Potential Mechanism of Dingji Fumai Decoction Against Atrial Fibrillation Based on Network Pharmacology, Molecular Docking, and Experimental Verification Integration Strategy

Monoterpene-chalcone conjugates and diarylheptanoids isolated from the seeds of Alpinia katsumadai Hayata with cytotoxic activity

Five undescribed monoterpene-chalcone conjugates (1-5), one undescribed hypothetical precursor of diarylheptanoid (6), two undescribed diarylheptanoids (7-8), and fourteen known compounds (9-22) were isolated from the seeds of Alpinia katsumadai. Their structures were elucidated through the interpretation of HRESIMS, NMR, ECD, and X-ray diffraction data. MTT assays on human cancer cell lines (HepG2, A549, SGC7901, and SW480) revealed that compounds 3-8, 11, and 13 exhibited broad-spectrum antiproliferative activities with IC50 values ranging from 3.59 to 21.78 μM. B cell lymphoma 2 was predicted as the target of sumadain C (11) by network pharmacology and verified by homogeneous time-resolved fluorescence assay and molecular docking.

Guanxin V Relieves Ventricular Remodeling by Inhibiting Inflammation: Implication from Virtual Screening, Systematic Pharmacology, Molecular Docking, and Experimental Validation

OBJECTIVE

To reveal the anti-inflammatory mechanism of Guanxin V, which is prescribed for ventricular remodeling in clinical practice.

METHODS

Guanxin V-, ventricular remodeling-, and inflammation-related targets were obtained through an integrated strategy of virtual screening and systematic pharmacology, and then the shared targets were visualised with a Venn diagram. Guanxin V network and the protein-protein interaction network were drawn, and enrichment analysis was conducted. Finally, the main results obtained from the integrated strategy were validated by molecular docking and in vivo experiments.

RESULTS

A total of 251, 11,425, and 15,246 Guanxin V-, ventricular remodeling-, and inflammation-related targets were acquired, respectively. Then, 211 shared targets were considered to contribute to the mechanism of ventricular remodeling treated by Guanxin V. Guanxin network and the protein-protein interaction network were drawn, and enrichment analysis showed some cardiovascular-related biological processes and signaling pathways. Molecular docking revealed that the Guanxin V-derived compounds could align with key targets. Final in vivo experiments proved that Guanxin V reverses ventricular remodeling by inhibiting inflammation.

CONCLUSION

Guanxin V relieves ventricular remodeling by regulating inflammation, which provides new ideas for the anti-ventricular remodeling mechanism of Guanxin V.

Immune landscape and regulatory mechanisms in human atherosclerotic coronary plaques: Evidence from single-cell and bulk transcriptomics

Atherosclerosis is a chronic immuno-inflammatory disease, however, the immune landscape and regulatory mechanisms have not been clear. We detected seven principal immune cell clusters with distinct phenotypic and spatial characteristics using single-cell RNA-sequencing of aortic immune cells from patients with acute coronary syndrome and stable angina pectoris. Then we acquired 265 differentially expressed immune-related genes and the high scores were mainly found in T cells and monocytes, which were differentially regulated in atherosclerotic coronary plaques. The CCL signaling pathway was the most relevant pattern in the T cells and CCL5-CCR1 and CCL5-CCR5 ligand-receptor pairs played a vital role in the CCL signaling pathway. Further comparative analysis indicated MCH-I signaling was the most relevant pattern in the T cells and HLA ligand-related ligand-receptor pairs played a vital role. Functional analysis of the single-cell and bulk transcriptomics pointed to multiple pathways, such as antigen presentation and immune response. Nineteen common differentially expressed immune-related genes were found in both immune cells and the human peripheral blood mononuclear cells. Nine common differentially expressed transcription factors were differentially expressed in both T cell and monocyte clusters from the coronary plaques and human peripheral blood mononuclear cells and the network demonstrated that CEBPB might play an essential role in the transcriptional regulation of atherosclerosis as a hub transcription factor. The definition of immune cell diversity and heterogeneity by single-cell level analysis of aortic immune cell subsets not only unveils cell-type-specific pathways and new immune mechanisms but also discovers the functional correlation of immune cells in human atherosclerosis. Our findings provide great promise for the discovery of novel molecular mechanisms and precise therapeutic targets for atherosclerosis.

