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Background: The resistance to endocrine therapy can lead to recurrence and metastasis of breast cancer (BC), affecting the survival period. Tiaogan Bushen Xiaoji (TGBSXJ) Formula, a traditional Chinese medicine (TCM) decoction, has been widely used in the treatment of estrogen receptor-positive (ER+) BC. However, the underlying mechanism of TGBSXJ Formula in ER+BC treatment has not been totally elucidated. Methods: Network pharmacology (NP) and RNA sequencing were used to predict the candidate ingredients and explore the potential targets of TGBSXJ Formula. Then, the results of NP and RNA sequencing were investigated by in vitro experiments. Results: Active ingredients of TGBSXJ Formula mainly included Mangiferin, Rutin, Anemarrhena asphodeloides saponin BII, Ganoderic acid A and Acacetin, etc. A protein-protein interaction (PPI) network was created based on the active ingredients of TGBSXJ Formula and target genes of ER+ BC, in which TGF-β, MMP2 and SMAD3 were defined as the hub genes. In vitro experiments showed that TGBSXJ Formula significantly inhibited the viability, colony ability and migration of ER+ BC cells, and significantly increased the sensitivity to TAM. Western blot analysis showed that TGBSXJ Formula significantly downregulated TGF-β, E-cadherin, MMP2, MMP9, N-cadherin, p-Smad2 and p-Smad3 in ER+ BC cells. Conclusion: TGBSXJ Formula increases the sensitivity of ER+ BC cells to TAM by inhibiting the TGF-β/Smad signaling pathway. [ABSTRACT FROM AUTHOR]

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The mechanism of MaiFuSheng (MFS) on inhibiting Nonalcoholic Fatty Liver Disease (NAFLD) were investigated based on the exploration of chemical compositions, the techniques of network pharmacology and molecular docking, and the validation using NAFLD mice model. The components of MFS were identified through UPLC-Zeno TOF-MS/MS. The Swiss Bioinformatics Research Platform were applied to obtain active components and potential targets of MFS. The DisGeNet and OMIM databases were used to screen disease targets of NAFLD. The intersection between disease targets and potential targets of MFS were obtained from Venn diagram, which were analyzed by constructing cross-target protein-protein interaction (PPI) network. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were conducted on Metascape database. The molecular docking about core targets and active components of MFS were carried out. Using high-fat diet (HFD)-induced C57BL/6J mice as NAFLD animal model to validate key targets. A total of 130 compounds were recognized, 54 active constituents and 176 potential targets of NAFLD were collected. The molecular docking experiments for the top 10 components with the targets are based on the degree value. We found docking models with the best binding energy for TNF-α with Quercetin, IL-17 with Asiatic acid, and IL-1β with Quercetin. We applied qPCR technique to detect above inflammation and lipid metabolism related indicators. Enrichment analysis demonstrated that MFS protects NAFLD via biological processes such as fatty acid transformation and positive regulation of lipid metabolism, as well as signaling pathways such as AGE-RAGE, HIF-1, and IL-17. Compared to the control groups, the model group's ALT, TG, and LDL-C indicators increased, whereas HDL-C indicators dropped (P<0.05) . MFS and Simvastatin treatment groups significantly reduced body weight, liver weight, and fat weight compared to the model groups (P<0.05). Higher doses resulted in significant reductions in serum levels and expression of TNF-α, IL-1β, and IL-17 (P<0.01). Compared to the control groups, the MFS treatment groups can minimize liver lipid accumulation by modulating the expression of lipid metabolism-related genes and improving hepatic fat breakdown. [ABSTRACT FROM AUTHOR]

Abnormal relaxation and contraction of intestinal smooth muscle can cause various intestinal diseases. Diarrhea is a common and important public health problem worldwide in epidemiology. Zingiber officinale Roscoe (fresh ginger) has been found to treat diarrhea, but the material basis and mechanism of action that inhibits intestinal peristalsis remain unclear. Metabolomics and serum pharmacology were used to identify differential metabolites, metabolic pathways, and pharmacodynamic substances, and were then combined with network pharmacology to explore the potential targets of ginger that inhibit intestinal peristalsis during diarrhea treatment, and the targets identified were verified using molecular docking and molecular dynamic simulation. We found that 25 active components of ginger (the six most relevant components), 35 potential key targets (three core targets), 40 differential metabolites (four key metabolites), and four major metabolic pathways were involved in the process by which ginger inhibits intestinal peristalsis during diarrhea treatment. This study reveals the complex mechanism of action and pharmacodynamic material basis of ginger in the inhibition of intestinal peristalsis, and this information helps in the development of new Chinese medicine to treat diarrhea and lays the foundation for the clinical application of ginger. [ABSTRACT FROM AUTHOR]

Bailing capsule (BLC), a drug that is clinically administered to modulate the autoimmune system, exhibits promising therapeutic potential in the treatment of thyroiditis. This study elucidates the chemical profile of BLC and its potential therapeutic mechanism in thyroiditis, leveraging network pharmacology and molecular docking techniques. Utilizing ultra‐high‐performance liquid chromatography coupled with linear trap‐Orbitrap mass spectrometry (UHPLC‐LTQ‐Orbitrap MS), 58 compounds were identified, the majority of which were nucleosides and amino acids. Utilizing the ultra‐high‐performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UHPLC QqQ MS/MS) strategy, 16 representative active components from six batches of BLCs were simultaneously determined. Network pharmacology analysis further revealed that the active components included 5′‐adenylate, guanosine, adenosine, cordycepin, inosine, 5′‐guanylic acid, and l‐lysine. Targets with higher connectivity included AKT1, MAPK3, RAC1, and PIK3CA. The signaling pathways primarily focused on thyroid hormone regulation and the Ras, PI3K/AKT, and MAPK pathways, all of which were intricately linked to inflammatory immunity and hormonal regulation. Molecular docking analysis corroborated the findings from network pharmacology, revealing that adenosine, guanosine, and cordycepin exhibited strong affinity toward AKT1, MAPK3, PIK3CA, and RAC1. Overall, this study successfully elucidated the material basis and preliminary mechanism underlying BLC's intervention in thyroiditis, thus laying a solid basis for further exploration of its in‐depth mechanisms. [ABSTRACT FROM AUTHOR]

Inflammation-induced osteoclast proliferation is a crucial contributor to impaired bone metabolism. Kurarinone (KR), a flavonoid extracted from the Radix Sophorae Flavescentis, exhibits notable anti-inflammatory properties. Nevertheless, the precise influence of KR on osteoclast formation remains unclear. This study's objective was to assess the impact of KR on osteoclast activity in vitro and unravel its underlying mechanism. Initially, a target network for KR-osteoclastogenesis-osteoporosis was constructed using network pharmacology. Subsequently, the intersecting targets were identified through the Venny platform and a PPI network was created using Cytoscape 3.9.1. Key targets within the network were identified employing topological algorithms. GO enrichment and KEGG pathway analysis were then performed on these targets to explore their specific functions and pathways. Additionally, molecular docking of potential core targets of KR was conducted, and the results were validated through cell experiments. A total of 83 target genes overlapped between KR and osteoclastogenesis-osteoporosis targets. Enrichment analysis revealed their role in inflammatory response, protein tyrosine kinase activity, osteoclast differentiation, and MAPK and NF-κB signaling pathways. PPI analysis and molecular docking demonstrate that key targets MAPK14 and MAPK8 exhibit more stable binding with KR compared to other proteins. In vitro experiments demonstrate that KR effectively inhibits osteoclast differentiation and bone resorption without cellular toxicity. It suppresses key osteoclast genes (NFATc1, c-Fos, TRAP, MMP9, Ctsk, Atp6v2), hinders IκB-α degradation, and inhibits ERK and JNK phosphorylation, while not affecting p38 phosphorylation. The results indicate that KR may inhibit osteoclast maturation and bone resorption by blocking NF-κB and MAPK signaling pathways, suggesting its potential as a natural therapeutic agent for osteoporosis. [ABSTRACT FROM AUTHOR]

The study aims to elucidate the pharmacological mechanisms of Sophorae Flavescentis Radix (SFR, Kushen) against ovarian cancer (OV) by employing an integrated approach that encompasses network pharmacology, molecular docking, and experimental validation. The effective components and potential targets of SFR were identified through screening the Traditional Chinese Medicine Systems Pharmacology (TSMSP) public database using network pharmacology. Core anti-OV targets were pinpointed using protein–protein interaction (PPI) networks. Datasets from The Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis (GEPIA) were used to investigate the mRNA and protein expressions of critical target genes in both normal and cancerous ovarian tissues, alongside their relationship to overall ovarian survival. Functional and pathway enrichment assessments of putative targets were carried out with Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The assessment of stable binding effects was conducted through molecular docking with quercetin, luteolin, and formononetin, and validated by anti-OV cell activity. The investigation identified 22 active SFR components yielding 152 potential targets following the intersection with known OV targets. Analysis of PPI network highlighted 13 crucial target genes, including tumor necrosis factor (TNF) and interleukin-1A (IL-1A). GO enrichment analysis covered 703 biological activities, 72 cellular components, and 144 chemical functions. The KEGG enrichment analysis suggested that anti-cancer effects of SFR are mediated by the TNF, interleukin-17 (IL-17), and AGE-RAGE signaling pathways. Molecular docking demonstrated that TNF and IL-1A were stable and strong binding to quercetin, luteolin, and formononetin, indicating that these stable structures significantly inhibited A2780 OV cell viability. This study demonstrated the ability of TNF and IL-1A combined with quercetin, luteolin, and formononetin to decrease the activity of OV cells, suggesting potential therapeutic effect against OV. [ABSTRACT FROM AUTHOR]

