Network pharmacology: curing causal mechanisms instead of treating symptoms

Discovery of bioactive compounds targeting endothelin A receptor and angiotensin II type 1 receptor in Gegen Qinlian decoction by co-immobilized receptor chromatography

An increased interest in multi-target compounds screening from complex matrices has revolutionized drug development paradigms, as these compounds often exhibit superior therapeutic efficacy and reduced off-target liabilities compared to the single-target compound. However, conventional discovery methods have been constrained by their singular focus on single-target screening methodologies. To address this limitation, we introduce a co-immobilization strategy tailored for G protein-coupled receptors(GPCRs) implicated in cardiovascular pathologies-specifically the endothelin A receptor (ETAR) and angiotensin II type 1 receptor(AT1R)-to facilitate the identification of multi-target compound within traditional herbal formulations. This innovative approach involves the oriented co-immobilization of ETAR and AT1R onto silica gel surfaces via histidine-tag anchoring, ensuring precise spatial orientation and functional integrity. Rigorous chromatographic characterization using receptor-specific ligands validated the dual-receptor column's functionality. Subsequent screening of Gegen Qinlian Decoction (GQD) identified puerarin as a novel multi-target compound capable of engaging both the two receptors. Zonal elution revealed that puerarin competes with native ligands for overlapping binding sites on ETAR and AT1R. Injection-amount-dependent method, demonstrated that puerarin binds ETAR and AT1R with association constants of 2.5 × 10⁵ M-1 and 2.0 × 10⁵ M-1, respectively. These findings validate our co-immobilization platform as a powerful tool for dissecting multi-target interactions in traditional Chinese medicines (TCMs), offering a transformative strategy to unlock the therapeutic potential of complex herbal mixtures.

Exploring the mechanism of Bruceine D against cervical cancer by network pharmacology and the effect of Bruceine D on the EGFR pathway

Cervical cancer (CC) remains a formidable challenge in oncology due to its high incidence and mortality rates. Despite recent advances in treatment, an immediate necessity exists for innovating advanced pharmacological interventions boasting augmented effectiveness. Bruceine D (BD), a quassinoid derived from the traditional Chinese medicinal plant Brucea javanica, has been demonstrated to possess notable anticancer properties against a range of malignant conditions, including lung, liver, leukemia, and pancreatic cancers. However, its specific effects on CC have not been thoroughly explored. This study sought to decode the effects of BD on CC through a combined method involving molecular docking analysis, network pharmacology, and data mining. From the PharmMapper database, we identified 58 potential targets of BD, and through GeneCards, we pinpointed 14 intersecting targets relevant to CC. A protein-protein interaction (PPI) network highlighted pivotal targets such as ESR1, HSP90AA1, ANXA5, EGFR, CASP7, and CCNA2. GO and KEGG enrichment analyses underscored significant biological processes and pathways, notably the EGFR signaling pathway. Molecular docking analysis revealed a strong binding affinity of BD to EGFR. Cell-based assays demonstrated that BD potently curtailed the viability, colony formation, adhesion, and mobility of Hela and Caski cells, escalating apoptosis in a dose-proportional manner. Supplementary evidence via western blot evaluations underscored BD's capability to obstruct the EGFR signaling pathway. These findings suggest that BD exerts potent anticancer effects against CC through multiple mechanisms, positioning it as a promising therapeutic agent for further investigation and clinical validation.

Network analysis and experimental validation analysis reveal the mechanism by which psoralen improves glucocorticoid-induced growth retardation

Glucocorticoids (GCs) are widely used, particularly concerning in pediatric patients. GC-induced growth retardation (GIGR) is one of its significant side effects. Endochondral ossification of growth plate chondrocytes is crucial for skeletal growth in children; excessive GCs inhibit growth plate development and longitudinal bone growth. Previous studies have shown that psoralen (PSO) has anti-osteoporotic effects, preserves cartilage homeostasis, and enhances chondrocyte proliferation. However, the specific mechanisms remain unclear. This study used network pharmacology and molecular docking to identify targets, followed by experimental validation to investigate how PSO affects damage to GC-induced growth plate chondrocytes. Results show that the PSO group exhibited significant increases in femoral length and growth plate size compared to the model group in rats. Additionally, testicular weight significantly increased in the PSO group compared to the model group. In vitro experiments demonstrated that PSO enhances proliferation and maintains cellular homeostasis in growth plate chondrocytes. Furthermore, experiments employing Western blotting, immunofluorescence, and other methods confirmed increased PI3K/AKT pathway activity, as well as elevated expression of cartilage-related proteins and reduced apoptotic proteins. Through network pharmacology, molecular docking, and experimental validation, we found that PSO stabilizes growth plate cell homeostasis and promotes cell proliferation by activating the PI3K/AKT signaling pathway. Therefore, PSO may be a potential therapeutic agent for improving GC-induced GIGR.

Zearalenone (ZEN) impairs motor function and induces neurotoxicity via inflammatory pathways: Evidence from zebrafish models and molecular docking studies

ZEN is a low-molecular-weight food contaminant that is frequently detected in various crops and regions due to its high thermal stability and persistence. It poses a significant threat to the biological nervous system. However, the molecular mechanisms underlying ZEN-induced neurotoxicity remain incompletely understood. To further explore this issue, this study focused on the effects of ZEN on the nervous system, particularly its key targets and related molecular mechanisms. The study combined network toxicology and molecular docking methods and performed behavioral analysis of zebrafish larvae exposed to ZEN. Firstly, motor capacity tests revealed that ZEN exposure significantly reduced the overall movement speed of zebrafish larvae during both photoperiod and dark cycles. We then identified 141 potential targets associated with ZEN-induced neurotoxicity from the GeneCards, OMIM, and DrugBank databases. Further screening using STRING and Cytoscape software extracted 25 key nodes, including TP53, AKT1, CASP3, MAPK3, and NFKB1. Analysis of GO and KEGG pathways suggested 20 of the most relevant signaling pathways and indicated that the core targets of ZEN-induced neurotoxicity were primarily involved in inflammatory pathways. Molecular docking using AutoDock further confirmed the strong binding affinity between ZEN and the targets. All six core target proteins exhibited strong binding affinity with ZEN, with binding energies of less than -7. In summary, the results of this study suggest that ZEN may impact cognitive dysfunction and neuropathy by activating neuroinflammatory signaling pathways, ultimately leading to neuronal death. This study provides important insights into the molecular mechanisms of ZEN-induced neurotoxicity and highlights the potential for prevention and treatment of diseases associated with exposure to ZEN and similar food contaminants.

Edaravone ameliorates inflammation in ischemic stroke mouse by regulating the CYP1A1 pathway through gut microbiota

Inflammation is one of the main contributors to post-stroke injuries, and the disorders of the gut-brain axis post-stroke can further induce inflammation. Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one, EDA) is widely utilized neuroprotective medication for ischemic stroke in Japan, China, India, and other countries. However, the effects of EDA on peripheral inflammation and gut-brain axis repair post-stroke have not been revealed yet. In this study, we employed network pharmacology to identify the potential anti-inflammatory targets and signaling pathways that EDA may influence in the treatment of ischemic stroke. Then, we used 16S rDNA sequencing and molecular docking techniques to determine whether the anti-inflammatory effects of EDA are dependent on the gut-brain axis. Using morphological and molecular biology methods, we investigate how EDA reduces inflammatory response after ischemic stroke through gut microbiota and its metabolites. We demonstrated that EDA alleviated central and peripheral inflammation and rescued gut microbiota dysbiosis post-stroke. Meanwhile, EDA also improved intestinal histological features and decreased intestinal inflammation of post-stroke. The network pharmacology, 16S rDNA sequencing, and molecular docking results revealed that EDA could bind with the ESR1 and thereby regulate the expression of CYP1A1. Furthermore, EDA regulated CYP1A1-related metabolism and decreased the level of 20-HETE post-stroke through gut microbiota. Our study confirmed that EDA alleviated central and peripheral inflammation post-stroke by inhibiting CYP1A1 and CYP1A1-related metabolic through gut microbiota. CYP1A1 was a candidate target for treating ischemic stroke.

Therapeutic potential of Platycodin D in allergic asthma through anti-inflammatory and anti-remodeling effects

BACKGROUND

Allergic asthma (AA) is a prevalent chronic respiratory disease characterized by airway hyperresponsiveness (AHR) and chronic inflammation, significantly impairing patients' quality of life.

PURPOSE

This study investigates the therapeutic effects of Platycodin D (PLD) on AA and its underlying mechanisms via the EGFR/PI3K/Akt signaling pathway.

METHODS

In vitro, BEAS-2B cells treated with IL-4 and IL-13 simulated asthma's inflammatory environment. Enzyme-linked immunosorbent assay (ELISA) assessed PLD's modulation of inflammatory factors, while Western blot (WB) analyzed its impact on airway remodeling proteins. Induced pluripotent stem cells (iPSC)-derived airway organoids (AOs) were used to evaluate PLD's effects on airway remodeling, observed through tissue staining and immunofluorescence. In vivo, an OVA-induced asthma mouse model was employed to assess PLD's therapeutic potential via lung function tests, serum biochemical analysis, and histopathology. Network pharmacology and transcriptomics predicted and validated PLD's target pathways.

RESULTS

In vivo experiments demonstrated that PLD significantly alleviated airway inflammation and remodeling in OVA-induced asthmatic mice. Specifically, treatment with 5 mg/kg PLD significantly reduced the number of inflammatory cells recovered from bronchoalveolar lavage fluid (BALF) compared to the model group (p < 0.05). Serum levels of IgE, IL-4, IL-5, IL-13, and IL-17A were markedly decreased following PLD treatment (p < 0.05). PLD also improved lung function by reducing airway resistance (RL) across all tested methacholine concentrations, with significant reductions at 5, 10, and 20 mg/mL doses (p < 0.05). Histological analysis revealed that PLD attenuated pathological changes in lung tissues, including goblet cell hyperplasia and collagen deposition. Western blot analysis confirmed that PLD significantly downregulated the expression of COL1A1 and α-SMA in lung tissues (p < 0.05), suggesting suppression of airway remodeling. In vitro, PLD inhibited the expression of IL-6, IL-8, COL1A1, and α-SMA in human bronchial epithelial (HBE) cells in a dose-dependent manner. Transcriptomic sequencing and RT-qPCR analysis further demonstrated that PLD downregulated key genes involved in the EGFR/PI3K/Akt pathway. Molecular docking showed high binding affinity between PLD and EGFR/PI3K proteins, supporting a potential mechanistic link.

CONCLUSION

PLD exerts therapeutic effects in allergic asthma by suppressing airway inflammation, improving lung function, and inhibiting airway remodeling. These effects are associated with the inhibition of the EGFR/PI3K/Akt signaling pathway. Our findings suggest that PLD may serve as a promising candidate for the treatment of allergic airway diseases.

Semen Ziziphi Spinosae alleviates cardiomyocyte apoptosis in rats with coronary heart disease via the AMPK/SIRT1/PGC-1α signaling pathway activation

BACKGROUND

Coronary heart disease (CHD) represents a significant cardiovascular condition, with its occurrence increasing as a result of alterations in lifestyle and dietary habits. Semen Ziziphi Spinosae (SZS) is commonly utilized for the management of disorders associated with the nervous system, including conditions like depression and insomnia. Recent research has revealed its potential therapeutic properties for cardiovascular issues. Nevertheless, there exists a limited amount of research addressing the mechanisms involved.

PURPOSE

This research seeks to explore the protective effects that SZS has on cardiac tissue, specifically within the framework of CHD. By conducting this investigation, the study aims to uncover the various mechanisms that play a role in these protective effects. This understanding could yield significant insights into how SZS may result in the preservation and enhancement of cardiac health in patients affected by CHD.

STUDY DESIGN

The study innovatively combines multiple advanced techniques. It first integrates UPLC-Q-TOF/MS analysis and network pharmacology to identify SZS components. In vitro experiments were conducted using H9c2 rat cardiomyocytes, and in vivo experiments used a CHD model in SD rats. Multiple assays were performed for multi - level and multi - dimensional validation.