The application and mechanism of Chinese medicine in the upstream treatment of atrial fibrillation

Upstream treatment of atrial fibrillation (AF, for short) is a new approach to the prevention and treatment of AF with non-antiarrhythmic drugs, which is essentially primary and secondary prevention of AF. The former refers to the prevention of AF by controlling risk factors such as diabetes, hypertension, and heart failure before AF occurs, and the latter mainly refers to targeting ion channels, inflammation, oxidative stress, and other pathways to reduce or reverse atrial electrical and structural remodeling, reduction of AF load, and reduction of the chance of AF occurrence or progression. More and more studies have shown that many traditional Chinese medicines, active ingredients of Chinese medicines, and Chinese herbal formulas have definite effects on the upstream treatment of AF, but their mechanisms of action are different. Therefore, we summarized the relevant literature on the application and mechanisms of Chinese medicine on the upstream treatment of AF in recent years, hoping to be helpful for subsequent studies.

IKBIP might be a potential prognostic biomarker for glioblastoma multiforme

BACKGROUND

Due to the negative association between inhibitor of nuclear factor-kB kinase-interacting protein (IKBIP) and survival in gliomas, this study aimed to comprehensively analyze the potential function of IKBIP in glioblastoma multiforme (GBM).

METHODS

GBM samples were retrieved from The Cancer Genome Atlas and Chinese Glioma Genome Atlas as training and validation cohorts, respectively, and survival and Cox regression analyses were conducted. Based on clinical indicators and IKBIP, three prognostic models were established and then verified using the validation dataset. Infiltrating immune cell analysis and single-sample gene set enrichment analysis were also conducted to explore the underlying mechanisms. Finally, the key findings were validated through molecular biology experiments.

RESULTS

Patients in the high IKBIP score group had poorer survival. Based on Cox regression and subgroup analyses, IKBIP was identified as an independent prognostic factor. Among the three models constructed, the model combining the IKBIP signature and clinical features displayed good performance in terms of discrimination, calibration, and model improvement capability in the training cohort. This model was also successfully validated in an external cohort from the CGGA. Further analysis revealed that many immune cells and related pathways were involved in the high-risk group. In vitro experiments revealed that the knockdown of IKBIP inhibited cell invasion and proliferation, and promoted their senescence.

CONCLUSIONS

The prognostic value of IKBIP and its positive impact on the invasiveness of GBM were identified, indicating that IKBIP may serve as an underlying target for the treatment of GBM.

Methyl eugenol protects the kidney from oxidative damage in mice by blocking the Nrf2 nuclear export signal through activation of the AMPK/GSK3β axis

Disrupted redox homeostasis contributes to renal ischemia-reperfusion (IR) injury. Abundant natural products can activate nuclear factor erythroid-2-related factor 2 (Nrf2), thereby providing therapeutic benefits. Methyl eugenol (ME), an analog of the phenolic compound eugenol, has the ability to induce Nrf2 activity. In this study, we investigated the protective effects of ME against renal oxidative damage in vivo and in vitro. An IR-induced acute kidney injury (AKI) model was established in mice. ME (20 mg·kg-1·d-1, i.p.) was administered to mice on 5 consecutive days before IR surgery. We showed that ME administration significantly attenuated renal destruction, improved the survival rate, reduced excessive oxidative stress and inhibited mitochondrial lesions in AKI mice. We further demonstrated that ME administration significantly enhanced Nrf2 activity and increased the expression of downstream antioxidative molecules. Similar results were observed in vitro in hypoxia/reoxygenation (HR)-exposed proximal tubule epithelial cells following pretreatment with ME (40 μmol·L-1). In both renal oxidative damage models, ME induced Nrf2 nuclear retention in tubular cells. Using specific inhibitors (CC and DIF-3) and molecular docking, we demonstrated that ME bound to the binding pocket of AMPK with high affinity and activated the AMPK/GSK3β axis, which in turn blocked the Nrf2 nuclear export signal. In addition, ME alleviated the development of renal fibrosis induced by nonfatal IR, which is frequently encountered in the clinic. In conclusion, we demonstrate that ME modulates the AMPK/GSK3β axis to regulate the cytoplasmic-nuclear translocation of Nrf2, resulting in Nrf2 nuclear retention and thereby enhancing antioxidant target gene transcription that protects the kidney from oxidative damage.

