Study on Anti-Type 2 Diabetes Mechanism of Sophora japonica L. based on Network Pharmacology and Molecular Docking

2021 ◽  
Vol 10 (04) ◽  
pp. 193-202
Author(s):  
镕泽 方
Keyword(s):  
Type 2 Diabetes ◽  
Molecular Docking ◽  
Network Pharmacology ◽  
Sophora Japonica

scholarly journals Simultaneous clustering analysis with molecular docking in network pharmacology for type 2 antidiabetic compounds

2018 ◽  
Vol 22 (1) ◽  
pp. 43
Author(s):  
Nur Azizah Komara Rifai ◽  
Farit Mochamad Afendi ◽  
I Made Sumertajaya
Keyword(s):  
Type 2 Diabetes ◽  
Molecular Docking ◽  
Protein Interactions ◽  
Binding Free Energy ◽  
Network Pharmacology ◽  
High Association ◽  
Target Proteins ◽  
Synthetic Drugs ◽  
Human Proteins

The database of drug compounds and human proteins plays a very important role in identifying the protein target and the compound in drug discovery. Recently, a network pharmacology approach was established by updating the research paradigm from the current “one disease-one target-one drug” to a new “drug-target-disease network”. Ligand-protein interactions can be analyzed quantitatively using simultaneous clustering and molecular docking. The docking method offers the ability to quickly and cheaply predict the ligand-protein binding free energy (DG) in structure-based virtual screening. Meanwhile, simultaneous clustering was used to find subgroups of compounds that exhibit a high correlation with subgroups of target proteins. This study is focused on the interaction between the 306 compounds from medicinal plants (brotowali Tinospora crispa, ginger Zingiber officinale, pare Momordica charantia, sembung Blumea balsamifera, synthetic drugs (FDA-approved) and the 21 significant human proteins associated with type 2 diabetes. We found that brotowali (B018), sembung (S031), pare (P231), and ginger (J036, J033) were close to the synthetic drugs and can possibly be developed as antidiabetic drug candidates. Likewise, the proteins AKT1, WFS1, APOE, EP300, PTH, GCG, and UBC which assemble each other and which have a high association with INS can be seen as target proteins that play a role in type 2 diabetes.

scholarly journals Research on Saponin Active Ingredient of Stir-Fried Dolichos Lablab L. Kernel for Treatment of Type-2 Diabetes Based on UHPLC-Q-Exactive Orbitrap MS and Network Pharmacology

2020 ◽  
Author(s):  
Han Jun ◽  
Liangzi Fang ◽  
Qinfang Zheng
Keyword(s):  
Type 2 Diabetes ◽  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Network Pharmacology ◽  
Dolichos Lablab ◽  
Q Exactive ◽  
Orbitrap Ms

Abstract BackgroundAlthough the clinical effect of stir-fried Dolichos lablab L. kernel has been approved in modern traditional Chinese medicine, existing associated studies mainly focus on its clinical studies and chemical ingredients. However, there are few studies on pharmacodynamics material basis and molecular mechanism of stirfried Dolichos lablab L. kernel in treatment of type-2 diabetes(T2DM), thus restricting the further development and utilization of stir-fried Dolichos lablab L. kernel.MethodsA qualitative analysis on saponin chemical ingredients of stir-fried Dolichos lablab L. kernel was performed using UHPLC-Q-Exactive Orbitrap MS. A total of 10 saponin ingredients were selected. Moreover, target screening, biological process and metabolism pathway analysis were accomplished by network pharmacology. Four key proteins(EGFR, IGF1, MAPK1 and PIK3R1) of type-2 diabetes were selected for molecular docking verification with saponin ingredients. Specifically, molecular dynamics simulation of ingredients which have strong bindings with proteins was conducted. ResultsIn this study, 16 saponin ingredients were identified from stir-fried Dolichos lablab L. kernel. There were 91 intersection targets and the KEGG pathway enrichment involved 20 relevant pathways. According to the molecular docking verification, saponin ingredients of stir-fried Dolichos lablab L. kernel can form stable binding with key protein targets. The molecular dynamics simulation further verifies stability and reasonability of the docking results. ConclusionsThis study provides references to identification of efficient ingredients of stir-fried Dolichos lablab L. kernel, screening of quality markers and explanation of relevant action mechanism by combining UHPLC-Q-Exactive Orbitrap MS and network pharmacology.

scholarly journals Mechanisms of Rhizoma Coptidis against type 2 diabetes mellitus explored by network pharmacology combined with molecular docking and experimental validation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenrong An ◽  
Yanqin Huang ◽  
Shouqiang Chen ◽  
Tao Teng ◽  
Yingning Shi ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Molecular Docking ◽  
Experimental Validation ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Active Compounds ◽  
Rhizoma Coptidis

AbstractThis study systematically explored the underlying mechanism of Rhizoma Coptidis against type 2 diabetes mellitus (T2DM) by using network pharmacology and molecular docking and experimental validation. We retrieved and screened active compounds of Rhizoma Coptidis and corresponding T2DM-related targets across multiple databases. PPI networks of the genes were constructed using STRING, and the core targets were screened via topological analysis. GO and KEGG enrichment analyses were performed by using DAVID. Finally, molecular docking and experimental studies were performed after bioinformatic analysis for verification. There were 14 active compounds and 19 core targets of Rhizoma Coptidis-T2DM, of which quercetin was identified as the main compound and IL6, VEGFA and TNF were the most significant core targets. GO and KEGG enrichment analyses showed that Rhizoma Coptidis ameliorated T2DM by regulating multiple biological processes and pathways. Docking studies indicated that IL6, VEGFA and TNF could stably bind with all active compounds of Rhizoma Coptidis. The results of our experiments revealed that Rhizoma Coptidis could inhibit the expression of IL6 and TNFα and enhance islet cell viability. This study suggests anti-inflammatory therapeutic effects of Rhizoma Coptidis on T2DM, thereby providing a scientific basis and new insight for further research on the antidiabetic effect of Rhizoma Coptidis.