METHODS

In the initial stage, the primary components of SZS and their possible mechanisms for combating CHD were examined through UPLC-Q-TOF/MS analysis in conjunction with network pharmacology approaches. For the in vitro investigation, an ischemia-hypoxia model was established utilizing H9c2 rat cardiomyocytes. The CCK-8 assay was used to assess myocardial injury markers. TUNEL staining and Western blot techniques were employed to confirm the impact of SZS treatment on apoptosis in H9c2 cells. The expression levels of proteins associated with the AMPK/SIRT1/PGC-1α signaling pathway were measured using RT-qPCR and Western blotting, and the results were validated with the AMPK inhibitor, compound C. In the in vivo segment, a model of coronary heart disease (CHD) in SD rats was established through the administration of a high-fat emulsion diet combined with pituitrin injections. Cardiac function in the rats was evaluated through electrocardiograms and echocardiograms. Pathological changes in the heart were observed utilizing TTC and H&E staining. Kits were implemented to measure the serum biochemical indicators in the rats.RT - qPCR and Western blotting were employed to measure the expression levels of proteins related to the AMPK/SIRT1/PGC - 1α signaling pathway.

RESULTS

The study identified 67 in vitro components, 27 blood - absorbed components, and 12 metabolic components of SZS. Network pharmacology analysis suggested the AMPK/SIRT1/PGC - 1α signaling pathway as a key mechanism. In vitro and in vivo experiments showed that SZS increased cell viability, reduced apoptosis, and activated the AMPK/SIRT1/PGC - 1α signaling pathway. Inhibiting AMPK abolished SZS's effects. SZS also improved cardiac function and reduced myocardial damage in rats with CHD.

CONCLUSION

This study for the first time highlights that Semen Ziziphi Spinosae plays a beneficial role in cardiovascular health by activating the AMPK/SIRT1/PGC-1α signaling pathway and reducing apoptosis in cardiomyocytes. These findings support its potential application in the treatment of CHD and other cardiac conditions.

A comprehensive pharmacology study reveals the molecular mechanisms underlying the antidepressant effects of Gastrodiae Rhizoma

BACKGROUND

Gastrodiae Rhizoma (GR) and its extract have been widely used in the treatment of depression, but the underlying mechanism of its antidepressant effects is unclear due to its numerous components.

PURPOSE

Revealing the cellular and molecular mechanisms underlying the antidepressant effects of GR through a comprehensive pharmacology-based in vivo and in vitro investigation.

METHODS

A mouse model of depression was established using chronic mild stress (CMS) procedure, and the antidepressant effects of GR were evaluated using systematic behavior. Metabolites in GR decoction and in mouse brain were identified by UPLC-QTOF-MS technology. Core components and targets of GR against MDD were screened based on network pharmacology analysis and molecular docking. The mechanism through which GR mitigated MDD was explored using transcriptome analysis, immunohistochemistry and western blotting in vitro and in vivo.

RESULTS

A total of 273 components were identified in the GR decoction, out of which 15 were detected in the brain of depressed mice treated with the GR decoction. We further identified nine key active ingredients, six essential targets, and fifth signaling pathways associated with the therapeutic effects of GR against MDD. We confirmed that the active ingredients of GR can target the neural stem/precursor cells (NSPCs) in the hippocampus of depressed mice to promote neurogenesis, as evidenced by a significant increase in the numbers of DCX+ cells, BrdU+ cells, BrdU+-DCX+ cells, and BrdU+-NeuN+ cells within the hippocampus of GR-treated mice compared to salinetreated mice under CMS exposure. Moreover, we have identified that the key active constituents of GR, namely gastrodin and parishin C, exert a targeted effect on EGFR to activate PI3K-Akt signaling in NSPCs, thereby facilitating proliferation and differentiation of NSPCs.

CONCLUSION

The antidepressant effect of GR involves the facilitation of PI3K/Akt-mediated neurogenesis through gastrodin and parishin C targeting EGFR in NSPCs.

β-Sitosterol inhibits osteoclast activity and reduces ovariectomy-induced bone loss by regulating the cAMP and NF-κB signaling pathways

BACKGROUND

β-Sitosterol, a prominent phytosterol present in numerous plant species, has been extensively studied for its potential health benefits, such as lipid-lowering, anxiolytic, and anti-inflammatory properties. Recently, the benefit of β-sitosterol on bone metabolism has been noted. The objective of the current study was to examine the impact of β-sitosterol on the skeletal system.

METHODS

Network pharmacology and molecular docking were used to predict how β-sitosterol may be used to treat osteoporosis. Cytotoxicity tests were conducted with different concentrations of β-sitosterol. The ability of β-sitosterol to inhibit osteoclast formation and function was evaluated, along with its potential molecular mechanism. An ovariectomized mouse model was used to assess the preventive effect of β-sitosterol on bone loss.

RESULTS

Network pharmacology analysis suggested that β-sitosterol could be a potential therapeutic treatment for osteoporosis by regulating the cAMP signaling pathway. β-sitosterol dose-dependently inhibited osteoclast differentiation and function without obvious cytotoxicity. Specifically, 20 μM β-sitosterol could obviously repress the number and size of osteoclasts, decrease the formation of F-actin belts, and reduce the bone-resorbing activity of osteoclasts. Some key signaling mediators, including PKA, c-Jun, NFATc1, p-CREB, and NF-κB, were downregulated by β-sitosterol. β-sitosterol acted by attenuating the cAMP and NF-κB signaling pathways. In vivo experiments confirmed β-sitosterol protected ovariectomy-induced bone loss though suppressing osteoclastic bone resorption.

CONCLUSION

β-sitosterol could inhibit the production and function of osteoclasts in vitro and reverse ovariectomy-induced bone loss. Thus, β-sitosterol could be a potential supplement for diseases with active bone resorption such as osteoporosis.

Macleaya cordata protopine total alkaloids as potential treatment for diarrhoea: Mechanistic insights and target identification

Diarrhoea remains a major public health concern, particularly affecting young children and livestock. Macleaya cordata protopine total alkaloids (MPTA), a standardized extract approved in China for poultry diarrhoea, has demonstrated anti-inflammatory properties in intestinal disorders. The study aims to investigate the antidiarrheal mechanism of MPTA using castor oil- and E. coli-induced diarrhoea models in mice. We first tested MPTA for acute oral toxicity. Subsequently, the effect of MPTA on castor oil- and E. coli-induced diarrhoea in mice based on LD50 results. Network pharmacology analysis and target competition assays (inhibitors and antagonists) were integrated to identify targets for MPTA's antidiarrheal effects. Molecular docking was used to verify the binding ability of MPTA components to these receptors. The LD50 of MPTA was determined to be 426.1 mg/kg. The optimal MPTA activity was found at 8 mg/kg in both castor oil and in infectious models. Network pharmacology analysis revealed potential targets and pathways of MPTA against intestinal motility. The impact of MPTA on cholinergic, serotonin, dopaminergic, and adrenergic receptors was assessed using standard inhibitors and agonists to induce intestinal smooth muscle contractions or relaxations. Molecular docking confirmed the binding ability of MPTA components to these receptors. In conclusion, MPTA exhibits significant antidiarrheal effects in both castor oil and E. coli-induced diarrhoea models. Its mechanism may involve modulation of cholinergic, serotonin, dopaminergic, and adrenergic receptors, as well as inhibition of ion channels and anti-inflammatory actions. These findings highlight the potential of MPTA as a novel therapeutic agent for diarrhoea.

Exploring the effective components and underlying mechanisms of Feiyanning formula in acute lung injury based on the pharmacokinetics, metabolomics and network pharmacology technology

This study aimed to explore the mechanisms of Feiyanning formula (FYN) on acute lung injury (ALI) using pharmacokinetics combined with network pharmacology strategy. Firstly, pharmacokinetic studies of 13 major bioactive components in normal and ALI mice were conducted using ultra-high performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-QQQ-MS/MS). Secondly, metabolomics was utilized to explore the metabolites affected by FYN. Finally, the network pharmacology was used to analyze the pharmacological mechanism of FYN's pharmacokinetic target components in ALI treatment, with western blotting (WB) experiment performed for verification. The pharmacokinetic results showed that compared to normal mice, the Cmax and AUC0-t of wogonin, oroxylin A, liquiritigenin, tetrandrine, and fangchinoline were significantly increased in ALI mice. The results of the lung tissue distribution showed that compared to normal mice, the AUC0-t of wogonin and oroxyloside was significantly increased in ALI mice; the Cmax of wogonoside and norwogonin was significantly increased in ALI mice. Metabolomics analysis showed that FYN may alleviate LPS-induced lung inflammation in mice by regulating related pathways including purine metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis in both serum and lung tissue. Network pharmacology identified 110 overlapping genes between the 13 absorbed components and ALI-related targets. In KEGG enrichment analysis, the PI3K/AKT signaling pathway was identified as a significant pathway. WB experiment confirmed that FYN reduced the expression ratios of p-PI3K/PI3K, p-AKT1/AKT1, p-EGFR/EGFR, and TLR4 levels in lung tissue of ALI mice. This study might offer a solid foundation for evaluating the clinical efficacy of FYN.

Epigenetics is involved in the pleiotropic effects of statins

INTRODUCTION

Statins have significantly reduced mortality from cardiovascular diseases by lowering serum cholesterol levels. Beyond their lipid-lowering effects, statins improve vascular function, reduce inflammation, decrease reactive oxygen species (ROS) formation, and stabilize atherosclerotic plaques. However, the mechanisms underlying these pleiotropic effects remain unclear.

AREA COVERED

This narrative review summarizes and discusses epigenetic mechanisms that may explain part of the pleiotropic effects of statins. This approach allows for a reevaluation of statin use beyond its cholesterol-lowering benefits. A structured search was conducted in the PubMed and Scopus databases using specific search terms, including articles published up to August 2024.

EXPERT OPINION

The pleiotropic effects of statins, including those mediated by the isoprenoid pathway, partially explain their clinical benefits. By inhibiting histone deacetylases (HDACs, the 'erasers') and DNA methyltransferases (DNMTs, the 'writers'), statins promote increased histone acetylation and reduced DNA methylation at gene promoter regions. These epigenetic modifications enhance chromatin accessibility, facilitating gene transcription and protecting the cardiovascular system. Further investigation into these epigenetic mechanisms could support the repositioning of statins for broader therapeutic applications. Statins may have benefits extending beyond their role in managing hypercholesterolemia, as their pleiotropic effects contribute to the prevention of cardiovascular disease-related mortality through mechanisms independent of LDL cholesterol reduction.

Scutellaria baicalensis Extracts Restrict Intestinal Epithelial Cell Ferroptosis by Regulating Lipid Peroxidation and GPX4/ACSL4 in Colitis

BACKGROUND

Ferroptosis in colonic epithelial cells has been implicated in the development of ulcerative colitis (UC) and the accompanying gut leakage. Scutellaria baicalensis Georgi (Scu) is widely used herb medicine for alleviating UC.

PURPOSE

We aimed to clarify the therapeutic effect of Scu on UC by inhibiting intestinal epithelial cell ferroptosis and explore its regulatory mechanisms on lipid peroxidation and the GPX4/ACSL4 pathways.

METHODS

UPLC-Q-TOF/MS was employed to analyze chemicals in the herbal extract and the colonic exposure of prototypes in Scu-treated mice. Additionally, the main compounds were quantified using HPLC-UV. The ameliorative effects of Scu were comprehensively explored in a UC mouse model established by feeding with dextran sulfate sodium (DSS). HPLC-MS based metabolomic studies were conducted to identify the differential metabolites in colon tissues from Scu or vehicle treated UC mice. Network pharmacology was conducted for target prediction and potential pathway analysis. In conjunction with these bioinformatic analyses, we performed RT-qPCR, immunofluorescence, immunohistochemistry and immunoblotting to elucidate the regulatory mechanisms of Scu on ferroptosis-related pathways in both in vivo and in vitro models.

RESULTS

78 chemical constituents in Scu were characterized, with 42 detected in the colonic tissues of Scu-treated mice. Scu could alleviate UC related symptoms in mice, including increased colon length and decreased pathological score. Furthermore, Scu inhibited pro-inflammatory cytokines and mediators, while improving gut barrier function by increasing the expression of ZO-1 and Occludin at both mRNA and protein levels. Based on metabolomic studies, a total of 71 differential metabolites exhibited a reversal trend following Scu administration. These findings, combined with results from network pharmacology, suggest that arachidonic acid (AA) metabolism and ferroptosis may serve as potential pathways for Scu intervention in UC. Further experiments indicated that the amelioratory actions of Scu on ferroptosis partially contributed to its modulation on lipid peroxidation and its regulatory influence on the GPX4/ASCL4 axis to ameliorate UC. When AA was administered at the same time as concurrently with Scu, the regulatory effects of Scu on ferroptosis, GPX4/ASCL4 axis, and its protective effects against UC were significantly reduced. Moreover, the inhibitory effect of Scu on ferroptosis was weakened when we knocked down GPX4 or overexpressed ACSL4 in vitro.

