Network Pharmacology Research Articles

Mechanism of Gastrodin against neurotoxicity based on network pharmacology, molecular docking and experimental verification

BackgroundDisorders of glutamate metabolism and excessive release participat in multiple neuronal pathologies including ischemic stroke (IS), Alzheimer's disease (AD), or Parkinson's disease (PD). Recently, herbal medicines have been widely used and have shown satisfactory results in the treatment of neurological disorders. Gastrodin is a traditional Chinese medicine (TCM) used for the treatment of nerve injuries, spinal cord injuries, and some central nervous system diseases as well. This research examines the neuroprotective effects of Gastrodin against glutamate-induced neurotoxicity in neuronal cells. MethodsThe HERB database was used to explore the active ingredients and target genes of Gastrodia Elata. The STRING database and Cytoscape software were used to screen and construct the Protein-Protein Interaction (PPI). Furthermore, we used molecular docking to predict the potential targets of Gastrodin. The effects of Gastrodin were revealed by western blot, calcium imaging, membrane clamp, CCK8 and flow cytometry. Neuronal oxidative stress and damage were assessed by measuring malondialdehyde (MDA) levels and superoxide dismutase (SOD) activity. Neuronal morphology was examined using Golgi-Cox staining. Finally, animal behavior was examined using novel object recognition and fear conditioning tests. ResultsWe have obtained 22 components such as TM10, TM17, TM25 (Gastrodin), and 281 targets such as AKT, EGFR, and CDK1 through network pharmacology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed these genes were significantly enriched in protein phosphorylation, protein serine/threonine/tyrosine kinase activity, apoptosis and HIF-1 signaling pathways, etc. A higher affinity between Gastrodin and AKT was revealed by PPI analysis and molecular docking. Further, Gastrodin significantly inhibited Ca2+ influxes and excitatory synaptic transmission in cortical neurons. In addition, Gastrodin effectively alleviated neuron apoptosis, oxidative stress and damage. ConclusionGastrodin has neuroprotective effects against glutamate-induced neurotoxicity.

Therapeutic mechanism and key active ingredients of Yinxing Mihuan Oral Solution in coronary heart disease comorbidity with anxiety: A network pharmacology and molecular docking approach.

Yinxing Mihuan Oral Solution (YMOS) is a Chinese patent medicine for treating coronary heart disease combined anxiety (CHDCA), but the molecular mechanism of its treatment is still unclear. This article aims to understand the molecular mechanism, optimize clinical drug use, and guide new drug development. Using the Swiss Target Prediction database, we obtained the main chemical composition of YMOS. Then we used network pharmacology to identify their potential targets. Network construction, coupled with protein-protein interaction and enrichment analysis was used to identify representative components and core targets. Finally, molecular docking simulation was conducted to further refine the drug-target interaction. Forty-two active chemicals were found in YMOS and 91 target genes related to CHDCA. The treatment effect was found to be associated with 1908 biological processes and 160 pathways, as revealed by the outcomes of the enrichment analysis. The potential therapeutic mechanisms of the drug are closely related to its antioxidant, anti-inflammatory, and vascular function regulation pathways, and the main core targets include albumin, tumor necrosis factor, TP53, AKT serine/threonine kinase 1, interleukin 1 beta, and vascular endothelial growth factor A. The potential molecular mechanisms of YMOS in CHDCA treatment were identified using network pharmacology and molecular docking approaches. The results reveal the systemic biological implications of YMOS. This study has systematically uncovered the molecular mechanism of YMOS for the first time, offering fresh insights for evidence-based clinical applications.

An Investigation of the Effect of the Traditional Naxi Herbal Formula Against Liver Cancer Through Network Pharmacology, Molecular Docking, and In Vitro Experiments

