Uncovering Mechanisms of Zanthoxylum piperitum Fruits for the Alleviation of Rheumatoid Arthritis Based on Network Pharmacology

Oh, Ki‐Kwang; Adnan, Md.; Cho, Dong-Ha

doi:10.3390/biology10080703

Cited by 10 publications

(8 citation statements)

References 53 publications

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“…Specifically, biological network models can serve as a paradigm to uncover the underlying causes of complex diseases [ 17 ]. Network pharmacology is an integrated analytical methodology to pioneer significant components (bioactives, proteins, diseases, and genes) [ 18 ]. With the development of bioinformatics, network pharmacology can decode the mechanism of action in complex biological systems through interdisciplinary studies, suggesting that network pharmacology is a convergent approach to shift from “one target, one compound” to “multiple targets, multiple compounds” [ 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study

Gupta

Min

et al. 2022

Cells

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The metabolites produced by the gut microbiota have been reported as crucial agents against obesity; however, their key targets have not been revealed completely in complex microbiome systems. Hence, the aim of this study was to decipher promising prebiotics, probiotics, postbiotics, and more importantly, key target(s) via a network pharmacology approach. First, we retrieved the metabolites related to gut microbes from the gutMGene database. Then, we performed a meta-analysis to identify metabolite-related targets via the similarity ensemble approach (SEA) and SwissTargetPrediction (STP), and obesity-related targets were identified by DisGeNET and OMIM databases. After selecting the overlapping targets, we adopted topological analysis to identify core targets against obesity. Furthermore, we employed the integrated networks to microbiota–substrate–metabolite–target (MSMT) via R Package. Finally, we performed a molecular docking test (MDT) to verify the binding affinity between metabolite(s) and target(s) with the Autodock 1.5.6 tool. Based on holistic viewpoints, we performed a filtering step to discover the core targets through topological analysis. Then, we implemented protein–protein interaction (PPI) networks with 342 overlapping target, another subnetwork was constructed with the top 30% degree centrality (DC), and the final core networks were obtained after screening the top 30% betweenness centrality (BC). The final core targets were IL6, AKT1, and ALB. We showed that the three core targets interacted with three other components via the MSMT network in alleviating obesity, i.e., four microbiota, two substrates, and six metabolites. The MDT confirmed that equol (postbiotics) converted from isoflavone (prebiotics) via Lactobacillus paracasei JS1 (probiotics) can bind the most stably on IL6 (target) compared with the other four metabolites (3-indolepropionic acid, trimethylamine oxide, butyrate, and acetate). In this study, we demonstrated that the promising substate (prebiotics), microbe (probiotics), metabolite (postbiotics), and target are suitable for obsesity treatment, providing a microbiome basis for further research.

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Section: Introductionmentioning

confidence: 99%

Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study

Gupta

Min

et al. 2022

Cells

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“…The percentage of each compound was calculated from the relative peak area of each compound in the chromatogram. The concept of integration was used in the ChemStation integrator algorithms (analyzed on September 24, 2021) (Oh et al, 2021).…”

Section: Methodsmentioning

confidence: 99%

“…The concept of integration was used in the ChemStation integrator algorithms (analyzed on September 24, 2021) (Oh et al, 2021).…”

Section: Gc-ms Analysis Conditionmentioning

confidence: 99%

A network pharmacology study to investigate bioactive compounds and signaling pathways of garlic ( Allium sativum L.) husk against type 2 diabetes mellitus

