[Application status and challenges of molecular docking in development of traditional Chinese medicine].

Traditional Chinese medicine is precious treasure of ancient Chinese science and a key to unlocking the treasure trove of Chinese civilization. To elucidate the efficacy and mechanism of traditional Chinese medicines, scientists have been engaged in the research on the molecular basis and regulatory targets. Molecular docking is a computer-aided drug design method capable of visualizing the interaction between components and target proteins. With the progress in the modernization of traditional Chinese medicine and the advancement of algorithms and computing power, molecular docking has become an essential approach in the development of new traditional Chinese medicines. This article summarizes the recent research progress in molecular docking in the development of traditional Chinese medicine, aiming to provide valuable references for further screening of active components and offering insights for improving the development of new traditional Chinese medicines.

Network pharmacology combined with metabolomics to explore the mechanism for Lonicerae Japonicae flos against respiratory syncytial virus.

BACKGROUND: Respiratory Syncytial Virus (RSV) stands out as a primary contributor to lower respiratory tract infections and hospitalizations, particularly in infants. Lonicerae japonicae flos (LJF), a traditional Chinese medicine renowned for its efficacy against various viral infections, including RSV, has been widely employed. Despite its common use, the precise therapeutic mechanism of LJF against RSV remains elusive. This study aimed to investigate the underlying mechanism of LJF against RSV through network pharmacology and metabolomics. METHODS: In this study, based on network pharmacology, potential targets related to LJF and RSV were obtained from PubChem and Swiss Target Prediction. The core targets and pathways were established and verified by enrichment analysis and molecular docking. The anti-RSV efficacy of LJF was determined by in vitro experiments. Additionally, metabolomics analysis was integrated, allowing for the identification of differential metabolites and their correlation with targets following LJF treatment in the context of RSV infection. RESULTS: A total of 23 active ingredients and 780 targets were obtained, of which 102 targets were associated with LJF anti-RSV. The construction of the corresponding Protein-Protein Interaction (PPI) network unveiled potential core targets, including STAT3, TNF, and AKT1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that LJF's anti-RSV effects primarily involve key pathways such as the PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, and FoxO signaling pathway. Molecular docking showed that ZINC03978781, 4,5'-Retro-.beta.,.beta.-Carotene -3,3'-dione, 4',5'-didehydro and 7-epi-Vogeloside had better binding ability. The cellular assay showed that the therapeutic index of LJF against RSV was 4.79. Furthermore, 18 metabolites were screened as potential biomarkers of LJF against RSV, and these metabolites were mainly involved in the pathways of purine metabolism, linoleic acid metabolism, alpha-linolenic acid metabolism, and other related pathways. CONCLUSIONS: The intergration of network pharmacology and metabolomics can clarify the active targets and related pathways of LJF against RSV, which could provide a valuable reference for further research and clinical application of LJF.

Prediction of the Active Components and Mechanism of Forsythia suspensa Leaf against Respiratory Syncytial Virus Based on Network Pharmacology.

Objective: Forsythia suspensa leaf (FSL) has been used as a health tea in China for centuries. Previous experiments have proved that FSL extract has a good effect on the antirespiratory syncytial virus (RSV) in vitro, but its exact mechanism is not clear. Therefore, this study aims to determine the active components and targets of FSL and further explore its anti-RSV mechanism. Methods: UPLC-Q-Exactive-MS was used to analyze the main chemical components of FSL. The compound disease target network, PPI, GO, and KEGG were used to obtain key targets and potential ways. Then, the molecular docking was verified by Schrödinger Maestro software. Next, the cell model of RSV infection was established, and the inhibitory effect of each drug on RSV was detected. Finally, western blotting was used to detect the effect of the active components of FSL on the expression of PI3K/AKT signaling pathway-related protein. Results: UPLC-Q-Exactive-MS analysis showed that there were 67 main chemical constituents in FSL, while network pharmacological analysis showed that there were 169 anti-RSV targets of the active components in FSL, involving 177 signal pathways, among which PI3K/AKT signal pathway played an important role in the anti-RSV process of FSL. The results of molecular docking showed that cryptochlorogenic acid, phillyrin, phillygenin, rutin, and rosmarinic acid had higher binding activities to TP53, STAT3, MAPK1, AKT1, and MAPK3, respectively. In vitro experiments showed that phillyrin and rosmarinic acid could effectively improve the survival rate of RSV-infected cells, increase the expression level of PI3K, and decrease the expression level of AKT. Conclusion: The active ingredients of FSL, phillyrin, and rosmarinic acid can play an anti-RSV role by inhibiting PI3K/AKT signaling pathway. This study provides reliable theoretical and experimental support for the anti-RSV treatment of FSL.

