Dataset Information

Network pharmacology and molecular docking-based study on exploring the potential mechanism of Lycium barbarum L: In the treatment of atherosclerosis.

ABSTRACT:

Background

Goji berries (Lycium barbarum L) are herbal medicine that have a long history of use and multiple pharmacological activities. In this study, we investigated the potential therapeutic effects of Goji berries on atherosclerosis (AS) using network pharmacology and molecular docking.

Methods

The active compounds of Goji berries were identified using the Traditional Chinese Medicine Systems Pharmacology platform, as well as the literature and the targets of each active compound were obtained using the Swiss Target Prediction database. The AS-related targets were collected from the GeneCards and OMIM databases to obtain the common targets of Goji berries and AS. The drug-compound-target-disease network and protein-protein interaction network were constructed using the Cytoscape software to obtain the core target proteins of Goji berries related to AS. Gene ontology analysis of the core targets and Kyoto encyclopedia of genes and genomes pathway enrichment analysis were performed by Metascape. The target-chemical correlations were verified using AutoDock molecular docking.

Results

After analysis, 44 active compounds within Goji berries were obtained that exhibit associations with AS. Among these, the proteins exhibiting the highest degrees of interaction within the compound-targeted protein protein-protein interaction network were AKT1, SRC, MAPK3, MAPK1, RELA, and STAT3. The gene ontology-biology process analysis showed that compound-targeted proteins were mainly involved in regulating small molecule metabolic process, cellular response to chemical stress, reactive oxygen species metabolic process, and regulation of inflammatory response. Kyoto encyclopedia of genes and genomes pathway mainly included lipid and AS in which AKT1, SRC, MAPK3, and MAPK1 were involved. Advanced glycation end-product-receptor for advanced glycation end-product signaling pathway in diabetic complications, Chagas disease, and pancreatic disease. Molecular docking assessment showed that fucosterol is bound to AKT1, MAPK3, and SRC.

Conclusion

This study demonstrates that network pharmacology and molecular docking analyses contribute to a better understanding of Goji berries active compounds and targets as potential therapeutic drugs for treating AS.

SUBMITTER: Qin X

PROVIDER: S-EPMC10627648 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Publications

Network pharmacology and molecular docking-based study on exploring the potential mechanism of Lycium barbarum L: In the treatment of atherosclerosis.

Qin Xinchen X Xie Zikai Z Chen Xi X Wang Xiaoxuan X Ma Lijuan L

Medicine 20231101 44

<h4>Background</h4>Goji berries (Lycium barbarum L) are herbal medicine that have a long history of use and multiple pharmacological activities. In this study, we investigated the potential therapeutic effects of Goji berries on atherosclerosis (AS) using network pharmacology and molecular docking.<h4>Methods</h4>The active compounds of Goji berries were identified using the Traditional Chinese Medicine Systems Pharmacology platform, as well as the literature and the targets of each active compo ...[more]

PMID: 37932998

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Project description:To explore the potential active compounds and molecular mechanism of Xuefu Zhuyu decoction (XFZYD) in the treatment of atherosclerosis (AS) based on network pharmacology and molecular docking. The effective components and action targets of XFZYD were screened by using TCMSP database. And then, the action targets of AS were collected by GeneCards database. The intersection targets between the effective components' targets of XFZYD and AS-related action targets were used to construct PPI networks. GO and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed on these intersection targets. Finally, molecular docking software was used to excavate the active compounds of the core targets VEGFA and AKT1. We detected 225 active components of XFZYD, and found that quercetin, kaempferol, luteolin, naringenin, β-sitosterol, isorhamnetin, stigmasterol, baicalein, nobiletin, and β-carotene are the potential active compounds of XFZYD; STAT3, IL6, JUN, VEGFA, MAPK14, and AKT1 are the core target proteins of the active compounds, among which VEGFA and AKT1 are the key target proteins. PPI network results showed that β-carotene, quercetin, kaempferol, luteolin, and naringenin had higher degree values and more corresponding targets than other 5 active compounds and had the stable binding ability to regulatory proteins VEGFA and AKT1. The core components β-carotene, quercetin, kaempferol, and luteolin exerted their therapeutic effects on AS by acting on the key target proteins VEGFA and AKT1 to regulate fluid shear stress and the AGE-RAGE signaling pathway and IL-17 signaling pathway of diabetic complications of AS. The molecular docking results showed that VEGFA and AKT1 had great docking ability with the targeted active compounds, and β-carotene is the best. The active components of XFZYD, including β -carotene, quercetin, kamanol, and luteolin, can act on VEGFA and AKT1. These active ingredients play a role in alleviating and treating AS by regulating fluid shear stress and participating in signaling pathways such AS AGE-RAGE of atherosclerosis and diabetes mellitus complicated with AS. β-carotene is a potential inhibitor of VEGFA and AKT1 and treats AS through antioxidant action.

Project description:BackgroundCurcumin shows great effects of inhibiting tumor cell proliferation, inducing apoptosis, inhibiting tumor metastasis, and inhibiting angiogenesis on a variety of tumors. However, the biological activity and possible mechanisms of curcumin in the treatment of retinoblastoma have not been fully elucidated. This study explored the potential therapeutic targets and pharmacological mechanisms of curcumin against retinoblastoma based on network pharmacology and molecular docking.MethodsThe genes corresponding to curcumin targets were screened from the HERB, PharmMapper, and SwissTargetPrediction databases. Protein-protein interaction (PPI) networks were constructed for the intersecting targets in the STRING database. Cytoscape 3.7.0 was used for network topology analysis and screening of important targets. R 4.1.0 software was used for Gene Ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of intersection targets. The molecular structures of curcumin and core target proteins were obtained from PubChem and PDB databases, and the two were preprocessed and molecularly docked using AutoDockTools and PyMOL software.ResultsThrough network data mining, we obtained 504 curcumin targets and 966 retinoblastoma disease targets, and 44 potential targets for curcumin treatment of retinoblastoma were obtained by mapping. Three core targets were obtained from network topology analysis. 462 biological processes, 21 cellular compositions, and 34 molecular functions were obtained by GO enrichment analysis. KEGG pathway analysis revealed 94 signaling pathways, mainly involving chemical carcinogenesis-receptor activation, chemical carcinogenesis-reactive oxygen species, viral carcinogenesis, Th17 cell differentiation, etc. The molecular docking results indicated that the binding energy of curcumin to the core targets was less than 0 kJ mol-1, among which the binding energy of RB1 and CDKN2A to curcumin was less than -5 kJ mol-1 with significant binding activity.ConclusionBased on molecular docking technology and network pharmacology, we initially revealed that curcumin exerts its therapeutic effects on retinoblastoma with multitarget, multipathway, and multibiological functions, providing a theoretical basis for subsequent studies.

Dataset Information

Network pharmacology and molecular docking-based study on exploring the potential mechanism of Lycium barbarum L: In the treatment of atherosclerosis.

Background

Methods

Results

Conclusion

Publications

Network pharmacology and molecular docking-based study on exploring the potential mechanism of Lycium barbarum L: In the treatment of atherosclerosis.

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