Integrative Network Pharmacology and Molecular Docking-Based Validation of Berberine as a Therapeutic Agent in Arsenic-Induced Cardiotoxicity.

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Exposure to arsenic (As) is a serious environmental and public health risk because it can cause systemic toxicity, which could lead to serious cardiovascular disease like heart failure, arrhythmias, and coronary heart disease (CHD). Exploring safer and multi-target therapeutic agents is gaining popularity as a result of the shortcomings of traditional therapies. The isoquinoline alkaloid berberine which is derived from plants, exhibits strong anti-inflammatory, antioxidant, and cardioprotective properties. This study employs an integrated network pharmacology and molecular docking approach to investigate the molecular mechanisms and therapeutic potential of berberine in arsenic-induced cardiotoxicity. Key genes target arsenic-induced cardiotoxicity and berberine, have been identified using the Swiss Target Prediction, Gene Cards, OMIM, and CTD databases. A protein-protein interaction (PPI) network was generated by analysing frequently intersecting genes with the STRING and Cytoscape tools. Shiny GO was used to conduct pathway enrichment analysis for the KEGG and Gene Ontology databases. Auto Dock was used to assess berberine's binding affinity. Berberine and arsenic-related cardiotoxicity shared 17 common targets. The primary targets were identified using Cytoscape ABL-1 (2G2F), CDK2 (1HCK), CYP19A1 (3EQM), ICAM-1 (4G6J), KIT (1T45), MAPK14 (3PY3), PGR (1A28), PTGS2 (5F19), RAC1 (3TH5), and SRC (2SRC). Enrichment analysis revealed TNF, VEGF, and AGE-RAGE signaling involvement, all of which are linked to oxidative stress, inflammation, and endothelial dysfunction. Binding affinity between berberine and the target was found to be ABL-1 (-9.2kcal/mol), PTGS2 (-8.8kcal/mol), SRC (-8.7kcal/mol), CYP19A1 (-8.6kcal/mol), KIT (-8.3kcal/mol), RAC1 (-7.9kcal/mol), CDK2 (-7.5kcal/mol), ICAM-1 (-7.2kcal/mol), MAPK (-6.8kcal/mol), PGR (-5.6kcal/mol). Berberine has multi-targeted therapeutic potential for arsenic-induced cardiotoxicity by modulating inflammatory and oxidative pathways. These results could support the possible usage of berberine in the treatment of cardiovascular diseases caused by arsenic and provide a mechanistic link for further experimental validation.

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Objective Exploring the preventive and therapeutic effects of dapagliflozin (DAPA) on gouty arthritis (GA) in rats, and revealing its potential mechanism of action. Methods Potential targets of DAPA were identified from DrugBank, Swiss Target Prediction, CTD, and PharmMapper databases. Targets associated with gouty arthritis (GA) were retrieved from Gene Cards, DisGeNET, and NCBI databases. By taking the intersection of these two sets, common targets of DAPA and GA were determined. These common targets were then subjected to Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Use the CB-DOCK2 online molecular docking platform to dock DAPA with the core target and perform visual analysis. Thirty-two SPF-grade male SD rats were randomly divided into four groups, with eight rats in each: a blank control group, a model group, a 20 mg/kg DAPA group, and a 40 mg/kg DAPA group. Rats received daily gavage administration of the corresponding medication for eight consecutive days. On the fifth day, monosodium urate (MSU) crystal suspension was injected into the left ankle joint to establish an acute GA model. Samples were collected one hour after the final gavage. The swelling of the ankle joints was recorded at various time points. Hematoxylin and eosin (HE) staining was used to observe pathological changes in the synovial tissue of the ankle joints. Enzyme-linked immunosorbent assay (ELISA) was conducted to measure the levels of inflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) in the peripheral blood of the rats. Western blotting was performed to detect the expression levels of signaling pathway proteins in the synovial tissue of the ankle joints. Results Based on network pharmacology analysis and molecular docking, it was found that targets were significantly enriched in the nucleotide binding oligomerization domain (NOD)-like receptor (NLR) signaling pathway, and the binding energies between the related core targets and DAPA were all <-7.0 kcal/mol. In animal experiments, regarding ankle joint swelling: compared with the model group, the 20 mg/kg DAPA group showed a significant reduction in ankle joint swelling at 72 hours post-modeling (p<0.05), and the 40 mg/kg DAPA group exhibited significant reductions in ankle joint swelling at both 48 and 72 hours post-modeling (p<0.01). For ankle joint HE staining: compared with the model group, DAPA-treated groups showed varying degrees of attenuation in pathological damage, including inflammatory cell infiltration, synovial tissue proliferation, and vascular proliferation in the ankle joints. Peripheral blood ELISA results: the levels of IL-1β and TNF-α in DAPA-treated groups were significantly lower than those in the model group (p<0.05). As for the protein expression levels of NOD-like receptor thermal protein domain-associated protein 3 (NLRP3) and cysteinyl aspartate-specific proteinase-1 (Caspase-1) in ankle joint synovium: compared with the model group, the expression of NLRP3 and Caspase-1 proteins was significantly reduced in DAPA-treated groups (p<0.05). Conclusion DAPA may alleviate the inflammatory response in acute GA in rats by inhibiting the NLRP3/Caspase-1 pathway.