Background/Objectives: The formula Chong-Lou-Yao-Fang (CLYF) is an herbal medicinal formulation developed by the indigenous Naxi people for treating liver cancer. This study was to reveal the biological activity, potential targets, and molecular mechanisms of CLYF for cancer treatment. Methods: Network pharmacology, microarray data analysis, survival analysis, and molecular docking were employed to predict potential compounds, targets, and pathways for the treatment of liver cancer. In vitro experiments and Western blot validation were conducted to confirm these predictions. Results: 35 key compounds and 20 core targets were screened from CLYF, involving signaling pathways for PI3K–Akt, MAPK, hepatitis B and C, which were effective for liver cancer treatment. Microarray data analysis and survival analysis indicated that EGFR and TP53 serve as promising biomarkers for diagnosis and prognosis in liver cancer. Molecular docking revealed stable binding between EGFR, TP53, and AKT1 with active ingredients. Cell experiments confirmed that CLYF-A suppressed cell proliferation, induced apoptosis, and caused cell cycle arrest in HepG2 cells, which were associated with a loss of mitochondrial membrane potential. Compared to the control group, the relative protein expression levels of EGFR and AKT1 significantly decreased following treatment with CLYF-A, while TP53 levels increased significantly. Conclusions: Verification of the anticancer activity of CLYF and its potential mechanisms may have important implications for anticancer therapies. Our results may provide a scientific basis for the clinical use of CLYF for cancer treatment and have important implications for developing pharmaceutical preparations, which also need more pharmacological experiments, clinical experiments, and in vivo experiments.

A Network Pharmacology Study on Mechanism of Total Flavonoids of Hippophae Rhamnoides in Treating Allergic Dermatitis via Regulation of IL-17 Signaling Pathways

Objective: This study aims to investigate the active ingredients and potential mechanisms of Total Flavonoids of Hippophae (TFH) in the treatment of Allergic Dermatitis (AD) using network pharmacology and molecular docking. Methods: The effective components and targets of TFH were identified using the TCMSP, Pub- Chem, and Pharmmapper databases. AD-related targets were screened through GeneCards, OMIM, and TTD databases, leading to the identification of TFH anti-AD related targets. The STRING database was utilized to obtain protein interaction relationships, and Cytoscape 3.9.0 software was employed to construct the protein-protein interaction network. GO and KEGG enrichment analyses were conducted to elucidate the biological processes and pathways involved. Molecular docking between key components and key targets was verified using AutoDock Tools 1.5.6 software. Results: The key components identified for anti-AD activity were Quercetin, Kaempferol, Cianidanol, and Epicatechin, while the key targets included MAPK8, MAPK10, MAPK14, AKT1, SRC, and EGFR. GO analysis indicated that TFH's anti-AD effects are primarily associated with hormone regulation, cellular processes, response to stimuli, organelles, and cytoplasm. KEGG enrichment analysis suggested that the key pathways involved are pathways in cancer, lipid and atherosclerosis, and the IL-17 signaling pathway, with a significant emphasis on the IL-17 signaling pathway. Molecular docking results demonstrated that the key active ingredients exhibited strong binding activity with all the key targets, with the highest binding affinities observed between kaempferol and MAPK14, epicatechin and MAPK14, and quercetin and AKT1. Conclusion: TFH exerts therapeutic effects on atopic dermatitis through multi-component, multitarget, and multi-pathway mechanisms involving inflammatory response, immune regulation, and apoptosis. This study provides valuable insights for the further development of drugs specifically targeting AD.

Quercetin inhibits mitophagy-mediated apoptosis and inflammatory response by targeting the PPARγ/PGC-1α/NF-κB axis to improve acute liver failure

BackgroundReactive oxygen species (ROS) from mitochondrial dysfunction are critical in triggering apoptosis and inflammation in acute liver failure (ALF). Quercetin (QUE), an antioxidant, is renowned for its therapeutic effects onliverdiseases. There are no studies on whether QUE regulates mitophagy level in hepatocytes to inhibit ALF. ObjectiveThis study investigates QUE’s protective effects on ALF and elucidates the mechanisms involved. MethodsThe ALF and hepatocyte inflammatory injury model was established using LPS and D-Galn. To predict potential targets and mechanisms of QUE in ALF treatment, transcriptomics, network pharmacology, molecular docking techniques, and ChIP were employed. The expression level related to mitophagy, apoptosis, and signaling pathways were detected by CCK8, IHC, IF staining, TUNEL, RT-qPCR, TEM, Western blotting, ELISA, and flow cytometry. ResultsNetwork pharmacology and transcriptomics revealed common targets between QUE and ALF. Enrichment analysis showed that the anti-ALF targets of QUE were significantly associated with mitochondria and NF-κB-related pathways. Subsequent experiments showed that QUE pretreatment significantly alleviated the loss of hepatocyte viability, enhanced mitochondrial membrane potential, activated mitophagy, and promoted the clearance of damaged mitochondria, thereby reducing ROS accumulation, significantly reducing cell apoptosis and inflammatory responses, reducing ALT and AST levels, and improving liver tissue pathology. Mechanistically, molecular docking, DARTS, and CETSA analyses confirmed that QUE directly binds to the PPARγ molecule, which reduced binding to IκB and significantly inhibit the NF-κB pathway to exert its protective effects. ConclusionIn short, our results provide the first evidence that QUE improves acute liver failure by promoting mitophagy through regulating the PPARγ/PGC-1α/NF-κB axis and inhibiting apoptosis and inflammatory responses mediated by mitochondrial dysfunction, which provides evidence for the potential of QUE in the treatment of ALF.

