Applications of Network Pharmacology in Traditional Chinese Medicine Research

Exploring the mechanism of baicalein on breast cancer based on network pharmacology, molecular docking and in vivo experiments

Breast cancer ranks among the most deadly gynecological cancers and presents a significant risk to women's health. Baicalein, a flavonoid extracted from Radix Scutellariae, has garnered significant interest due to its potential anti-cancer properties. However, further research is required to determine the precise anti-cancer mechanisms of baicalein. Hence, we investigated the anti-tumor properties and underlying mechanisms of baicalein in breast cancer, utilizing both network pharmacology and experimental approaches. The effects of baicalein on cellular proliferation, the cell cycle, and apoptosis were assessed through MTT assays, plate cloning, and flow cytometry techniques. Furthermore, network pharmacology was employed to identify the primary target and pathway associated with baicalein in the context of breast cancer. The validation of these target and the elucidation of baicalein anti-breast cancer mechanisms were carried out using Western blotting, qRT-PCR, molecular docking, CETSA assays, and IHC. Behavioral experiments were conducted to assess the physical changes and toxicity of baicalein in model mice. Our findings demonstrated that baicalein significantly reduced the growth of both MCF-7 and MDA-MB-231 cell lines in a dose-dependent manner, inhibited cell proliferation, induced G0/G1 phase arrest, and triggered apoptosis. Notably, SRC serves as a therapeutic target for baicalein, with the Hippo pathway identified as a crucial mechanism of action in this context. Intraperitoneal injection of baicalein has been demonstrated to effectively inhibit tumor growth, while concurrently ameliorating splenomegaly and enhancing the fatigue resistance of the model mice. The findings confirm that baicalein was a potential drug for the treatment of breast cancer.

Study on the Material Basis and Mechanisms of Achyrocline satureioides in the Treatment of Nonsmall Cell Lung Cancer Based on Network Pharmacology and Spatial Metabolomics

Achyrocline satureioides have good therapeutic effects on nonsmall cell lung cancer (NSCLC). Nevertheless, it is still challenging to elucidate the active ingredients and mechanism of action due to their complex chemical composition. To address this, we innovatively combined network pharmacology with spatial metabolomics to comprehensively investigate the active components and the action mechanism in the present study. First, metabolomics of cells treated with the methanol extract of A. satureioides (ASM) utilizing high-resolution ultrahigh-performance liquid chromatography tandem mass spectrometry (HR-UHPLC-MS/MS) revealed 32 changed metabolites and 7 enriched metabolic pathways, confirming the anti-NSCLC effect of ASM and its impact on endogenous metabolites at the cellular level. Then, 69 chemical components in the ASM were identified using HR-UHPLC-MS/MS, followed by the screening of 6 core components and 10 core targets of anti-NSCLC with the help of network pharmacology and molecular docking. Lastly, quercetin, the most abundant compound among the six core active ingredients, was chosen for evaluating its anti-NSCLC effect and the potential mechanism using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). 51 altered endogenous metabolites were screened, and pathway enrichment analysis results were consistent with cell metabolomics, corroborating our network pharmacology predictions. In addition, we also observed the accumulation of three metabolites of quercetin in the tumor tissues. Network pharmacology combined with MSI elucidated the metabolic mechanisms by which A. satureioides treats NSCLC, offering new insights into herbal cancer therapies.

Integrating metabolomics, network pharmacology and pharmacological verification analysis provides new insights into the anti-inflammatory and anti-tussive properties of Fritillaria cirrhosa bulbs

ETHNOPHARMACOLOGICAL RELEVANCE

Fritillaria cirrhosa bulbs, referred to as Chuanbeimu in traditional Chinese medicine (TCM), are extensively used for recognized anti-inflammatory and anti-tussive effects. Both Songbei (SB) and Qingbei (QB), which are from this plant, have been used separately in medicine. However, the differences and similarities in their bioactive components and anti-inflammatory effects remain unclear.

OBJECTIVE

We aimed to analyse the metabolic profiles of F. cirrhosa bulbs across different growth years and explore the anti-inflammatory and anti-tussive properties of two distinct medicinal materials.

METHODS

With nontargeted metabolic technology, the main components of bulbs were detected. Principal component analysis (PCA) and pathway enrichment analysis were carried out to determine the differentially expressed metabolites between growth years. Network pharmacology was subsequently used to analyse the relationships among the components, diseases, key targets, and metabolic pathways by constructing a network model. The effects of drug-containing serum on cellular inflammatory factors were analysed through in vitro assays.

RESULTS

A total of 1349 compounds were identified from the different bulb samples. PCA revealed metabolic differences between SB bulbs (1- and 2-year-old) and QB bulbs (3-, 4-, and 5-year-old). Notably, 4-methoxycinnamaldehyde, tenuifoliside A, LysoPC 20:4, and morpholine-4-carboximidamide hydrobromide were identified as potential components for distinguishing SB and QB. Network pharmacology revealed more common targets related to anti-inflammatory (PPARG, PPARA, PTGS1, and XDH) and anti-tussive (PPARG, PTGS1, PPARA, OPRM1, DRD2, SLC6A4, and HTR2A) effects in SB than in QB. KEGG analysis revealed that inflammation and cough, including tryptophan metabolism and arachidonic acid metabolism, were enriched in the SB group. Cellular assays revealed anti-inflammatory effects, with SB having greater effects on IL-6 and QB on TNF-α and IL-1β having overall anti-inflammatory effects.

CONCLUSION

By integrating metabolomic and network analyses, the traditional classification of F. cirrhosa into SB and QB based on bulb characteristics and the observed differences are justified to a certain extent. This study provides new insights, guiding the clinical use of these treatments for inflammation and cough.

Network pharmacology and in silico approach to study the mechanism of quercetin against breast cancer

Breast cancer is a significant health concern among females with an estimated 2.3 million cases reported worldwide in 2022. Traditional treatment methods have now developed resistance and various adverse effects, highlighting an urgent need for attention. Therefore, it is advisable to substitute these conventional therapies with innovative medications. Quercetin is a flavonoid, commonly found in various vegetables and fruits and have been shown to possess anti-cancer properties. Network pharmacology is a comprehensive approach that has significantly assisted in investigating the potential of quercetin as a therapeutic option for breast cancer. The first step includes target fishing for quercetin-targeted genes in breast cancer through various online available databases. All intersecting genes were analysed for the phenotypic- genotypic correlation via online VarElect analysis tool. Using the result from the result the GO enrichment and pathway enrichment analysis was done on 52 common genes; followed by PPI network construction and based on topological parameters top 8 genes were filtered. Based on theVenny2.1 and then GEPIA and HPA analysis the key target were identifies as ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4 and ABCG2. Further, Molecular docking was done to investigate the possible interaction of the identified gene with quercetin. Our finding shows quercetin is the potential natural drug that can treat breast cancer effectively. Quercetin interacts with ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 at cellular as well as molecular level. The ADMET analysis suggests the bioavaibility of quercetin is around 0.55. Suggesting that quercetin satisfies drug-likeness rules but may face challenges like low bioavailability, which can be enhanced through structural modifications or formulations (e.g., nanoparticles). The molecular docking result assures the interaction of quercetin with the ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 with the binding affinity of - 7.2, - 10.1, - 10.4, - 8.0, - 8.2, - 8.2, - 9.0 and - 8.9 respectively. These results suggest quercetin has a stable interaction with the ABCC4 gene. Considering this interaction the quercetin molecules can rescue the cellular condition by inducing apoptosis, inhibiting proliferation, and suppressing metastasis. Quercetin, a natural compound found in fruits and vegetables, has been found to have significant therapeutic roles in treating breast cancer. It inhibits cell cycle arrest, promotes apoptosis, and reduces blood vessel formation. It also reverses drug resistance and has antioxidant and anti-inflammatory properties. This study concludes that the therapeutic influence of quercetin plays a significant role in treating breast cancer and aids in the advancement of the clinical application of quercetin in future studies.

Graphical Abstract

Network pharmacology and molecular docking reveal the mechanism of action of Bergapten against non‑small cell lung cancer

Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide, necessitating new treatment approaches with minimal side effects. In the present study, the potential of Bergapten (5-methoxypsoralen), a natural furanocoumarin compound, as a therapeutic agent against NSCLC was investigated by using network pharmacology, molecular docking and in vitro validation. Bergapten targets were identified using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and SwissTarget databases, whilst lung cancer-related targets were sourced from GeneCards and DisGeNET. Protein-protein interaction analysis and molecular docking were performed to identify key targets. The inhibitory effects of Bergapten on lung cancer cells were assessed using Cell Counting Kit-8 assays, wound healing assays, cell migration experiments, flow cytometry and western blotting. SC79 was used to verify the regulation of Bergapten on the PI3K/AKT pathway. Network pharmacology identified 51 targets, one signaling pathway and four Gene Ontology projects associated with the action of Bergapten against NSCLC. Key targets identified included glycogen synthase kinase-3β, Janus kinase 2, phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α and protein tyrosine kinase 2. In vitro experiments demonstrated that Bergapten significantly inhibited cell viability, promoted apoptosis, induced cellular senescence and inhibited the PI3K/AKT signaling pathway in NSCLC cells. In conclusion, Bergapten exerts its anti-NSCLC effects through the PI3K/AKT pathway, promoting cell senescence and inhibiting inflammation. These findings suggest that Bergapten has potential as a therapeutic agent for NSCLC.

Shanyao regulates the PI3K/AKT/P21 pathway to promote oogonial stem cell proliferation and stemness restoration to alleviate premature ovarian insufficiency

ETHNOPHARMACOLOGICAL RELEVANCE

Shanyao (SY, yam, Rhizoma Dioscoreae, the dried rhizome of Dioscorea oppositifolia L.) was recorded in the Chinese pharmacopoeia and was often used in the treatment of premature ovarian insufficiency (POI).

AIM OF STUDY

To evaluate the efficacy of shanyao in cyclophosphamide (CTX)-induced POI and explore its potential mechanism of action.

MATERIAL AND METHODS

We employed network pharmacology, Liquid Chromatograph Mass Spectrometer (LC-MS), and molecular docking methods to identify active compounds and core targets, and predict the mechanism of shanyao for treating POI. The mechanism was subsequently validated through a series of experiments. Female Sprague-Dawley (SD) rats were randomly divided into five groups: control (CON), model, estradiol valerate (EV), low-dose shanyao, and high-dose shanyao. An experimental rat model of POI was established using cyclophosphamide and treated with either shanyao or EV for a duration of two months. We assessed the efficacy of shanyao in vivo through methods such as weighing, Enzyme-linked Immunosorbent Assay (ELISA), and Hematoxylin and Eosin (H&E) staining. Oogonial stem cells (OSCs) were isolated, after modeling, treated them with a serum containing either shanyao or EV. Using methods such as CCK8 assay, immunofluorescence staining, flow cytometry (FCM) analysis, and Western blot analysis to verify the mechanism of shanyao in treating POI.

RESULTS

In this study, we found that after treatment with shanyao, the general condition of POI rats was improved, body weight and the ratio of ovarian weight to body weight were increased, FSH, E2 and AMH levels were improved, primary follicles and preantral follicles were significantly increased, atretic follicles were decreased. However, the number of antral follicles and fresh corpus luteum was no statistical difference. We identified 10 active compounds of shanyao that act on 220 target genes, 176 of which are associated with POI. Denudatin B and Kadsurenone were finally identified as core components. Through topological analysis, 18 key targets were selected, and ultimately PI3K, CCND1, and CDK4 were identified as core targets. Molecular docking results showed that core components had good binding energy with core targets. The results of GO and KEGG enrichment analysis mainly focus on cell cycle regulation and PI3K/AKT signaling pathway. A series of molecular biology experiments confirmed that after shanyao treatment, the phosphorylation level of PI3K and AKT in POI rats were increased, P21 was inhibited, PI3K/AKT/P21 signaling pathway was activated, and the expression levels of CCND1 and CDK4 were increased. At the same time, the expression of Oct4, fragilis and Mvh of ovarian stem cells was up-regulated.