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  • Abstract
  • Cite Count Icon 217
  • 10.1161/circulationaha.107.189622
State of the science conference: Initiative to decrease cardiovascular risk and increase quality of care for patients living with HIV/AIDS: executive summary.
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Revolutionary New Concepts in the Prevention and Treatment of Cardiovascular Disease
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We have reached a limit in our ability to reduce the incidence of coronary heart disease (CHD) and cardiovascular disease (CVD) utilizing the traditional evaluation, prevention, and treatment strategies for the top five cardiovascular risk factors – hypertension, diabetes mellitus (DM), dyslipidemia, obesity, and smoking. Statistics show that approximately 50% of patients will have CHD or myocardial infarction (MI) despite “normal” levels of these five risk factors as traditionally defined. A more logical and in-depth understanding is required of these top risk factors, including the evaluation of a 24-hour ambulatory blood pressure monitoring (24-hour ABM), advanced lipid testing, and more sophisticated parameters to evaluate dysglycemia and visceral obesity with effects of adipokines and of the three finite vascular responses: inflammation, oxidative stress, and immune vascular dysfunction related to numerous internal and external vascular insults. Understanding translational cardiovascular medicine to correlate the CHD risk factors to the presence or absence of vascular injury and disease with noninvasive vascular testing will allow for early identification, prevention, and treatment of CHD and CVD.

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Investigating the Molecular Mechanisms of Resveratrol in Treating Cardiometabolic Multimorbidity: A Network Pharmacology and Bioinformatics Approach with Molecular Docking Validation.
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Resveratrol is a potent phytochemical known for its potential in treating cardiometabolic multimorbidity. However, its underlying mechanisms remain unclear. Our study systematically investigates the effects of resveratrol on cardiometabolic multimorbidity and elucidates its mechanisms using network pharmacology and molecular docking techniques. We screened cardiometabolic multimorbidity-related targets using the OMIM, GeneCards, and DisGeNET databases, and utilized the DSigDB drug characterization database to predict resveratrol's effects on cardiometabolic multimorbidity. Target identification for resveratrol was conducted using the TCMSP, SymMap, DrugBank, Swiss Target Prediction, CTD, and UniProt databases. SwissADME and ADMETlab 2.0 simulations were used to predict drug similarity and toxicity profiles of resveratrol. Protein-protein interaction (PPI) networks were constructed using Cytoscape 3.9.1 software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were performed via the DAVID online platform, and target-pathway networks were established. Molecular docking validated interactions between core targets and resveratrol, followed by molecular dynamics simulations on the optimal core proteins identified through docking. Differential analysis using the GEO dataset validated resveratrol as a core target in cardiometabolic multimorbidity. A total of 585 cardiometabolic multimorbidity target genes were identified, and the predicted results indicated that the phytochemical resveratrol could be a major therapeutic agent for cardiometabolic multimorbidity. SwissADME simulations showed that resveratrol has potential drug-like activity with minimal toxicity. Additionally, 6703 targets of resveratrol were screened. GO and KEGG analyses revealed that the main biological processes involved included positive regulation of cell proliferation, positive regulation of gene expression, and response to estradiol. Significant pathways related to MAPK and PI3K-Akt signaling pathways were also identified. Molecular docking and molecular dynamics simulations demonstrated strong interactions between resveratrol and core targets such as MAPK and EGFR. This study predicts potential targets and pathways of resveratrol in treating cardiometabolic multimorbidity, offering a new research direction for understanding its molecular mechanisms. Additionally, it establishes a theoretical foundation for the clinical application of resveratrol.