2022

Journal of Food Biochemistry

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During garlic harvest, much husk has been generated, nearly all husk is discarded as unnecessary by-products. However, in Korean folk remedies, Allium sativum L. husk (ASLH) extracts have been used as a reliever against type 2 diabetes mellitus (T2DM).Currently, its significant mechanisms against T2DM remain unclear. Thus, the aim of this study is to investigate the characteristics of its key signaling pathways, targets, and compounds. The compounds in ASLH were analyzed by gas chromatographymass spectrum (GC-MS) and confirmed drug-like compounds (DLCs) in silico. Then, protein-protein interaction (PPI) networks and signaling pathways, targets, compounds are constructed, visualized by using RStudio. Finally, we performed a molecular docking test (MDT) to identify the key mechanism(s), target(s), and compound(s) of ASLH on T2DM. A total of 23 compounds in ASLH were identified by GC-MS, and all compounds were accepted by Lipinski's rule. The 23 compounds were associated with 521 targets and retrieved 4,736 T2DM-related targets by Online Mendelian Inheritance in Man (OMIM) and DisGeNET. The final overlapping 87 targets were obtained between compounds-targets and T2DM-related targets. The number of 13 signaling pathways, 33 targets, and 19 compounds of ASLH were associated with T2DM. In parallel, MDT revealed four potential compounds: (1) 9-hexacosene, (2) 2- (([2-ethylhexyl]oxy)carbonyl)benzoic acid, (3) clionasterol, (4) 4-methyl-2-phenylpyrimidine on PPAR signaling pathway. Overall, the four compounds from ASLH might show an anti-T2DM synergistic effect by activating the PPAR signaling pathway or inactivating the phospholipase D signaling pathway. In this study, we suggest that ASLH might be considered a health-promising resource from both nutraceutical and pharmaceutical perspectives. Practical applicationsAllium sativum L. husk (ASLH) has been regarded as wastes that come from garlic (Allium sativum L.). During the harvesting period of garlic, a considerable amount of ASLH is a severe problem in farm communities. Particularly, garlic bioactive compounds are well documented including organosulfur compounds. Conversely, at

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“…Some researchers explored the association between TCM and diabetes using network analysis and molecular docking [ 36 ]. Oh et al investigated the bioactivities of Zanthoxylum piperitum fruits in treating rheumatoid arthritis based on network pharmacology [ 37 ]. Previous studies showed that computer-aided learning is an appropriate method for pharmaceutical research.…”

Section: Introductionmentioning

confidence: 99%

Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis

Kang

Wang³

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Background. Clinical research found that TCM is therapeutic in treating gastric cancer. Clearing heat is the most common method, while some antirheumatic medicines are widely used in treatment as well. To explore the pharmacological mechanism, we researched the comparison between heat-clearing medicine and antirheumatic medicine in treating gastric cancer. Methods. First, related ingredients and targets were searched, respectively, and are shown in an active ingredient-target network. Combining the relevant targets of gastric cancer, we constructed a PPI network and MCODE network. Then, GO and KEGG enrichment analyses were conducted. Molecular docking experiments were performed to verify the affinity of targets and ligands. Finally, we analyzed the tumor immune infiltration on gene expression, somatic CNA, and clinical outcome. Results. A total of 31 ingredients and 90 targets of heat-clearing medicine, 31 ingredients and 186 targets of antirheumatic medicine, and 12,155 targets of gastric cancer were collected. Antirheumatic medicine ranked the top in all the enrichment analyses. In the KEGG pathway, both types of medicines were related to pathways in cancer. In the KEGG map, AR, MMP2, ERBB2, and TP53 were the most crucial targets. Key targets and ligands were docked with low binding energy. Analysis of tumor immune infiltration showed that the expressions of AR and ERBB2 were correlated with the abundance of immune infiltration and made a difference in clinical outcomes. Conclusions. Quercetin is an important ingredient in both heat-clearing medicine and antirheumatic medicine. AR signaling pathway exists in both types of medicines. The mechanism of the antitumor effect in antirheumatic medicine was similar to trastuzumab, a targeted drug aimed at ERBB2. Both types of medicines were significant in tumor immune infiltration. The immunology of gastric tumor deserves further research.

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Uncovering Mechanisms of Zanthoxylum piperitum Fruits for the Alleviation of Rheumatoid Arthritis Based on Network Pharmacology

Cited by 10 publications

References 53 publications

Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study

Elucidation of Prebiotics, Probiotics, Postbiotics, and Target from Gut Microbiota to Alleviate Obesity via Network Pharmacology Study

A network pharmacology study to investigate bioactive compounds and signaling pathways of garlic ( Allium sativum L.) husk against type 2 diabetes mellitus

Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis

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