-related diseases. Furthermore, addition of JDTL to INS-1 and HepG2 cell cultures stimulated cellular mRNA-level and protein-level expression leading to enhanced production of IRS1, Akt, and PI3K. In summary, here JDTL bioactive ingredients, potential targets, and molecular mechanisms underlying JDTL anti-T2DM effects were identified using a multi-component, multi-target, and multi-channel analytical approach, thus providing an important scientific foundation to facilitate development of new drugs mechanistic strategies for preventing and treating T2DM.

An Advanced Systems Pharmacology Strategy Reveals AKR1B1, MMP2, PTGER3 as Key Genes in the Competing Endogenous RNA Network of Compound Kushen Injection Treating Gastric Carcinoma by Integrated Bioinformatics and Experimental Verification

Gastric carcinoma (GC) is a severe tumor of the digestive tract with high morbidity and mortality and poor prognosis, for which novel treatment options are urgently needed. Compound Kushen injection (CKI), a classical injection of Chinese medicine, has been widely used to treat various tumors in clinical practice for decades. In recent years, a growing number of studies have confirmed that CKI has a beneficial therapeutic effect on GC, However, there are few reports on the potential molecular mechanism of action. Here, using systems pharmacology combined with proteomics analysis as a core concept, we identified the ceRNA network, key targets and signaling pathways regulated by CKI in the treatment of GC. To further explore the role of these key targets in the development of GC, we performed a meta-analysis to compare the expression differences between GC and normal gastric mucosa tissues. Functional enrichment analysis was further used to understand the biological pathways significantly regulated by the key genes. In addition, we determined the significance of the key genes in the prognosis of GC by survival analysis and immune infiltration analysis. Finally, molecular docking simulation was performed to verify the combination of CKI components and key targets. The anti-gastric cancer effect of CKI and its key targets was verified by in vivo and in vitro experiments. The analysis of ceRNA network of CKI on GC revealed that the potential molecular mechanism of CKI can regulate PI3K/AKT and Toll-like receptor signaling pathways by interfering with hub genes such as AKR1B1, MMP2 and PTGERR3. In conclusion, this study not only partially highlighted the molecular mechanism of CKI in GC therapy but also provided a novel and advanced systems pharmacology strategy to explore the mechanisms of traditional Chinese medicine formulations.

Integrating Network Pharmacology and Experimental Verification to Explore the Mechanism of Effect of Zuojin Pills in Pancreatic Cancer Treatment

Background and Aim

Pancreatic cancer is one of the most malignant tumors worldwide. Zuojin pills (ZJP), a traditional Chinese medicine (TCM) formula, which can treat a variety of cancers. However, the active compounds present in ZJP and the potential mechanisms through which ZJP acts against pancreatic cancer have not been thoroughly investigated.

Methods

Data on pancreatic cancer-related genes, bioactive compounds, and potential targets of ZJP were downloaded from public databases. Bioinformatics analysis, including protein–protein interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, was conducted to identify important components, potential targets, and signaling pathways through which ZJP affects pancreatic cancer. The results of this analysis were verified by in vitro experiments.

Results

The network pharmacology analysis results showed that 41 compounds and 130 putative target genes of ZJP were associated with anti-pancreatic cancer effects. ZJP may exert its inhibitory effects against pancreatic cancer by acting on key targets such as JUN, TP53, and MAPK1. Moreover, KEGG analysis indicated that the anti-pancreatic cancer effect of ZJP was mediated by multiple pathways, such as the PI3K-AKT, IL-17, TNF, HIF-1, and P53 signaling pathways. Among these, the PI3K-AKT signaling pathway, which included the highest number of enriched genes, may play a more important role in treating pancreatic cancer. The in vitro results showed that ZJP significantly inhibits the cell cycle and cell proliferation through the PI3K/AKT/caspase pathway and that it can induce apoptosis of pancreatic cancer cells, consistent with the results predicted by network pharmacological methods.

Conclusion

This study preliminarily investigated the pharmacological effects of ZJP, which appear to be mediated by multiple compounds, targets and pathways, and its potential therapeutic effect on pancreatic cancer. Importantly, our work provides a promising approach for the identification of compounds in TCM and the characterization of therapeutic mechanisms.

