Network Pharmacology Method Research Articles

Ocular adverse events associated with GLP-1 receptor agonists: a real-world study based on the FAERS database and network pharmacology

ABSTRACT Objective This study evaluates the risk of ocular adverse events (AEs) associated with glucagon-like peptide-1 receptor agonists (GLP-1 RAs) using data from the FDA Adverse Event Reporting System (FAERS) and network pharmacology methods. Methods FAERS data from 2004 to 2024 were analyzed for ocular AEs linked to GLP-1 RA treatments. Disproportionality analysis (Reporting Odds Ratio, ROR) was used to identify signals, and a drug-gene interaction network explored potential mechanisms. Results Among 17,785,793 FAERS reports, semaglutide and lixisenatide were significantly associated with ocular AEs, with RORs of 1.25 (95% CI, 1.20-1.31) and 1.96 (95% CI, 1.70-2.27), respectively. Commonly reported AEs included blurred vision, visual impairment, and diabetic retinopathy, with some AEs occurring as early as 10 days after treatment initiation. Gene enrichment analysis highlighted potential links between GLP-1-related genes and ocular AEs. Conclusion The widespread use of GLP-1 RAs has raised concerns regarding their ophthalmic safety. This study contributes new evidence from real-world data, suggesting that semaglutide and lixisenatide are associated with significant risks of ocular AEs. Further experimental studies are warranted to elucidate the underlying mechanisms and confirm these associations.

Network pharmacology and molecular docking to explore the potential molecular mechanism of chlorogenic acid treatment of oral squamous cell carcinoma.

Oral squamous cell carcinoma (OSCC) is a tumor type with a high mortality rate. Chlorogenic acid, abundant in resources and widely utilized in cancer treatments, has seen limited studies regarding its efficacy against OSCC. This paper investigates chlorogenic acid's mechanism in treating OSCC, aiming to guide the development of novel drugs. The study employed network pharmacology, molecular docking, and survival analysis methods. Network pharmacological analysis revealed chlorogenic acid targets 23 OSCC-related proteins, including ESR1, MMP2, MMP9, SRC, MAPK8, MAPK1, CDC42, ERBB2, ATM, and BRAF. Molecular docking simulations indicated that the primary target exhibits significant binding capacity with chlorogenic acid, with MMP9 associated with tumor migration and angiogenesis standing out. Survival analysis demonstrated that the downregulation of most primary targets correlates with improved survival rates in OSCC patients. Enrichment analysis of therapeutic targets highlighted the pivotal role of MAPK-ERK and MAPK-JNK signaling pathways in chlorogenic acid's efficacy against OSCC. This paper predicts chlorogenic acid's potential targets and proposes its molecular mechanism in treating OSCC, offering a theoretical foundation for its application in OSCC treatment. We used traditional Chinese medicine, a disease pharmacology-related information base, and an analysis platform to predict targets. The Cytoscape 3.9.1 and STING databases were used to address common targets for drugs and diseases, establish networks of protein interaction relationships, and screen core targets. Meastro11.5 was used for molecular docking simulation. R4.2.2 was used for survival analysis and joint target enrichment analysis. Network pharmacological analysis identified chlorogenic acid acting on 23 OSCC targets. Molecular docking simulations revealed a strong binding affinity of chlorogenic acid compounds with these targets, particularly MMP9, essential for tumor migration and angiogenesis. Survival analysis indicated that the downregulation of most core targets was correlated with improved OSCC patient survival. Enrichment analysis of therapeutic targets highlighted the critical roles of the MAPK-ERK and MAPK-JNK signaling pathways in the effectiveness of chlorogenic acid against OSCC. This study predicted the potential targets of chlorogenic acid in OSCC treatment and hypothesized its molecular mechanism, offering a theoretical foundation for its use in OSCC therapy.

Mechanism of Asperosaponin VI Related to EGFR/MMP9/AKT/PI3K Pathway in Treatment of Rheumtoid Arthritis.

