Network pharmacology, a promising approach to reveal the pharmacology mechanism of Chinese medicine formula

Elucidating the mechanism of action of astragalus polysaccharide on ionizing radiation-induced myocardial damage based on network pharmacology and experimental research

Due to the unavoidable impact of ionizing radiation on the heart located near the mediastinum, varying degrees of myocardial damage may occur. As a result, the clinical application of radiotherapy in cancer treatment is significantly limited. However, the molecular mechanisms underlying radiation-induced heart disease (RIHD) are not yet fully understood, and there is a lack of disease-specific treatment strategies. Astragalus polysaccharide (APS), is an active compound abundant in the traditional Chinese herb Astragalus membranaceus (Fisch.) Bunge (AS), has been shown to have cardioprotective effects against various cardiovascular diseases. Thus, this study aims to investigate the potential cardioprotective effect of APS on RIHD and its underlying molecular mechanisms. The network pharmacology results indicated that 9 core genes were identified from the biological network of the effective components of AS acting on RIHD. The results of GO enrichment analysis showed that these hub genes were mainly involved in biological processes such as cell apoptosis, cell proliferation, inflammatory response, and response to external stimuli. The results of KEGG enrichment analysis showed that these hub genes mainly regulated the occurrence of RIHD through pathways such as the EGFR signaling pathway, PI3K/Akt signaling pathway, IL-17 signaling pathway, and so on. In molecular docking analysis, we found that AKT1 and mTOR had good and stable binding abilities with the three types of glucosides rich in AS. The results of in vitro and in vivo experiments all showed that APS could not only improve cardiac dysfunction, myocardial injury, inflammatory response, and myocardial fibrosis in RIHD rats, but also alleviated apoptosis and atrophy of H9C2 cells under ionizing radiation stimulation. In addition, we also found that APS improved the accumulation of autophagic flux induced by ionizing radiation, which could be confirmed by the reversal of Beclin1, p62, LC3B proteins and accelerated degradation of accumulated autophagic vesicles. Rapamycin (Rap) was a classic autophagy flux inducer that could attenuate the improvement effect of APS on H9C2 cell apoptosis under ionizing radiation stimulation. Finally, we found that APS could reverse the inhibition of PI3K/Akt/mTOR signaling pathway activity by ionizing radiation in vitro, thereby improving ionizing radiation-induced autophagy flux accumulation, cardiomyocyte apoptosis, and atrophy. All in all, this study provides important evidence for understanding the molecular mechanisms of the cross-talk between autophagy and apoptosis, and provides new directions and insights for APS combined with autophagy regulators as a therapeutic strategy for RIHD.

The multi-target mechanism of action of Selaginella doederleinii Hieron in the treatment of nasopharyngeal carcinoma: a network pharmacology and multi-omics analysis

Nasopharyngeal carcinoma (NPC) presents significant treatment challenges due to its complex etiology and late-stage diagnosis. The traditional Chinese medicine Selaginella doederleinii Hieron (S. doederleinii) has shown potentiality in NPC treatment due to its multi-target, multi-pathway anti-cancer mechanisms. First, we identified NPC related target genes from databases like GeneCards, OMIM, and DisGeNET, and performed WGCNA analysis on the GSE53819 dataset to identify several important gene modules related to NPC. Active components and their targets in S. doederleinii were screened from the TCMSP and other databases, identifying 32 overlapping genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these genes are primarily involved in critical biological processes like protein phosphorylation and cell cycle regulation. A protein-protein interaction network was constructed, and cytoHubba identified six key genes (BCL2, MAPK14, ABCB1, PLK1, ATM, HMOX1). Kaplan-Meier analysis and immune infiltration analysis further showed that these key genes are closely related to the prognosis and immune microenvironment of NPC patients. Single-cell RNA sequencing analysis revealed the expression distribution of key genes across different immune cell types and explored their roles in the differentiation process of malignant cells through pseudotime trajectory analysis. Molecular docking and dynamics simulation results indicated that the Berberine-MAPK14 and Matairesinol-PLK1 complexes have high binding affinity and stability. Binding free energy calculations confirmed the stability of these complexes. Based on our comprehensive multi-level analysis, the active components of S. doederleinii may play a significant role in the treatment of NPC through multi-pathway and multi-target synergistic effects.

Integrated approach with UHPLC-Q-Exactive-tandem mass spectrometry, network analysis, and molecular docking to determine potential active compounds and mechanisms of Rhizoma Musae decoction in osteoarthritis treatment

Objective

This study aimed to identify the potential active compounds in Rhizoma Musae decoction and understand their mechanisms of action in osteoarthritis treatment.

Methods

UHPLC-Q-Exactive-MS/MS technology was used for an in-depth analysis of the chemical compounds present in Rhizoma Musae decoction. A network analysis approach was used to construct a comprehensive network of compounds, targets, and pathways, which provided insights into the molecular mechanisms of Rhizoma Musae decoction in osteoarthritis treatment.

Results

The integrated analysis revealed the presence of 534 chemical compounds in Rhizoma Musae decoction, with 7beta-hydroxyrutaecarpine, 7,8-dihydroxycoumarin, pinocembrin diacetate, and scopoletin being identified as potential active compounds. Potential targets such as GAPDH, AKT1, TNF, IL6, and SRC were implicated in key pathways including MAPK signaling pathway, lipid and atherosclerosis, PI3K-Akt signaling pathway, and IL-17 signaling pathway. Molecular docking studies showed significant binding affinity between the core targets and key components. In vitro cell experiments have demonstrated that RM decoction can enhance cell proliferation and upregulates the expression of TNFα, IL-6, and SRC, while down-regulating the expression of GAPDH and AKT1.

Conclusion

The potential active compounds present in Rhizoma Musae decoction influence specific targets and signaling pathways involved in osteoarthritis pathogenesis, providing new insights for the functional development and utilization of RM.

Xiaohuafuning tang intervenes liver-depression-and-spleen-deficiency syndrome chronic-atrophic-gastritis by reshaping amino acid metabolism through gut Microbiota

BACKGROUND

Xiaohua Funing Tang (XHFND) is a decoction formula of traditional Chinese medicine (TCM) and possesses the potential to manage chronic atrophic gastritis (CAG) with liver depression and spleen deficiency (LDSD), but the mechanisms were still unclear.

PURPOSE

Our aim is to reveal the overall synergistic mechanisms of XHFND against CAG with LDSD.

METHODS

Based on a CAG rat model with LDSD, this study combined metabolomics, gut microbiota, and network pharmacology techniques to demonstrate the XHFND mechanisms with multiple components and targets.

RESULTS

Through the integration analysis of gut microbiome and metabolome using metorigin, we found that XHFND regulates arginine metabolism levels in the urea cycle by regulating the gut ecological environment and the host. The XHFND mainly promotes aspartate 1 metabolism by regulating the abundance of odoribacter, bacteroides, phocaeicola, lachnospire, and intestinimonas, intervened in the imbalance of arginine metabolism in CAG rats with LDSD, suppresses the pathogenic Th17 cell differentiation, and inhibits the gastric mucosa damage in rats. Through Cytoscape analysis of network pharmacology and metabolomics integration, we found that XHFND might regulate host phospholipid metabolism through PTEN and PIK3CA to inhibit the PI3K-AKT-TSC axis and then inhibit mTORC1 to control arginine metabolism in the urea cycle and produce polyamines, thereby inhibiting the pathogenic Th17 cell differentiation and preventing rat gastric mucosa damage. Intervention in arginine metabolism in the urea cycle is the primary pathway in which XHFND exerts its therapeutic effects. XHFND may mainly control the pathogenic Th17 cell differentiation in the gastric mucosa of model rats through the pathway.

CONCLUSION

This study indicated that XHFND might intervene in treating CAG with LDSD from multiple levels and perspectives to suppress the pathogenic Th17 cell differentiation, which aligns with the characteristics of TCM treatment. This study presents experimental evidence for the clinical use of XHFND and promotes the development of drugs for the therapy of CAG with LDSD.

Q-Marker Prediction of Astragali Complanati Semen Based on Fingerprint and Network Pharmacology

BACKGROUND

Astragali Complanati, known in Chinese as Shayuanzi, is a common medicinal material in traditional Chinese medicine, mainly used for tonifying the kidney, supporting yang, consolidating essence, reducing urine, and other diseases.

OBJECTIVE

The ultra performance liquid chromatography (UPLC) fingerprint of Astragali Complanati Semen (ACS) was established, and the Q-markers of ACS were analyzed by network pharmacology.

METHODS

First, a UPLC fingerprint detection method was established for ACS, and the common peaks were identified by UPLC-MS/MS. The "component-target-pathway" network relationships of characteristic components of ACS were constructed by network pharmacology, and the potential quality markers (Q-markers) were predicted.

RESULTS

A total of 24 common peaks were identified from the UPLC fingerprint of ACS, and 12 chromatographic peaks were identified by UPLC-MS/MS. A total of 12 Q-markers candidate components were screened out. Through network pharmacological analysis, it is predicted that myricetin 3-O-β-D-xylopyranosyl-(1-2)-[α-L-rhamnopyranosyl-(1-6)]-β-D-glucopyranoside, myricetin 3-O-β-D-xylopyranosyl(1-2)-β-D-glucopyranoside, myricetin 3-β-D-glucopyranoside, cannabiscitrin, laricitrin-3-O-glucoside, leucoside, complanatoside B, complanatuside, complanatuside 6''-malonate, clycosin, rhamnocitrin 3-O-β-D-apiofuranosyl(1→2)-β-D-glucopyranoside, and 3-O-[5'''-O-feruloyl-beta-D-apiofuranosyl(1'''->2'')-beta-D-glucopyranosyl] rhamnocitrin are the Q-markers of ACS.

CONCLUSION

The method established in this study was accurate, reliable, simple, and practical and could be used as a reference method for ACS quality detection. Twelve Q-markers selected by network pharmacology could provide support and references for ACS QC.

Mechanism of action of total saponin Achyranthes in treating knee osteoarthritis explored using network pharmacology and animal experimentation

Objectives

Knee osteoarthritis (KOA) is a persistent degenerative disease affecting the joints, significantly reducing the quality of life for individuals afflicted. This study explores the therapeutic effects of total saponin Achranthes (TSA) on KOA rats and its underlying mechanism.

Materials and Methods

Forty-eight rats were randomly assigned to six experimental groups: a blank control group, a model group, a sham-operated group, and a TSA treatment group (low, medium, and high dose), with eight rats in each group. The rats were treated continuously for four weeks. The degree of joint swelling was quantified, and the Lequesne MG score was evaluated. Network pharmacology approaches were employed to pinpoint potential TSA targets and related pathways for managing KOA. Additionally, histopathological examinations were conducted on the knee cartilage of the rats. Serum levels of TNF-α and IL-1β were assessed through the ELISA assay.

Results

The network pharmacology results indicate that TSA may effectively treat KOA through the MAPK and PI3K/Akt signaling pathways. Moreover, TSA significantly decreased the serum concentrations of pro-inflammatory cytokines such as TNF-α and IL-1β, and TSA down-regulated the P38 MAPK, PI3K/Akt, and NF-κB pathways, whereas the KOA model showed up-regulation. The treatment also significantly reduced MMP-9, MMP-13, and ADAMTS-5 protein levels.

Conclusion

TSA can potentially ameliorate inflammation, safeguard knee cartilage tissue, and alleviate symptoms of KOA by inhibiting the MAPK/Akt/NF-κB signaling pathway.