scholarly journals DECIPHERING THE ACTION MECHANISM OF INDONESIA HERBAL DECOCTION IN THE TREATMENT OF TYPE II DIABETES USING A NETWORK PHARMACOLOGY APPROACH

2017 ◽  
Vol 9 (3) ◽  
pp. 243
Author(s):  
Peter Juma Ochieng ◽  
Wisnu Ananta Kusuma ◽  
Mohamad Rafi ◽  
Tony Sumaryada
Keyword(s):  
Type 2 Diabetes ◽  
Molecular Docking ◽  
Profile Analysis ◽  
Synergetic Effect ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Action Mechanism ◽  
Pharmacological Mechanism ◽  
Dietary Starch

Objective: The aim of this research was to investigate action mechanism of Indonesia herbal decoctions in the treatment of Type 2 Diabetes (T2D) using network pharmacology approaches.Methods: Drug target profile analysis via Markov clustering was performed to identify the potent antidiabetic ingredients in the four herbs. Network target base identification of multicomponent synergy was applied to predict the ingredients synergetic effect. The multi-level and integrated target networks were contracted to identify the herbs major ingredients and their presumed targets. Further enrichment analysis and molecular docking were performed to validate network targets.Results: 278 ingredients from the four herbs were linked to antidiabetic drugs with an overall clustering success rate of 98.58% and 5 ingredient pairs had significant synergetic effects. Enrichment analysis demonstrates herbs candidate presumed targets were frequently involved in the significant biological process and pathways associated with progression of Type 2 diabetes (T2D) diseases. Finally, molecular docking validation revealed there was high binding site similarity between momordicoside F2 (78%), beta-sitosterol (67%) and cis-N-Feruloyltyramine (67%) with miglitol drug. In addition, the four ligands presented the higher binding affinity to Maltase-glucoamylase (MGA) receptor an enzyme responsible for the digestion of dietary starch to glucose.Conclusion: This study revealed the pharmacological mechanism of action of Indonesia herbal decoctions in the treatment of Type 2 diabetes. The herbs major presumed target played a significant biological role in the progression of Type 2 diabetes (T2D) while major herbal ingredients indicates the potential of curing Type 2 diabetes by inhibiting Maltase-glucoamylase (MGA) activity.

2469-PUB: Exploring the Mechanisms of Berberine against Type 2 Diabetes Mellitus and Its Complications by Network Pharmacology

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 2469-PUB
Author(s):  
SHA DI ◽  
LIN HAN ◽  
LINHUA ZHAO ◽  
XIAOLIN TONG
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Network Pharmacology

scholarly journals Use of Network Pharmacology to Explore the Mechanism of Gegen (Puerariae lobatae Radix) in the Treatment of Type 2 Diabetes Mellitus Associated with Hyperlipidemia

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Guozhen Yuan ◽  
Shuai Shi ◽  
Qiulei Jia ◽  
Jingjing Shi ◽  
Shuqing Shi ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Signaling Pathway ◽  
Fluid Shear Stress ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Active Ingredients

Rapid increases in metabolic disorders, such as type 2 diabetes mellitus (T2DM) and hyperlipidemia, are becoming a substantial challenge to worldwide public health. Traditional Chinese medicine has a long history and abundant experience in the treatment of diabetes and hyperlipidemia, and Puerariae lobatae Radix (known as Gegen in Chinese) is one of the most prevalent Chinese herbs applied to treat these diseases. The underlying mechanism by which Gegen simultaneously treats diabetes and hyperlipidemia, however, has not been clearly elucidated to date. Therefore, we systematically explored the potential mechanism of Gegen in the treatment of T2DM complicated with hyperlipidemia based on network pharmacology. We screened the potential targets of Gegen, T2DM, and hyperlipidemia in several online databases. Then, the hub targets were analyzed by performing protein-protein interaction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment assays, and finally, the complicated connections among compounds, targets, and pathways were visualized in Cytoscape. We found that isoflavones, including daidzein, genistein, and puerarin, as well as β-sitosterol, are the key active ingredients of Gegen responsible for its antidiabetic and antihyperlipidemia effects, which mainly target AKR1B1, EGFR, ESR, TNF, NOS3, MAPK3, PPAR, CYP19A1, INS, IL6, and SORD and multiple pathways, such as the PI3K-Akt signaling pathway; the AGE-RAGE signaling pathway in diabetic complications, fluid shear stress, and atherosclerosis; the PPAR signaling pathway; insulin resistance; the HIF-1 signaling pathway; the TNF signaling pathway; and others. These active ingredients also target multiple biological processes, including the regulation of glucose and lipid metabolism, the maintenance of metabolic homeostasis, and anti-inflammatory and antioxidant pathways. In conclusion, Gegen is a promising therapeutic phytomedicine for T2DM with hyperlipidemia that targets multiple proteins, biological processes, and pathways.

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