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

This study aimed to evaluate the pharmacological mechanism of Hedyotis diffusa Willd against CRC (colorectal cancer) using network pharmacological analysis combined with experimental validation. The active components and potential targets of Hedyotis diffusa Willd were screened from the tax compliance management program public database using network pharmacology. The core anti-CRC targets were screened using a protein-protein interaction (PPI) network. The mRNA and protein expression of core target genes in normal colon and CRC tissues and their relationship with overall CRC survival were evaluated using The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Functional and pathway enrichment analyses of the potential targets were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The first six core targets with stable binding were molecular-docked with the active components quercetin and β-sitosterol. Finally, the results of network pharmacology were verified using in vitro experiments. In total, 149 potential targets were identified by searching for seven types of active components and the intersection of all potential and CRC targets. PPI network analysis showed that ten target genes, including tumor protein p53 (TP53) and recombinant cyclin D1 (CCND1), were pivotal genes. GO enrichment analysis involved 2043 biological processes, 52 cellular components, and 191 molecular functions. KEGG enrichment analysis indicated that the anticancer effects of H. alba were mediated by tumor necrosis factor, interleukin-17, and nuclear factor-κB (NF-κB) signaling pathways. Validation of key targets showed that the validation results for most core genes were consistent with those in this study. Molecular docking revealed that the ten core target proteins could be well combined with quercetin and β-sitosterol and the structure remained stable after binding. The results of the in vitro experiment showed that β-sitosterol inhibited proliferation and induced apoptosis in SW620 cells. This study identified a potential target plant for CRC through network pharmacology and in vitro validation. [ABSTRACT FROM AUTHOR]

The purpose of this study is to investigate the ingredients and mechanisms through which Dalbergiae Odoriferae Lignum (DOL) reduces adriamycin-induced cardiotoxicity. DOL's ingredients and drug targets were acquired from Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), and adriamycin-induced cardiotoxicity disease targets were gathered from GeneCards and National Center for Biotechnology Information (NCBI). The therapeutic targets of DOL against adriamycin-induced cardiotoxicity were identified by intersecting drug and disease targets. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted using R. Subsequently, core targets were determined and used for molecular docking with DOL ingredients. In vitro and in vivo experiments validated DOL's primary ingredients against adriamycin-induced cardiotoxicity efficacy. Western blot and immunohistochemistry verified its impact on target protein. After intersecting 530 drug targets and 51 disease targets, 19 therapeutic targets for DOL alleviated adriamycin-induced cardiotoxicity were received. Molecular docking demonstrated that DOL primary ingredient formononetin had a robust binding affinity for nitric oxide synthase 3 (NOS3). Experimental results showed that formononetin effectively mitigated adriamycin-induced cardiotoxicity. Additionally, western blot and immunohistochemistry showed that formononetin improved NOS3 expression. The network pharmacology and experimentation suggest that the primary ingredient of DOL, formononetin, may target NOS3 to act as a therapeutic agent for adriamycin-induced cardiotoxicity. [ABSTRACT FROM AUTHOR]

Hyperlipidemia is a metabolic disorder characterized by abnormal lipid metabolism, resulting in lipid accumulation in the plasma. According to reports, medicinal and edible plants can reduce the risk of metabolic diseases such as hyperlipidemia. This study investigates the effects and mechanisms of Astragalus membranaceus extract (AME), Hippophae rhamnoides L. extract (HRE), and Taraxacum mongolicum Hand. Mazz extract (TME) on hyperlipidemia. Active compounds and potential gene targets of AME, HRE, and TME were screened using LC-MS and TCMSP databases, and hyperlipidemia targets were detected from the OMIM and DisGeNet databases. A drug-target pathway disease network was constructed through protein interactions, GO enrichment, and KEGG pathway analysis. Finally, the lipid-lowering effects of three extracts were validated through in vitro HepG2 cell and in vivo animal experiments. The results show that LC-MS and network pharmacology methodologies identified 41 compounds and 140 targets. KEGG analysis indicated that the PI3K-Akt and MAPK signaling pathways significantly treat hyperlipidemia with AHT. In vitro experiments have shown that AHT is composed of a ratio of AME:HRE:TME = 3:1:2. HepG2 cell and animal experiments revealed that AHT exhibits strong lipid-lowering and antioxidant properties, significantly regulating the levels of total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC). It is worth noting that AHT can effectively downregulate the protein expression levels of p-AKT/AKT and p-PI3K/PI3K and upregulate the protein expression levels of p-AMPK/AMPK and SIRT1, verifying the results predicted by network pharmacology. This study presents a novel approach to utilizing these natural plant extracts as safe and effective treatments for hyperlipidemia. [ABSTRACT FROM AUTHOR]

Catechins, a class of polyphenolic compounds found in tea, have attracted significant attention due to their numerous health benefits, particularly for the treatment and protection of hypertension. However, the potential targets and mechanisms of action of catechins in combating hypertension remain unclear. This study systematically investigates the anti-hypertensive mechanisms of tea catechins using network pharmacology, molecular docking, and molecular dynamics simulation techniques. The results indicate that 23 potential anti-hypertensive targets for eight catechin components were predicted through public databases. The analysis of protein–protein interaction (PPI) identified three key targets (MMP9, BCL2, and HIF1A). KEGG pathway and GO enrichment analyses revealed that these key targets play significant roles in regulating vascular smooth muscle contraction, promoting angiogenesis, and mediating vascular endothelial growth factor receptor signaling. The molecular docking results demonstrate that the key targets (MMP9, BCL2, and HIF1A) effectively bind with catechin components (CG, GCG, ECG, and EGCG) through hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations further confirmed the stability of the binding between catechins and the targets. This study systematically elucidates the potential mechanisms by which tea catechins treat anti-hypertension and provides a theoretical basis for the development and application of tea catechins as functional additives for the prevention of hypertension. [ABSTRACT FROM AUTHOR]

To explain the effect and mechanism of cordycepin (COR) in resisting acute kidney injury (AKI). Network pharmacology was employed to analyze the correlations between COR, AKI, and pyroptosis, as well as the action target of COR. A mouse model of AKI was established by ischemia reperfusion injury (IRI), and after treatment with COR, the renal function, tissue inflammatory cytokine levels, and pyroptosis‐related signals were detected in mice. In in‐vitro experiments, damage of renal macrophages was caused by the oxygen‐glucose deprivation model, and pyroptosis indicators and inflammatory cytokine levels were assayed after COR treatment. Network pharmacological analysis revealed that nuclear factor kappa‐B (NF‐κB) was the primary action target of COR and that COR could inhibit kidney injury and tissue inflammation during IRI by inhibiting NF‐κB‐mediated gasdermin D cleavage. When NF‐κB was inhibited, the effect of COR was weakened. COR in renal macrophages could inhibit pyroptosis and lower the levels of inflammatory cytokines, whose effect was associated with NF‐κB. Our study finds that COR can play an anti‐inflammatory role and inhibit the progression of AKI through the NF‐κB‐mediated pyroptosis, which represents its nephroprotective mechanism. [ABSTRACT FROM AUTHOR]

Necrotic enteritis (NE) is a critical disease affecting broiler health, with Clostridium perfringens as its primary pathogen. Polygonum hydropiper compound extract (PHCE), formulated based on traditional Chinese veterinary principles, contains primarily flavonoids with antibacterial, anti-inflammatory, and antioxidant properties. However, PHCE's efficacy against Clostridium perfringens-induced NE and its underlying mechanism remain unclear. This study employed network pharmacology and molecular docking to predict PHCE's potential mechanisms in treating NE, followed by determining its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against Clostridium perfringens (C. perf). Subsequently, the effects of various PHCE doses on intestinal damage, antioxidant capacity, and inflammatory factors in C. perf-infected broilers were assessed. Network pharmacology and molecular docking suggested that PHCE's therapeutic mechanism for NE involves the NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammasome signaling pathway, with flavonoids such as quercetin, kaempferol, and isorhamnetin as key active components. PHCE exhibited an MIC of 3.13 mg/mL and an MBC of 12.5 mg/mL against C. perf. High PHCE doses effectively reduced intestinal damage scores in both the jejunum and ileum, accompanied by attenuated intestinal pathological changes. Additionally, the high dose significantly increased superoxide dismutase (SOD) levels while decreasing malondialdehyde (MDA), hydrogen peroxide (H2O2), tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6) in the jejunum and ileum (p < 0.01 or p < 0.05). PHCE also modulated the expression of caspase-1, IL-1β, gasdermin D (GSDMD), and NLRP3 mRNA, key components of the NLRP3 inflammasome signaling pathway, in both intestinal segments. These findings collectively indicate that PHCE protects against C. perf-induced oxidative stress and inflammatory damage in NE. By enhancing antioxidant capacity, PHCE likely reduces oxidative stress and inflammatory responses, subsequently modulating NLRP3 inflammasome signaling pathway key factor expression. Overall, this research provides valuable insights into the protective mechanism of the herbal compound PHCE and its potential benefits for avian health. [ABSTRACT FROM AUTHOR]

The seeds of ginkgo biloba L (GB) have been widely used worldwide. This study investigated the bioefficacies of whole GB seed powder (WGP) retaining the full nutrients of ginkgo against aging, atherosclerosis, and fatigue. The experimental results indicated that WGP lowered brain monoamine oxidase and serum malondialdehyde levels, enhanced thymus/spleen indexes, and improved learning ability, and delayed aging in senescent mice. WGP regulated lipid levels and prevented atherosclerosis by reducing triglycerides, lowering low-density lipoprotein cholesterol, increasing high-density lipoprotein cholesterol, and decreasing the atherosclerosis index. WGP improved exercise performance by reducing blood lactate accumulation and extending exhaustive swimming and climbing times, improved energy storage by increasing muscle/liver glycogen levels, and relieved physical fatigue. Network pharmacology analysis revealed 270 potential targets of WGP that play roles in cellular pathways related to inflammation inhibition, metabolism regulation, and anti-cellular senescence, etc. Protein-protein interaction analysis identified 10 hub genes, including FOS, ESR1, MAPK8, and SP1 targets. Molecular docking and molecular dynamics simulations showed that the bioactive compounds of WGP bound well to the targets. This study suggests that WGP exerts prominent health-promoting effects through multiple components, targets, and pathways. [ABSTRACT FROM AUTHOR]