To explore the mechanism of action of asperosaponin VI (AVI) in the treatment of rheumatoid arthritis (RA) and validate it in ex vivo experiments using network pharmacology and molecular docking methods. The predicted targets of AVI were obtained from PharmMaper, UniProt and SwissTarget Prediction platforms, the disease targets were collected from Online Mendelian Inheritance in Man, Therapeutic Target Database and GeneCards databases, the intersection targets of AVI and RA were obtained from Venny 2.1.0, and the protein-protein interaction (PPI) network was obtained from STRING database, which was analyzed by Cytoscape software and screened to obtain the core targets. Cytoscape software was used to analyze PPI network and screen the core targets. Based on the Database for Annotation, Visualization and Integrated Discovery database, Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed, and Cytoscape software was used to construct the "Disease-Pathway-Target-Drug" network, which was finally verified by molecular docking and animal experiments. Network pharmacological studies showed that AVI was able to modulate 289 targets, with 102 targets for the potential treatment of RA, with the core pathway being the AKT/PI3K signaling pathway, and the core targets being the epidermal growth factor receptor (EGFR) and matrix metalloproteinase 9 (MMP9). Molecular docking results showed that AVI could produce strong binding with both of the 2 core targets. In vitro cellular experiments showed that AVI reduced nitric oxide, prostaglandin E2, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and IL-1 β levels (P<0.05) and inhibited cyclooxygenase-2, nitric oxide synthase, EGFR, MMP9, phosphorylated phosphoinositide 3-kinase (p-PI3K), and phosphorylated serine-threonine kinase (p-AKT) proteins (P<0.05). The results of in vivo studies showed that AVI improved RA score and foot swelling thickness and decreased TNF-α, IL-6, p-PI3K and p-AKT levels in RA rats (P<0.05). AVI exerts anti-inflammatory and anti-RA effects which might be related to the EGFR/MMP9/AKT/PI3K pathway.

Unveiling the efficacy and mechanism of Danggui-Shaoyao-San in treating nephrotic syndrome: A meta-analysis and network pharmacology study

Aim of the studyThe purpose of this study was to investigate the efficacy and mechanism of DSS in treating nephrotic syndrome through meta-analysis and network pharmacology methods. Materials and methodsTo conduct a comprehensive search for randomized controlled trials on the efficacy of Danggui Shaoyao San (DSS) in the treatment of nephrotic syndrome, we searched across eight electronic databases from their establishment to May 1, 2023. The Cochrane Collaboration's Risk of Bias 2 tool was used to evaluate the quality of evidence regarding bias risk and outcomes. Statistical analysis was performed using RevMan software (version 5.4). Furthermore, network pharmacology was employed to validate the underlying mechanism. ResultsThis study included 14 articles that involved 1256 patients with nephrotic syndrome. The clinical efficacy of DSS against nephrotic syndrome was significantly higher than that of Western medical treatment alone. In comparison with the control groups, which were administered Western medicines alone, the use of DSS significantly increased plasma albumin levels (mean difference [MD] = 4.32, 95 % confidence interval [CI] [2.37, 6.24], p < 0.00001) and reduced 24 h urinary protein excretion (MD = −0.92, 95 % CI [−1.11, −0.73], p < 0.00001), total cholesterol levels (MD = −1.23, 95 % CI [−1.76, −0.70], p < 0.00001), triglyceride levels (MD = −0.37, 95 % CI [−0.54, −0.20], p < 0.00001). Furthermore, the combination of DSS with Western medicines achieved better control of adverse reactions in comparison with the control groups (relative risk = 0.37, 95 % CI [0.29, 0.49], p < 0.00001). Network pharmacology analysis identified 39 important active compounds and 18 core target genes involved in the treatment of primary nephrotic syndrome by DSS. Gene Ontology enrichment analysis identified 2126 biological processes, 64 cellular components, and 115 molecular functions, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified 149 signaling pathways. Key active compounds include ginsenoside Rg5, ginsenoside Rg1, schisandrin A, berberine, gallic acid, quercetin, and β-sitosterol, while potential core target genes include IL6, AKT1, TNF, VEGFA, IL1B, and TP53. KEGG pathway analysis indicated that DSS is involved in multiple mechanisms, such as neural development, synaptic plasticity, programmed cell death, inflammation, and immunity. ConclusionsDSS has higher efficacy and safety in the treatment of nephrotic syndrome and acts on nephrotic syndrome via mechanisms that involve multiple targets, components, and pathways.

Asiatic acid induces lung cancer toxicity by triggering SRC-mediated ferroptosis

Ferroptosis is a recently discovered form of regulated cell death that shows promise as a novel approach for inducing tumor cell death in cancer treatment, with significant research potential. Asiatic acid (AA), a key component of the traditional Chinese medicine Centella asiatica, has been identified as having potential therapeutic benefits for various diseases, particularly cancer. Non-small cell lung cancer (NSCLC) is a challenging and prevalent form of cancer to treat. In our study, we utilized network pharmacology, molecular docking, and experimental methods to investigate the potential of AA in treating NSCLC and to elucidate its role in inhibiting cancer through the ferroptosis pathway. Through network pharmacology analysis, we identified that AA targets the core NSCLC protein SRC through the ferroptosis pathway. Our experiments demonstrated that treatment with AA led to increased iron accumulation, mitochondrial membrane potential, and expression of ferroptosis markers glutathione peroxidase 4 (GPX4), ferritin heavy chain 1 (FTH1), and acyl-CoA synthetase long chain family member 4 (ACSL4) in NSCLC cells, confirming the induction of ferroptosis. In conclusion, AA has the potential to target SRC and induce NSCLC cell death through the ferroptosis pathway, offering a promising approach for cancer treatment.

