Uncovering the mechanism of resveratrol in the treatment of diabetic kidney disease based on network pharmacology, molecular docking, and experimental validation

Anti-inflammatory effects of resveratrol in treating interstitial cystitis/bladder pain syndrome: a multi-faceted approach integrating network pharmacology, molecular docking, and experimental validation

This study aims to investigate the anti-inflammatory effects of Resveratrol (RES) in the treatment of Interstitial Cystitis/Bladder Pain Syndrome (IC/BPS) by integrating network pharmacology, molecular docking, and experimental validation. Potential targets of RES were identified using DrugBank and SwissTargetPrediction, while IC/BPS-related targets were obtained from DisGeNET and Genecards. Molecular docking was performed using UCSF Chimera and SwissDock to validate the binding affinity of RES to key targets. Experimental validation involved treating TNF-α induced urothelial cells with RES, followed by assessments using RT-qPCR, ELISA, and Western blotting. A total of 86 drug targets and 211 disease targets were analyzed, leading to the identification of 8 key therapeutic targets for RES in IC/BPS treatment. Molecular docking revealed a strong affinity of RES for ESR2, with notable interactions also observed with SHBG, PTGS2, PPARG, KIT, PI3KCA, and AKT1. In vitro experiments confirmed that RES significantly alleviated the inflammatory response in TNF-α-induced urothelial cells, normalizing the expression levels of ESR2, SHBG, PPARG, and AKT1. RES can modulate critical pathways involving ESR2, SHBG, PPARG, and AKT1, highlighting its potential as a therapeutic agent for IC/BPS. This study provides a theoretical foundation for the clinical application of RES in treating IC/BPS.

Exploring the mechanism of Epimedium in treating diabetic nephropathy based on network pharmacology and experimental validation study

Diabetic nephropathy (DN) is a severe complication of diabetes, characterized by chronic inflammation, metabolic disturbances, and progressive renal damage. Natural perennial herb, such as Epimedium, has shown potential therapeutic effects on DN, but its underlying mechanisms remain unclear. This study aimed to explore the pharmacological mechanisms of Epimedium in the treatment of DN through network pharmacology, molecular docking, and experimental validation. Active components of Epimedium were identified using TCMSP and SwissTargetPrediction databases, while DN-related targets were retrieved from GeneCards, DisGeNET, OMIM, and TTD databases. Overlapping targets were analyzed via PPI network and Cytoscape's cytoHubba plugin to identify hub genes. GO and KEGG enrichment analyses were conducted to explore functional pathways. Molecular docking validated the binding affinity between key targets and active components. Finally, high-glucose-induced HK-2 cell injury models were used to verify the protective effects of Epimedium through RT-qPCR, western blotting, and mitochondrial function assays. A total of 224 overlapping targets were identified, with AKT1, TNF, HSP90AA1, and SRC serving as key hub genes. GO and KEGG analyses revealed significant enrichment in pathways such as the PI3K-Akt signaling pathway and lipid metabolism. Molecular docking demonstrated strong interactions between Epimedium components and hub targets. Experimental validation showed that Epimedium restored nephrin and WT1 protein levels, mitigated mitochondrial dysfunction, and reversed high-glucose-induced overexpression of key targets. Epimedium exerts therapeutic effects on DN through multi-target interactions, primarily via the PI3K-Akt pathway, highlighting its potential as a novel treatment for DN.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10616-025-00748-0.

Network toxicological and molecular docking in investigating the mechanisms of toxicity of agricultural chemical pyraclostrobin

The safety of agricultural products is significant to human health. Pyraclostrobin (PYR), a common methoxycarbonyl fungicide, is a crucial role in the prevention of fungal infections during the transport and storage of agricultural products, including vegetables and fruits. Using a multi-analytical approach, integrating toxicological database mining, protein-protein interaction (PPI) network analysis, and molecular docking, this study aimed to elucidate the molecular mechanisms underlying the toxicity of PYR. A total of 162 and 129 targets were identified for cancer and kidney injury, respectively, with PPI analysis pinpointing five vital targets per condition. Functional enrichment through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway annotations revealed significant associations with pathways related to prostate cancer and renal impairment pathways. Molecular docking confirmed PYR's binding affinity to these targets, indicating its potential role in disease pathogenesis. Our findings underscore the imperative for stringent safety assessments of PYR, particularly concerning the risks posed by chronic exposure, and emphasize the urgency for further research to inform public health and environmental policies.

Dendrobium nobile lindl extract modulates integrin αIIbβ3-mediated signaling pathways to inhibit platelet activation and thrombosis

ETHNOPHARMACOLOGICAL RELEVANCE

Dendrobium nobile Lindl. (DNL) is a promising medicinal plant. It has the traditional medicinal effects of promoting blood circulation and resolving stasis, as well as regulating the meridians and collaterals.

AIM OF THE STUDY

We studyed how DNL extract was involved in platelet activation and thrombosis and used network pharmacology and molecular docking analysis to help clarify the underlying mechanisms.

MATERIALS AND METHODS

The effect of DNL extract on platelet aggregation and ATP release function was examined by aggregometer; The effect of DNL extract on the binding of PAC-1 and fibrinogen to integrin was determined by flow cytometry; The effect of DNL extract on "outside-in" platelet signals was detected by platelet adhesion, spreading and clot retraction; Key compounds and major targets of platelet interactions with DNL extract were analyzed by network pharmacology and molecular docking and verified against related pathway proteins by western blotting; The effect of DNL extract on thrombosis was tested by mesenteric artery embolism model.

RESULTS

DNL extract exhibited inhibition of platelet function and PAC-1 and fibrinogen binding to integrin αIIbβ3. In addition, it delayed FeCl3-induced mesenteric artery thrombosis without affecting the clotting time and the hemostatic time of tail in mice. The detection of platelet "inside-out" and "outside-in" signaling by Western blot further confirmed the inhibitory effect of DNL extract on platelet activation.

CONCLUSIONS

DNL extract may affect the thrombosis process by inhibiting platelet activation via inhibiting integrin αⅡbβ3-mediated bidirectional signaling pathway proteins.

Effects and Mechanisms of Paeoniflorin in Relieving Neuropathic Pain: Network Pharmacological Analysis and Experimental Validation

Neuropathic pain (NP) is a prevalent condition that can lead to a variety of complications, significantly impacting patients' quality of life. Previous studies have confirmed that paeoniflorin (PF) demonstrates both therapeutic pain relief and neuroprotective effects. However, its therapeutic efficacy in managing NP remains to be thoroughly investigated. We conducted a systematic study to explore the underlying mechanisms of PF in the treatment of NP through combining network pharmacological analysis with experimental validation. Our studies revealed that PF alleviates NP through a multifaceted approach, mainly involving protein kinase C (PKC), serotonin receptors, calcium signaling pathways, inflammatory mediator regulation of transient receptor potential (TRP) channels, and G-protein coupled receptor signaling pathways. Additionally, our animal experiments indicated that PF reduces pain-related behavior on spinal nerve ligation-induced NP in rats by modulating the PKCε-TRPV1 pathway. PF was found to inhibit the expression of inflammatory factors such as interleukin 6 and tumor necrosis factor α, as well as the activation of microglia, thereby alleviating NP. These findings suggest a potential therapeutic role for PF in the treatment of NP, providing a valuable reference for clinical applications.

Urate-lowering effect of delphinidin-3-glucoside in red kidney beans via binding to the FAD site of the XO enzyme

BACKGROUND

The incidence of hyperuricemia (HUA) is increasing globally, posing serious health risks. The discovery of natural urate-lowering agents is urgently needed.