Systematic analysis of the mechanism of hydroxysafflor yellow A for treating ischemic stroke based on network pharmacology technology

In this study, we analyzed the mechanism of hydroxysafflor yellow A (HSYA) for treating ischemic stroke (IS) based on network pharmacology tools, and verified the kernel targets via animal experiments. The targets of HSYA were collected via PharmMapper server and the IS-related targets were searched using Genecards, Online Mendelian Inheritance in Man, Therapeutic Target, and Disgenet databases. The targets identified from the above two steps were overlapped to acquire candidate targets involved in the effects of HSYA for treating IS. Subsequently, the Database for Annotation, Visualization, and Integrated Discovery was used for gene ontology analysis and the Kyoto encyclopedia of genes and genomes pathway analysis. Cytoscape 3.7.1 was applied to establish the component-target-pathway network. Potential core targets were obtained by protein-protein interaction analysis. Furthermore, Autodock Vina was used to identify core genes, and animal experiments was used to verify the expression level of core genes. On the basis of the modified neurologic severity score and the results of 2,3,5-Triphenyltetrazolium chloride and Hematoxylin-eosin staining, we confirmed that HSYA reduced the infarct volume in rats and protected neuronal cells in the hippocampal region after IS. Western blot and immunohistochemical staining showed that HSYA increased the expression of epidermal growth factor receptor, hypoxia inducible factor 1 alpha, and endothelial nitric oxide synthase (P < 0.05). The effects of HSYA on IS are mediated through several targets and pathways related to the regulation of oxidative stress and the renewal of cell and blood vessels while improving post-ischemic brain impairment.

Network pharmacology-based identification of the key mechanism of quercetin acting on hemochromatosis

Hemochromatosis is an iron overload disease, which lacks nutritional intervention strategies. This study explored the protective effect of quercetin on hemochromatosis and its possible mechanism through network pharmacology. We used Online Mendelian Inheritance in Man to screen the disease targets of hemochromatosis, and further constructed a potential protein interaction network through STITCH. The above-mentioned targets revealed by Gene enrichment analysis have played a significant role in ferroptosis, mineral absorption, basal cell carcinoma, and related signal pathways. Besides, the drug likeness of quercetin obtained by Comparative Toxicogenomics Database was evaluated by Traditional Chinese Medicine Systems Pharmacology, and potential drug targets identified by PharmMapper and similar compounds identified by PubChem were selected for further research. Moreover, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed the relationship between quercetin and glycosylation. Furthermore, we performed experiments to verify that the protective effect of quercetin on iron overload cells is to inhibit the production of reactive oxygen species, limit intracellular iron, and degrade glycosaminoglycans. Finally, iron-induced intracellular iron overload caused ferroptosis, and quercetin and fisetin were potential ferroptosis inhibitors. In conclusion, our study revealed the correlation between hemochromatosis and ferroptosis, provided the relationship between the target of quercetin and glycosylation, and verified that quercetin and its similar compounds interfere with iron overload related disease. Our research may provide novel insights for quercetin and its structurally similar compounds as a potential nutritional supplement for iron overload related diseases.

Integrated Systems Pharmacology and Surface Plasmon Resonance Approaches to Reveal the Synergistic Effect of Multiple Components of Gu-Ben-Ke-Chuan Decoction on Chronic Bronchitis

Introduction

Gu-Ben-Ke-Chuan (GBKC) decoction, a well-known prescription composed of seven herbs, has been widely used for treating chronic bronchitis (CB). However, the pharmacological constituents of GBKC and the underlying mechanisms by which these components act on CB remain unclear.

Methods

Ultra-high-pressure liquid chromatography coupled with linear ion trap–Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap) was first employed to rapidly identify compounds from GBKC. Thereafter, network pharmacology and molecular docking analyses were performed to identify the potential active constituents, candidate targets, and major pathways. Finally, the affinities between the key compounds and targets were verified via surface plasmon resonance (SPR) analysis. In addition, the anti-inflammatory effect of GBKC was verified using an LPS-induced inflammatory cell model based on the predicted results.

Results

A total of 53 major compounds were identified in the GBKC decoction. After network pharmacology-based virtual screening, 141 major targets and 39 main compounds were identified to be effective in the treatment of CB. The major targets were highly enriched in the tumor necrosis factor (TNF) signaling pathway, suggesting that GBKC could attenuate the inflammatory response in patients with CB. Furthermore, molecular docking results indicated that 20 pairs of components and target proteins relevant to the TNF pathway exhibited notable interactions. Among them, eight compound-target pairs exhibited good affinity as per SPR analysis. In addition, the production of interleukin 6 and TNF-α in LPS-induced MH-S cells was suppressed after GBKC treatment.