Evaluation of the Mechanism of Yishan Formula in Treating Breast Cancer Based on Network Pharmacology and Experimental Verification.

Yishan formula (YSF) has a significant effect on the treatment of breast cancer, which can improve the quality of life and prolong the survival of patients with breast cancer; however, its mechanism of action is unknown. In this study, network pharmacology and molecular docking methods have been used to explore the potential pharmacological effects of the YSF, and the predicted targets have been validated by in vitro experiments. Active components and targets of the YSF were obtained from the TCMSP and Swiss target prediction website. Four databases, namely GeneCards, OMIM, TTD, and DisGeNET, were used to search for disease targets. The Cytoscape v3.9.0 software was utilized to draw the network of drug-component-target and selected core targets. DAVID database was used to analyze the biological functions and pathways of key targets. Finally, molecular docking and in vitro experiments have been used to verify the hub genes. Through data collection from the database, 157 active components and 618 genes implicated in breast cancer were obtained and treated using the YSF. After screening, the main active components (kaempferol, quercetin, isorhamnetin, dinatin, luteolin, and tamarixetin) and key genes (AKT1, TP53, TNF, IL6, EGFR, SRC, VEGFA, STAT3, MAPK3, and JUN) were obtained. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the YSF could affect the progression of breast cancer by regulating biological processes, such as signal transduction, cell proliferation and apoptosis, protein phosphorylation, as well as PI3K-Akt, Rap1, MAPK, FOXO, HIF-1, and other related signaling pathways. Molecular docking suggested that IL6 with isorhamnetin, MAPK3 with kaempferol, and EGFR with luteolin have strong binding energy. The experiment further verified that YSF can control the development of breast cancer by inhibiting the expression of the hub genes. This study showed that resistance to breast cancer may be achieved by the synergy of multiple active components, target genes, and signal pathways, which can provide new avenues for breast cancer-targeted therapy.

Unraveling Cordia myxa’s anti-malarial potential: integrative insights from network pharmacology, molecular modeling, and machine learning

Malaria is a potentially fatal infective illness caused due to parasites that belong to the Plasmodium genus, which are transferred to humans with the help of the stings of affected female Anopheles mosquitoes, and it persists as a serious public wellness problem worldwide. Cordia myxa is a medicinal plant that possesses various medicinal characteristics like antimicrobial, anti-inflammation, antioxidant, and antidiabetic activities, which makes it an important natural resource for the therapy of different maladies in traditional medicine. In this investigation, a certain network pharmacology method has been utilized to identify the potent active components, possible targets as well as signaling pathways present in C. myxa in relation to malaria therapy. The active compounds were submitted to molecular docking approaches to validate their successful activity against the potential targets. The study concluded that three constituents named cosmosiin, stigmastanol, robinetin, and quercetin were highly active and could regulate the expression of Interleukin 6 (IL6) and Cysteine-aspartic acid protease 3 (CASP3), which may act as a potential therapeutic target for malaria treatment. These analyses are validated by molecular dynamics simulation which reflects on the overall structural stability of the intermolecular conformation and interactions. These results can also be witnessed in simulation-based trajectories binding free energies, which concluded the significant role of electrostatic and van der Waals energies in total intermolecular interactions. Finally, we utilized machine learning to predict the anti-malarial activity of C. myxa compounds, comparing them with approved drugs. Using the Chemprop model and MAIP predictions, we assessed ten compounds, revealing their potential as lead anti-malarial agents. This study establishes a groundwork for comprehending the function of the anti-malaria action of C. myxa.

Based on Spectrum-Effect Relationship, Network Pharmacology, and Molecular Docking, the Material Basis and Mechanism of Antioxidant Effect of Miao Medicine Indigofera stachyoides Lindl Were Studied.