CONCLUSION

The active compounds of shanyao can regulate the PI3K/AKT/P21 signaling pathway, promote the proliferation of oogonial stem cells, stemness restoration, and delay ovarian aging. This study provides valuable insights into shanyao treatment for POI.

Gypenosides alleviate oxidative stress in the hippocampus, promote mitophagy, and mitigate depressive-like behaviors induced by CUMS via SIRT1

ETHNOPHARMACOLOGICAL RELEVANCE

The use and efficacy of Gynostemma [Gynostemma pentaphyllum (Thunb.) Makino], a versatile traditional Chinese herb, was first documented in the renowned pharmacopoeia, "Compendium of Materia Medica". Gypenosides (Gps), saponin components are the primary constituents responsible for its biological activities and clinical effects, which include antioxidant, immunoregulatory, antitumor, and neuroprotective properties. Pharmacological studies have shown that Gps has the potential to combat depression. However, the exact molecular mechanisms underlying its antidepressant effects remain unclear.

AIM OF THE STUDY

This study aims to elucidate the mechanisms underlying the antidepressant effects of Gps through antioxidative stress, utilizing an integrated approach that includes network pharmacology, molecular simulations, and experimental validation.

MATERIALS AND METHODS

Sprague-Dawley rats were subjected to chronic unpredictable mild stress (CUMS) and were orally administered doses of Gps (50 and 100 mg/kg) and fluoxetine (10 mg/kg). The regulatory effects of Gps on depression-like behaviors in CUMS rats and their impact on oxidative stress levels in the hippocampus region were evaluated. Network pharmacology was used to investigate the mechanisms by which Gps affects oxidative stress in depression, and was accompanied by molecular docking and dynamics simulations. CUMS rats were treated orally with Gps (100 mg/kg) and injected with EX527 for rescue experiments to validate the role of SIRT1 in antioxidative stress and evaluate the impact of Gps on mitophagy.

RESULTS

Gps ameliorated depression-like behaviors induced by CUMS in rats. The improvements observed included an increased sucrose preference, reduced immobility time in the tail suspension and forced swim tests, and an increased movement distance in the open-field test. Additionally, Gps effectively reduced reactive oxygen species, malondialdehyde, and 8-hydroxy-2'-deoxyguanosine levels in the hippocampus, while increasing the contents of ATP, catalase, superoxide dismutase, and glutathione, indicating an increased capacity for antioxidative stress in the hippocampus. Furthermore, Gps increased the number of neuronal cells in the hippocampal CA1 region and the level of mitochondrial autophagy, with SIRT1 as a potential key target. Inhibition of SIRT1 expression by exposure to EX527 reversed the beneficial effects of Gps, further validating the critical role of SIRT1 in the regulation of oxidative stress and improving depression-like behavior.

CONCLUSION

Gps improved the antioxidative stress capacity of the hippocampus and promoted mitophagy in CUMS rats through SIRT1, thus protecting hippocampal neurons and improving depression-like behavior.

Review on ginseng and its potential active substance G-Rg2 against age-related diseases: Traditional efficacy and mechanism

ETHNOPHARMACOLOGICAL RELEVANCE

According to the Shen Nong Herbal Classic, Ginseng (Panax ginseng C.A. Meyer) is documented to possess life-prolonging effects and is extensively utilized in traditional Chinese medicine for the treatment of various ailments such as qi deficiency, temper deficiency, insomnia, and forgetfulness. Ginseng is commonly employed for replenishing qi and nourishing blood, fortifying the body and augmenting immunity; it has demonstrated efficacy in alleviating fatigue, enhancing memory, and retarding aging. Furthermore, it exhibits a notable ameliorative impact on age-related conditions including cardiovascular diseases and neurodegenerative disorders. One of its active constituents - ginsenoside Rg2 (G-Rg2) - exhibits potential therapeutic efficacy in addressing these ailments.

AIM OF THE REVIEW

The aim of this review is to explore the traditional efficacy of ginseng in anti-aging diseases and the modern pharmacological mechanism of its potential active substance G-Rg2, in order to provide strong theoretical support for further elucidating the mechanism of its anti-aging effect.

METHODS

This review provides a comprehensive analysis of the traditional efficacy of ginseng and the potential mechanisms underlying the anti-age-related disease properties of G-Rg2, based on an extensive literature review up to March 12, 2024, from PubMed, Web of Science, Scopus, Cochrane, and Google Scholar databases. Potential anti-aging mechanisms of G-Rg2 were predicted using network pharmacology and molecular docking analysis techniques.

RESULTS

In traditional Chinese medicine theory, ginseng has been shown to improve aging-related diseases with a variety of effects, including tonifying qi, strengthening the spleen and stomach, nourishing yin, regulating yin and yang, as well as calming the mind. Its potential active ingredient G-Rg2 has demonstrated significant therapeutic potential in age-related diseases, especially central nervous system and cardiovascular diseases. G-Rg2 exhibited a variety of pharmacological activities, including anti-apoptotic, anti-inflammatory and antioxidant effects. Meanwhile, the network pharmacological analyses and molecular docking results were consistent with the existing literature review, further validating the potential efficacy of G-Rg2 as an anti-aging agent.

CONCLUSION

The review firstly explores the ameliorative effects of ginseng on a wide range of age-related diseases based on TCM theories. Secondly, the article focuses on the remarkable significance and value demonstrated by G-Rg2 in age-related cardiovascular and neurodegenerative diseases. Consequently, G-Rg2 has broad prospects for development in intervening in aging and treating age-related health problems.

Investigating the molecular mechanism of epimedium herb in treating rheumatoid arthritis through network pharmacology, molecular docking, and experimental validation

This study attempted to explore the molecular mechanism of Epimedium herb (EH) on rheumatoid arthritis (RA) treatment. We employed network pharmacology, molecular docking, and HPLC analysis to investigate the molecular mechanisms underlying the efficacy of EH in treating RA. To assess the efficacy of EH intervention, RA fibroblast-like synoviocytes (RA-FLS) and collagen-induced arthritis (CIA) mouse models were utilized. Ultimately, the active compounds icariin, luteolin, quercetin, and kaempferol were identified, with interleukin-1β (IL-1β), IL-6, tumor necrosis factor-alpha (TNF-α), and matrix metalloproteinase-9 (MMP-9) emerging as key targets of EH for RA. These targets were found to be downregulated in both in vitro and in vivo experiments following EH intervention. Furthermore, EH treatment induced apoptosis, reduced metastasis and invasion in RA-FLS, and ameliorated arthritis-related symptoms while regulating Th17 and Treg cells in CIA mice.

Gastric schwannoma with post-surgical gastroparesis: a case report and literature review

Gastric schwannoma is a relatively rare submucosal mesenchymal tumor with low probability of metastasis and arises from Schwann cells of the gastrointestinal nervous plexus. Surgical therapy is the main treatment of gastric schwannoma with symptoms or malignant tendency. Gastroparesis is a potential complication following gastrointestinal surgery, which is a clinical syndrome caused by gastric emptying disorder and characterized by nausea, vomiting, and bloating, resulting in insufficient nutrient intake. Generally, post-surgical etiology is the main potential etiology of gastroparesis, while the most common underlying etiology is diabetes mellitus. So far, reports of gastroparesis arising from resection of gastric schwannoma are rare. We present an 80-year-old woman who was diagnosed with gastrointestinal stromal tumor (GIST) primarily and has undergone laparoscopic wedge-shaped gastrectomy. The pathological and immunohistochemical examination ultimately established the diagnosis of gastric schwannoma. The patient experienced belching, nausea, vomiting, and bloating 1 week after the surgery and confirmed as gastroparesis through gastrointestinal series and gastroscopic examination. A series of treatments were performed, including correcting fluid-electrolyte disorders and vitamin deficiencies, and nutritional support and pharmacological treatments. The patient ultimately recovered well, and the relevant literatures were reviewed to identify and handle similar cases hereafter.

In vivo and in vitro study on the regulatory mechanism of XiaoChaiHu decoction on PANoptosis in sepsis-induced cardiomyopathy

ETHNOPHARMACOLOGICAL RELEVANCE

In accordance with the tenets of traditional Chinese medicine, sepsis is categorized into three distinct syndromes: heat syndrome, blood stasis syndrome, and deficiency syndrome. Xiaochaihu decoction (XCHD) has many functions, including the capacity to protect the liver, cholagogue, antipyretic, anti-inflammatory, and anti-pathogenic microorganisms. XCHD exerts the effect of clearing heat and reconciling Shaoyang. The XCHD contains many efficacious active ingredients, yet the mechanism of sepsis-induced cardiomyopathy (SIC) remains elusive.

AIM OF THE STUDY

To investigate the molecular mechanisms underlying the protective effects of XCHD against SIC using an integrated approach combining network pharmacology and molecular biology techniques.

MATERIALS AND METHODS

Network pharmacology methods identified the active ingredients, target proteins, and pathways affected by XCHD in the context of SIC. We conducted in vivo experiments using mice with lipopolysaccharide-induced SIC, evaluating cardiac function through echocardiography and histology. XCHD-containing serum was analyzed to determine its principal active components using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The effects of XCHD-containing serum on SIC were further tested in vitro in LPS-treated H9c2 cardiac cells. Protein expression levels were quantified via Western blotting and enzyme-linked immunosorbent assay (ELISA). Additionally, molecular docking was performed between the active components and ZBP1, a potential target protein. Overexpression of ZBP1 in H9c2 cells allowed for a deeper exploration of its role in modulating SIC-associated gene expression.

RESULTS

UPLC-MS/MS identified 31 shared XCHD and XCHD-containing serum components. These included organic acids, terpenoids, and flavonoids, which have been identified as the active components of XCHD. Our findings revealed that XCHD alleviated LPS-induced myocardial injury, improved cardiac function, and preserved cardiomyocyte morphology in mice. In vitro studies, we demonstrated that XCHD-containing serum significantly suppressed the expression of inflammatory cytokines (IL-6, IL-1β, and TNF-α) in LPS-induced H9c2 cells. Mechanistic investigations showed that XCHD downregulated genes associated with PANoptosis, a novel cell death pathway, suggesting its protective role in sepsis-damaged hearts. Conversely, overexpression of ZBP1 abolished the protective effects of XCHD and amplified PANoptosis-related gene expression.

CONCLUSIONS

Our study provides the first evidence supporting the protective effects of XCHD against SIC, both in vitro and in vivo. The underlying mechanism involves the inhibition of ZBP1-initiated PANoptosis, offering new insights into treating SIC using XCHD.

Taoren Honghua Decoction alleviates atherosclerosis by inducing autophagy and inhibiting the PI3K-AKT signaling pathway to regulate cholesterol efflux and inflammatory responses

BACKGROUND

Taoren Honghua Decoction (THD) is a traditional Chinese formula known for enhancing blood circulation and demonstrating clinical efficacy in the treatment of cardiovascular and cerebrovascular diseases. However, the primary active components and the underlying mechanisms by which THD exerts its therapeutic effects on atherosclerosis (AS) remain insufficiently characterized.