OBJECTIVE

To discover natural urate-lowering agents and investigate their effect and action mechanisms for ameliorating HUA.

METHODS

Our study comprehensively explored the association between the intake of 13 specific legume varieties in the US population. A composition-target-metabolic (C-T-M) pathway network was constructed to identify key agents and their interactions with key proteins, which were verified by molecular dynamics simulations (MD) and surface plasmon resonance (SPR). Biochemical, in vitro, and in vivo metabolomic studies in male ICR mice were conducted to examine the effects of the key agent in red kidney beans on uric acid production and other metabolisms.

RESULTS

We found that consuming red kidney beans was robustly negatively associated with the risk of HUA. Based on the C-T-M network, delphinidin-3-glucoside (Dp-3G) was identified as the key agent in red kidney beans, focusing on its binding to xanthine oxidase (XO) enzyme. This interaction was subsequently verified by MD and SPR, revealing that Dp-3G binds to the FAD site of the XO enzyme, thereby blocking electron transfer during enzyme catalysis involving Moco, [2Fe-2S], and FAD. Dp-3G consistently reduces uric acid production under biochemical, in vitro, and in vivo conditions and reverses metabolic abnormalities related to HUA in mice, including methionine, proline, and folate.

CONCLUSIONS

This study identifies Dp-3G, a novel natural agent enriched in red kidney beans, as capable of occupying the FAD site of the XO enzyme, thereby interfering with uric acid synthesis, and suggesting its potential for preventing and treating HUA.

Galangin reduces MPTP-induced dopamine neuron injury via the autophagy dependent-PI3K/AKT pathway

Introduction

Research has confirmed that Galangin can attenuate autophagy and protect dopaminergic neurons. This study aims to clarify whether Galangin attenuates dopaminergic neuron injury by regulating the PI3K/AKT pathway in Parkinson's disease (PD) model mice.

Methods

The study explores the mitigating effects of Galangin on PD processes by administering 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) to induce the condition. Techniques including network analysis, transcriptomic analysis, rotarod test, enzyme-linked immunosorbent assay (ELISA), qRT-PCR, western blotting, immunohistochemistry, immunofluorescence, and hematoxylin-eosin (HE) were employed to unveil the molecular changes induced by Galangin.

Results

The network pharmacological analysis showed 301 targets related to Galangin, and 2,858 genes related to PD. Galangin treatment can improve the motor coordination of PD model mice, reduce damage to neurons in the brain, improve the antioxidant capacity and reduce the inflammatory damage of brain tissue. Additionally, Galangin suppressed mRNA expression of PD markers (IL-1β, TNF-α, IL-6, SRC and PTGS2), elevated protein levels of GSH-Px, SOD, P-PI3K, P-CREB, P-AKT, TH, BDNF and P62, while decreasing α-syn, SRC, MDA, Beclin-1 and LC3B expression. Moreover, the expression of significantly different genes in the Galangin-treated group and model group analyzed by transcriptomics was basically consistent with the qRT-PCR verification results.

Conclusion

Galangin supresses Beclin-1-dependent autophagy and upregulates the PI3K/AKT signaling pathway to attenuate the neuroinflammatory injury and improve motor coordination ability in PD mice induced by MPTP.

USP14-Dependent IGF1R Aggravates High Glucose-Induced Diabetic Retinopathy by Upregulating BAP1

Diabetic retinopathy (DR) is a microvascular complication of diabetes. Insulin-like growth factor 1 receptor (IGF1R) has been implicated in the pathogenesis of DR; however, the underlying mechanism remains unclear. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to assess IGF1R mRNA expression. Western blotting assays were performed to analyze the protein expression of IGF1R, ubiquitin-specific peptidase 14 (USP14), and BRCA1-associated protein 1 (BAP1). Cell viability, apoptosis, interleukin-1 beta (IL-1β), and tumor necrosis factor-alpha (TNF-α) levels were analyzed using cell counting kit-8 assay, flow cytometry, and enzyme-linked immunosorbent assays, respectively. Fluorescent microscopy and flow cytometry were performed for reactive oxygen species (ROS) level assessment, and colorimetric assays for iron (Fe2+) and glutathione (GSH) levels. Co-immunoprecipitation assays and/or colocalization techniques were employed to validate the association of IGF1R with USP14 and BAP1. Treatment with high glucose (HG) increased the protein expression of IGF1R, USP14, and BAP1 in ARPE-19 cells. Silencing of IGF1R mitigated HG-induced apoptosis, inflammatory response, and ferroptosis in ARPE-19 cells. USP14 was found to stabilize IGF1R protein expression through deubiquitination. Overexpression of USP14 exacerbated HG-induced cellular injury, whereas silencing of USP14 protected ARPE-19 cells by reducing IGF1R expression. Interaction between IGF1R and BAP1 was confirmed in ARPE-19 cells and IGF1R silencing protected cells from HG-induced injury by regulating BAP1 expression. Thus, USP14-dependent regulation of IGF1R expression and its interaction with BAP1 play a crucial role in the pathogenesis of high glucose-induced diabetic retinopathy.

Serum metabolic profiling of patients with diabetic kidney disease based on gas chromatography-mass spectrometry

Introduction

Given the increasing incidence rate of diabetic kidney disease (DKD), there is an urgent need for methods to diagnose and treat DKD in clinics.

Methods

Serum samples were collected from 56 DKD patients and 32 healthy controls (HCs) at the First Affiliated Hospital of Ningbo University, and the metabolic profiles were obtained through untargeted metabolomics using gas chromatography mass spectrometry. The data were then analyzed using principal components analysis, orthogonal partial least-squares discriminant analysis, Pearson correlation analysis, and receiver operating characteristic (ROC) curve.

Results

It was found that the serum metabolic profiles of the DKD patients were significantly different from those of the HCs. A total of 68 potential differential metabolites were identified that were involved in arginine biosynthesis, ascorbate and aldarate metabolism, and galactose metabolism, among others; a total of 31 differential metabolites were also identified between early-stage (EDG) and late-stage (LDG) DKD patients. Additionally, 30 significant metabolic differences were observed among the EDG, LDG, and HC groups. Based on Pearson correlation analysis between the abundances of the differential metabolites and clinical markers (estimated glomerular filtration rate, blood urea nitrogen, serum creatinine, and urinary albumin/creatinine ratio) and area under the ROC curve (AUROC) analysis, the AUROC values of myoinositol and gluconic acid were found to be 0.992 and 0.991, respectively, which can be used to distinguish DKD patients from HCs.

Discussion

These results indicate that myoinositol and gluconic acid could possibly be used as biomarkers of DKD.

Network pharmacology and molecular docking technology-based predictive study and potential targets analysis of icariin for the treatment of diabetic nephropathy

OBJECTIVE

Epimedium glycoside is a flavonoid compound in Epimedium, which has been found to alleviate various chronic diseases. The effect and mechanism of icariin on the treatment of diabetes nephropathy still need to be clarified. In this study, we conducted network pharmacology and molecular docking analysis to reveal the mechanism of icariin treating DKD, and then validated its efficacy using a cell model.

METHOD

The structure and targets of icariin were screened using Traditional Chinese Medicine Systems Pharmacology (TCMSP), and their targets were annotated. Retrieve DKD targets from OMIM, GeneCards, and TTD databases. We constructed a protein-protein interaction (PPI) network using the STRING platform and visualized the results using Cytoscape 3.9.1 software. We also conducted GO and KEGG enrichment analysis on icariin and then performed molecular docking between icariin and key targets. Finally, we established a cell model of DKD to evaluate the efficacy of icariin in treating DKD.

