The mechanism research on the anti‐liver fibrosis of emodin based on network pharmacology

Liang, Baoyu; Gao, Liyuan; Wang, Feixia; Li, Zhanghao; Li, Yujia; Tan, Shanzhong; Chen, Anping; Zhang, Zili; Sun, Lixia; Zhang, Feng; Zheng, Shizhong

doi:10.1002/iub.2523

Cited by 15 publications

(7 citation statements)

References 50 publications

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“…First, we sketched molecular structures with ChemDraw 14.0. Then the molecules were minimized using Tripos Field ( White, 1977 ; Motoc et al, 1986 ; Waltho et al, 1988 ; Clark et al, 1989 ; Purohit et al, 2020 ) in Sybyl-X 2.0 ( SYBYL, 2012 ; Liang et al, 2021 ). The lowest energy structures were further optimized by undergoing ( Turner et al, 2017 ) (PM7) ( Stewart, 2013 ; Turner et al, 2017 ) in Molecular Orbital PACkage (MOPAC 2016) method.…”

Section: Methodsmentioning

confidence: 99%

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

Nie

Xia

et al. 2022

Front. Chem.

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As a potent zinc chelator, hydroxamic acid has been applied in the design of inhibitors of zinc metalloenzyme, such as histone deacetylases (HDACs). A series of hydroxamic acids with HDAC inhibitory activities were subjected to the QSRR (Quantitative Structure–Retention Relationships) study. Experimental data in combination with calculated molecular descriptors were used for the development of the QSRR model. Specially, we employed PCA (principal component analysis) to accomplish dimension reduction of descriptors and utilized the principal components of compounds (16 training compounds, 4 validation compounds and 7 test compounds) to execute GA (genetic algorithm)-BP (error backpropagation) algorithm. We performed double cross-validation approach for obtaining a more convincing model. Moreover, we introduced molecular interaction-based features (molecular docking scores) as a new type of molecular descriptor to represent the interactions between analytes and the mobile phase. Our results indicated that the incorporation of molecular interaction-based features significantly improved the accuracy of the QSRR model, (R2 value is 0.842, RMSEP value is 0.440, and MAE value is 0.573). Our study not only developed QSRR model for the prediction of the retention time of hydroxamic acid in HPLC but also proved the feasibility of using molecular interaction-based features as molecular descriptors.

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Section: Methodsmentioning

confidence: 99%

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

Nie

Xia

et al. 2022

Front. Chem.

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“…In contrast, Scutellaria baicalensis decoction has a preventive effect on liver injury, which may be related to the involvement in the metabolism of some tryptophan to reduce oxidative stress and inhibit collagen regeneration [ 127 ]. Emodin extracted from various anthraquinones further affects the fibrotic process by inhibiting epithelial-mesenchymal transition (EMT), reducing Ly6C hi macrophage infiltration Ly6C hi [ 128 ], mediating the p53 signaling pathway to induce HSC apoptosis and the TLR4 pathway to slow down inflammation production and lipid deposition in NAFLD models [ 129 , 130 ]. Moreover, all three can mediate the NF-kB pathway, inhibit the TGF- β and the levels of inflammatory factors such as TNF- α , and antagonize the profibrotic effects of the inflammatory response [ 129 – 135 ].…”

Section: Tcm Therapeutic Perspectivesmentioning

confidence: 99%

“…Emodin extracted from various anthraquinones further affects the fibrotic process by inhibiting epithelial-mesenchymal transition (EMT), reducing Ly6C hi macrophage infiltration Ly6C hi [ 128 ], mediating the p53 signaling pathway to induce HSC apoptosis and the TLR4 pathway to slow down inflammation production and lipid deposition in NAFLD models [ 129 , 130 ]. Moreover, all three can mediate the NF-kB pathway, inhibit the TGF- β and the levels of inflammatory factors such as TNF- α , and antagonize the profibrotic effects of the inflammatory response [ 129 – 135 ]. Studies have shown that ursolic acid (UA) can regulate EMT or MFB via Rho [ 136 , 137 ], improve the integrity of the intestinal barrier, reduce intestinal flora disorders [ 138 , 139 ], and modulate the NOX4/NLRP3 inflammatory vesicle signaling pathway to attenuate liver fibrosis [ 140 ].…”

Section: Tcm Therapeutic Perspectivesmentioning

confidence: 99%

Pathogenesis of Liver Fibrosis and Its TCM Therapeutic Perspectives

Nan

Lian

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Liver fibrosis is a pathological process of abnormal tissue proliferation in the liver caused by various pathogenic factors, which will further develop into cirrhosis or even hepatocellular carcinoma if liver injury is not intervened in time. As a diffuse progressive liver disease, its clinical manifestations are mostly excessive deposition of collagen-rich extracellular matrix resulting in scar formation due to liver injury. Hepatic fibrosis can be caused by hepatitis B and C, fatty liver, alcohol, and rare diseases such as hemochromatosis. As the metabolic center of the body, the liver regulates various vital activities. During the development of fibrosis, it is influenced by many other factors in addition to the central event of hepatic stellate cell activation. Currently, with the increasing understanding of TCM, the advantages of TCM with multiple components, pathways, and targets have been demonstrated. In this review, we will describe the factors influencing liver fibrosis, focusing on the effects of cells, intestinal flora, iron death, signaling pathways, autophagy and angiogenesis on liver fibrosis, and the therapeutic effects of herbal medicine on liver fibrosis.

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“…The energy was calculated using the SYBYLÀ X 2.0 package [33] with Tripos force field and Gasteiger-Marsili charge. The binding energy of two molecules (A and B) was the difference in the free energies before and after binding: ΔG = G(Ligand-Macromolecule) -G(Ligand) -G(Macromolecule) [34] .…”

Section: Docking Simulationmentioning

confidence: 99%

Insight into the Stereocontrol of DNA Polymerase‐Catalysed Reaction by Chiral Cobalt Complexes

et al. 2022

Adv Synth Catal

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Enantiomers of chiral substances typically have distinct biological activities, thus, the explorations of biochemical processes at the enantiomeric level has very high significance. This study investigated DNA polymerase-catalyzed reaction modulated by various types of chiral cobalt complexes. The experimental data showed that polymerase reactions were inhibited or accelerated in the presence of KMore importantly, the stereocontrol of bioreactivity was found to be different for the enantiomers, which was reflected in their ability to bind to the polymerase reaction system. The docking simulation illustrated that the acceleration or inhibition of polymerase reaction could be correlated with diverse electrostatic energy induced by the attached metal chelates, whereas the different stereocontrol of bioreactivity for the enantiomers was attributed to a discrepancy of Van der Waals interactions between the enantiomer and polymerase catalytic sites.

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The mechanism research on the anti‐liver fibrosis of emodin based on network pharmacology

Cited by 15 publications

References 50 publications

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

Development of QSRR model for hydroxamic acids using PCA-GA-BP algorithm incorporated with molecular interaction-based features

Pathogenesis of Liver Fibrosis and Its TCM Therapeutic Perspectives

Insight into the Stereocontrol of DNA Polymerase‐Catalysed Reaction by Chiral Cobalt Complexes

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