Deciphering the Anti-Diabetic Potential of Gymnema Sylvestre Using Integrated Computer-Aided Drug Design and Network Pharmacology

This study explores novel therapeutic avenues for diabetes, a global health concern marked by elevated blood glucose levels. We investigated the anti-diabetic potential of Gymnema Sylvestre's bioactive compounds, including Gymnemic acid I, Stigmasterol, Deacylgymnemic acid, Beta-Amyrin acetate, Longispinogenin, Gymnemic acid II, Gymnemic acid, Gymnemic acid X, Gymnemaside VI, Phytic acid and Gymnemic acid X. Employing network pharmacology, molecular docking and molecular dynamics (MD), we elucidated the potential mechanism of action. SwissTargetPrediction identified targets for bioactive constituents, while DisGeNET provided diabetes-related targets. A GeneVenn diagram revealed 397 common potential targets for diabetes management. The protein-protein interaction network, constructed via the STRING database, underwent topological analysis in Cytoscape, identifying AKT1, SRC, TNF, PPARG and IL1B as top targets. Gene ontology analysis using FunRich identified crucial roles of screened targets in integrin family cell surface interactions and glypican pathways for diabetes management. Molecular interactions and binding affinities with the top target, AKT1, were assessed, with Gymnemic acid I displaying the least binding energy (-9.813) with H- and non-H-bond interactions. Molecular dynamics simulations provided insights into the distinct behaviours of Gymnemic acid I within the protein complex. In conclusion, our study elucidates the potential anti-diabetic mechanism of Gymnemic acid I, underscoring the need for further in vitro, in vivo and clinical studies to validate our findings.

Exploring the Molecular Mechanism by which Kaempferol Attenuates Sepsis-related Acute Respiratory Distress Syndrome Based on Network Pharmacology and Experimental Verification

BACKGROUND

Sepsis-related acute respiratory distress syndrome (ARDS) is a fatal disease without effective therapy. Kaempferol is a flavonoid compound extracted from natural plant products; it exerts numerous pharmacological effects. Kaempferol attenuates sepsis-related ARDS; however, the underlying protective mechanism has not been elucidated completely.

OBJECTIVES

This study aimed to use network pharmacology and experimental verification to investigate the mechanisms by which kaempferol attenuates sepsis-related ARDS.

METHODS

We screened the targets of kaempferol by PharMapper, Swiss Target Prediction, and CTD database. We identified the targets of sepsis-related ARDS by GeneCards, DisGeNet, OMIM, and TTD. The Weishengxin platform was used to map the targets of both kaempferol and sepsis-related ARDS. We created a Venn diagram to identify the intersection targets. We constructed the "component-intersection targets-disease" network diagram using Cytoscape 3.9.1 software. The intersection targets were imported into the STRING database for developing the protein-protein interaction network. Metascape was used for the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. We selected the leading 20 KEGG pathways to establish the KEGG relationship network. Finally, we performed experimental verification to confirm our prediction results.

RESULTS

Through database screening, we obtained 502, 360, and 78 kaempferol targets, disease targets of sepsis-related ARDS, and intersection targets, respectively. The core targets consisted of tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, albumin (ALB), IL-1β, and AKT serine/ threonine kinase (AKT)1. GO enrichment analysis identified 426 items, which were principally involved in response to lipopolysaccharide, regulation of inflammatory response, inflammatory response, positive regulation of cell migration, positive regulation of cell adhesion, positive regulation of protein phosphorylation, response to hormone, regulation of reactive oxygen species (ROS) metabolic process, negative regulation of apoptotic signaling pathway, and response to decreased oxygen levels. KEGG enrichment analysis identified 151 pathways. After eliminating the disease and generalized pathways, we obtained the hypoxia-inducible factor 1 (HIF-1), nuclear factor κB (NF-κB), and phosphoinositide 3-kinase (PI3K)-Akt signaling pathways. Our experimental verification confirmed that kaempferol blocked the HIF-1, NFκκB, and PI3K-Akt signaling pathways, diminished TNF-α, IL-1β, and IL-6 expressions, suppressed ROS production, and inhibited apoptosis in lipopolysaccharide (LPS)-induced murine alveolar macrophage (MH-S) cells.

CONCLUSION

Kaempferol can reduce inflammatory response, ROS production, and cell apoptosis by acting on the HIF-1, NF-κB, and PI3K-Akt signaling pathways, thereby alleviating sepsis- related ARDS.

Linarin Identified as a Bioactive Compound of Lycii Cortex Ameliorates Insulin Resistance and Inflammation Through the c-FOS/ARG2 Signaling Axis

Insulin resistance (IR) is a central pathophysiological process underlying numerous chronic metabolic disorders, including type 2 diabetes and obesity. Lycii Cortex, a widely used traditional Chinese herb, has demonstrated potential benefits in preventing and managing diabetes and IR. Whereas, the specific bioactive compounds responsible for these protective effects and their underlying mechanisms of action remain elusive. This study aimed to identify the bioactive components within Lycii Cortex that contribute to its anti-diabetic effects and to elucidate the molecular mechanisms underlying its beneficial actions on insulin resistance. Network pharmacology and molecular docking analyses were employed to identify the potential active compounds in Lycii Cortex and their corresponding target proteins. An in vitro model of IR was established using palmitic acid (PA)-treated HepG2 cells. Cell viability was assessed using the CCK-8 assay, while glucose uptake was evaluated by 2-NBDG staining and extracellular glucose measurement. To validate the in vitro findings, an in vivo model of obesity-induced IR was established using high-fat diet (HFD)-fed mice. The network pharmacology analysis preliminarily identified 13 candidate chemicals and 10 hub LyC and IR-related genes (LIRRGs). Molecular docking analysis demonstrates that Linarin as the potential active component exhibits the greatest potential to target c-FOS for preventing obesity-induced IR. Enrichment analysis suggested that Linarin-targeted pathways are correlated with inflammation. In vitro experimental validation demonstrated that Linarin was capable of protecting against PA-induced IR in HepG2 cells evidenced by improving glucose uptake ability and reducing extracellular glucose content. Additionally, we found that Linarin ablated PA-induced increase in the expression of c-FOS and inflammatory cytokines. Furthermore, in PA-treated cells, silencing c-FOS markedly improved glucose consumption, and reduced inflammation and Arginase 2 (ARG2) expression. Similarly, as exposure to PA, silencing ARG2 also ameliorated glucose uptake and inflammation, while not affecting c-FOS expression. In vivo experiments further showed that Linarin administration remarkably improved glucose tolerance and insulin sensitivity, and reduced the fat mass and body weight in HFD-induced obese mice. In this study, Linarin has been identified as the bioactive compound of Lycii Cortex to ameliorate obesity-related IR and inflammation through the c-FOS/ARG2 signaling cascade. These findings underscore the therapeutic potential of Linarin and provide valuable insights into developing novel intervention strategies for type 2 diabetes therapy.

Mechanism of Fangji Huangqi decoction against acute kidney injury based on network pharmacology and experimental validation

BACKGROUND

Fangji Huangqi Decoction (FJHQD), a famous Traditional Chinese Medicine (TCM) formula, has been widely applied in improving renal function. However, the interaction of bioactives from FJHQD with the targets involved in acute renal injury (AKI) has not been elucidated yet.

PURPOSE

A network pharmacology-based approach combined with molecular docking and in vitro and in vivo validation was performed to determine the bioactives, key targets, and potential pharmacological mechanism of FJHQD against AKI.

MATERIALS AND METHODS

The model of mouse renal ischemic reperfusion was adopted to verify the curative effect of FJHQD against renal injury. FJHQD was analyzed and separated by Ultra-High performance liquid chromatography (UHPLC). Bioactives and potential targets of FJHQD, as well as AKI-related targets, were retrieved from public databases. Crucial bioactive ingredients, potential targets, and signaling pathways were acquired through bioinformatics analysis, including protein-protein interaction (PPI), as well as the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Subsequently, molecular docking was carried out to predict the combination of active compounds with core targets. Besides, in vivo and vitro experiments were conducted to verify the findings.

RESULTS

A total of 20 bioactive ingredients of FJHQD (top 10 positive ion and negative ion compounds) and 274 FJHQD-AKI overlaped targets were screened. Bioinformatics analysis revealed that apoptosis mediated by PI3K-AKT signaling pathway might play an important role in FJHQD against AKI. Further experiments showed that FJHQD alleviated I/R-induced renal injury and OGD/R induced TEC apoptosis by activating PI3K-AKT signaling pathway. Moreover, molecular docking suggested (9Z,12Z,14E)-16-Hydroxy-9,12,14-octadecatrienoic acid, 2-Hydroxyacetophenone, Liquiritigenin, (S)-[10]-Gingerol and Isookanin-7-O-glucoside may be potential candidate agents, among which, PIK3CA interacted with Liquiritigenin, (S)-[10]-Gingerol, Isookanin-7-O-glucoside and 2-Hydroxyacetophenone respectively. AKT1 interacted with (9Z,12Z,14E)-16-Hydroxy-9,12,14-octadecatrienoic acid and 2-Hydroxyacetophenone. Cell experiments showed that the most important ingredient of FJHQD, Liquiritigenin, could inhibit the TEC apoptosis and up-regulate PI3K-Akt signaling pathway, which further confirmed the prediction by network pharmacology strategy and molecular docking.

CONCLUSION

Our results comprehensively illustrated the bioactives, potential targets, and molecular mechanism of FJHQD against AKI. It also provided a promising strategy to uncover the scientific basis and therapeutic mechanism of TCM formulae in treating diseases.

Mechanism of Action of Tongjiang Mixture for Treating Reflux Esophagitis: A Study Using Serum Pharmacochemistry and Network Pharmacology

Tongjiang Mixture (TJM) is a traditional Chinese formula for treating reflux esophagitis (RE). Nevertheless, its active ingredients and potential pharmacological mechanisms are not yet clearly elucidated. This study will identify the active ingredients of TJM using serum pharmacochemistry and to elucidate the mechanism on RE through network pharmacology. The blood-borne ingredients of TJM are identified by the Ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometer. Subsequently, a "compound-target-disease" network is established and obtained core targets associated with TJM and RE. Then, the potential signaling pathways are forecasted through the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Finally, the rat model of RE is established to verify the results predicted by network pharmacology through animal experiments. Fifteen blood-borne ingredients of TJM are identified, with eight active ingredients-namely Tangeretin, Tricin, Palmati, Berberine, Limonin, Evodiamine, Tetrahydropalmatine and Rutecarpine - making significant contributions to its efficacy. Moreover, TJM is predicted to act on 193 targets related to RE, involving AKT1, HSP90AA1, PIK3CA, and other targets, which enriches mainly in PI3K/AKT /NF-κB signaling. Additionally, TJM can alleviate inflammation of the esophageal mucosa, reduce pathological damage, and increase gastric pH. It can downregulate PI3K, AKT, and NF-κB mRNA transcription levels and reduce the protein expression of PI3K, AKT, and NF-κB. Furthermore, it can inhibit the overproduction of IL-6, TNF-α and IL-17. TJM can alleviate immune-inflammatory responses and ameliorate RE by restraining the PI3K/AKT pathway and its downstream NF-κB.

Network Pharmacology, Molecular Docking, and Experimental Validation on Guiluoshi Anzang Decoction Against Premature Ovarian Insufficiency

BACKGROUND AND OBJECTIVES

Premature Ovarian Insufficiency (POI) is a disease suffered by women under the age of 40 when ovarian function has declined, seriously affecting both the physical and mental health of women. Guiluoshi Anzang decoction (GLSAZD) has been used for a long time and has a unique therapeutic effect on improving ovarian function. This study aims to investigate the mechanism of GLSAZD in treating POI through network pharmacology, molecular docking, and experimental verification.