Bioinformatics and network pharmacology discover the molecular mechanism of Liuwei Dihuang pills in treating cerebral palsy.

A collection of chronic central motor, postural, and activity restriction symptoms are referred to as cerebral palsy (CP). Previous research suggests that a number of perinatal variables, including hypoxia, may be linked to CP. And the pathophysiological process that causes brain injury in growing fetuses is mostly caused by amniotic fluid infection and intra-amniotic inflammation. Still, there is still much to learn about the molecular mechanism of CP. The goal of this study was to identify the molecular mechanism of Liuwei Dihuang pill (LWDHP) in the treatment of CP using network pharmacology and bioinformatics. The Chinese medicine database provided the LWDHP components and targets, the CP illness gene data set was gathered from a disease, and the expression profile of children with CP was chosen from anther database. Using the Kyoto Encyclopedia of Genes and Genomes and gene ontology databases, a network of interactions between proteins was created, and functional enrichment analysis was carried out. Analysis of traditional Chinese medicine found that the key active ingredients of LWDHP are quercetin, Stigmasterol and kaempferol. Through enrichment analysis, it was found that the hub genes for LWDHP treatment of CP are CXCL8, MMP9, EGF, PTGS2, SPP1, BCL2L1, MMP1, and AR. K EGG analysis found that LWDHP treatment of CP mainly regulates PI3K-Akt signaling pathway, IL-17 signaling pathway, Jak-STAT signaling pathway, NF-kappa B signaling pathway, etc. To summarize, LWDHP regulates immunological and inflammatory variables through a variety of components, targets, and signaling pathways, which plays a significant role in the development and management of CP.

Study on the anti-atherosclerosis mechanisms of Tanyu Tongzhi formula based on network pharmacology, Mendelian randomization, and experimental verification

Context Tanyu Tongzhi Formula (TTF) exhibits potential against atherosclerosis; however, its mechanisms remain unclear. Objective This study explores the pharmacological mechanisms of TTF in treating atherosclerosis. Materials and methods Network pharmacology, molecular docking, mendelian randomization (MR), and liquid chromatography-mass spectrometry (LC-MS) analyses were utilized to reveal potential targets and compounds of TTF against atherosclerosis. After exploring the appropriate concentration of TTF to treat HCAECs using Cell Counting Kit-8 (CCK-8), the HCAECs were divided into three groups: control, oxidized low-density lipoprotein (ox-LDL, 50 μg/mL), and ox-LDL (50 μg/mL) + TTF (1 mg/mL). After 24-h incubation, the efficacy of TTF was verified by CCK-8, Oil red O staining, and ELISA. The expression of key targets was detected by real-time polymerase chain reaction (qPCR) and western blotting. Results A total of 137 active compounds and 127 potential TTF targets against atherosclerosis were identified. MR identified ALB, TNF, PPARα, and PPARγ as key targets. Molecular docking indicated that baicalin, naringenin, and curcumin exhibited suitable binding activities to these targets, further confirming by LC-MS analysis. The IC50 of TTF in HCAECs was 18.25 mg/mL. TTF treatment significantly improved atherosclerosis by enhancing cell viability, reducing lipid accumulation, and inhibiting inflammation factors (IL6, IL1B and TNF-α) in ox-LDL-treated HCAECs. Moreover, qPCR or western blotting indicated that TTF could up-regulate PPARα and PPARγ while down-regulate TNF expression. Discussion and conclusions Our results revealed active compounds, key pathways, and core targets of TTF against atherosclerosis, providing experimental support for its application in treating of atherosclerosis.

Integrating network pharmacology, molecular docking, and experimental validation to reveal the mechanism of Radix Rehmanniae in psoriasis.

