Network Pharmacology Analysis Research Articles

Explore the active ingredients and potential mechanism of action on Actinidia arguta leaves against T2DM by integration of serum pharmacochemistry and network pharmacology

BackgroundActinidia arguta leaves (AAL) are traditionally consumed as a vegetable and as tea in folk China and Korea. Previous studies have reported the anti-diabetic effect of AAL, but its bioactive components and mechanism of action are still unclear. Aim of the studyThis study aims to identify the hypoglycemic active components of AAL by combining serum pharmacochemistry and network pharmacology and to elucidate its possible mechanism of action. MethodsFirstly, the effective components in mice serum samples were characterized by UPLC-Q/TOF-MSE. Furthermore, based on these active ingredients, network pharmacology analysis was performed to establish an “H-C-T-P-D” interaction network and reveal possible biological mechanisms. Finally, the affinity between serum AAL components and the main proteins in the important pathways above was investigated through molecular docking analysis. ResultsSerum pharmacochemistry analysis showed that 69 compounds in the serum samples were identified, including 23 prototypes and 46 metabolites. The metabolic reactions mainly included deglycosylation, dehydration, hydrogenation, methylation, acetylation, glucuronidation, and sulfation. Network pharmacology analysis showed that the key components quercetin, pinoresinol diglucoside, and 5-O-trans-p-coumaroyl quinic acid butyl ester mainly acted on the core targets PTGS2, HRAS, RELA, PRKCA, and BCL2 targets and through the PI3K-Akt signaling pathway, endocrine resistance, and MAPK signaling pathway to exert a hypoglycemic effect. Likewise, molecular docking results showed that the three potential active ingredients had good binding effects on the five key targets. ConclusionThis study provides a basis for elucidating the pharmacodynamic substance basis of AA against T2DM and further exploring the mechanism of action.

Insights into the molecular mechanisms of Spirulina platensis against rheumatoid arthritis through integrative serum pharmacochemistry and network pharmacology analysis

Spirulina platensis traditionally and increasingly consumed as a premium food and complementary medicine in many Asian countries on account of its nutritive and pharmacological attributes. So far, Spirulina holds promise as a potential therapeutic agent for RA alleviation. However, the mechanistic basis of S. platensis against RA remains poorly clarified.The research strategy featuring serum pharmacochemistry and network pharmacology was constructed to pinpoint the potential bioactive components and efficiency mechanisms of S. platensis against RA. Firstly, a rat model of RA was established using Complete Freund's Adjuvant (CFA). Secondly, serum migrating components following Spirulina administration were profiled and relatively quantified as monitoring indexes for Spirulina bioavailability. Using network pharmacology strategy, potential target genes of transitional components and associated pathways were predicted. Lastly, the control mechanisms of S. platensis in CFA model were verified through a series of serum and synovial biochemical markers along with master RA-related pathways by western blotting. Nineteen circulating compounds, including four prototypes and fifteen metabolites were profiled and selected as candidate efficacy compounds successfully absorbed and maintained considerable concentrations in Spirulina-treated sera creating a great opportunity to exert the anti-RA potential. Among which, fatty acids and their conjugated metabolites represented the most relevant and abundant circulating metabolites. Regarding network pharmacology findings, the top predictive targets highly correlated with RA were NFKB, NLRP3, TNF, MMP-9, TLR4 and VEGFA. Relatedly, KEGG analysis dissected PI3K-Akt signaling pathway, MAPK signaling pathway, osteoclasts (OCs) differentiation and VEGF signaling pathway as the top-ranked RA pathways. Our efficacy experimental findings emphasized that Spirulina markedly downregulated the inflammatory mediators (IL-1, IL-6, IL-17, TNF-α and MMP-9) levels. Following Spirulina treatment, western blotting detected significant alterations in RA master proteins as TLR4, NLRP3, VEGF, Pro caspases-1, Caspase-1, and NF-κB p65. This integrated work illuminates the molecular mechanisms and efficacy constituents of S. platensis as referenced templates against RA. In the light of the above, systematized information on the metabolic fate of the absorbable Spirulina metabolites should be expanded through in-depth pharmacokinetics research for highly targeted drugs. In a broader sense, future investigations and adequate evidence should be explored to broaden the therapeutic strategies scenario in the era of personalized medicine to achieve a comprehensive “treat-to-target” approach which, undoubtedly, is of a great significance in the clinical settings.