METHODS

In this study, the active ingredients of Guiluoshi Anzang Decoction and the targets of POI were obtained from TCMSP, BATMANN-TCM, Uniprot, GeneCards, and other databases, and network pharmacology analysis was performed. Molecular docking was conducted to validate the affinity of the main active ingredient of GLSAZD to key POI targets. A POI SD rat model was established, and HE staining, ELISA, Real-time PCR, and Western blot experiments were performed to verify the predicted core targets and the therapeutic effects.

RESULTS

10 core targets and the top 5 ingredients were screened out. Molecular docking showed core targets AKT1, CASP3, TNF, TP53, and IL6 had stable binding with the core 5 ingredients quercetin, kaempferol, beta-sitosterol, luteolin, and Stigmasterol. GO and KEGG enrichment analysis demonstrated the mechanism involved in the positive regulation of gene expression, PI3K-AKT signaling pathway, and apoptosis signaling pathways. Animal experiments indicated GLSAZD could up-regulate the protein expression of p-PI3K and p-AKT1 and the mRNA expression of STAT3 and VEGF, down-regulate TP53 and Cleaved Caspase-3 protein expression in rat`s ovarian tissues and serum TNF-α and IL-6 protein levels, activate PI3K-AKT signaling pathway and inhibit the apoptosis signaling pathway.

CONCLUSION

GLSAZD treats POI through multi-component, multi-target, and multi-pathway approaches. This study provided evidence for its clinical application in treating POI and shed light on the study of traditional medicine of the Guangxi Zhuang Autonomous Region in China.

Network Pharmacological Analysis of Hydroxychloroquine Intervention in the Treatment of Iga Nephropathy

BACKGROUND

IgA nephropathy (IgAN) is the most prevalent primary glomerulonephritis globally and has a high propensity to develop into end-stage renal disease (ESRD). Hydroxychloroquine has been proven to reduce proteinuria in IgAN patients, but the precise mechanism remains unclear. Therefore, network pharmacology was used to investigate the mechanism.

METHODS

PubChem and SwissADME databases were utilized to acquire the structure of hydroxychloroquine. The SwissTargetPrediction, PharmMapper, DrugBank, TargetNet, and BATMAN-TCM databases were then utilized to obtain the targets. The target genes related to IgAN were then gathered from the databases, which included GeneCards, PHARMGKB, DrugBank, OMIM, and DisGeNET. Common targets were obtained by UniProt. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to define the main molecular mechanisms and pathways. Furthermore, a protein-protein interaction (PPI) network was constructed using the STRING tool, and the core targets were obtained by Cytoscape. Finally, molecular docking between the core targets and hydroxychloroquine was performed.

RESULTS

167 common target genes were acquired by overlapping. The core targets were TNF, ALB, IL1B, JUN, FOS, SRC, and MMP9. The GO and KEGG results showed the targets to be related to the production of inflammatory cytokines and chemokines and were engaged in the toll-like receptor (TLR) signaling pathway. At the same time, the molecular docking results showed that the core targets all combined with hydroxychloroquine closely.

CONCLUSION

This study proved that hydroxychloroquine may treat IgAN through the TLR signaling pathway, and the restraint of TNF, TLR, IL1B, and JUN may be essential for the treatment.

Exploring the Therapeutic Potentials and Molecular Mechanisms of Coscinium fenestratum Alkaloids in Ulcerative Colitis: An Integrative Network Pharmacology and Molecular Docking Approach

Coscinium fenestratum, a medicinal plant traditionally used in Southeast Asia, exerts protective effects against various inflammatory diseases, primarily due to its rich alkaloid content. Despite substantial evidence supporting its anti-inflammatory properties, the biological activities of C. fenestratum are unclear. This study aimed to elucidate anticolitis mechanisms of C. fenestratum alkaloids (CFAs) using an integrative approach of network pharmacology and molecular docking analyses. Key active alkaloids and core target genes were identified through pharmacological and protein-protein interaction networks. The core targets were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways to determine the functional properties of active CFA. Finally, the binding affinity of the key compounds with the core targets was determined using molecular docking. The results showed that 11 active CFAs interactively interfered with 10 hub genes related to ulcerative colitis, including prostaglandin-endoperoxide synthase 2 (PTGS2), selectin E (SELE), kinase insert domain receptor (KDR), fms-related receptor tyrosine kinase 1 (FLT1), intracellular adhesion molecule 1 (ICAM1), C-X-C motif chemokine receptor 4 (CXCR4), hypoxia-inducible factor-1 (HIF1A), matrix metalloproteinase (MMP)-2, MMP3, and MMP9, which were functionally involved in the immunological response, tumor necrosis factor signaling pathway, and interleukin-17 signaling pathway. The molecular docking results indicated that CFA compounds had a strong binding affinity for the hub genes. The findings reveal, for the first time, a therapeutic role of CFA in alleviating ulcerative colitis through its predicted interactions with relevant biological targets.

Investigation into the Potential Mechanism of Radix Paeoniae Rubra Against Ischemic Stroke Based on Network Pharmacology

BACKGROUND

Radix Paeoniae Rubra (RPR), an edible and medicinal Traditional Chinese Medicine (TCM), is extensively employed in therapeutic interventions of cardiovascular and cerebrovascular diseases. However, the curative effect of RPR on ischemic stroke remains ambiguous. This work integrated network pharmacology, molecular docking, and experimental validation to explore the mechanisms of RPR in treating ischemic stroke.

METHODS

In this study, we preliminarily elucidated the therapeutic effect and mechanism of RPR on ischemic stroke through network pharmacology, molecular docking analysis, and experimental verification.

RESULTS

The results indicated that RPR improved the neurological deficit scores, decreased the size of infarcts, and reduced brain edema symptoms in the tMCAO mice model. Furthermore, through network pharmacology and molecular docking, four core targets (MAPK3, TNF-α, MAPK14, and JNK) closely related to RPR's treatment of ischemic stroke were identified, exhibiting strong affinity with two key active components of RPR: albiflorin (AF) and β-sitosterol (BSS). The Western blot showed the potential mechanism of RPR treatment for ischemic stroke by regulating the MAPK signaling pathway. Moreover, RPR and its main active ingredients exhibited a significant inhibitory effect on platelets.

CONCLUSION

In conclusion, this study revealed that RPR alleviates ischemic injury by activating the MAPK signaling pathway, and its protective effect may partly stem from inhibiting platelet activation. This work may provide a scientific basis for the development and utilization of RPR as a natural edible material to prevent ischemic stroke and anti-platelet therapy.

Network pharmacology and anticancer mechanism study of Dendrobium nobile dendrobine in the treatment of colorectal cancer

OBJECTIVE

This study aims to explore the potential targets and anticancer mechanisms of dendrobine from Dendrobium nobile in the treatment of colorectal cancer through network pharmacology, and to experimentally validate its specific effects.

METHODS

Initially, potential targets of dendrobine were identified using the ITCM Traditional Chinese Medicine database, while colorectal cancer-related genes were obtained from the NCBI Gene database, with the intersection of these datasets taken for further analysis. Functional enrichment analysis was conducted using the Metascape database, and a protein-protein interaction (PPI) network was constructed. Additionally, cell culture, cell proliferation assays, and wound healing assays were performed. The Wnt/β-catenin and NF-κB/COX-2/PGE2 signaling pathways were analyzed using PCR and Western blot experiments.

RESULTS

The PPI network constructed from 152 intersecting genes revealed that these genes play crucial roles in processes such as cell proliferation, apoptosis, and signal transduction. Cell-based assays demonstrated that dendrobine significantly inhibits the proliferation and migration of colorectal cancer cells. Furthermore, PCR and Western blot results indicated that dendrobine suppresses colorectal cancer cell proliferation and migration by modulating the Wnt/β-catenin and NF-κB/COX-2/PGE2 signaling pathways.

CONCLUSION

Dendrobine exhibits significant anticancer potential against colorectal cancer by regulating the Wnt/β-catenin and NF-κB/COX-2/PGE2 signaling pathways, providing a theoretical foundation and experimental evidence for its therapeutic application in colorectal cancer.

Introduced paeoniflorin reduces the main toxicity induced by diosbulbin B, the major toxic compound of Dioscorea bulbifera L.: involved inhibiting inflammation and ferroptosis

Rhizoma Dioscoreae Bulbiferae (HYZ) is a widely utilized herb in clinical practice, known for its significant biological activities. However, the associated hepatotoxicity poses limitations to its application. Our previous research indicated that the effective mitigation of HYZ-induced hepatotoxicity through the concoction with Radix Paeoniae Alba medicinal juice involves the incorporation of paeoniflorin (Pae) and a reduction in diosbulbin B (DB), the primary toxic compound in HYZ. This finding suggests that the introduced Pae may exert a direct attenuating effect on DB. In light of this, this study represents the first investigation into Pae's detoxification effect against DB-induced hepatotoxicity after administration for 2 months in mice vivo while also exploring underlying mechanisms related to inflammation and ferroptosis based on network pharmacology results. Our findings demonstrate that Pae significantly alleviates DB-induced hepatotoxicity in a dose-dependent manner. Western blotting and ELISA analyses revealed that Pae effectively reversed elevated levels of hepatic inflammation-related markers-such as NF-κB, p38 MAPK, NLRP3, TNF-α, and IL-1β-as well as excessively high concentrations of ferroptosis-related MDA and Fe2+. Furthermore, it restored low levels of GSH, SOD, GPX4, and FTH1. In summary, introduced Pae substantially mitigated DB-induced hepatotoxicity by inhibiting both hepatocyte inflammation and ferroptosis.

Efficacy and safety of TACE combined with traditional Chinese medicine versus TACE alone in hepatocellular carcinoma: bayesian network meta-analysis and pharmacological mechanisms study

PURPOSE

This study investigates the clinical benefits of integrating traditional Chinese medicine (TCM) with Transarterial Chemoembolization (TACE) in hepatocellular carcinoma (HCC) treatment via meta-analysis and an exploration of network pharmacology analysis (NPA).

METHODS

A comprehensive search across different databases retrieved all randomized controlled trials (RCTs) evaluating TCM combined with TACE for HCC. Meta-analysis included 39 RCTs to assess the intervention effects. The bayesian network meta-analysis observed the relative efficacy and potential ranking of various interventions. Active compounds and target genes from frequently used TCM were sourced from the TCMSP database, while HCC disease targets were collected from five public disease databases. Regulatory networks connecting target genes with active components of key herbs were constructed. Following the identification of key genes, we conducted analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to enrich our understanding of their functions. NPA and molecular docking methods were refined to reveal potential interactions between TCM components and their specific targets.

RESULTS

The combination of TCM with TACE significantly enhances the efficacy and safety of HCC treatment, improving the overall response rate, disease control rate, and overall survival rate, while also reducing the incidence of adverse events. Among the TCM evaluated, Ganfu Formula proved to be the most effective in enhancing patient response rates. Analysis of all included medicinal herbs identified 10 pivotal TCMs and 17 core genes. GO analysis revealed their significance in protein interactions, whereas KEGG analysis highlighted their role in crucial oncological pathways. NPA and molecular docking techniques elucidate the underlying mechanisms of action of TCM components.

CONCLUSION

Adding TCM to TACE protocols significantly enhances treatment outcomes and safety in HCC patients by modulating tumor biology and systemic immune responses, highlighting its potential as an effective adjunct therapy. These findings support the inclusion of TCM in standard care regimens, offering potential for improved management of HCC.