Chlorogenic acid suppresses miR-460a in the regulation of Bcl-2, causing interleukin-1ß reduction in thiram exposed chondrocytes via caspase-3/caspase-7 pathway.

BACKGROUND: Apoptosis is thought to be involved in all processes, including normal cell cycle, immune system, atrophy, embryonic development, and chemical-induced cellular damage. However, if the normal apoptotic process fails, the results might be disastrous, e.g., chondrocytes damage in tibial dyschondroplasia (TD). TD is a worldwide issue in the poultry sector due to thiram toxicity. Thiram (Tetramethyl thiuram disulfide) is a dithiocarbamate pesticide and fungicide commonly used in horticulture to treat grains meant for seed protection and preservation. PURPOSE: According to prior studies, chlorogenic acid (CGA) is becoming essential for regulating apoptosis. But still, the specific role of CGA in chondrocyte cells remains unclear. The present study explored the molecular mechanism of CGA on chondrocytes' apoptosis with B-cell lymphoma 2 signaling under the effect of miR-460a. METHODS: An in vivo and in vitro study was performed according to our previously developed methodology. Flow cytometry, western blotting, reverse transcription-quantitative polymerase chain reaction, and immunofluorescence assay were used to investigate the involvement of apoptosis and inflammasome related pathways. RESULTS: The CGA decreased the apoptosis rate with the deactivation of miR-460a, accompanied by the activation of Bcl-2. The high expression of miR-460a reduced the cell viability of chondrocytes in vitro and in vivo, that led to the interleukin-1ß production. While the apoptotic executioners (caspase-3 and caspase-7) acted upstream in miR-460a overexpressing cells, and its depletion downgraded these executioners. The CGA administrated cells negatively regulated miR-460a expression and thus indicating the deactivation of the apoptotic and inflammasome related pathways. CONCLUSION: Chlorogenic acid had a negative effect on miR-460a, setting off specific feedback to regulate apoptotic and inflammasome pathways, which might be a key feature for chondrocytes' survival.

Discovery of Biomarkers and Potential Mechanisms of Agarwood Incense Smoke Intervention by Untargeted Metabolomics and Network Pharmacology.

BACKGROUND: Agarwood, as a traditional Chinese medicine, has great potential value for the treatment of tranquilization. However, its potential mechanisms and biomarkers are still unclear. METHODS: In this study, ultra-high performance liquid chromatography-quadrupole-Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap-MS)-based metabonomics was adopted to discover the potential biomarkers in mice after agarwood incense smoke (AIS) intervention. Furthermore, the chemical components in agarwood were identified based on UHPLC-Q-Exactive Orbitrap-MS. The global view of potential compound-target-pathway (C-T-B) network was constructed through network pharmacology to understand the potentially material basis of biomarkers. RESULTS: Metabolic profiling indicated that the metabolic changed significantly in mice serum after AIS intervention. A total of 18 potential biomarkers closely related to insomnia and emotional disease were identified, mainly involving in tryptophan metabolism, arginine and proline metabolism, cysteine and methionine metabolism and steroid hormone biosynthesis pathways. A total of 138 components in agarwood were identified based on UHPLC-Q-Exactive Orbitrap-MS. The results showed that mainly compounds such as flidersia type 2-(2-phenylethyl) chromones (FTPECs) and sesquiterpenes exerted good docking abilities with key target proteins, which were involved in multiple diseases including depression and hypnosis. CONCLUSION: In conclusion, this study enhanced current understanding of the change of metabolic markers after AIS intervention. Meanwhile, it also confirmed the feasibility of combining metabolomics and network pharmacology to identify active components and elucidate the material basis of biomarkers and mechanisms.

Chlorogenic acid suppresses mitochondrial apoptotic effectors Bax/Bak to counteract Nod-like receptor pyrin domain 3 (NLRP3) inflammasome in thiram exposed chondrocytes.