Integrative network pharmacology and experimental verification to reveal the anti-inflammatory mechanism of ginsenoside Rh4

Inflammation is an innate immune response to infection, and it is the main factor causing bodily injury and other complications in the pathological process. Ginsenoside Rh4 (G-Rh4), a minor ginsenoside of Panax ginseng C. A. Meyer and Panax notoginseng, has excellent pharmacological properties. However, many of its major pharmacological mechanisms, including anti-inflammatory actions, remain unrevealed. In this study, network pharmacology and an experimental approach were employed to elucidate the drug target and pathways of G-Rh4 in treating inflammation. The potential targets of G-Rh4 were selected from the multi-source databases, and 58 overlapping gene symbols related to G-Rh4 and inflammation were obtained for generating a protein–protein interaction (PPI) network. Molecular docking revealed the high affinities between key proteins and G-Rh4. Gene ontology (GO) and pathway enrichment analyses were used to analyze the screened core targets and explore the target–pathway networks. It was found that the JAK-STAT signaling pathway, TNF signaling pathway, NF-κB signaling pathway, and PI3K-Akt signaling pathway may be the key and main pathways of G-Rh4 to treat inflammation. Additionally, the potential molecular mechanisms of G-Rh4 predicted from network pharmacology analysis were validated in RAW264.7 cells. RT-PCR, Western blot, and ELISA analysis indicated that G-Rh4 significantly inhibited the production of pro-inflammatory cytokines such as TNF-α, IL-6, and IL-1β, as well as inflammation-related enzymes in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Moreover, in vitro experiments evaluated that Ginsenoside Rh4 exerts anti-inflammatory effects via the NF-κB and STAT3 signaling pathways. It is believed that our study will provide the basic scientific evidence that G-Rh4 has potential anti-inflammatory effects for further clinical studies.

Potential Mechanisms of Shu Gan Jie Yu Capsule in the Treatment of Mild to Moderate Depression Based on Systemic Pharmacology and Current Evidence

Background

Shu Gan Jie Yu (SGJY) capsule has a good effect on relieving depressive symptoms in China. However, the mechanism of action is still unclear. Therefore, systemic pharmacology and molecular docking approaches were used to clarify its corresponding antidepressant mechanisms.

Methods

Traditional Chinese Medicine Database and Analysis Platform (TCMSP), the Encyclopedia of Traditional Chinese Medicine (ETCM), and Swiss Target Prediction servers were used to screen and predict the bioactive components of the SGJY capsule and their antidepressive targets. Mild to moderate depression (MMD) related genes were obtained from GeneCards and DisGeNET databases. A network of bioactive components-therapeutic targets of the SGJY capsule was established by STRING 11.5 and Cytoscape 3.9.0 software. Gene function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by utilizing Database for Annotation, Visualization, and Integrated Discovery (DAVID) platform. Active components were taken to dock with the hypothetical proteins by iGEMDOCK and SwissDock, and the docking details were visually displayed by UCSF Chimera software. Then, the related research literature of the SGJY capsule was reviewed, summarized, sorted, and analyzed, including experimental evidence and clinical experience.

Results

Seven active components and 45 intersection targets were included in the study. PPI network had genuinely uncovered the potential therapeutic targets, such as AKT1, HSP90AA1, ESR1, EGFR, and PTGS2. KEGG pathway analysis showed that the mechanism of the SGJY capsule on MMD was mainly involved in the PI3K-Akt signaling pathway.

Conclusions

In this study, we have successfully predicted the biochemically active constituents, potential therapeutic targets, and comprehensively predicted the related drug-gene interaction of the SGJY capsule for treating MMD and provided a basis for subsequent experiments.

Ligand fishing based on tubular microchannel modified with monoamine oxidase B for screening of the enzyme's inhibitors from Crocus sativus and Edgeworthia gardneri

A novel strategy of performing ligand fishing with enzyme-modified open tubular microchannel was proposed for screening bioactive components present in medicinal plants. Monoamine oxidase B was immobilized onto the surface of the microchannel for the first time to specifically extract its ligands when the plant's extracts solution flows through the channel. The thermal and the storage stability of immobilized monoamine oxidase B were significantly enhanced after immobilization. Crocin I and Ⅱ were extracted from Crocus sativus, and tiliroside was extracted from Edgeworthia gardneri. All the three compounds were inhibitors of the enzyme with the half-maximal inhibitory concentration values of 26.70 ± 0.91, 19.88 ± 2.78, and 15.65 ± 0.85 μM, respectively. The enzyme inhibition kinetics and molecular docking were investigated. This is the first report on the inhibitory effects of tiliroside and crocin Ⅱ. The novel ligand fishing method proposed in this work possesses advantages of rapidness, high efficiency, and tiny sample consumption compared to routine ligand fishing, with promising potential for screening active natural products in complex mixtures.

Pharmacological mechanisms of sodium-glucose co-transporter 2 inhibitors in heart failure with preserved ejection fraction

Background

More and more evidence indicates sodium-glucose co-transporter 2 inhibitors (SGLT2is) may display clinical benefits for heart failure with preserved ejection fraction (HFpEF). However, the mechanisms of the action remain unclear.