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

Background: The objective of this research was to investigate how the combination of semen coicis extract and PD-1 inhibitors can potentially work together to enhance the anti-tumor effects, with a focus on understanding the underlying mechanism. Methods: We obtained the active components and specific targets of semen coicis in the treatment of NSCLC from various databases, namely TCMSP, GeneCard, and OMIM. By utilizing the STRING database and Cytoscape software, we established a protein interaction network (PPI) for the active ingredient of semen coicis and the target genes related to NSCLC. To explore the potential pathways involved, we conducted gene ontology (GO) and biological pathway (KEGG) enrichment analyses, which were further supported by molecular docking technology. Additionally, we conducted cyto-inhibition experiments to verify the inhibitory effects of semen coicis alone or in combination with a PD-1 inhibitor on A549 cells, along with examining the associated pathways. Furthermore, we investigated the synergistic mechanism of these two drugs through cytokine release experiments and the PD-L1 expression study on A549 cells. Results: Semen coicis contains two main active components, Omaine and (S)-4-Nonanolide. Its primary targets include PIK3R1, PIK3CD, PIK3CA, AKT2, and mTOR. Molecular docking experiments confirmed that these ingredients and targets form stable bonds. In vitro experiments showed that semen coicis demonstrates inhibitory effects against A549 cells, and this effect was further enhanced when combined with PD-1 inhibitors. PCR and WB analysis confirmed that the inhibition of the PI3K-AKT-mTOR pathway may contribute to this effect. Additionally, semen coicis was observed to decrease the levels of IFN-γ, IL-6, and TNF-α, promoting the recovery of the human anti-tumor immune response. And semen coicis could inhibit the induced expression of PD‑L1 of A549 cells stimulated by IFN‑γ as well. Conclusion: Semen coicis not only has the ability to kill tumor cells directly but also alleviates the immunosuppression found in the tumor microenvironment. Additionally, it collaboratively enhances the effectiveness of PD-1 inhibitors against tumors by blocking the activation of PI3K-AKT-mTOR. [ABSTRACT FROM AUTHOR]

PurposeEvaluate for perturbed signaling pathways associated with subgroups of patients with low versus high levels of state anxiety. These pathways were compared to the pathways identified across eight network pharmacology studies of the anxiolytic effect(s) of a variety of compounds.MethodsAdult outpatients had a diagnosis of breast, gastrointestinal, gynecological, or lung cancer; had received chemotherapy within the preceding four weeks; and were scheduled to receive at least two additional cycles of chemotherapy. Latent profile analysis was used to identify subgroups of patients with distinct anxiety profiles based on Spielberger State Anxiety Inventory scores that were obtained six times over two cycles of chemotherapy. Blood samples were processed using RNA sequencing (i.e., RNA-seq sample, n = 244) and microarray (i.e., microarray sample; n = 256) technologies. Pathway perturbations were assessed using pathway impact analysis. Fisher's combined probability method was used to combine test results using a false discovery rate of 0.01.ResultsIn the RNA-seq sample, 62.3% and 37.7% of the patients were in the low- and high-anxiety classes, respectively. In the microarray sample, 61.3% and 38.7% were in the low and high-anxiety classes, respectively. Forty-one perturbed signaling pathways were identified. Eight of these pathways were common to those identified in the network pharmacology studies.ConclusionsFindings increase our knowledge of the molecular mechanisms that underlie anxiety in patients receiving chemotherapy. This study provides initial insights into how anxiety in patients with cancer may share common mechanisms with anxiety in patients with other clinical conditions.

Objective: Network pharmacology, molecular docking technology, and CCK8, wound healing, cell invasion, plate colony formation assay were used to explore the effect of apigenin in the treatment of gastric cancer. Methods: The ChEMBL, UniProt, and GeneCards databases and jvenn tools were used to obtain the potential anticancer targets of apigenin. Then, the PPI network analysis, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment analysis of key targets were used to investigate the mechanism, and Auto dock software was used for further molecular docking. Lastly, the inhibitory effect of apigenin on gastric cancer cells was verified through cell counting kit-8 (CCK8) experiments. Results: There were 52 potential targets of apigenin in the treatment of gastric cancer. GO analysis showed that apigenin might exert its anti-gastric cancer mechanism by regulating signal transduction, chemical synaptic transmission, and proteolysis. KEGG analysis showed that apigenin played a role by regulating the neural active ligand receptor interaction, nitrogen metabolism and other signaling pathways. The molecular docking results showed that the binding energy of ligand and receptor was: AChE|−9.1|>MAOA|−8.8|>CA2|−7.4|>DPP4|−7.3|>CA1|−7.2|=GRM5|−7.2|>ADA|−6.8|>CASP3|−5.8|, indicating that the ligand and receptor had good binding affinity. In vitro tests exhibited that apigenin possessed significant inhibitory effect on gastric cancer cell lines, which might be due to its ability to reducing the expression of MAOA, DPP4, AChE and increasing the expression of CA2. Conclusion: Apigenin has the effect of anti-gastric cancer, and the main targets involved in its effect are AChE, CA1, CA2, CASP3, ADA, MAOA, DPP4, GRM5, which shows the advantages of apigenin in multi-component, multi-target, and multi-channel, and provides a reference for the follow-up study of the anti-gastric cancer effect of apigenin.

Objective: It was elucidated the anti-inflammatory active components and their mechanisms of action in the fruits of Diospyros lotus. Methods: Ultra-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was used to qualitatively analyze the chemical constituents of Diospyros lotus fruits, and combined with network pharmacology to explore the potential anti-inflammatory active components and their mechanisms of action, and validated the results by molecular docking. Results: A total of 26 flavonoid compounds, including 10 myricetin derivatives, 7 quercetin derivatives, 4 kaempferol derivatives, 2 apigenin derivatives, and 3 other flavonoid compounds, were identified from extract of D. lotus fruits based on molecular ion peaks and mass spectrometry cleavage characteristics in negative ion mode, among which 12 compounds were reported for the first time in the fruits. Network pharmacological analysis showed that compounds myricetin 3-sambubioside, myricetin 3-(2G-rhamnosylrutinoside), morin, myricetin 3-rhamnosyl-(1->2)-rhamnoside, isorhamnetin-3-O-glucoside, myricetin, quercetin, naringenin, apigenin and kaempferol had potential anti-inflammatory activities and exerted anti-inflammatory effects mainly related to PI3K-Akt, EGFR tyrosine kinase inhibitor resistance and cancer signaling pathway. Molecular docking showed that the active components stably docked with the key targets, and the results were consistent with the network pharmacological predictions. Conclusion: Flavonoids in D. lotus extracts have potential anti-inflammatory effects and are useful as adjunctive preventive agents in inflammatory diseases.

Background Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths. The current prevention and treatment situation remains critical. It is of scientific significance to explore new therapeutic agents for HCC. Objective To analyze the mechanism of wogonin on HCC by network pharmacology and to verify it in vitro. Methods The drug targets of wogonin were searched in TCMSP database, and the disease targets of HCC were collected from TTD, GenCard, OMIM, DisGent databases. The collected drug targets and disease targets were intersected as potential targets for drug intervention in diseases. R software was used for enrichment analysis of intersection targets, STRING database and Cytoscape software were used to construct protein interaction network and screen core targets. The core targets were further analyzed in GIEPA database. Finally, the preliminary analysis results were verified by in vitro experiments, including cell activity determination using CCK-8 kit, cell proliferation determination using plate clone formation experiment, cell migration determination using scoring test, protein expression level determination using Western-blotting (WB) assay. Results The AMDE characteristics of wogonin were found to be in accordance with the rules for small molecule drug formation and the toxicity analysis showed no toxicity. A total of 135 wogonin targets and 8 238 HCC targets were collected, and 113 targets were intersected. Through the analysis of the core genes of TOP10 screened by the constructed protein interaction network, it was found that the mRNA levels of CDK1 and SRC in liver cancer tissues were higher than those in normal liver tissues (P

Abstract Background Pisum sativum (PS) is a universal legume plant utilized for both human and animal consumption, particularly its seeds, known as green peas. The processing of PS in food industries and households produces a significant amount of waste that needs to be valorized. Methods In this study, the metabolite profiles of the 70% ethanolic extracts of PS wastes, namely peels (PSP) and a combination of leaves and stems (PSLS), were investigated by liquid chromatography-electrospray ionization-quadrupole time-of-flight tandem mass spectrometry (LC-ESI-QTOF-MS/MS) followed by molecular networking. Results Different classes of metabolites were identified, being flavonoids and their derivatives, along with phenolic acids, the most abundant categories. Additionally, a comprehensive network pharmacology strategy was applied to elucidate potentially active metabolites, key targets, and the pathways involved in cytotoxic activity against breast cancer. This cytotoxic activity was investigated in MCF-7 and MCF-10a cell lines. Results revealed that PSLS extract exhibited a potent cytotoxic activity with a good selectivity index (IC50 = 17.67 and selectivity index of 3.51), compared to the reference drug doxorubicin (IC50 = 2.69 µg/mL and selectivity index of 5.28). Whereas PSP extract appeared to be less potent and selective (IC50 = 32.92 µg/mL and selectivity index of 1.62). A similar performance was also observed for several polyphenolics isolated from the PSLS extract, including methyl cis p-coumarate, trans p-coumaric acid, and liquiritigenin/ 7-methyl liquiritigenin mixture. Methyl cis p-coumarate showed the most potent cytotoxic activity against MCF-7 cell line and the highest selectivity (IC50 = 1.18 µg/mL (6.91 µM) and selectivity index of 27.42). The network pharmacology study revealed that the isolated compounds could interact with several breast cancer-associated protein targets including carbonic anhydrases 1, 2, 4, 9, and 12, as well as aldo-keto reductase family 1 member B1, adenosine A3 receptor, protein tyrosine phosphatase non-receptor type 1, and estrogen receptor 2. Conclusion The uncovered therapeutic potential of PSLS and its metabolite constituents pave the way for an efficient and mindful PS waste valorization, calling for further in-vitro and in-vivo research. Graphical Abstract

Abstract G Protein-Coupled Receptors (GPCRs) are integral membrane proteins that have gained considerable attention as drug targets, particularly in cancer treatment. In this study, we explored the capacity of bioactive compounds derived from Gnetum gnemon (GG) for the development of of pharmaceuticals targeting GPCRs within the context of cancer therapy. Integrated approach combined network pharmacology and molecular docking to identify and validate the underlying pharmacological mechanisms. We retrieved targets for GG-derived compounds and GPCRs-related cancer from databases. Subsequently, we established a protein-protein interaction (PPI) network by mapping the shared targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to predict the mechanism of action of these targets. Molecular docking was conducted to validate our findings. We identified a total of 265 targets associated with GG-derived bioactive compounds for the treatment of GPCRs-related cancer. Functional enrichment analysis revealed the promising therapeutic effects of these targets on GPCRs-related cancer pathways. The PPI network analysis identified hub targets, including MAPK3, SRC, EGFR, STAT3, ESR1, MTOR, CCND1, and PPARG, which demonstrate as treatment targets for GPCRs-related cancer using GG-derived compounds. Additionally, molecular docking experiments demonstrated the strong binding affinity of gnetin A, gnetin C, (-)-viniferin, and resveratrol dimer, thus inhibiting MAPK3, SRC, EGFR, and MTOR. Survival analysis established the clinical prognostic relevance of identified hub genes in cancer. This study presents a novel approach for comprehending the therapeutic mechanisms of GG-derived active compounds and thereby paving the way for their prospective clinical applications in the field of cancer treatment.