CONCLUSION

The ameliorative effect of Scu in UC is closely related to the regulation of lipid peroxidation and GPX4/ASCL4 mediated intestinal epithelial ferroptosis.

Shenfu injection ameliorates hepatic ischemia-reperfusion injury through induction of ferroptosis via JAK2/STAT3 pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Shenfu injection (SF) is a traditional Chinese medicine (TCM) compound preparation developed from the Shenfu decoction, which is described in the ancient Chinese medical book "Ji Sheng Fang" from the Song Dynasty. It is composed of two traditional Chinese medicines: Ginseng Radix et Rhizoma Rubra (G. Radix) and Aconiti Lateralis Radix Preparata (A. Lateralis). SF is renowned for its effects of restoring yang, rescuing adverse conditions, replenishing qi and consolidating deficiency. Research indicated that SF may enhance the recovery from Hepatic ischemia-reperfusion injury (HIRI), although its potential pharmacological mechanisms remain to be clearly defined.

AIM OF THE STUDY

To explore the pharmacological effects and mechanisms of SF in the treatment of HIRI.

MATERIALS AND METHODS

This study employed network pharmacology alongside both in vivo and in vitro experimental validation. It involved retrieving drug ingredients and targets from a database, constructing networks of chemical composition-targets- pathways and protein-protein interactions to pinpoint key targets. To evaluate the binding affinity between active ingredients and their respective targets, molecular docking was employed. Further, the study predicted potential targets and signaling pathways influenced by SF through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Finally, in vivo and in vitro experimental validation were performed using the HIRI mouse model and the oxygen-glucose deprivation/reperfusion (OGD/R)-induced AML12 cells model.

RESULTS

Findings from in vivo experiments indicated that SF could markedly lower serum glutamic pyruvic transaminase (ALT) and glutamic oxaloacetic transaminase (AST) levels, improve hepatic histopathological damage, reduce the count of myeloperoxidase (MPO) positive cells, and decrease the levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) in HIRI mice. Moreover, we investigated ferroptosis-related biomarkers and found that pretreatment with SF could significantly reduce the levels of reactive oxygen species (ROS), malondialdehyde (MDA), and iron in both HIRI mice and OGD/R-induced AML12 cells. Furthermore, it boosted the activity of superoxide dismutase (SOD) and glutathione (GSH), upregulated the protein expression of glutathione Peroxidase 4 (GPX4), and elevated the mRNA expression of GPX4, solute carrier family 7 member 11 (SLC7A11), and prostaglandin-endoperoxide synthase 2 (PTGS2) in both in vivo and in vitro. The findings from the network pharmacology analysis showed that 51 active components of SF were effective against HIRI and 257 potential intersecting target points. Further screening identified five key targets: AKT1, IL-1β, TNF, STAT3, and PTGS2. KEGG pathway analysis enriched for signaling pathways such as JAK2/STAT3. Additionally, the outcomes of molecular docking revealed a significant binding affinity among the four primary active components of SF and their respective targets. Western blotting results indicated that SF could inhibit the activation of the JAK2/STAT3 pathway in HIRI mice and OGD/R-induced AML12 cells.

CONCLUSION

Through network pharmacology, molecular docking and in vivo and in vitro experiments, it was preliminarily demonstrated that SF attenuates HIRI through the induction of ferroptosis via JAK2/STAT3 pathway.

Network pharmacology analysis reveals that coumestrol targets ZYX to inhibit ferroptosis and alleviate acute pancreatitis

AIM

The therapeutic effect of CMS on acute pancreatitis (AP) and the mechanism of targeting Zyxin (ZYX) to regulate ferroptosis in acinar cells.

METHODS

To assess the therapeutic effects of CMS in AP, we established caerulein-induced AP and caerulein plus LPS-induced SAP mouse models. Subsequently, weighted gene co-expression network analysis (WGCNA) and network pharmacology analysis were used to investigate the mechanism and target of CMS in the treatment of AP. Molecular docking and cell biology techniques were used to explore the molecular mechanisms by which CMS mitigated ferroptosis in AP animal and cell models.

RESULTS

CMS could alleviate the pathological damage of AP and SAP, inhibit ferroptosis and reduce inflammatory response. ZYX was an important target for CMS in the treatment of AP, and CMS could specifically bind to ZYX, down-regulate ZYX expression, and reduce TGF-β/SMAD pathway activity, thereby inhibiting acinar cell ferroptosis and improving pancreatic injury in AP. And we found that ZYX overexpression counteracted the inhibitory effects of CMS on TGF-β/Smad signaling and ferroptosis processes.

CONCLUSION

These results suggested that coumestrol targeting ZYX regulated the TGF-β/SMAD pathway, inhibited ferroptosis in acinar cells, and alleviated AP. Our research provided new drugs and targets for the treatment of AP.

Network pharmacology and experimental validation to elucidate the mechanism of the treatment of polycystic ovary syndrome with insulin resistance by Resina Draconis

BACKGROUND

Resina Draconis(RD) is a traditional Chinese medicine that activates blood circulation and removes blood stasis. Modern pharmacological studies have proved that RD has hypoglycaemic, pancreatic islets-protective, oestrogenic activity, anti-inflammatory, antibacterial and anti-tumour effects. Studies have shown that insulin resistance (IR) is the core pathological mechanism of polycystic ovary syndrome (PCOS), and RD can lower blood glucose to ameliorate IR, which has achieved significant results in the treatment of diabetes. However, the mechanism of action of RD in the treatment of PCOS-IR is still unclear.

METHODS

Network pharmacology analysis was used to predict the potential therapeutic targets of the active ingredients of RD. Experimental validation used a rat model of insulin resistance in PCOS; PCOS-IR symptoms were assessed, ovarian pathology was evaluated, and serum levels of insulin and sex hormones were determined. Expression levels of the PI3K, p-PI3K, Akt, p-Akt, GLUT4, FOXO3a, and P27 proteins were also measured in rat ovaries, along with mRNA expression levels of PI3K, Akt, GLUT4, FOXO3a, and P27.

RESULTS

Network pharmacological analyses indicated that the PI3K/Akt signalling pathway may play an important role in the treatment of PCOS-IR rats with RD. Experiments in PCOS-IR rats showed that RD significantly reversed insulin resistance, improved pathological changes in the ovaries, increased serum levels of follicle stimulating hormone (FSH) and estradiol (E2), and decreased levels of luteinizing hormone (LH), testosterone (T) and insulin. In addition, RD increased the levels of PI3K, p-PI3K, Akt, p-Akt and GLUT4, and decreased the levels of FOXO3a and P27 in the ovarian tissues of PCOS-IR rats, suggesting that RD may improve the symptoms of PCOS-IR in rats through the PI3K/Akt signalling pathway.

CONCLUSION

RD might improve insulin resistance and ovarian function in PCOS-IR by upregulating PI3K, p-PI3K, Akt, p-Akt and GLUT4 expression and downregulating FOXO3a and P27, thereby activating the PI3K/Akt signaling pathway. RD also regulated the LH/FSH ratio, increased E2 levels, reduced LH and T levels, and alleviated PCOS-IR symptoms in a rat PCOS-IR model.

Hedyotis chrysotricha aqueous extract inhibits hepatitis B surface antigen and viral replication via hepatocyte nuclear factor 4α regulation

BACKGROUND

Chronic hepatitis B virus (HBV) infection continues to pose a significant global public health challenge, as current antiviral treatments have not yet succeeded in completely eradicating the virus. Traditional Chinese Medicine (TCM) offers unique advantages in treating chronic hepatitis B. Furthermore, the aqueous extract of Hedyotis chrysotricha (Palib.) Merr (HCM), a synonym of Exallage chrysotricha (Palib.) Neupane & N.Wikstr., has shown potential anti-HBV properties. Nevertheless, its pharmacological effects and precise mechanisms of action remain unclear.

PURPOSE

We aim to evaluate the anti-HBV efficacy of the aqueous extract of HCM and investigate its underlying mechanisms.

STUDY DESIGN

Ultra performance liquid chromatography-triple time-of-flight mass spectrometry (UPLC-Triple-TOF/MS) was used to identify the HCM components, and the anti-HBV efficacy of HCM was evaluated using a transgenic HBV mouse model, as well as the HepG2.2.15 and HepAD38 HBV cell lines.

METHODS

We first identified the chemical components of HCM using UPLC-Triple-TOF/MS, combined with relevant reference standards. Quantification was achieved using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), followed by methodology validation. We used a transgenic HBV mouse model along with the HepG2.2.15 and HepAD38 HBV cell lines to assess its anti-HBV efficacy. Besides, network pharmacology, molecular docking and transcriptomics were employed to explore the underlying anti-HBV mechanisms.

RESULTS

UPLC analysis, using authentic reference standards, identified 19 major chemical components in HCM, including isorhamnetin, monotropein, sesamoside, and kaempferol, which were newly identified as components in this matrix. Our study demonstrates that HCM significantly inhibited HBV replication and transcription in both the transgenic HBV mouse model and HBV cell lines, with a notable reduction in HBsAg levels and the potential inhibition of cccDNA, which serves as a stable viral DNA reservoir in the nucleus of infected hepatocytes, driving the replication and persistence of HBV. Further analysis using network pharmacology and transcriptomic approaches suggests that the anti-hepatitis B mechanism may involve the upregulation of the phosphatidylinositol 3-kinase - protein kinase B (PI3K-AKT) and mitogen-activated protein kinase - extracellular signal-regulated kinase 1 and 2 (MAPK-ERK1/2) pathways. Additionally, hepatocyte nuclear factor 4α (HNF4α) was shown to play a critical role in HBV inhibition, with its function negatively regulated by the PI3K-AKT and MAPK-ERK1/2 pathways.

CONCLUSION

The aqueous extract of HCM not only inhibits HBV replication and transcription but also significantly suppresses HBsAg levels. The underlying mechanism likely involves the concurrent activation of the PI3K-AKT and MAPK-ERK1/2 pathways, resulting in the inhibition of HNF4α activity, which in turn suppresses HBV.

Huaxian formula alleviates nickel oxide nanoparticle-induced pulmonary fibrosis via PI3K/AKT signaling

As a progressive fibrotic lung disorder with high mortality, pulmonary fibrosis (PF) suffers from inadequate treatment options. While the traditional Chinese medicine (TCM) formulation Huaxian Formula (HXF) demonstrates multi-target therapeutic potential against PF, the identity of its active components and their mechanistic basis of action require systematic investigation. To elucidate the therapeutic effects and pharmacological mechanisms of HXF in treating PF induced by nickel oxide nanoparticles (nano NiO), utilizing network pharmacology (NP), molecular docking, as well as in vivo and in vitro experiments. A comprehensive analysis of authoritative databases identified 121 active compounds, 202 potential therapeutic targets, and 1664 PF-related genes. Among these, 105 overlapping targets were found between HXF and PF. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses identified the PI3K/AKT signaling pathway as both a pivotal mechanism in PF pathogenesis and a primary target of HXF's therapeutic effects. Molecular docking studies revealed that the six core compounds (quercetin, luteolin, kaempferol, β-sitosterol, isorhamnetin, and formononetin) of HXF exhibited strong binding affinity to proteins involved in the PI3K/AKT pathway. In the rat and A549 cell model, HXF treatment reduced collagen deposition and downregulated the expression of type I collagen (Col-I). Mechanistically, HXF inhibited the phosphorylation of PI3K and AKT. Collectively, these findings suggested that HXF alleviated PF by modulating the PI3K/AKT signaling pathway, providing valuable insights and methods for the development of TCM for PF.

The Inhibitory Effect of the Active Ingredients in the Bushen Huoxue Formula on the IL-17A Signaling Pathway and Its Alleviating Effect on Osteoarthritis

Objective

Osteoarthritis (OA) stands as a prevalent degenerative disease worldwide. Despite the demonstrated therapeutic efficacy of the Bushen Huoxue formula (BSHXF) in treating OA, its underlying mechanism remains elusive. Network pharmacology is commonly employed for investigating drug-disease associations and processes. In this study, we employed network pharmacology alongside in vitro and in vivo experiments to elucidate the molecular mechanism by which BSHXF treats OA.

