Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia

Bisht, Anand Singh; Tewari, D. P.; Kumar, Sanjay; Chandra, Subhash

doi:10.1007/s11030-023-10684-w

Cited by 14 publications

(5 citation statements)

References 74 publications

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“…The structural stability of the protein is related to hydrogen bond integrity and stability. 30 From the overall MD simulation (RMSD, RMSF, radius of gyration, number of hydrogen bonds), we concluded that diosgenin and luteolin were relatively stable complexes, showing good binding affinity. The combination of drugs and proteins did not affect the protein conformation.…”

Section: Discussionmentioning

confidence: 86%

A Network Pharmacology and Molecular Dynamics Simulation-Based Study of Qing Run Hua Jie Decoction in Interstitial Pneumonia Treatment

Li,

Lian,

Lin

et al. 2024

IDR

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Objective This study is dedicated to revealing the potential mechanism of Qin Run Hua Jie (QRHJ) decoction in Interstitial pneumonia (IP) treatment. Methods The TCMSP database predicted the chemical components and targets of QRHJ decoction, and the IP-related genes were from the Genecards database. Cytoscape software was used to establish the interaction network. R package clusterProfiler was utilized for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The molecular docking analysis of target proteins and the corresponding active pharmaceutical ingredients in the core position of the interaction network was conducted. Then, molecular dynamics (MD) simulations of a potential active substance and its key targets were performed. The binding efficiency of EGFR and luteolin, HIF1A and diosgenin was detected by cellular thermal shift assay (CETSA), and protein expression was measured by Western blot. CCK-8 was used to detect cell activity. Results A total of 153 active ingredients, 127 targets and 362 IP-related genes were obtained. KEGG enrichment analysis identified IP-related signaling pathways including HIF-1 signaling pathway and TNF signaling pathway. The two key components luteolin and diosgenin stably bound to the key targets EGFR and HIF1A. Cell experiments further showed that EGFR and luteolin, HIF1A and diosgenin bound to exert anti-fibrotic effects. Conclusion As an active ingredient of QRHJ decoction, luteolin and diosgenin may exert therapeutic effect on IP through binding to the key target EGFR and HIF1A. This work initially revealed the key molecular mechanism of QRHJ decoction in IP treatment and offered theoretical evidence.

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Section: Discussionmentioning

confidence: 86%

A Network Pharmacology and Molecular Dynamics Simulation-Based Study of Qing Run Hua Jie Decoction in Interstitial Pneumonia Treatment

Li,

Lian,

Lin

et al. 2024

IDR

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“…Hydrogen bonds play a crucial role in stabilizing a protein–ligand complex by forming highly specific interactions between a ligand and a receptor. They play an essential role in drug specificity, metabolism, and drug absorption in drug design [ 76 ]. Moreover, the protein–ligand complexes exhibited remarkable structural stability at a temperature of 298.15 K. Most amino acids should exhibit an RMSF value of less than 2 Å in optimal circumstances.…”

Section: Discussionmentioning

confidence: 99%

Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling

Ullah,

Sun,

et al. 2024

Nutrients

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Physical fatigue (peripheral fatigue), which affects a considerable portion of the world population, is a decline in the ability of muscle fibers to contract effectively due to alterations in the regulatory processes of muscle action potentials. However, it lacks an efficacious therapeutic intervention. The present study explored bioactive compounds and the mechanism of action of Citrus reticulata peel (CR-P) in treating physical fatigue by utilizing network pharmacology (NP), molecular docking, and simulation-based molecular dynamics (MD). The bioactive ingredients of CR-P and prospective targets of CR-P and physical fatigue were obtained from various databases. A PPI network was generated by the STRING database, while the key overlapping targets were analyzed for enrichment by adopting KEGG and GO. The binding affinities of bioactive ingredients to the hub targets were determined by molecular docking. The results were further validated by MD simulation. Five bioactive compounds were screened, and 56 key overlapping targets were identified for CR-P and physical fatigue, whereas the hub targets with a greater degree in the PPI network were AKT1, TP53, STAT3, MTOR, KRAS, HRAS, JAK2, IL6, EGFR, and ESR1. The findings of the enrichment analysis indicated significant enrichment of the targets in three key signaling pathways, namely PI3K-AKT, MAPK, and JAK-STAT. The molecular docking and MD simulation results revealed that the bioactive compounds of CR-P exhibit a stronger affinity for interacting with the hub targets. The present work suggests that bioactive compounds of CR-P, specifically Hesperetin and Sitosterol, may ameliorate physical fatigue via the PI3K-AKT signaling pathway by targeting AKT1, KRAS, and MTOR proteins.

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“…For ATC treatment, it is crucial to identify key targets in the mechanism of action of Digitalis. Network pharmacology-grounded in systems biology and the network analysis of biological systems-focuses on selecting specific signaling nodes for drug design to target multiple targets . Researchers have utilized network pharmacology to discover active compounds in drugs and traditional Chinese medicine (TCM), analyze drug combination laws and formula pairings, and elucidate the overall mechanisms of action. , This approach combines the roles of target and effector molecules and can accurately predict the therapeutic efficacy and mechanism of action of drugs .…”

Section: Introductionmentioning

confidence: 99%

Incorporating Network Pharmacology and Experimental Validation to Identify Bioactive Compounds and Potential Mechanisms of Digitalis in Treating Anaplastic Thyroid Cancer

Zhu,

Liang,

Guo

et al. 2024

ACS Omega

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Anaplastic thyroid cancer (ATC) is one of the most lethal malignant tumors for which there is no effective treatment. There are an increasing number of studies on herbal medicine for treating malignant tumors, and the classic botanical medicine Digitalis and its active ingredients for treating heart failure and arrhythmias have been revealed to have significant antitumor efficacy against a wide range of malignant tumors. However, the main components of Digitalis and the molecular mechanisms of its anti-ATC effects have not been extensively studied. Here, we screened the main components and core targets of Digitalis and verified the relationship between the active components and targets through network pharmacology, molecular docking, and experimental validation. These experiments showed that the active ingredients of Digitalis inhibit ATC cell activity and lead to ATC cell death through the apoptotic pathway.

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Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia

Cited by 14 publications

References 74 publications

A Network Pharmacology and Molecular Dynamics Simulation-Based Study of Qing Run Hua Jie Decoction in Interstitial Pneumonia Treatment

A Network Pharmacology and Molecular Dynamics Simulation-Based Study of Qing Run Hua Jie Decoction in Interstitial Pneumonia Treatment

Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling

Incorporating Network Pharmacology and Experimental Validation to Identify Bioactive Compounds and Potential Mechanisms of Digitalis in Treating Anaplastic Thyroid Cancer

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