Hongling Du,1– 3 Shunjie Zhang,1 Kezhu Yuan,4 Zhirui Yang,5 Mingquan Wu4 1Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China; 2Department of Pharmacy, Sichuan Public Health Clinical Center, Chengdu, Sichuan, People’s Republic of China; 3State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy School, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, People’s Republic of China; 4Department of Pharmacy, Sichuan Orthopedic Hospital, Chengdu, Sichuan, People’s Republic of China; 5Department of Nuclear Medicine, Chengdu Second People’s Hospital, Chengdu, Sichuan, People’s Republic of ChinaCorrespondence: Mingquan Wu, Department of Pharmacy, Sichuan Orthopedic Hospital, Chengdu, Sichuan, People’s Republic of China, Email 18782976939@163.comBackground: Rehmanniae Radix (RR) has received attention for its antithrombotic effect. However, few studies have independently explored the bioactive components responsible for its antithrombotic bioactivity and the potential mechanism. We aimed to reveal the antithrombotic mechanisms of RR by using metabolomics integrated with network pharmacology.Methods: A thrombosis model was established by intraperitoneal injection of type I carrageenan in rats, and antithrombotic function was evaluated at different doses of RR. Metabolomics was used to identify the differential metabolites in the serum. Network pharmacology was then applied to identify the potential targets for the antithrombotic activity of the RR. An integrated network of metabolomics and network pharmacology was constructed using Cytoscape. Finally, key targets were verified using molecular docking.Results: RR at 5.4 g/kg significantly alleviated the thrombosis. Thirteen potentially significant metabolites were involved in the therapeutic effects of RR against thrombosis, most of which were regulated for recovery after RR treatment. An integrated analysis of metabolomics and network pharmacology showed that the antithrombosis effect of RR was closely associated with the regulation of PLA2G2A, PTGS1, ALOX5, and CYP2C9. Molecular docking showed high affinity between the key targets and components of RR. We speculated that the components of RR, such as catalpol, ferulic acid methyl ester, and methyl 4-hydroxycinnamate, might act on key proteins, including PLA2G2A, PTGS1, and ALOX5, to exert antithrombosis effects.Conclusion: This study confirmed the antithrombotic effect of high-dose RR, revealed the antithrombotic mechanism and potential material basis, and laid the foundation for the antithrombotic clinical application of RR. Furthermore, it provides a successful case reference for screening natural herbal components and exploring their potential pharmacological mechanisms.Keywords: Rehmanniae radix, antithrombotic effects, metabolomics, network pharmacology

Quan-Ai Zhang,1,&ast; Wang-Sheng Luo,2,&ast; Ji Li,3,&ast; Qi-Wen Zhang,1 Qin Guo,1 Jian Chen,3– 5 Zhi-Qiang Liang3 1The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China; 2Department of Cardiology, the First Affiliated Hospital of University of South China, Hengyang, People’s Republic of China; 3Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China; 4Anhui Province Rural Revitalization Collaborative Technical Service Center, Huangshan University, Huangshan, People’s Republic of China; 5Department of Public Health, International College, Krirk University, Bangkok, Thailand&ast;These authors contributed equally to this workCorrespondence: Jian Chen; Zhi-Qiang Liang, Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, People’s Republic of China, Email alexandercj@126.com; liangzhiqiang006@163.comIntroduction: Acupuncture may help treat diabetes mellitus (DM), diabetic peripheral neuropathy (DPN), and adjunct therapy for cancer, but the biological mechanisms and immune-related genes involved are unclear; this study aims to clarify these aspects.Methods: Comprehensive gene expression analysis revealed differentially expressed genes (DEGs) among DM, DPN, and control samples. Key genes from WGCNA were intersected with DEGs and acupuncture targets. Inflammatory responses, immune processes, signaling pathways, immune cell infiltration, and microRNA–gene interactions were studied. Hub immune-related genes’ dysregulation was analyzed for copy number variation and gene methylation. A pan-cancer nomogram model was created to predict survival based on various factors, linking hub genes to cancer properties.Results: Our analysis found 3,217 and 2,191 DEGs in DM/control and DPN/DM comparisons, respectively, and identified 1,830 potential acupuncture targets. We pinpointed 21 key genes in DM and 43 in DPN, involved in inflammatory responses, immune processes, CAMKK2, and cAMP signaling pathways. Distinct immune cell infiltration patterns, including M0 and M2 macrophages, neutrophils, and follicular helper T cells, were noted. Further analysis revealed microRNAs and TF genes interacting with immune hub genes in both conditions. Dysregulation of eight hub immune-related genes was linked to copy number variation and gene methylation, correlating with cancer prognosis. Co-occurrence of single nucleotide variations and oncogenic mutations was observed in these genes. The pan-cancer nomogram model showed strong prognostic capabilities, and a significant association was found between the eight genes and cancer properties like angiogenesis, EMT, and cell cycle progression.Discussion: Our findings underscore the pivotal roles of MAPK3, IL1RN, SOD2, CTSD, ESR1, SLC1A1, NPY, and CCR2 in the immune response mediated by acupuncture in the context of DM, DPN, and adjunct therapy for cancer. Keywords: acupuncture, text mining, network pharmacology, immune, diabetic peripheral neuropathy, cancer

Min-Dong Du,1,2,&ast; Kai-Yi He,3,&ast; Si-Qi Fan,3 Jin-Yi Li,3 Jin-Fu Liu,3 Zi-Qiang Lei,3 Gang Qin3 1Department of Osteoarthrosis, Xing-An Jieshou Orthopedics Hospital, Guilin, People’s Republic of China; 2Department of Orthopaedic Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China; 3Department of Osteoarthrosis, The First Affiliated Hospital of Guangxi Traditional Chinese Medical University, Nanning, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Gang Qin, Department of Osteoarthrosis, The First Affiliated Hospital of Guangxi Traditional Chinese Medical University, 89-9 Dongge Road, Nanning, Guangxi, 530023, People’s Republic of China, Tel +86-771-5361264, Email qqvvcbgq6016@163.comBackground: Cyperus rotundus (CR) is widely used in traditional Chinese medicine to prevent and treat a variety of diseases. However, its functions and mechanism of action in osteoarthritis (OA) has not been elucidated. Here, a comprehensive strategy combining network pharmacology, molecular docking, molecular dynamics simulation and in vitro experiments was used to address this issue.Methods: The bioactive ingredients of CR were screened in TCMSP database, and the potential targets of these ingredients were obtained through Swiss Target Prediction database. Genes in OA pathogenesis were collected through GeneCards, OMIM and DisGeNET databases. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed using DAVID database. STRING database and Cytoscape 3.10 software were used to construct “component-target-pathway” network, and predict the core targets affected by CR. The binding affinity between bioactive components and the core targets was evaluated by molecular docking and molecular dynamics simulation. The therapeutic activity of kaempferol on chondrocytes in inflammatory conditions was verified by in vitro experiments.Results: Fifteen CR bioactive ingredients were obtained, targeting 192 OA-related genes. A series of biological processes, cell components, molecular functions and pathways were predicted to be modulated by CR components. The core targets of CR in OA treatment were AKT serine/threonine kinase 1 (AKT1), interleukin 1 beta (IL1B), SRC proto-oncogene, non-receptor tyrosine kinase (SRC), BCL2 apoptosis regulator (BCL2), signal transducer and activator of transcription 3 (STAT3), epidermal growth factor receptor (EGFR), hypoxia-inducible factor 1 subunit alpha (HIF1A), matrix metallopeptidase 9 (MMP9), estrogen receptor 1 (ESR1) and PPARG orthologs from vertebrates (PPARG), and the main bioactive ingredients of CR showed good binding affinity with these targets. In addition, kaempferol, one of the CR bioactive components, weakens the effects of IL-1β on the viability, apoptosis and inflammation of chondrocytes.Conclusion: Theoretically, CR has great potential to ameliorate the symptoms and progression of OA, via multiple components, multiple targets, and multiple downstream pathways. Keywords: osteoarthritis, Cyperus rotundus, network pharmacology, molecular docking

Abstract Hypertension is the most prevalent cardiovascular disease, affecting one-third of adults. All antihypertensive drugs have potential side effects. Gut metabolites influence hypertension. The objective of this study was to identify antihypertensive gut metabolites through network pharmacology and molecular docking techniques and to validate their antihypertensive mechanisms via in vitro experiments. A total of 10 core antihypertensive targets and 18 gut metabolites that act on hypertension were identified. Four groups of protein metabolites, namely, CXCL8-baicalein, CXCL8-baicalin, CYP1A1-urolithin A, and PTGS2-equol, which have binding energies of − 7.7, − 8.5, − 7.2, and − 8.8 kcal-mol−1, respectively, were found to have relatively high affinities. Based on its drug-likeness properties in silico and toxicological properties, equol was identified as a potential antihypertensive metabolite. On the basis of the results of network pharmacology and molecular docking, equol may exert antihypertensive effects by regulating the IL-17 signaling pathway and PTGS2. A phenylephrine-induced H9c2 cell model was subsequently utilized to verify that equol inhibits cell hypertrophy (P