Methods

Based on the TCMSP database, active components of BSHXF were screened, and OA-related targets were retrieved from GeneCard and DisGeNET to construct a "component-target-pathway" network using Cytoscape. Core target functions and pathways (KEGG/GO) were analyzed through STRING and Metascape, while component-target binding affinity was validated via Autodock. For in vitro experiments, an IL-1β-induced chondrocyte inflammation model was established, and key protein expression was detected by Western blot and immunofluorescence. For in vivo experiments, an OA model was created by medial meniscectomy of the knee joint in rats, and therapeutic efficacy was assessed using histological staining and micro-CT.

Results

This study screened 89 active ingredients of BSHXF and identified 189 common targets. Network pharmacological analysis revealed luteolin and tanshinone IIA as the most crucial active ingredients in treating OA with BSHXF. The potential mechanisms of action for BSHXF in OA treatment involve inflammation inhibition, immune function regulation, and resistance to oxidative stress, with a significant regulatory role played by the IL-17 signaling pathway. Molecular docking results demonstrated luteolin's strong binding affinity to key targets such as B-cell lymphoma 2 (Bcl-2), Matrix metalloproteinase-9 (Mmp-9), and IL-6.In vitro experiments demonstrated that BSHXF significantly suppressed IL-1β-induced inflammatory responses in chondrocytes, downregulating IL-17A expression (p < 0.05), reducing the expression of MMP-9 (p < 0.05) and IL-6 (p < 0.05), and inhibiting apoptosis. Additionally, in vivo experiments revealed that the high-dose BSHXF group (150 mg/kg) markedly alleviated cartilage damage in OA rats, with OARSI scores significantly decreased compared to the model group (p < 0.05). Micro-CT analysis showed that BSHXF inhibited osteophyte formation and ameliorated OA pathological conditions.

Conclusion

BSHXF has the potential to alleviate OA by suppressing inflammation, inhibiting cartilage apoptosis and hindering extracellular matrix degradation via the IL-17 signaling pathway. Our study elucidated the molecular mechanisms underlying the therapeutic effects of BSHXF on OA, thus highlighting its further research implications as a novel drug candidate.

Exploring the antitumor potential of cucurbitacin B in hepatocellular carcinoma through network pharmacology, molecular docking, and molecular dynamics simulations

Cucurbitacin B exhibits promising anticancer activity across various cancers; however, its precise mechanism remains unclear. This study integrates network pharmacology, molecular docking, and dynamics simulations to elucidate CuB's multitarget therapeutic mechanisms against HCC. Potential CuB targets were retrieved from CTD, HERB, SwissTargetPrediction, ETCM, and PharmMapper databases. HCC-related genes were sourced from GEO datasets (GSE216613, GSE101685, GSE62232, GSE46408), GeneCard, DisGeNET, OMIM, and TTD. Intersecting targets were analyzed via PPI networks (STRING/Cytoscape), followed by GO/KEGG enrichment (DAVID). Molecular docking (Autodock Vina), ADMET evaluation (ADMETlab 2.0), and molecular dynamics simulations (Amber20) validated interactions. Core targets were further verified using GEPIA, HPA, cBioPortal, and TIMER databases. A total of 139 shared targets were identified between CuB and HCC. Key targets included EGFR, MTOR, MMP9, HSP90AB1, STAT3, and TNF. KEGG pathway analysis revealed significant enrichment in the phosphatidylinositol 3-kinase/protein kinase B (PI3K-Akt) signaling pathway, alongside cancer-related pathways (e.g., lipid metabolism, EGFR tyrosine kinase inhibitor resistance). Molecular docking confirmed strong binding (energy < - 5.0 kcal/mol) between CuB and core targets (e.g., MTOR: - 8.2 kcal/mol; HSP90AB1: - 7.9 kcal/mol). ADMET profiling indicated favorable pharmacokinetic properties, and molecular dynamics simulations demonstrated stable ligand-receptor complexes (RMSD < 2.5 Å). External validation highlighted differential expression (HSP90AB1, TNF) and clinical correlations (CCND1, EGFR) in HCC. CuB exerts antitumor effects in HCC through multitarget modulation, primarily via PI3K-Akt signaling and interactions with EGFR, MTOR, and HSP90AB1. This study provides a mechanistic foundation for CuB's therapeutic potential in HCC, guiding future experimental and clinical investigations.

Aryl Organophosphate Esters and Hemostatic Disruption: Identifying Risk through Machine Learning and Experimental Validation

Organophosphate esters (OPEs) have emerged as a significant environmental concern due to their widespread occurrence and potential human health risks. The presence of OPEs in human blood suggests direct interactions with hematological components, which may compromise hemostatic balance and lead to adverse health outcomes. Despite the critical role of hemostatic balance in maintaining blood stability, the effects of OPEs on this system remain poorly understood. This investigation was undertaken to delineate the effects and potential mechanisms of OPEs that modulate hemostasis, utilizing in silico approach and high-throughput in vitro investigation. We analyzed 85 environmentally prevalent OPEs for their structural descriptors and affinity for proteins essential to hemostatic function. The multiple linear regression implicated aryl-OPEs, distinguished by their benzene ring scaffold, as potent disruptors of hemostatic balance. This analysis result was rigorously validated through the in vitro hemostatic balance assays. Further investigation through network toxicology, artificial intelligence (α-Fold) algorithms, and an agonist cotreatment assay revealed proliferator-activated receptor γ (PPARγ) as a key mediator of aryl-OPEs induced hemostatic disruption. By integrating in vitro experimental insights with in vivo exposure data, we concluded that specific aryl-OPEs, such as bisphenol a bis (diphenyl phosphate) (BDP) and cresyl diphenyl phosphate (CDP), pose a moderate risk to the hemostatic balance of the general population. Our findings not only contribute to the prioritization of OPEs risk management but also establish a methodology for assessing the hematological toxicity of emerging pollutants.

Synergistic Network Pharmacology: Preclinical Validation and Clinical Safety in Acute Ischemic Stroke

BACKGROUND

Most human disease definitions, except for rare and communicable diseases, are based on symptoms in specific organs, not on causal molecular mechanisms. This limits treatments to imprecise symptomatic approaches with high numbers needed to treat. Systems medicine, instead, has a holistic approach and defines diseases in an organ-agnostic manner on the basis of associated risk genes, their encoded proteins, and protein-protein interactions. Dysregulation of such disease modules is best corrected by multitarget, synergistic network pharmacology. Here we test this principle in acute ischemic stroke, a highly unmet medical indication without any approved neuroprotective drug so far.

METHODS

We extend 3 validated risk genes, neuronal nitric oxide synthase (NOS1), NADPH oxidase 5 (NOX5), and soluble guanylate cyclase (sGC), to a single disease module. For preclinical validation, we used C57/Bl6 mice and humanized NOX5-knock-in mice because NOX5 is not present in the mouse genome despite playing a key role in early stroke. Because up to 70% of patients with stroke have diabetes or prediabetes as an aggravating comorbidity, we also induced diabetes in these mice to model the increased clinical risk for hemorrhagic transformation.

RESULTS

We found that a triple-drug combination of a NOX inhibitor, a nitric oxide synthase inhibitor, and an sGC activator reduced infarct size and, in diabetic animals, also prevented hemorrhagic transformation. Reducing each individual compound dose to subthreshold levels still resulted in full protection when combined, typical for supra-additive network pharmacology. To examine clinical safety, 3 drugs, either marketed for sGC or repurposed for nitric oxide synthase and NADPH oxidase, were administered to healthy volunteers in a phase I trial.

CONCLUSIONS

Our data establish that a mechanism-based network pharmacology approach is effective and clinically safe, warranting a currently ongoing first-in-class neuroprotective phase II interventional trial.

REGISTRATION

URL: https://clinicaltrials.gov/study/NCT05762146?term=repo-stroke&rank=1; Unique Identifier: NCT05762146.

Potential of Sivelestat for Pulmonary Arterial Hypertension Treatment: Network Pharmacology-Based Target Identification and Mechanistic Exploration

Background

Sivelestat is a specific neutrophil elastase inhibitor that is currently approved for the treatment of acute lung injury and acute respiratory distress syndrome. Given sivelestat's established anti-inflammatory and antioxidant properties, its efficacy in treating pulmonary arterial hypertension (PAH) remains uncertain. This study aims to investigate the potential of sivelestat as a treatment for PAH.

Methods

Sivelestat's effects on PAH were evaluated using hypoxia-induced rat models (10% O2, 4 weeks) and pulmonary arterial endothelial/smooth muscle cells (1% O2). Rats received sivelestat (20-100 mg/kg) for 2 weeks, with hemodynamic (RVSP) and vascular remodeling (%WT) assessments. In vitro, sivelestat (50-200 μM) suppressed hypoxia-driven proliferation (CCK-8, EdU), migration (Transwell), and angiogenesis. Molecular validation via qPCR/Western blot confirmed reduced expression of key targets (IGF1R, JAK1, JAK2, PDGFRB).

Results

Through predictive analysis, we identified 595 potential genes associated with sivelestat in the treatment of PAH. Notably, ERBB2, IGF1R, JAK1, JAK2, PDGFRB, and PTPN11 emerged as key hub genes. In vivo experiments demonstrated that administration of sivelestat at a dose of 100 mg/kg significantly reduced PAH and improved pulmonary vascular remodeling. In vitro experiments indicated that sivelestat effectively decreased the proliferation and migration of PAECs and PASMCs induced by hypoxia.

Conclusion

Sivelestat has the potential to treat PAH through various targets and pathways. We have initially elucidated the molecular mechanism by which sivelestat acts in the treatment of PAH and have conducted preliminary validation through molecular docking studies and experimental approaches.

Network toxicology and molecular docking to investigate the mechanism of bisphenol A toxicity in human diabetic cardiomyopathy

Bisphenol A (BPA), a ubiquitous endocrine-disrupting chemical, is widely used in polymers, plasticizers, and food packaging, raising significant concerns for human health. Growing evidence links BPA exposure to cardiovascular diseases, including diabetic cardiomyopathy (DCM), a severe complication of diabetes characterized by myocardial dysfunction. This study employs an integrative approach combining network toxicology and molecular docking to elucidate the molecular mechanisms underlying BPA-induced DCM. Using computational tools such as ADMETlab2.0, ProTox3.0, GeneCards, OMIM, Swiss Target Prediction, and ChEMBL databases, we systematically predicted BPA's potential to induce DCM and constructed comprehensive disease and BPA target libraries. Venn diagram analysis identified 93 potential targets associated with BPA-induced DCM, and a robust BPA regulatory network was established using Cytoscape. Functional enrichment analyses revealed significant involvement of oxidative stress, insulin signaling, and metabolic pathways in BPA toxicity. Molecular docking simulations demonstrated stable binding interactions between BPA and core targets (INS, AKT1, PPARG, STAT3, PPARA, MMP9), with binding energies ranging from -5.3 to -7.5 kcal/mol. Our findings indicate that BPA may induce DCM through key genes and pathways, including cGMP-PKG signaling pathway, insulin signaling pathway, AMPK signaling pathway, and HIF-1 signaling pathway. This study provides a novel theoretical framework for understanding the molecular pathogenesis of BPA-induced DCM and highlights the potential of network toxicology in identifying toxic pathways for uncharacterized environmental compounds. These insights offer potential targets for preventive and therapeutic strategies against BPA-associated cardiovascular complications.

5,7,2',6'- Tetrahydroxyflavone affects the progression of ovarian cancer via hsa-miR-495-3p-ACTB/HSP90AA1 pathway

BACKGROUND

Scutellariae Radix (SR), a traditional Chinese medicine, has been shown to have potential anti-cancer properties.

PURPOSE

To explore the mechanism of inhibiting ovarian cancer (OC) progression by SR.

METHODS

The key active ingredient (5,7,2',6'-Tetrahydroxyflavone, TF) and key targets (ACTB and HSP90AA1) of SR were screened by the network pharmacology method. CCK-8 reagent, Transwell assay, and Annexin-V-FITC kit were used to evaluate the effects of TF on OC cell viability, migration, and apoptosis. The upstream microRNAs (miRNAs) of ACTB and HSP90AA1 were predicted by the starBase database. Important miRNAs related to OC were mined using gene expression datasets in the GEO database. RT-qPCR and Western blotting experiments were used to detect miRNA or gene expression.