Indigofera stachyoides Lindl (IS.Lindl, Xuerensen in Chinese) is a traditional medicine frequently utilized by ethnic minorities; nevertheless, the chemicals responsible for these effects have not been identified. Ultraperformance liquid chromatography (UPLC) was utilized to establish the fingerprints of various origins. Free radical scavenging in 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) and 2,2-biazobis(3-ethyl-phenylpropylthiazole-6-sulfonate) diammonium salt (ABTS) assays was used to evaluate the antioxidant activity. Partial least-squares regression analysis (PLSR) and gray correlation analysis (GRA) were utilized to determine the spectral-effect relationship in order to screen the antioxidant pharmacodynamic components. The corresponding targets were obtained from Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Integrated Traditional Chinese Medicine (ITCM). Disease-related targets for antioxidants were collected from GeneCards and Online Mendelian Inheritance in Man (OMIM) databases. The PPI interaction network analysis, GO enrichment analysis, and KEGG pathway analysis were established using the online analysis platform, and Autodock software assisted in aligning the components with important targets. The fingerprint profile revealed 32 common peaks, and eight standards were identified using standard comparison, with similarity ranging from 0.920 to 0.995. The primary antioxidant components include proanthocyanidin B1, epicatechin, and proanthocyanidin B3. Important targets include EGFR, CASP3, IL6, PTGS2, and TNF. Important signaling pathways include the AGE-RAGE signaling pathways in diabetic complications, the MAPK signaling pathway, the IL-17 signaling pathway, and the pathways in cancer. The results of molecular docking technology showed that the main active ingredients of the drug could bind well to the core target. In this study, we successfully established the spectral-effect relationship of IS.Lindl and clarified the effective substances of IS.Lindl. Through network pharmacology and molecular docking methods, it was clear that IS.Lindl plays an antioxidant role through multicomponent, multitarget, and multipathway synergy.

Mechanism of action of "cistanche deserticola-Polygala" in treating Alzheimer's disease based on network pharmacology methods and molecular docking analysis.

This article used network pharmacology, molecular docking, GEO analysis, and Gene Set Enrichment Analysis to obtain 38 main chemical components and 66 corresponding targets involved in Alzheimer's disease (AD) treatment in "Cistanche deserticola-Polygala". Through further Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis, we obtained AD signalling pathways, calcium signalling pathways, and other signalling pathways related to the treatment of AD with "Cistanche deserticola-Polygala". Molecular docking showed that most of the core chemical components had good binding ability with the core targets. This article aims to reveal the mechanism of "Cistanche deserticola-Polygala" in treating AD and provide a basis for the treatment of AD with "Cistanche deserticola-Polygala".

From Life's Essential 8 to metabolic syndrome: insights from NHANES database and network pharmacology analysis of quercetin.

Metabolic syndrome (MetS), or syndrome X, is a collection of metabolic illnesses that affect the body's health, particularly insulin resistance and obesity. The prevalence of MetS is on the rise, particularly among younger individuals. Quercetin, a natural flavonoid found in many traditional Chinese medicines, can impact various pathways to disrupt the pathological advancement of MetS with few negative effects. The American Heart Association recently introduced a cardiovascular health assessment termed Life's Essential 8 (LE8), which might impact the treatment of MetS. Quercetin targets and their functions in MetS pathways were identified using a network pharmacology method and molecular docking techniques. The study examined quercetin's direct and indirect interactions with proteins linked to the pathogenic processes of MetS. Data were collected regarding the American Heart Association's LE8 cardiovascular health indicators, which include health behaviors (diet, physical activity, nicotine exposure, and sleep) and health factors (body mass index, non-high-density lipoprotein cholesterol, blood glucose, and blood pressure). The study assessed the connection between LE8 and the occurrence of MetS, taking into account dietary quercetin consumption as a variable of interest. The negative correlation between MetS and LE8 indicates that individuals with higher LE8 scores are less likely to develop MetS. Individuals in the fully adjusted highest group (LE8 ≥ 80) demonstrated a 79% lower likelihood of developing MetS than those in the lowest group (OR = 0.21; 95% CI, 0.17-0.26, p < 0.0001). Network pharmacology and molecular docking results show that quercetin may exert its therapeutic effects by modulating various biological response processes, including those related to xenobiotic stimuli, bacterial molecules, lipopolysaccharides, and oxidative stimuli. These processes involve key pathways associated with diabetic complications, such as the AGE-RAGE signaling pathway, pathways related to diabetic complications, and pathways involved in lipids and atherosclerosis. Therefore, quercetin may reduce cardiovascular risk, improve glucose-lipid metabolism, and alleviate insulin resistance and other biological processes by influencing multiple aspects of the lipid profile, blood glucose, and insulin resistance, ultimately impacting the links between LE8 score and MetS. This study discovered that an optimal LE8 score is a marker of adopting a lifestyle of wellness and is connected with a reduced likelihood of developing MetS. Quercetin acts on core targets such as IL6, BCL2, TP53, IL1B, MAPK1, and CCL2, and then plays a therapeutic role in regulating lipid metabolism, anti-inflammation, immunomodulation, autophagy, etc., through the pathways of diabetic complications, lipids, atherosclerosis, etc., and has the characteristics of multi-targets, multi-pathways, and multi-functions in regulating interventions for MetS.