SYSTEMATIC REVIEW REGISTRATION

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024571280.

Network pharmacology combined with experimental validation reveals the mechanism of action of cangerzisan on allergic rhinitis

ETHNOPHARMACOLOGICAL RELEVANCE

Allergic rhinitis (AR) stands as a non-infectious inflammatory condition affecting the nasal mucosa, marked by bouts of sneezing, nasal itching, and congestion. This ailment afflicts individuals across all age groups and poses challenges for effective treatment due to its chronic nature. Cangerzisan (CEZS), documented in the Jishengfang compendium, represents a traditional Chinese medicinal formula long utilized for AR management.

AIM OF THE STUDY

Investigating mechanism beneath therapeutic effect of CEZS in alleviating AR.

MATERIALS AND METHODS

The main active components in CEZS were determined by High Performance Liquid Chromatography (HPLC).The active constituents of CEZS and their corresponding targets were identified through an exhaustive screening process employing TCMSP database. To identify targets relevant to AR, GeneCards, OMIM, and DisGeNET databases were thoroughly applied. Protein-protein interaction (PPI) network was assembled utilizing STRING platform. Potential signaling pathways influenced by CEZS were delineated through GO and KEGG enrichment analyses. Subsequently, an AR model was induced by administering aluminum hydroxide (Al(OH)3) and ovalbumin (OVA) for affecting basal and local sensitization, respectively, facilitating experimental validation of the principal signaling pathways.

RESULTS

There were 61 active constituents identified within CEZS, targeting a pool of 129 entities associated with AR treatment. Pathways analysis of KEGG revealed that CEZS potentially inhibits AR advancement via modulating TLR4 signaling pathway. Animal experiments demonstrated that CEZS effectively alleviated symptom scores in guinea pigs with AR. Moreover, it exhibited notable improvements in serum immune and inflammatory factors levels, as well as reduced inflammatory infiltration within nasal mucosa, including goblet and mast cells. CEZS was found to enhance GATA-3 expression while reducing T-bet expression, thereby modulating the TH1/TH2 immune balance. Additionally, CEZS downregulated HMGB1, TLR4, and p-NF-κB/NF-κB protein expressions within nasal mucosa of guinea pigs.

CONCLUSIONS

The therapeutic mechanism of CEZS against AR involves rectifying TH1/TH2 immune imbalance and upregulating inflammatory and immune factors through modulating key proteins expression within TLR4 pathway. This targeted regulation effectively impedes AR progression.

Triphala ameliorates cognitive deficits and anxiety via activation of the Nrf2/HO-1 axis in chronic sleep-deprived mice

Triphala is renowned for its curative attributes and has been utilized for centuries to address diverse health ailments. Moreover, the active component of Triphala, polyphenols, is widely recognized for its excellent pharmacological activities, such as anti-inflammatory properties, and has been utilized as a potential natural remedy. However, the precise mechanism through which Triphala alleviates cognitive dysfunction and anxiety induced by chronic sleep deprivation (SD) remains restricted. The objective of this investigation is to examine and clarify the potential mechanism of action that underlies the therapeutic benefits of Triphala in addressing cognitive dysfunction and anxiety induced by chronic SD. Our results demonstrated that Triphala significantly alleviates chronic SD-induced behavioral abnormalities. Additionally, Triphala was highly effective at preventing histopathological or morphological damage to neurons located in the hippocampus. The therapeutic effects of Triphala in treating cognitive dysfunction and anxiety induced by chronic SD involve the modulation of several biological pathways, including inflammation and immune responses, oxidative stress, cell growth and differentiation, metabolism, and neurotransmitter communication. Moreover, our study illustrated that Triphala increased the nuclear translocation of nuclear factor erythroid 2-related factor 2 (Nrf2) and significantly activated the Nrf2/hemeoxygenase-1 (HO-1) axis. Additionally, the neuroprotective properties of Triphala were found to be counteracted by the Nrf2 inhibitor ML385. Our study represented the first to unveil that Triphala exerts therapeutic benefits in alleviating chronic SD-induced cognitive deficits and anxiety by activation of the Nrf2/HO-1 axis. Triphala emerges as a promising nutraceutical ingredient for mitigating cognitive deficits and anxiety linked to chronic SD.

Cardioprotective effect of Saussurea involucrata injection against Doxorubicin-induced cardiotoxicity by network pharmacology analysis and experimental verification

Doxorubicin (Dox) is widely utilized in the clinical treatment of various cancers. Despite its efficacy, Dox induces numerous adverse effects in humans with significant cardiotoxicity, posing a major limitation to its use. Saussurea involucrata injection (SII), derived from Saussurea involucrata, exhibits notable anti-inflammatory and anti-oxidative stress properties. However, its potential protective effects against Dox-induced cardiotoxicity (DIC) remain unexplored. In this study, we investigate the ability of SII to mitigate DIC and elucidate the underlying mechanisms through experimental research and network pharmacology analysis. Results from both in vitro and in vivo experiments reveal that SII treatment significantly improves Dox-induced cardiac dysfunction, reducing pathological alterations and fibrosis in cardiomyocytes. Moreover, SII has cardioprotective effects by diminishing the inflammation, oxidative stress, and apoptosis triggered by Dox. Network pharmacological analysis further shows that SII downregulates P53 protein expression by activating the AKT/MDM2 signaling pathway, thus attenuating DIC. In conclusion, this study confirms that SII mitigates DIC through downregulation of the AKT/MDM2/P53 signaling pathway, suggesting a promising therapeutic strategy for alleviating DIC.

Ganoderic acid a alleviates Aβ25-35-induced HT22 cell apoptosis through the ERK/MAPK pathway: a system pharmacology and in vitro experimental validation

Alzheimer's disease (AD) is a neurodegenerative disorder that occurs with aging. Ganoderma lucidum (Curtis.) P. Karst. (G. lucidum) is a traditional medicinal fungus believed to nourish the brain and anti-aging. Ganoderic acid A (GAA), a triterpenoid from G. lucidum, has demonstrated natural neuroprotective effects. This study aims to explore the therapeutic effect and molecular mechanism of GAA on AD. Systematic network pharmacology identified 95 targets, 8 biological functions, and multiple pathways. The results highlighted MAPK family members as core genes, with MAPK1 (ERK2) showing the highest binding affinity to GAA in molecular docking. In vitro experiments revealed that GAA dose-dependently increased the viability of Aβ25-35-injured HT22 cells and inhibited MAPK pathway-related protein expression. Similar to FR180204, 100 µM GAA significantly reversed ERK protein expression, oxidative stress markers, and mitochondrial damage in AD cell model. GAA also downregulated cleaved caspase-3 protein levels, apoptosis rates, Aβ and p-Tau expression by inhibiting the ERK signaling pathway. The therapeutic effect of GAA on AD was predicted and validated through network pharmacology and in vitro experiments. The ability of GAA to inhibit apoptosis via the ERK/MAPK signaling pathway positions it as a promising candidate for AD treatment.

Network pharmacology integrated with experimental validation to elucidate the mechanisms of action of the Guizhi-Gancao Decoction in the treatment of phenylephrine-induced cardiac hypertrophy

CONTEXT

The mechanisms of Traditional Chinese Medicine (TCM) Guizhi-Gancao Decoction (GGD) remain unknown.

OBJECTIVE

This study explores the mechanisms of GGD against cardiac hypertrophy.

MATERIALS AND METHODS

Network pharmacology analysis was carried out to identify the potential targets of GGD. In vivo experiments, C57BL/6J mice were divided into Con, phenylephrine (PE, 10 mg/kg/d), 2-chloroadenosine (CADO, the stable analogue of adenosine, 2 mg/kg/d), GGD (5.4 g/kg/d) and GGD (5.4 g/kg/d) + CGS15943 (a nonselective adenosine receptor antagonist, 4 mg/kg/d). In vitro experiments, primary neonatal rat cardiomyocytes (NRCM) were divided into Con, PE (100 µM), CADO (5 µM), GGD (10-5 g/mL) and GGD (10-5 g/mL) + CGS15943 (5 µM). Ultrasound, H&E and Masson staining, hypertrophic genes expression and cell surface area were conducted to verify the GGD efficacy. Adenosine receptors (ADORs) expression were tested via real-time polymerase chain reaction (PCR), western blotting and immunofluorescence analysis.

RESULTS

Network pharmacology identified ADORs among those of the core targets of GGD. In vitro experiments demonstrated that GGD attenuated PE-induced increased surface area (with an EC50 of 5.484 × 10-6 g/mL). In vivo data shown that GGD attenuated PE-induced ventricular wall thickening. In vitro and in vivo data indicated that GGD alleviated PE-induced hypertrophic gene expression (e.g., ANP, BNP and MYH7/MYH6), A1AR over-expression and A2aAR down-expression. Moreover, CADO exerts effects similar to GGD, whereas CGS15943 eliminated most effects of GGD.

DISCUSSION AND CONCLUSIONS

Our findings suggest the mechanism by which GGD inhibits cardiac hypertrophy, highlighting regulation of ADORs as a potential therapeutic strategy for HF.

A stepwise integrated strategy to explore quality markers of Qishen Yiqi dripping pills against myocardial ischemia

BACKGROUND

Numerous experiments and clinical practices have demonstrated the effectiveness of Qishen Yiqi dripping pills (QSYQ) on myocardial ischemia (MI). However, the bioactive ingredients and mechanisms remain unclear, leading to huge gaps between quality control and biological effect of QSYQ. Discovering quality markers (Q-markers) based on effective components is crucial for ensuring stable quality and clinical effectiveness of QSYQ.

PURPOSE

To explore Q-markers of QSYQ against MI by a stepwise strategy integrating serum pharmacochemistry, network pharmacology, metabolomics, quantitative analysis, and cell experiments.

METHODS

Firstly, liquid/gas chromatography-mass spectrometry was applied to characterize chemical profiles of QSYQ in vitro and in vivo. Based on the serum migrating constituents, a component-target-MI interaction network was constructed. Subsequently, pharmacodynamics and metabolomics were conducted to evaluate cardioprotective effect and potential mechanism of QSYQ. Next, conjoint analysis of network pharmacology and metabolomics was performed to screen candidate Q-markers. Finally, the measurability and bioactivity were validated to justify their usage as Q-markers.

RESULTS

A total of 97 components were identified in QSYQ, 24 prototypes of which were detected in serum. The "component-target-disease" interaction network was constructed based on serum migrating constituents. Pharmacodynamic results showed that QSYQ effectively improved cardiac function, attenuated inflammatory cell infiltration, alleviated myocardial fibrosis, and reduced the levels of myocardial enzymes and oxidative stress in MI rats. Metabolomics study demonstrated that 59 metabolites were markedly altered in MI rats, 25 of which were significantly reversely regulated by QSYQ. After integrative analysis of network pharmacology and metabolomics, 12 components were selected as candidate Q-markers of QSYQ, and the contents were quantified. These candidate Q-markers displayed synergistic protective effects against H2O2-induced injury in H9c2 cells. Taken together, 12 components with properties of transitivity and traceability, effectiveness, measurability, and compatibility contribution were defined as representative Q-markers of QSYQ, including Astragaloside IV, Ononin, Calycosin, Formononetin, Rosmarinic acid, Cryptotanshinone, Salvianolic acid A, Tanshinol, Ginsenoside Rb1, Ginsenoside Rg1, Nerolidol, and Santalol.

CONCLUSION

In this study, a novel stepwise integrated strategy was presented for discovering Q-markers related to therapeutic effects of traditional Chinese medicine prescriptions. Twelve comprehensive and representative Q-markers of QSYQ were identified for the first time to improve its quality control.

