A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies

Ni, Mengwei; Liu, Xinkui; Meng, Ziqi; Jia, Shanshan; Liu, Yingying; Zhou, Wei; Wu, Jiarui; Zhang, Jingyuan; Guo, Siyu; Li, Jialin; Wang, Haojia; Zhang, Xiaomeng

doi:10.1186/s12906-020-02939-y

Cited by 6 publications

(5 citation statements)

References 94 publications

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“…The effect of AGPS on the pathway network was analyzed in human glioma cells by sequencing and bioinformatics analysis, and it was discovered that AGPS silencing regulated tumor-related signaling pathways, such as the PI3K/Akt, Toll-like receptor, focal adhesion and VEGF signaling pathways. These aforementioned results were further validated by RT-qPCR, where significantly upregulated expression levels of THBS1 and ITGA11, and downregulated expression levels of SPP1, VEGFA, EGFR, IL7R, CXCL8, PTGS2 and SDC4, were all identified; all of these are crucial genes involved in the aforementioned signaling pathways, and have been found to serve roles in tumor metastasis and angiogenesis ( 18 – 23 ).…”

Section: Discussionmentioning

confidence: 75%

Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

Chen

Zhang

et al. 2020

Oncol Lett

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Alkylglycerone phosphate synthase (AGPS) is a key enzyme for ether ester synthesis and acts as an oncogene in malignant tumors. The present study aimed to investigate the effect of AGPS silencing on the expression levels of long non-coding RNAs (lncRNAs) and the co-expression with mRNAs in glioma U251 cells using microarray analysis. Furthermore, the underlying biological functions of crucial lncRNAs identified were investigated. It was discovered that in vitro U251 cell proliferation was suppressed following the genetic silencing of AGPS. Differentially expressed lncRNAs and mRNAs in U251 cells were sequenced following AGPS silencing. The results from the Gene Ontology analysis identified that the co-expressed mRNAs were mainly involved in biological processes, such as 'cellular response to hypoxia', 'extracellular matrix organization' and 'PERK-mediated unfolded protein response'. In addition, Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis revealed that the co-expressed mRNAs were the most enriched in the 'AGE/RAGE signaling pathway in diabetic conditions'. Additionally, the PI3K/Akt and epidermal growth factor receptor signaling pathways serve important roles in tumor processes, for example carcinogenesis and angiogenesis. Furthermore, it was identified that the lncRNA AK093732 served a vital role in the regulatory network and the core pathway in this network regulated by this lncRNA was discovered to be the 'Cytokine-cytokine receptor interaction'. In conclusion, the findings of the present study suggested that AGPS may affect cell proliferation and the degree of malignancy. In addition, the identified lncRNAs and their co-expressed mRNAs screened using microarrays may have significant biological effects in the occurrence, development and metastasis of glioma, and thus may be novel markers of glioma.

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Section: Discussionmentioning

confidence: 75%

Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

Chen

Zhang

et al. 2020

Oncol Lett

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“…The two-dimensional structures of naringin were obtained from the PubChem Database, and AdipoR1 was obtained from the RCSB PDB database. Molecular docking was conducted by using AutoDock Vina software according to the published methods, and the results were analyzed by using PyMOL …”

Section: Methodsmentioning

confidence: 99%

“…Molecular docking was conducted by using AutoDock Vina software according to the published methods, and the results were analyzed by using PyMOL. 21 Statistical Analysis. All experimental data were analyzed using GraphPad Prism 8 and SPSS 21 software.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Naringin Promotes Skeletal Muscle Fiber Remodeling by the AdipoR1-APPL1-AMPK Signaling Pathway

Zhang²,

Song

et al. 2021

J. Agric. Food Chem.

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Naringin, a natural flavonoid mainly found in citrus fruit, has been reported to exert a positive effect on improving skeletal muscle health. However, the effects and potential mechanisms of naringin on skeletal muscle fiber switching is still unclear. Here, we discovered that oral administration of naringin increased the low-speed running time, four-limb hanging time, body oxygen consumption in mice, enhanced aerobic enzyme activity, MyHC I expression, and slow-twitch fiber percentage in mice skeletal muscle. By contrast, naringin decreased α-GPDH enzyme activity, MyHC IIb expression, and fast-twitch fiber percentage. Moreover, naringin increased the concentration of serum adiponectin and activated the expression of AdipoR1, APPL1, AMPK, and PGC-1α. Furthermore, by the in vitro experiment and AdipoR1 knockdown, we found that inhibition of the AdipoR1 signaling pathway significantly reduced the effect of naringin on slow-twitch fiber-/fast-twitch fiber-related gene and protein expression. In conclusion, our results indicated that naringin could induce skeletal muscle fiber transition from fast twitch to slow twitch via the AdipoR1 signaling pathway. This study may provide new strategy for improving exercise endurance and slow muscle fiber deficiency-related diseases.