Network Pharmacology and Molecular Docking to Explore the Mechanism of Action of Danxiong Huoxue Tablets for the Prevention and Treatment of Heterotopic Ossification

Background: Danxiong Huoxue tablets have been used clinically to prevent and treat Heterotopic Ossification (HO) after total hip arthroplasty, but its therapeutic mechanism is not clear. background: Danxiong Huoxue Tablets has been used clinically to prevent and treat heterotopic ossification (HO) after total hip arthroplasty, but its therapeutic mechanism is not clear. Objectives: This study investigated the potential mechanism of action of Danxiong Huoxue tablets against HO using network pharmacology and molecular docking methods. Methods: The TCMID and SymMap databases and the existing literature were used to screen the active ingredients and targets of Danxiong Huoxue tablets, and the targets of heterotopic ossification were obtained from Gene Cards, DisGeNET, and PharmGkb databases. The PPI network diagram was constructed using the String database and Cytoscape 3.9.1 software. Finally, the core targets were analyzed by GO and KEGG enrichment and validated by molecular docking. Results: A total of 39 active ingredients and 328 corresponding targets of Danxiong Huoxue tablets were identified, which were enriched in signaling pathways, such as PI3K/Akt and MAPK. Molecular docking verified that there was good binding activity between the core targets and the corresponding components. Conclusion: Danxiong Huoxue tablets may prevent and treat HO by acting on key targets, such as SRC, AKT1, JUN, and TNF, and regulating the PI3K/Akt signaling pathway and MAPK signaling pathway.

Integrating protein interaction and pathway crosstalk network reveals a promising therapeutic approach for psoriasis through apoptosis induction

Psoriasis is a complex inflammatory skin disease manifested by altered proliferation and differentiation of keratinocytes with dysfunctional apoptosis. This study aimed to identify regulatory factors and comprehend the underlying mechanisms of inefficient apoptosis to open up promising therapeutic approaches. Incorporating human protein interactions, apoptosis proteins, and physical relationships of psoriasis-apoptosis proteins helped us to generate a psoriasis-apoptosis interaction (SAI) network. Subsequently, topological and functional analyses of the SAI network revealed effective proteins, functional modules, hub motifs, dysregulated pathways and transcriptional gene regulatory factors. Network pharmacology, molecular docking and molecular dynamics simulation methods identified the potential drug-target interactions. RELA, MAPK1, MAPK3, MMP9, IL1B, AKT1 and STAT1 were revealed as effective proteins. The MAPK1-MAPK3-RELA motif was identified as a hub regulator in the crosstalk between 41 pathways. Among all pathways, “lipid and atherosclerosis” was found to be the predominant pathway. Acetylcysteine, arsenic-trioxide, β-elemene, bortezomib and curcumin were identified as potential drugs to inhibit pathway crosstalk. Experimental verifications were performed using the literature search, GSE13355 and GSE14905 microarray datasets. Drug-protein-pathway interactions associated with apoptosis were deciphered. These findings highlight the role of hub motif-mediated pathway-pathway crosstalk associated with apoptosis in the complexity of psoriasis and suggest crosstalk inhibition as an effective therapeutic approach.

Mechanisms of Action of the Herba Salviae Chinensis-Fructus Akebiae Pair in the Treatment of Non-small Cell Lung Cancer based on a Network Pharmacology Study

Objective: To study the active ingredients and mechanism of action of "Herba Salviae Chinensis-Fructus Akebiae" drug pair in the treatment of non-small cell lung cancer (NSCLC) by using network pharmacology to provide theoretical basis for clinical application. Methods: The TCMSP (Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform) was used to obtain the active ingredients and targets of "Herba Salviae Chinensis-Fructus Akebiae", and the results were analyzed by the Genecard (https://genecard, org/) database, the Online Mendelian Inheritance Network (OMI), the Genecard database, the Genecard database, and the Online Mendelian Inheritance Network. We searched the Genecard (https://genecard, org/) database and the Online Mendelian Inheritance in Man (OMIM) database (http://omim. org/) for non-small cell lung cancer (NSCLC) disease targets by selecting "NSCLC" as a keyword, and then obtained the results of the "Herba Salviae Chinensis-Fructus Akebiae" drug pair by using venn. We used venn to obtain the intersecting targets of the drug pair "Herba Salviae Chinensis-Fructus Akebiae" and NSCLC, and then used the STRING database and Cytoscape to construct a common target visualization network diagram. The gene (GO) enrichment analysis and KEGG enrichment analysis were realized with the help of metascape database and Microbiology platform. Results: Five active ingredients of Ishiminokan-Precipitant were obtained, and 3695 non-small cell lung cancer targets and 123 common targets were obtained. GO analysis showed that the process of GO enrichment was mainly related to the regulation of responses to inorganic substances, transcriptional regulatory complexes, cytokine receptor binding, etc. KEGG enrichment showed that the process of KEGG enrichment was mainly through Pathways in Cancer, ILRT, and cytokine receptor binding. KEGG enrichment showed that KEGG mainly exerted anti-cancer effects through pathways in cancer and IL-17 signaling pathway. Conclusion: Using the method of network pharmacology, it is proved that the drug pair "Herba Salviae Chinensis-Fructus Akebiae" can exert therapeutic effects on NSCLC through multi-components, multi-targets, and multi-pathways, and provides the theoretical basis for the clinical application.