BCPT perspectives on studies involving natural products, traditional Chinese medicine and systems pharmacology

Natural products constitute a vast source of bioactive compounds with the potential of providing valuable insight for future medicines. However, from a pharmacological perspective, natural product studies are also often accompanied by serious limitations due to, for example, the complex nature of biological extracts, the challenge of reproducibly characterizing the extract and providing an exhaustive list of constituents and, consequently, the difficulties in linking the observed pharmacological effects to specific chemical entities. The present paper discusses the major challenges of studies with natural products and provides a guideline to be followed by authors submitting research findings involving data from natural products, and their derivatives, to Basic & Clinical Pharmacology & Toxicology.

Integrating network pharmacology and experimental validation to investigate the effects and mechanism of Renshen Shouwu decoction for ameliorating Alzheimer's disease

CONTEXT

The mechanism of Renshen Shouwu Decoction (RSSW) in treating Alzheimer's disease (AD) remains unknown.

OBJECTIVE

This study investigates the effects and mechanism of RSSW for ameliorating AD.

MATERIALS AND METHODS

Ten SAMR1 mice and 40 SAMP8 mice were divided into five groups: control (SAMR1), model (SAMP8), positive drug (Donepezil, 1.3 mg/kg/d), and RSSW (Low-dose, 117 mg/kg/d; High-dose, 234 mg/kg/d). Starting from 6 months of age, the medications were administered intragastrically for a total of 60 days. Subsequently, memory improvement in rapidly aging mice was assessed using the novel object recognition test and Morris water maze test. Through the identification of absorbed blood components and analysis of network pharmacology, active ingredients and potential targets involved in the treatment of AD were identified. Finally, AD-related biological indicators were detected using western blotting and ELISA.

RESULT

Our results demonstrated that RSSW effectively ameliorated memory impairments, inhibited tau hyperphosphorylation, and reduced β-amyloid plaque deposition in SAMP8 mice. Thirty absorbed blood components in RSSW were identified, revealing identified 96 major targets that play a key role in alleviating AD. Notably, the obtained main targets were highly enriched in SIRT1-mediated signaling pathways. Subsequent experimental validation confirmed that RSSW activated the SIRT1/NF-κB, SIRT1/AMPK, and SIRT1/p53 signaling cascades. Nine potential active ingredients were predicted through molecular docking.

DISCUSSION AND CONCLUSIONS

Our research findings suggest the mechanism of RSSW treatment for AD, which ameliorates memory impairments by reducing cortical tissue inflammation and apoptosis.

Anti-depression molecular mechanism elucidation of the phytochemicals in edible flower of Hemerocallis citrina Baroni

The edible flower of Hemerocallis citrina Baroni, commonly known as "Huang Huacai" in China, has anti-depressant effects. However, targets and molecular mechanisms of Hemerocallis citrina Baroni edible flowers (HEF) in depression treatment are still unclear. The potential anti-depression targets in HEF were identified by the intersecting results from typical drug databases. The network construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis were carried out for core targets. The molecular docking was conducted to predict the binding affinity between the active components and the central targets. The intersecting results indicated that there were 24 active components in HEF, with 449 anti-depression targets identified. After screening through degree centrality (DC), betweenness centrality (BC), and closeness centrality (CC), 166 core targets were determined. Tumor protein 53 (TP53) and interleukin 6 (IL-6) had the highest degree values. The results of GO enrichment analysis associated with anti-depression revealed that the biological processes were negative regulation of osteoclast differentiation and positive regulation of phosphorus metabolic process. KEGG enrichment analysis results revealed that pathways, such as the phosphatidylinositol 3‑kinase-protein kinase B (PI3K-Akt) signaling pathway and mitogen-activated protein kinase (MAPK) signaling pathway, were primarily associated with anti-depression. Molecular docking results indicated that the top 10 active ingredients in HEF could bind to the central targets. This study applied network pharmacology to unveil the potential anti-depressive mechanisms of HEF, providing a theoretical basis for further exploration of the effective components in H. citrina edible flower parts.

Mechanism of Xue-Jie-San treating Crohn's disease complicated by atherosclerosis: Network pharmacology, molecular docking and experimental validation

BACKGROUND

Crohn's disease (CD), as a chronic systemic inflammatory disease, is strongly associated with the development of premature atherosclerosis (AS). Atherosclerotic cardiovascular disease, including coronary heart disease, myocardial infarction and stroke, is a lethal complication of CD. Nowadays, there is a lack of effective monotherapy for CD complicated by AS.

PURPOSE

To explore the underlying effects and mechanisms of Xue-Jie-San (XJS) on treating CD complicated by AS via network pharmacology and experimental validation.

METHODS

The targets of XJS components were obtained from TCMSP, ETCM and PubChem databases as well as the disease genes of CD and AS from GeneCards, DisGeNET and OMIM databases. The core targets were screened out from the drug-disease common targets identified by protein-protein interaction (PPI) network analysis and then analyzed with GO and KEGG enrichment. The interaction between core target and XJS component was detected by molecular docking and molecular dynamics simulation. Subsequently, the core targets were validated via GEO datasets and their biological functions were confirmed in vitro. Nile red staining was used to evaluated lipid accumulation in human umbilical vein endothelial cells (HUVECs) challenged by lipopolysaccharide (LPS) combined with oxidized low-density lipoprotein (ox-LDL). Levels of pro-inflammatory cytokines were examined by enzyme-linked immunosorbent assay. Chemokine CCL2 and CXCL8 were detected by immunofluorescence staining. The activity of the TLR4/Myd88/NF-κB signaling pathway was assessed using Western blot.

RESULTS

In total, 26 common target genes of XJS, CD and AS were found. Among them, 11 core genes were identified by PPI network analysis. The effects of XJS treating CD complicated by AS were mainly mediated by the lipid and atherosclerosis pathway, inflammatory bowel disease pathway and toll-like receptor signaling pathway. Molecular docking and molecular dynamics simulation displayed strong binding affinity between XJS component and the core target. Six core genes including TLR4, IL-1β, TNF, ICAM1, CCL2 and CXCL8 were validated by GEO datasets. In vitro, the effects of XJS on reducing lipid accumulation, secretion of IL-1β, IL6, TNF-α, CCL2 and CXCL8, and the protein expressions of TLR4, Myd88, p-p65 and ICAM1 were verified.

CONCLUSION

XJS is a potential candidate drug for the treatment of CD complicated by AS. The underlying mechanisms involve mitigation of lipid accumulation-mediated endothelial dysfunction and blockage of immune inflammatory response by targeting TLR4.

Peimine induces apoptosis of glioblastoma cells through regulation of the PI3K/AKT signaling pathway

Glioblastoma (GBM) is one of the most malignant forms of intracranial tumors, with high mortality rates and invariably poor prognosis, due to the limited clinical treatment strategies available. As a natural compound, peimine's favorable pharmacological activities have been widely revealed. However, potential inhibitory effects of peimine on GBM have not been explored. In the present study, both in vitro and in vivo experiments were performed to elucidate the effects of peimine on GBM and to further delineate the underlying molecular mechanism of action. Different doses (0, 25 and 50 µM) of peimine were added to U87 cells, before MTT, colony formation, wound healing, Transwell migration and invasion, reactive oxygen species and mitochondrial transmembrane potential assays were used to measure proliferation, migration, invasion and apoptosis. Furthermore, western blotting was used to examine the possible effects of peimine on the expression of proteins associated with apoptosis and the PI3K/AKT signaling pathway. Subsequently, a GBM mouse xenograft model was used to assess the effects of peimine in vivo. The findings showed that peimine inhibited GBM proliferation, migration and invasion in a dose-dependent manner, whilst also inducing apoptosis. Peimine also reduced tumor growth in vivo. Mechanistically, peimine downregulated the expression of Bcl-2 and Caspase 3, whilst upregulating the protein expression levels of p53, Bax and Cleaved-Caspase 3 in a dose-dependent manner. In addition, PI3K and AKT phosphorylation levels were found to be decreased by peimine in a dose-dependent manner. In conclusion, these findings suggest that peimine may limit GBM growth by regulating the PI3K/AKT signaling pathway both in vitro and in vivo. These findings may have promising clinical implications.

Yishen paidu pills attenuates 5/6 nephrectomy induced kidney disease via inhibiting the PI3K/AKT/mTOR signaling pathway

Introduction

Chronic kidney disease (CKD) is a substantial global health issue with high morbidity and mortality. Yishen Paidu Pills (YSPDP) are effective concentrated water pills composed of four herbs developed by Wuhan Union Hospital to treat CKD. However, the mechanism of YSPDP action is largely unknown. This study combined metabolomics, network pharmacology, transcriptomics, and experimental verification to elucidate and identify the effects and potential mechanisms of YSPDP against CKD.

Methods

Firstly, we used metabolomics analyses to identify the chemical components of YSPDP. Then, network pharmacology was conducted and indicated the predicted signaling pathways regulated by YSPDP. Next, we conducted a 5/6 subtotal nephrectomy (5/6 SNx) rat model and treated these rats with YSPDP or Losartan for 10 weeks to evaluate the effect of YSPDP on CKD. To further analyze the underlying mechanism of YSPDP in CKD, the kidney tissues of 5/6 SNx rats treated with vehicle and YSPDP were performed with transcriptome sequencing. Finally, the western blot was performed to validate the signaling pathways of YSPDP against CKD.

Results

Twenty-four classes of chemicals were identified by metabolomics in YSPDP. YSPDP markedly hindered CKD progression, characterized by the restoration of body weight and serum albumin levels, improved renal function, diminished tissue injury, and hampered renal fibrosis in 5/6 SNx rats. The efficacy of YSPDP in ameliorating the progression of CKD was comparable to that of losartan. Furthermore, network pharmacology, transcriptomics, and functional enrichment analysis indicated the PI3K/AKT/mTOR signaling pathway was the key pathway regulated by YSPDP. Western blot validated the inhibition of PI3K/AKT/mTOR signaling in the kidney of 5/6 SNx rats treated by YSPDP.

Conclusion

The study identified the chemicals of YSPDP and revealed that YSPDP prevented the progression of CKD by inhibiting PI3K/AKT/mTOR signaling in 5/6 SNx rats.

Cepharanthine as an effective small cell lung cancer inhibitor: integrated insights from network pharmacology, RNA sequencing, and experimental validation

Background

Small cell lung cancer (SCLC) is an aggressive malignancy with limited treatment options and poor prognosis, underscoring the need for new therapeutic agents.

Methods

A library of 640 natural products was screened for anti-proliferative activity in SCLC cells. The effects of Cepharanthine (CE) on SCLC cells were assessed in vitro and in vivo. Network pharmacology and RNA sequencing (RNA-seq) were used to elucidate the molecular mechanisms. Pathway enrichment analysis was performed using Gene Set Enrichment Analysis (GSEA) with Hallmark and Reactome gene sets. Protein-protein interaction (PPI) networks, along with the Cytoscape cytoHubba plugin, were used to identify key hub genes. RT-PCR and Western blotting were employed to validate mRNA and protein expression. Molecular docking studies assessed the binding affinity of CE to potential targets. Bioinformatics analyses, including expression profiling, prognostic evaluation, and loss-of-function studies, were used to explore the role of specific genes in SCLC.