RESULT

A total of 77 icariin targets were associated with DKD. The GO and KEGG enrichment results showed that the therapeutic effect of icariin on DKD was significantly correlated with inflammatory response, cell apoptosis, epithelial-mesenchymal transition, and PI3K/AKT signaling pathway. The molecular docking results indicate that icariin has a high affinity for key targets EGER, AKT1, and IGF1. Cell experiments showed that icariin inhibited high glucose-induced EMT, fibrosis-related proteins, levels of inflammatory factors TGF-β1, IL-6, and TNF-α, as well as phosphorylation of phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT) in renal tubular epithelial cells. In addition, icariin inhibited the increase in EGER and AKT1 mRNA levels caused by high glucose and alleviated the decrease in IGF1 mRNA levels.

CONCLUSION

Epimedium glycoside may protect DKD by targeting EGER, AKT1, and IGF1 to inhibit PI3K/AKT signaling, but the specific mechanism needs further exploration.

Combining Network Pharmacology, Molecular Docking and Experimental Validation to Explore the Effects and Mechanisms of Indirubin on Acute Lymphoblastic Leukemia

Purpose

To investigate the effects and underlying mechanisms of indirubin in treating ALL using network pharmacology and experimental validation.

Methods

Potential targets of indirubin- and ALL-related genes were identified using public databases. Core genes were filtered through protein-protein interaction analysis in Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the potential mechanisms of indirubin against ALL. Drug-disease-functional annotation-signaling pathway network maps were constructed. Molecular docking between indirubin and core proteins was performed using AutoDock Vina software. Finally, both in vitro and in vivo experiments were performed to validate these findings.

Results

PPI network analysis identified eight potential core targets of indirubin in ALL: AKT1, CASP3, and the mammalian target of rapamycin. GO and KEGG enrichment analyses suggested that the mechanism of action of indirubin against ALL involves multiple biological functions and signaling pathways, with the PI3K-AKT pathway likely playing a central role. Molecular docking findings further confirmed the strong binding affinity of indirubin for the core targets. Both in vitro and in vivo experiments demonstrated that indirubin inhibited ALL cell proliferation and induced cell cycle arrest and apoptosis; the underlying mechanism may involve the PI3K-AKT signaling pathway.

Conclusion

The action and mechanism of indirubin in ALL through network pharmacology, as well as in vivo and in vitro experimental validation were elucidated, offering new insights and potential therapeutic avenues for the treatment of ALL.

Exploring the potential mechanism of B-phycoerythrin on DSS-induced colitis and colitis-associated bone loss based on network pharmacology, molecular docking, and experimental validation

B-phycoerythrin (B-PE), a pigment protein, has found extensive applications in the food, pharmaceutical, and cosmetic industries. However, the effects and potential mechanisms of B-PE on colitis and colitis-associated bone loss remain unclear. Thus, the aim of this study was to investigate the pharmacological mechanisms of B-PE against colitis and colitis-associated bone loss using network pharmacology analysis, molecular docking, and experimental validation. Based on public databases, 99 common targets of B-PE against inflammatory bowel disease and osteoporosis were predicted. The protein-protein interaction network identified 16 core targets, including TNF, AKT1, EGFR, etc., as hub targets. Additionally, functional enrichment analyses and molecular docking results revealed that the PI3K/AKT signaling pathway may serve as a potential signaling pathway for B-PE in the treatment of colitis and colitis-associated bone loss. Furthermore, pharmacological experiments indicated that B-PE not only reversed the elevated expression of TNF-α, IL-1β, MMP9, and CXCL8a, and the reduced expression of ZO-1, E-cadherin, COL1A1, and RUNX2 in the DSS-induced colitis zebrafish model, but also enhanced the phosphorylation of PI3K and AKT, thereby mitigating inflammatory response and promoting osteogenesis. In conclusion, this study provides a theoretical basis for considering B-PE as a promising candidate for the treatment of colitis and colitis-associated bone loss.

The Many Facets of PPAR-γ Agonism in Obesity and Associated Comorbidities: Benefits, Risks, Challenges, and Future Directions

PURPOSE OF REVIEW

Obesity is strongly associated with cardiometabolic disorders and certain malignancies, emphasizing the key role of adipose tissue in human health. While incretin mimetics have shown effectiveness in glycemic control and weight loss, a holistic strategy for combating obesity and associated comorbidities remains elusive. This review explores peroxisome proliferator-activated receptor gamma (PPAR-γ) agonism as a potential therapeutic approach, highlighting its benefits, addressing its limitations, and outlining future directions for developing more effective treatment strategies.

RECENT FINDINGS

Both natural and synthetic PPAR-γ agonists hold significant therapeutic potential as insulin sensitizers, while also demonstrating anti-inflammatory properties and playing a critical role in regulating lipid metabolism. However, the clinical use of natural agonists is limited by poor bioavailability, while synthetic agents like thiazolidinediones are associated with adverse effects, including fluid retention, weight gain, and bone loss. Current research is focused on developing modified, tissue-specific PPAR-γ agonists, as well as dual PPAR-α/PPAR-γ agonists, with improved safety profiles to mitigate these side effects. Nanotechnology-based drug delivery systems also hold promise for enhancing bioavailability and therapeutic efficacy. Furthermore, the transformative potential of machine learning and artificial intelligence offers opportunities to accelerate advancements in this field. PPAR-γ agonists exhibit significant potential in addressing metabolic syndrome, cardiovascular disease, and cancer. However, their clinical use is restricted by safety concerns and suboptimal pharmacokinetics. Innovations in modified PPAR-γ agonists, nanotechnology-based delivery systems, and computational tools hold promise for creating safer and more effective therapeutic options for obesity and its associated disorders.

Exploring the osteogenic effects of simiao wan through activation of the PI3K/AKT pathway in osteoblasts

ETHNOPHARMACOLOGICAL RELEVANCE

Osteoporosis (OP) is a degenerative bone disease commonly associated with reduced bone density and increased fracture risk.

AIM OF THE STUDY

This study aimed to validate the therapeutic effects of Simiao wan (SMW) on OP and explore the underlying mechanism, particularly focusing on the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway.

MATERIALS AND METHODS

The chemical components of SMW were identified using UPLC-Q-TOF-MS/MS. The obtained compounds were then input into the TCMSP, TargetNet, and SwissTargetPrediction databases to predict potential targets. OP-related targets were collected from the GeneCards and DisGeNET databases, and intersecting targets were identified through a Venn diagram. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the intersecting targets using the Database for Annotation, Visualization and Integrated Discovery (DAVID). SMW extract was subsequently used to treat osteoblasts in vitro, and its toxicity on osteoblasts was assessed using Cell Counting Kit-8 (CCK-8) and lactate dehydrogenase (LDH) release assays. Osteoblast differentiation and activity were further evaluated using alizarin red staining, alkaline phosphatase staining, and Western blot analyses to validate the activation of network pharmacological signaling pathways.

RESULTS

A total of 121 potential targets were identified for SMW in the treatment of OP, with AKT1 as the primary target. The PI3K/AKT pathway emerged as a key signaling pathway potentially involved in SMW's therapeutic effects o OP. Toxicity assessments showed no significant toxicity of SMW on osteoblasts. Additionally, SMW promoted osteoblast proliferation, alkaline phosphatase activity, calcium nodule deposition, and the expression of osteogenic markers (osteocalcin (OCN), runt-related transcription factor 2 (RunX2), and collagen I), and activated the PI3K/AKT signaling pathway. The PI3K/AKT pathway inhibitor LY294002 partially reversed the SMW-induced mineral deposition and expression of OCN, RunX2, and collagen I.