RESULTS

TF inhibited OC cell viability/migration and induced apoptosis in a concentration-dependent manner. Hsa-miR-495-3p was identified to be a key miRNA in OC, whose expression was lacking in OC cells. ACTB and HSP90AA1 expressed highly in OC cells. Hsa-miR-495-3p mimics reduced ACTB and HSP90AA1 expression. Hsa-miR-495-3p inhibitor and overexpression of ACTB or HSP90AA1 reversed the inhibitory effect of TF on OC cells.

CONCLUSION

TF, an active ingredient of SR, hindered OC progression through the hsa-miR-495-3p-ACTB/HSP90AA1 pathway.

Curcumin alleviates LPS-induced WI-38 cell inflammation injury by regulating PTGS2 expression

BACKGROUND

Infantile pneumonia is a common infectious disease affecting infants and young children, which can lead to severe complications such as heart failure, significantly increasing morbidity and mortality rates among affected populations. Curcumin (CUR), a prominent natural polyphenol found in turmeric and other species of Curcuma, exhibits anti-inflammatory, antioxidant, and anticancer properties. Consequently, CUR has been hoped to be a therapeutic or preventive agent for several main human diseases. This study aims to explore the effects of CUR on lipopolysaccharide (LPS)-treated Wistsar Institute (WI)-38 cells.

METHODS

The cell vitality, proliferation, and apoptosis were assessed by cell counting kit-8 (CCK8) assay, 5-ethynyl-2'-deoxyuridine (EdU), and flow cytometry assays. Inflammation and oxidative stress were examined by measuring interleukins (IL)-6, IL-1β, tumor necrosis factor α (TNF-α), malondialdehyde (MDA), and superoxide dismutase (SOD) levels using the corresponding enzyme-linked immunosorbent assay (ELISA) test kits. The network pharmacology and molecule docking were carried out to predict the critical targets and potential therapeutic mechanisms of CUR in infantile pneumonia. The key target genes were predicted using PPI in the CUR protected-infantile pneumonia effect. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to exhibit the biological function. The results of prediction were confirmed in vitro experiments.

RESULTS

LPS inhibited the vitality, proliferation, and SOD levels of WI-38 cells and facilitated the cell apoptosis, IL-6, IL-1β, TNF-α, and MDA levels. CUR abolished LPS-induced regulation WI-38 cell biological functions. Besides, the 16 hub genes from potential target genes of CUR and infantile pneumonia were screened. Moreover, six hub genes (enhanced green fluorescent protein (EGFP), v-akt murine thymoma viral oncogene homolog 1 (AKT1), prostaglandin endoperoxide synthase (PTGS2), signal transducer and activator of transcription 3 (STAT3), matrix metalloproteinase 9 (MMP9), and tumor necrosis factor (TNF)) in the CUR-protected-infantile pneumonia effect were identified by PPI analysis. The therapeutic effects of CUR on infantile pneumonia might relate to anti-viral and anti-inflammatory effects predicted by GO and KEGG enrichment analysis. Interestingly, CUR repressed LPS-stimulated facilitation of PTGS2 expression. The molecular docking demonstrated that PTGS2 could directly bind to CUR. The PTGS2 levels were inhibited by CUR treatment and negatively related to the time after WI-38 cells were treated with cycloheximide (CHX). PTGS2 knockdown could promote LPS-induced injury in WI-38 cells. CUR expedited cell vitality and proliferation and suppressed cell apoptosis, inflammation, and oxidative stress in LPS-induced WI-38 cells via down-regulating PTGS2.

CONCLUSION

CUR attenuates LPS-induced WI-38 cell injury by downregulating PTGS2. CUR may be the potential drug for alleviating LPS-induced WI-38 cell inflammation damage via regulating PTGS2 expression.

Integrating network pharmacology and experimental validation to advance psoriasis treatment: Multi-target mechanistic elucidation of medicinal herbs and natural compounds

BACKGROUND

Psoriasis, a chronic immune-mediated inflammatory disease (IMID), presents significant therapeutic challenges, necessitating exploration of alternative treatments like medicinal herbs (MH) and natural compounds (NC). Network pharmacology offers predictive insights, yet a systematic evaluation connecting these predictions with experimental validation outcomes specifically for MH/NC in psoriasis is lacking. This review specifically fills this gap by comprehensively integrating and analyzing studies that combine network pharmacology predictions with subsequent experimental validation.

METHODS

A systematic literature search identified 44 studies employing both network pharmacology and in vitro or in vivo experimental methods for MH/NC targeting psoriasis. This review provides a systematic analysis of the specific network pharmacology platforms, predicted targets/pathways, in vivo and in vitro experimental validation models, and key biomarker changes reported across these integrated studies. Methodological approaches and the consistency between predictions and empirical findings were critically evaluated.

RESULTS

This first comprehensive analysis reveals that network pharmacology predictions regarding MH/NC mechanisms in psoriasis are frequently corroborated by experimental data. Key signaling pathways, including the IL-17/IL-23 axis, MAPK, and NF-κB, emerge as consistently predicted and experimentally validated targets across diverse natural products. The review maps the specific network pharmacology tools and experimental designs utilized, establishing a methodological benchmark for the field and highlighting the successful synergy between computational prediction and empirical verification.

CONCLUSION

By systematically integrating and critically assessing the linkage between network pharmacology predictions and experimental validation for MH/NC in psoriasis, this review offers a unique clarification of the current, validated state-of-the-art, differentiating it from previous literature. It confirms network pharmacology's predictive power for natural products, identifies robustly validated therapeutic pathways, and provides a crucial benchmark, offering data-driven insights for future research into artificial intelligence-enhanced natural product-based therapies for psoriasis and other IMIDs.

Comprehensive network pharmacology and experimentation to unveil the therapeutic efficacy and mechanisms of gypenoside LI in anaplastic thyroid cancer

BACKGROUND

Anaplastic thyroid cancer (ATC) is a markedly invasive subtype of thyroid cancer with a poor prognosis. The Gynostemma pentaphyllum-derived Gypenoside LI (Gyp LI) can inhibit the growth and metastasis of various tumors. This study was designed to evaluate the pharmacological mechanisms of Gyp LI against ATC via network pharmacology analysis combined with experimental verification.

METHODS

Core targets and signaling pathways were obtained by using the network pharmacological analysis method. Utilizing a combination of in vitro and in vivo methodologies, we conducted a rigorous examination to ascertain the suppressive impact of Gyp LI on the ATC cell lines, specifically 8305 C and C643. Then used western blotting and immunohistochemistry to analyze the inhibitory effects of Gyp LI on SRC kinase and its downstream signaling pathways.

RESULTS

Through integrative analysis of Gyp LI and ATC-target interactions, 78 candidate targets were identified. Network-based protein-protein interaction (PPI) analysis, combined with molecular docking, pinpointed HSP90AA1, SRC, and CASP3 as pivotal hub genes modulated by Gyp LI. KEGG enrichment analysis further emphasized the PI3K/AKT pathway, highlighting its critical involvement in ATC therapy. Gyp LI significantly inhibits ATC cell proliferation, migration, and invasion while inducing apoptosis, likely via modulation of the SRC/PI3K/AKT axis. Moreover, it enhances iodine uptake in ATC cells by regulating the sodium-iodide symporter pathway.

CONCLUSIONS

Gyp LI effectively inhibits ATC progression by modulating SRC/PI3K/AKT signaling, enhancing apoptosis, and promoting iodine uptake, offering potential therapeutic benefits for ATC treatment.

1, 8-Cineole Ameliorated Staphylococcus aureus-Induced Pneumonia through Modulation of TRP-KYN and Arginine-NO Reprogramming

1, 8-Cineole (Cin), a cyclic monoterpenoid derived from tea trees and eucalyptus species, exhibits diverse pharmacological properties. Yet, its therapeutic impact and underlying mechanism against Staphylococcus aureus (S. aureus) pneumonia remain to be elucidated. In this study, metabolomics based on UPLC-MS/MS was integrated with network pharmacology, molecular biology, and molecular docking to investigate the effects of Cin. The findings demonstrated that Cin markedly reduced mortality and lung bacterial load, lessened pulmonary damage while suppressing the levels of proinflammatory factors, including tumor necrosis factor α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) in the bronchoalveolar lavage fluid (BALF) of infected mice. Additionally, 19 metabolites, primarily involved in tryptophan metabolism and arginine biosynthesis, were notably modified by Cin via suppressing the enzymatic activity of indoleamine 2, 3-dioxygenase 1 (IDO1) and inducible nitric oxide synthase (iNOS), thereby attenuating the inflammatory response. Notably, knockdown of IDO1 or iNOS significantly diminished the anti-inflammation effect of Cin. In conclusion, our study validates the therapeutic potential of Cin against S. aureus pneumonia via anti-inflammation by downregulating IDO1 and iNOS. Our results provide a theoretical basis of natural substances applied in bacterial pneumonia treatment.

Transcriptomic analysis and experiment to verify the mechanism of Xiaoyao san in the treatment of irritable bowel syndrome with depression

ETHNOPHARMACOLOGICAL RELEVANCE

Xiaoyao san (XYS) is a classic traditional Chinese medicine compound first recorded in "Taiping Huimin Heji Ju Fang". Traditionally, it is used to treat irritable bowel syndrome (IBS) and depression. However, its mechanism of action in treating IBS patients with depressive symptoms is still unclear.

AIM OF THE STUDY

This study aimed to investigate the effects of XYS on intestinal and depressive symptoms in IBS and explore the mechanisms through transcriptomic analysis and pharmacological experiments.

MATERIALS AND METHODS

IBS was induced in mice through a combination of chronic unpredictable mild stress and intragastric senna leaf stimulation. We evaluated six depressive parameters, examined colon tissue with hematoxylin and eosin staining and transmission electron microscopy, analyzed related proteins using western blotting, and performed transcriptomics on brain and intestinal tissues. The possible mechanism of action was speculated by network analysis of transcriptome results and further verified using the IBS model.

RESULTS

The results show that XYS restored mouse weight, reduced intestinal symptoms and sensitivity, suppressed villous loss and atrophy, and enhanced the integrity of the intestinal mucosal barrier. Notably, XYS decreased the depression-like behavior. Transcriptomic analysis combined with pharmacological experiments revealed that XYS inhibited the expression of proteins related to the intestinal ACT1/TRAF6/P38MAPK/AP-1 signaling pathway while activating the brain's DRD2/TH signaling pathway and increasing dopamine release in the brain.

CONCLUSIONS

XYS may regulate the brain-gut axis function and improve intestinal and depressive symptoms in IBS model mice through the intestinal ACT1/TRAF6/P38MAPK/AP-1 signaling pathway and the brain DRD2/TH signaling pathway.

Coagulin-L alleviates hepatic stellate cells activation and angiogenesis through modulation of the PI3K/AKT pathway during liver fibrosis

Fibrosis, a wound healing response in chronic liver diseases, is a potential therapeutic target during the disease progression. The activation of hepatic stellate cells (HSCs) plays a central role in liver fibrosis and depicts phenotypic change during fibrosis progression. Coagulin-L, a withanolide from Withania coagulans, has shown diverse biological activities, including anti-hyperglycemic and anti-dyslipidemic effects. However, its therapeutic efficacy against HSC activation, pathological angiogenesis and liver fibrosis is unknown. This study investigates the effects of Coagulin-L on HSC activation, pathological angiogenesis and validates these findings in vivo using a methionine and choline-deficient (MCD) diet-induced liver fibrosis model in C57BL/6 mice. Therapeutic efficacy of Coagulin-L was studied using transforming growth factor beta (TGF-β) activated HSC cell line LX-2 in vitro. Network pharmacology was used for target prediction, followed by Human umbilical vein endothelial cells (HUVEC) cell based angiogenic assays. The validation studies were carried out in a mice model of MCD diet induced liver fibrosis using serum biochemistry, histopathological assessment and immunohistochemistry methods. We found that Coagulin-L mitigated TGF-β induced activation of stellate cells and exhibited anti-angiogenic effects by downregulation of vascular endothelial growth factor (VEGF) expression and secretion from stellate cells with inhibition of the PI3K/AKT signaling pathway. In the MCD diet-induced liver fibrosis model, Coagulin-L alleviated liver injury, improved liver function, and reduced collagen deposition. Collectively, our results underscored the anti-fibrotic and anti-angiogenic effects of Coagulin-L in vitro and in vivo liver fibrosis models, thereby indicating its therapeutic potential in chronic liver diseases including metabolic dysfunctional-associated steatohepatitis (MASH).