Conclusion

This study successfully clarified the mechanism of action of GBKC against CB, which demonstrated that the integrated strategy described above is reliable for identifying the active compounds and mechanisms responsible for the pharmacological activities of GBKC decoction.

Analysis of astaxanthin molecular targets based on network pharmacological strategies

In order to further explore the potential pharmacological activity of astaxanthin (AST), network pharmacological approaches were employed in this work to systematically investigate its affinity targets, perturbed signaling pathways, and related disease applications. First, potential targets were captured based on AST chemical structure information. Enrichment analysis was then performed using bioinformatics tools to predict the biological processes and diseases in which AST targets are involved. The results suggest that AST is involved in steroid hormone metabolism, and the regulation of glucocorticoids may be one of the potential mechanisms of its known therapeutic effects on depression and insulin resistance. Molecular docking experiments confirmed that AST can form stable binding to several key nodes (SRD5A2, STS, AKR1C2, HSD11B1, and CYP17A1) in steroid hormone biosynthesis. More importantly, the molecular targets of AST were the most significantly associated with endometriosis. Functionally, grouped analysis of key therapeutic nodes was carried out by establishing the interaction network between drug targets and disease targets. While exerting inflammatory effects, the regulation of estrogen and other semiochemicals by targeting steroid metabolism may be the biological basis for the potential treatment of endometriosis with AST. This work provides a theoretical basis for further exploring the pharmacological mechanisms of AST and development of new therapeutic applications. PRACTICAL APPLICATIONS: In this study, systematic pharmacological methods were used to identify the potential therapeutic effects and associated mechanisms of astaxanthin, providing a bioinformatics basis for further exploration of astaxanthin's new pharmacological properties in foods.

Prediction of Targets of Curculigoside A in Osteoporosis and Rheumatoid Arthritis Using Network Pharmacology and Experimental Verification

Purpose

Network pharmacology is considered to be the next-generation drug development model that uses bioinformatics to predict and identify multiple drug targets and interactions in diseases. Here, network pharmacology was used to investigate the mechanism by which Curculigoside A (CA) acts in rheumatoid arthritis (RA) and osteoporosis.

Methods

First, TCMSP and SwissADME were applied to predict the druggability of CA. Then, potential targets were identified from overlapping data in SwissTarget and TargetNet, and targets were analyzed using Genemania and DAVID6.8 to obtain information about the GO and KEGG pathways. Ultimately, the drug-target-pathway network was identified after using Cytoscape 3.0 for visualization. Besides, qPCR was used to validate the predicted five major genes targets (EGFR, MAP2K1, MMP2, FGFR1, and MCL1).

Results

The results of TCMSP and SwissADME demonstrated that CA exhibits good druggability; 26 potential protein targets were classified by SwissTarget and TargetNet. The results of Genemania and DAVID6.8 indicated that CA probably caused anti-osteoporosis and anti-RA effects by regulating some biological pathways, especially nitrogen metabolism, estrogen signaling pathway, Rap1 signaling pathway, and PI3K/Akt signaling pathway. Besides, the result of Cytoscape 3.0 showed that the 26 targets participate in osteoporosis and RA-related pathways, metabolism, and other physiological processes. In vitro induced inflammation cell model experiments, the qPCR results showed that CA pretreatment significantly decreased the expression of EGFR, MAP2K1, MMP2, FGFR1, and MCL1 genes.

Conclusion

These results suggested that network pharmacology may provide possible mechanism of how CA exerts therapeutic effects in osteoporosis and RA.

Systemic elucidation on the potential bioactive compounds and hypoglycemic mechanism of Polygonum multiflorum based on network pharmacology

BACKGROUND

Diabetes is a complex metabolic disease characterized by hyperglycemia, plaguing the whole world. However, the action mode of multi-component and multi-target for traditional Chinese medicine (TCM) could be a promising treatment of diabetes mellitus. According to the previous research, the TCM of Polygonum multiflorum (PM) showed noteworthy hypoglycemic effect. Up to now, its hypoglycemic active ingredients and mechanism of action are not yet clear. In this study, network pharmacology was employed to elucidate the potential bioactive compounds and hypoglycemic mechanism of PM.