OBJECTIVE

This study aims to systematically validate the protective effects of THD on AS and elucidate its potential molecular mechanisms through an integrative approach involving network pharmacology, in vivo, and in vitro experiments.

METHODS

The main active ingredients and corresponding targets of all traditional Chinese medicines in THD were collected from the TCSMP and BATMAN-TCM databases. Potential targets of AS were identified using the OMIM, DrugBank, DisGeNET, and CTD databases, and AS microarray gene data were obtained from the GEO database. A drug active ingredient-target relationship network and a PPI network were constructed using Cytoscape 3.9.2 software. The molecular functions of the core targets were annotated through GO and KEGG enrichment analyses to further elucidate the potential molecular mechanisms of THD's anti-AS effects. The ApoE-/-mouse AS model was constructed through a high-fat diet (HFD), and RAW264.7 macrophage model was induced with ox-LDL to further validate the results of network pharmacology.

RESULTS

Network pharmacology analysis revealed that the main five active ingredients of THD include quercetin, apigenin, luteolin, kaempferol, and tanshinone IIA. Subsequently, by analyzing the intersection genes of the main active ingredient targets of THD and the AS targets, a total of ten core targets were identified: TP53, PPARG, JUN, AKT1, INS, IL6, SIRT1, TNF, ESR1, and STAT3. These are considered the core targets of THD in the treatment of AS. The GO and KEGG enrichment analysis results indicate that THD may exert anti-AS effects by regulating lipid metabolism and the PI3K-AKT signaling pathway. In vivo and in vitro experiments showed that THD reduced circulating lipid levels, decreased intraplaque lipid accumulation, and increased intraplaque collagen fiber content in HFD-induced ApoE-/- mice. Additionally, THD reduced ox-LDL-induced macrophage-derived foam cell formation, inhibited the expression of inflammatory factors IL-6 and TNF-α, and promoted the expression of cholesterol efflux regulatory proteins PPARγ, ABCA1, and ABCG1. Notably, the autophagy inhibitor 3-MA reversed these effects, confirming that THD's action involves autophagy activation, evidenced by increased LC3II/I and decreased p62 levels.

CONCLUSION

This study demonstrates that THD exerts significant anti-AS effects through the inhibition of the PI3K/AKT signaling pathway and the activation of autophagy, thereby promoting cholesterol efflux and mitigating inflammation. By integrating network pharmacology with experimental validation, these findings provide a comprehensive understanding of THD's mechanisms in treating AS and offer a solid theoretical basis for its potential clinical application.

Computational screening and molecular dynamics of natural compounds targeting the SH2 domain of STAT3: a multitarget approach using network pharmacology

SH2 (Src Homology 2) domains play a crucial role in phosphotyrosine-mediated signaling and have emerged as promising drug targets, particularly in cancer therapy. STAT3 (Signal Transducer and Activator of Transcription 3), which contains an SH2 domain, plays a pivotal role in cancer progression and immune evasion because it facilitates the dimerization of STAT3, which is essential for their activation and subsequent nuclear translocation. SH2 domain-mediated STAT3 inhibition disrupts this binding, reduces phosphorylation of STAT3, and impairs dimerization. This study employed an in silico approach to screen potential natural compounds that could target the SH2 domain of STAT3 and inhibit its function. The phytomolecules (182455) were retrieved from the ZINC 15 database and were docked using various modes like HTVS, SP, and XP. The phytomolecules exhibiting higher binding affinity were selected. MM-GBSA was performed to determine binding free energy, and the QikProp tool was utilized to assess the pharmacokinetic properties of potential hit compounds, narrowing down the list of candidates. Molecular dynamics simulations, thermal MM-GBSA, and WaterMap analysis were performed on compounds that exhibited favorable binding affinities and pharmacokinetic characteristics. Based on docking scores and binding interactions, ZINC255200449, ZINC299817570, ZINC31167114, and ZINC67910988 were identified as potential STAT3 inhibitors. ZINC67910988 demonstrated superior stability in molecular dynamics simulation and WaterMap analysis. Furthermore, DFT was performed to determine energetic and electronic properties, and HOMO and LUMO sites were predicted for electronic structure calculation. Additionally, network pharmacology was performed to map the compounds' interactions within biological networks, highlighting their multitarget potential. Compound-target networks elucidate the relationships between compounds and multiple targets, along with their associated pathways and help to minimize off-target effects. The identified lead compound showed strong potential as a STAT3 inhibitor, warranting further validation through in vitro and in vivo studies.

Potential role of formononetin as a novel natural agent in Alzheimer's disease and osteoporosis comorbidity

BACKGROUND

The growing aging population has led to an increase in the prevalence of Alzheimer's disease (AD) and osteoporosis (OP), both of which significantly impair quality of life. The comorbid nature of these conditions suggests a shared genetic etiology, the understanding of which is crucial for developing targeted therapies.

OBJECTIVE

This study aims to explore the shared genetic etiology underlying AD and OP, using a system biology approach to identify potential therapeutic targets and natural compounds for treatment.

METHODS

We employed Weighted Gene Co-Expression Network Analysis (WGCNA) with molecular docking strategies to uncover the genetic links between AD and OP. MT2A and CACNA1C were identified as key pleiotropic hub genes potentially linking AD and OP. Molecular docking was utilized to screen for compounds with therapeutic potential, leading to the identification of formononetin as a compound with significant binding affinity to these hub genes. Quantitative real-time PCR (qRT-PCR) validation was conducted to confirm the gene expression changes in disease models.

RESULTS

Our study indicate that formononetin exhibits strong binding affinity to the identified hub genes, MT2A and CACNA1C. qRT-PCR validation confirmed the upregulation of these genes in disease models, which was mitigated upon treatment with formononetin, suggesting a reversal of disease markers.

CONCLUSIONS

This study advances our understanding of the genetic intersections between AD and OP and positions formononetin as a promising natural agent for further translational research. Formononetin's multi-target potential makes it a valuable candidate for managing these comorbid conditions, meriting further investigation and development as a therapeutic strategy.

Exploring Asthma Mechanism of Belamcanda Chinensis by "Dose-effect Weighted Coefficient" Network Pharmacology and Experiment Validation

BACKGROUND

Asthma is a chronic inflammatory disease of the airways that seriously endangers human health. Belamcanda chinensis (BC), a traditional Chinese medicine, has been used to counteract asthma as it has been shown to possess anti-inflammatory and regulatory immunity properties.

OBJECTIVE

The study aimed to investigate the mechanisms of action of BC in the treatment of asthma; a "dose-effect weighted coefficient" network pharmacology method was established to predict potential active compounds.

METHODS

Information on the components and content of BC was obtained by UPLC-QEOrbitrap- MS spectrometry. Based on BC content, oral bioavailability, and molecular docking binding energy, dose-effect weighting coefficients were constructed. With the degree greater than average as the index, a protein-protein interaction (PPI) database was used to obtain the core key targets for asthma under dose-effect weighting. GO function and KEGG pathway analyses of the core targets were performed using DAVID software. Finally, MTT and ELISA assays were used to assess the effects of active components on 16HBE cell proliferation.

RESULTS

The experimental results using the 16HBE model demonstrated BC to have a potential protective effect on asthma. Network pharmacology showed SYK, AKT1, and ALOX5 to be the main key targets, and Fc epsilon RI as the promising signaling pathway. Eight components, such as tectoridin, mangiferin, luteolin, and isovitexin were the main active compounds, Finally, we analyzed the LPS-induced 16HBE proliferation of each active ingredient. Based on the activity verification study, all five predicted components promoted the proliferation of 16HBE cells. These five compounds can be used as potential quality markers for asthma.

CONCLUSION

This study provides a virtual and practical method for the simple and rapid screening of active ingredients in natural products.

Network pharmacology and experimental validation to explore the pharmacological mechanism of saw palmetto and its core ingredients in benign prostatic hyperplasia treatment

Benign prostatic hyperplasia (BPH) is a prevalent urological condition that predominantly affects the geriatric male population, resulting in lower urinary tract symptoms. Saw palmetto is a traditional Chinese medicine for treating BPH. This study aimed to investigate the potential therapeutic mechanisms of saw palmetto in BPH treatment. The active ingredients and potential targets of saw palmetto were obtained through the TCMSP database. BPH-related targets were retrieved from the GeneCards database. PPI, GO, and KEEG analyses were performed to predict the potential therapeutic mechanism. The active ingredient-common target and common target-pathway networks were constructed by Cytoscape software. Molecular docking and cellular experiments were carried out to further validate the potential mechanism. We obtained 13 active components in saw palmetto and 56 common targets in BPH treatment. KEEG analysis showed that the estrogen signaling pathway was the most enriched and exhibited a close association with BPH. PPI analysis, along with ingredient-target and target-pathway network analyses, indicated that stigmasterol was the core ingredient and PGR, NCOA1, and NCOA2 were identified as the hub genes mediating the effects of saw palmetto against BPH. In addition, molecular docking showed that stigmasterol had strong binding to PGR, NCOA1, and NCOA2. Cellular experiments revealed that stigmasterol significantly increased the percentage of BPH-1 cells in the G0/G1 phase and inhibited cell viability and division. Furthermore, it notably reduced the expression of PGR, NCOA1, and NCOA2. Saw palmetto might inhibit cell viability and division by suppressing the expression of PGR, NCOA1, and NCOA2, thereby playing a therapeutic role in treating BPH.

Unveiling the Mechanisms and Therapeutic Effects of Xiaoyao Sanjie Decoction in Triple-Negative Breast Cancer: A Network Pharmacology and Experimental Validation Approach

Purpose

Triple-negative breast cancer (TNBC) is a disease associated with high incidence and high mortality, which is a major problem threatening women's health. Xiaoyao Sanjie Decoction (XYSJD) exhibits remarkable therapeutic efficacy on TNBC; however, the underlying mechanism is unclear. This study verified the efficacy of XYSJD and its active component in the treatment of TNBC and explored its potential mechanism.

Methods

Ultra-high performance liquid chromatography-hybrid quadrupole orbitrap mass spectrometry (UHPLC-Q Exactive HFX-MS) was applied to explore the main chemical constituents of XYSJD. The key targets and potential mechanisms of XYSJD in the treatment of TNBC were predicted through network pharmacology, bioinformatics analysis and molecular docking. The effects of XYSJD against TNBC cells were evaluated by CCK-8 assay, EdU assay, wound healing assay, transwell assay, Hoechst-PI staining and flow cytometry. The mechanism of action was validated by Western blot analysis. Finally, the effect and mechanism of XYSJD and Que on TNBC were further verified by the tumor formation model.

Results

UHPLC-Q Exactive HFX-MS identified a total of 9 compounds in XYSJD. Network pharmacological methods identified 206 targets for anti-TNBC. Bioinformatics analysis suggests that the EZH2/AKT1 signaling pathway might play an important role in the effects of XYSJD against TNBC. Gene Ontology enrichment analysis showed that the biological process of XYSJD in TNBC treatment mainly involved apoptosis. XYSJD and Que were observed to have a good anticancer effect in vivo and in vitro. In addition, quercetin could induce the apoptosis of TNBC cells by decreased the expression levels of EZH2/AKT1 signaling pathway. Furthermore, AKT1 overexpression, treatment with the AKT activator (SC79) and EZH2 overexpression could reverse apoptosis induced by quercetin in TNBC cells.

Conclusion

This study revealed the anti-TNBC efficacy of XYSJD. Quercetin, the effective component of XYSJD, promoted apoptosis of TNBC cells via blockade of the EZH2/AKT1 signaling pathway. These findings aim to provide a more reliable basis for the clinical application of XYSJD in the treatment of TNBC.