Radix Rehmanniae (RR) plays an important role in treating psoriasis. However, the active compounds of RR and potential mechanisms are unclear. The current study was designed to investigate the potential active ingredients, targets, and mechanisms of RR in treating psoriasis through network pharmacology, molecular docking, and vitro experiments. Initially, the TCMSP database and literature retrieval were used to access the active ingredients of RR. The psoriasis target proteins were obtained from Therapeutic Target Database, OMIM, GeneCards, and DrugBank databases. The target proteins were then converted into target genes using Uniprot. Secondly, overlapping genes were obtained through Venn online tool. Then, protein-protein interactions network diagram is finished by STRING database. Next, Cytoscape software was used to acquire the top 10 hub proteins; gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis were then used to predict possible mechanisms. Afterwards, molecular docking validation of the active ingredients with the main targets was performed by AutoDock software. Finally, lipopolysaccharides induced RAW264.7, to assess the effects and molecular mechanisms by MTT, RT-qPCR, and Western blot assays. Overall, there are 20 effective compounds and 33 targets involved in biological processes including apoptosis, intracellular signaling, vasodilation, and mitogen-activated protein kinase (MAPK) signaling cascade. The docking results showed strong binding capacity between the active ingredients and targets. We verified aucubin as the key active ingredient, tumor necrosis factor α, and IL6 as the core targets, and focused on the p38MAPK protein pathway. Cellular experiments showed that aucubin down-regulated the phosphorylated p38MAP protein and reduced the expression of tumor necrosis factor α mRNA, IL6 mRNA, and IL1βmRNA. In summary, RR is featured with multicomponent, multi-target, and multi-pathway in treating psoriasis; the preliminary mechanism may be associated with the down-regulation of p38MAPK phosphorylation and curbing the expression of inflammatory factor by aucubin. This paper provides the scientific basis for Traditional Chinese medicine treating psoriasis.

Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network

Background/Objectives: Acute myeloid leukemia (AML) is characterized by therapeutic failure and long-term risk for disease relapses. As several therapeutic targets participate in networks, they can rewire to eventually evade single-target drugs. Hence, multi-targeting approaches are considered on the expectation that interference with many different components could synergistically hinder activation of alternative pathways and demolish the network one-off, leading to complete disease remission. Methods: Herein, we established a network-based, computer-aided approach for the rational design of drug combinations and de novo agents that interact with many AML network components simultaneously. Results: A reconstructed AML network guided the selection of suitable protein hubs and corresponding multi-targeting strategies. For proteins responsive to existing drugs, a greedy algorithm identified the minimum amount of compounds targeting the maximum number of hubs. We predicted permissible combinations of amiodarone, artenimol, fostamatinib, ponatinib, procaine, and vismodegib that interfere with 3–8 hubs, and we elucidated the pharmacological mode of action of procaine on DNMT3A. For proteins that do not respond to any approved drugs, namely cyclins A1, D2, and E1, we used structure-based de novo drug design to generate a novel triple-targeting compound of the chemical formula C15H15NO5, with favorable pharmacological and drug-like properties. Conclusions: Overall, by integrating network and structural pharmacology with molecular modeling, we determined two complementary strategies with the potential to annihilate the AML network, one in the form of repurposable drug combinations and the other as a de novo synthesized triple-targeting agent. These target–drug interactions could be prioritized for preclinical and clinical testing toward precision medicine for AML.

Erianin inhibits the progression of pancreatic cancer by directly targeting AKT and ASK1

BackgroundPancreatic cancer is a malignant tumor of the digestive tract with a high mortality rate. Erianin has antitumor activity, but the regulatory targets and mechanism of action in pancreatic cancer are unclear. The objective of this study was to evaluate the anti-pancreatic cancer activity of Erianin and explore its underlying mechanisms.MethodsA network pharmacology approach was used to investigate the mechanism of action of Erianin in pancreatic cancer cells. Cell proliferation was analyzed using CCK8, colony-formation, and EdU proliferation assays. Cell migration was evaluated through wound healing and transwell assays, as well as determination of the protein expression levels of EMT markers and β-catenin. Apoptosis and the cell cycle were measured using flow cytometry and JC-1 staining, respectively. The protein expression levels of p-Rb, CyclinB1, P21, Cleaved-PARP, and Cleaved-Caspase3 were assessed using western blotting. RNA sequencing (RNA-seq) and bioinformatics analyses were performed to elucidate the mechanism underlying the action of Erianin in pancreatic cancer. Western blotting was used to examine the expression levels of key proteins in the AKT, JNK, and p38 MAPK signaling pathways. Molecular docking and CETSA were used to test hypotheses. The tumor-suppressive ability of Erianin in vivo was assessed using a tumor-bearing assay in nude mice.ResultsNetwork pharmacology revealed that Erianin inhibited pancreatic cancer through multiple pathways. Erianin significantly inhibited pancreatic cancer cell proliferation and migration while promoting intracellular ROS and inducing apoptosis. Mechanistically, Erianin inhibited pancreatic cancer cell proliferation by regulating the AKT/FOXO1 and ASK1/JNK/p38 MAPK signaling pathways. In vivo experiments showed that Erianin inhibited subcutaneous tumor growth and promoted tumor tissue apoptosis in nude mice.ConclusionsThe component-target-pathway network revealed that Erianin exerted anti-cancer effects through multiple components, targets, and pathways. Erianin inhibited the proliferation and migration of pancreatic cancer cells and induced apoptosis through the AKT/FOXO1 and ASK1/JNK/p38 MAPK signaling pathways. These results indicate that Erianin is a promising agent for pancreatic cancer treatment.