Results

CE was identified as a promising SCLC inhibitor. In vitro, CE significantly inhibited SCLC cell proliferation, colony formation, migration, and invasion, while promoting apoptosis. In vivo, CE treatment notably reduced tumor volume in xenograft models. Network pharmacology identified 60 potential target genes, with enrichment analysis indicating their involvement in cholesterol metabolism regulation. RNA-seq and experimental validation further confirmed that CE inhibits cholesterol synthesis in SCLC cells by downregulating key enzymes, including HMGCR, HMGCS1, IDI1, FDFT1, and SQLE. Molecular docking studies confirmed the binding of CE to these enzymes. Additionally, these enzymes were found to be highly expressed in SCLC cells, with elevated levels of HMGCS1, HMGCR, and IDI1 correlating with poor prognosis. Functional assays revealed that silencing these genes significantly suppressed SCLC cell proliferation.

Conclusion

This study identifies CE as a potential therapeutic agent for SCLC, acting through the suppression of cholesterol synthesis, and uncovers novel therapeutic targets for the treatment of this aggressive cancer.

Predicting the therapeutic role and potential mechanisms of Indole-3-acetic acid in diminished ovarian reserve based on network pharmacology and molecular docking

BACKGROUND

Indole-3-acetic acid (IAA), an indole analog produced by intestinal microorganisms metabolizing tryptophan, has anti-inflammatory and antioxidant properties and thus has potential applications in ovarian protection, although the exact mechanism is unknown. The present study preliminarily investigated the pharmacological mechanism of IAA in alleviating diminished ovarian reserve (DOR) by network pharmacology and molecular docking.

METHODS

Relevant target proteins of IAA were searched in SwissTargetPrediction, PharmMapper, TargetNet, BATMAN-TCM, and SuperPred databases. The potential targets of DOR were obtained from GeneCards, DisGenet, OMIM, and Drugbank databases. Both common targets were then imported into the String website to construct a PPI network, and these targets were analyzed for GO and KEGG enrichment. Finally, we utilized molecular docking to validate the possible binding conformations between IAA and the candidate targets. We used in vitro experiments to preliminarily investigate the effects of IAA on DOR.

RESULTS

We obtained 88 potential targets for IAA and DOR interaction. We received 16 pivotal targets by constructed protein interaction screening. KEGG enrichment analysis mainly included the AGE-RAGE signaling pathway, IL-17 signaling pathway, Chemical carcinogenesis-reactive oxygen species in diabetic complications, etc. GO functional analysis showed that IAA treatment of DOR may involve biological processes such as response to external stimuli, hypoxia, gene expression, and regulation of enzyme activity. Molecular docking and in vitro experiments further revealed the potential effects of IAA on MMP2, TNF-α, AKT1, HSP90AA1, and NF-κ B.

CONCLUSION

We preliminarily revealed the potential protective effects of IAA against DOR through multiple targets and pathways, which provides a new research strategy for the molecular mechanism of IAA to alleviate DOR in the future. However, further studies need to demonstrate whether IAA can be used as a compound to prevent and treat DOR.

Deciphering mechanism of Buyang Huanwu Decoction in regulating macrophage polarization to alleviate atherosclerosis via virtual screening and experimental verification

ETHNOPHARMACOLOGICAL RELEVANCE

Buyang Huanwu Decoction (BYHWD), a traditional prescription known for its Supplementing Qi and Promoting Blood Circulation, has demonstrated noteworthy therapeutic roles in regulating macrophage polarization to atherosclerosis (AS). However, its underlying mechanisms remain unknown.

AIM OF THE STUDY

The purpose of this paper was to decipher mechanism of BYHWD in regulating macrophage polarization to alleviate AS.

MATERIALS AND METHODS

A comprehensive virtual screening strategy, incorporating network pharmacology and batch molecular docking, combined with experimental validation techniques, was employed to systematically elucidate the underlying mechanism of BYHWD regulating macrophage polarization to alleviate AS.

RESULTS

Firstly, based on high-fat diet induced AS model in apolipoprotein E-deficient mice, it was found that BYHWD can significantly regulate macrophage polarization to alleviate AS. Then, the network pharmacological analysis revealed that the core targets of BYHWD regulating macrophage polarization to alleviate AS mainly involved TP53, AKT1 and BCL2. The mitochondrial function and metabolism were the main biological processes. Meanwhile, the main chemical components were identified as 3-O-p-coumaroylquinic acid, D-mandelonitrile, Ellagic acid, Ferulic acid, 5-hydroxy-L-tryptophan zwitterion, Isoliquiritigenin, Senkyunolide-F, Anofinic acid, Trimethylhydroquinone and Senkyunolide-E by batch molecular docking strategy. Further, the in vitro experiments demonstrated that BYHWD not only regulated macrophage polarization and alleviated macrophage foam formation but also modulated mitochondrial function and the expression of TP53, p-AKT, and BCL2 proteins. Finally, multivariate statistical analysis confirmed that the ameliorative effect of BYHWD on AS was closely related to mitochondrial function and macrophage polarization regulated by TP53, AKT1 and BCL2.

CONCLUSIONS

BYHWD could activate key targets, including TP53, AKT1, and BCL2, to alleviate mitochondrial dysfunction and regulate macrophage polarization, thereby improving AS. The 10 active compounds of BYHWD, including 5-hydroxy-L-tryptophan zwitterion and Isoliquiritigenin, played an important role in regulating macrophages polarization to alleviate AS.

WenTongGanPi decoction alleviates diarrhea-predominant irritable bowel syndrome by improving intestinal barrier

ETHNOPHARMACOLOGICAL RELEVANCE

WenTongGanPi Decoction (WTGPD) is a representative medical practice of the Fuyang School of Traditional Chinese Medicine (TCM), which originated from the classical Lu's Guizhi method. WTGPD places emphasis on the balance and functionality of yang qi, and is effective in treating TCM symptoms related to liver qi stagnation and spleen yang deficiency. In TCM, diarrhea-predominant irritable bowel syndrome (IBS-D) is often diagnosed as liver depression and spleen deficiency, and the use of WTGPD has shown significant therapeutic effect. However, the underlying mechanism of WTGPD treating IBS-D remains unclear.

AIM OF THE STUDY

To explore the effect and mechanism of WTGPD in the treatment of IBS-D.

MATERIALS AND METHODS

An IBS-D model with liver depression and spleen deficiency was constructed by chronic immobilization stress stimulation and sennae folium aqueous gavage. The impact of WTGPD on IBS-D rats was evaluated through measurements of body weight, fecal water content, and abdominal withdrawal reflex (AWR). Intestinal permeability was assessed using hematoxylin-eosin (HE), alcian blue-periodic acid schiff (AB-PAS), immunofluorescence (IF) staining, and quantitative real-time PCR (qRT-PCR). The components of WTGPD were analyzed using UPLC-Q-TOF-MS. The underlying mechanisms were investigated through network pharmacology, transcriptomics sequencing, western blot (WB), molecular docking, and 16S rRNA sequencing.

RESULTS

WTGPD treatment effectively alleviated diarrhea and abnormal pain in IBS-D rats (P < 0.05). It enhanced the intestinal barrier function by improving colonic structure and increasing the expression of tight junction proteins (P < 0.05). A total of 155 components were identified in WTGPD. Both network pharmacology and transcriptomics sequencing analysis highlighted MAPK as the key signaling pathway in WTGPD's anti-IBS-D effect. The WB results showed a significant decrease in p-p38, p-ERK and p-JNK expression after WTGPD treatment (P < 0.0001). Guanosine, adenosine and hesperetin in WTGPD may be involved in regulating the phosphorylation of p38, ERK and JNK. Additionally, WTGPD significantly enhanced microbial diversity and increased the production of colonic valeric acid in IBS-D rats (P < 0.01).

CONCLUSION

In conclusion, our findings suggest that WTGPD can effectively alleviate IBS-D and improve intestinal barrier likely via inhibiting MAPK signal pathway and improving micobial dysbiosis.

Research landscape and pharmacological mechanisms of traditional Chinese medicines in treating and preventing urolithiasis: Unearthing an anti-urolithic treasure trove

ETHNOPHARMACOLOGICAL RELEVANCE

Urolithiasis represents a predominant concern within urology due to its high recurrence rate and consequential surgical complications. Traditional Chinese Medicine (TCM), with a history spanning over 2000 years in treating kidney diseases, not only offers a less invasive and cost-effective option for treating and preventing urolithiasis, but also serves as a pharmacological treasure trove for the development of anti-urolithic drugs.

AIM OF THE STUDY

With the continuous deepening of research on the anti-urolithic effects of Chinese medicines, the pharmacological mechanisms of TCMs against urolithiasis are continuously evolving. Therefore, it is essential to summarize the current research status, clinical effectiveness, and mechanisms of TCM in treating and preventing urolithiasis, to ascertain its potential in anti-urolithic treatments, and to provide a reference for future anti-urolithiasis drug research.

METHODS

The electronic databases such as PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI) have been utilized to retrieve relevant literature spanning from 2000 to September 2023, using keywords "Traditional Chinese Medicine" and "Urolithiasis". Then we conducted a visual analysis of the current status of related research, as well as a systematic organization of the therapeutic effects and underlying mechanisms of anti-urolithic TCMs.

RESULTS

Through the organization of research models, therapeutic effects, and active ingredients of 31 potential anti-urolithic TCMs, we have systematically summarized the underlying mechanisms of TCMs in management of urolithiasis. Mechanistically, Chinese herbs facilitate stone expulsion by enhancing diuresis, instigating anti-spasmodic effects, and promoting ureteral peristalsis when addressing calculi. They also harbor the potential to dissolve pre-existing stones. In terms of stone recurrence prevention, TCM compounds obstruct stone formation through targeting the sequence of crystal adhesion, nucleation, growth, and aggregation to inhibit stone formation. Additionally, TCM's significant roles include stifling oxidative stress, augmenting urinary stone inhibitors, and harmonizing oxalate metabolism, all of which are critical actions in stone prevention.

CONCLUSION

The anti-urolithic mechanism of TCM is multifaceted. Investigating the anti-urolithiasis mechanisms of TCM not only illuminates the potential of Chinese medicine in treating and preventing urolithiasis, but also uncovers active molecules and targets for drug treatment against calculus formation.

Jianwei Xiaoyan granule ameliorates chronic atrophic gastritis by regulating HIF-1α-VEGF pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Jianwei Xiaoyan Granule (JWXYG) is the traditional Chinese medicine preparation in Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, which has been widely used in clinical treatment of chronic atrophic gastritis (CAG). However, the material basis and potential mechanism of JWXYG in the treatment of CAG are not clear.

PURPOSE

To explore the material basis and potential mechanism of JWXYG in the treatment of CAG.

METHODS

In this study, the components of JWXYG were analyzed by HPLC-Q-TOF-MS/MS. Then, the CAG model in rats established by a composite modeling method and MC cell model induced by MNNG were used to explore the improvement effect of JWXYG on CAG. Finally, the potential mechanism of JWXYG in the treatment of CAG was preliminarily predicted based on network pharmacology and validated experimentally.

RESULTS

Thirty-one components of JWXYG were analyzed through HPLC-Q-TOF-MS/MS, such as albiflorin, paeoniflorin, lobetyolin firstly. Research results in vivo showed that the gastric mucosa became thinner, intestinal metaplasia appeared, the number of glands was reduced, the serum levels of PG I and PG II increased and the contents of G17 and IL-6 reduced in CAG model rats. After 4 weeks of JWXYG (2.70 g/kg) administration, these conditions were significantly improved. In addition, cell viability, migration, and invasion of MNNG-induced MC cells was inhibited by JWXYG treatment (800 μg/mL). Furthermore, the results of network pharmacology indicated that HIF-1 and VEGF signaling pathways might play important roles in the therapeutic process. Then the results of Western blot, immunohistochemistry and immunofluorescence confirmed that with JWXYG treatment, the increased expression of HIF-1α, VEGF and VEGFR2 in gastric issue of CAG rats were restrained. Eventually, potential components of JWXYG in the treatment of CAG were predicted through molecular docking to elucidate the material basis.