METHODS

First, the compounds with good pharmacokinetic properties were screened from the self-established library of PM, and the targets of these compounds were predicted and collected through database. Relevant targets of diabetes were summarized by searching database. The intersection targets of compound-targets and disease-targets were obtained soon. Secondly, the interaction net between the compounds and the filtered targets was established. These key targets were enriched and analyzed by protein-protein interactions (PPI) analysis, molecular docking verification. Thirdly, the key genes were used to find the biologic pathway and explain the therapeutic mechanism by genome ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis. Lastly, the part of potential bioactive compounds were under enzyme activity inhibition tests.

RESULTS

In this study, 29 hypoglycemic components and 63 hypoglycemic targets of PM were filtrated based on online network database. Then the component-target interaction network was constructed and five key components resveratrol, apigenin, kaempferol, quercetin and luteolin were further obtained. Sequential studies turned out, AKT1, EGFR, ESR1, PTGS2, MMP9, MAPK14, and KDR were the common key targets. Docking studies indicated that the bioactive compounds could stably bind the pockets of target proteins. There were 38 metabolic pathways, including regulation of lipolysis in adipocytes, prolactin signaling pathway, TNF signaling pathway, VEGF signaling pathway, FoxO signaling pathway, estrogen signaling pathway, linoleic acid metabolism, Rap1 signaling pathway, arachidonic acid metabolism, and osteoclast differentiation closely connected with the hypoglycemic mechanism of PM. And the enzyme activity inhibition tests showed the bioactive ingredients have great hypoglycemic activity.

CONCLUSION

In summary, the study used systems pharmacology to elucidate the main hypoglycemic components and mechanism of PM. The work provided a scientific basis for the further hypoglycemic effect research of PM and its monomer components, but also provided a reference for the secondary development of PM.

Haimufang decoction, a Chinese medicine formula for lung cancer, arrests cell cycle, stimulates apoptosis in NCI-H1975 cells, and induces M1 polarization in RAW 264.7 macrophage cells

BACKGROUND

Lung cancer has the highest morbidity and mortality in the world and novel treatment strategies are still needed. Haimufang decoction (HMF) is a patented clinical prescription of traditional Chinese medicine for lung cancer treatment. HMF is composed of four herbs and has been applied clinically in advanced cancer patients. However, its therapeutic mechanisms are still unclear. This study aims to elucidate the possible mechanisms of HMF for the treatment of lung cancer.

METHODS

3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay was applied for evaluating the proliferative effect of HMF in lung cancer cells and monocyte macrophage RAW264.7 cells. Flow cytometer was used to detect the effects of HMF on cell cycle and apoptosis, and western blotting was employed to explore the potential apoptotic mechanisms of HMF on lung cancer cells. For immunomodulatory effect, co-culture system was used to detect the activation of macrophage RAW264.7 cells when treated with HMF, and neutral red assay was used to measure the effect of HMF on the phagocytosis of the activated macrophages. Enzyme linked immunosorbent assay, flow cytometer, and immunofluorescence staining method were employed for the investigation on the underlying mechanisms of the immunomodulatory effect on RAW264.7 induced by HMF.

RESULTS

HMF inhibited the proliferation, induced S phase cell cycle arrest, and stimulated apoptosis in lung cancer NCI-H1975 cells, while had negligible cytotoxicity on macrophage RAW264.7 cells. Moreover, HMF could activate macrophage RAW264.7 cells and promote the inhibition activity of RAW264.7 cells against lung cancer cells. And also, HMF activated macrophages and increased their phagocytic activity in a concentration-dependent manner. HMF increased the expression of macrophage activation marker CD40, the level of nitric oxide, the generation of intracellular reactive oxygen species, as well as M1 macrophages cytokines including tumor necrosis factor-α, interleukin-1β, interleukin 12 p70, and interleukin 6. Further investigation showed that HMF induced M1 but not M2 phenotype polarization in RAW264.7 cells.

CONCLUSIONS

HMF can mainly exert anticancer activity via (1) cytotoxicity to human lung cancer cells by proliferation inhibition, cell cycle arrest, and apoptosis induction; and also via (2) immunomodulation via macrophage cells activation and M1 phenotype polarization induction.