Exploring the Potential Effects and Mechanism of Astragalus Membranaceus in Treating Ischemic Heart Failure Based on Network Pharmacology and Experimental Verification.

Astragalus membranaceus (AM) is a traditional Chinese medicine that has been clinically utilized as an adjunctive therapy for the treatment of myocardial ischemia and heart failure; however, its precise molecular mechanism of action remains unknown. This study aims to investigate the potential pharmacological effects and molecular mechanism of AM in the treatment of ischemic heart failure (IHF) using network pharmacology methods, molecular docking technology, and in vitro experiments. The active components and targets of AM were obtained from the TCMSP databases, while the disease targets of IHF were retrieved from GeneCards and OMIM databases. The analysis of overlapping targets between AM and IHF mainly included active compounds-targets network, PPI network, and GO and KEGG enrichment analysis. The association between active compounds and target proteins was verified through molecular docking. Additionally, an in vitro experimental model was used to evaluate the accuracy of the forecast results. The network pharmacological analysis revealed that quercetin, kaempferol, 7-Omethylisomucronulatol, formononetin, and isorhamnetin were the core active components of AM in treating IHF. The core targets included AKT1, IL6, IL1B, PTGS2, CASP3, MMP9, and HIF1A. The molecular docking results demonstrated a strong binding affinity between these active components and targets. The KEGG pathway analysis suggested that the PI3K-AKT signaling pathway might play a central role in mediating AM's therapeutic effects on IHF. In vitro experiments demonstrated that AM treatment enhanced cell viability, reduced heart failure biomarkers, and suppressed cell apoptosis. Furthermore, the western blot analyses indicated that AM treatment effectively regulated AKT1 phosphorylation in an experimental model of IHF. Through integrated network pharmacological analysis, molecular docking technology, and in vitro experimental validation, it was demonstrated that AM can effectively mitigate IHF through activating PI3K-AKT signaling pathway. These findings significantly advance our understanding of the molecular mechanisms in IHF treatment and contribute further to promoting the clinical application of AM.

Baicalin Ameliorates Depression-like Behaviors via Inhibiting Neuroinflammation and Apoptosis in Mice

Depression is a common neuropsychiatric disease which brings an increasing burden to all countries globally. Baicalin, a flavonoid extracted from the dried roots of Scutellaria, has been reported to exert anti-inflammatory, antioxidant, and neuroprotective effects in the treatment of depression. However, the potential biological mechanisms underlying its antidepressant effect are still unclear. In the present study, we conducted extensive research on the potential mechanisms of baicalin’s antidepressant effect using the methods of network pharmacology, including overlapped terms-based analysis, protein–protein interaction (PPI) network topology analysis, and enrichment analysis. Moreover, these results were further verified through molecular docking, weighted gene co-expression network analysis (WGCNA), differential gene expression analysis, and subsequent animal experiments. We identified forty-one genes as the targets of baicalin in the treatment of depression, among which AKT1, IL6, TP53, IL1B, and CASP3 have higher centrality in the more core position. Meanwhile, the roles of peripheral genes derived from direct potential targets were also observed. Our study suggested that biological processes, such as inflammatory reaction, apoptosis, and oxidative stress, may be involved in the therapeutic process of baicalin on depression. These mechanisms were validated at the level of structure, gene, protein, and signaling pathway in the present study. Taken together, these findings propose a new perspective on the potential mechanisms underlying baicalin’s antidepressant effect, and also provide a new basis and clarified perspective for its clinical application.

