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

Potential of natural products in inflammation: biological activities, structure-activity relationships, and mechanistic targets

A balance between the development and suppression of inflammation can always be found in the body. When this balance is disturbed, a strong inflammatory response can damage the body. It sometimes is necessary to use drugs with a significant anti-inflammatory effect, such as nonsteroidal anti-inflammatory drugs and steroid hormones, to control inflammation in the body. However, the existing anti-inflammatory drugs have many adverse effects, which can be deadly in severe cases, making research into new safer and more effective anti-inflammatory drugs necessary. Currently, numerous types of natural products with anti-inflammatory activity and distinct structural features are available, and these natural products have great potential for the development of novel anti-inflammatory drugs. This review summarizes 260 natural products and their derivatives with anti-inflammatory activities in the last two decades, classified by their active ingredients, and focuses on their structure-activity relationships in anti-inflammation to lay the foundation for subsequent new drug development. We also elucidate the mechanisms and pathways of natural products that exert anti-inflammatory effects via network pharmacology predictions, providing direction for identifying subsequent targets of anti-inflammatory natural products.

Flavokawain C inhibits proliferation and migration of liver cancer cells through FAK/PI3K/AKT signaling pathway

PURPOSE

This study investigated the potential applicability and the underlying mechanisms of flavokawain C, a natural compound derived from kava extracts, in liver cancer treatment.

METHODS

Drug distribution experiment used to demonstrate the preferential tissues enrichment of flavokawain C. Cell proliferation, apoptosis and migration effect of flavokawain C were determined by MTT, colony formation, EdU staining, cell adhesion, transwell, flow cytometry and western blot assay. The mechanism was explored by comet assay, immunofluorescence assay, RNA-seq-based Kyoto encyclopedia of genes and genomes analysis, molecular dynamics, bioinformatics analysis and western blot assay. The anticancer effect of flavokawain C was further confirmed by xenograft tumor model.

RESULTS

The studies first demonstrated the preferential enrichment of flavokawain C within liver tissues in vivo. The findings demonstrated that flavokawain C significantly inhibited proliferation and migration of liver cancer cells, induced cellular apoptosis, and triggered intense DNA damage along with strong DNA damage response. The findings from RNA-seq-based KEGG analysis, molecular dynamics, bioinformatics analysis, and western blot assay mechanistically indicated that treatment with flavokawain C notably suppressed the FAK/PI3K/AKT signaling pathway in liver cancer cells. This effect was attributed to the induction of gene changes and the binding of flavokawain C to the ATP sites of FAK and PI3K, resulting in the inhibition of their phosphorylation. Additionally, flavokawain C also displayed the strong capacity to inhibit Huh-7-derived xenograft tumor growth in mice with minimal adverse effects.

CONCLUSIONS

These findings identified that flavokawain C is a promising anticancer agent for liver cancer treatment.

Mechanism and Progress of Natural Products in the Treatment of NAFLD-Related Fibrosis

Nonalcoholic fatty liver disease (NAFLD) has emerged as the most prevalent chronic liver disorder worldwide, with liver fibrosis (LF) serving as a pivotal juncture in NAFLD progression. Natural products have demonstrated substantial antifibrotic properties, ushering in novel avenues for NAFLD treatment. This study provides a comprehensive review of the potential of natural products as antifibrotic agents, including flavonoids, polyphenol compounds, and terpenoids, with specific emphasis on the role of Baicalin in NAFLD-associated fibrosis. Mechanistically, these natural products have exhibited the capacity to target a multitude of signaling pathways, including Hedgehog, Wnt/β-catenin, TGF-β1, and NF-κB. Moreover, they can augment the activities of antioxidant enzymes, inhibit pro-fibrotic factors, and diminish fibrosis markers. In conclusion, this review underscores the considerable potential of natural products in addressing NAFLD-related liver fibrosis through multifaceted mechanisms. Nonetheless, it underscores the imperative need for further clinical investigation to authenticate their effectiveness, offering invaluable insights for future therapeutic advancements in this domain.

Hepatoprotective effect of total flavonoids from Carthamus tinctorius L. leaves against carbon tetrachloride-induced chronic liver injury in mice

Carthamus tinctorius L. leaves, a waste product after Carthami flos production, are rich in flavonoids. Total flavonoids from C. tinctorius L. leaves (TFCTLL) exhibited the protective effect on acute liver injury in mice in previous studies. The aim of the present study was to evaluate the hepatoprotective effect of TFCTLL on chronic liver injury (CLI) and investigate the underlying mechanism. The chemical components of TFCTLL were identified by UPLC-Q-TOF/MS, and their migration into blood was evaluated. The protective effect of TFCTLL on CLI was evaluated by antioxidative and anti-inflammatory experiments in vitro, network pharmacology and a carbon tetrachloride (CCl4)-induced CLI mouse model. We indentified 18 chemical components in the TFCTLL samples and 4 components in plasma. TFCTLL showed significant anti-inflammatory activity and antioxidant capacity in vitro and in vivo. TFCTLL administration prominently improved the liver function and structure, decreased the mRNA expression levels of TLR2, TLR3, TLR4, NF-κB p65, IRF3, AKT1, TRIF, PI3K, MyD88, IL-1β and TNF-α and inhibited the protein expression and nuclear translocation of NF-κB p65 in mice with CLI. The molecular docking results showed that components in plasma had high binding affinity for the targets TLR4, PI3K and AKT1. Therefore, TFCTLL has a protective effect against CCl4-induced CLI, and the underlying mechanisms may be related to antioxidation, anti-inflammation and modulation of the TLRs/NF-κB and PI3K/AKT pathways.