Systemic pharmacology understanding of the key mechanism of Sedum sarmentosum Bunge in treating hepatitis

Sedum sarmentosum Bunge is a Traditional Chinese Medicine that is widely used in treating hepatitis, whereas the detailed mechanisms have not been fully interpreted. A systemic pharmacology method including absorption, distribution, metabolism and elimination screening, drug targeting, interaction network plotting, and enrichment analysis was applied for exploring the underlying mechanisms of Sedum sarmentosum Bunge in the treatment of hepatitis. A total of 47 ingredients were identified in Sedum sarmentosum Bunge, and 5 active ingredients (DFV, isorhamnetin, beta-sitosterol, luteolin and quercetin) were screened out with the criteria of oral bioavailability (OB) ≥ 30% and drug-likeness (DL) ≥ 0.18. Those 5 ingredients interacted with 170 targets, 163 of which were hepatitis-related. By compound-target-disease network plotting, protein-protein interaction network plotting and enrichment analysis, the pathways that the 5 ingredients engaged in during hepatitis development and progression were investigated, such as threonine-protein kinase signaling. The integrated systemic pharmacology analysis facilitates the in-depth understanding of Sedum sarmentosum Bunge in the hepatitis treatment, which also paves the way for further knowledge of the molecular mechanism of Sedum sarmentosum Bunge in treating hepatitis.

Network Pharmacology-Based Prediction and Verification of the Active Ingredients and Potential Targets of Zuojinwan for Treating Colorectal Cancer

Background

Zuojinwan (ZJW), a famous Chinese medicine formula, has been widely used to treat colorectal cancer (CRC). However, its bioactive compounds, potential targets, and molecular mechanism remain largely elusive.

Aim

A network pharmacology-based strategy combined with molecular docking studies and in vitro validation were employed to investigate bioactive compounds, potential targets, and molecular mechanism of ZJW against CRC.

Materials and Methods

Bioactive compounds and potential targets of ZJW, as well as related genes of CRC, were acquired from public databases. Important ingredients, potential targets, and signaling pathways were determined through bioinformatics analysis, including protein-protein interaction (PPI), the Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, molecular docking and cell experiments were performed to further verify the findings.

Results

A total of 36 bioactive ingredients of ZJW and 163 gene targets of ZJW were identified. The network analysis revealed that quercetin, baicalein, wogonin, beta-sitosterol, and isorhamnetin may be candidate agents. The AKT1, JUN, CDKN1A, BCL2L1, and NCOA1 could become potential drug targets. The KEGG indicated that PI3K-AKT signaling pathway may play an important role in the effect of ZJW against CRC. Molecular docking suggested that quercetin, baicalein, and wogonin combined well with AKT1 and JUN. The in vitro experiment showed that quercetin, the most important ingredient of ZJW, could induce apoptosis of HCT116 cells through PI3K-Akt signaling pathway. This finding was congruent with the prediction obtained through the network pharmacology approach.

Conclusion

This study comprehensively illuminated the active ingredients, potential targets, and molecular mechanism of ZJW against CRC. It also provided a promising approach to uncover the scientific basis and therapeutic mechanism of traditional Chinese medicine (TCM) formula treating for disease.

A bioinformatics investigation into molecular mechanism of Yinzhihuang granules for treating hepatitis B by network pharmacology and molecular docking verification

Yinzhihuang granules (YZHG) is a patented Chinese medicine for the treatment of hepatitis B. This study aimed to investigate the intrinsic mechanisms of YZHG in the treatment of hepatitis B and to provide new evidence and insights for its clinical application. The chemical compounds of YZHG were searched in the CNKI and PUBMED databases, and their putative targets were then predicted through a search of the SuperPred and Swiss Target Prediction databases. In addition, the targets of hepatitis B were obtained from TTD, PharmGKB and DisGeNET. The abovementioned data were visualized using Cytoscape 3.7.1, and network construction identified a total of 13 potential targets of YZHG in the treatment of hepatitis B. Molecular docking verification showed that CDK6, CDK2, TP53 and BRCA1 might be strongly correlated with hepatitis B treatment. Furthermore, GO and KEGG analyses indicated that the treatment of hepatitis B by YZHG might be related to positive regulation of transcription, positive regulation of gene expression, the hepatitis B pathway and the viral carcinogenesis pathway. Network pharmacology intuitively shows the multicomponent, multitarget and multichannel pharmacological effects of YZHG in the treatment of hepatitis B and provides a scientific basis for its mechanism of action.