Searching for Hub Genes of Quince–Basil Co-Administration Against Atherosclerosis Using Bioinformatics Analysis and Experimental Validation

Background: Atherosclerosis (AS) has one of the highest rates of morbidity and death globally. Cydonia oblonga Mill. (quince, COM) and Ocimum basilicum L. (basil, OB) are Uyghur medicines that are often used for anti-inflammatory, anti-tumor, and cardiovascular disease treatment. This study aimed to uncover the hub genes of the quince-basil co-administration against AS and validate them. Methods: Network pharmacology analysis and bioinformatics analysis methods were utilized to map the network and obtain four hub genes. Experiments were performed in vivo and in vitro using HUVEC and zebrafish to validate the therapeutic effect of COM-OB co-administration against AS. Finally, the hub genes were validated by Western blot. Results: Screening by network pharmacology analysis and bioinformatics analysis obtained a total of 3302 drug targets, 1963 disease targets, and 1630 DEGs. A series of bioinformatic analyses were utilized to ultimately screen four hub genes, and the stability was also verified by molecular docking and molecular dynamics. COM-OB total flavonoids co-administration significantly decreased PA-induced lipid deposition in HUVEC and reduced high cholesterol-induced fat accumulation in zebrafish. Western blot results showed that COM-OB co-administration significantly affected the expression of hub genes. Conclusions: The study identified and validated four hub genes, COL1A1, COL3A1, BGLAP, and NOX4, thus providing a rationale for the treatment of AS with COM and OB co-administration.

Banxia xiexin decoction prevents the development of gastric cancer.

In China banxia xiexin decoction (BXD) has been used in treating gastric cancer (GC) for thousands of years and BXD has a good role in reversing GC histopathology, but its chemical composition and action mechanism are still unknown. To investigate the mechanism of action of BXD against GC based on transcriptomics, network pharmacology, in vivo and in vitro experiments. The transplanted tumor model was prepared, and the nude mouse were pathologically examined after administration, and hematoxylin-eosin staining was performed. The active ingredients of BXD were quality controlled and identified using ultra-performance liquid chromatography tandem quadrupole electrostatic field orbitrap mass spectrometry (UPLC-Q-Orbitrap MS/MS), and traditional Chinese medicines systems pharmacology platform, drug bank and the Swiss target prediction platform to predict the relevant targets, the differentially expressed genes (DEGs) of GC were screened by RNA-seq sequencing, and the overlapping targets were analyzed to obtain the key targets and pathways. Cell Counting Kit-8, apoptosis assay, cell migration and Realtime fluorescence quantitative polymerase chain reaction were used for in vitro experiments. All dosing groups inhibited the growth of transplanted tumors in laboratory-bred strain nude, with the capecitabine group and the BXD medium-dose group being the best. A total of 29 compounds and 859 potential targets in BXD were identified by UPLC-Q-Orbitrap MS/MS and network pharmacology, RNA-seq sequencing found 4767 GC DEGs, which were combined with network pharmacology and analyzed 246 potential therapeutic targets were obtained and pathway results showed that BXD may against GC through the Phosphoinositide 3-kinase (PI3K)/protein kinase B (AKt) signaling pathway. In vitro cellular experiments confirmed that BXD-containing serum and LY294002 could inhibit the proliferation of GC cells, promote apoptosis, and inhibit the migration of GC cells by decreasing the expression of EGFR, PIK3CA, IL6, BCL2 and AKT1 in the PI3K-Akt pathway in MGC-803 expression. BXD has the effect of inhibiting tumor growth rate and delaying the development of GC. Its mechanism of action may be related to the regulation of PI3K-Akt signaling pathway.