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“…Clinical trials have demonstrated that Bruceae fructus can improve the effectiveness of treatment in patients with clinically advanced non-small cell lung cancer. [ 8 , 9 ] Bruceae fructus bitol is a key active component of the plant. [ 10 ] Bruceae fructus bitol has been shown in studies to suppress breast cancer, nasopharyngeal cancer, lung cancer, and other malignant tumors.…”

Section: Introductionmentioning

confidence: 99%

Prediction of network pharmacology, molecular docking-based strategy, and vitro assays to determine potential pharmacological mechanism of Dioscoreae bulbiferae and Bruceae fructus against laryngocarcinoma

Wu,

Zhu,

Cao

et al. 2023

Medicine

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Background: Based on network pharmacology, molecular docking, and vitro assays, investigate the probable pharmacological mechanism of Dioscoreae bulbiferae and Bruceae fructus in the treatment of laryngocarcinoma. Methods: The active components and targets of Dioscoreae bulbiferae and Bruceae fructus were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. Targets linked with laryngocarcinoma were gathered from the GeneCards, DisGeNET, and DrugBank databases. The String database was utilized to build a protein–protein interaction network of common medication and illness targets, after which the core targets were filtered out. The Metascape database served for gene ontology enrichment and Kyoto encyclopedia of genes and genomes pathway analysis of common targets. AutoDock then performed molecular docking between the essential component and the vital target. To investigate the biological effects of diosbulbin B, we assessed the viability of laryngocarcinoma cells after diosbulbin B therapy using the Mahalanobis Taguchi system technique. Following that, we looked at how diosbulbin B affected colony formation after 14 days of culture of treated cells. Flow cytometry was utilized to detect apoptosis in order to examine the influence of diosbulbin B on laryngocarcinoma cell apoptosis. Results: According to a study of the literature, the fundamental components of Dioscoreae bulbiferae and Bruceae fructus in the treatment of laryngocarcinoma include brusatol and diosbulbin B, which may operate on core targets such as cyclin D1, Cyclin Dependent Kinase Inhibitor 1A, and E2F Transcription Factor 1. The significant pathways discovered using Kyoto encyclopedia of genes and genomes enrichment analysis were the phosphoinositide 3-kinase-protein kinase B signaling route, the tumor necrosis factor signaling pathway, and so on. These pathways primarily influence the development and prognosis of laryngeal cancer by controlling cell growth, cell proliferation, angiogenesis, tumorigenesis, and metastasis. The molecular docking studies revealed that the affinity between the heart and crucial targets was robust. The results of vitro assays indicate that diosbulbin B suppressed Hep-2 cell activity in a concentration-dependent manner. Besides, diosbulbin B has powerful antiproliferative properties in Hep-2 cells. Flow cytometry results showed that diosbulbin B promoted laryngocarcinoma cell apoptosis in a concentration-dependent manner. Conclusion: The article delivered a preliminary discussion of the probable mechanism of Dioscoreae bulbiferae and Bruceae fructus in the treatment of laryngocarcinoma, which can serve as a theoretical basis and evidence for subsequent experimental investigation.

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A bioinformatics investigation into the pharmacological mechanisms of javanica oil emulsion injection in non-small cell lung cancer based on network pharmacology methodologies

Cited by 6 publications

References 94 publications

Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

Naringin Promotes Skeletal Muscle Fiber Remodeling by the AdipoR1-APPL1-AMPK Signaling Pathway

Prediction of network pharmacology, molecular docking-based strategy, and vitro assays to determine potential pharmacological mechanism of Dioscoreae bulbiferae and Bruceae fructus against laryngocarcinoma

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