Elucidating the Mechanism of Action of Salvia miltiorrhiza for the Treatment of Acute Pancreatitis Based on Network Pharmacology and Molecular Docking Technology

Zhu, Kunyao; Zhang, Man; Long, Jiafu; Zhang, Shuqi; Luo, Huali

doi:10.1155/2021/8323661

Cited by 7 publications

(5 citation statements)

References 35 publications

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“…NCOA1, ESR1, and ESR2 are enriched in the estrogen signaling pathway. Studies have shown that NCOA1 is involved in the acute inflammatory process of AP through the regulation of IL-17 [ 60 ]. Both ESR1 and ESR2 can mediate anti-inflammatory actions.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of Magnolia Volatile Oil in the Treatment of Acute Pancreatitis Based on GC‐MS, Network Pharmacology, and Molecular Docking

Huang

Liu

et al. 2023

Evidence-Based Complementary and Alternative Medicine

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Objective. Magnoliae officinalis cortex (MOC) is one of the most frequently used traditional Chinese medicine (TCM) for the treatment of acute pancreatitis (AP). Magnolia volatile oil (MVO) is considered to be one of the main active ingredients in MOC for AP treatment. However, the underlying mechanism of MVO in AP therapy is unknown. Methods. An integrated strategy of gas chromatography-mass spectrum (GC-MS), network pharmacology, and molecular docking simulation was employed to predict underlying mechanism of MVO in AP treatment. First, the compounds of MVO were identified by GC-MS, and the targets of the identified characteristic compounds were collected from several databases, as well as AP-related targets. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out to obtain the mechanism. Moreover, the binding activity between core therapeutic targets and their corresponding compounds was evaluated by molecular docking simulation. Results. GC-MS results showed a total of 35 compounds that appeared in at least 18 out of 20 chromatograms were considered as characteristic compounds of MVO, and 33 compounds of those were identified. Network analysis demonstrated that 33 compounds regulated 142 AP-related targets. Of those, 8 compounds (α-eudesmol, γ-eudesmol, (−)-terpinen-4-ol, terpineol, hinesol, linalool, borneol, and β-eudesmol) and 8 targets (TNF, IL-1β, PPARγ, PPARα, PTGS2, NCOA1, CNR1, and ESR1) have a close relationship with AP treatment and were recognized as the key active compounds and the core therapeutic targets, respectively. The 142 targets were involved in both inflammation and calcium overload-related biological pathways, such as neuroactive ligand-receptor interaction, estrogen, MAPK, and calcium signaling pathway. Moreover, molecular docking simulation indicated that the 8 core therapeutic targets strongly interacted with their corresponding compounds. Conclusions. In summary, the present study elucidated that the efficacy of MVO in AP treatment might be attributed to anti-inflammation and inhibition of calcium overload through multicomponents and multitargets.

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Section: Discussionmentioning

confidence: 99%

Mechanism of Magnolia Volatile Oil in the Treatment of Acute Pancreatitis Based on GC‐MS, Network Pharmacology, and Molecular Docking

Huang

Liu

et al. 2023

Evidence-Based Complementary and Alternative Medicine

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“…Molecular docking technology docks known small-molecule active substances with related target proteins, which can clarify the mechanism of action between active TCM ingredients and targets at the molecular level [ 43 , 44 ]. At present, molecular docking technology plays an important role in elucidating the mechanism of action between active ingredients of TCM [ 45 , 46 ] and related target proteins in many diseases, such as cardiovascular disease [ 25 ] and cancer [ 26 ]. Therefore, we conducted preliminary screening with reference to the five principles of drug-like standards and other screening conditions of “drug similarity” and obtained 22 compounds.…”

Section: Discussionmentioning

confidence: 99%

Virtual screening–molecular docking–activity evaluation of Ailanthus altissima (Mill.) swingle bark in the treatment of ulcerative colitis