Abstract Patients with gastric cancer (GC) are more susceptible to coronavirus disease 2019 (COVID-19), which further worsens their already challenging prognosis. However, there are no effective treatment options for these patients. Lentinan is a potent bioactive component with antiviral and antitumor effects. We hypothesized that lentinan might exert powerful pharmacological effects in patients with GC and COVID-19. In this study, a prognostic model of patients with GC/COVID-19 was constructed and used to apply a network pharmacology approach to reveal biological functions, drug targets, and molecular mechanisms of the action of lentinan against GC/COVID-19. Clinical analysis revealed key prognostic genes in patients with GC/COVID-19. The results of network pharmacology analysis suggested that the therapeutic effect of lentinan on GC/COVID-19 mainly involves the modulation of several neutrophil-related biological processes, as well as the nucleotide-binding and oligomerization domain-like receptor and interleukin-17 signaling pathways. In addition, C-X-C motif chemokine ligand 8, vascular endothelial growth factor A, ribonuclease 3, and F2 were identified as key genes of lentinan against GC/COVID-19. Key prognostic genes were identified in patients with GC/COVID-19 through the construction of a prognostic model. Pharmacological functions and signaling pathways of lentinan against GC/COVID-19 were revealed. These included the regulation of neutrophils and NOD-like receptor signaling pathways. The findings provide the first published evidence of the potential value of lentinan as a complementary therapy for GC/COVID-19.

Jiayue Zhou,1,2 Yingxiang Wu,1,2 Zhiyan Lu,1,2 Yan Wang1,2 1Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, Yunnan Province, 671000, People’s Republic of China; 2National-Local Joint Engineering Research Center of Entomoceutics, Dali University, Dali, Yunnan Province, 671000, People’s Republic of ChinaCorrespondence: Yan Wang, Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Dali University, Dali, Yunnan Province, 671000, People’s Republic of China, Tel +86 0872-2257401, Email jessica9428@sina.comPurpose: Rodgersia sambucifolia Hemsl (also known as Yantuo) is a traditional Chinese medicine commonly utilized as a medicinal herb with its rhizomes, mainly used to regulate the immune function of the human body. However, relatively few studies have investigated its active components and potential mechanisms of action in vivo.Methods: First, the chemical composition in vitro was identified and analyzed using the UPLC-Q-TOF MS/MS technique. Cyclophosphamide (CTX) was then administered intraperitoneally to rats to establish an immunosuppression model. Physiological and biochemical parameters, organ indices, and histopathological findings were evaluated for efficacy. Subsequently, potential biomarkers in rat serum were identified using multivariate statistical analysis and enriched and topologized using online platforms such as MetaboAnalyst and KEGG to reveal the critical metabolic pathways and their roles in the immunomodulatory network. Finally, the integrated analysis of components in vivo and in vitro, along with metabolic pathways, was performed using network pharmacology and molecular docking technology to elucidate the mechanisms of their roles in organismal immunity.Results: A total of 28 chemical components in vitro were identified, while pharmacodynamic experiments confirmed the immunomodulatory effects of Yantuo, especially in the high-dose administration group. Metabolomics analysis showed that 37 potential immune-related biomarkers were identified in positive and negative ion modes, involving 16 metabolic pathways such as arginine biosynthesis, pyrimidine metabolism, and riboflavin metabolism. The results of network pharmacology and molecular docking indicated that Yantuo may affect 7-O-galloyl-catechin, Cynaroside, Quercetin-7-O-beta-D-glucopyranoside, and 1.6-bis-O-galloyl-beta-D-glucose through interactions with the immune system, with significant pathways of action including galactose metabolism, glycolysis/gluconeogenesis, pyrimidine metabolism, and riboflavin metabolism.Conclusion: In our experiments, we confirmed the organismal modulatory effect of Yantuo on immunocompromised rats, clarified the key components, target proteins, and pathways of its possible action, and provided possibilities for follow-up studies. Keywords: immunosuppression, Yantuo, metabolomics, network pharmacology, molecular docking

Wenyi Li,1,2 Zhenguo Liu,1 Min Song,1 Zhenpeng Shi,1 Jihang Zhang,3 Junyu Zhou,1 Yidan Liu,1 Yun Qiao,4 Deshan Liu4 1First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China; 2Research Center for Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, People’s Republic of China; 3Traditional Chinese Medicine College, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China; 4Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, People’s Republic of ChinaCorrespondence: Deshan Liu, Department of Traditional Chinese Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People’s Republic of China, Tel +86 18560087381, Email liudeshan@sdu.edu.cnContext: Diabetic nephropathy (DN) and cognitive dysfunction (CD) are common complications of diabetes. Yi-Qi-Bu-Shen Recipe (YQBS) can effectively reduce blood glucose, improve insulin resistance, and delay the progression of diabetic complications. The underlying mechanisms of its effects need to be further studied.Objective: This study elucidates the mechanism of YQBS in DN with CD through network pharmacology and experimental validation.Materials and Methods: Protein-protein interaction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Male Sprague-Dawley (SD) rats were divided into 6 groups: model, YQBS (2, 4, 8 g/kg), positive control (metformin, 200 mg/kg), and control; the DN model was established by high sugar and high fat diet combined with intraperitoneal streptozotocin injection. After the DN model was established, the rats were gavaged for 10 weeks. Serum, kidneys, and hippocampus tissues were collected to measure the expression levels of TLR4, NF-κB, TNF-α, and IL-6.Results: The network pharmacology analysis showed that quercetin and kaempferol were the main active components of YQBS. TNF and IL-6 were the key targets, and TLR4/NF-κB pathway was crucial to YQBS in treating DN complicated with CD. Experimental validation showed that the intervention of YQBS can reduce TNF-α and IL-6 in serum, and also significantly decreases the protein expression of TLR4 and NF-κB.Conclusion: YQBS exerts anti-inflammatory effects on DN with CD through TLR4/NF-κB pathway. This study provides a biological basis for the scientific usage of YQBS in inflammation diseases and supplies experimental evidence for future traditional Chinese medicine development.Keywords: Yiqi Bushen Recipe, diabetes nephropathy, cognitive dysfunction, network pharmacology, inflammation

Objective: To provide the mechanism-based pharmacotherapy of the Huatan Qushi formula (HTQS formula), for the health management and treatment of non-alcoholic fatty liver disease (NAFLD). Methods: A rat model of NAFLD was employed to examine the efficacy and safety of the HTQS formula. In vivo active components and potential mechanisms of the HTQS formula were identified using UPLC‒MS/MS combined with network pharmacology. The influence of the HTQS formula on the dominating proteins in PI3K/Akt pathway was validated in vivo using western blot. Finally, 16S rRNA sequencing of the gut microbiome was conducted followed by targeted metabolomics detecting fecal short-chain fatty acids (SCFAs) and bile acids to determine the impact of the HTQS formula on gut microbiota. Results: The HTQS formula reduced weight gain and hepatic steatosis in NAFLD rats and decreased serum total cholesterol (TC), triglycerides, blood glucose, and insulin resistance (IR) without causing liver or kidney injury. We detected 28 components using UPLC‒MS/MS and identified 439 shared targets between NAFLD and the HTQS formula. Primarily, we focused on the PI3K/Akt signaling pathway based on protein‒protein interaction network analysis. We validated that the HTQS formula inhibited liver steatosis and inflammation by increasing the phosphorylation levels of PI3K, AKT, P27, GSK3β in the PI3K/Akt signaling pathway. 16S rRNA sequencing revealed that the HTQS formula reduced the abundance of the genus Family_XIII_AD3011_group, which was positively correlated with IR and taurodeoxycholic acid. In addition, Lachnospiraceae_UCG_010 inversely correlated with TC and five bile acids, which could be essential to the therapeutic effect of the HTQS formula against NAFLD. Conclusions: The HTQS formula proved to be an effective pharmacotherapy for NAFLD without causing liver or kidney injury. Multiple potent components of the HTQS formula could alleviate liver steatosis and lipid metabolism disorder by modulating the PI3K/Akt signaling pathway and restoring gut microbiota composition.

Yule Wang,&ast; Bei Li,&ast; Yingjuan Zhang,&ast; Ruiling Lu, Qianzhuo Wang, Yue Gao Zhejiang Key Laboratory of Traditional Chinese Medicine for the Prevention and Treatment of Senile Chronic Diseases, Department of Geriatrics, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Yue Gao, Zhejiang Key Laboratory of Traditional Chinese Medicine for the Prevention and Treatment of Senile Chronic Diseases, Department of Geriatrics, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, 261 huansha Road, Shangcheng District, Hangzhou, 310006, People’s Republic of China, Email gaoyue@hospital.westlake.edu.cnBackground: Acute lung injury (ALI) is a life-threatening clinical syndrome with high mortality. Currently, the safe and effective therapies for ALI patients are still limited. Qingfei Huoxue decoction (QFHXD) is a hospital agreement prescription for treating pulmonary diseases and displays a remarkable efficacy. However, the pharmacological effect of QFHXD on preventing lipopolysaccharide (LPS)-induced ALI has yet to be reported, let alone questions of potential molecular mechanisms and anti-ALI active substances.Methods: To answer the above-mentioned questions, histopathological observation and kit detection were performed to estimate the protective effect of QFHXD pretreatment against LPS-induced ALI. Based on comprehensive chemical profiling of QFHXD, a network pharmacology strategy and experimental validation were integrated to elucidate the underlying functional mechanisms. The potential anti-ALI active components were identified by molecular docking. The anti-ALI activity of narirutin and its anti-inflammatory mechanism were further validated using animal and molecular experiments.Results: Pretreatment with different doses of QFHXD effectively mitigated histopathological lesions and systemic inflammation caused by LPS stimulation. A detailed analysis of established compound-target-disease network revealed the strong correlation between anti-ALI action of QFHXD and inflammatory mechanisms. Compared with the model group, QFHXD intervention markedly restrained the abnormally increased transcription and protein levels of pro-inflammatory factors (TLR4, NF-κB, IL-6, IL-1β, and TNF-α) in lung tissues of ALI mice. The results of molecular docking highlighted the anti-ALI potential of narirutin targeting to TLR4 and NF-κB p65. In addition to the protective effect of narirutin on suppressing LPS-induced pathological changes, we found that narirutin pretreatment effectively normalized the disordered protein levels of above pro-inflammatory factors of ALI mice.Conclusion: These interesting findings indicate the beneficial effects of QFHXD and its active component narirutin against ALI partly via regulating TLR4/NF-κB mediated inflammation. This work contributes to the development of novel medications for ALI patients. Keywords: Qingfei Huoxue decoction, narirutin, LPS-induced acute lung injury, network pharmacology, TLR4/NF-κB pathway, inflammatory response