Oxyresveratrol Improves Cognitive Impairments and Episodic-like Memory through Modulating Neuroinflammation and PI3K-Akt Signaling Pathway in LPS-Induced Mice.

Oxyresveratrol is one of the active ingredients derived from mulberry branch with strong anti-inflammatory bioactivity. In this research, we want to explore if oxyresveratrol can improve cognitive impairments and episodic-like memory and its mechanism. In LPS-induced BV-2 cells, 25 μM OXY can significantly inhibit the expression of NO and alter the M1/M2 polarization by regulating M1/M2 phenotype makers. In vivo, OXY (50, 100 mg/kg) significantly reversed cognitive impairments and alleviated neuronal injuries caused by neuroinflammation. According to network pharmacology analysis, OXY alleviated neuroinflammation via the PI3K-Akt pathway. In general, the research revealed that OXY can improve cognitive impairments and episodic-like memory through alleviating LPS-induced neuroinflammation and regulating the PI3K-Akt signaling pathway.

Kavain alleviates choroidal neovascularization via decreasing the activity of the HIF-1α/VEGF-A/VEGFR2 signaling pathway and inhibiting inflammation

Purpose: Neovascular age-related macular degeneration (nAMD) is a prevalent cause of blindness in the elderly. Standard treatment includes anti-vascular endothelial growth factor (VEGF) drugs, including Bevacizumab, Ranibizumab, and Aflibercept. However, anti-VEGF drugs may have limited efficacy and cause drug resistance. Recently, inflammation has been identified as one of the main risk factors in the progression of AMD. This study explores whether Kavain, an anti-inflammatory molecule from Piper methysticum, can treat choroidal neovascularization (CNV). Materials and methods: Various experiments were conducted to assess the Kavain’s toxicity. The impact of Kavain on in vitro cultured endothelial cells was examined through 5-Ethynyl-20-deoxyuridine (EdU) assays, transwell migration assays, and tube formation assays. The therapeutic effects of Kavain on CNV were investigated using a Laser-induced CNV mice model. Laser burns, approximately two papillary diameters away from the mouse optic nerve, were uniformly induced (532 nm wavelength, 0.1 s duration, 120 mW power, and 50 µm spot size). To elucidate the mechanism of Kavain, network pharmacology analysis, molecular docking, and western blots were performed. Results: Kavain exhibited no apparent toxicity both in vitro and in vivo. Kavain significantly decreased endothelial cell viability, proliferation, migration, and tube formation ability in a dose-dependent manner compared to the hypoxia groups (P<0.05). Kavain alleviated CNV in the laser-induced CNV mouse model compared to the control groups (P<0.05). These effects were statistically significantly enhanced in the Kavain plus Aflibercept groups (P<0.05). Following Kavain administration, the expression levels of various inflammatory factors were markedly reduced in retinal pigment epithelium (RPE) /choroid complexes (P<0.05). Mechanistically, we proved that Kavain decreased the activity of the hypoxia-inducible factor 1 α (HIF-1 α)/VEGF-A/VEGF receptor 2 (VEGFR2) signaling pathway. Conclusions: Our study is the first to demonstrate Kavain's potential as a promising treatment for nAMD, owing to its dual effects of anti-inflammation and anti-angiogenesis.

Icariin ameliorates LPS-induced acute lung injury in mice via complement C5a-C5aR1 and TLR4 signaling pathways

Acute lung injury (ALI) is an acute respiratory-related progressive disorder, which lacks specific pharmacotherapy. Icariin (ICA) has been shown to be effective in treating ALI. However, the targets and pharmacological mechanisms underlying the effects of ICA in the treatment of ALI are relatively lacking. Based on network pharmacology and molecular docking analyses, the gene functions and potential target pathways of ICA in the treatment of ALI were determined. In addition, the underlying mechanisms of ICA were verified by immunohistochemistry, immunofluorescence, quantitative Real-time PCR, and Western blot in LPS-induced ALI mice. The biological processes targeted by ICA in the treatment of ALI included the pathological changes, inflammatory response, and cell signal transduction. Network pharmacology, molecular docking, and in vivo experimental results revealed that ICA inhibited the complement C5a-C5aR1 axis, TLR4 mediated NF-κB, MAPK, and JAK2-STAT3 signaling pathways related gene and protein expressions, and decreased inflammatory cytokine, chemokine, adhesion molecule expressions, and mitochondrial apoptosis in LPS-induced ALI.