Ma,

Liu,

et al. 2023

BMC Complement Med Ther

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Background The dried bark of Ailanthus altissima (Mill.) Swingle is widely used in traditional Chinese medicine for the treatment of ulcerative colitis. The objective of this study was to explore the therapeutic basis of the dried bark of Ailanthus altissima (Mill.) Swingle for the treatment of ulcerative colitis based on Virtual Screening–Molecular Docking–Activity Evaluation technology. Methods By searching the Traditional Chinese Medicine Systems Pharmacology TCMSP Database and Analysis Platform, 89 compounds were obtained from the chemical components of the dried bark of Ailanthus altissima (Mill.) Swingle. Then, after preliminarily screening the compounds based on Lipinski’s rule of five and other relevant conditions, the AutoDock Vina molecular docking software was used to evaluate the affinity of the compounds to ulcerative colitis-related target proteins and their binding modes through use of the scoring function to identify the best candidate compounds. Further verification of the compound’s properties was achieved through in vitro experiments. Results Twenty-two compounds obtained from the secondary screening were molecularly docked with ulcerative colitis-related target proteins (IL-1R, TLR, EGFR, TGFR, and Wnt) using AutoDock Vina. The free energies of the highest scoring compounds binding to the active cavity of human IL-1R, TLR, EGFR, TGFR, and Wnt proteins were − 8.7, − 8.0, − 9.2, − 7.7, and − 8.5 kcal/mol, respectively. The potential compounds, dehydrocrebanine, ailanthone, and kaempferol, were obtained through scoring function and docking mode analysis. Furthermore, the potential compound ailanthone (1, 3, and 10 µM) was found to have no significant effect on cell proliferation, though at 10 µM it reduced the level of pro-inflammatory factors caused by lipopolysaccharide. Conclusion Among the active components of the dried bark of Ailanthus altissima (Mill.) Swingle, ailanthone plays a major role in its anti-inflammatory properties. The present study shows that ailanthone has advantages in cell proliferation and in inhibiting of inflammation, but further animal research is needed to confirm its pharmaceutical potential.

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“…Genes. Finally, KEGG functional enrichment analysis was performed on these target genes [59]. Te reliability of the predictions was further assessed to know whether enriched pathways were classical and critical pathways in unstable angina.…”

Section: Validation Of the Function Of Targetmentioning

confidence: 99%

A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris

Dan

et al. 2022

Computational Intelligence and Neuroscience

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MicroRNAs (miRNAs) are important types of noncoding RNAs, and there is a lack of holistic and systematic understanding of the functions they play in disease. We proposed a research strategy, including two parts network analysis and network modelling, to analyze, model, and predict the regulatory network of miRNAs from a network perspective, using unstable angina pectoris as an example. In the network analysis section, we proposed the WGCNA & SimCluster method using both correlation and similarity to find hub miRNAs, and validation on two datasets showed better results than the methods using correlation or similarity alone. In the network modelling section, we used six knowledge graph or graph neural network models for link prediction of three types of edges and multilabel classification of two types of nodes. Comparative experiments showed that the RotatE model was a good model for link prediction, while the RGCN model was the best model for multilabel classification. Potential target genes were predicted for hub miRNAs and validation of hub miRNA-target gene interactions, target genes as biomarkers and target gene functions were performed using a three-step validation approach. In conclusion, our study provides a new strategy to analyze and model miRNA regulatory networks.

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Elucidating the Mechanism of Action of Salvia miltiorrhiza for the Treatment of Acute Pancreatitis Based on Network Pharmacology and Molecular Docking Technology

Cited by 7 publications

References 35 publications

Mechanism of Magnolia Volatile Oil in the Treatment of Acute Pancreatitis Based on GC‐MS, Network Pharmacology, and Molecular Docking

Mechanism of Magnolia Volatile Oil in the Treatment of Acute Pancreatitis Based on GC‐MS, Network Pharmacology, and Molecular Docking

Virtual screening–molecular docking–activity evaluation of Ailanthus altissima (Mill.) swingle bark in the treatment of ulcerative colitis

A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris

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