Dynamics simulation and in vitro studies of betulinic acid derivative with liver X receptor

Molecular dynamics simulation of the dominant conformational conjugate was performed for 40 ns and 100 ns via Amber software based on molecular docking by Sybyl software. Because the RMSD and RMSF of 100 ns MD simulation were higher than that of 40 ns MD simulation, the 40 ns was reasonable and credible for MD simulation. The binding free energy and decomposition free energy of the two systems of betulinic acid, com3 with liver X receptor was calculated by the MM_GBSA and MM_PBSA methods, respectively. The results showed that the two systems reached equilibrium and convergence at 20 ns, both stable at about 2 Å, and exhibited low volatility in the range of amino acid 270 to 370 (RMSF <1 Å). The binding energy of com3 (ΔG_bind = -68.02 kcal/mol by the MM_GBSA method or -55.50 kcal/mol by the MM_PBSA method) with the liver X receptor was lower than that of betulinic acid (ΔG_bind = -55.70 kcal/mol or -42.73 kcal/mol) respectively, and van der Waals force was the most important main driving force, which was consistent with molecular docking and previous experiments. Hydrophobic groups and aromatic rings can be introduced appropriately in structure optimization to increase the van der Waals force and π-π accumulation effect of betulinic acid and liver X receptor, which is conducive to binding and thereby increasing antitumor activity. The clone formation assay and results of western blotting indicated that BA derivative com3 exposure inhibited cell proliferation may relate to the regulation of the AKT/mTOR pathway in 7721 cells. This study clarifies the dynamic interaction mode and potential mechanism of betulinic acid and its derivatives with the liver X receptor, which provides a new idea for the rapid screening of liver X receptor agonists from traditional Chinese medicines.Communicated by Ramaswamy H. Sarma.

Development of Novel Herbal Compound Formulations Targeting Neuroinflammation: Network Pharmacology, Molecular Docking, and Experimental Verification

Neuroinflammation plays an important role in the onset and progression of neurodegenerative diseases. The multicomponent and multitarget approach may provide a practical strategy to address the complex pathological mechanisms of neuroinflammation. This study aimed to develop synergistic herbal compound formulas to attenuate neuroinflammation using integrated network pharmacology, molecular docking, and experimental bioassays. Eight phytochemicals with anti-neuroinflammatory potential were selected in the present study. A compound-gene target-signaling pathway network was constructed to illustrate the mechanisms of action of each phytochemical and the interactions among them at the molecular level. Molecular docking was performed to verify the binding affinity of each phytochemical and its key gene targets. An experimental study was conducted to identify synergistic interactions among the eight phytochemicals, and the associated molecular mechanisms were examined by immunoblotting based on the findings from the network pharmacology analysis. Two paired combinations, andrographolide and 6-shogaol (AN-SG) (IC50 = 2.85 μg/mL), and baicalein-6-shogaol (BA-SG) (IC50 = 3.28 μg/mL), were found to synergistically (combination index <1) inhibit the lipopolysaccharides (LPS)-induced nitric oxide production in microglia N11 cells. Network pharmacology analysis suggested that MAPK14, MAPK8, and NOS3 were the top three relevant gene targets for the three phytochemicals, and molecular docking demonstrated strong binding affinities of the phytochemicals to their coded proteins. Immunoblotting suggested that the AN-SG and BA-SG both showed prominent effects in inhibiting inducible nitric oxide synthase (iNOS) (p < 0.01 and p < 0.05, respectively) and MAPKp-p38 (both p < 0.05) compared with those induced by the LPS stimulation only. The AN-SG combination exhibited greater inhibitions of the protein expressions of iNOS (p < 0.05 vs. individual components), which may partly explain the mechanisms of the synergy observed. This study established a practical approach to developing novel herbal-compound formulations using integrated network pharmacology analysis, molecular docking, and experimental bioassays. The study provides a scientific basis and new insight into the two synergistic combinations against neuroinflammation.

A comprehensive review of emodin in fibrosis treatment

Emodin is the main pharmacodynamic components of rhubarb, with significant pharmacological effects and clinical efficacy.Emodin has a variety of therapy effects, such as anti-cancer, anti-fibrosis effects, and is widely used to treat encephalitis, diabetic cataract and organ fibrosis. Several studies have shown that emodin has a good treatment effect on organ fibrosis, but the mechanism is complex. Moreover, the evidence of some studies is conflicting and confusing. This paper reviewed the mechanism, pharmacokinetics and toxicology of emodin in fibrosis treatment, and briefly discussed relevant cutting-edge new formulations to improve the efficacy, the result can provide some reference for future study.