CONCLUSION

SMW demonstrated effective multi-target and multi-pathway therapeutic potential in the treatment of OP, with a significant impact on the PI3K/AKT signaling pathway.

Dehydrodiisoeugenol inhibits PDGF-BB-induced proliferation and migration of human pulmonary artery smooth muscle cells via the mTOR/HIF1-α/HK2 signaling pathway

Abnormal proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) leading to pulmonary vascular remodeling are critical factors in the development of pulmonary hypertension (pH). Dehydrodiisoeugenol (DEH), a natural phenolic compound, is renowned for its antioxidant and anti-inflammatory properties. However, the precise role and mechanisms of DEH in PH remain unclear. In this study, human PASMCs were exposed to PDGF-BB for 48 h to establish an in vitro model. Subsequently, cells were treated with DEH, and assessments of cell proliferation, migration, and apoptosis were performed using CCK-8/EdU assays, scratch/transwell assays, and flow cytometry. The results showed that PDGF-BB induced phenotypic modulation, proliferation, and migration of PASMCs while reducing apoptosis. Treatment with DEH effectively reversed these effects. Bioinformatics analysis identified mTOR as a target of DEH action. Western blot experiments were conducted to evaluate the expression of proteins involved in the mTOR/HIF1-α/HK2 signaling pathway, suggesting that DEH modulates this pathway by targeting and inhibiting mTOR. After treating cells with mTOR inhibitors, cellular glycolysis was assessed using the extracellular acidification rate (ECAR) assay. The results indicated that inhibition of mTOR phosphorylation decreased aerobic glycolysis in PASMCs and suppressed cell proliferation, migration, and apoptosis resistance, regardless of PDGF-BB treatment. Activation of mTOR reversed the inhibition of PDGF-BB-induced PASMC-related protein expression by DEH. These findings suggest that DEH inhibits aerobic glycolysis in PDGF-BB-induced PASMCs through the mTOR/HIF1-α/HK2 signaling pathway, thereby suppressing cell proliferation, migration, and resistance to apoptosis. Consequently, DEH holds promise as a novel therapeutic agent for treating pulmonary arterial hypertension.

Sodium butyrate regulates macrophage polarization by TGR5/β-arrestin2 in vitro

BACKGROUND

Macrophages play an important role in the pathogenesis of ulcerative colitis (UC). We will explore the effects of sodium butyrate (SB) on macrophage function.

METHODS

The targets of butyric acid were identified using SwissTargetPrediction database and surface plasmon resonance (SPR). Limited proteolysis mass spectrometry (Lip-MS) was used to further investigate the binding sites of butyric acid with its targets and molecular docking was employed to simulate their binding modes. Macrophage polarization model was established with lipopolysaccharide (LPS) in vitro. Takeda G protein-coupled receptor 5 (TGR5) and β-arrestin2 expression and macrophage polarization markers were detected with or without SB.

RESULTS

TGR5 was identified as the target of butyric acid. Moreover, the amino acid regions 275-286 and 321-330 of TGR5 (GPBAR1 [275-286] and GPBAR1 [321-330]) were the potential binding regions for butyric acid. Based on molecular docking analysis, butyric acid formed effective hydrogen-bonding interactions with ASP-284 and TYR-287 of TGR5. In cell experiments, LPS inhibited the expression of TGR5, β-arrestin2, IL-10, ARG1, and CD206 and increased the expression of IL-1β, iNOS, and CD86, while SB reversed the effect of LPS. SBI-115, a TGR5 antagonist, and knockdown of β-arrestin2 inhibited the effect of sodium butyrate. INT-777, a TGR5 agonist, reversed the inhibitory effect of knockdown of β-arrestin2.

CONCLUSION

SB inhibited M1-like polarization and promoted M2-like polarization induced by LPS via TGR5/β-arrestin2 in RAW264.7 cells and TGR5 was the target of SB.

Narciclasine attenuates sepsis-associated acute kidney injury through the ESR1/S100A11 axis

Narciclasine (Ncs) was effective in sepsis management due to its antioxidant properties. The present study dissected the protective effects of Ncs against sepsis-associated acute kidney injury (SA-AKI) and the molecular mechanisms. The SA-AKI mice were developed using cecum ligation and puncture and pretreated with Ncs and adenoviruses. Human renal microvascular endothelial cells (RMECs) were induced with LPS and treated with Ncs. Ncs alleviated proximal tubular dilatation, interstitial widening, and necrosis in renal tissues and reduced the renal injury marker and pro-inflammatory cytokine levels in the serum of SA-AKI mice. Ncs promoted the expression of ZO-1, VE-cadherin, and CD31 and the activities of SOD, GSH-Px, and CAT, and inhibited the levels of pro-inflammatory cytokines, and apoptosis rate in LPS-treated RMECs. Estrogen receptor 1 (ESR1) was a target protein of Ncs, and S100 calcium-binding protein A11 (S100A11) was a target of the transcription factor ESR1. Ncs blocked transcription of S100A11 by inhibiting ESR1. Silencing of S100A11 overturned the deteriorating effects of ESR1 overexpression on SA-AKI progression in vivo and RMEC injury in vitro. These findings suggest that Ncs may ameliorate SA-AKI by repressing the ESR1/S100A11 signaling, providing a novel perspective for research on SA-AKI.

Network Pharmacology, Molecular Docking, and Molecular Dynamics Study to Explore the Effect of Resveratrol on Type 2 Diabetes

This network pharmacology study represents a significant step in understanding the potential of Resveratrol as an antidiabetic agent and its molecular targets. Targets for Type 2 diabetes were obtained from the MalaCards and DisGeNET databases, while targets for Resveratrol were sourced from the STP and CTD databases. Subsequently, we performed matching to identify common disease-compound targets. The identified genes were analyzed using the ShinGO-0.76.3 database for functional enrichment analysis and KEGG pathway mapping. A protein-protein interaction network was then constructed using Cytoscape software, and hub genes were identified. These hub genes were subjected to molecular docking and dynamic simulations using AutoDock Vina and Gromacs software. According to functional enrichment and KEGG pathway analysis, Resveratrol influences insulin receptors, endoplasmic reticulum functions, and oxidoreductase activity and is involved in the estrogen and HIF-1 pathways. Ten hub genes were identified, including ESR1, PTGS2, SRC, NOS3, MMP9, IGF1R, CYP19A1, MTOR, MMP2, and PIK3CA. The proteins associated with these genes exhibited high interaction with Resveratrol in the molecular docking analysis, and molecular dynamics showed a stable interaction of Resveratrol with ESR1, MMP9, PIK3CA, and PTGS2. In conclusion, our work enhances the understanding of the antidiabetic activity of Resveratrol, which future studies should experimentally corroborate.