CONCLUSION

JWXYG could inhibit angiogenesis by regulating HIF-1α-VEGF pathway to exert therapeutic effects on CAG. Our study explored the potential mechanisms and material basis of JWXYG in the treatment of CAG and provides experimental data for the clinical rational application of JWXYG.

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

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

Tinosporae Radix attenuates acute pharyngitis by regulating glycerophospholipid metabolism and inflammatory responses through PI3K-Akt signaling pathway

Introduction

With the onset of the COVID-19 pandemic, the incidence and prevalence of acute pharyngitis (AP) have increased significantly. Tinosporae Radix (TR) is a vital medication utilized in the treatment of pharyngeal and laryngeal ailments, especially AP. The study endeavors to explore unclear molecular mechanisms of TR in addressing AP.

Methods

Network pharmacology and metabolomics analyses of effect of TR on AP were conducted, and apossible pathway was validated both in vivo using the acute pharyngitis rat model and in vitro using the LPS-induced RAW264.7 cells model, through techniques such as histopathological examinations, immunohistochemical technology, ELISA, RT-qPCR, and Western blotting to systematically explore the possible mechanisms underlying the inhibition of AP by TR.

Results and discussion

Network pharmacology analysis identified several key targets, including PIK3CA, IL6, AKT1, TNF, and PTGS2, alongside pivotal signaling pathways such as IL-17, TNF, Hepatitis B, nuclear factor kappa B (NF-κB), Influenza A, and the PI3K-Akt pathway. Most of them are closely associated with inflammation. Then, wide-target metabolomics analysis showed that TR downregulated substances within the glycerophospholipid metabolic pathway, and modulated the PI3K-Akt pathway. The integrated findings from network pharmacology and metabolomics underscored the pivotal role of the PI3K-Akt signaling pathway and the attenuation of inflammatory responses. Finally, in vitro and in vivo experiments have shown that TR can inhibit inflammatory factors such as IL-6, TNF - α, and COX-2, downregulate targets such as PI3K and AKT on the PI3K-Akt signaling pathway, and thereby alleviate the inflammatory response of AP. Our study demonstrated that TR exerts an anti-AP effect through suppression of release of inflammatory factors and modulation of glycerophospholipid metabolism via suppressing the PI3K-Akt signaling pathway.

Elucidating hydroxysafflor yellow A's multi-target mechanisms against alcoholic liver disease through integrative pharmacology

BACKGROUND

Alcoholic liver disease (ALD) significantly contributes to global liver-related morbidity and mortality. Natural products play a crucial role in the prevention and treatment of ALD. Hydroxysafflor yellow A (HSYA), a unique and primary component of Safflower (Carthamus tinctorius l.), exhibits diverse pharmacological activities. However, the impact and mechanism of HSYA on ALD have not been fully elucidated.

PURPOSE

The purpose of this study was to employ an integrative pharmacology approach to assess the multi-targeted mechanism of HSYA against ALD.

METHODS

Network pharmacology and molecular docking techniques were used to analyze the potential therapeutic signaling pathways and targets of HSYA against ALD. An ALD model in zebrafish larvae was established. Larvae were pretreated with HSYA and then exposed to ethanol. Liver injury was measured by fluorescence expression analysis in the liver-specific transgenic zebrafish line Tg (fabp10a:DsRed) and liver tissue H&E staining. Liver steatosis was determined by whole-mount oil red O staining and TG level. Additionally, an ethanol-induced hepatocyte injury model was established in vitro to observe hepatocyte damage (cell viability, ALT level), lipid accumulation (oil red O staining, TC and TG), and oxidative stress (ROS, MDA, GPx and SOD) in HepG2 cells treated with or without HSYA. Finally, qRT-PCR combined with network pharmacology and molecular docking was employed to validate the effects of HSYA on targets.

RESULTS

HSYA exhibited a significant, dose-dependent improvement in ethanol-induced liver injury in zebrafish larvae and HepG2 cells. Network pharmacology analysis revealed that HSYA may exert pharmacological effects against ALD through 341 potential targets. These targets are involved in various signaling pathways, including lipid metabolism and atherosclerosis, PI3K-Akt signaling pathway, MAPK signaling pathway, and ALD itself. Molecular docking studies displayed that HSYA had a strong binding affinity toward the domains of IL1B, IL6, TNF, PPARA, PPARG, HMGCR and ADH5. qRT-PCR assays demonstrated that HSYA effectively reversed the ethanol-induced aberrant gene expression of SREBF1, FASN, ACACA, CPT1A, PPARA, IL1B, IL6, TNFα, ADH5, and ALDH2 in vivo and in vitro.

CONCLUSION

This study offers a comprehensive investigation into the anti-ALD mechanisms of HSYA using an integrative pharmacology approach. The potential targets of HSYA may be implicated in enhancing ethanol catabolism, reducing lipid accumulation, mitigating oxidative stress, and inhibiting inflammatory response.

Comprehensive Investigation of Homology and Heterogeneity Between Aurantii Fructus and Aurantii Fructus Immaturus Using Chemometrics Combined with Network Pharmacology

Aurantii Fructus (AF) and Aurantii Fructus Immaturus (AFI) are distinct herbs outlined by the Chinese Pharmacopoeia. They are sourced from the same plant but harvested at different times, resulting in differences in efficacy. It is important to avoid mixing them clinically and to distinguish between the two. Furthermore, dissimilar cultivation conditions may cause variability in the quality of herbs, so it is vital to differentiate drugs from dissimilar origins. In this study, two plants, AF and AFI from different provinces, were comparatively analyzed based on High Performance Liquid Chromatography (HPLC) fingerprints and classified using chemometric methods. The results indicate that the two medicines can be clearly distinguished. Also, AF and AFI grown in different locations can be distinguished. Ten chemical markers were screened, and their variations were determined, including eriocitrin, narirutin, naringin, meranzin hydrate, naringenin, hesperidin, nobiletin, tangeretin, neohesperidin, and poncirin. Subsequent network pharmacology correlated the screened chemical components with the biological network of the organism. The material basis of the difference in efficacy of the two homologous herbs was explored from the perspective of changes in chemical composition. This study provides a reference for formulating quality evaluation standards for AF and AFI and lays a foundation for the efficacy-related quality research of the two.

Exploration of potential antidiabetic and antioxidant components from the branches of Mitragyna diversifolia and possible mechanism

In this study, sixteen compounds were isolated from the branches of Mitragyna diversifolia, including twelve triterpenes (1-12), a phenolic compound (13), and three flavonoids (14-16). Among them, compounds 1-7, and 10-16 were reported for the first time from this plant. Compounds 7, 14, and 15 exhibited significant inhibitory activities against α-glucosidase, with IC50 values of 18.48 ± 2.74, 12.14 ± 1.58 and 35.77 ± 4.52 µM, respectively. Furthermore, the inhibitory kinetics of α-glucosidase revealed that all fractions, active compounds 7, 14, and 15 belong to the mix inhibition type. In molecular docking, the analysis showed that compounds 13, 14, 15, and 16 possessed superior binding capacities with α-glucosidase (-8.3, -9.6, -9.9, and -9.2 kcal/mol, respectively). The results of the glucose uptake experiment indicated that only compound 14 showed a significant promotion effect on the glucose uptake rate of 3T3-L1 adipocytes (P < 0.05). Meanwhile, compounds 13, 14, 15, and 16 possessed potent antioxidant abilities with DPPH, ABTS, and FRAP. In DNA and protein oxidative damage assays, compound 15 had a stronger effect than the positive control Vc. The network-based pharmacological analysis platform was used to predict the diabetes-related target proteins of active compounds 7, 13, 14, 15, and 16, and two candidate targets (ALB and PPARG) related to their therapeutic effects on diabetes were identified.

Study on the mechanism of Shenmai injection in the treatment of sepsis

Shenmai injection (SMI) is widely used in the clinical treatment of sepsis, but its mechanism is not yet clear. This study aimed to explore the molecular mechanism through network pharmacology, bioinformatics, and molecular docking technologies. The active ingredients and targets of SMI were screened through traditional Chinese medicine databases and the Swiss Target Prediction database, respectively. The disease genes were searched using GEO and GeneCards databases, and Venn mapping was used to screen potential therapeutic targets. The key targets were selected using Cytoscape 3.9.1 software. The BioGPS database was used to evaluate the expression of these targets in tissues/cells. The DAVID database is used for enrichment analysis. Molecular docking technology was used to evaluate the interaction between these targets and core active ingredients. 122 potential therapeutic targets and 28 key targets were identified. Forty-six potential therapeutic targets showed highly specific expression in 40 tissues/cells. The PI3K-AKT, RAP1, and MAPK signalling pathways are highly enriched. The molecular docking results showed good interactions. This study systematically analysed the mechanism of SMI in treating sepsis, involving multiple targets and pathways, possibly related to anti-inflammatory, anti-oxidative stress, and immune regulation, providing reference value for future basic research of sepsis.

Investigating Xiaochaihu Decoction's fever-relieving mechanism via network pharmacology, molecular docking, dynamics simulation, and experiments

Xiaochaihu Decoction（XCHD）is a classic prescription for the treatment of fever, but the mechanism is not clear. In this study, We elucidated the mechanism of action through network pharmacology and molecular docking. A rat fever model was established to verify the prediction results of network pharmacology. The analysis revealed that 120 intersection targets existed between XCHD and fever. The TP53, STAT3, RELA, MAPK1, AKT1, TNF and MAPK14 as potential core targets of XCHD in fever treatment. GO and KEGG pathway enrichment analyses indicated that XCHD may act through pathways such as the AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, IL-17 signaling pathway. Molecular docking results demonstrated that quercetin, kaempferol, β-sitosterol, stigmasterol and baicalein exhibited strong binding activity to key targets. Animal experiments showed that XCHD significantly reduced body temperature and levels of IL-1β, IL-6, TNF-α, NO, PGE2, and cAMP in rats with fever. Importantly, no significant difference was observed between the XCHD self-emulsifying nano phase plus suspension phase and XCHD group. XCHD exerts its therapeutic effects on fever through a multi-ingredient, multi-target, and multi-pathway approach.

Isoliquiritigenin alleviates SLC7A11-mediated efferocytosis inhibition to promote wounds healing in diabetes

The healing process of chronic wounds often progresses slowly and is fraught with challenges, imposing increasing economic burdens and physical suffering on patients. Managing persistent wound inflammation and stimulating angiogenesis are crucial elements in promoting wound healing. Plants have been playing a key role in traditional medicine, and their abundant bioactive components continually inspire the development and innovation of new drugs. Isoliquiritigenin (ISL), a flavonoid compound derived from licorice roots known as chalcone, has demonstrated multifaceted pharmacological potential. However, its effects on diabetic wounds and the detailed mechanisms remain to be investigated. Through in-depth exploration using network pharmacology, we successfully predicted potential therapeutic targets of ISL for ischemic diseases. The revealed mechanisms primarily focused on the critical pathway of efferocytosis. Subsequent in vivo experiments demonstrated that ISL significantly enhanced the efferocytosis of dendritic cells (DC), improving the functional behaviors of endothelial cells. Further research indicated that ISL promoted DC efferocytosis by regulating SLC7A11-mediated glycolysis. Notably, the overexpression of SLC7A11 diminished the positive effects of ISL, suggesting a potential antagonistic role of SLC7A11 in the regulatory process. In the wounds of diabetic mice, we observed that ISL accelerated DC efferocytosis and angiogenesis, resulting in faster wound closure and better tissue repair. In summary, this study not only demonstrates the broad potential of ISL in managing diabetic wounds but also delves deeply into its mechanisms, laying a solid theoretical foundation for future clinical applications.