Network pharmacological analysis on the mechanism of Linggui Zhugan decoction for nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD), represents a chronic progressive disease that imposes a significant burden on patients and the healthcare system. Linggui Zhugan decoction (LGZGD) plays a substantial role in treating NAFLD, but its exact molecular mechanism is unknown. Using network pharmacology, this study aimed to investigate the mechanism of action of LGZGD in treating NAFLD. Active ingredients and targets were identified through the integration of data from the TCMSP, GEO, GeneCards, and OMIM databases. Cytoscape 3.9.1 software, in conjunction with the STRING platform, was employed to construct network diagrams and screen core targets. The enrichment analysis of gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways were conducted by using the R. Molecular docking of the active ingredients and core targets was performed with AutoDock Vina software. We obtained 93 and 112 active ingredients and potential targets using the bioinformatic analysis of LGZGD in treating NAFLD. The primary ingredients of LGZGD included quercetin, kaempferol, and naringenin. The core targets were identified AKT1, MYC, HSP90AA1, HIF1A, ESR1, TP53, and STAT3. Gene ontology function enrichment analysis revealed associations with responses to nutrient and oxygen levels, nuclear receptor activity, and ligand-activated transcription factor activity. Kyoto Encyclopedia of Genes and Genomes signaling pathway analysis implicated the involvement of the PI3K-Akt, IL-17, TNF, Th17 cell differentiation, HIF-1, and TLR signaling pathways. Molecular docking studies indicated strong binding affinities between active ingredients and targets. LGZGD intervenes in NAFLD through a multi-ingredient, multi-target, and multi-pathway approach. Treatment with LGZGD can improve insulin resistance, oxidative stress, inflammation, and lipid metabolism associated with NAFLD.

Network pharmacology analysis and experimental validation of Xiao-Qing-Long-Tang’s therapeutic effects against neutrophilic asthma

BackgroundXiao-Qing-Long-Tang (XQLT), a classical Chinese herbal medicine formula, has been extensively used for allergic asthma treatment. However, there is limited research on its anti-inflammatory effects and mechanisms specifically in neutrophilic asthma (NA). PurposeThis study aims to investigate the potential therapeutic effects of XQLT against NA using a combination of network pharmacology and experimental validation. Study designBy utilizing traditional Chinese medicine and disease databases, we constructed an XQLT-asthma network to identify potential targets of XQLT for NA. In the experimental phase, we utilized an ovalbumin (OVA)/lipopolysaccharide (LPS)-induced model for neutrophilic asthma and examined the therapeutic effects of XQLT. ResultsOur research identified 174 bioactive components within XQLT and obtained 140 target genes of XQLT against asthma. Functional enrichment analysis revealed that these target genes were primarily associated with inflammation and cytokines. In the experimental validation, mice induced with OVA-LPS showcased eosinophilic and neutrophilic cell infiltration in peri-bronchial areas, elevated levels of IL-4 and IL-17 in both serum and lung, increased percentages of Th2 and Th17 cells in the spleen, as well as elevated levels of CD11b+ and CD103+ dendritic cells (DCs) within the lung. Treatment with XQLT effectively reduced IL-4 and IL-17 levels, decreased the percentages of Th2, Th17, CD11b+, and CD103+ DCs, and improved inflammatory cell infiltrations in lung tissues. These findings serve as a foundation for the potential clinical application of XQLT in neutrophilic asthma.

Dihydrocapsaicin suppresses the STING-mediated accumulation of ROS and NLRP3 inflammasome and alleviates apoptosis after ischemia-reperfusion injury of perforator skin flap.