Objective: To investigate the differences in chemical composition between ethanol extracts from Lonicera japonica flos (EELF) and L. japonica leaves (EELL) and their potential anti-aging components and mechanisms. Methods: The chemical compositions of EELF and EELL were determined by ultra-high performance liquid chromatography-quadrupole electrostatic field orbitrap mass spectrometry (UPLC-QE-orbitrap-MS). The effect of feeding Escherichia coli OP50 culture containing different concentrations of EELF or EELL on the life span, mobility, reproductive capacity and oxidant stress resistance of Caenorhabditis elegans was investigated. The potential anti-aging mechanism of EELF and EELL was explored through network pharmacology. Results: A total of 122 compounds were identified in EELF and EELL, including 35 organic acids, 27 flavonoids, 37 iridoid compounds and 23 other compounds. The chemical compositions of EELF and EELL were roughly the same, and the contents of chlorogenic acid and total phenolic acid were also roughly same. The contents of total flavonoids, isochlorogenic acid C and luteolin in EELL were significantly higher than those in EELF, while the content of isochlorogenic acid A was significantly lower than that in EELF. EELF and EELL at all concentrations improved oxidative and thermal stress resistance, prolonged the life span, enhanced the motility and reproductive capacity of the nematode, and decreased the levels of reactive oxygen species (ROS) and lipofuscin. A total of 16 potential bioactive components from EELF and EELL and 59 potential anti-aging targets for them were identified, and the core targets were signal transducer and activator of transcription 3 (STAT3), serine/threonine kinase 1 (AKT1), epidermal growth factor receptor (EGFR), steroid receptor coactivator (SRC), cysteinyl aspartate specific proteinase 3 (CASP3), and tumor necrosis factor (TNF). The anti-aging effect could be exerted by suppressing cancer, reducing lipid and alleviating atherosclerosis through the regulation of the phosphatidyl-inositol 3-kinase/serine-threonine kinase (PI3K/AKT) signaling pathway. Conclusion: EELF and EELL have similar chemical compositions, exert similar anti-aging effects, and have multi-pathway and multi-target characteristics, which provides a reference for their deep development and utilization.

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

Jiali Wang,1,2 Yiqing Liu,3 Chengkui Xiu,1 Xue Wang,1 Yinan Liu,1 Yanhong Hu,1 Jing Yang,1 Yan Lei1 1Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China; 2Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, People’s Republic of China; 3National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of ChinaCorrespondence: Yan Lei; Jing Yang, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, People’s Republic of China, Tel +13651217893 ; +15901070286, Email 13651217893@163.com; yangjingdr@163.comObjective: To explore the mechanism of the traditional Chinese medicine (TCM), Zhizhu granule (ZZG), in treating metabolic syndrome (MS) based on network pharmacology and pharmacodynamic experiment.Materials and Methods: Network pharmacology combined with a pharmacodynamic experiment was used to elucidate the therapeutic mechanism of ZZG in MS. Serum samples were collected from rats with MS, induced by a high-sugar-fat-salt diet (HSFSD) combined with streptozotocin (STZ), to measure the levels of biochemical markers. The glucose (GLU), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), systolic blood pressure (SBP), and diastolic blood pressure (DBP) were detected. The liver tissue of rats was used for histological examination and Western blot analysis.Results: Network pharmacology analysis generated 69 drug-disease common targets and 10 hub genes closely related to ZZG against MS. KEGG pathway analysis revealed that the PI3K/AKT signaling pathway was the most potential pathway, which took part in the therapeutic mechanisms. In the animal experiments section, the therapeutic effect of ZZG on MS and the therapeutic pathway of ZZG on MS were verified. ZZG could significantly decrease the body weight, TC, TG, LDL-C and GLU levels in MS rats (all p< 0.01), alleviate hepatocyte steatosis and decrease liver lipid droplet deposition. Western blot analysis indicated that compared with the model group, the expression levels of PI3K, AKT, and IRS-1 protein were significantly increased (all p< 0.05), and the FOXO-1 was significantly decreased (all p< 0.05) in the ZZG group.Conclusion: ZZG can improve glucose-lipid metabolism disorder in rats with metabolic syndrome. The reported results provide experimental evidence for ZZG in the treatment of MS.Keywords: metabolic syndrome, network pharmacology, Zhizhu granule, pharmacodynamic experiment, PI3K/AKT pathway

Abstract Breast Cancer (BC) is the most common cause of cancer-associated deaths in females worldwide. Despite advancements in BC treatment driven by extensive characterization of its molecular hallmarks, challenges such as drug resistance, tumor relapse, and metastasis persist. Therefore, there is an urgent need for alternative treatment approaches with multi-modal efficacy to overcome these hurdles. In this context, natural bioactives are increasingly recognized for their pivotal role as anti-cancer compounds. This study focuses on predicting molecular targets for key herbal phytoconstituents—gallic acid, piperine, quercetin, resveratrol, and beta-sitosterol—present in the polyherbal formulation, Krishnadi Churna. Using an in-silico network pharmacology model, key genes were identified and docked against these marker compounds and controls. Mammary carcinoma emerged as the most significant phenotype of the putative targets. Analysis of an online database revealed that out of 135 predicted targets, 134 were mutated in breast cancer patients. Notably, ESR1, CYP19A1, and EGFR were identified as key genes which are known to regulate the BC progression. Docking studies demonstrated that the herbal phytoconstituents had similar or better docking scores than positive controls for these key genes, with convincing protein-ligand interactions confirmed by molecular dynamics simulations, MM/GBSA and free energy landscape (FEL) analysis. Overall, this study highlights the predictive potential of herbal phytoconstituents in targeting BC genes, suggesting their promise as a basis for developing new therapeutic formulations for BC.

Abstract IMPHY000797 derivatives have been well known for their efficacy in various diseases. Moreover, IMPHY000797 derivatives have been found to modulate such genes involved in multiple neurological disorders. Hence, this study seeks to identify such genes and the probable molecular mechanism that could be involved in the pathogenesis of Parkinson’s disease. The study utilized various biological tools such as DisGeNET, STRING, Swiss target predictor, Cytoscape, AutoDock 4.2, Schrodinger suite, ClueGo, and GUSAR. All the reported genes were obtained using DisGeNET, and further, the common genes were incorporated into the STRING to get the KEGG pathway, and all the data was converted to a protein/pathway network via Cytoscape. The clustering of the genes was performed for the gene-enriched data using two-sided hypergeometrics (p-value). The binding affinity of the IMPHY000797 was verified with the highest regulated 25 proteins via utilizing the “Monte Carlo iterated search technique” and the “Emodel and Glide score” function. Three thousand five hundred eighty-three genes were identified for Parkinson’s disease and 31 genes for IMPHY000797 compound, among which 25 common genes were identified. Further, the “FOXO-signaling pathway” was identified to be a modulated pathway. Among the 25 proteins, the highest modulated genes and highest binding affinity were exhibited by SIRT3, FOXO1, and PPARGC1A with the compound IMPHY000797. Further, rat toxicity analysis provided the efficacy and safety of the compound. The study was required to identify the probable molecular mechanism, which needs more confirmation from other studies, which is still a significant hit-back.

Abstract Aim To explore, using network pharmacology and RNA-seq technologies, potential active targets and mechanisms underpinning Radix Bupleuri’s effectiveness during sepsis treatment. Methods Following the Sepsis-3.0 criteria, the research cohort, comprising 23 sepsis patients and 10 healthy participants, was obtained from public databases. Peripheral blood samples were collected and subjected to RNA-seq analysis. Active ingredients and potential targets of Radix Bupleuri were identified using the Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine 2.0 (BATMAN-TCM 2.0) database and TCMSP database. Subsequently, protein-protein interaction (PPI) network construction, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted to explore cross-targets between disease and drugs. Survival analysis of key targets was performed using the GSE65682 dataset, and single-cell RNA-seq was employed for cellular localization analysis of key genes. Finally, molecular docking and Molecular dynamics simulation of the core target was conducted. Results Differential expression analysis revealed 4253 genes associated with sepsis. Seventy-six active components and 1030 potential targets of Radix Bupleuri were identified. PPI, GO, and pathway enrichment analyses indicated involvement in the regulation of transmembrane transport, monatomic ion transport, and MAPK signaling. Survival curve analysis identified PIK3CD, ARRB2, SUCLG1, and SPI1 as key targets associated with lower mortality in the high expression group, while higher mortality was observed in the high PNP and FURIN expression groups. Single-cell RNA sequencing unveiled the cellular localization of PIK3CD, PNP, SPI1, and FURIN within macrophages, while ARRB2 and SUCLG1 exhibited localization in both macrophages and T-cells. Subsequent molecular docking and Molecular dynamics simulation indicated a potential binding interaction for Carvone-PIK3CD, Encecalin-ARRB2, Lauric Acid-SUCLG1, Pulegone-FURIN, Nootkatone-SPI1, and Saikogenin F-PNP. Conclusion Radix Bupleuri could modulate immune function by affecting PIK3CD, ARRB2, SUCLG1, FURIN, SPI1, and PNP, thereby potentially improving the prognosis of sepsis.