The effectiveness and safety of Chinese medicines for the treatment of uveitis: A protocol for systematic review and meta-analysis

BACKGROUND

Uveitis is an inflammatory and heterogeneous ocular disorder and has a profound impact on patients' life, work and family. There are substantial costs to the countries and individuals associated with treatment of the complications of uveitis and blindness. Conventional therapies did not lead to satisfactory outcomes for uveitis and are associated with substantial adverse events (AEs). Emerging evidences have proved the important value and potential prospect of Chinese medicines and its compound in uveitis. However, although Chinese medicines are widely used in uveitis, its therapeutic effect and safety are still controversial. It is, therefore, timely to perform an objective and normative systematic review to assess the efficacy and safety of Chinese medicines in treating uveitis on current research.

METHODS

The systematic review will include all of the randomized controlled trials (RCT) on the efficacy and safety of Chinese medicines for uveitis. A relevant literature search by sensitive search strategies was conducted using the following electronic databases from their inception to September 30, 2019: PubMed, Web of Science, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), Wanfang Database, China Science and Technology Journal database (VIP) and Chinese Biomedical Literature database (CBM). The strategy combines treatment terms and disease: that is, "Medicine, Chinese Traditional" (e.g., "Medicine, Chinese Traditional", TCM, Traditional Chinese medicine, Zhong Yi Xue) and uveitis. We will also search registers of clinical trials, potential gray literature, and conference abstracts. There are no limits on language and publication status. The literature screening, data extraction, and quality assessment will be conducted by 2 reviewers independently. The reporting quality and risk of bias will be assessed by other two researchers. Best-corrected visual acuity (BCVA) and improvement in disease activity were assessed as the primary outcome. The secondary outcomes will include laboratory efficacy indexes, score changes in the National Eye Institute Visual Functioning Questionnaire 25 (NEI-VFQ 25), uveitis-related tissue damage or complications, concurrent requirement of corticosteroids, immunosuppressive drugs or biologics, and AEs of treatment. Meta-analysis will be performed using RevMan5.3 software provided by the Cochrane Collaboration.

RESULTS

This study will provide a comprehensive review based on current evidence of Chinese medicines treatment for uveitis in several aspects, including BCVA and improvement in disease activity, laboratory efficacy indexes, score changes in the NEI-VFQ 25, uveitis-related tissue damage or complications, etc. CONCLUSION:: The conclusion of this study will provide evidence to determine whether Chinese medicines are an effective and safe intervention for patients with uveitis.

ETHICS AND DISSEMINATION

It is not necessary to obtain ethical approval for this study, given that this protocol is for a systematic review. The systematic review will be published in a peer-reviewed journal, presented at conferences and will be shared on social media platforms.

PROSPERO REGISTRATION NUMBER

PROSPERO CRD42020153620.

An integrated metabolism in vivo analysis and network pharmacology in UC rats reveal anti-ulcerative colitis effects from Sophora flavescens EtOAc extract

Ulcerative colitis (UC), an immune system disease, is characterized by long duration and easy relapse. Sophora flavescens (S. flavescens), also named "Kushen", is a traditional Chinese medicine, widely used to treat UC in clinics. Alkaloids and flavonoids are the main constituents of S. flavescens. Previous studies indicated that the effects of S. flavescens against UC mainly attribute to its alkaloids. In view of the clinical applications of its flavonoids and our preliminary experiments on the effects of S. flavescens treatment, we speculated that flavonoids also could exert an anti-UC effect, but its efficacy and mechanism are still not yet to be revealed. Herein, we examined the pharmacodynamic effects of the ethyl acetate (EtOAc) extract of S. flavescens EtOAc (SFE) against dextran sodium sulfate-induced UC rats for the first time. Pharmacodynamic effects indicated that SFE could significantly alleviate the loss in the body weight and shortening of the colon length, reduce colon bleeding and improve colon tissue damage of UC rats. A total of 28 prototypes and 41 metabolites were unambiguously or tentatively detected in rat's plasma and urine. Among them, 28 prototypes and 3 phase I metabolites shared 40 UC targets, the targets contributed to 51 metabolic pathways in 5 modules. Additionally, genistein, formononetin, isokurarinone, kurarinone, maackiain, kushenol N, trifolirnizin, kuraridin and norkurarinone were suggested to be potential active compounds in SFE for treating UC by comprehensively investigating the results of network pharmacology analysis, metabolic analysis in vivo, and previous researches. Finally, a combination of metabolic analysis in vivo with network pharmacology can elucidate the material basis and pharmacodynamic effect of traditional Chinese medicines, and lay the foundation for further clarify the anti-UC mechanism of SFE.