Gegen Qinlian Decoction Attenuates Colitis-Associated Colorectal Cancer via Suppressing TLR4 Signaling Pathway Based on Network Pharmacology and In Vivo/In Vitro Experimental Validation

Background: Gegen Qinlian Decoction (GQD), is used for intestinal disorders like ulcerative colitis, irritable bowel syndrome, and colorectal cancer. But the precise mechanisms underlying its anti-inflammatory and anti-tumor effects are not fully elucidated. Methods: Use network pharmacology to identify targets and pathways of GQD. In vivo (azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colitis-associated colorectal cancer (CAC) mouse model) and in vitro (lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages) experiments were conducted to explore GQD's anti-inflammatory and anti-tumor effects. We monitored mouse body weight and disease activity index (DAI), and evaluated colon cancer tissues using hematoxylin and eosin staining. Expression of Ki67 and F4/80 was determined by immunohistochemistry analysis. The protein levels of TLR4 signaling pathway were assessed by western blotting analysis. Enzyme-linked immunosorbent assay measured IL-1β, IL-6, and TNF-α levels. Immunofluorescence (IF) staining visualized NF-κB and IRF3 translocation. Results: There were 18, 9, 24 and 77 active ingredients in the four herbs of GQD, respectively, targeting 435, 156, 485 and 691 genes. Through data platform analysis, it was concluded that there were 1104 target genes of GQD and 2022 target genes of CAC. Moreover, there were 99 intersecting genes between GQD and CAC. The core targets of GQD contained NFKB1, IL1B, IL6, TLR4, and TNF, and GQD reduced inflammation by inhibiting the TLR4 signaling pathway. In vivo experiment, GQD increased mouse body weight, lowered DAI scores, while also alleviating histopathological changes in the colon and decreasing the expressions of Ki67 and F4/80 in the AOM/DSS-induced mice. GQD reduced IL-1β, IL-6, and TNF-α levels in the serum and downregulated TLR4, MyD88, and phosphorylation of IκBα, P65, and IRF3 in the colon tissue from AOM/DSS-induced mice. In vitro, GQD suppressed pro-inflammatory cytokines and TLR4 signaling pathway in the LPS-induced RAW264.7 cells, and combined with TAK242, it further reduced the phosphorylation of IκBα, P65. Conclusions: GQD mitigated CAC by inhibiting the TLR4 signaling pathway, offering a potential therapeutic approach for CAC management.

Elucidating the role of gut microbiota metabolites in diabetes by employing network pharmacology

BACKGROUND

Extensive research has underscored the criticality of preserving diversity and equilibrium within the gut microbiota for optimal human health. However, the precise mechanisms by which the metabolites and targets of the gut microbiota exert their effects remain largely unexplored. This study utilizes a network pharmacology methodology to elucidate the intricate interplay between the microbiota, metabolites, and targets in the context of DM, thereby facilitating a more comprehensive comprehension of this multifaceted disease.

METHODS

In this study, we initially extracted metabolite information of gut microbiota metabolites from the gutMGene database. Subsequently, we employed the SEA and STP databases to discern targets that are intricately associated with these metabolites. Furthermore, we leveraged prominent databases such as Genecard, DisGeNET, and OMIM to identify targets related to diabetes. A protein-protein interaction (PPI) network was established to screen core targets. Additionally, we conducted comprehensive GO and KEGG enrichment analyses utilizing the DAVID database. Moreover, a network illustrating the relationship among microbiota-substrate-metabolite-target was established.

RESULTS

We identified a total of 48 overlapping targets between gut microbiota metabolites and diabetes. Subsequently, we selected IL6, AKT1 and PPARG as core targets for the treatment of diabetes. Through the construction of the MSMT comprehensive network, we discovered that the three core targets exert therapeutic effects on diabetes through interactions with 8 metabolites, 3 substrates, and 5 gut microbiota. Additionally, GO analysis revealed that gut microbiota metabolites primarily regulate oxidative stress, inflammation and cell proliferation. KEGG analysis results indicated that IL-17, PI3K/AKT, HIF-1, and VEGF are the main signaling pathways involved in DM.

CONCLUSION

Gut microbiota metabolites primarily exert their therapeutic effects on diabetes through the IL6, AKT1, and PPARG targets. The mechanisms of gut microbiota metabolites regulating DM might involve signaling pathways such as IL-17 pathways, HIF-1 pathways and VEGF pathways.

A network pharmacology approach-based decoding of Resveratrol's anti-fibrotic mechanisms

BACKGROUND

Inhalation of crystalline silica (CS) frequently leads to chronic lung inflammation and pulmonary fibrosis (PF), a condition with limited effective treatments. Resveratrol (Res) has demonstrated potential in PF treatment; however, its underlying mechanisms remain incompletely elucidated.

PURPOSE

This study represents the first comprehensive attempt to uncover the novel mechanisms underlying Res's anti-fibrotic effects against PF through an innovative, integrated approach combining network pharmacology and experimental validation.

METHODS

We employed network pharmacology to investigate the holistic pharmacological mechanism of Res, then validated the predicted pharmacological effects using in vivo and in vitro studies.

RESULTS

In total, 216 genes were identified to be simultaneously associated with PF and Res. An integrated bioinformatics analysis implicated a crucial role of the autophagy signaling pathway in dominating PF, with AMPK and mTOR showing high docking scores. Animal studies revealed that Res significantly alleviated silica-induced lung damage in silicotic mice, with decreased collagen I (Col-I) levels and reduced expression of vimentin and α-SMA. In-depth investigation demonstrated that Res modulated CS-dysregulated autophagy by targeting the AMPK/mTOR pathway. in vitro, Res treatment significantly reduced lactate dehydrogenase (LDH), TNF-α, and TGF-β levels and improved cell viability of Raw264.7 cells post-CS exposure. Notably, Res was demonstrated to suppress fibroblast-to-myofibroblast transition via mediating macrophage autophagy through the AMPK/mTOR pathway.

CONCLUSION

Res can alleviate CS-induced PF by targeting AMPK in the autophagy signaling pathway, which sheds light on Res' therapeutic potential in treating PF.

Decoding the anti-hypertensive mechanism of α-mangostin based on network pharmacology, molecular docking and experimental validation

BACKGROUND

Hypertension is a leading risk factor for disability and deaths worldwide. Evidence indicates that alpha-mangostin(α-MG) can reduce blood pressure and improve target organ damage. Nonetheless, its pharmacological targets and potential mechanisms of action remain inadequately elucidated.

METHOD

We used SwissTargetPrediction to identify α-MG's drug targets and DisGeNET, GeneCards, CTD, and GEO databases for hypertension-related targets, and then determined antihypertensive therapeutic targets of α-MG by intersecting these targets. GO functional enrichment analysis, KEGG pathway analysis, and disease association analysis were conducted using the DAVID database and R package "clusterprofile", visualized with Cytoscape software. The binding affinity of α-MG to identified targets was confirmed through molecular docking using Autodock Vina v.1.2.2 software. The impact of α-MG on target genes was validated using an Angiotensin II-induced hypertensive mouse model and RT-qPCR.

RESULTS

A total of 51 potential antihypertensive therapeutic targets for α-MG were identified by intersecting 109 drug targets with 821 disease targets. Furthermore, 10 cellular component terms, 10 disease terms, and the top 20 enriched biological processes, molecular functions, and KEGG pathways related to α-MG's antihypertensive effects were documented. Molecular docking studies indicated a strong binding affinity of α-MG with the HSP90AA1 domain. In Ang II-induced hypertensive mice aorta, treatment with α-MG effectively reversed the aberrant mRNA expression of TNF, HSP90AA1, NFKB1, PPARG, SIRT1, PTGS2, and RELA.

CONCLUSION

Our analyses showed that TNF, HSP90AA1, NFKB1, PPARG, SIRT1, PTGS2, and RELA might be α-MG's potential therapeutic targets for hypertension, laying groundwork for further investigation into its pharmacological mechanisms and clinical uses.