A Study and In Vitro Evaluation of the Bioactive Compounds of Broad Bean Sprouts for the Treatment of Parkinson's Syndrome

Levodopa (LD) is the first discovered and the most promising and effective medication for Parkinson's disease (PD). As the first identified natural source of LD, Vicia faba L. (broad beans), especially its sprouts, has been confirmed to contain many other potential bioactive compounds that could also be therapeutic for PD. In this study, the bioactive components obtained from broad bean sprout extraction (BSE) that could be beneficial for PD treatment were screened, and the related mechanisms were explored. Solvent extraction combined with column chromatography was used to isolate bioactive fractions and monomer compounds, while UPLC-ESI-MS/MS, HRESI-MS and (1H, 13C) NMR were employed for compound identification. Network pharmacology techniques were applied to screen for potential mechanisms. A total of 52 compounds were identified in a 50% MeOH extract of broad bean sprouts. Moreover, twelve compounds were isolated and identified from ethyl acetate and n-butanol portions, including caffeic acid (1), trans-3-indoleacrylic acid (2), p-coumaric acid (3), protocatechualdehyde (4), isovitexin (5), isoquercetin (6), grosvenorine (7), kaempferol-3-O-rutinoside (8), isoschaftoside (9), narcissin (10), kaempferitrin (11) and trigonelline HCl (12). Compounds 2, 4, 7, 8 and 12 were isolated from Vicia faba L. for the first time. The potential mechanisms were determined by analyzing 557 drug targets, 2334 disease targets and 199 intersections between them using a protein-protein interaction (PPI) network, gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment. Further in vitro experiments confirmed that caffeic acid (compound 1) and p-coumaric acid (compound 3) have neuroprotective effects in 6-hydroxydopamine-treated SH-SY5Y cells and lipopolysaccharide-treated PC-12 cells through anti-inflammatory and antioxidant mechanisms. In conclusion, this study explored effective components in broad bean sprouts and performed in vitro evaluations.

Combining single-cell RNA sequencing and network pharmacology to explore the target of cangfu daotan decoction in the treatment of obese polycystic ovary syndrome from an immune perspective

Background

Polycystic ovary syndrome (PCOS) is a heterogeneous gynecological endocrine disorder linked to immunity. Cangfu Daotan Decoction (CFDT), a classic Chinese medicine prescription, is particularly effective in treating PCOS, specifically in patients with obesity; however, its specific mechanism remains unclear.

Methods

Part 1: Peripheral blood mononuclear cells were collected on egg retrieval day from obese and normal-weight patients with PCOS and healthy women undergoing in vitro fertilization (IVF)-embryo transfer. Next, scRNA-seq was performed to screen the key genes of bese patients with PCOS. Part 2: Active ingredients of CFDT and obesity-related PCOS targets were identified based on public databases, and the binding ability between the active ingredients and targets was analyzed. Part 3: This part was a monocentric, randomized controlled trial. The obese women with PCOS were randomized to CFDT (6 packets/day) or placebo, and the healthy women were included in the blank control group (43 cases per group). The clinical manifestations and laboratory outcomes among the three groups were compared.

Results

Based on the scRNA-seq data from Part 1, CYLD, ARPC3, CXCR4, RORA, JUN, FGL2, ZEB2, GNLY, FTL, SMAD3, IL7R, KIR2DL1, CTSD, BTG2, CCL5, HLA, RETN, CTSZ, and NCF2 were potential key genes associated with obese PCOS were identified. The proportions of T, B, and natural killer cells were higher in patients with PCOS compared to healthy women, with even higher proportions observed in obese patients with PCOS. Gene ontology and the Kyoto encyclopedia of genes and genomes analysis depicted that the differentially expressed genes were related to immune regulation pathways. Network pharmacology analysis identified that the key active components in CFDT were quercetin, carvacrol, β-sitosterol, cholesterol, and nobiletin, and TP53, AKT1, STAT3, JUN, SRC, etc. were the core targets. The core targets and their enrichment pathways overlapped with those in Part 1. Clinical trials in Part 3 found that CFDT reduced the dosage of gonadotropins use in patients with PCOS, increased the number of high-quality embryos, and improved the ongoing pregnancy rate.

Conclusion

CFDT can improve the immune microenvironment of patients to some extent, reduce their economic burden, and enhance IVF outcomes. The improvement in the immune microenvironment in obese patients with PCOS may be linked to targets such as JUN and AKT.

Identification of active ingredients in Naomaitai capsules using high-resolution mass spectrometry unite molecular network analysis and prediction of their action mechanisms

RATIONALE

Although Naomaitai capsule (NMC) is widely used in clinical practice and has a good curative effect for cerebral infarction, its material basis and mechanism of action remain unclear.

METHODS

In this study, ultra-high-performance liquid chromatography (UHPLC) coupled with quadrupole Orbitrap MS technology was used to analyse the in vivo and in vitro components of NMC, and the Global Natural Products Social Molecular Networking website was used to further analyse the components of NMC. Next, systems biology approaches were employed to investigate the mechanism of action of NMC. Finally, molecular docking technology was used to verify the network pharmacological results.

RESULTS

In total, 177 compounds were identified in vitro, including 65 terpenoids, 62 flavonoids, 25 organic acids and 11 quinones. 64 compounds were identified in the blood of mice, and the main active components included ginkgolide C, ginkgolide A, ligustilide, tanshinone IIB, olmelin, emodin and puerarin. The main targets in vivo included TP53, SRC, STAT3, PIK3CA and PIK3R1.

CONCLUSIONS

In conclusion, this study has revealed that NMC acts on multiple targets in the body through various active components, exerting synergistic effects in the treatment of CI. Its mechanism of action may involve inhibiting neuronal apoptosis, oxidative stress and inflammatory responses as well as reducing cerebral vascular permeability and promoting cerebral vascular regeneration.

Using broadly targeted plant metabolomics technology combined with network pharmacology to explore the mechanism of action of the Yishen Gushu formula in the treatment of postmenopausal osteoporosis in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Yishen Gushu Formula (YSGSF) is composed of Epimedium, prepared Rehmannia, Drynaria, Eucommia, Dodder, ginseng, Astragalus, Ligusticum wallichii, Aucklandia and Panax notoginseng. It can improve bone mineral density by regulating bone metabolism. However, the mechanism of YSGSF in the treatment of Postmenopausal osteoporosis (PMOP) remains unclear.

AIM OF THE STUDY

The compounds, targets, and molecular mechanisms of YSGSF in the treatment of PMOP were investigated using broad-spectrum target metabolomics from plants, combined with network pharmacology and animal studies, leading to a discussion on a novel approach to understanding YSGSF's action in PMOP treatment.

MATERIALS AND METHODS

Using ultra-performance liquid chromatography coupled with triple quadrupole-linear ion trap tandem mass spectrometry (UPLC-QTRAP-MS/MS) within a comprehensive targeted metabolomics framework, the active constituents of YSGSF were identified. This, alongside network pharmacology and molecular docking, facilitated the identification of critical signaling pathways and targets pertinent to YSGSF's therapeutic effect on PMOP. Subsequently, an animal model for PMOP was developed. Following intervention grouping, rats' weight changes were recorded; serum bone metabolic factors were assessed via ELISA; bone microstructure was examined using HE staining and Micro-CT; and key signaling pathway proteins and genes were analyzed through immunohistochemistry to validate YSGSF's potential mechanism in PMOP treatment.

RESULTS

A total of 84 main active components of YSGSF were identified. The key signaling pathways affected by YSGSF in the treatment of PMOP were the TNF and IL-7 signaling pathways, closely related to TNF-α, IL-1β, c-jun and other protein targets. The results of animal experiments showed that YSGSF could downregulate the expression of TNF-a, IL-1β and c-Jun proinflammatory factors by regulating the TNF and IL-7 signaling pathways and regulate the inflammatory response, osteocyte differentiation and apoptosis to control the development of PMOP.

CONCLUSION

YSGSF activates the TNF-α and IL-7 signaling pathways in PMOP rats, reducing TNF-α and IL-1β levels, the c-Jun inflammatory response, and osteocyte differentiation and apoptosis, thus playing a significant role in treating PMOP.

Inhibition of M2 tumor-associated macrophages polarization by modulating the Wnt/β-catenin pathway as a possible liver cancer therapy method

The problem of liver cancer is becoming increasingly important due to the epidemic of metabolic diseases and persistent high alcohol consumption. This determines great attention to the development and improvement of methods for early diagnosis and treatment of liver cancer. Huang et al presented a study in the World Journal of Gastroenterology, in which they showed that the use of the traditional Chinese medicine Calculus bovis (CB) can suppress tumor growth in mice by inhibiting M2 tumor-associated macrophages (TAM) through modulating the activity of the Wnt/β-catenin pathway. The interaction of CB components with the Wnt/β-catenin pathway, M2 TAM polarization, and tumor dynamics were studied using network pharmacology, transcriptomics, and molecular docking. It is now generally accepted that the polarization of TAM and the differentiation of the functions of M1 and M2 phagocytes are of great importance for the progression of neoplasms. It is assumed that M2 TAM promote proliferation and migration of tumor cells. Attempts to medicinally influence the Wnt/β-catenin pathway in order to modulate phagocyte polarization now belong to one of the most promising areas of immunotherapy of oncological diseases. Undoubtedly, the work of the Chinese authors deserves attention and further development.

Integrative analysis of the efficacy and pharmacological mechanism of Xuefu Zhuyu decoction in idiopathic pulmonary fibrosis via evidence-based medicine, bioinformatics, and experimental verification

Objective

We used evidence-based medicine, bioinformatics and experimental verification to comprehensively analyze the efficacy and pharmacological mechanism of Xuefu Zhuyu decoction (XFZYD) in the treatment of idiopathic pulmonary fibrosis (IPF).

Methods

Major databases were retrieved for randomized controlled trials (RCTs) of XFZYD treating IPF to perform meta-analysis. Active ingredients and target genes of XFZYD were identified from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). IPF-related differentially expressed genes (DEGs) were identified from the Gene Expression Omnibus (GEO) database. The RGUI software was utilized for Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The ingredient-target and protein-protein interaction (PPI) networks were achieved through Cytoscape software and the STRING database to identify the key compounds and target proteins. Molecular docking was performed using AutoDockTool and AutoDock Vina software. The effect between key compounds and target proteins was verified in animal experiments.

Results

Six RCTs were included for meta-analysis, which uncovered that the total effective rate of clinical efficacy was higher in the experimental group than control group. Then, 156 active ingredients and 254 target genes of XFZYD, and 1,566 IPF-related DEGs were identified. The intersection analysis identified 48 target genes correlating with 130 active ingredients of XFZYD treating IPF. GO functional enrichment, KEGG pathway enrichment, ingredient-target network and PPI network were achieved. Following the identification of key compounds and target proteins, we performed molecular docking. Ultimately, our research focused on the key compound quercetin for experimental validation to assess its interactions with two key target proteins, JUN and PTGS2.

Conclusion

The effectiveness of XFZYD on IPF has been substantiated through evidence-based medicine. The pharmacological mechanism of XFZYD for IPF treatment involves a complex interplay of various compounds and targets, with quercetin exerting pronounced impacts on JUN and PTGS2 proteins.