Pharmacological Network Analysis of the Functions and Mechanism of Quercetin From Jisuikang (JSK) in Spinal Cord Injury (SCI)

Neuroinflammation, especially microglia/macrophage activation, is a hallmark of spinal cord injury (SCI). Jisuikang (JSK) is a clinical experiential Chinese herbal formula for SCI therapy containing Huangqi (Astragali Radix), Danggui (Angelica sinensis Radix), Chishao (Paeoniae Radix Rubra), Dilong (earthworm, Pheretima aspergillum), Chuanxiong (Chuanxiong Rhizoma), Taoren (Persicae Seman) and Honghua (Carthami Flos). Eighteen active ingredients in 6 herbs of JSK were found to be correlated with inflammation, spinal injury and other diseases. These 18 active ingredients target 5464 genes according to the PubChem database. Through comparing differentially expressed genes between SCI and normal samples using GSE datasets, 50 hub genes were identified. These hub-genes were enriched in oxidative stress response and inflammation response. The herb-compound-target, herb-compound-signalling and compound-target-signalling networks were generated and quercetin was identified as the hub compound. A concentration of 25 μM quercetin showed no cytotoxicity but significantly protected microglial cells from LPS-induced inhibition of cell viability. LPS stimulation elevated the levels of iNOS, IL-1β and TNF-α but decreased IL-10 levels, whereas quercetin significantly attenuated LPS-induced alterations in these factors. Moreover, quercetin targeted gene, IL1R1 was reduced by quercetin as predicted. Overexpression of IL1R1 further increased LPS-induced inflammation, which could be partly reversed by quercetin treatment. In vivo, quercetin improved histopathological alterations, inflammation and promoted M2 macrophage polarisation post-injury, whereas IL1R1 overexpression partially attenuated the beneficial effects of quercetin on the rat SCI model. Collectively, quercetin, the main ingredient compound of JSK, protects against LPS-induced cell viability inhibition and cellular inflammation, which could be partially attenuated by IL1R1 overexpression.

Exploring the mechanism of Suxin Hugan Fang in treating ulcerative colitis based on network pharmacology

As a traditional Chinese medicine formula used in clinical practice for an extended period, Suxin-Hugan-Fang (SXHGF) exhibits excellent anti-inflammatory properties. However, the efficacy of SXHGF in treating ulcerative colitis (UC) and its mechanism of action are still unclear. In this study, the therapeutic effects of SXHGF on UC were evaluated using network pharmacology and experimental validation, while also investigating its mechanism of action. By administering DSS to C57BL/6 mice to construct a mouse model of ulcerative colitis, the therapeutic effect of SXHGF on ulcerative colitis was evaluated based on weight loss percentage, disease activity index, colon length changes, and pathological conditions as indicators. The main chemical components of SXHGF were determined by LC-MS-QTOF method. The potential targets and mechanisms of action of SXHGF in the treatment of UC were inferred using bioinformatics methods, and further validated through ELISA, IHC, and Western blotting assays. The experimental results demonstrate that SXHGF can suppress oxidative stress and oxidative damage in the colon tissue of UC mice, and alleviate DSS-induced ulcerative colitis by inhibiting the JAK2/STAT3 and NFκB pathways.

Therapeutic Effect of Shikimic Acid on Heat Stress-Induced Myocardial Damage: Assessment via Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Experiments

Background: Rising global temperatures have been linked to an increased incidence of heat stress (HS)-induced myocardial damage.

METHODS

This study aimed to investigate the therapeutic potential of shikimic acid (SA) on HS-induced myocardial damage using network pharmacology, molecular docking, molecular dynamics (MD) simulations, and in vitro experiments.

RESULTS

Network pharmacology analysis indicated that SA significantly attenuates the inflammatory response to HS by modulating 60 targets, including TNF, IL-6, and STAT3, which are enriched in the PI3K/AKT signaling pathway. Molecular docking and MD simulation analyses demonstrated that SA forms stable complexes with TNF (-6.642 kcal/mol) and IL-6 (-7.261 kcal/mol), with no significant conformational changes over a 100 ns simulation period. In vitro experiments demonstrated that SA, within the concentration range of 250 μM to 31.25 μM, significantly promoted the proliferation of normal HL-1 cells by an average of 31.0%. Moreover, it enhanced the survival rate of HL-1 cells exposed to 43 °C for 3 h by approximately 59.9% and downregulated the expression of Hsp90 and Hsp70. Additionally, this concentration range of SA reduced the expression of TNF-α, IL-6, TLR2, and COL1A1.

CONCLUSIONS

These findings offer evidence for the therapeutic potential of SA in HS-induced myocardial damage.

The Potential Compounds in Lansium parasiticum Leaf Extract for Breast Cancer Therapy: Metabolite Profiling, Pharmacological Network Analysis and In Silico Validation

OBJECTIVE

This study aims to identify the compounds found in Lansium parasiticum leaf extract (LPLE) and explain its activity in the context of breast cancer prevention and therapy using a pharmacological network approach and its validation in silico to understand the molecular mechanisms involved.

METHODS

Identification of compounds in LPLE is done using Liquid Chromatography Tandem Mass Spectrophotometry (LC-MS/MS). We also identified absorption and bioavailability profiles using ADMET software. Predictions about the molecular mechanisms of the anti-cancer compounds of LPLE were made through a network pharmacological approach involving devices such as Cytoscape 3.9.1, GeneCards, Disgenet, STRING 2.0.0, the Kyoto Encyclopedia of Genes and Genomes (KEGG) path, and SRplot. Interactions between potential compounds with TP53 receptors were analyzed using site-specific molecular docking, using PyRx Autodock Vina 9.0 and Biovia Discovery Studio.

RESULT

A total of 24 active compounds were successfully identified through LC-MS/MS. The results of the pharmacological network analysis of these compounds showed that there are four substances that have potential against the potential target gene of breast cancer, namely dihydrotestosterone with 8 target genes, Oxoberberine with 8 targets, Pregnenolone with 1 target gene, and Quercetine with 16 targets. The results of in silico validation revealed that the four compounds showed strong affinity to TP53, even higher than their original ligaments.

CONCLUSION

The study successfully identified the active compounds in Lansium parasiticum leaf extract (LPLE) that have potential in the prevention and treatment of breast cancer.

Targeting ferroptosis in treating traumatic brain injury: Harnessing the power of traditional Chinese medicine

Traumatic brain injury (TBI) exhibits high prevalence and mortality, but current treatments remain suboptimal. Traditional Chinese medicine (TCM) has long been effectively used for TBI intervention. Moreover, the recently discovered iron-dependent cell death pathway, known as ferroptosis, characterized by lipid peroxidation, as a key target in TCM-based treatments for TBI. This review provides a comprehensive overview of the latest advancements in TCM strategies targeting ferroptosis in TBI therapy, covering natural product monomers, classic formulas, and acupuncture/moxibustion. The review also addresses current challenges and outlines future research directions to further advance the development and application of TBI management strategies.

Exploring the Antidiabetic Potential of Salvia officinalis Using Network Pharmacology, Molecular Docking and ADME/Drug-Likeness Predictions

A combination of network pharmacology, molecular docking and ADME/drug-likeness predictions was employed to explore the potential of Salvia officinalis compounds to interact with key targets involved in the pathogenesis of T2DM. These were predicted using the SwissTargetPrediction, Similarity Ensemble Approach and BindingDB databases. Networks were constructed using the STRING online tool and Cytoscape (v.3.9.1) software. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis and molecular docking were performed using DAVID, SHINEGO 0.77 and MOE suite, respectively. ADME/drug-likeness parameters were computed using SwissADME and Molsoft L.L.C. The top-ranking targets were CTNNB1, JUN, ESR1, RELA, NR3C1, CREB1, PPARG, PTGS2, CYP3A4, MMP9, UGT2B7, CYP2C19, SLCO1B1, AR, CYP19A1, PARP1, CYP1A2, CYP1B1, HSD17B1, and GSK3B. Apigenin, caffeic acid, oleanolic acid, rosmarinic acid, hispidulin, and salvianolic acid B showed the highest degree of connections in the compound-target network. Gene enrichment analysis identified pathways involved in insulin resistance, adherens junctions, metabolic processes, IL-17, TNF-α, cAMP, relaxin, and AGE-RAGE in diabetic complications. Rosmarinic acid, caffeic acid, and salvianolic acid B showed the most promising interactions with PTGS2, DPP4, AMY1A, PTB1B, PPARG, GSK3B and RELA. Overall, this study enhances understanding of the antidiabetic activity of S. officinalis and provides further insights for future drug discovery purposes.

Research progress of traditional Chinese medicine compound "Chaihu Shugan Powder" in the treatment of premenstrual syndrome

BACKGROUND

This paper aims to conduct a comprehensive and insightful review and analysis of the potential targets and corresponding pathways of Chaihu Shugan Powder (CSP) for the treatment of premenstrual syndrome (PMS) using a network pharmacology approach. The review will encompass traditional applications, active ingredients of Chinese medicines, clinical applications, pharmacological mechanisms, and active ingredients.

METHODS

The active ingredients, pharmacological mechanisms, and clinical applications of the herbal ingredients in the CSP formulation were summarized by searching the literature, and the main signaling pathways of the CSP formulation for the treatment of PMS were identified by network pharmacological studies.

RESULTS

CSP is a representative traditional Chinese medicine formula known for its liver detoxification properties and its effectiveness in alleviating depression. It is also recognized as one of the most widely used formulas for treating PMS. In this study, we systematically summarized the active ingredients and pharmacological mechanisms of the 7 traditional Chinese medicine components present in CSP. Through network pharmacology analysis, we identified 75 common targets of CSP relevant to the treatment of PMS. These targets were predominantly concentrated within 17 specific signaling pathways, elucidating the potential molecular mechanisms underlying CSP's therapeutic effects on PMS.

CONCLUSION

In this paper, we have reviewed CSP and PMS, investigated the potential targets and corresponding pathways of CSP for the treatment of PMS, and systematically summarized the active ingredients and pharmacological mechanisms of 7 herbal components. In addition, 17 pathways of CSP for PMS were identified for future research and clinical application. However, the specific mechanism of action of CSP for the treatment of PMS is only based on literature and online pharmacological studies, and no basic or clinical experiments have been conducted. In addition, CSP has many components with complex and varied interactions, and the effects of certain compounds may be overlooked. Based on the present findings, it is beneficial to further explore the mechanism of action of the new effector compounds and the prospect of their application in basic research and clinical trials. In conclusion, the revelation of new effector compounds and mechanisms of action is conducive to the further clinical application of CSP, the discovery of new targets for PMS, and the modernization of Chinese medicine.

Exploring the therapeutic mechanisms of resveratrol for treating arecoline-induced malignant transformation in oral epithelial cells: insights into hub targets

BACKGROUND

Betel nut chewing is a significant risk factor for oral cancer due to arecoline, its primary active component. Resveratrol, a non-flavonoid polyphenol, possesses anti-cancer properties. It has been shown to inhibit arecoline-induced oral malignant cells in preliminary experiments but the underlying mechanism remains unclear. This research therefore aimed to explore the potential therapeutic targets of resveratrol in treating arecoline-induced oral cancer.

METHODS

Data mining identified common targets and hub targets of resveratrol in arecoline-induced oral cancer. Gene set variation analysis (GSVA) was used to score and validate the expression and clinical significance of these hub targets in head and neck cancer (HNC) tissues. Molecular docking analysis was conducted on the hub targets. The effect of resveratrol intervention on hub targets was verified by experiments.