Research on erchen tang in the treatment of community-acquired pneumonia based on chemical molecular mechanisms of quercetin and kaempferol: PI3K/AKT/NF-κB protein signaling

Streptococcus pneumoniae is the most common pathogen of community-acquired pneumonia (CAP). This study aimed to investigate into the effects of compounds in Erchen Tang (also known as Erchen Decoction, ECD) on the expression of inflammatory factors, as well as proteins associated with the key signaling pathways. The expression changes of proteins pertinent to those potential pathways were meticulously detected using Gene Cards, OMIM database, STRING database, and GO and KEGG enrichment analyses. The findings indicated that both quercetin and kaempferol are highly competitive components in ECD. Additionally, these natural compounds were found to diminish the expression levels of inflammatory factors such as tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). Extensive research has demonstrated that quercetin and kaempferol play a pivotal role in the therapeutic efficacy of ECD for the treatment of CAP. They achieve this by exerting anti-inflammatory and immunomodulatory effects, primarily through the inhibition of the PI3K/AKT/NF-κB signaling pathway's activation. This groundbreaking discovery not only offers a novel molecular mechanism explanation for the application of Erchen Decoction in combating community-acquired pneumonia but also lays a solid theoretical foundation for the development of innovative anti-pneumonia medications that are centered around quercetin and kaempferol.

Understanding dosage effects of traditional Chinese medicine using network analysis

Background

Traditional Chinese Medicine (TCM) prescriptions are complex, multi-botanical drug systems in which dosage critically influences therapeutic efficacy. While network pharmacology is widely used to analyze TCM mechanisms, existing methods ignore the dosage of botanical drugs, a key limitation that may skew predictions. This study investigates how integrating dosage data alters network analysis outputs, addressing a fundamental gap in understanding TCM's dosage-dependent effects.

Methods

Our analysis compared dosage-weighted and traditional non-dosage network approaches across 94 traditional Chinese medicine (TCM) prescriptions. We developed four custom indicators to quantify differences throughout the network pipeline: Dedis (input distance difference), DeSD (input standard deviation difference), DeDT (drug target prediction difference), and DePy (pathway prediction difference). The interrelationships among these indicators were examined to indicate when dosage adjustments influence predictions. A detailed case study further demonstrated the impact of dosage modifications on predictive outcomes.

Results

Among the indicators with inputs difference, Dedis, but not DeSD, exhibited a statistically significant relationship with output predictions, with target differences (DeDT) ranging from 0% to 68.9% and pathway differences (DePy) ranging from 0% to 74.6%. The interrelationships between these indicators were visualized using a clock model representation. The case study further demonstrated the impact of dosage on network outputs, revealing dosage refined both the predicted drug targets for individual botanical drugs and the subsequent pathway analysis results.

Conclusion

Our study demonstrated that dosage significantly influences the outcomes of network analysis, with Dedis serving as a reliable indicator of whether such changes would occur. Specifically, changes resulting from dosage-dependent refinement of both drug target prediction and pathway analysis were observed.

Quercetin down-regulates MCP-1 expression in autoimmune myocarditis via ERK1/2-C/EBPβ pathway: An integrative approach using network pharmacology and experimental models

Myocarditis is one of the common causes of sudden death in adolescents, and autoimmune response and inflammation play an essential role in the development of myocarditis. Quercetin is a natural flavonoid compound with anti-inflammatory and cardioprotective effects. However, the mechanism of quercetin in autoimmune myocarditis remains unclear. This study observed that quercetin significantly improved cardiac function, inflammation and fibrosis in mice with experimental autoimmune myocarditis (EAM). In addition, Network pharmacology predicts the key target C/EBPβ and signalling pathway MAPK for quercetin treatment of autoimmune myocarditis. CESTA and DARTS experiments verified that quercetin and C/EBPβ have strong binding ability. It is shown that quercetin down-regulates MCP-1 expression in H9C2 cells by dephosphorylation of ERK1/2 and C/EBPβ. Specifically, quercetin reduced the binding of C/EBPβ to the MCP-1 promoter, resulting in decreased expression of MCP-1, which was associated with decreased ERK1/2 dependent phosphorylation at the C/EBPβ threonine 188 site. This inhibitory effect of quercetin could be further enhanced by the ERK1/2 inhibitor PD98059. The biological relevance of this regulatory network is demonstrated in EAM mice. In conclusion, these results illustrate the protective effect of quercetin against autoimmune myocarditis. A novel regulatory mechanism was revealed, namely the down-regulation of MCP-1 through the ERK1/2-C/EBPβ axis. This provides a new therapeutic strategy for autoimmune myocarditis.

Effectiveness of herbal medicine for liver cancer treatment as revealed by a bibliometric and visualization analysis

Background

Liver cancer is highly prevalent worldwide. However, current medical treatments remain insufficient. Although herbal medicine has a long history and extensive expertise in treating liver cancer, the literature in this field has not been thoroughly explored. This study aims to assess and analyze the distribution patterns and key research areas of publications concerning herbal medicine for liver cancer.

Methods

Literature on herbal medicine and liver cancer published between January 1, 2008, and September 28, 2024, was collected for this research. Excel, CiteSpace 6.4.R1, VOSviewer 1.6.20, Scimago Graphica, and Bibliometrix 4.1 were used for data analysis.

Result

The study examines 634 academic articles on herbal medicine for liver cancer, with the majority contributed by Chinese researchers, particularly from Shanghai University of Traditional Chinese Medicine. Wang Ning is the most productive author, possessing the highest h-index. The JOURNAL OF ETHNOPHARMACOLOGY has the most publications and the highest h-index. Journals publishing on herbal medicine and liver cancer are primarily in the fields of molecular biology and immunology, whereas the cited journals are mainly in the fields of environment, toxicology, and nutrition. Keyword clustering analysis indicates that "NF kappa B" and apoptosis have long been the main research topics in this field. Analysis of emergent words suggests that "network pharmacology", antioxidants, "adjuvant therapy", and "molecular docking" may become significant research topics in the near future.

Conclusion

This analysis provides a comprehensive overview of the current status, primary focuses, and emerging trends in research related to herbal medicine and liver cancer.

Astragali Radix-Curcumae Rhizoma normalizes tumor blood vessels by HIF-1α to anti-tumor metastasis in colon cancer

BACKGROUND

Abnormal tumor blood vessels can significantly promote the malignant progression of tumors, prompting researchers to focus on drugs that normalize these vessels for clinical treatment. The combination of the Qi-tonifying drug Astragali Radix and the blood-activating drug Curcumae Rhizoma, referred to as AC, exhibited significant anti-tumor metastasis effects. However, the association between the anti-tumor metastasis effect of AC and its potential role in regulating tumor vascular remodeling warrants further exploration.

PURPOSE

This study aimed to elucidate the mechanism through which AC induces tumor blood vessel normalization in colon cancer (CC).

METHODS

The potential active components of AC were identified through UPLC-MS/MS. An orthotopic transplantation model of CC was established in BALB/c mice using the CT26-Lucifer cell line, and the effects of AC were evaluated using IVIS imaging, hematoxylin and eosin (H&E) staining, and immunohistochemistry. Network pharmacology and molecular biology analyses were employed to identify the potential direct targets of AC. Subsequently, RT-PCR and Western blotting techniques were utilized to validate the findings obtained from network pharmacology. Furthermore, ELISA and other methodologies were used to investigate glycolysis-related indicators, along with immunofluorescence technology to demonstrate changes in vascular leakage and perfusion characteristics associated with blood vessel normalization.

RESULTS

We identified HIF-1α as a potential direct target of AC. This interaction influences the glycolytic processes in both tumor cells and tumor-associated endothelial cells (TECs) by directly binding to HIF-1α and modulating its nuclear translocation, thereby determining the integrity of TEC junctions. Mechanistically, AC directly regulates the key enzyme PFKFB3 in glycolysis by modulating HIF-1α expression and inhibiting its nuclear translocation. This action reduces tumor glycolytic flux, decreases the internalization of VE-cad, and influences the expression of downstream matrix metalloproteinases (MMPs), thereby strengthening the adherens and tight junctions between TECs and restoring vascular integrity.

CONCLUSION

This study presents novel findings that AC can regulate glycolysis through the inhibition of HIF-1α nuclear translocation, thereby promoting the normalization of tumor blood vessels and effectively inhibiting tumor metastasis. These results suggested that AC may serve as an effective therapeutic agent for normalizing tumor blood vessels.

Association and mechanism of montelukast on sleep disorders: insights from NHANES 2005-2018 data analysis and a network pharmacology study

BACKGROUND

Studies have suggested associations between montelukast and increased risks of sleep disorders, including overall sleeping problems and insomnia. However, the results of observational studies are not consistent. Understanding these associations is crucial, particularly in patients solely diagnosed with allergic rhinitis, where montelukast use remains prevalent.

OBJECTIVE

This study aimed to assess whether montelukast exposure is associated with sleep disorders and elucidate the possible molecular mechanism.

METHOD

We conducted a cross-sectional study of 16,520 adults from the National Health and Nutrition Examination Survey (NHANES) 2005-2018. Multivariable regression was used to evaluate the association between montelukast exposure and sleep disorder. Network pharmacology was conducted to identify the mechanisms of montelukast on sleep disorders.

RESULTS

Montelukast exposure had a higher prevalence of sleep disorders (25.28%). In a multivariable logistic regression model adjusted for sociodemographic, behavioral, and health characteristics, montelukast exposure was associated with sleep disorders (odds ratio [OR]: 1.72; confidence interval [CI]: 1.32-2.26). Network pharmacology was identified 39 intersection targets and 17 core targets of montelukast on sleep disorders. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested montelukast mainly works through multiple pathways in chemical carcinogenesis-receptor activation, cancer, estrogen signaling pathway, etc.

CONCLUSIONS

The study implies a potential positive association between long-term montelukast exposure and sleep disorders through multi-faceted mechanisms. It is suggested that attention be given to the possibility of sleep disorders in patients undergoing prolonged montelukast therapy.

Study on the mechanism of Trichosanthes kirilowii Maxim. against COPD based on serum chemical composition analysis, network pharmacology, and experimental study

BACKGROUND

Trichiosanthis Pericarpium (TP) is the dried ripe peel of Trichosanthes kirilowii Maxim., also known as gualoupi in Chinese, effectively clears heat and transforms phlegm. Traditional Chinese medicine (TCM) prescriptions that contain TP are widely used in clinical practice to treat respiratory diseases, including chronic obstructive pulmonary disease (COPD). However, the active ingredients of TP and the potential targets and mechanisms of action of TP against COPD have not been sufficiently investigated.

PURPOSE

This study aimed to determine the active ingredients of TP and the potential targets and mechanisms of action of TP against COPD.

STUDY DESIGN

The initial phase comprised the screening of potential active ingredients in TP, this was followed by the evaluation of their pharmacodynamic effects through both in vivo and in vitro experiments. Subsequently, network pharmacology and molecular docking were utilized to predict the key targets and associated pathways, which were later validated through animal-related experiments. Finally, the pharmacodynamic basis of TP interacting with the relevant target was identified using surface plasmon resonance (SPR).

METHODS

The potential active ingredients of TP were predicted by serum chemical composition analysis. The pharmacodynamic effect of Total Flavonoids of Trichiosanthis Pericarpium (TPTF) against COPD was demonstrated by in vivo and in vitro experiments. The targets and pathways of TPTF for COPD were predicted using network pharmacology and confirmed preliminarily by molecular docking techniques. The critical targets and pathways of TPTF against COPD were validated by Western blot and SPR. The active ingredients of TPTF were selected and identified through SPR.

RESULTS

The main active ingredients of TP are flavonoids, which are evaluated through serum chemical composition analysis. TPTF has been demonstrated to be effective in inhibiting inflammation and mucus hypersecretion in both in vivo and in vitro models of COPD. The targets of TPTF against COPD are focused on the EGFR/PI3K/AKT signaling pathway according to Network pharmacology, and the prediction was subsequently validated in the COPD mice. The flavonoids of TP that specifically target on EGFR include Luteolin-7-O-β-d-glucoside, Quercetin-3-O-β-rutinoside, and Apigenin-7-O-glucoside.