Resveratrol: Challenges and prospects in extraction and hybridization with nanoparticles, polymers, and bio-ceramics

Resveratrol (RSV), a bioactive natural phenolic compound found in plants, fruits, and vegetables, has garnered significant attention in pharmaceutical, food, and cosmetic industries due to its remarkable biological and pharmacological activities. Despite its potential in treating various diseases, its poor pharmacokinetic properties, such as low solubility, stability, bioavailability, and susceptibility to rapid oxidation, limit its biomedical applications. Recent advancements focus on incorporating resveratrol into innovative materials like nanoparticles, polymers, and bio-ceramics to enhance its properties and bioavailability. In this review, an exhaustive literature search was conducted from PubMed, Google Scholar, Science Direct, Scopus, and Web of Science databases to explore these advancements, to compares conventional and innovative extraction methods, and to highlights resveratrol's therapeutic potential, including its anti-inflammatory, anti-oxidative, anti-cancerogenic, antidiabetic, neuroprotective, and cardio-protective properties. Additionally, we discuss the challenges and prospects of hybrid materials combining resveratrol with nanoparticles, polymers, and bio-ceramics for therapeutic applications. Rigorous studies are still needed to confirm their clinical efficacy.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Ginkgo Biloba Bioactive Phytochemicals against Age-Related Diseases: Evidence from a Stepwise, High-Throughput Research Platform

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.

(-)-Epicatechin gallate prevented atherosclerosis by reducing abnormal proliferation of VSMCs and oxidative stress of AML 12 cells

(-)-Epicatechin gallate (ECG) is beneficial to the treatment of cardiovascular diseases (CVDs), especially atherosclerosis (AS) through antioxidant stress, but there is a lack of detailed mechanism research. In this study, the therapeutic target of ECG was determined by crossing the drug target and disease target of CVDs and AS. The combination ability of ECG with important targets was verified by Discovery Studio software. The abnormal proliferation of vascular smooth muscle cells (VSMCs) induced by Ang-II and the oxidative damage of AML 12 induced by H2O2 were established to verify the reliability of ECG intervention on the target protein. A total of 120 ECG targets for the treatment of CVDs-AS were predicted by network pharmacology. The results of molecular docking showed that ECG has strong binding force with VEGFA, MMP-9, CASP3 and MMP-2 domains. In vitro experiments confirmed that ECG significantly reduced the expression of VEGFA, MMP-9, CASP3 and MMP-2 in Ang-II-induced VSMCs, and also blocked the abnormal proliferation, oxidative stress and inflammatory reaction of VSMCs by inhibiting the phosphorylation of PI3K signaling pathway. At the same time, ECG also interfered with H2O2-induced oxidative damage of AML 12 cells, decreased the expression of ROS and MDA and cell foaming, and increased the activities of antioxidant enzymes such as SOD, thus playing a protective role.

B. glomerulata promotes neuroprotection against ischemic stroke by inhibiting apoptosis through the activation of PI3K/AKT/mTOR pathway

BACKGROUND

Brassaiopsis glomerulata (Blum) Regel (B.glomerulata) is recognized as a traditional Chinese medicine (TCM) primarily used for promoting blood circulation and removing stasis. It is frequently utilized in the treatment of injuries resulting from falls and bumps.

PURPOSE

Despite its effective use in clinical treatment for ischemic stroke (IS), there are currently no reports on its composition and mechanism of action, which affects its promotion. The study investigated the chemical components and molecular mechanisms of B.glomerulata, with the following components: UPLC-Q-TOF-MS, network pharmacology Analysis and experimental verification in vivo and vitro.

METHODS

The effect of B.glomerulata on interfering with ischemic stroke was assessed on MCAO/R rats and ORD cell model. Then the compositional analysis was conducted using UPLC-Q-TOF-MS. Furthermore, network pharmacology and molecular docking techniques were explored to identify potential targets and pathways. The predicted mechanisms of action were ultimately confirmed by immunohistochemistry and protein blotting.

RESULTS

B. glomerulata exhibited neuroprotective effects in MCAO/R rats by reductions in hippocampal and cortical neuronal damage, brain infarction, and cerebral edema. Both in vivo and in vitro experiments demonstrated that it decreased ROS and MDA levels, increased SOD and GSH levels, thereby inhibiting oxidative stress. Moreover, the improvements in neuronal morphology and the modulation of Nissl bodies suggested a potential mechanism underlying its neuroprotective action. Additionally, B.glomerulata exhibited concentration-dependent reductions in Bax and Caspase-3 expressions, along with increases in GFAP, Bcl2/Bax ratio, p-PI3K, p-AKT, and p-mTOR levels.

CONCLUSION

B.glomerulata exhibited neuroprotective effects against cerebral ischemia-reperfusion injury both in vivo and in vitro. It prevented oxidative stress damage and inhibited apoptosis of ischemic stroke through the PI3K/AKT/mTOR pathway.

The role of artificial intelligence in the development of anticancer therapeutics from natural polyphenols: Current advances and future prospects

Natural polyphenols, abundant in the human diet, are derived from a wide variety of sources. Numerous preclinical studies have demonstrated their significant anticancer properties against various malignancies, making them valuable resources for drug development. However, traditional experimental methods for developing anticancer therapies from natural polyphenols are time-consuming and labor-intensive. Recently, artificial intelligence has shown promising advancements in drug discovery. Integrating AI technologies into the development process for natural polyphenols can substantially reduce development time and enhance efficiency. In this study, we review the crucial roles of natural polyphenols in anticancer treatment and explore the potential of AI technologies to aid in drug development. Specifically, we discuss the application of AI in key stages such as drug structure prediction, virtual drug screening, prediction of biological activity, and drug-target protein interaction, highlighting the potential to revolutionize the development of natural polyphenol-based anticancer therapies.

Green Tea Polyphenol (-)-Epicatechin Pretreatment Mitigates Hepatic Steatosis in an In Vitro MASLD Model

Metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), is becoming more prominent globally due to an increase in the prevalence of obesity, dyslipidemia, and type 2 diabetes. A great deal of studies have proposed potential treatments for MASLD, with few of them demonstrating promising results. The aim of this study was to investigate the potential effects of (-)-epicatechin (EPI) on the development of MASLD in an in vitro model using the HepG2 cell line by determining the metabolic viability of the cells and the levels of PPARα, PPARγ, and GSH. HepG2 cells were pretreated with 10, 30, 50, and 100 μM EPI for 4 h to assess the potential effects of EPI on lipid metabolism. A MASLD cell culture model was established using HepG2 hepatocytes which were exposed to 1.5 mM oleic acid (OA) for 24 h. Moreover, colorimetric MTS assay was used in order to determine the metabolic viability of the cells, PPARα and PPARγ protein levels were determined using enzyme-linked immunosorbent assay (ELISA), and lipid accumulation was visualized using the Oil Red O Staining method. Also, the levels of intracellular glutathione (GSH) were measured to determine the level of oxidative stress. EPI was shown to increase the metabolic viability of the cells treated with OA. The metabolic viability of HepG2 cells, after 24 h incubation with OA, was significantly decreased, with a metabolic viability of 71%, compared to the cells pretreated with EPI, where the metabolic viability was 74-86% with respect to the concentration of EPI used in the experiment. Furthermore, the levels of PPARα, PPARγ, and GSH exhibited a decrease in response to increasing EPI concentrations. Pretreatment with EPI has demonstrated a great effect on the levels of PPARα, PPARγ, and GSH in vitro. Therefore, considering that EPI mediates lipid metabolism in MASLD, it should be considered a promising hepatoprotective agent in future research.

[Euonymus alatus delays progression of diabetic kidney disease in mice by regulating EGFR tyrosine kinase inhibitor resistance signaling pathway]

OBJECTIVE

To explore the therapeutic mechanism of Euonymus alatus for diabetic kidney disease (DKD).