Avascular necrosis frequently occurs as a complication following surgery involving the distal perforator flap. Dihydrocapsaicin (DHC) can protect tissue from ischemia-reperfusion (I/R) injury, but its specific role in multizone perforator flaps remains unclear. In this study, the prospective target of DHC in the context of I/R injury was predicted using network pharmacology analysis. Flap viability was determined through survival area analysis, laser Doppler blood flow, angiograms, and histological examination. The expressions of angiogenesis, apoptosis, NLR family pyrin domain containing 3 (NLRP3) inflammasome, oxidative stress, and molecules related to cyclic guanosine monophosphate (GMP)-adenosine monophosphate synthase (cGAS)-interferon gene stimulant (STING) pathway were assessed using western blotting, immunofluorescence, TUNEL staining, and dihydroethidium (DHE) staining. Our finding revealed that DHC promoted the perforator flap survival, which involves the cGAS-STING pathway, oxidative stress, NLRP3 inflammasome, apoptosis, and angiogenesis. DHC induced oxidative stress resistance and suppressed the NLRP3 inflammasome, preventing apoptosis in vascular endothelial cells. Through regulation of STING pathway, DHC controlled oxidative stress in endothelial cells and NLRP3 levels in ischemic flaps. However, activation of the cGAS-STING pathway led to the accumulation of reactive oxygen species (ROS) and NLRP3 inflammasome, thereby diminishing the protective role of DHC. DHC enhanced the survival of multidomain perforator flaps by suppressing the cGAS-STING pathway, oxidative stress, and the formation of NLRP3 inflammasome. These findings unveil a potentially novel mechanism with clinical significance for promoting the survival of multidomain perforator flaps.

Elucidation of the key therapeutic targets and potential mechanisms of Andrographolide multi-targets against osteoarthritis via network pharmacological analysis and experimental validation

ObjectiveOur purpose is to unveil Andrographolide's potential multi-target and multi-mechanism therapeutic effects in treating OA via systematic network pharmacological analysis and cell experimental validation. Materials and MethodsInitially, we gathered data from Andrographolide and OA-related databases to obtain information on Andrographolide's biological properties and the targets linked with OA. We developed a bioinformatic network about Andrographolide and OA, whereby we analyzed the network to identify potential therapeutic targets and mechanisms of action of Andrographolide. Subsequently, we used molecular docking to analyze the binding sites of Andrographolide to the target proteins. At the same time, SDF-1 was used to construct an OA cell model to verify the therapeutic effect of Andrographolide on OA and its effect on target proteins. ResultsOur experimental results show that Andrographolide has excellent pharmaceutical properties, by Lipinski's rules for drugs, suggesting that this compound can be considered to have a high therapeutic potential in drug development. 233 targets were preliminarily investigated, the mechanisms through which Andrographolide targets OA primarily involve the TNF signaling pathway, PI3K-AKT signaling pathway, IL-17 signaling pathway, and TLR signaling pathway. These mechanisms target OA by influencing immune and inflammatory responses in the joints, regulating apoptosis to prevent chondrocyte death. Finally, TNF-α, STAT3, TP53, IL-6, JUN, IL-1β, HIF-1α, TGF-β1, and AKT1 were identified as 9 key targets of Andrographolide anti-OA. In addition, our molecular docking analyzes with cell experimental validation further confirm the network pharmacology results. According to our molecular docking results, Andrographolide can bind to all the hub target proteins and has a good binding ability (binding energy < -5 kcal/mol), with the strongest binding affinity to AKT1 of −9.2 kcal/ mol. The results of cell experiments showed that Andrographolide treatment significantly increased the cell viability and the expression of COL2A1 and ACAN proteins. Moreover, 30 μM Andrographolide significantly reversed SDF-1-induced increases in the protein expression of TNF-α, STAT3, TP53, IL-6, JUN, IL-1β, HIF-1α, and TGF-β1, and decreases in the protein expression of AKT1. ConclusionThis study provides a comprehensive understanding of the potential therapeutic targets and mechanisms of action of Andrographolide in OA treatment. Our findings suggest that Andrographolide is a promising candidate for drug development in the management of OA.

Identification of the Role of Mume fructus in Treating Nocturnal Asthma Based on Network Pharmacology and In vitro Investigation