Hepatoprotective action mechanism and quantification of soyasaponin Bb in Abri Herba by HPLC and network pharmacology

Ethnopharmacological relevanceThe herb of Abrus cantoniensis Hance (AC) is an important Traditional Chinese Medicine (TCM) and is also used as an herbal tea with hepatoprotective action. Soyasaponin Bb is one of the pharmacodynamic substances of AC for the herb's effective pharmacological activity. This study aims to investigate the anti-fibrotic and hepatoprotective activities of soyasaponin Bb in vivo and in vitro experiments, mechanism by network pharmacology and quantification by HPLC. Materials and methodsHigh-performance liquid chromatography (HPLC) was applied to evaluate the quality of the herb and determine the contents of soyasaponin Bb from different sources and parts of the AC. In vivo experiments were conducted to induce an acute liver injury model by injecting CCl4 into mice, and an in vitro hepatic fibrosis model was established by cultivating LX-2 cells with TGF-β1. These models were used to explore the anti-fibrotic and hepatoprotective effects of soyasaponin Bb and its underlying mechanisms. In addition, the potential target genes corresponding to soyasaponin Bb were identified using the Swiss Target Prediction database through network pharmacology methods. Meanwhile, hepatic fibrosis targets were screened using the GeneCards, TTD, and OMIM disease databases. The STING database was used to construct the protein-protein interaction (PPI) network of soyasaponin Bb-hepatic fibrosis. The soyasaponin Bb-hepatic fibrosis disease target-pathway network was constructed using Cytoscape 3.9.1 software. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to enrich and analyze the common targets of the drug and the disease, aiming to identify the potential targets and pathways involved in the anti-fibrotic and hepatoprotective effects of soyasaponin Bb. ResultsThe content of soyasaponin Bb varied across different sources, with the roots containing the highest concentration, up to 0.2480%. In vivo experiments showed that soyasaponin Bb had a protective effect against CCl4-induced acute liver injury, effectively inhibiting the increase in ALT and AST levels and slowing down the hepatocyte inflammatory damage caused by CCl4. Soyasaponin Bb also down-regulated MDA levels and up-regulated SOD levels, indicating a certain antioxidant capacity. In vitro cell experiments showed that soyasaponin Bb could effectively inhibit the proliferation of HSC-LX2 cells induced by TGF-β1 by regulating the TGF-β1/α-SMA pathway, significantly down-regulate the protein expression of TGF-β1 and α-SMA, while also reducing the levels of inflammatory cytokines IL-6 and IL-1β. Further network pharmacology analysis suggested that soyasaponin Bb can exert anti-fibrosis activity by regulating the IBD signaling pathway, Th17 signaling pathway, Hepatitis B signaling pathway, and JAK-STAT signaling pathway. ConclusionSoyasaponin Bb is primarily distributed in the root of AC, and it has a strong protective effect against CCl4-induced acute liver injury. It can reduce the level of inflammatory factors, relieve inflammation, and exert anti-fibrotic activity by regulating the TGF-β1/α-SMA pathway. Its potential anti-hepatic fibrosis mechanism has been investigated through network pharmacology.

Identification and screening of potential anti-pneumonia active ingredients and targets of Qing-Kai-Ling oral liquid via UHPLC-Q-Exactive Orbitrap mass spectrometry based on data post-processing

Qing-Kai-Ling oral liquid is commonly used clinically for the treatment of fever and upper respiratory tract infection. Moreover, studies have shown that Qing-Kai-Ling oral liquid has an anti-pneumonia effect. However, owing to its complex pharmacodynamic material basis, its pharmacological research and clinical application are limited. To address this problem, the chemical constituents of Qing-Kai-Ling oral liquid were identified by ultra-high performance liquid chromatography quadrupole-Exactive Orbitrap mass (UHPLC-Q-Exactive Orbitrap MS) and network pharmacology methods, which were used to predict its potential anti-pneumonia target and signalling pathway. A total of 150 compounds were identified and tentatively characterized, including 35 amino acids and their derivatives, 36 organic acids, 20 terpenoids, 20 alkaloids, 12 glycosides, 7 flavonoids, and 20 others. Among them, 14 compounds were accurately identified by comparing their retention time and mass spectrum data with those of reference substances. Additionally, we performed molecular simulation calculations via Density Function Theory to determine the plausibility of the compound cleavage reactions and further confirm compound structures. Furthermore, 90 key targets were screened through network pharmacology, with the particular focus on the PI3K-AKT, MAPK and TNF signalling pathways. This method achieved the first comprehensive identification of the chemical composition of Qing-Kai-Ling oral liquid and elucidated its potential mechanism of anti-pneumonia. The results provide valuable reference and data support for pharmacodynamic substance research and quality control.