METHODS

TCMSP, PubChem and Swiss Target Prediction databases were used to obtain the active ingredients in Euonymus alatus and their targets. GEO database and R language were used to analyze the differentially expressed genes in DKD. The therapeutic targets of DKD were obtained using GeneCards, DisGeNet, OMIM and TTD databases. The protein-protein interaction network and the "drug-component-target-disease" network were constructed for analyzing the topological properties of the core targets, which were functionally annotated using GO and KEGG pathway enrichment analyses. Molecular docking was performed for the core targets and the main pharmacologically active components, and the results were verified in db/db mice.

RESULTS

Analysis of GSE96804, GSE30528 and GSE30529 datasets (including 60 DKD patients and 45 normal samples) identified 111 differentially expressed genes in DKD. Network pharmacology analysis obtained 161 intersecting genes between the target genes of Euonymus alatus and DKD, including the key core target genes SRC, EGFR, and AKT1. The core active ingredients of Euonymus alatus were quercetin, kaempferol, diosmetin, and naringenin, which were associated with responses to xenobiotic stimulionus and protein phosphorylation and regulated EGFR tyrosine kinase inhibitor resistance pathways. Molecular docking suggested good binding activities of the core active components of Euonymus alatus with the core targets. In db/db mouse models of DKD, treatment with Euonymus alatus obviously ameliorated kidney pathologies, significantly inhibited renal expressions of SRC, EGFR and AKT1, and delayed the progression of DKD.

CONCLUSION

Euonymus alatus contains multiple active ingredients such as quercetin, kakaferol, diosmetin, naringenin, which regulate the expressions of SRC, EGFR, and AKT1 to affect the EGFR tyrosine kinase inhibitor resistance signaling pathway to delay the progression of DKD.

The role of metabolic memory in diabetic kidney disease: identification of key genes and therapeutic targets

Diabetic kidney disease (DKD) is characterized by complex pathogenesis and poor prognosis; therefore, an exploration of novel etiological factors may be beneficial. Despite glycemic control, the persistence of transient hyperglycemia still induces vascular complications due to metabolic memory. However, its contribution to DKD remains unclear. Using single-cell RNA sequencing data from the Gene Expression Omnibus (GEO) database, we clustered 12 cell types and employed enrichment analysis and a cell‒cell communication network. Fibrosis, a characteristic of DKD, was found to be associated with metabolic memory. To further identify genes related to metabolic memory and fibrosis in DKD, we combined the above datasets from humans with a rat renal fibrosis model and mouse models of metabolic memory. After overlapping, NDRG1, NR4A1, KCNC4 and ZFP36 were selected. Pharmacology analysis and molecular docking revealed that pioglitazone and resveratrol were possible agents affecting these hub genes. Based on the ex vivo results, NDRG1 was selected for further study. Knockdown of NDRG1 reduced TGF-β expression in human kidney-2 cells (HK-2 cells). Compared to that in patients who had diabetes for more than 10 years but not DKD, NDRG1 expression in blood samples was upregulated in DKD patients. In summary, NDRG1 is a key gene involved in regulating fibrosis in DKD from a metabolic memory perspective. Bioinformatics analysis combined with experimental validation provided reliable evidence for identifying metabolic memory in DKD patients.

Qigui-Yishen decoction delays renal fibrosis in mice with chronic kidney disease by regulating TM and PAI-1

OBJECTIVE

To explore the mechanism of Qigui-Yishen decoction in delaying renal fibrosis in mice by regulating thrombin regulatory protein (Thrombomodulin, TM) and plasminogen activator inhibitor-1 (PAI-1) based on network pharmacology.

METHODS

The active ingredients of Qigui Yishen decoction and their target molecules associated with chronic kidney disease (CKD) were retrieved from websites and databases, sorted out, and screened, and the possible targets of Qigui Yishen decoction for reducing CKD renal fibrosis were predicted and analyzed. Forty Institute of Cancer research (ICR) rats were used to establish a unilateral ureteral obstruction (UUO) model, and divided into several groups: sham operation group, model group, high concentration decoction group (1 g/mL), low concentration decoction group (0.46 g/mL), and benazepril group (0.1 g/mL). At the end of the experiment, the levels of serum creatinine (Scr) and blood urea nitrogen (BUN) were detected. Masson staining was used to observe changes in the renal interstitial fibrosis index. Immunohistochemistry and western blot were used to detect the expressions of TM, PAI-1, transforming growth factor-β1 (TGF-β1) and collagen I (Col I) in kidney tissues, and the differences between groups were compared.

RESULTS

Qigui Yishen decoction contains 42 effective ingredients such as sitosterol, mannitol, and quercetin, with 662 drug targets and 16154 disease targets. Analysis revealed 570 potential targets, including TM4SF19, PAIP1, TGF-β1, and Col I-AI. Compared to the sham operation group, all treatment groups exhibited increased Scr and BUN levels (P<0.05) and enhanced renal interstitial fibrosis (P<0.05) after UUO model establishment. Moreover, immunohistochemical results showed significant increases in PAI-1, TGF-β1, and Col I (all P<0.05), and a significant decrease in TM expression (P<0.05). Compared to the model group, the high concentration decoction group, low concentration decoction group and benazepril group had no significant difference in Scr and BUN values (P>0.05), but the renal interstitial fibrosis index was lower (P<0.05). Also, the relative expressions of PAI-1, TGF-β1 and Col I in the kidney tissue of mice were decreased, while the relative expression of TM was increased (P<0.05).

CONCLUSION

Qigi Yishen decoction has the characteristics of multiple components and multiple targets, and can play a role in delaying renal fibrosis by regulating the expression of PAI-1, TGF-β1, Col I, and TM.

Glucose-modified BSA/procyanidin C1 NPs penetrate the blood-brain barrier and alleviate neuroinflammation in Alzheimer's disease models

Alzheimer's disease (AD) is a chronic neurodegenerative disease with high prevalence, long duration and poor prognosis. The blood-brain barrier (BBB) is a physiologic barrier in the central nervous system, which hinders the entry of most drugs into the brain from the blood, thus affecting the efficacy of drugs for AD. Natural products are recognized as one of the promising and unique therapeutic approaches to treat AD. To improve the efficiency and therapeutic effect of the drug across the BBB, a natural polyphenolic compound, procyanidin C-1 (C1) was encapsulated in glucose-functionalized bovine serum albumin (BSA) nanoparticles to construct Glu-BSA/C1 NPs in our study. Glu-BSA/C1 NPs exhibited good stability, slow release, biocompatibility and antioxidant properties. In addition, Glu-BSA/C1 NPs penetrated the BBB, accumulated in the brain by targeting Glut1, and maintained the BBB integrity both in vitro and in vivo. Moreover, Glu-BSA/C1 NPs alleviated memory impairment of 5 × FAD mice by reducing Aβ deposition and Tau phosphorylation and promoting neurogenesis. Mechanistically, Glu-BSA/C1 NPs significantly activated the PI3K/AKT pathway and inhibited the NLRP3/Caspase-1/IL-1β pathway thereby suppressing neuroinflammation. Taken together, Glu-BSA/C1 NPs could penetrate the BBB and mitigate neuroinflammation in AD, which provides a new therapeutic approach targeting AD.