RESULTS

Sixty-one common targets and 15 hub targets were identified. Hub targets were highly expressed in HNC and were associated with unfavorable prognoses. They played a role in HNC metastasis, epithelial-mesenchymal transition, and invasion. Their expression also affected immune cell infiltration and correlated negatively with sensitivity to chemotherapeutic agents such as bleomycin and docetaxel. Experiments demonstrated that resveratrol down-regulated the expression of the hub targets, inhibited their proliferation and invasion, and induced apoptosis.

CONCLUSION

Resveratrol inhibits the arecoline-induced malignant phenotype of oral epithelial cells by regulating the expression of some target genes, suggesting that resveratrol may be used not only as an adjuvant treatment for oral cancer, but also as an adjuvant for oral cancer prevention due to its low toxicity and high efficacy. © 2024 Society of Chemical Industry.

Network pharmacological analysis and experimental study of cucurbitacin B in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is a malignant tumor with a high incidence and poor prognosis. Cucurbitacin B (CuB) is a tetracyclic triterpenoid small-molecule compound extracted from plants, such as Cucurbitaceae and Brassicaceae, which has powerful anticancer effects. However, the effect and mechanism of CuB on OSCC remain unclear. Within the framework of the current study, network pharmacology was used to analyze the relationship between CuB and OSCC. The network pharmacology analysis showed that CuB and OSCC share 134 common targets; among them, PIK3R1, SRC, STAT3, AKT1, and MAPK1 are the key targets. The molecular docking analysis showed that CuB binds five target proteins. The results of the enrichment analysis showed that CuB exerted effects on OSCC through various pathways; of these pathways, PI3K-AKT was the most important pathway. The results of the in vitro cell experiments showed that CuB could inhibit the proliferation and migration of SCC25 and CAL27 cells, block the cell cycle in the G2 phase, induce cell apoptosis, and regulate the protein expression of the PI3K-AKT signaling pathway. The results of the in vivo animal experiments showed that CuB could inhibit 4NQO-induced oral cancer in mice. Therefore, network pharmacology, molecular docking, cell experiments, and animal experiments showed that CuB could play a role in OSCC by regulating multiple targets and pathways.

A Dataset for Constructing the Network Pharmacology of Overactive Bladder and Its Application to Reveal the Potential Therapeutic Targets of Rhynchophylline

Objectives: Network pharmacology is essential for understanding the multi-target and multi-pathway therapeutic mechanisms of traditional Chinese medicine. This study aims to evaluate the influence of database quality on target identification and to explore the therapeutic potential of rhynchophylline (Rhy) in treating overactive bladder (OAB). Methods: An OAB dataset was constructed through extensive literature screening. Using this dataset, we applied network pharmacology to predict potential targets for Rhy, which is known for its therapeutic effects but lacks a well-defined target profile. Predicted targets were validated through in vitro experiments, including DARTS and CETSA. Results: Our analysis identified Rhy as a potential modulator of the M3 receptor and TRPM8 channel in the treatment of OAB. Validation experiments confirmed the interaction between Rhy and these targets. Additionally, the GeneCards database predicted other targets that are not directly linked to OAB, corroborated by the literature. Conclusions: We established a more accurate and comprehensive dataset of OAB targets, enhancing the reliability of target identification for drug treatments. This study underscores the importance of database quality in network pharmacology and contributes to the potential therapeutic strategies for OAB.

AI empowering traditional Chinese medicine?

For centuries, Traditional Chinese Medicine (TCM) has been a prominent treatment method in China, incorporating acupuncture, herbal remedies, massage, and dietary therapy to promote holistic health and healing. TCM has played a major role in drug discovery, with over 60% of small-molecule drugs approved by the FDA from 1981 to 2019 being derived from natural products. However, TCM modernization faces challenges such as data standardization and the complexity of TCM formulations. The establishment of comprehensive TCM databases has significantly improved the efficiency and accuracy of TCM research, enabling easier access to information on TCM ingredients and encouraging interdisciplinary collaborations. These databases have revolutionized TCM research, facilitating advancements in TCM modernization and patient care. In addition, advancements in AI algorithms and database data quality have accelerated progress in AI for TCM. The application of AI in TCM encompasses a wide range of areas, including herbal screening and new drug discovery, diagnostic and treatment principles, pharmacological mechanisms, network pharmacology, and the incorporation of innovative AI technologies. AI also has the potential to enable personalized medicine by identifying patterns and correlations in patient data, leading to more accurate diagnoses and tailored treatments. The potential benefits of AI for TCM are vast and diverse, promising continued progress and innovation in the field.

Network pharmacology study and in vitro experimental validation of Xiaojianzhong decoction against gastric cancer

BACKGROUND

Cancer is one of the most serious threats to human health worldwide. Conventional treatments such as surgery and chemotherapy are associated with some drawbacks. In recent years, traditional Chinese medicine treatment has been increasingly advocated by patients and attracted attention from clinicians, and has become an indispensable part of the comprehensive treatment for gastric cancer.

AIM

To investigate the mechanism of Xiaojianzhong decoction (XJZ) in the treatment of gastric cancer (GC) by utilizing network pharmacology and experimental validation, so as to provide a theoretical basis for later experimental research.

METHODS

We analyzed the mechanism and targets of XJZ in the treatment of GC through network pharmacology and bioinformatics. Subsequently, we verified the impact of XJZ treatment on the proliferative ability of GC cells through CCK-8, apoptosis, cell cycle, and clone formation assays. Additionally, we performed Western blot analysis and real-time quantitative PCR to assess the protein and mRNA expression of the core proteins.

RESULTS

XJZ mainly regulates IL6, PTGS2, CCL2, MMP9, MMP2, HMOX1, and other target genes and pathways in cancer to treat GC. The inhibition of cell viability, the increase of apoptosis, the blockage of the cell cycle at the G0/G1 phase, and the inhibition of the ability of cell clone formation were observed in AGS and HGC-27 cells after XJZ treatment. In addition, XJZ induced a decrease in the mRNA expression of IL6, PTGS2, MMP9, MMP2, and CCL2, and an increase in the mRNA expression of HOMX1. XJZ significantly inhibited the expression of IL6, PTGS2, MMP9, MMP2, and CCL2 proteins and promoted the expression of the heme oxygenase-1 protein.

CONCLUSION

XJZ exerts therapeutic effects against GC through multiple components, multiple targets, and multiple pathways. Our findings provide a new idea and scientific basis for further research on the molecular mechanisms underlying the therapeutic effects of XJZ in the treatment of GC.

Integrative approach using network pharmacology, bioinformatics, and experimental methods to explore the mechanism of cantharidin in treating colorectal cancer

Cantharidin, a terpenoid produced by blister beetles, has been used in traditional Chinese medicine to treat various ailments and cancers. However, its biological activity, impact, and anticancer mechanisms remain unclear. The Cantharidin chemical gene connections were identified using various databases. The GSE21815 dataset was used to collect the gene expression information. Differential gene analysis and gene ontology analyses were performed. Gene set enrichment analysis was used to assess the activation of disease pathways. Weighted gene co-expression network analysis and differential analysis were used to identify illness-associated genes, examine differential genes, and discover therapeutic targets via protein-protein interactions. MCODE analysis of major subgroup networks was used to identify critical genes influenced by Cantharidin, examine variations in the expression of key clustered genes in colorectal cancer vs. control samples, and describe the subject operators. Single-cell GSE188711 dataset was preprocessed to investigate Cantharidin's therapeutic targets and signaling pathways in colorectal cancer. Single-cell RNA sequencing was utilized to identify 22 cell clusters and marker genes for two different cell types in each cluster. The effects of different Cantharidin concentrations on colorectal cancer cells were studied in vitro. One hundred and ninety-seven Cantharidin-associated target genes and 480 critical genes implicated in the development of the illness were identified. Cantharidin significantly inhibited the proliferation and migration of HCT116 cells and promoted apoptosis at certain concentrations. Patients on current therapy develop inherent and acquired resistance. Our study suggests that Cantharidin may play an anti-CRC role by modulating immune function.

Transplanting network pharmacology technology into food science research: A comprehensive review on uncovering food-sourced functional factors and their health benefits

Network pharmacology is an emerging interdisciplinary research method. The application of network pharmacology to reveal the nutritional effects and mechanisms of active ingredients in food is of great significance in promoting the development of functional food, facilitating personalized nutrition, and exploring the mechanisms of food health effects. This article systematically reviews the application of network pharmacology in the field of food science using a literature review method. The application progress of network pharmacology in food science is discussed, and the mechanisms of functional factors in food on the basis of network pharmacology are explored. Additionally, the limitations and challenges of network pharmacology are discussed, and future directions and application prospects are proposed. Network pharmacology serves as an important tool to reveal the mechanisms of action and health benefits of functional factors in food. It helps to conduct in-depth research on the biological activities of individual ingredients, composite foods, and compounds in food, and assessment of the potential health effects of food components. Moreover, it can help to control and enhance their functionality through relevant information during the production and processing of samples to guarantee food safety. The application of network pharmacology in exploring the mechanisms of functional factors in food is further analyzed and summarized. Combining machine learning, artificial intelligence, clinical experiments, and in vitro validation, the achievement transformation of functional factor in food driven by network pharmacology is of great significance for the future development of network pharmacology research.

Potential molecular metabolic mechanisms underlying the effects of cimifugin in gastric cancer through single-cell and bulk RNA sequencing combined with network pharmacology

Background

Gastric cancer (GC) is a leading cause of cancer-related mortality worldwide, posing a significant clinical challenge due to its complex tumor microenvironment (TME) and metabolic heterogeneity. Despite continuous improvements in treatment strategies including surgery, chemotherapy, and targeted therapies, the metabolic reprogramming in GC continues to impede treatment efficacy, highlighting an urgent need for the development of novel therapeutic strategies. This persistent issue underscores the urgent need for novel therapeutic approaches that can effectively address the diverse and dynamic characteristics of GC. Cimifugin, a traditional Chinese medicine (TCM), has garnered attention for its potential role in alleviating inflammation, neurological disorders, pain, and metabolic disorders. Its multi-targeting properties and minimal side effects suggest a broad potential for cancer management, which is currently being explored. This study aims to delineate the molecular mechanisms that cimifugin may impact within the TME and metabolic pathways of GC, with the expectation of contributing to a deeper understanding of GC and the development of innovative treatment strategies.

Methods

We identified the GC-related TME cell types and metabolic profiles and pathways by using relevant data from the single-cell RNA sequencing (scRNA-seq) database GSE134520 and the stomach adenocarcinoma (STAD) data set from The Cancer Genome Atlas (TCGA). We also assessed the effects of cimifugin on MKN28 cell proliferation, invasion, and migration. By using six public platforms, we comprehensively predicted the potential biological targets of cimifugin. Clinical prognosis and immunohistochemistry (IHC), molecular docking, and dynamics simulations were used to confirm the clinical relevance and stability of the aforementioned targets.

Results

Cimifugin inhibited MKN28 cell proliferation, migration, and invasion. Cimifugin may potentially act on various metabolic pathways in GC, including folate biosynthesis, xenobiotic metabolism via cytochrome P450 (CYP), glutathione metabolism, steroid hormone biosynthesis, and tryptophan metabolism. Cimifugin was noted to stably bind to three significant core targets associated with metabolic reprogramming in GC: AKR1C2, MAOB, and PDE2A; all three targets were strongly expressed in endocrince cells, pit mucous cells (PMCs), and common myeloid progenitors (CMPs).