CONCLUSION

This study demonstrates significant progress in understanding how the pharmacodynamic basis and mechanisms of TP improve COPD. The pharmacodynamic ingredients were identified as TPTF through predictions of serum chemical composition, experimental validation, and identification of SPR. The pharmacodynamic mechanisms were also derived from a comprehensive approach that combined network pharmacology, molecular docking predictions, experimental validation, and SPR identification. The innovative integration of different strategies has led to new findings that flavonoid glycosides, such as Luteolin-7-O-β-d-glucoside, Quercetin-3-O-β-rutinoside, and Apigenin-7-O-glucoside in TPTF, enhance the improvement of COPD by reducing inflammation and mucus hypersecretion associated with the EGFR/PI3K/AKT and EGFR/STAT3 signaling pathways.

The Potential Hepatocyte Differentiation Targets and MSC Proliferation by FH1

The main cause of acute liver failure (ALF) is hepatocellular necrosis, which induces liver repair dysfunction and leads to high mortality. In recent years, studies have increasingly shown that stem cell-derived hepatocyte-like cells (HLCs) can be used for treatment in animal models of ALF. Notably, a hepatocyte differentiation strategy based on the small-molecule compound functional hit 1 (FH1) successfully replaces HGF to promote the maturation of HLCs, but the underlying mechanism is still unclear. In this study, we used network pharmacology analysis to clarify the important role of the HGF/c-Met signalling pathway in FH1-induced hepatocyte (FH1-iHeps) differentiation. After FH1 was added to mesenchymal stem/stromal cells (MSCs), proliferation and cell cycle progression were rescued by treatment with a tyrosine kinase (c-Met) inhibitor. Additionally, c-Met signalling in MSCs was significantly increased by treatment with FH1, as shown by the increased c-Met, p-p38, p-AKT and p-ERK1/2 protein levels. FH1-iHeps efficiently improved the liver function of mice with acute liver injury and prolonged their lifespan. These data provide new insight into the mechanisms regulating the stemness properties of human umbilical cord-derived stem cells (hUC-MSCs) and reveal a previously unrecognised link between FH1 and c-Met in directing hepatocyte differentiation.

Beta-boswellic acid facilitates diabetic wound healing by targeting STAT3 and inhibiting ferroptosis in fibroblasts

Objective

Diabetic wounds are a severe complication of diabetes, with persistently high incidence and mortality rates, often leading to severe clinical outcomes such as amputation. Beta-boswellic acid (β-BA) is a plant-derived pentacyclic triterpene with activities of inflammatory control and ferroptosis regulation. However, the protective effect of β-BA on DW has not been described.

Method

We employed network analysis approaches and molecular docking to predict the potential targets and pathways of β-BA in the treatment of diabetic wounds (DW). Both in vitro and in vivo models were established, including high-glucose-induced fibroblast models and diabetic rat wound models. The effects of β-BA on diabetic wounds were investigated through CCK-8 assay, wound healing assay, immunofluorescence staining, western blotting, fluorescent probe analysis, gross observation, and histopathological experiments.

Result

In this study, we predicted potential targets for β-BA using public databases and identified 29 key genes, with STAT3 being the most significant. GO analysis revealed that these targets are involved in biological processes closely related to ferroptosis, such as regulation of inflammatory response and lipid metabolism. Our results showed that HG induced ferroptosis in HSFs, as evidenced by decreased cell viability, altered GSH/MDA, Fe2+, and ROS levels, and changes in the expression of ferroptosis-related genes ACSL4 and GPX4. Notably, treatment with the ferroptosis inhibitor Ferr-1 partly reversed these effects. CCK-8 assays showed that β-BA improved HSFs viability in a concentration-dependent manner. Immunofluoresc-ence staining and further biochemical analyses demonstrated that β-BA reduced Fe2+ and lipid peroxide levels, prevented oxidative damage, and improved cell migration ability impaired by HG. Western blot analysis confirmed that β-BA reversed the changes in ACSL4 and GPX4 expression induced by HG. Molecular docking validated the potential binding between β-BA and STAT3. Western blot analysis revealed that β-BA increased the level of phosphorylated STAT3 in HSFs. Introducing a STAT3 inhibitor diminished the beneficial effects of β-BA on HG-induced cell dysfunction and suppressed its protective effect against ferroptosis. Finally, we assessed the efficacy of β-BA in the treatment of diabetic wounds in rats. BA administration accelerated wound closure, reduced inflammatory cell infiltration, improved granulation tissue arrangement, and increased collagen deposition. Immunohistochemical staining showed that BA upregulated the number of STAT3-positive cells and upregulated the number of GPX4-positive cells in the wounds, suggesting that BA can inhibit ferroptosis and accelerate wound healing in diabetic rats.

Conclusion

Our findings suggested that β-BA may exert its therapeutic effects on diabetic wounds by targeting STAT3 and inhibiting ferroptosis.

Comprehensive characterisation of bioactive compounds in Boletus edulis as functional foods to improve muscle atrophy; through whole plant targeted metabolomics, network pharmacology, in vivo and in vitro experiments, molecular docking and molecular dynamics analysis

ETHNOPHARMACOLOGICAL SIGNIFICANCE

Boletus edulis (BE) is a naturally occurring fungus that has been traditionally used in ancient Chinese herbal medicine. It is a key component of the formula 'Shujin Pill', commonly prescribed for the treatment or relief of muscular dystrophy. However, the specific efficacy of BE within Shujin Pill or its primary active components remains unclear.

AIMS OF THE STUDY

This study aims to elucidate the biological function and molecular mechanisms of BE in alleviating muscular atrophy in mice. We employed a comprehensive approach, integrating metabolomics, network pharmacological analysis, molecular docking, molecular dynamics simulation, and in vivo and in vitro experimental validation, to verify these effects.

MATERIALS AND METHODS

The bioactive components in BE were quantified by UPLC-QTOF-MS/MS. To evaluate the muscle function indexes after 14 days of action of different doses of BE and to analyze the pathological changes in muscle tissue. Enabling network pharmacology to analyze the potential active components in BE for the alleviation of muscle atrophy, using computer molecular simulation for docking scores, molecular dynamics simulation to assist in the validation of the active components in BE, and in vitro experiments for the validation of the active components.

RESULT

BE administered alone was able to slow down Lipopolysaccharide (LPS)-induced muscle atrophy. 996 non-volatile components were detected in BE by metabolomics, and GAPDH, TP53, AKT1, TNF-α and IL-6 were more strongly associated with muscle atrophy by using web-based pharmacological analyses. Folic acid, Cycloartenol and Sesamin active ingredients have greater potential to treat or alleviate muscle atrophy, molecular docking, molecular dynamics detected that Sesamin and AKT both have high binding energy, in vitro using C2C12 skeletal muscle cells to verify the efficacy of Sesamin and BE, found that in the presence of the LY294002 (PI3K inhibitor) and GSK21417 (AKT inhibitor) treatment conditions, the elimination of the up-regulation of the PI3K/AKT signaling pathway by Sesamin and BE and loss of biological efficacy. It suggests that BE may slow down or treat muscle atrophy through the PI3K/AKT signaling pathway, in which Sesamin plays a major role. Meanwhile BE and Sesamin were able to enhance the antioxidant level of C2C12 skeletal muscle cells.

Clostridium butyricum Regulates the Inflammatory and Immunoregulatory Pathway Through NFKB1 in Colorectal Cancer Treatment

Colorectal cancer (CRC) ranks among the top three most prevalent malignancies globally and is a leading cause of cancer-related mortality. Traditional therapeutic approaches usually cause significant adverse effects, highlighting the urgent demand for alternative, more effective treatments. Probiotics have gained attentions as potential cancer therapy due to their beneficial impacts on host health. Clostridium butyricum (Cl. butyricum) has shown anticancer properties in recent studies, though the underlying mechanisms remain inadequately understood. This study presents an integrative analysis of network pharmacology and proteomics to elucidate the key targets of Cl. butyricum in CRC treatment. The network pharmacology analysis identified 72 overlapping genes, and functional analysis of these genes indicated that most pathways were related to pathways in cancer and inflammation, and butyrate emerging as the pivotal product of Cl. butyricum due to its strong associations with the identified hub genes. In parallel, proteomics analysis revealed 168 differential expressed proteins (DEPs) in Cl. butyricum-treated HCT-116 cells, comprising 78 upregulated and 90 downregulated proteins. These DEPs were primarily enriched in apoptosis and inflammatory pathways. PPI analysis further highlighted NFKB1 as key contributors to the anticancer effects of Cl. butyricum. The integrative analysis revealed a significant convergence of pathways enrichment patterns, particularly in inflammatory and immune-related pathways. Computational and experimental validation identified NFKB1 as a pivotal molecular target in CRC intervention. These collective findings elucidate the mechanistic basis of the antitumor properties of Cl. butyricum, highlighting its regulatory effects on NFKB1 through both inflammatory and, to a lesser extent, immunoregulatory pathways.

Exploring the mechanism of Cynanchum paniculatum (Bunge) Kitag's therapeutic strategy for rheumatoid arthritis: integrating network pharmacology, molecular docking and in vivo experiments

Rheumatoid arthritis (RA) is a chronic inflammatory disorder characterized by joint swelling, cartilage degradation, and joint deformity. The traditional Chinese herb Cynanchum paniculatum (Bunge) Kitag has been utilized in the management of RA, but the underlying mechanisms are unknown. This study utilized network pharmacology analysis to identify 26 active compounds associated with RA treatment and elucidate their interactions with 23 critical targets linked to RA. Subsequently, molecular docking studies revealed eight compounds with the capacity to bind to multiple key targets, with butyl isobutyl phthalate and geranyl acetone emerging as the most promising candidates based on their drug-likeness properties. To validate these findings, a rat model of adjuvant-induced arthritis was employed. Oral administration of geranyl acetone led to a significant reduction in paw swelling and pro-inflammatory markers, including TNF-α, IL-6, IL-1β, and MPO. Furthermore, it resulted in histological improvements in ankle tissues, all without adverse effects on weight or immune organs. Mechanistically, geranyl acetone was found to impede the progression of RA by modulating the TLR4/MyD88/NF-κB signaling pathway. In conclusion, C. paniculatum demonstrates substantial therapeutic potential for RA due to its multi-target and multi-pathway activities. Moreover, geranyl acetone, when used as a standalone agent, exhibits significant promise in alleviating RA symptoms, offering a compelling avenue for further research and potential clinical applications.

Soybean Sprout Peptides Alleviate Obesity via PI3K-Akt and JAK-STAT Pathway Modulation, Gut Microbiota Regulation, and Metabolic Reprogramming

Obesity is a growing global health concern associated with severe metabolic disorders, necessitating the development of safer and more effective therapeutic strategies. Soybean sprout peptides (SSPs), derived from germinated soybeans, are bioactive compounds with potential antiobesity effects. This study aimed to investigate the molecular mechanisms of SSPs through an integrated approach combining network pharmacology, molecular docking, and in vivo experiments. SSP sequences were identified using UPLC-Orbitrap-MS/MS, and their bioactivity was predicted using PeptideRanker. Network pharmacology identified key SSP targets, including AKT1, SRC, STAT3, ESR1, FOS, and NFKB1, which are implicated in the PI3K-Akt and JAK-STAT pathways. Molecular docking validated strong interactions between SSPs and these targets. In vivo, SSP administration significantly reduced body weight gain, abdominal fat accumulation, and serum lipid abnormalities in high-fat-diet-induced obese mice while modulating gut microbiota composition by restoring the Firmicutes-to-Bacteroidetes ratio and reducing pathogenic taxa. Fecal metabolomics revealed that SSP alleviated oxidative stress and improved amino acid metabolism, contributing to its antiobesity effects. These findings suggest that SSP holds promise as a functional food ingredient or nutraceutical for obesity prevention and management.

The mechanism of Weiqi decoction treating gastric cancer: a work based on network pharmacology and experimental verification

BACKGROUND

Weiqi Decoction (WQD) is an empirical prescription traditionally used in China for the treatment of precancerous gastric cancer (GC) lesions. This study aimed to elucidate the potential pharmacological mechanisms of WQD in GC therapy.