Discovery of a novel homoisoflavonoid derivative 5g for anti-osteoclastic bone loss via targeting FGFR1

Several flavonoids have been shown to exert anti-osteoporosis activity. However, the structure-activity relationship and the mechanism of anti-osteoporosis activity of flavonoids remain unknown. In this study, we prepared a series of novel homoisoflavonoid (HIF) derivatives to evaluate their inhibitory effects on osteoclastogenesis using TRAP-activity in vitro assay. Then, the preliminary structure-activity relationship was studied. Among the evaluated novel flavonoids, derivative 5g exerted the most inhibitory bioactivity on primary osteoclast differentiation without interfering with osteogenesis. It was hence selected for further in vitro, in vivo and mechanism of action investigation. Results show that 5g likely directly binds to the fibroblast growth factor receptor 1 (FGFR1), decreasing the activation of ERK1/2 and IκBα/NF-κB signaling pathways, which in turn blocks osteoclastogenesis in vitro and osteoclastic bone loss in vivo. Our study shows that homoisoflavonoid (HIF) derivatives 5g can serve as a potential novel candidate for treating osteoporosis via inhibition of FGFR1.

PPARG and the PTEN-PI3K/AKT Signaling Axis May Cofunction in Promoting Chemosensitivity in Hypopharyngeal Squamous Cell Carcinoma

It has been demonstrated that PPARG may interact with the PTEN-PI3K/AKT pathway, contributing to its involvement in the chemotherapy treatment of hypopharyngeal squamous cell carcinoma (HSCC). However, the underlying mechanism remains largely unknown. In this study, gene expression profiles of 17 HSCC patients, comprising 8 chemotherapy-sensitive patients (CSP) and 9 chemotherapy-nonsensitive patients (CNSP), were collected and analyzed to investigate expression patterns, correlations, influencing factors of the PPARG-PTEN-PI3K/AKT pathway, and its role in regulating chemosensitivity. The results revealed significantly increased expression (p < 0.04) of AKT1, AKT2, AKT3, PIK3CA, PPARG, and PTEN in the CSP group compared to the CNSP group. Specifically, AKT2 exhibited significant overexpression in tumor tissue (p = 0.01), while AKT2, AKT3, PPARG, and PTEN displayed significant increases in normal tissue (p ≤ 0.04). Positive correlations (R ∈ [0.43, 0.71], p < 0.014) were observed between PIK3CA, AKT1, AKT2, AKT3, and PTEN, with AKT2, AKT3, and PTEN also showing significant correlations with PPARG (R ∈ [0.35, 0.47], p < 0.04). Age, gender, and disease stage had no influence on PPARG, PIK3CA, and PTEN expression, but they may affect AKT expressions. Pathway analysis revealed that PPARG may interact with the PTEN-PI3K/AKT signaling pathway, playing a crucial role in regulating chemosensitivity in the normal tissue microenvironment. Our results suggest that AKT1 and PIK3CA may be associated with chemosensitivity in HSCC tumor cells, while PPARG and PTEN might exhibit a correlation with a specific segment of the PI3K/AKT pathway, potentially influencing chemosensitivity in the normal tissue microenvironment of HSCC patients.

Role of Gut Microbiota, Immune Imbalance, and Allostatic Load in the Occurrence and Development of Diabetic Kidney Disease

Diabetic kidney disease (DKD) is a prevailing complication arising from diabetes mellitus. Unfortunately, there are no trustworthy and efficacious treatment modalities currently available. In recent times, compelling evidence has emerged regarding the intricate correlation between the kidney and the gut microbiota, which is considered the largest immune organ within the human physique. Various investigations have demonstrated that the perturbation of the gut microbiota and its associated metabolites potentially underlie the etiology and progression of DKD. This phenomenon may transpire through perturbation of both the innate and the adaptive immunity, leading to a burdensome allostatic load on the body and ultimately culminating in the development of DKD. Within this literature review, we aim to delve into the intricate interplay between the gut microbiota, its metabolites, and the immune system in the context of DKD. Furthermore, we strive to explore and elucidate potential chemical interventions that could hold promise for the treatment of DKD, thereby offering invaluable insights and directions for future research endeavors.

Shuangshen Ningxin capsule alleviates myocardial ischemia-reperfusion injury in miniature pigs by modulating mitophagy: network pharmacology and experiments in vivo

BACKGROUND

Myocardial ischemia/reperfusion injury (MI/RI) is involved in a variety of pathological states for which there is no effective treatment exists. Shuangshen Ningxin (SSNX) capsule which is developed by Xiyuan Hospital, Chinese Academy of Traditional Chinese Medicine has been demonstrated to alleviate MI/RI, but its mechanism remains to be further elucidated.

METHODS

The MI/RI miniature pigs model was constructed to assess the pharmacodynamics of SSNX by blocking the proximal blood flow of the left anterior descending branch of the cardiac coronary artery through an interventional balloon. The principal chemical compounds and potential targets of SSNX were screened by HPLC-MS and SwissTargetPrediction. The targets of MI/RI were identified based on Online Mendelian Inheritance in Man (OMIM) and GeneCards. Cytoscape 3.9.0 was applied to construct a protein-protein interaction (PPI) network, and Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using metascape. To further validate the mechanism of SSNX, Molecular docking, Transmission electron microscopy, and Western blot analysis were used to test the effectiveness of targets in related pathways.

RESULTS

Our results indicated that SSNX significantly improved cardiac function, attenuated myocardial I/R injury. Through network analysis, a total of 15 active components and 201 targets were obtained from SSNX, 75 of which are potential targets for the treatment of MI/RI. KEGG and MCODE analysis showed that SSNX is involved in the mitophagy signaling pathway, and ginsenoside Rg1, ginsenoside Rb1 and ginsenoside Rb2 are key components associated with the mitophagy. Further experimental results proved that SSNX protected mitochondrial structure and function, and significantly reduced the expression of mitophagy-related proteins PTEN-induced putative kinase 1 (PINK1), Parkin, FUN14 domain containing 1 (FUNDC1) and Bcl-2/E1B-19 kDa interacting protein 3 (BNIP3) in MI/RI miniature pigs.

CONCLUSION

In our study, the integration of network pharmacology and experiments in vivo demonstrated that SSNX interfered with MI/RI by inhibiting mitophagy.

Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

Hydroquinine has antimicrobial potential with demonstrated activity against several bacteria, including multidrug-resistant (MDR) P. aeruginosa reference strains. Despite this, there is limited evidence confirming the antibacterial activity of hydroquinine against clinical isolates and the underlying mechanism of action. Here, we aimed to investigate the antibacterial effect of hydroquinine in clinical P. aeruginosa strains using phenotypic antimicrobial susceptibility testing and synergistic testing. In addition, we examined the potential inhibitory mechanisms against MDR P. aeruginosa isolates using informatic-driven molecular docking analysis in combination with RT-qPCR. We uncovered that hydroquinine inhibits and kills clinical P. aeruginosa at 2.50 mg/mL (MIC) and 5.00 mg/mL (MBC), respectively. Hydroquinine also showed partial synergistic effects with ceftazidime against clinical MDR P. aeruginosa strains. Using SwissDock, we identified potential interactions between arginine deiminase (ADI)-pathway-related proteins and hydroquinine. Furthermore, using RT-qPCR, we found that hydroquinine directly affects the mRNA expression of arc operon. We demonstrated that the ADI-related genes, including the arginine/ornithine antiporter (arcD) and the three enzymes (arginine deiminase (arcA), ornithine transcarbamylase (arcB), and carbamate kinase (arcC)), were significantly downregulated at a half MIC of hydroquinine. This study is the first report that the ADI-related proteins are potential molecular targets for the inhibitory effect of hydroquinine against clinically isolated MDR P. aeruginosa strains.