Abstract Background Prostate cancer is the most common oncological disease in men and one of leading causes of death worldwide. Growing evidence has demonstrated the effectiveness of mung bean bioactive compounds in suppressing various cancer cells. However, their effects and underlying mechanisms on prostate cancer have not been verified. The present study aimed to investigate the therapeutical effects and underlying mechanisms of mung bean compounds against prostate cancer. Results The results revealed that 56 proteins related to prostate cancer could be modulated by mung bean, including several vital proteins of SRC (Sarcoma), Mitogen-Activated Protein Kinase 8 (MAPK8), Heat shock protein 90 kDa alpha member A1 (HSP90AA1), and Harvey Rat sarcoma virus (HRAS). It was also found that the potential pathways associated with prostate cancer pathogenesis comprising pyrimidine metabolism, nitrogen metabolism, and prolactin signaling pathways. Of 19 mung bean compounds docked to four key proteins reveal three promising compound (dulcinoside, peonidin-3-glucoside, and chlorogenic acid) with lower binding affinity score of − 7.7, − 12.2, − 9.0, and − 6.5 kcal/mol against SRC, MAPK8, HSP90AA1, and HRAS, respectively in their site of action. Dynamic simulation results also showed values of − 36.52 ± 2.93, − 35.93 ± 1.67, and − 35.77 ± 1.17 kJ/mol for Dulcinoside-SRC, Dulcinoside-MAPK8, and P3G-HSP90AA1 complexes, respectively. The binding of the compound occur in stable and flexible with the proteins. Moreover, all mung bean compounds predicted to have good ADMET properties. Conclusions The study concluded that dulcinoside, peonidin-3-glucoside, and chlorogenic acid potentially exhibited anticancer activity against prostate cancer in silico. Nevertheless, further studies such as in vitro and in vivo are needed to optimize and prove the efficacy of the mung brand and its compounds against prostate cancer. Graphical abstract

AIM: To investigate the mechanism of action of Qingxuan Runmu Yin(QRY)in the treatment of dry eye(DE)based on transcriptomics and network pharmacology, and to validate the efficacy and key targets of QRY through a animal model of DE.METHODS:RNA-sequencing(RNA-seq)technology was used to detect differentially expressed genes(DEGs)between mice in the DE group and mice in the normal control group, the active ingredients and potential targets of QRY were screened through database, and gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were carried out after overlapping the results and obtaining key targets. Additionally, “drug-component-target signaling pathways” network was built and the protein-protein interaction(PPI)was analyzed. Mice were examined for Schirmer I test(SⅠt), tear film breakup time(BUT), and corneal fluorescein staining(FL)every 7 d from the beginning of the animal experiments. Hematoxylin-eosin staining(HE)was performed to observe pathologic changes in mouse corneal tissues. Enzyme linked immunosorbent assay(ELISA), Western blot and quantitative real-time polymerase chain reaction(qRT-PCR)were performed to verify the mRNA and protein expression levels of the core targets in mouse corneal tissues.RESULTS:Totally 2 234 DEGs, 233 active ingredients and 457 related targets of QRY were collected, with a total of 64 key targets obtained. GO function and KEGG pathway results showed that QRY was closely related to inflammatory mediators, and 19 core targets such as interleukin-1β(IL-1β)were screened by PPI network construction; SⅠt, BUT and FL results in the QRY group were statistically significantly different compared with the model group(all P

Abstract Hypertension has become a major contributor to the morbidity and mortality of cardiovascular diseases worldwide. Despite the evidence of the anti‐hypertensive effect of gastrodia‐uncaria granules (GUG) in hypertensive patients, little is known about its potential therapeutic targets as well as the underlying mechanism. GUG components were sourced from TCMSP and HERB, with bioactive ingredients screened. Hypertension‐related targets were gathered from DisGeNET, OMIM, GeneCards, CTD, and GEO. The STRING database constructed a protein–protein interaction network, visualized by Cytoscape 3.7.1. Core targets were analyzed via GO and KEGG using R package ClusterProfiler. Molecular docking with AutodockVina 1.2.2 revealed favorable binding affinities. In vivo studies on hypertensive mice and rats validated network pharmacology findings. GUG yielded 228 active ingredients and 1190 targets, intersecting with 373 hypertension‐related genes. PPI network analysis identified five core genes: AKT1, TNF‐α, GAPDH, IL‐6, and ALB. Top enriched GO terms and KEGG pathways associated with the anti‐hypertensive properties of GUG were documented. Molecular docking indicated stable binding of core components to targets. In vivo study showed that GUG could improve vascular relaxation, alleviate vascular remodeling, and lower blood pressure in hypertensive animal models possibly through inhibiting inflammatory factors such as AKT1, mTOR, and CCND1. Integrated network pharmacology and in vivo experiment showed that GUG may exert anti‐hypertensive effects by inhibiting inflammation response, which provides some clues for understanding the effect and mechanisms of GUG in the treatment of hypertension.

Abstract Background Current prostate cancer treatments are associated with life-threatening side effects, prompting the search for effective and safer alternatives. Aspilia pluriseta Schweinf. ex Engl. has previously shown anticancer activity in lung and liver cancer cell lines. This study investigated its potential for prostate cancer. Methods A crude extract of A. pluriseta root was prepared using dichloromethane/methanol (1:1 v/v) and partitioned into hexane, ethyl acetate, and water fractions. The MTT assay was used to assess the antiproliferative activity of the fractions. The active fractions were tested at 6.25–200 µg/ml on human prostate cancer DU-145 cells and non-cancerous Vero E6 cells. Qualitative phytochemical and gas chromatography-mass spectrometry (GC-MS) analyses were conducted to identify chemical compounds. Network pharmacology was employed to predict molecular targets and modes of action of the identified chemical compounds, with subsequent validation through molecular docking and real-time PCR. Results Active extracts included crude dichloromethane/methanol, hexane, and ethyl acetate fractions, inhibiting DU-145 cell proliferation with IC50 values of 16.94, 20.06, and 24.14 µg/ml, respectively. Selectivity indices were determined to be 6.04 (crude), 3.62 (hexane), and 6.68 (ethyl acetate). Identified phytochemicals comprised phenols, terpenoids, flavonoids, tannins, sterols, and saponins. GC-MS analysis revealed seventy-nine (79) compounds, with seven (7) meeting ideal drug candidate parameters; their hub gene targets included MAPK3, MAPK1, IL6, TP53, ESR1, PTGS2, MMP9, MDM2, AR, and MAP2K1, implicating regulation of PI3K/Akt, MAPK, and p53 signaling pathways as potential modes of action. Core compounds such as 1-heneicosanol, lanosterol, andrographolide, and retinoic acid exhibited strong binding activities, particularly lanosterol with MAPK21 (-9.7 kcal/mol), ESR1 (-8.9 kcal/mol), and MAPK3 (-8.8 kcal/mol). Treatment with A. pluriseta downregulated AR expression and upregulated p53, while also downregulating CDK1 and BCL-2 and upregulating caspase-3. Conclusions A. pluriseta extracts inhibited DU-145 cell growth without causing cellular toxicity, suggesting great potential for development as an anti-prostate cancer agent. However, further in vitro and in vivo experiments are recommended.

Abstract A main feature of neurodegenerative diseases is the loss of neurons. One of the most prevalent neurodegenerative illnesses is Parkinson disease (PD). Although several medications are already approved to treat neurodegenerative disorders, most of them only address associated symptoms. The main aim of the current study was to examine the neuroprotective efficacy and underlying mechanism of Lobophytum sp. crude extract in a rotenone-induced rat model of neurodegeneration mimicking PD in humans. The influence of the treatment on antioxidant, inflammatory, and apoptotic markers was assessed in addition to the investigation of TH (tyrosine hydroxylase) immunochemistry, histopathological changes, and α-synuclein. Metabolomic profiling of Lobophytum sp. crude extract was done by using High-Resolution Liquid Chromatography coupled with Mass Spectrometry (HR-LC–ESI–MS), which revealed the presence of 20 compounds (1–20) belonging to several classes of secondary metabolites including diterpenoids, sesquiterpenoids, steroids, and steroid glycosides. From our experimental results, we report that Lobophytum sp. extract conferred neuroprotection against rotenone-induced PD by inhibiting ROS formation, apoptosis, and inflammatory mediators including IL-6, IL-1β, and TNF-α, NF-кB, and subsequent neurodegeneration as evidenced by decreased α-synuclein deposition and enhanced tyrosine hydroxylase immunoreactivity. Moreover, a computational network pharmacology study was performed for the dereplicated compounds from Lobophytum sp. using PubChem, SwissTarget Prediction, STRING, DisGeNET, and ShinyGO databases. Among the studied genes, CYP19A1 was the top gene related to Parkinson’s disease. Dendrinolide compounds annotated a high number of parkinsonism genes. The vascular endothelial growth factor (VEGF) pathway was the top signaling pathway related to the studied genes. Therefore, we speculate that Lobophytum sp. extract, owing to its pleiotropic mechanisms, could be further developed as a possible therapeutic drug for treating Parkinson's disease.

Abstract Background Modified Si-Miao granule (mSMG), a traditional Chinese medicine, is beneficial for T2DM and insulin resistance (IR), but the underlying mechanism remains unknown. Methods Using network pharmacology, we screened the compounds of mSMG and identified its targets and pathway on hepatic IR in T2DM. Using molecular docking, we identified the affinity between the compounds and hub target TNF-α. Then these were verified in KK-Ay mice and HepG2 cells. Results 50 compounds and 170 targets of mSMG against IR in T2DM were screened, and 9 hub targets such as TNF and MAPK8 were identified. 170 targets were mainly enriched in insulin resistance and TNF pathway, so we speculated that mSMG might act on TNF-α, JNK1 and then regulate insulin signaling to mitigate IR. Experimental validation proved that mSMG ameliorated hyperglycemia, IR, and TNF-α, enhanced glucose consumption and glycogen synthesis, relieved the phosphorylation of JNK1 and IRS-2 (Ser388), and elevated the phosphorylation of Akt (Ser473) and GSK-3β (Ser9) and GLUT2 expression in KK-Ay mice. Molecular docking further showed berberine from mSMG had excellent binding capacity with TNF-α. Then, in vitro validation experiments, we found that 20% mSMG-MS or 50 μM berberine had little effect in IR-HepG2 cell viability, but significantly increased glucose consumption and glycogen synthesis and regulated TNF-α/JNK1/IRS-2 pathway. Conclusion Network pharmacology and molecular docking help us predict potential mechanism of mSMG and further guide experimental validation. mSMG and its representative compound berberine improve hepatic IR and glycogen synthesis, and its mechanism may be related to the inhibition of TNF-α/JNK1/IRS-2 pathway.