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

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.

An optimized herbal combination for the treatment of liver fibrosis: Hub genes, bioactive ingredients, and molecular mechanisms

ETHNOPHARMACOLOGICAL RELEVANCE

Liver fibrosis is a chronic liver disease that can lead to cirrhosis, liver failure, and hepatocellular carcinoma, and it is associated with long-term adverse outcomes and mortality. As a primary resource for complementary and alternative medicine, traditional Chinese medicine (TCM) has accumulated a large number of effective formulas for the treatment of liver fibrosis in clinical practice. However, studies on how to systematically optimize TCM formulas are still lacking.

AIM OF THE REVIEW

To provide a methodological reference for the systematic optimization of TCM formulae against liver fibrosis and explored the underlying molecular mechanisms; To provide an efficient method for searching for lead compounds from natural sources and developing from herbal medicines; To enable clinicians and patients to make more reasonable choices and promote the effective treatment toward those patients with liver fibrosis.

MATERIALS AND METHODS

TCM formulas related to treating liver fibrosis were collected from the Web of Science, PubMed, the China National Knowledge Infrastructure (CNKI), Wan Fang, and the Chinese Scientific Journals Database (VIP). Furthermore, the TCM compatibility patterns were mined using association analysis. The core TCM combinations were found by designing an optimized formulas algorithm. Finally, the hub target proteins, potential molecular mechanisms, and active compounds were explored through integrative pharmacology and docking-based inverse virtual screening (IVS) approaches.

RESULTS

We found that the herbs for reinforcing deficiency, activating blood, removing blood stasis, and clearing heat were the basis of TCM formulae patterns. Furthermore, the combination of Salviae Miltiorrhizae (Salvia miltiorrhiza Bunge; Chinese salvia/Danshen), Astragali Radix (Astragalus membranaceus (Fisch.) Bunge; Astragalus/Huangqi), and Radix Bupleuri (Bupleurum chinense DC.; Bupleurum/Chaihu) was identified as core groups. A total of six targets (TNF, STAT3, EGFR, IL2, ICAM1, PTGS2) play a pivotal role in TCM-mediated liver fibrosis inhibition. (-)-Cryptotanshinone, Tanshinaldehyde, Ononin, Thymol, Daidzein, and Formononetin were identified as active compounds in TCM. And mechanistically, TCM could affect the development of liver fibrosis by regulating inflammation, immunity, angiogenesis, antioxidants, and involvement in TNF, MicroRNAs, Jak-STAT, NF-kappa B, and C-type lectin receptors (CLRs) signaling pathways. Molecular docking results showed that key components had good potential to bind to the target genes.

CONCLUSION

In summary, this study provides a methodological reference for the systematic optimization of TCM formulae and exploration of underlying molecular mechanisms.

The combination of Lonicerae Japonicae Flos and Forsythiae Fructus herb-pair alleviated inflammation in liver fibrosis

Objective: To explore the active components and epigenetic regulation mechanism underlying the anti-inflammatory effects of Lonicerae Japonicae Flos and Forsythiae Fructus herb-pair (LFP) in carbon tetrachloride (CCl₄)-induced rat liver fibrosis.

Methods: The main active ingredients and disease-related gene targets of LFP were determined using TCMSP and UniProt, and liver fibrosis disease targets were screened in the GeneCards database. A network was constructed with Cytoscape 3.8.0 and the STRING database, and potential protein functions were analyzed using bioinformatics analysis. Based on these analyses, we determined the main active ingredients of LFP and evaluated their effects in a CCl₄-induced rat liver fibrosis model. Serum biochemical indices were measured using commercial kits, hepatocyte tissue damage and collagen deposition were evaluated by histopathological studies, and myofibroblast activation and inflammation were detected by reverse transcription-polymerase chain reaction (RT-PCR) and western blotting. High-performance liquid chromatography-mass spectrometry was performed to determine the levels of homocysteine, reduced glutathione, and oxidized glutathione, which are involved in inflammation and oxidative stress.

Results: The main active components of LFP were quercetin, kaempferol, and luteolin, and its main targets were α-smooth muscle actin, cyclooxygenase-2, formyl-peptide receptor-2, prostaglandin-endoperoxide synthase 1, nuclear receptor coactivator-2, interleukinβ, tumor necrosis factor α, CXC motif chemokine ligand 14, and transforming growth factor β1. A combination of quercetin, kaempferol, and luteolin alleviated the symptoms of liver fibrosis.

Conclusion: The results of this study support the role of LFP in the treatment of liver fibrosis, and reveal that LFP reduces collagen formation, inflammation, and oxidative stress. This study suggests a potential mechanism of action of LFP in the treatment of liver fibrosis.

Pathogenesis of Liver Fibrosis and Its TCM Therapeutic Perspectives

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.