Conclusions

We verified the pharmacological effects of cimifugin on GC cell proliferation, invasion, and migration. AKR1C2, MAOB, and PDE2A were identified as the key targets of cimifugin in GC-related metabolic reprogramming and pathogenesis. Our research provides preliminary insights into the potential therapeutic effects of cimifugin, which could be considered for future exploration in the context of GC treatment.

Exploring the Effects and Potential Mechanisms of Hesperidin for the Treatment of CPT-11-Induced Diarrhea: Network Pharmacology, Molecular Docking, and Experimental Validation

Chemotherapy-induced diarrhea (CID) is a potentially serious side effect that often occurs during anticancer therapy and is caused by the toxic effects of chemotherapeutic drugs on the gastrointestinal tract, resulting in increased frequency of bowel movements and fluid contents. Among these agents, irinotecan (CPT-11) is most commonly associated with CID. Hesperidin (HPD), a flavonoid glycoside found predominantly in citrus fruits, has anti-oxidation properties and anti-inflammation properties that may benefit CID management. Nevertheless, its potential mechanism is still uncertain. In this study, we firstly evaluated the pharmacodynamics of HPD for the treatment of CID in a mouse model, then used network pharmacology and molecular docking methods to excavate the mechanism of HPD in relieving CID, and finally further proved the predicted mechanism through molecular biology experiments. The results demonstrate that HPD significantly alleviated diarrhea, weight loss, colonic pathological damage, oxidative stress, and inflammation in CID mice. In addition, 74 potential targets for HPD intervention in CID were verified by network pharmacology, with the top 10 key targets being AKT1, CASP3, ALB, EGFR, HSP90AA1, MMP9, ESR1, ANXA5, PPARG, and IGF1. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the PI3K-Akt pathway, FoxO pathway, MAPK pathway, TNF pathway, and Ras pathway were most relevant to the HPD potential treatment of CID genes. The molecular docking results showed that HPD had good binding to seven apoptosis-related targets, including AKT1, ANXA5, CASP3, HSP90AA1, IGF1, MMP9, and PPARG. Moreover, we verified apoptosis by TdT-mediated dUTP nick-end labeling (TUNEL) staining and immunohistochemistry, and the hypothesis about the proteins above was further verified by Western blotting in vivo experiments. Overall, this study elucidates the potential and underlying mechanisms of HPD in alleviating CID.

Sinomenine Alleviates Rheumatoid Arthritis by Suppressing the PI3K-Akt Signaling Pathway, as Demonstrated Through Network Pharmacology, Molecular Docking, and Experimental Validation

Purpose

Sinomenine (SIN) is commonly used in Traditional Chinese Medicine (TCM) as a respected remedy for rheumatoid arthritis (RA). Nevertheless, the therapeutic mechanism of SIN in RA remains incompletely understood. This study aimed to delve into the molecular mechanism of SIN in the treatment of RA.

Methods

The potential targets of SIN were predicted using the TCMSP server, STITCH database, and SwissTarget Prediction. Differentially expressed genes (DEGs) in RA were obtained from the GEO database. Enrichment analyses and molecular docking were conducted to explore the potential mechanism of SIN in the treatment of RA. In vitro and in vivo studies were conducted to validate the intervention effects of SIN on rheumatoid arthritis, as determined through network pharmacology analyses.

Results

A total of 39 potential targets associated with the therapeutic effects of SIN in RA were identified. Enrichment analysis revealed that these potential targets are primarily enriched in PI3K-Akt signaling pathway, and the molecular docking suggests that SIN may act on specific proteins in the pathway. Experimental results have shown that exposure to SIN inhibits cytokine secretion, promotes apoptosis, reduces metastasis and invasion, and blocks the activation of the PI3K-Akt signaling pathway in RA fibroblast-like synoviocytes (RA-FLS). Moreover, SIN treatment alleviated arthritis-related symptoms and regulated the differentiation of CD4+ T cells in the spleen of collagen-induced arthritis (CIA) mice.

Conclusion

By utilizing network pharmacology, molecular modeling, and in vitro/in vivo validation, this study demonstrates that SIN can alleviate RA by inhibiting the PI3K-Akt signaling pathway. These findings enhance the understanding of the therapeutic mechanisms of SIN in RA, offering a stronger theoretical foundation for its future clinical application.

Plantaginis Semen Ameliorates Hyperuricemia Induced by Potassium Oxonate

Plantaginis semen is the dried ripe seed of Plantago asiatica L. or Plantago depressa Willd., which has a long history in alleviating hyperuricemia (HUA) and chronic kidney diseases. While the major chemical ingredients and mechanism remained to be illustrated. Therefore, this work aimed to elucidate the chemicals and working mechanisms of PS for HUA. UPLC-QE-Orbitrap-MS was applied to identify the main components of PS in vitro and in vivo. RNA sequencing (RNA-seq) was conducted to explore the gene expression profile, and the genes involved were further confirmed by real-time quantitative PCR (RT-qPCR). A total of 39 components were identified from PS, and 13 of them were detected in the rat serum after treating the rat with PS. The kidney tissue injury and serum uric acid (UA), xanthine oxidase (XOD), and cytokine levels were reversed by PS. Meanwhile, renal urate anion transporter 1 (Urat1) and glucose transporter 9 (Glut9) levels were reversed with PS treatment. RNA-seq analysis showed that the PPAR signaling pathway; glycine, serine, and threonine metabolism signaling pathway; and fatty acid metabolism signaling pathway were significantly modified by PS treatment. Further, the gene expression of Slc7a8, Pck1, Mgll, and Bhmt were significantly elevated, and Fkbp5 was downregulated, consistent with RNA-seq results. The PPAR signaling pathway involved Pparα, Pparγ, Lpl, Plin5, Atgl, and Hsl were elevated by PS treatment. URAT1 and PPARα proteins levels were confirmed by Western blotting. In conclusion, this study elucidates the chemical profile and working mechanisms of PS for prevention and therapy of HUA and provides a promising traditional Chinese medicine agency for HUA prophylaxis.

Exploring the pharmacological potential of Lepionurus sylvestris blume: from folklore medicinal usage to modern drug development strategies using in vitro and in silico analyses

BACKGROUND

Lepionurus sylvestris Blume has a long history of folklore medicinal usage against various ailments. However, studies on these plants were neglected particularly their pharmacological potential.

METHODS

The crude extract was identified using LC-MS analysis. In vitro assays were carried out to determine the properties of antioxidant, anti-microbial, and anti-cancer. Further, network pharmacology was proposed to evaluate the potential targets of the compounds against breast cancer and type II diabetes. Molecular docking and molecular dynamic simulation were used to determine the potential compounds for the drug formulation of diabetes.

RESULTS

Various bioactive compounds were identfied using LC-MS and Galiposin, Fujikinetin, Boeravinone B, 4-Deoxybryaquinone, and Norbaeocystin were described for the first time from the plant. Determination of antioxidant potential showed that the IC50 value of ABTS, DPPH, and phosphomolybdate was 24.33 µg/ml, 37.81 µg/ml, 60.35 µg/ml, and reducing power assays 1.185. The antibacterial activity against Streptococcus pyogenes, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli was determined, and the minimum inhibition concentration (MIC) was found to be 5.3 mg/ml, 3.47 mg/ml, 3.33 mg/ml, and 2.7 mg/ml respectively, revealing the extracts as effective antibacterial agents. The IC50 values for the plant extract were determined to be 26 µg/ml, 30.52 µg/ml, and 24.39 µg/ml for HeLa, MCF-7, and K-562 cells, respectively, and the increasing concentration of the plant extract increased LDH release. Furthermore, the in silico network pharmacology, molecular docking which had the highest docking score for GAPDH and HIF-1 target proteins of -9.3 kcal/mol, and - 11.3 kcal/mol binding affinities, and molecular dynamic simulation analysis revealed the bioactive compound Boeravinone B present in the plant was significant for the treatment of various ailments.

CONCLUSION

Based on our findings, plant extracts could be a promising option for developing new drug formulations.

[Xionggui Decoction alleviates heart failure in mice with myocardial infarction by inhibiting oxidative stress-induced cardiomyocyte apoptosis]

OBJECTIVE

To explore the protective effect of Xionggui Decoction against cardiac myopathy in a mouse model of heart failure following myocardial infarction (MI) and explore the underlying mechanism.

METHODS

We searched TCMSP, GeneCards, and CTD databases for the targets of active ingredients Xionggui Decoction and heart failure, and the intersecting targets were analyzed with GO and KEGG pathway enrichment analysis using DAVID database. In a mouse model of heart failure following acute MI induced by coronary artery ligation, the cardiac protective effects of 3 g/kg Xionggui Decoction were evaluated by assessing cardiac function, cardiac myopathy and ventricular remodeling of the mice using HE staining, Masson staining, RT-qPCR, and immunohistochemistry. We also tested the effect of Xionggui Decoction at 50 and 100 μg/mL on tertbutylhydrogen peroxide (TBHP)-induced apoptosis of H9C2 cells using CCK8 assay, detection kits for ROS, MDA, SOD, JC-1 and Hoechst 33342/PI staining.

RESULTS

Network pharmacological analysis identified 62 potential targets of Xionggui Decoction for treatment of heart failure, and the core targets included PTGS2, ESR1, caspase-3, PPARG, HSP90AA1, BCL2, JUN, and GSK3B, which were involved in cell apoptosis and the AGE-RAGE, P53, PI3K-Akt, and VEGF signaling pathways. In the mouse models of heart failure, treatment with Xionggui Decoction significantly alleviated cardiac myopathy and ventricular remodeling, obviously improved heart function of the mice, lowered myocardial expressions of caspase-3 and BAX, and enhanced the expression of BCL2. In H9C2 cells, Xionggui Decoction significantly alleviated TBHP-induced cell apoptosis by inhibiting oxidative stress in the cells.

CONCLUSION

Xionggui Decoction can alleviate myocardial injury and improve cardiac function in mice with heart failure following acute MI possibly by inhibiting cardiomyocyte apoptosis induced by oxidative stress.