BACKGROUND: Tibial dyschondroplasia (TD) is a common disease characterized by proliferation and the deterioration of growth plate's chondrocytes due to widespread utilization of thiram in the agriculture and industrial sector. PURPOSE: In recent years, Nod-like receptor pyrin domain 3 (NLRP3) inflammasome has become a dilemma in the occurrence of many diseases. According to many research investigations, NLRP3 inflammasome has been linked to various diseases caused by pesticides and environmental toxins. Its involvement in such conditions opens up new treatment approaches. However, the role of the NLRP3 inflammasome in the development of TD is not fully understood under the impact of chlorogenic acid (CGA). METHODS: Chondrocytes were cultured with our previously developed methodology from growth plates. After morphological and molecular identification, chondrocytes were split into different groups to investigate the efficacy of chlorogenic acid. Cell apoptosis was determined through flow cytometry and Tunnel assay. Furthermore, RT-qPCR, immunofluorescence, and western blotting techniques were used to check marker genes and proteins expression. RESULTS: In thiram-induced TD, Bax/Bak activation persuade a parallel pathway, mediated by the NLRP3 base inflammasome. It is worth mentioning that the apoptotic executioners (caspase-3 and caspase-7) act upstream for inflammasome. Furthermore, chondrocytes' ability to undergo mitochondrial apoptosis was governed by anti-apoptotic members, e.g., Bcl-2 and Bcl-xl. Equilibrium of these anti-apoptotic proteins ensured appropriate regulation of apoptosis during the development and survival of chondrocytes. CONCLUSION: Chondrocytes have ability to undergo Bax/Bak-mediated apoptosis and generate pro-inflammatory signals, e.g., NLRP3 in thiram-induced TD. So, the Nod-like receptor pyrin domain 3 is the potential target to eliminate TD at all stages of pathology, while drugs, e.g., CGA, can significantly improve chondrocytes' survival by targeting these pro-inflammatory signals.

Anti-Respiratory Syncytial Virus Mechanism of Houttuynia cordata Thunb Exploration based on Network Pharmacology.

BACKGROUND AND OBJECTIVE: Respiratory Syncytial Virus (RSV) is the leading cause of infant lower respiratory tract infections with no mature vaccines and medicines available. Pneumonia caused by RSV kills many infants every year. There are unique advantages of Traditional Chinese Medicine (TCM) to fight against the virus. Houttuynia cordata Thunb is a commonly used antivirus medicine in TCM, but its mechanism has not been investigated. The current study explores the anti-RSV mechanism of H. cordata Thunb by means of network pharmacology and bioinformatics. METHODS: The candidate compounds of H. cordata Thunb and the potential targets were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), PubMed, CNKI, PubChem Database, and Swiss Target Prediction database. Then the potential targets and pathways of H. cordata Thunb against RSV were screened by GeneCards, GenCLiP 3, and NCBI Database. We developed a Protein-Protein Interactions (PPI) Network and Compound-Target-Pathway Network through the Cytoscape software. Furthermore, core targets were preliminary verified by Gene Expression Omnibus (GEO) database by bioinformatics methods. At last, the first six pathways were screened out to draw a map of the main target signal pathways. RESULTS: A total of 12 potentially active compounds and 47 potential interaction targets were screened. PPI Network and data from GEO showed that IL-6, STAT3, TNF, AKT1, PTGS2, SRC, and MAPK3 may play a core role in the antivirus process. KEGG enrichment pathway analysis predicted that H. cordata Thunb exerted its anti-RSV effect by regulating TNF, Rap1, HIF-1, PI3KAkt, MAPK, and VEGF signaling pathways. CONCLUSION: This study preliminarily predicted the main active compounds, targets and related pathways of H. cordata Thunb in the treatment of RSV-induced diseases, which laid a good foundation for further revealing its mechanism.

The Separation of Antler Polypeptide and Its Effects on the Proliferation and Osteogenetic Differentiation of Bone Marrow Mesenchymal Stem Cells.

BACKGROUND: Colla Cornus Cervi (CCC) has been used as a traditional Chinese medicine in the treatment of osteoporosis and osteonecrosis of the femoral head. However, the bioavailability of CCC is seriously limited owing to its large molecular weight and complex ingredients. In the present study, antler polypeptide was separated from CCC, and the effects of antler polypeptide on rat bone marrow mesenchymal stem cells (BMSCs) were investigated. METHODS: Antler polypeptide was separated from Colla Cornus Cervi by ultrafiltration into different samples according to the molecular weight. The total peptide content of these samples was determined by the biuret method. The content of antler polypeptide in different samples was quantified by high-performance liquid chromatography (HPLC). The effects of antler polypeptide at different concentrations on the proliferation, cell cycle, alkaline phosphatase activity, and BMP7 expression of BMSCs were investigated. RESULTS: Antler polypeptide was separated by ultrafiltration into different samples: A (molecular weight <800 Da), B (molecular weight 800-1500 Da), and C (molecular weight >1500 Da). The total peptide contents of A, B, and C were 0.602 mg/mL, 8.976 mg/mL, and 38.88 mg/mL. Antler polypeptide B eluted at 14.279∼15.351 min showed that the content of antler polypeptide was significantly higher than that of A and C with a peak area of 933.80927. The BMSCs proliferation rate (84.66%) of polypeptide B was the highest at the concentration of 1.578 × 10-2 g/mL. Antler polypeptide B significantly promoted the proliferation of BMSCs with a proliferation index of 38.68%, which was significantly higher than that of the other groups. Antler polypeptide B significantly enhanced the activity of alkaline phosphatase in BMSCs compared to that of the blank group (P < 0.001). Antler polypeptide B increased the BMP7 protein expression in BMSCs. CONCLUSIONS: Results suggested that antler polypeptide may promote the proliferation and osteogenic differentiation of BMSCs. Our study lays an experimental foundation for the further development and application of antler polypeptide in medicine.