Dan’e fukang decoction reduces hemorrhage in a rat model of mifepristone induced incomplete abortion and may correlate with cell adhesion molecule signaling interference

Ethnopharmacological relevanceDan’e fukang decoction (DFD) is a traditional Chinese medicine formula. DFD obtains 10 herbs, including Salvia yunnanensis C.H.Wright (Zidanshen), Curcuma zedoaria (Christm.) Roscoe (Ezhu), Angelica sinensis (Oliv.) Diels (Danggui), Cyperus rotundus L. (Xiangfuzi), Corydalis yanhusuo (Y.H.Chou & Chun C. Hsu) W.T.Wang ex Z.Y.Su & C.Y.Wu, Bupleurum marginatum Wall. ex DC. (Yanhusuo), Sparganium stoloniferum (Buch.-Ham. ex Graebn.) Buch.-Ham. ex Juz. (Sanleng), Panax notoginseng (Burkill) F.H.Chen (Sanqi), Paeonia lactiflora Pall. (Shaoyao) and Glycyrrhiza uralensis Fisch. (Gancao). DFD is now clinically used for the treatment of menstrual irregularities, dysmenorrhea and menstrual discomfort caused by blood stasis and easing of endometriosis. Based on this, it is reasonable to presume that DFD may be effective in treating incomplete abortion and reducing postpartum bleeding, but no specific studies have been reported so far. Aim of the studyTo investigate the efficacy of Dan’e fukang decoction (DFD) in reducing prolonged vaginal bleeding followed by mifepristone induced incomplete abortion and explore the mechanisms of action of DFD in treating incomplete abortion. MethodsAn incomplete abortion model of rat was established by single intragastrically administered 8.5 mg/kg mifepristone on the 7th day of pregnancy. From the 8th day of pregnancy, the abortive rats were administered solvent, a positive control drug, or different doses of DFD, respectively for seven consecutive days. The efficacy of DFD was assessed by measuring the vaginal bleeding volume of the rats. Four coagulation parameters and platelet counts were measured. Hematoxylin and eosin (HE) staining was performed to evaluate pathological changes in the uterine embryos. Serum levels of progesterone and estrogen were measured using ELISA. Network pharmacology and transcriptomics were used to predict potential targets and pathways for DFD to reduce hemorrhage. The levels of mRNA related to cell adhesion molecules (CAMs) were detected by RT-qPCR. The levels of progesterone and estrogen receptors and the proteins associated with CAMs pathway in uterine tissues were detected by Western Blot. ResultsDFD significantly reduced the volume of vaginal bleeding of the abortive rats and significantly downgraded the pathological scores of uterine embryos. DFD significantly increased serum levels of E2, and had no impact on serum levels of P4 and the protein expression of ER and PR in the uteri of the abortive rats. Pathways in cancer, lipid, focal adhesion and immune-related signaling were predicted to be influenced by DFD via the analysis of network pharmacology. The CAMs signaling was found the most critical pathway regulated by both mifepristone and DFD via RNA-seq assay, followed by axon guidance, basal cell carcinoma, hippo signaling pathway and neuroactive ligand-receptor interaction. Combining the two analytical methods, ICAM-1 was predicted likely the key targeted gene by DFD. Finally, DFD was validated to decrease the protein expression of ICAM-1, ITGB2, ITGB7 and RASSF5 in the uterine tissues, which correlated to suppress the CAMs signaling pathway. ConclusionDFD significantly reduced hemorrhage. DFD significantly increased the serum levels of E2 and inhibited CAMs signaling pathway, which was likely to be involved in the mechanism of action of DFD facilitating residual uterine embryo expulsion in the rat model of incomplete abortion.