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The Mechanism of Propofol in Treating Depression-like Behaviors Based on Network Pharmacology and Experimental Validation
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Objective: To explore the potential mechanism of propofol in improving antidepressant-like behavior through network pharmacology and animal experimental validation, providing theoretical and experimental support for the development of novel antidepressant drugs based on propofol. Methods: 1. The targets of propofol and the disease targets of depression were screened through Swiss Target prediction, Super-pred, SEA, Drugbank, CTD, GeneCards, OMIM, and TTD databases. A protein-protein interaction (PPI) network was constructed, and the core targets were screened and visualized using CytoScape 3.10.2 software. Additionally, GO and KEGG enrichment analyses of the intersection targets were performed using the Metascape database. 2. Thirty male C57BL/6 mice were randomly divided into the CON group, LH model group, and PRO treatment group, with 10 mice in each group. The sucrose preference test, forced swim test, and tail suspension test were conducted to determine whether the depression model was successfully established and to assess the improvement effect of propofol on antidepressant-like behavior. 3. The pathological morphological changes of hippocampal neurons in the three groups of mice were observed through HE staining experiments. The expression of mGluR5 protein in the hippocampus was analyzed by Western blot. Results: 1. Network pharmacology analysis indicated that propofol may exert antidepressant effects by acting on core genes such as ALB, ESR1, NFKB1, HSP90AB1, and EGFR. These core target genes were mainly enriched in biological processes such as synaptic transmission and membrane potential regulation; they involved cellular components such as GABA receptor complexes and synaptic membranes; and they included molecular functions such as neurotransmitter receptor activity. Additionally, propofol may exert antidepressant effects through signaling pathways such as neuroactive ligand-receptor interaction, morphine addiction, and GABAergic synapse. 2. Compared with the CON group, the sucrose preference rate of mice in the LH model group significantly decreased, while the immobility time in the forced swim test and tail suspension test significantly increased. Compared with the LH model group, the sucrose preference rate of mice in the PRO treatment group significantly increased, and the immobility time significantly decreased. 3. The HE results showed that compared with the CON group, the number of neurons in the LH group decreased, with loose arrangement, pycnotic and deeply stained nuclei with blurred boundaries. However, the number of necrotic neurons in the PRO group significantly decreased. The Western blot results showed that compared with the CON group, the expression level of mGluR5 protein in the LH model group significantly increased, while it significantly decreased in the PRO treatment group compared with the LH model group. Conclusion: Propofol may exert antidepressant effects by regulating the expression of mGluR5, improving antidepressant-like behavior, and reducing hippocampal neuronal necrosis.

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  • 10.1097/md.0000000000028787
The molecular mechanism of Ligusticum wallichii for improving idiopathic pulmonary fibrosis
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  • Medicine
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Background:At present, there was no evidence that any drugs other than lung transplantation can effectively treat Idiopathic Pulmonary Fibrosis (IPF). Ligusticum wallichii, or Chinese name Chuan xiong has been widely used in different fibrosis fields. Our aim is to use network pharmacology and molecular docking to explore the pharmacological mechanism of the Traditional Chinese medicine (TCM) Ligusticum wallichii to improve IPF.Materials and methods:The main chemical components and targets of Ligusticum wallichii were obtained from TCMSP, Swiss Target Prediction and Phammapper databases, and the targets were uniformly regulated in the Uniprot protein database after the combination. The main targets of IPF were obtained through Gencards, OMIM, TTD and DRUGBANK databases, and protein interaction analysis was carried out by using String to build PPI network. Metascape platform was used to analyze its involved biological processes and pathways, and Cytoscape3.8.2 software was used to construct “component-IPF target-pathway” network. And molecular docking verification was conducted through Auto Dock software.Results:The active ingredients of Ligusticum wallichii were Myricanone, Wallichilide, Perlolyrine, Senkyunone, Mandenol, Sitosterol and FA. The core targets for it to improve IPF were MAPK1, MAPK14, SRC, BCL2L1, MDM2, PTGS2, TGFB2, F2, MMP2, MMP9, and so on. The molecular docking verification showed that the molecular docking affinity of the core active compounds in Ligusticum wallichii (Myricanone, wallichilide, Perlolyrine) was <0 with MAPK1, MAPK14, and SRC. Perlolyrine has the strongest molecular docking ability, and its docking ability with SRC (−6.59 kJ/mol) is particularly prominent. Its biological pathway to improve IPF was mainly acted on the pathways in cancer, proteoglycans in cancer, and endocrine resistance, etc.Conclusions:This study preliminarily identified the various molecular targets and multiple pathways of Ligusticum wallichii to improve IPF.