Initiation of Apoptotic Pathway by the Cell-Free Supernatant Synthesized from Weissella cibaria Through In-Silico and In-Vitro Methods

Globally, colorectal cancer is the most prevalent type of cancer. Even though multiple treatments such as surgery, radiation, chemotherapy, and immunotherapy are available, the adverse effects caused in patients seem remarkable. Therefore, the current work was deliberated to prepare the metabolites (cell-free supernatant-CFS) from Weissella cibaria RK-3-1 to conduct in-silico and in-vitro-based anticancer assays. First, the active biomolecules present in the CFS were screened using a GC-MS analyzer. In addition, in-silico-based pharmacokinetic and docking studies were performed to confirm the anticancer potential of metabolites. In-silico results suggested that the bioactive compounds such as filicinic acid, dibutyl phthalate, and 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl present in CFS possessed significant molecular docking interactions with anticancer hub proteins. Furthermore, in-vitro results displayed the inhibition of cell proliferation in HT-29 cells at an IC50 value of 22.5 ± 1.3 µg/ml with the least significant effect on HEK-293 cell lines. Moreover, bacterial metabolites-controlled cell proliferation during the cell cycle's synthesis phase (S). Furthermore, the gene expression results confirm the increased expression of Bad, Bax, Bcl2, caspase-3, and cytochrome-C genes involved in the intrinsic apoptotic pathway. Hence, our findings from the in-silico and the in-vitro study confirm the anticancer potential of cell free-supernatant synthesized by W. cibaria.

iTRAQ-based quantitative proteomics revealing the therapeutic mechanism of a medicinal and edible formula YH0618 in reducing doxorubicin-induced alopecia by targeting keratins and TGF-β/Smad3 pathway

YH0618, a medicinal and edible formulation, has demonstrated the potential to alleviate doxorubicin-induced alopecia in animal studies and clinical trials. However, the mechanisms underlying its therapeutic effects remain unexplored. The objective of this study was to ascertain possible therapeutic targets of YH0618 in the treatment of doxorubicin-induced alopecia. The assessment of hair loss was conducted through the measurement of the proportion of the affected area and the examination of skin histology. Isobaric tags for relative and absolute quantification (iTRAQ) in quantitative proteomics was employed to discern proteins that exhibited variable expressions. The major proteins associated with doxorubicin-induced alopecia were identified using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The interaction network of the differentially expressed proteins was constructed using the STRING database and the Python software. The study analyzed a total of 3894 proteins extracted from the skin tissue of mice. Doxorubicin treatment resulted in the upregulation of 18 distinct proteins, whereas one differential protein was found to be downregulated. The above effects were reinstated after the administration of the YH0618 therapy. The bioinformatic study revealed that the identified proteins exhibited enrichment in many biological processes, including staphylococcus aureus infection, estrogen signaling route, pyruvate metabolism, chemical carcinogenesis, and PPAR signaling pathway. The results of Western blot revealed that the levels of keratin 81 (Krt81), keratin 34 (Krt34), keratin 33a (Krt33a), and Sma and MAD-related protein 3 (Smad3) were upregulated in response to doxorubicin treatment, and were attenuated by the administration of YH0618. These four proteins are likely to correlate with DOX-induced alopecia and serve as promising therapeutic targets for YH0618. This work presents significant insights and empirical evidence for comprehending the process underlying chemotherapy-induced alopecia, paving the way for exploring innovative therapeutic or preventive strategies employing herbal items.

Tianma-Gouteng pair ameliorates the cognitive deficits on two transgenic mouse models of Alzheimer's disease

ETHNOPHARMACOLOGICAL RELEVANCE

Alzheimer's disease (AD) is a progressive neurodegenerative disease. Tianma-Gouteng Pair (TGP), commonly prescribed as a pair-herbs, can be found in many Chinese medicine formulae to treat brain diseases. However, the neuroprotective effects and molecular mechanisms of TGP remained unexplored.

AIM OF THE STUDY

This study investigated the difference between the TgCRND8 and 5 × FAD transgenic mice, the anti-AD effects of TGP, and underlying molecular mechanisms of TGP against AD through the two mouse models.

METHODS

Briefly, three-month-old TgCRND8 and 5 × FAD mice were orally administered with TGP for 4 and 6 months, respectively. Behavioral tests were carried out to determine the neuropsychological functions. Moreover, immunofluorescence and western blotting assays were undertaken to reveal the molecular mechanisms of TGP.

RESULTS

Although TgCRND8 and 5 × FAD mice had different beta-amyloid (Aβ) burdens, neuroinflammation status, and cognition impairments, TGP exerted neuroprotective effects against AD in the two models. In detail, behavioral tests revealed that TGP treatment markedly ameliorated the anxiety-like behavior, attenuated the recognition memory deficits, and increased the spatial learning ability as well as the reference memory of TgCRND8 and 5 × FAD mice. Moreover, TGP treatment could regulate the beta-amyloid precursor protein (APP) processing by inhibiting the Aβ production enzymes such as β- and γ-secretases and activating Aβ degrading enzyme to reduce Aβ accumulation. In addition, TGP reduced the Aβ42 level, the ratio of Aβ42/Αβ40, Aβ accumulation, and tau hyperphosphorylation in both the 5 × FAD and TgCRND8 mouse models. Furthermore, TGP ameliorated neuroinflammation by decreasing the densities of activated microglia and astrocytes, and inhibiting the production of inflammatory cytokines. TGP upregulated the SIRT1 and AMPK, and downregulated sterol response element binding protein 2 (SREBP2) in the brain of TgCRND8 mice and deactivation of the EPhA4 and c-Abl in the brain tissues of 5 × FAD mice.

CONCLUSION

Our experiments for the first time revealed the neuroprotective effects and molecular mechanism of TGP on 5 × FAD and TgCRND8 transgenic mouse models of different AD stages. TGP decreased the level of Aβ aggregates, improved the tauopathy, and reduced the neuroinflammation by regulation of the SIRT1/AMPK/SREBP2 axis and deactivation of EPhA4/c-Abl signaling pathway in the brains of TgCRND8 and 5 × FAD mice, respectively. All these findings unequivocally confirmed that the TGP would be promising in developing into an anti-AD therapeutic pharmaceutical.

Unraveling the mechanism of malancao in treating ulcerative colitis: A multi-omics approach

BACKGROUND

Malancao (MLC) is a traditional Chinese medicine with a long history of utilization in treating ulcerative colitis (UC). Nevertheless, the precise molecular mechanisms underlying its efficacy remain elusive. This study leveraged ultra-high-performance liquid chromatography coupled with exactive mass spectrometry (UHPLC-QE-MS), network pharmacology, molecular docking (MD), and gene microarray analysis to discern the bioactive constituents and the potential mechanism of action of MLC in UC management.

AIM

To determine the ingredients related to MLC for treatment of UC using multiple databases to obtain potential targets for fishing.

METHODS

This research employs UHPLC-QE-MS for the identification of bioactive compounds present in MLC plant samples. Furthermore, the study integrates the identified MLC compound-related targets with publicly available databases to elucidate common drug disease targets. Additionally, the R programming language is utilized to predict the central targets and molecular pathways that MLC may impact in the treatment of UC. Finally, MD are conducted using AutoDock Vina software to assess the affinity of bioactive components to the main targets and confirm their therapeutic potential.

RESULTS

Firstly, through a comprehensive analysis of UHPLC-QE-MS data and public database resources, we identified 146 drug-disease cross targets related to 11 bioactive components. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis highlighted that common disease drug targets are primarily involved in oxidative stress management, lipid metabolism, atherosclerosis, and other processes. They also affect AGE-RAGE and apoptosis signaling pathways. Secondly, by analyzing the differences in diseases, we identified key research targets. These core targets are related to 11 active substances, including active ingredients such as quercetin and luteolin. Finally, MD analysis revealed the stability of compound-protein binding, particularly between JUN-Luteolin, JUN-Quercetin, HSP90AA1-Wogonin, and HSP90AA1-Rhein. Therefore, this suggests that MLC may help alleviate intestinal inflammation in UC, restore abnormal lipid accumulation, and regulate the expression levels of core proteins in the intestine.

CONCLUSION

The utilization of MLC has demonstrated notable therapeutic efficacy in the management of UC by means of the compound target interaction pathway. The amalgamation of botanical resources, metabolomics, natural products, MD, and gene chip technology presents a propitious methodology for investigating therapeutic targets of herbal medicines and discerning novel bioactive constituents.

Utilizing network pharmacology, molecular docking, and animal models to explore the therapeutic potential of the WenYang FuYuan recipe for cerebral ischemia-reperfusion injury through AGE-RAGE and NF-κB/p38MAPK signaling pathway modulation

BACKGROUND

Stroke is a debilitating condition with high morbidity, disability, and mortality that significantly affects the quality of life of patients. In China, the WenYang FuYuan recipe is widely used to treat ischemic stroke. However, the underlying mechanism remains unknown, so exploring the potential mechanism of action of this formula is of great practical significance for stroke treatment.

OBJECTIVE

This study employed network pharmacology, molecular docking, and in vivo experiments to clarify the active ingredients, potential targets, and molecular mechanisms of the WenYang FuYuan recipe in cerebral ischemia-reperfusion injury, with a view to providing a solid scientific foundation for the subsequent study of this recipe.

MATERIALS AND METHODS

Active ingredients of the WenYang FuYuan recipe were screened using the traditional Chinese medicine systems pharmacology database and analysis platform. Network pharmacology approaches were used to explore the potential targets and mechanisms of action of the WenYang FuYuan recipe for the treatment of cerebral ischemia-reperfusion injury. The Middle Cerebral Artery Occlusion/Reperfusion 2 h Sprague Dawley rat model was prepared, and TTC staining and modified neurological severity score were applied to examine the neurological deficits in rats. HE staining and Nissl staining were applied to examine the pathological changes in rats. Immunofluorescence labeling and Elisa assay were applied to examine the expression levels of certain proteins and associated factors, while qRT-PCR and Western blotting were applied to examine the expression levels of linked proteins and mRNAs in disease-related signaling pathways.

RESULTS

We identified 62 key active ingredients in the WenYang FuYuan recipe, with 222 highly significant I/R targets, forming 138 pairs of medication components and component-targets, with the top five being Quercetin, Kaempferol, Luteolin, β-sitosterol, and Stigmasterol. The key targets included TP53, RELA, TNF, STAT1, and MAPK14 (p38MAPK). Targets related to cerebral ischemia-reperfusion injury were enriched in chemical responses, enzyme binding, endomembrane system, while enriched pathways included lipid and atherosclerosis, fluid shear stress and atherosclerosis, AGE-RAGE signaling in diabetic complications. In addition, the main five active ingredients and targets in the WenYang FuYuan recipe showed high binding affinity (e.g. Stigmasterol and MAPK14, total energy <-10.5 Kcal/mol). In animal experiments, the WenYang FuYuan recipe reduced brain tissue damage, increased the number of surviving neurons, and down-regulated S100β and RAGE protein expression. Moreover, the relative expression levels of key targets such as TP53, RELA and p38MAPK mRNA were significantly down-regulated in the WenYang FuYuan recipe group, and serum IL-6 and TNF-a factor levels were reduced. After WenYang FuYuan recipe treatment, the AGE-RAGE signaling pathway and downstream NF-kB/p38MAPK signaling pathway-related proteins were significantly modulated.

CONCLUSION

This study utilized network pharmacology, molecular docking, and animal experiments to identify the potential mechanism of the WenYang FuYuan recipe, which may be associated with the regulation of the AGE-RAGE signaling pathway and the inhibition of target proteins and mRNAs in the downstream NF-kB/p38MAPK pathway.

Anti-Melanogenic Activity of Ethanolic Extract from Garcinia atroviridis Fruits Using In Vitro Experiments, Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Melanin, the pigment responsible for human skin color, increases susceptibility to UV radiation, leading to excessive melanin production and hyperpigmentation disorders. This study investigated the ethanolic extract of Garcinia atroviridis fruits for its phenolic and flavonoid contents, antioxidant activity, and impact on melanogenesis pathways using qRT-PCR and Western blot analysis. Utilizing network pharmacology, molecular docking, and dynamics simulations, researchers explored G. atroviridis fruit extract's active compounds, targets, and pharmacological effects on hyperpigmentation. G. atroviridis fruit extract exhibited antioxidant properties, scavenging DPPH• and ABTS•+ radicals radicals and chelating copper. It inhibited cellular tyrosinase activity and melanin content in stimulated B16F10 cells, downregulating TYR, TRP-1, phosphorylated CREB, CREB, and MITF proteins along with transcription levels of MITF, TYR, and TRP-2. LC-MS analysis identified thirty-three metabolites, with seventeen compounds selected for further investigation. Network pharmacology revealed 41 hyperpigmentation-associated genes and identified significant GO terms and KEGG pathways, including cancer-related pathways. Kaempferol-3-O-α-L-rhamnoside exhibited high binding affinity against MAPK3/ERK1, potentially regulating melanogenesis by inhibiting tyrosinase activity. Stable ligand-protein interactions in molecular dynamics simulations supported these findings. Overall, this study suggests that the ethanolic extract of G. atroviridis fruits possesses significant antioxidant, tyrosinase inhibitory, and anti-melanogenic properties mediated through key molecular targets and pathways.