Mechanistic Insights into the Antioxidant Potential of Sugarcane Vinegar Polyphenols: A Combined Approach of DPPH-UPLC-MS, Network Pharmacology and Molecular Docking

Mechanistic Insights into the Antioxidant Potential of Sugarcane Vinegar Polyphenols: A Combined Approach of DPPH-UPLC-MS, Network Pharmacology and Molecular Docking

Application of Network Pharmacology, Molecular Docking, and In Vitro Experimental Evaluation to Decipher the Anti-Inflammatory Mechanisms of Cirsium japonicum

Cirsium japonicum, a traditional herb, exhibits significant anti-inflammatory activity. However, the main components and potential mechanisms of C. japonicum remain unclear. The aim of this study is to investigate the anti-inflammatory mechanism of Cirsium japonicum through network pharmacology and cellular experiments. The effective components of and potential targets for the anti-inflammatory activity of C. japonicum were identified using a traditional Chinese medicine systematic pharmacology database, the TCMSP analysis platform, and the GeneCards database. The drug–component–target–disease network diagram was constructed using Cytoscape 3.8.0 software, while the protein interaction network diagram was created using the STRING database and Cytoscape 3.8.0 software. Gene ontology (GO) enrichment and KEGG pathway enrichment analysis were carried out using the DAVID database. Molecular docking between key targets and active components was constructed with AutoDock 4.2.6 software to determine the best binding target. The results revealed that 14 active components of C. japonicum targeted 171 anti-inflammatory proteins. GO function enrichment analysis yielded 173 items, while KEGG pathway enrichment analysis identified 48 signaling pathways related to inflammation regulation. Molecular docking showed a strong affinity of sitosterol, stigmasterol, and other components with key targets such as peroxisome proliferator-activated receptor α recombinant protein (PPARA) and cyclooxygenase-2 (PTGS2). Vanillin, one active ingredient of C. japonicum, inhibited the release of lipopolysaccharide (LPS)-induced inflammatory factors in RAW264.7 cells. These findings suggest that C. japonicum may exert its anti-inflammatory effects by modulating the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signal pathway (PI3K-Akt) and apoptin signal pathway, highlighting the multi-component, multi-target, and multi-channel molecular mechanism underlying its anti-inflammatory properties. Finally, the anti-inflammatory effect of vanillin, an effective component of C. japonicum, was verified by cell experiments. This study provides a new understanding of the pharmacological mechanisms of C. japonicum in the treatment of inflammatory conditions.

Synthesis of novel (R)-Carvone-1,2,3-triazole hybrids: Network pharmacology, molecular docking, and dynamics simulation targeting tumor protein markers

Cancer poses a global health crisis with increasing incidence and mortality rates, urging the development of novel anti-cancer therapies. 1,2,3-triazoles, recognized for their diverse biological activities, offer promising avenues for drug discovery targeting critical proteins associated with various cancer types. In this study, various derivatives of 1,2,3-triazoles were synthesized and their anti-cancer potential was tested under both in-silico and in-vitro conditions. The synthesized derivatives 9a-h show IC50 values in the range of 25–100 µM against various cancer cell lines. Incorporating the 4-nitro-phenyl group at the N1 position of the triazole nucleus 9d resulted in increased activity compared to other synthesized 1,2,3-triazoles against HT-1080 and MCF-7. A network pharmacology study was conducted to predict the breast cancer targets of the synthesized regioisomers. The results indicate that the proteins SRC, MYC, and HSP90AA1 are most likely the breast cancer targets of the synthesized compounds. To study the binding effect of synthesized compounds on the selected targets, a molecular docking study was conducted and it revealed that both synthesized compounds have good binding affinity towards SRC (< -7.0 kcal/mol). Also, the synthesized compounds showed no violations at any of the drug-likeness filters during the ADME study. Finally, molecular dynamics simulation was carried out to determine the stability of interaction between the protein and ligand for a 200 ns duration. The SRC complexed with compound 9d showed more stability during MD simulation with few interactions being maintained throughout the simulation time. Therefore, compound 9d could be a promising drug candidate for cancer chemotherapy.

Analysis of pharmacological effects and mechanisms of compound essential oils via GC-MS and network pharmacology.

Aromatherapy based on essential oil (EO) has been widely used for alleviating pain and intense where no compound EO reports its application on pharmacological effects. In order to explore the active pharmaceutical ingredients (API) and mechanism of a compound EO, a blend of Artemisia argyi, Boswellia carterii, Commiphora myrrha, Cinnamomum cassia, Zingiber oj-jicinale, and Ilex pubescens EO, in treating neck and shoulder pain (NSP). Network pharmacology hyphenated with mice model was employed to investigate. Gas chromatography-mass spectrometry (GC-MS) was applied for the identification of constituents in compound EO. Lastly, transdermal absorption of compound EO was studied before verifying analgesic and anti-inflammatory effects in mice. Totally, 75 compounds were tentatively identified through GC-MS, predicting 46 potential analgesic targets. Moreover, 11 core targets were obtained through network topology screening. Animal test resulted that the compound EO had significantly stronger anti-inflammatory and analgesic effects compared to single EO. Multiple API in compound EO affected on targets and exerted therapeutic effects on NSP through multiple pathways. Afterwards, eucalyptol, camphor, and borneol from compound EO exhibited a sustained-release effect, which provide scientific basis to illustrate the application of compound EO in clinical.