Effects of dietary coated cysteamine hydrochloride on pork color in finishing pigs.

BACKGROUND: Coated cysteamine hydrochloride (CC) was applied as a feed additive in animal production. The influence and the mechanisms of CC used as a feed additive in promoting meat quality in finishing pigs were investigated. RESULTS: Dietary CC supplementation increased (P < 0.05) the a* and H* values and reduced (P < 0.05) the L* value in the longissimus dorsi muscles at 48 h postmortem (P < 0.05). The deoxymyoglobin content was enhanced (P < 0.05) and the metmyoglobin and malondialdehyde contents were reduced (P < 0.05) in pigs fed the dietary CC. Pigs fed a dietary CC of 0.035 g kg-1 had a lower cooking loss (P < 0.05) and a higher a* (24 h) value in the longissimus dorsi muscles than pigs on control treatment. The messenger RNA expression of superoxide dismutase 1 was upregulated (P < 0.05) in the longissimus dorsi. CONCLUSION: Dietary supplementation with CC could improve antioxidant status and delay meat discoloration by improving glutathione levels and antioxidase activity after longer chill storage (for 48 h after slaughter). Dietary supplementation with CC at 0.035 g kg-1 may promote the stability of pork color by reducing oxidation. © 2017 Society of Chemical Industry.

Mesenchymal stem cells alleviate TNBS-induced colitis by modulating inflammatory and autoimmune responses.

AIM: To investigate the potential therapeutic effects of mesenchymal stem cells (MSCs) in inflammatory bowel disease (IBD), we transplanted MSCs into an experimental model of IBD. METHODS: A rectal enema of trinitrobenzene sulfonic acid (TNBS) (100 mg/kg body weight) was administered to female BALB/c mice. Bone marrow mesenchymal stem cells (BMSCs) were derived from male green fluorescent protein (GFP) transgenic mice and were transplanted intravenously into the experimental animals after disease onset. Clinical activity scores and histological changes were evaluated. GFP and Sex determining region Y gene (SRY) expression were used for cell tracking. Ki67 positive cells and Lgr5-expressing cells were determined to measure proliferative activity. Inflammatory response was determined by measuring the levels of different inflammatory mediators in the colon and serum. The inflammatory cytokines included tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-6, IL-17, IL-4, IL-10, and transforming growth factor (TGF-ß). Master regulators of Th1 cells (T-box expressed in T cells, T-bet), Th17 cells (retinoid related orphan receptor gamma(t), RORγt), Th2 cells (GATA family of transcription factors 3, GATA3) and regulatory T cells (forkhead box P3, Foxp3) were also determined. RESULTS: Systemic infusion of GFP-BMSCs ameliorated the clinical and histopathologic severity of colitis, including body weight loss, diarrhea and inflammation, and increased survival (P < 0.05). The cell tracking study showed that MSCs homed to the injured colon. MSCs promoted proliferation of intestinal epithelial cells and differentiation of intestinal stem cells (P < 0.01). This therapeutic effect was mainly mediated by down-regulation of both Th1-Th17-driven autoimmune and inflammatory responses (IL-2, TNF-α, IFN-γ, T-bet; IL-6, IL-17, RORγt), and by up-regulation of Th2 activities (IL-4, IL-10, GATA-3) (P < 0.05). MSCs also induced activated CD4(+)CD25(+)Foxp3(+) regulatory T cells (TGF-ß, IL-10, Foxp3) with a suppressive capacity on Th1-Th17 effecter responses and promoted Th2 differentiation in vivo (P < 0.05). CONCLUSION: MSCs are key regulators of immune and inflammatory responses and may be an attractive candidate for cell-based therapy of IBD.