Resveratrol activates MAPK/ERK pathway to regulate oestrogen metabolism in type I endometrial cancer

OBJECTIVE

Endometrial cancer (EC) is an oestrogen-dependent tumour, the occurrence of which is closely related to an imbalance of oestrogen homeostasis. Our previous studies explored the effects of Resveratrol(Res) on oestrogen metabolism. However, systematic research on the exact mechanism of action of Res is still lacking. Based on network pharmacology, molecular docking and animal experiments, the effects and molecular mechanisms of Res on endometrial cancer were investigated.

METHODS

The target of Res was obtained from the high-throughput experiment and reference-guided database of TCM (HERB) and the Encyclopedia of Traditional Chinese Medicine (ETCM) databases, and the target of endometrial cancer was obtained by using the Genecards database. Venny map was used to obtain the intersection target of Res in the treatment of endometrial cancer, and the protein interaction network of the intersection target was constructed by importing the data into the STRING database. Then, the drug-disease-target interaction network was constructed based on Cytoscape 3.9.1 software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for intersection targets using the OmicShare cloud platform. Res and core targets were analysed by molecular docking. EC model mice induced by MNNG were randomly divided into the control group, Res group, MNNG group, MNNG + Res group, and MNNG + Res + MAPK/ERKi group. The protein levels of ERK and p-ERK in the mouse uterus were detected by Western blot. The levels of E1, E2, E3, 16-epiE3, 17-epiE3, 2-MeOE1, 4-MeOE1, 2-MeOE2, 4-MeOE2, 3-MeOE1, 2-OHE1, 4-OHE1, 2-OHE2, 4-OHE2, and 16α-OHE1 in the serum and endometrial tissue of mice were measured by LC‒MS/MS.

RESULTS

A total of 174 intersection targets of Res anti-endometrial cancer were obtained. The signalling pathways analysed by KEGG enrichment included the AGE-RAGE signalling pathway in diabetic complications, the PI3K-Akt signalling pathway and the MAPK signalling pathway. The top 10 core targets were MAPK3, JUN, TP53, CASP3, TNF, IL1B, AKT1, FOS, VEGFA and INS. Molecular docking showed that in addition to TNF, other targets had good affinity for Res, and the binding activity with MAPK3 was stable. Western blot results showed that Res increased the phosphorylation level of ERK and that MAPK/ERKi decreased ERK activation. In the LC-MS/MS analysis, the levels of 2-MeOE1, 2-MeOE2 and 4-MeOE1 in serum and uterine tissue showed a significantly decreasing trend in the MNNG group, while that of 4-OHE2 was increased (P < 0.05). The concentrations of 4-MeOE1 in serum and 2-MeOE1 and 2-MeOE2 in the endometrial tissue of mice were significantly increased after Res treatment, and those of 4-OHE2 in the serum and uterus of mice were significantly decreased (P < 0.05). Meanwhile, in the MAPK/ERKi intervention group, the effect of Res on the reversal of oestrogen homeostasis imbalance was obviously weakened.

CONCLUSION

Res has multiple targets and multiple approaches in the treatment of endometrial cancer. In this study, it was found that Res regulates oestrogen metabolism by activating the MAPK/ERK pathway. This finding provides a new perspective for subsequent research on the treatment of endometrial cancer.

Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species

Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.

Long COVID-19 gastrointestinal related disorders and traditional Chinese medicine: A network target-based approach

The significant number of individuals impacted by the pandemic makes prolonged symptoms after COVID-19 a matter of considerable concern. These are numerous and affect multiple organ systems. According to the World Health Organization (WHO), prolonged gastrointestinal issues are a crucial part of post-COVID-19 syndrome. The resulting disruption of homeostasis underscores the need for a therapeutic approach based on compounds that can simultaneously affect more than one target/node. The present review aimed to check for nutraceuticals possessing multiple molecular mechanisms helpful in relieving Long COVID-19-specific gastrointestinal symptoms. Specific plants used in Keywords Chinese Medicine (TCM) expected to be included in the WHO Global Medical Compendium were selected based on the following criteria: (1) they are widely used in the Western world as natural remedies and complementary medicine adjuvants; (2) their import and trade are regulated by specific laws that ensure quality and safety (3) have the potential to be beneficial in alleviating intestinal issues associated with Long COVID-19. Searches were performed in PubMed, Elsevier, Google Scholar, Scopus, Science Direct, and ResearchGate up to 2023. Cinnamomum cassia, Glycyrrhiza uralensis, Magnolia officinalis, Poria cocos, Salvia miltiorrhiza, Scutellaria baicalensis, and Zingiber officinalis were identified as the most promising for their potential impact on inflammation and oxidative stress. Based on the molecular mechanisms of the phytocomplexes and isolated compounds of the considered plants, their clinical use may lead to benefits in gastrointestinal diseases associated with Long COVID-19, thanks to a multiorgan and multitarget approach.

Deciphering the Systemic Impact of Herbal Medicines on Allergic Rhinitis: A Network Pharmacological Approach

Allergic rhinitis (AR) is a systemic allergic disease that has a considerable impact on patients' quality of life. Current treatments include antihistamines and nasal steroids; however, their long-term use often causes undesirable side effects. In this context, traditional Asian medicine (TAM), with its multi-compound, multi-target herbal medicines (medicinal plants), offers a promising alternative. However, the complexity of these multi-compound traits poses challenges in understanding the overall mechanisms and efficacy of herbal medicines. Here, we demonstrate the efficacy and underlying mechanisms of these multi-compound herbal medicines specifically used for AR at a systemic level. We utilized a modified term frequency-inverse document frequency method to select AR-specific herbs and constructed an herb-compound-target network using reliable databases and computational methods, such as the Quantitative Estimate of Drug-likeness for compound filtering, STITCH database for compound-target interaction prediction (with a high confidence score threshold of 0.7), and DisGeNET and CTD databases for disease-gene association analysis. Through this network, we conducted AR-related targets and pathway analyses, as well as clustering analysis based on target-level information of the herbs. Gene ontology enrichment analysis was conducted using a protein-protein interaction network. Our research identified 14 AR-specific herbs and analyzed whether AR-specific herbs are highly related to previously known AR-related genes and pathways. AR-specific herbs were found to target several genes related to inflammation and AR pathogenesis, such as PTGS2, HRH1, and TBXA2R. Pathway analysis revealed that AR-specific herbs were associated with multiple AR-related pathways, including cytokine signaling, immune response, and allergic inflammation. Additionally, clustering analysis based on target similarity identified three distinct subgroups of AR-specific herbs, corroborated by a protein-protein interaction network. Group 1 herbs were associated with the regulation of inflammatory responses to antigenic stimuli, while Group 2 herbs were related to the detection of chemical stimuli involved in the sensory perception of bitter taste. Group 3 herbs were distinctly associated with antigen processing and presentation and NIK/NF-kappa B signaling. This study decodes the principles of TAM herbal configurations for AR using a network pharmacological approach, providing a holistic understanding of drug effects beyond specific pathways.

Paeoniflorin improves ulcerative colitis via regulation of PI3K‑AKT based on network pharmacology analysis

Paeoniflorin (PF) is the primary component derived from Paeonia lactiflora and white peony root and has been used widely for the treatment of ulcerative colitis (UC) in China. UC primarily manifests as a chronic inflammatory response in the intestine. In the present study, a network pharmacology approach was used to explore the specific effects and underlying mechanisms of action of PF in the treatment of UC. A research strategy based on network pharmacology, combining target prediction, network construction, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and molecular docking simulation was used to predict the targets of PF. A total of 288 potential targets of PF and 599 UC-related targets were identified. A total of 60 therapeutic targets of PF against UC were identified. Of these, 20 core targets were obtained by protein-protein interaction network construction. GO and KEGG pathway analyses showed that PF alleviated UC through EGFR tyrosine kinase inhibitor resistance, the IL-17 signaling pathway, and the PI3K/AKT signaling pathway. Molecular docking simulation showed that AKT1 and EGFR had good binding energy with PF. Animal-based experiments revealed that the administration of PF ameliorated the colonic pathological damage in a dextran sulfate sodium-induced mouse model, resulting in lower levels of proinflammatory cytokines including IL-1β, IL-6, and TNF-α, and higher levels of IL-10 and TGF-β. PF decreased the mRNA and protein expression levels of AKT1, EGFR, mTOR, and PI3K. These findings suggested that PF plays a therapeutic protective role in the treatment of UC by regulating the PI3K/AKT signaling pathway.

Exploring the potential mechanism of Heng-Gu-Gu-Shang-Yu-He-Ji therapy for osteoporosis based on network pharmacology and transcriptomics

ETHNOPHARMACOLOGICAL RELEVANCE

Heng-Gu-Gu-Shang-Yu-He-Ji (Osteoking, OK) is a well-known formula for fracture therapy. In clinic, OK is effective in treating fractures while alleviating osteoporosis (OP) symptoms. However, active components of OK and the associated molecular mechanisms remain not fully elucidated.

AIM OF THE STUDY

This study aims to systematically evaluate the anti-osteoporosis efficacy of OK and for the first time combine network pharmacology with high-throughput whole gene transcriptome sequencing to study its underlying mechanism.

MATERIALS AND METHODS

In this study, the osteoporosis model was established by the castration of both ovaries. The level of serum bone turnover factor was detected by enzyme-linked immunosorbent assay. Micro-CT and HE staining were used to observe the changes of bone histopathology, and nano-indentation technique was used to detect the biomechanical properties of rat bone. The main active Chemical components of OK were identified using UPLC-DAD. Efficacy verification and mechanism exploration were conducted by network pharmacology, molecular docking, whole gene transcriptomics and in vivo experiments.

RESULTS

In our study, OK significantly improved bone microarchitecture and bone biomechanical parameters in OVX rats, reduced osteoclast indexes such as C-telopeptide of type I collage (CTX-I) and increased Osteoprotegerin (OPG)/Receptor activator of NF-κB ligand (RANKL) levels. Mechanistically, PI3K/AKT pathway was a common pathway for genome enrichment analysis (KEGG) of both network pharmacology and RNA-seq studies. G protein-β-like protein (GβL), Ribosomal-protein S6 kinase homolog 2 (S6K2), and Phosphoinositide 3-kinase (PI3K) appeared differentially expression in the PI3K-AKT signaling pathway. These results were also confirmed by qRT-PCR and immunohistochemistry.

CONCLUSIONS

OK may be used to treat osteoporosis, at least partly by activating PI3K/AKT/mTORC1 signaling pathway.

Prospect of research on anti-atherosclerosis effect of main components of traditional Chinese medicine Yiqi Huoxue Huatan recipe through gut microbiota: A review

The incidence and mortality rates of cardiovascular diseases are on the rise globally, posing a severe threat to human health. Atherosclerosis (AS) is considered a multi-factorial inflammatory disease and the main pathological basis of cardiovascular and cerebrovascular diseases, as well as the leading cause of death. Dysbiosis of the gut microbiota can induce and exacerbate inflammatory reactions, accelerate metabolic disorders and immune function decline, and affect the progression and prognosis of AS-related diseases. The Chinese herbal medicine clinicians frequently utilize Yiqi Huoxue Huatan recipe, an effective therapeutic approach for the management of AS. This article reviews the correlation between the main components of Yiqi Huoxue Huatan recipe and the gut microbiota and AS to provide new directions and a theoretical basis for the prevention and treatment of AS.