Systems pharmacology reveals the mechanism of activity of Ge-Gen-Qin-Lian decoction against LPS-induced acute lung injury: A novel strategy for exploring active components and effective mechanism of TCM formulae

Acute lung injury (ALI), a severe and life-threatening inflammation of the lung, with high morbidity and mortality, underscoring the urgent need for novel treatments. Ge-Gen-Qin-Lian decoction (GQD), a classic Chinese herbal formula, has been widely used to treat intestine-related diseases in the clinic for centuries. In recent years, a growing number of studies have found that GQD has a favorable anti-inflammatory effect. With the further study on the viscera microbiota, the link between the lungs and the gut-the gut-lung axis has been established. Based on the theory of the gut-lung axis, we used systems pharmacology to explore the effects and mechanisms of GQD treatment in ALI. Hypothesizing that GQD inhibits ALI progression, we used the experimental model of lipopolysaccharide (LPS)-induced ALI in Balb/c mice to evaluate the therapeutic potential of GQD. Our results showed that GQD exerted protective effects against LPS-induced ALI by reducing pulmonary edema and microvascular permeability. Meanwhile, GQD can downregulate the expression of LPS-induced TNF-α, IL-1β, and IL-6 in lung tissue, bronchoalveolar lavage fluid (BLAF), and serum. To further understand the molecular mechanism of GQD in the treatment of ALI, we used the network pharmacology to predict the disease targets of the active components of GQD. Lung tissue and serum samples of the mice were separately analyzed by transcriptomics and metabolomics. KEGG pathway analysis of network pharmacology and transcriptomics indicated that PI3K/Akt signaling pathway was significantly enriched, suggesting that it may be the main regulatory pathway for GQD treatment of ALI. By immunohistochemical analysis and apoptosis detection, it was verified that GQD can inhibit ALI apoptosis through PI3K/Akt signaling pathway. Then, we used the PI3K inhibitor LY294002 to block the PI3K/Akt signaling pathway, and reversely verified that the PI3K/Akt signaling pathway is the main pathway of GQD anti-ALI. In addition, differential metabolites in mice serum samples indicate that GQD can inhibit the inflammatory process of ALI by reversing the imbalance of energy metabolism. Our study showed that, GQD did have a better therapeutic effect on ALI, and initially elucidated its molecular mechanism. Thus, GQD could be exploited to develop novel therapeutics for ALI. Moreover, our study also provides a novel strategy to explore active components and effective mechanism of TCM formula combined with TCM theory to treat ALI.

Network pharmacology analysis of Chaihu Lizhong Tang treating non-alcoholic fatty liver disease

BACKGROUND

In this study, the network pharmacological methods were used to predict the target of active components of Chaihu Lizhong Tang (CHLZT) in the treatment of non-alcoholic fatty liver disease (NAFLD).

METHOD

The active components of "CHLZT", their targets, and NAFLD related targets were screened by multiple databases, and the potential targets of "CHLZT" in the treatment of NAFLD were predicted. The active component-target network of "CHLZT" was constructed by Cytoscape software. The potential target of "CHLZT" for the treatment of NAFLD constructed protein-protein interaction (PPI) network in the Search Tool for the Retrieval of Interacting Genes Database (STRING). The hub genes of "CHLZT" in the treatment of NAFLD were screened by network topological parameters, and the results were verified by molecular docking. "ClusterProfiler" in R was used for Gene Ontology (GO) analysis and KEGG pathway enrichment analysis.

RESULTS

OB ≥ 30 % and DL ≥ 0.18 were selected as the screening criteria of active components. A total of 83 active components and 456 targets were selected. Based on the evaluation of topological parameters of degree network, five hub genes for interaction with "CHLZT" therapy for NAFLD were screened, that is, AKT1, ALB, IL6, EGFR, and CASP3. The results of molecular docking showed that the active components in "CHLZT" had a good binding ability with the key targets. The enrichment analysis results showed that the treatment of NAFLD with "CHLZT" mainly involved in cofactor binding, protease binding, AGE-RAGE signaling pathway in diabetic complications, and IL-17 signaling pathway, which mediated the potential mechanism of "CHLZT" intervention in NAFLD.

CONCLUSION

The molecular mechanism of "CHLZT" in the treatment of NAFLD indicated the synergistic features of multi-component, multi-target, and multi-pathway of traditional Chinese medicine, which provided an important scientific basis for further elucidating the mechanism of "CHLZT" in the treatment of NAFLD.