Abstract Objective: Mume fructus is commonly used in traditional Chinese medicine to treat nocturnal asthma symptoms. However, the molecular mechanisms underlying its effects on nocturnal asthma have not yet been established. This study evaluated the therapeutic mechanisms of Mume fructus in treating nocturnal asthma. Materials and Methods: Network pharmacology was used to investigate the chemical composition, critical targets, and potential mechanisms of action of Mume fructus in treating nocturnal asthma. “Mume fructus” and “nocturnal asthma” were used as keywords to search the relevant databases. The 16HBE and RAW264.7 cells were treated with various concentrations of Mume fructus and lipopolysaccharides (LPSs). Data provided included analyses of cell viability detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide, cell proliferation and apoptosis detected by 5-ethynyl-2’-deoxyuridine and Hoechst 33342, messenger ribonucleic acid (mRNA) levels obtained by real-time polymerase chain reaction, and protein expression detected by Western blotting. Additionally, immunofluorescence was used to detect nuclear translocation. Results: Network pharmacology analyses were mainly enriched in nuclear factor kappa B (NF-κB), mitogen-activated protein kinase (MAPK) pathway, and interleukin (IL)-6. Mume fructus and LPS had no effect on viability, proliferation, and apoptosis in 16HBE and RAW264.7 cells under certain concentration conditions. Mume fructus counteracted LPS-stimulated mRNA and protein expression of IL-6. In addition, Mume fructus treatment prevented the LPS-induced phosphorylation of NF-κB and MAPK pathways, as well as the nuclear translocation of NF-κB p-p65 in the 16HBE and RAW264.7 cells. Conclusions: Mume fructus can treat nocturnal asthma by regulating the NF-κB and MAPK pathways and counteracting IL-6 expression. These findings provide a scientific basis for the use of Mume fructus in the treatment of nocturnal asthma.

Identification of novel AKT1 inhibitors from Sapria himalayana bioactive compounds using structure-based virtual screening and molecular dynamics simulations

Through the experimental and computational analyses, the present study sought to elucidate the chemical composition and anticancer potential of Sapria himalayana plant extract (SHPE). An in vitro analysis of the plant extract was carried out to determine the anticancer potential. Further, network pharmacology, molecular docking, and molecular dynamic simulation were employed to evaluate the potential phytochemical compounds for cervical cancer (CC) drug formulations. The SHPE exhibited anti-cancerous potential through inhibition properties against cancer cell lines. The LC-MS profiling showed the presence of 14 compounds in SHPE. Using network pharmacology analysis, AKT1 (AKT serine/threonine kinase 1) is identified as the possible potential target, and EGFR (Epidermal Growth Factor Receptor) is identified as the possible key signal pathway. The major targets were determined to be AKT1, EGFR by topological analysis and molecular docking. An in silico interaction of phytoconstituents employing molecular docking demonstrated a high binding inclination of ergoloid mesylate and Ergosta-5,7,9(11),22-tetraen-3-ol, (3.beta.,22E)- with binding affinities of -15.5 kcal/mol, and -11.3 kcal/mol respectively. Further, MD simulation and PCA analyses showed that the phytochemicals possessed significant binding efficacy with CC protein. These results point the way for more investigation into SHPE compound’s potential as CC treatment.Graphical

Anti-Cholinergic Effects of the Phenolic Extract from the Astragalus crenatus Plant: A Computational and Network Pharmacology Study.

Investigations into cholinesterase inhibition have received attention from researchers in recent years for the treatment of Alzheimer's disease. Cholinesterase enzymes, namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), hold pivotal significance in Alzheimer's disease (AD) treatment. In this study, we utilized the ethanolic extract of Astragalus crenatus followed by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to separate and identify at least 21 compounds in the extract. Rosmarinic acid exhibited the highest concentration (96.675 ± 1.3 mg/g extract), succeeded by hesperidin (79.613 ± 1.2 mg/g extract), hesperetin (75.102 ± 1.4 mg/g extract), rutin (68.156 ± 1.6 mg/g extract), chlorogenic acid (67.645 ± 1.5 mg/g extract), fisetin (66.647 ± 2.3 mg/g extract), and hyperoside (63.173 ± 1.5 mg/g extract). A. crenatus extract efficiently inhibited both AChE and BChE activities in a dosage-dependent manner. Molecular docking was employed to scrutinize the anticholinesterase mechanisms of the identified phytocompounds. Notably, a network pharmacology analysis was executed for the most efficacious compound. Based on binding energies, hesperidin emerged as the most potent inhibitor against both AChE and BChE, exhibiting scores of -10.5 Kcal/mol and -9.8 Kcal/mol, respectively. Due to its dual inhibition of AChE and BChE activities, hesperidin from Astragalus crenatus holds promise for the development of novel therapeutics aimed at neurological disorders, particularly AD.