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  • Research Article
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  • 10.3390/biology13050315
Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Analysis Reveal Insights into the Molecular Mechanism of Cordia myxa in the Treatment of Liver Cancer.
  • May 1, 2024
  • Biology
  • Li Li + 6 more

Traditional treatments of cancer have faced various challenges, including toxicity, medication resistance, and financial burdens. On the other hand, bioactive phytochemicals employed in complementary alternative medicine have recently gained interest due to their ability to control a wide range of molecular pathways while being less harmful. As a result, we used a network pharmacology approach to study the possible regulatory mechanisms of active constituents of Cordia myxa for the treatment of liver cancer (LC). Active constituents were retrieved from the IMPPAT database and the literature review, and their targets were retrieved from the STITCH and Swiss Target Prediction databases. LC-related targets were retrieved from expression datasets (GSE39791, GSE76427, GSE22058, GSE87630, and GSE112790) through gene expression omnibus (GEO). The DAVID Gene Ontology (GO) database was used to annotate target proteins, while the Kyoto Encyclopedia and Genome Database (KEGG) was used to analyze signaling pathway enrichment. STRING and Cytoscape were used to create protein-protein interaction networks (PPI), while the degree scoring algorithm of CytoHubba was used to identify hub genes. The GEPIA2 server was used for survival analysis, and PyRx was used for molecular docking analysis. Survival and network analysis revealed that five genes named heat shot protein 90 AA1 (HSP90AA1), estrogen receptor 1 (ESR1), cytochrome P450 3A4 (CYP3A4), cyclin-dependent kinase 1 (CDK1), and matrix metalloproteinase-9 (MMP9) are linked with the survival of LC patients. Finally, we conclude that four extremely active ingredients, namely cosmosiin, rosmarinic acid, quercetin, and rubinin influence the expression of HSP90AA1, which may serve as a potential therapeutic target for LC. These results were further validated by molecular dynamics simulation analysis, which predicted the complexes with highly stable dynamics. The residues of the targeted protein showed a highly stable nature except for the N-terminal domain without affecting the drug binding. An integrated network pharmacology and docking study demonstrated that C. myxa had a promising preventative effect on LC by working on cancer-related signaling pathways.

  • Research Article
  • Cite Count Icon 17
  • 10.3389/fphar.2022.950749
Therapeutic mechanism of Curcuma aromatica Salisb. rhizome against coronary heart disease based on integrated network pharmacology, pharmacological evaluation and lipidomics
  • Aug 9, 2022
  • Frontiers in Pharmacology
  • Chenghao Fei + 10 more

Curcuma aromatica Salisb. rhizome (CASR) has multifunctional characteristics worldwide and a long history of use as a botanical drug with. Currently, it is often used clinically to treat coronary heart disease (CHD) caused by blood stasis syndrome. However, the therapeutic mechanism of CASR in the treatment of CHD remains poorly understood. In study, the main chemical constituents of CASR were analyzed using UPLC-Q-TOF-MS/MS. Then, its potential therapeutic mechanism against CHD was predicted. Subsequently, pharmacological evaluation was performed using CHD rat model. Finally, a lipidomics approach was applied to explore the different lipid metabolites to verify the regulation of CASR on lipid metabolism disorders in CHD. A total of 35 compounds was identified from CASR. Seventeen active components and 51 potential targets related to CHD were screened by network pharmacology, involving 13 key pathways. In vivo experiments showed that CASR could significantly improve myocardial infarction, blood stasis, and blood lipid levels and regulate the PI3K/AKT/mTOR signaling pathway in CHD rats. Lipidomics further showed that CASR could regulate abnormal sphingolipid, glycerophospholipid, and glycerolipid metabolism in CHD rats. The therapeutic mechanism of CASR against CHD was initially elucidated and included the regulation of lipid metabolism. Its effects may be attributed to active ingredients, such as curzerene, isoprocurcumenol, and (+)-curcumenol. This study reveals the characteristics of multi-component and multi-pathway of CASR in the treatment of CHD, which provides a basis for the follow-up development and utilization of CASR.

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