Methods

A systematic pharmacology-based strategy was applied for predicting the potential molecular mechanisms of SGLT2is in HFpEF. The potential targets of SGLT2is and HFpEF were contained from diverse databases. After networks were constructed, Metascape was applied to functional enrichment. Moreover, the key findings were validated through molecular docking.

Results

We obtained 487 SGLT2is related targets and 1505 HFpEF related targets. The networks showed the complex relationship of HFpEF-target-HFpEF. The results of functional enrichment analysis suggested that several biological processes, including muscle system process, inflammatory response, vasculature development, heart development, regulation of MAPK cascade, positive regulation of ion transport, negative regulation of cell population proliferation, cellular response to nitrogen compound, apoptotic signaling pathway, multicellular organismal homeostasis, response to oxidative stress, regulation of cell adhesion, positive regulation of cell death, response to growth factor, and cellular response to lipid, and signaling pathways, such as cardiomyopathy, cAMP signaling pathway, cytokine-cytokine receptor interaction, apoptosis, MAPK signaling pathway, HIF-1 signaling pathway, calcium signaling pathway, and NF-kappa B signaling pathway. Finally, we validated the interactions and combinations of SGLT2is and core targets.

Conclusion

SGLT2is play the potential role of anti-HFpEF through the direct or indirect synergy of multiple targets and pathways. Our study promotes the explanation of the molecular mechanisms of SGLT2is in HFpEF.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12872-022-02693-8.

Guanxin V alleviates acute myocardial infarction by restraining oxidative stress damage, apoptosis, and fibrosis through the TGF-β1 signalling pathway

BACKGROUND

Oxidative stress, apoptosis, and fibrosis have important roles in acute myocardial infarction, which is the main cause of global morbidity and mortality. Guanxin V significantly ameliorates acute myocardial infarction, the underlying mechanism, however, is still unclear.

PURPOSE

In this study, we detected the anti-oxidative, anti-apoptotic, and anti-fibrosis effects of Guanxin V on acute myocardial infarction.

METHODS

We used left anterior descending coronary artery ligation to construct an acute myocardial infarction model. Cardiac function, heart weight, infarction size, and histopathology were measured. Cardiomyocytes were treated with hydrogen peroxide to build an in vitro model. Cell apoptosis, fibrosis, and reactive oxygen species-related markers were tested. We observed the mitochondrial ultrastructure through transmission electron microscopy. The levels of collagens and TGF-β1 signalling were measured. The lentiviral vector containing the full-length TGF-β1 sequence was administered to investigate the rescue role of Guanxin V.

RESULTS

Guanxin V significantly decreased apoptosis and inhibited oxidative stress damage and fibrosis in acute myocardial infarction. Hydrogen peroxide could stimulate cardiomyocytes to produce reactive oxygen species and Guanxin V could significantly reverse hydrogen peroxide-induced cell damage, inhibit oxidative stress damage, apoptosis, and fibrosis, and enhance mitochondrial dynamic balance. Mechanistically, Guanxin V attenuated oxidative stress damage, apoptosis, and fibrosis induced by the TGF-β1 signalling pathway activation.

CONCLUSIONS

Guanxin V effectively relieved apoptosis, oxidative stress damage, and fibrosis through down-regulating the TGF-β1 signalling pathway, which enhances the knowledge of the cellular and molecular mechanism of Guanxin V in treating acute myocardial infarction.

Guanxin V Acts as an Antioxidant in Ventricular Remodeling

Background: Our previous studies have shown that Guanxin V (GXV) is safe and effective in the treatment of ventricular remodeling (VR), but its mechanism related to oxidative stress has not been studied deeply.

Methods: We applied integrating virtual screening and network pharmacology strategy to obtain the GXV-, VR-, and oxidative stress-related targets at first, and then highlighted the shared targets. We built the networks and conducted enrichment analysis. Finally, the main results were validated by molecular docking and solid experiments.

Results: We obtained 251, 11,425, and 9,727 GXV-, VR-, and oxidative stress-related targets, respectively. GXV-component-target-VR and protein–protein interaction networks showed the potential mechanism of GXV in the treatment of VR. The following enrichment analysis results gathered many biological processes and “two GXV pathways” of oxidative stress-related to VR. All our main results were validated by molecular docking and solid experiments.

Conclusion: GXV could be prescribed for VR through the mechanism, including complex interactions between related components and targets, as predicted by virtual screening and network pharmacology and validated by molecular docking and solid experiments. Our study promotes the explanation of the biological mechanism of GXV for VR.