EXPLORATION OF THE ACTIVE COMPOUNDS OF MORINGA OLEIFERA LAM AS HIV-1 REVERSE TRANSCRIPTASE INHIBITOR: A NETWORK PHARMACOLOGY AND MOLECULAR DOCKING APPROACH

Objective: This study aims to predict the active compound of Moringa oleifera for the treatment of Human Immunodeficiency Virus (HIV), specifically targeting the HIV-1 reverse transcriptase (HIV-1 RT) enzyme using network pharmacology and molecular docking approach. Methods: The active ingredients of M. oleifera, were screened from the Knapsack database. Subsequently, HIV-1 RT and its related target compounds were retrieved from the Genecard database. The analysis of common targets involved protein-protein interactions (PPI) analysis using string databases and constructing interaction IDs using Cytoscape software. Gene Ontology (GO) functional and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. Molecular docking studies were conducted using AutoDock Vina software to validate the results of the network pharmacological analysis. Results: A total of 63 active ingredients and 8601 targets related to HIV-1 RT were identified. The network analysis, encompassing GO and KEGG enrichment, revealed strong associations of common targets with key signaling pathways such as Tumor Necrosis Factor (TNF), Toll Like Receptor (TLR), and apoptosis. Additionally, 11 compounds of M. oleifera including apigenin, benzyl isothiocyanate, benzylamine, caffeic acid, ferulic acid, epicatechin, kaempferol, gallic acid, luteolin, syringic acid and vanillin were identified as potential vital compounds. Molecular docking analysis highlighted apigenin and kaempferol as the most promising compounds, exhibiting the lowest binding affinity to the HIV-1 RT enzyme. These compounds correlated with caspase-3(CASP3), caspase-9 (CASP9), and BCL2 Apoptosis Regulator (BAX) protein, stimulating cell apoptosis through multiple pathways. Conclusion: The study highlighted that apigenin and kaempferol are potential compound of M. oleifera in HIV-1 treatment through inhibition activity at HIV-1 RT Enzyme.

Investigating the Mechanism of Chufan Yishen Formula in Treating Depression through Network Pharmacology and Experimental Verification.

Objective: To investigate the antidepressant effect and potential mechanism of the Chufan Yishen Formula (CFYS) through network pharmacology, molecular docking, and experimental verification. Methods: The active ingredients and their target genes of CFYS were identified through Traditional Chinese Medicine Systems Pharmacology (TCMSP) and TCM-ID. We obtained the differentially expressed genes in patients with depression from the GEO database and screened out the genes intersecting with the target genes of CFYS to construct the PPI network. The key pathways were selected through STRING and KEGG. Then, molecular docking and experimental verification were performed. Results: A total of 113 effective components and 195 target genes were obtained. After intersecting the target genes with the differentially expressed genes in patients with depression, we obtained 37 differential target genes, among which HMOX1, VEGFA, etc., were the key genes. After enriching the differential target genes by KEGG, we found that the "chemical carcinogenesis-reactive oxygen species" pathway was the key pathway for the CFYS antidepressant effect. Besides, VEGFA might be a key marker for depression. Experimental verification found that CFYS could significantly improve the behavioral indicators of rats with depression models, including improving the antioxidant enzyme activity and increasing VEGFA levels. The results are consistent with the network pharmacology analysis. Conclusions: CFYS treatment for depression is a multicomponent, multitarget, and multipathway complex process, which may mainly exert an antidepressant effect by improving the neuron antioxidant stress response and regulating VEGFA levels.

Network pharmacology and experimental verification study on the mechanism of Hedyotis diffusa Willd in treating colorectal cancer.

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.

Network Pharmacology Analysis and Molecular Docking to Identify the Mechanism of Kuntai Capsules: Brief Research on Its Action in Premature Ovarian Insufficiency