Effect of particle size on dissolution of different chemical components in Codonopsis pilosula.

Codonopsis pilosula (Franch.) Nannf. is a traditional herb for treating immunosuppression. C. pilosula boiling powder (CP-BP) contains particles of a small size made from C. pilosula decoction pieces (CP-DP). It is still unclear how changes in particle size during the decoction process affect the dissolution of various chemical components in C. pilosula. Herein, an ultra-high-performance liquid chromatography-quadrupole-Exactive Orbitrap mass spectrometry technique was established to characterize the components of CP-BP and CP-DP decoctions. The contents of the components were evaluated based on the relative peak area, extract yield, and alcohol solubility rate. A total of 71 compounds were finally identified, and their content in the CP-BP decoction was generally higher than that in the CP-DP decoction. Alkaloids had the highest average content, whereas terpenoids were the most affected by changes in particle size. In addition, immunosuppression was used as model to investigate whether these changes have practical significance. The results of network pharmacology suggested that the phosphoinositide 3-kinase (PI3K)-Akt pathway may be a potential pathway of C. pilosula for treating immunosuppression. The results of molecular docking indicated that compounds with large content variations have good docking affinity with key targets (epidermal growth factor receptor [EGFR], prostaglandin-endoperoxide synthase 2 [PTGS2], and peroxisome proliferator-activated receptor gamma [PPARG]). These results provide an important reference for further development and use of C. pilosula.

Wuzi Yanzong Decoction Ameliorates Oligoasthenozoospermia by Up-Regulating Methyltransferaseand IncreasingSpata, Bcl, and Pik3Series GenesMethylationLevel.

Wuzi Yanzong decoction (WZYZD) belongs to the traditional formula for treatingmale infertility caused by oligoasthenozoospermia (OLI). This research aims to elucidate the therapeutic substance basis and potential pharmacological mechanisms of WZYZD in treating OLI.A total of 52 chemical ingredients were identified from WZYZD.HEand TUNEL staining demonstrated that WZYZD can markedly alleviate OLI.Immunofluorescence analysis showed that WZYZD can significantly increase the expression levels of DNMT3A, PIWIL1, SETDB1, and PRMT5. Methyl capture sequencingproved that WZYZD can markedly upregulate the methylated level of Spata, Bcl,and Pik3series genes. Network pharmacology analysis proved that WZYZD can ameliorate OLI through BCL-2 and PI3K-AKT signaling pathways. The immunofluorescence assay of BCL-2 and SPATA18 proved the aforementioned results.The potential mechanism of WZYZD in treating OLImainly involved recruiting methyltransferase DNMT3A, PIWIL1, PRMT5, and SETDB1 and increasing the methylation degree of Spata, Bcl, and Pik3series genes.

Integrative Network Pharmacology, Molecular Docking, and Dynamics Simulations Reveal the Mechanisms of Cinnamomum tamala in Diabetic Nephropathy Treatment: An In Silico Study

Diabetic nephropathy (DN) is a serious diabetes-related complication leading to kidney damage. Cinnamomum tamala (CT), traditionally used in managing diabetes and kidney disorders, has shown potential in treating DN, although its active compounds and mechanisms are not fully understood. This study aims to identify CT’s bioactive compounds and explore their therapeutic mechanisms in DN. Active compounds in CT were identified using the Indian Medicinal Plants, Phytochemicals and Therapeutics database, and their potential targets were predicted with PharmMapper. DN-related targets were sourced from GeneCards, and therapeutic targets were identified by intersecting the compound–target and disease–target data. Bioinformatics analyses, including the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment studies, were performed on these targets. A protein–protein interaction network was constructed using STRING and Cytoscape. Molecular docking and dynamics simulations validated the most promising compound–target interactions. Six active compounds in CT were identified, along with 347 potential therapeutic targets, of which 70 were DN-relevant. Key targets like MMP9, EGFR, and AKT1 were highlighted, and the PPAR and PI3K-AKT signaling pathways were identified as the primary mechanisms through which CT may treat DN. CT shows promise in treating DN by modulating key pathways related to cellular development, inflammation, and metabolism.