Changhong Xu,1,&ast; Yun Deng,1,&ast; Jiangwei Man,1,&ast; Huabin Wang,1 Tuanjie Che,2 Liyun Ding,3 Li Yang1 1Department of Urology, Institute of Urology, Gansu Province Clinical Research Center for Urinary System Disease, Lanzhou University Second Hospital, Lanzhou, Gansu, 730030, People’s Republic of China; 2Innovation Center of Functional Genomics and Molecular Diagnostics Technology of Gansu Province, Lanzhou, People’s Republic of China; 3School of Physical Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Li Yang, Department of Urology, Institute of Urology, Gansu Province Clinical Research Center for Urinary System Disease, Lanzhou University Second Hospital, Lanzhou, Gansu, 730030, People’s Republic of China, Email ery_yangli@lzu.edu.cnObjective: This study investigates the targets, pathways, and mechanisms of Schisandrin B (Sch B) in alleviating renal ischemia-reperfusion injury (RIRI) using RNA sequencing and network pharmacology.Methods: The effects of Sch B on RIRI were assessed using hematoxylin-eosin (HE) and periodic acid-Schiff (PAS) staining, along with measurements of blood creatinine and urea nitrogen (BUN). Differential gene expression in mouse models treated with RIRI and Sch B+RIRI was analyzed through RNA-Seq. Key processes, targets, and pathways were examined using network pharmacology techniques. The antioxidant capacity of Sch B was evaluated using assays for reactive oxygen species (ROS), mitochondrial superoxide, and JC-1 membrane potential. Molecular docking was employed to verify the interactions between key targets and Sch B, and the expression of these targets and pathway was confirmed using qRT-PCR, Western blot, and immunofluorescence.Results: Sch B pre-treatment significantly reduced renal pathological damage, inflammatory response, and apoptosis in a mouse RIRI model. Pathological damage scores dropped from 4.33 ± 0.33 in the I/R group to 2.17 ± 0.17 and 1.5 ± 0.22 in Sch B-treated groups (p < 0.01). Creatinine and BUN levels were also reduced (from 144.6 ± 21.05 μmol/L and 53.51 ± 2.34 mg/dL to 50.44 ± 5.61 μmol/L and 17.18 ± 0.96 mg/dL, p < 0.05). Transcriptomic analysis identified four key targets (AKT1, ALB, ACE, CCL5) and the PI3K/AKT pathway. Experimental validation confirmed Sch B modulated these targets, reducing apoptosis and oxidative stress, and enhancing renal recovery.Conclusion: Sch B reduces oxidative stress, inflammation, and apoptosis by modulating key targets such as AKT1, ALB, ACE, and CCL5, while activating the PI3K/AKT pathway, leading to improved renal recovery in RIRI.Keywords: renal ischemia-reperfusion injury, schisandrin B, transcriptomics, network pharmacology, PI3K/AKT pathway

Objective: To evaluate the effect of trigonelline on bleomycin-induced idiopathic pulmonary fibrosis (IPF) and to explore its underlying mechanisms using network pharmacology. Methods: IPF was induced in C57BL/6 mice by a single intratracheal instillation of bleomycin (5 mg/kg). Trigonelline was administered at doses of 25, 50, and 100 mg/kg/day orally from the 2nd day post-bleomycin induction up to the 14th day. In IPF-induced mice, lung coefficient, immune cell infiltration in bronchoalveolar lavage fluid, and oxidative stress were measured. Histological alterations in lung tissues were also assessed. Moreover, network pharmacology approach was conducted to reveal molecular interactions of bleomycin and trigonelline with targets of IPF. Results: Trigonelline treatment reduced bleomycin-induced oxidative stress and immune cell infiltration, and mitigated physiological changes in the lung tissues of mice. Moreover, trigonelline alleviated bleomycin-induced histological alterations in lung tissues. Network pharmacology analysis showed that bleomycin and trigonelline interacted with IPF targets, such as NFKB1, HDAC2, HIF1A, and TLR4. Conclusions: The interaction of trigonelline with key IPF targets and its ameliorative effects on lung damage and oxidative stress highlight its potential in treating IPF. It may be considered an antifibrotic agent for further clinical development.

Abstract Metformin, a widely used anti-diabetic agent, has shown significant anti-cancer properties as reported in in various cancers, including acute myeloid leukemia. However, the detailed mechanisms by which metformin influences acute myeloid leukemia remain unrevealed. Employing a synergistic approach of network pharmacology and experimental validation, this study systematically identifies and analyzes potential metformin targets and AML-related genes. These findings are then cross-referenced with biomedical databases to construct a target-gene network, providing insights into metformin's pharmacodynamics in AML treatment. Protein–Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses are utilized. Results show metformin's effectiveness in inhibiting AML cell proliferation and inducing apoptosis through the AKT/HIF1A/PDK1 signaling pathway. This research provides insights into metformin's clinical application in AML treatment.

Abstract Objective In this study, we evaluated the molecular mechanisms of HuangQiSiJunZi Decoction (HQSJZD) for treating triple-negative breast cancer (TNBC) using network pharmacology and bioinformatics analyses. Methods Effective chemical components together with action targets of HQSJZD were selected based on the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Meanwhile, differentially expressed genes (DEGs) were extracted from TNBC sample data in The Cancer Genome Atlas (TCGA) database. Additionally, we built a protein-protein interaction (PPI) network and acquired hub genes. Gene Expression Omnibus(GEO) datasets were utilized to verify the accuracy of hub gene expression. Additionally, enrichment analyses were conducted on key genes. Furthermore, TNBC severity-related high-risk factors were screened through univariate together with multivariate Cox regressions; next, the logistic regression prediction model was built. Moreover, differential levels of 22 immune cell types in TNBC tissues compared with normal tissues were analyzed. The hub gene levels within pan-cancer and the human body were subsequently visualized and analyzed. Finally, quantitative PCR (RT-qPCR) was used to validate the correlation of the hub genes in TNBC cells. Results The study predicted 256 targets of active ingredients and 1791 DEGs in TNBC, and obtained 16 hub genes against TNBC. The prognostic signature based on FOS, MMP9, and PGR was independent in predicting survival. A total of seven types of immune cells, such as CD4 + memory T cells, showed a significant difference in infiltration (p

Abstract Background Nomilin is a limonoid compound known for its multiple biological activities, but its role in triple negative breast cancer (TNBC) remains unclear. This study aims to uncover the potential therapeutic effect of nomilin on TNBC and elucidate the specific mechanism of its action. Methods We employed weighted gene co-expression network analysis (WGCNA), differential expression analysis, and the GeneCards database to identify potential targets for TNBC. Simultaneously, we utilized the Swiss Target Prediction, ChEMBL, and STITCH databases to identify potential targets of nomilin. The core targets and mechanisms of nomilin against TNBC were predicted through protein-protein interaction (PPI) network analysis, molecular docking, and enrichment analysis. The results of the network pharmacology were corroborated by conducting experiments. Results A total of 17,204 TNBC targets were screened, and 301 potential targets of nomilin were identified. Through the PPI network, eight core targets of nomilin against TNBC were pinpointed, namely BCL2, Caspase3, CyclinD1, EGFR, HSP90AA1, KRAS, PARP1, and TNF. Molecular docking, molecular dynamics simulation and proteome microarray revealed that nomilin exhibits strong binding activity to these core proteins. Enrichment analysis results indicated that the anti-TNBC effect of nomilin is associated with PI3K/Akt pathway. In vitro and in vivo experiments have demonstrated that nomilin inhibits TNBC cell proliferation and migration while promoting cell apoptosis through the PI3K/Akt pathway. Conclusion For the first time, the research effectively discovered the objectives and mechanisms of nomilin in combating TNBC using network pharmacology, molecular docking, molecular dynamics simulation, proteome microarray and experimental confirmation, presenting a hopeful approach for treating TNBC. Graphical Abstract

Abstract Diabetes, a global health concern, poses increasing mortality risks. The pathogenesis of diabetes involves multiple mechanisms, with oxidative stress being one of the key contributors. As synthetic drugs have various side effects, which can be minimized by using herbal plants. This study focuses on the In vitro antioxidant potential, α-amylase inhibition potential, identification of bioactive compounds, and hub genes in diabetes treatment mechanism by using C. tinctorius Extraction of C. tinctorious lead and flower was performed using different solvents (Distilled water, methanol, chloroform, and Dimethyl ether). After extraction different concentrations range from 25–200 mg/mL) was made and checked against activities. The antioxidant potential was assessed using 2, 2-diphenyl-1-picrylhydrazyl (DPPH), total phenolic contents (TPC), and total antioxidant capacity (TAC) assays, while antidiabetic activity was evaluated through α-amylase inhibition assay. Phytochemicals was identified by GC–MS analysis, followed by ADMET screening and network pharmacology analysis using Swiss Target Prediction, Gene Card, DesGeNet, DAVID, STRING, Cytoscape, and drug revitalization databases. Results revealed positive correlations with DPPH, TAC, and TPC. Methanol extract exhibited the highest inhibitory concentration. Screening of 46 compounds was performed by studying their pharmacokinetic properties which revealed 9 compounds effective against 204 diabetes targets. Moreover, their network analysis identified four hub genes, including AKT1, JUN, EGFR, and MMP9. These genes found highly associated with drugs like Colchicine and Serotobenine. Revitalization analysis also highlighted four genes (EGFR, PTGS2, AKT1, and MMP9) strongly correlated with FDA-approved drugs. The study suggests C. tinctorius methanol extract is a potential source for novel drugs. Graphical Abstract