Natural hydrogen gas and engineered microalgae prevent acute lung injury in sepsis

BackgroundHydrogen gas and microalgae both exist in the natural environment. We aimed to integrate hydrogen gas and biology nano microalgae together to expand the treatment options in sepsis. MethodsPhosphoproteomics, metabolomics and proteomics data were obtained from mice undergoing cecum ligation and puncture (CLP) and inhalation of hydrogen gas. All omics analysis procedure were accordance with standards. Multi R packages were used in single cell and spatial transcriptomics analysis to identify primary cells expressing targeted genes, and the genes’ co-expression relationships in sepsis related lung landscape. Then, network pharmacology method was used to identify candidate drugs. We used hydrophobic-force-driving self-assembly method to construct dihydroquercetin (DQ) nanoparticle. To cooperate with molecular hydrogen, ammonia borane (B) was added to DQ surface. Then, Chlorella vulgaris (C) was used as biological carrier to improve self-assembly nanoparticle. Vivo and vitro experiments were both conducted to evaluate anti-inflammation, anti-ferroptosis, anti-infection and organ protection capability. ResultsAs a result, we identified Esam and Zo-1 were target phosphorylation proteins for molecular hydrogen treatment in lung. Ferroptosis and glutathione metabolism were two target pathways. Chlorella vulgaris improved the dispersion of DQB and reconstructed morphological features of DQB, formed DQB@C nano-system (size = 307.3 nm, zeta potential = −22mv), with well infection-responsive hydrogen release capability and biosafety. In addition, DQB@C was able to decrease oxidative stress and inflammation factors accumulation in lung cells. Through increasing expression level of Slc7a11/xCT and decreasing Cox2 level to participate with the regulation of ferroptosis. Also, DQB@C played lung and multi organ protection and anti-inflammation roles on CLP mice. ConclusionOur research proposed DQB@C as a novel biology nano-system with enormous potential on treatment for sepsis related acute lung injury to solve the limitation of hydrogen gas utilization in clinics.

Exploring the mechanism of action of Bidens pilosa L. in combating hepatic fibrosis through network pharmacology and molecular docking: An observational study.

Based on network pharmacology and molecular docking methods, to explore the possible targets and mechanisms of Bidens pilosa L. in treatment of liver fibrosis. The TCMSP, GeneCard, OMIM, TTD and DrugBank databases were used to obtain the targets of Bidens pilosa L and liver fibrosis, than the intersection targets were screened out by Venny 2.1.0, the protein-protein interaction (PPI) network and the core targets were obtained by the STRING database. Use Cytoscape3.7.2 software to draw the "traditional Chinese medicine-component-target-disease" network. The DAVID database platform was explored to analyze the biological process and pathway, and predict the anti-liver fibrosis mechanism of Bidens pilosa L. AutoDock and PyMol were used to verify the molecular docking between the active ingredients of Bidens pilosa L. and the core targets. Six active components of Bidens pilosa L. and 106 intersection targets were screened. PIK3R1, HSP90AA1, SRC, TP53, AKT1, RELA and other core targets were screened by PPI network analysis. The results of GO and KEGG enrichment analysis showed that the anti-liver fibrosis of Bidens pilosa L mainly involved in the regulation and negative regulation of apoptosis process, positive regulation of protein kinase B signal transduction, positive regulation of cell migration and other biological processes. Pathways acting on cancer, fluid shear stress and atherosclerosis, lipids and atherosclerosis, PI3K-AKT signaling pathway, MAPK signaling pathway and other signaling pathways. Molecular docking showed that the active components of Bidens pilosa L. displayed good binding activity with core target proteins, and the average binding energy was -7.47 kcal/mol. The possible mechanism of the active components against liver fibrosis is to regulate the PI3K-AKT, MAPK, and other signaling pathways by acting on core targets such as PIK3R1, HSP90AA1, SRC, TP53, AKT1, RELA, and induce the apoptosis of activated HSC cells to reverse and improve liver fibrosis.

Elucidation of the molecular mechanism of type 2 diabetes mellitus affecting the progression of nonalcoholic steatohepatitis using bioinformatics and network pharmacology: A review.

Increasing evidence suggests that patients with diabetes are at increased risk of developing nonalcoholic steatohepatitis (NASH), but the underlying mechanisms that affect the progression of NASH remain unclear. In this study, we used bioinformatics and network pharmacology methods to explore the differentially expressed genes of NASH and the related genes of type 2 diabetes mellitus, and a total of 46 common targets were obtained. Gene ontology showed that the common targets were mainly involved in biological processes such as glucocorticoid, hormone, and bacterium responses. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis signal pathways were mainly in colorectal cancer, amphetamine addition, the peroxisome proliferator-activated receptor signaling pathway, and the toll-like receptor signaling pathway. The protein-protein interaction network identified 8 hub genes, and the co-expression network was analyzed to obtain 7 related functions and mutual proportions of hub genes. A total of 120 transcription factors were predicted for hub genes. Hub genes were closely related to immune cells, including neutropils and eosinophils. In addition, we identified 15 potential candidate drugs based on hub genes that are promising for the treatment of NASH. Type 2 diabetes mellitus can affect the progression of NASH by changing hormone levels and inflammatory responses through multiple targets and signaling pathways. Eight hub genes are expected to be potential targets for subsequent treatment.