Objective. This study aimed to explore the therapeutic targets and related pathways of Kuntai capsules (KTCs) for premature ovarian insufficiency (POI) using network pharmacology and molecular docking. Methods. The active components and their targets of KTCs were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) website, and disease therapeutic targets of POI were downloaded from DisGeNET, GeneCards, and OMIM databases and combined with the disease differential genes of POI microarray dataset from the Gene Expression Omnibus (GEO) database. The intersecting genes of drug potential therapeutic targets and disease therapeutic targets were uploaded to the STRING database to form a protein-protein interaction network. Also, the possible pathway of KTCs in the treatment of POI was explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis; through the core therapeutic targets, the corresponding active ingredients of KTCs were found. Finally molecular docking was conducted to verify the accuracy of the drug action. Results. 120 potential therapeutic targets of KTCs for POI were found. The bioinformatics analysis revealed that KTCs may regulate the recruitment, growth, and development of follicles by controlling various pathways such as fluid shear stress, atherosclerosis, PI3K/AKT, and p53 signaling. They can inhibit granulosa cell atrophy and apoptosis, promote follicle maturation, regulate follicle sensitivity to follicle-stimulating hormone, and ultimately impact ovarian function. The core therapeutic targets were TP53, AKT1, and TNF, and the corresponding active ingredients were quercetin, kaempferol, and stigmasterol. The molecular docking results showed that all the root mean square deviations were less than 2. Conclusions. KTCs improve ovarian function probably by acting on regulating the recruitment of follicles, reducing the apoptosis of granulosa cells, promoting their growth and development, reducing oxidative stress damage, and improving the sensitivity of follicles to FSH.

Integrating network pharmacology with molecular docking to rationalize the ethnomedicinal use of Alchornea laxiflora (Benth.) Pax & K. Hoffm. for efficient treatment of depression.

Background: Alchornea laxiflora (Benth.) Pax & K. Hoffm. (A. laxiflora) has been indicated in traditional medicine to treat depression. However, scientific rationalization is still lacking. Hence, this study aimed to investigate the antidepressant potential of A. laxiflora using network pharmacology and molecular docking analysis. Materials and methods: The active compounds and potential targets of A. laxiflora and depression-related targets were retrieved from public databases, such as PubMed, PubChem, DisGeNET, GeneCards, OMIM, SwissTargetprediction, BindingDB, STRING, and DAVID. Essential bioactive compounds, potential targets, and signaling pathways were predicted using in silico analysis, including BA-TAR, PPI, BA-TAR-PATH network construction, and GO and KEGG pathway enrichment analysis. Later on, with molecular docking analysis, the interaction of essential bioactive compounds of A. laxiflora and predicted core targets of depression were verified. Results: The network pharmacology approach identified 15 active compounds, a total of 219 compound-related targets, and 14,574 depression-related targets with 200 intersecting targets between them. SRC, EGFR, PIK3R1, AKT1, and MAPK1 were the core targets, whereas 3-acetyloleanolic acid and 3-acetylursolic acid were the most active compounds of A. laxiflora with anti-depressant potential. GO functional enrichment analysis revealed 129 GO terms, including 82 biological processes, 14 cellular components, and 34 molecular function terms. KEGG pathway enrichment analysis yielded significantly enriched 108 signaling pathways. Out of them, PI3K-Akt and MAPK signaling pathways might have a key role in treating depression. Molecular docking analysis results exhibited that core targets of depression, such as SRC, EGFR, PIK3R1, AKT1, and MAPK1, bind stably with the analyzed bioactive compounds of A. laxiflora. Conclusion: The present study elucidates the bioactive compounds, potential targets, and pertinent mechanism of action of A. laxiflora in treating depression. A. laxiflora might exert an antidepressant effect by regulating PI3K-Akt and MAPK signaling pathways. However, further investigations are required to validate.

Integrated Serum Pharmacochemistry and Network Pharmacological Analysis Used To Explore Possible Anti-Aging Mechanisms of the Ginsenosides

Although constitutive ginsenosides are credited with ginseng's remarkable anti-aging efficacy, the mechanism of action and bioactive components of ginsenosides are unclear. The goal of the study was to examine the effect of ginsenosides on D-galactose (D-gal)-induced aging in rats and to figure out the underlying molecular mechanism using serum pharmacochemistry and network pharmacology. Using behavioral, biochemical indexes, and histological analysis, ginsenosides were evaluated for their anti-aging effects in rats induced by D-gal, and effective ingredients absorbed in the blood were examined by ultra-performance liquid chromatography quadrupole time of flight coupled with mass spectrometry (UPLC-Q/TOF-MS) before being subjected to network pharmacology analysis. As well as improving spatial learning and memory skills, Ginsenosides are known to regulate malondialdehyde (MDA), glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) activity. In addition, it improved the ultrastructure of neurons in D-gal-induced rats' hippocampus. Seventy-four absorption components and metabolites of ginsenosides were identified in aging rat serum. According to a network pharmacology study, ginsenosides have anti-aging properties by modulating the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) and mitogen-activated protein kinases (MAPK) signaling pathways. The potential mechanisms of the anti-aging effect of ginsenosides involve multiple components, targets, and pathways. These findings serve as a foundation for further research into the processes behind ginsenoside's anti-aging impact.