METHODS

Active ingredients, corresponding targets, and GC-related genes were identified using public databases. A protein-protein interaction (PPI) network was constructed via the STRING database, and functional enrichment analyses were conducted using the DAVID platform. Gene expression and survival analyses were performed using the GEPIA database. Molecular docking was conducted with AutoDock Vina and visualized using PyMOL. The effects of WQD on GC cell viability, proliferation, migration, and invasion were evaluated through CCK-8, colony formation, and Transwell assays.

RESULTS

WQD contained 43 active ingredients targeting 751 potential genes, including 458 GC-related targets. Quercetin, luteolin, and kaempferol were identified as key active compounds. PPI network analysis revealed nine core targets, including TP53 and SRC, which may mediate the anti-GC effects of WQD. GO enrichment analysis indicated involvement in 726 biological processes, 91 cellular components, and 177 molecular functions, while KEGG pathway analysis suggested modulation of the AGE-RAGE, PI3K-Akt, and HIF-1 signaling pathways. GEPIA database analysis confirmed that EP300, HSP90AA1, HSP90AB1, SRC, and TP53 were highly expressed in GC. Molecular docking demonstrated strong binding affinities between the key active compounds and core targets. In vitro experiments further validated that WQD extract inhibited GC cell viability, proliferation, migration, and invasion.

CONCLUSION

WQD exhibits therapeutic potential against GC by regulating multiple targets and signaling pathways. These findings provide mechanistic insights into the pharmacological actions of WQD in GC treatment.

Integrating network pharmacology and in vivo pharmacological validation to explore the gastroprotective mechanism of Sotetsuflavone against indomethacin-induced gastric ulcer in rats: Involvement of JAK2/STAT3 pathway

Sotetsuflavone (SF) is an antioxidant flavonoid derived from the Cycas thouarsii R.Br. plant. Although SF regulates numerous cellular pathways influencing inflammation, its antiinflammatory benefits against gastric ulcers are less well-studied. Hence, it is imperative to thoroughly understand the potential gastroprotective mechanisms of SF. This study aimed to explore the effectiveness of SF against indomethacin (IND)-induced gastric ulcers. Network analysis and molecular docking were used to identify the specific targets and pathways related to SF and stomach ulcers. To validate the in vivo pharmacological action of SF, 36 rats were divided into six groups. Ulcer index (UI), protective percentage (PP), gastric mucosal mediators, oxidant/antioxidant status, and inflammatory markers (MIF, M-CSF, and AIF-1) were assessed. Additionally, the expression of PI3K, Akt, Siah2, SOCS3, JAK2, and STAT3 was determined. Stomach histopathology and immunohistochemistry were done. Network pharmacology detected 46 overlapping targets between SF and stomach ulcers, with HIF1A as the primary target among the top hubs. The network also revealed that JAK/STAT, PI3K/Akt, and HIF-1A signaling are among the top 50 markedly enriched KEGG pathways. Furthermore, docking results confirmed that SF has a strong binding affinity towards SOCS3, JAK2, STAT3, M-CSF (CSF-1), and AIF-1. Therefore, we hypothesized that the JAK2/STAT3 pathway may be primarily responsible for SF antiinflammatory action. Through up-regulating SOCS3, SF altered the PI3K/Akt pathway, mitigating oxidative stress, blocking the outflow of inflammatory mediators, and impeding gastric ulcer development. Overall, SF, by the SOCS3-mediated JAK2/STAT3 suppression, might considerably reduce oxidative stress, inflammation, and ulceration caused by indomethacin in the stomach.

Dl-3-n-butylphthalide ameliorates diabetic foot ulcer by inhibiting apoptosis and promoting angiogenesis

BACKGROUND

Diabetic foot ulcers (DFU) are estimated to affect about 18.6 million people worldwide annually. The pathogenesis of DFU is complex, and the available drugs are not effective. Dl-3-n-butylphthalide (NBP) is a synthetic mixture of racemates used in China for the treatment of ischemic stroke. It was initially isolated from the seeds of Apium graveolens Linn, with studies showing its potential role in treating diabetes and its complications.

AIM

To predict and validate the mechanism by which NBP treats DFU.

METHODS

Network pharmacological analysis was performed to identify pharmacological targets and signaling pathways mediating the treatment effect of NBP on DFU. In vivo and in vitro experiments were conducted to validate the therapeutic effects and mechanisms of NBP on DFU.

RESULTS

Network pharmacology analysis identified 26 pharmacological targets of NBP and predicted that NBP could treat DFU partially by modulating apoptosis and vascular signaling pathways. Results from animal experiments showed that NBP significantly improved DFU by increasing neovascularization and fibroblast proliferation. In vitro tests demonstrated that NBP treatment promoted the migration and proliferation of human umbilical vein endothelial cells and human dermal fibroblasts, while inhibiting the apoptosis of human umbilical vein endothelial cells, human dermal fibroblasts, and human keratinocytes cells.

CONCLUSION

This study found that NBP could treat DFU by decreasing the rate of apoptosis and increasing angiogenesis via the advanced glycation end products-receptor of advanced glycation end products signaling pathway and binding to the heme oxygenase 1, caspase 3, B cell leukemia/lymphoma 2, brain derived neurotrophic factor, and nuclear factor erythroid 2 L2 genes.

Aripiprazole alleviates the high prolactin levels induced by amisulpride via distinct molecular mechanisms: a network pharmacology and molecular docking study

BACKGROUND

Amisulpride, a unique atypical antipsychotic, significantly increases prolactin secretion during schizophrenia treatment, resulting in adverse effects that reduce patient quality of life and treatment adherence. Aripiprazole, a partial dopamine D2 receptor agonist, reduces prolactin elevation induced by antipsychotic drugs used for schizophrenia treatment. The molecular targets and mechanisms underlying the contrasting effects of these two drugs on prolactin regulation are unclear. The objective of this study was to systematically explore the molecular mechanisms of prolactin regulation by aripiprazole and amisulpride using network pharmacology and molecular docking techniques.

METHODS

Relevant targets of amisulpride and aripiprazole and for schizophrenia and elevated prolactin treatment were obtained from online databases and screened for significance. A protein-protein interaction network was constructed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the core targets were performed to identify key biological processes and signaling pathways, and a target-pathway-drug integrated network was established. The binding affinities of amisulpride and aripiprazole with core targets were predicted using molecular docking analyses.

RESULTS

Screening and matching drug and disease targets combined with GO and KEGG pathway enrichment analyses revealed several key signaling pathways involved in prolactin regulation, including MAPK, PI3K/AKT, and dopamine receptor pathways. The core targets of aripiprazole include MAPK3, PPARG, DRD2, and ESR1, and amisulpride primarily targets MMP9, CDC42, mTOR, and AKT1. Molecular docking analysis demonstrated that aripiprazole and amisulpride have high binding affinities for their respective targets, supporting the hypothesis that these drugs regulate prolactin levels through target-ligand interactions.

CONCLUSION

These findings highlight the distinct signaling pathways and molecular networks involved in prolactin regulation by aripiprazole and amisulpride and provide new insights into the mechanisms of these drugs in schizophrenia treatment. Further pharmacological and clinical research is needed to validate the complex regulatory networks and in vivo effects.

A Multi-Level Study on the Anti-Lung Cancer Mechanism of Peiminine, a Key Component of Fritillaria ussuriensis Maxim.: Integrating Quality Analysis, Network Pharmacology, Bioinformatics Analysis, and Experimental Validation

Globally, lung cancer is the primary cause of deaths associated with cancer; however, current therapies are costly and toxic, highlighting the need for novel treatments. Peiminine (Verticinone), a key bioactive compound derived from Fritillaria ussuriensis Maxim., has demonstrated diverse biological activities. However, the precise pharmacological mechanisms underlying its anti-lung cancer effects remain unclear. The objective of this study was to quantify the content of peiminine in Fritillaria ussuriensis Maxim. from different geographical regions using UHPLC-MS/MS and to elucidate the anti-lung cancer mechanisms of peiminine through network pharmacology, bioinformatics, and in vitro experiments. The content of peiminine in Fritillaria ussuriensis Maxim. from various regions was determined using UHPLC-MS/MS. Potential target genes associated with peiminine and lung cancer were systematically screened from multiple databases. To identify core genes, we set up a PPI (protein-protein interaction) network, followed by in-depth analyses of their corresponding target proteins. Survival analysis, molecular docking, and dynamics simulations were used to explore potential anti-cancer mechanisms. In vitro experiments on human H1299 NSCLC cells assessed peiminine's anti-tumor activity and measured key gene transcription levels. UHPLC-MS/MS analysis revealed that Fritillaria ussuriensis Maxim. from Mudanjiang (Heilongjiang Province) exhibited the highest peiminine content. Network pharmacological analysis identified PIK3CG, SRC, JAK3, AKT2, and PRKCA as key potential targets of peiminine in lung cancer treatment. Molecular docking results demonstrated strong binding affinities between peiminine and PIK3CG, SRC, and JAK3; these results were further confirmed using molecular dynamics simulations. Survival analysis indicated that a high AKT2 and PRKCA expression correlated with bad prognosis in lung cancer patients. In vitro, peiminine inhibited H1299 cell viability and regulated genes involved in the PI3K-Akt pathway (PI3K, AKT, and PTEN) and apoptosis (Bcl-2, Bax), suggesting that it may induce its effects via PI3K-Akt pathway inhibition. Peiminine from Fritillaria ussuriensis Maxim. exhibits significant anti-lung cancer potential by targeting key genes such as PIK3CG, SRC, and JAK3, as well as by modulating the PI3K-Akt signaling pathway and apoptosis-related genes. These results lay a foundation for further investigations into peiminine as a potentially effective therapeutic option for treating lung cancer. Additionally, the identified targets (PIK3CG, SRC, JAK3, AKT2, and PRKCA) may function as possible biomarkers for predicting lung cancer prognosis and guiding personalized therapy.

Integrated network pharmacology, proteomics, molecular docking, and experiments in vivo and in vitro to explore the efficacy and potential mechanism of bufalin against hepatocellular carcinoma angiogenesis

ETHNOPHARMACOLOGICAL RELEVANCE

Bufalin is a potent bioactive compound extracted from the venom of toads such as Bufo gargarizans. It has rich pharmacological effects, and its traditional applications mainly include anti-cancer, anti-inflammatory and analgesic, especially in cancer treatment, which has been a hot topic of research. Prior research has suggested that bufalin may have anti-tumor angiogenic effects. However, the efficacy and mechanism of bufalin inhibiting hepatocellular carcinoma (HCC) angiogenesis have yet to be further investigated.

AIM OF THE STUDY

An extensive detailed strategy via network pharmacology, proteomics, histopathological analysis, molecular docking, in vitro experiments, and in vivo magnetic resonance imaging (MRI) examinations were adopted to investigate the efficacy and mechanisms of bufalin against HCC angiogenesis.

MATERIALS AND METHODS

Micro-vessel density (MVD) and intravoxel incoherent motion (IVIM) perfusion-related parameters based on magnetic resonance diffusion-weighted imaging were used to identify the effect of bufalin against HCC angiogenesis. Potential bufalin and HCC targets were gathered from appropriate databases. The STRING database was used to construct the target protein interaction networks. The "clusterprofiler" package (version 4.2.2) in R was applied to conduct the target-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology (GO) analysis. Network pharmacology and proteomics were integrated to identify key targets and pathways related to bufalin against HCC angiogenesis. Molecular docking and Western Blot were utilized to validate the findings.

RESULTS

Analysis through IVIM and MVD showed that bufalin could inhibit HCC angiogenesis in nude mice models. A total of 159 common targets of bufalin and HCC were identified by network pharmacology. GO analysis revealed that these targets focused on multiple angiogenesis-related biological processes, including endothelial cell proliferation and migration, sprouting angiogenesis, and regulation of angiogenesis. The KEGG enrichment results suggested that bufalin could regulate multiple signaling pathways to inhibit HCC angiogenesis, including VEGF, MAPK, PI3K-Akt, mTOR, and HIF-1 signaling pathways. MAPK1, MAPK14, PRKCA, EIF4E, and APEX1 might be critical targets in regulating the above pathways. The molecular docking and Western blot analysis verified the effects of bufalin on target proteins.

CONCLUSION

This study demonstrated that bufalin might inhibit HCC angiogenesis by regulating multiple targets and pathways. These findings offer theoretical insights and experimental foundations for the clinical application and commercial development of bufalin in the treatment of HCC.