Integrated network pharmacology and pharmacological investigations to explore the potential mechanism of Ding-Chuan-Tang against chronic obstructive pulmonary disease

Ethnopharmacological relevanceDing-Chuan-Tang (Abbreviated as DCT) is frequently prescribed for treatment of respiratory diseases, including chronic obstructive pulmonary disease (COPD), which is characterized by coughing, wheezing, and chest tightness in traditional Chinese medicine (TCM). However, the potential mechanism of DCT has not been investigated. Aim of studyThe aim of the study is to explore the efficiency of DCT in the treatment of COPD in vivo and in vitro, and to illustrate the possible mechanism against COPD. MethodsCOPD model was induced by exposure of mice to cigarette smoke (CS) for 16 weeks. Enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay, Western blot, etc., were used to explore the efficiency and mechanisms of DCT. Network pharmacology analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, etc., was performed to explore the potential targets in the treatment of DCT on COPD. ResultsDCT significantly alleviated pulmonary pathological changes in mouse COPD model, and inhibited inflammatory response induced by CS and LPS in vivo and in vitro. Network pharmacology analysis suggested that DCT alleviated COPD via inhibiting inflammation by regulating PI3K-AKT pathway. In cell-based models, DCT suppressed the phosphorylation of PI3K and AKT, which further regulated its downstream targets Nrf2 and NF-κB, and inhibited inflammatory response. ConclusionsDCT effectively attenuated COPD in the mouse model induced by CS. The therapeutic mechanism of DCT against COPD was closely associated with the regulation of PI3K-AKT pathway and its downstream transcription factors, Nrf2 and NF-κB.

Mechanisms of Action of Potentilla discolor Bunge in Type 2 Diabetes Mellitus Based on Network Pharmacology and Experimental Verification in Drosophila.

Type 2 diabetes mellitus (T2DM) is associated with reduced insulin uptake and glucose metabolic capacity. Potentilla discolor Bunge (PDB) has been used to treat T2DM; however, the fundamental biological mechanisms remain unclear. This study aimed to understand the active ingredients, potential targets, and underlying mechanisms through which PDB treats T2DM. Components and action targets were predicted using network pharmacology and molecular docking analyses. PDB extracts were prepared and validated through pharmacological intervention in a Cg>InRK1409A diabetes Drosophila model. Network pharmacology and molecular docking analyses were used to identify the key components and core targets of PDB in the treatment of T2DM, which were subsequently verified in animal experiments. Network pharmacology analysis revealed five effective compounds made up of 107 T2DM-related therapeutic targets and seven protein-protein interaction network core molecules. Molecular docking results showed that quercetin has a strong preference for interleukin-1 beta (IL1B), IL6, RAC-alpha serine/threonine-protein kinase 1 (AKT1), and cellular tumor antigen p53; kaempferol exhibited superior binding to tumor necrosis factor and AKT1; β-sitosterol demonstrated pronounced binding to Caspase-3 (CASP3). High-performance liquid chromatography data quantified quercetin, kaempferol, and β-sitosterol at proportions of 0.030%, 0.025%, and 0.076%, respectively. The animal experiments revealed that PDB had no effect on the development, viability, or fertility of Drosophila and it ameliorated glycolipid metabolism disorders in the diabetes Cg>InRK1409A fly. Furthermore, PDB improved the body size and weight of Drosophila, suggesting its potential to alleviate insulin resistance. Moreover, PDB improved Akt phosphorylation and suppressed CASP3 activity to improve insulin resistance in Drosophila with T2DM. Our findings suggest that PDB ameliorates diabetes metabolism disorders in the fly model by enhancing Akt activity and suppressing CASP3 expression. This will facilitate the development of key drug targets and a potential therapeutic strategy for the clinical treatment of T2DM and related metabolic diseases.