[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.

Pyroptosis -related potential diagnostic biomarkers in steroid-induced osteonecrosis of the femoral head.

PURPOSE: Steroid-induced necrosis of the femoral head (SONFH) is a refractory orthopedic hip disease occurring in young and middle-aged people, with glucocorticoids being the most common cause. Previous experimental studies have shown that cell pyroptosis may be involved in the pathological process of SONFH, but its pathogenesis in SONFH is still unclear. This study aims to screen and validate potential pyroptosis-related genes in SONFH diagnosis by bioinformatics analysis to further elucidate the mechanism of pyroptosis in SONFH. METHODS: There were 33 pyroptosis-related genes obtained from the prior reviews. The mRNA expression was downloaded from GSE123568 dataset in the Gene Expression Omnibus (GEO) database, including 10 non-SONFH (following steroid administration) samples and 30 SONFH samples. The pyroptosis-related differentially expressed genes involved in SONFH were identified with "affy" and "limma" R package by intersecting the GSE123568 dataset with pyroptosis genes. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the pyroptosis-related differentially expressed genes involved in SONFH were conducted by "clusterProfiler" R package and visualized by "GOplot" R package. Then, the correlations between the expression levels of the pyroptosis-related differentially expressed genes involved in SONFH were confirmed with "corrplot" R package. Moreover, the protein-protein interaction (PPI) network was analysed by using GeneMANIA database. Next, The ROC curve of pyroptosis-related differentially expressed genes were analyzed by "pROC" R package. RESULTS: A total of 10 pyroptosis-related differentially expressed genes were identified between the peripheral blood samples of SONFH patients and non-SONFH patients based on the defined criteria, including 20 upregulated genes and 10 downregulated genes. The GO and KEGG pathway enrichment analyses revealed that these 10 pyroptosis-related differentially expressed genes involved in SONFH were particularly enriched in cysteine-type endopeptidase activity involved in apoptotic process, positive regulation of interleukin-1 beta secretion and NOD-like receptor signaling pathway. Correlation analysis revealed significant correlations among the 10 differentially expressed pyroptosis-related genes involved in SONFH. The PPI results demonstrated that the 10 pyroptosis-related differentially expressed genes interacted with each other. Compared to non-SONFH samples, these pyroptosis-related differentially expressed genes had good predictive diagnostic efficacy (AUC = 1.000, CI = 1.000-1.000) in the SONFH samples, and NLRP1 had the highest diagnostic value (AUC: 0.953) in the SONFH samples. CONCLUSIONS: There were 10 potential pyroptosis-related differentially expressed genes involved in SONFH were identified via bioinformatics analysis, which might serve as potential diagnostic biomarkers because they regulated pyroptosis. These results expand the understanding of SONFH associated with pyroptosis and provide new insights to further explore the mechanism of action and diagnosis of pyroptosis associated in SONFH.

Blockade of MMP-2 and MMP-9 inhibits corneal lymphangiogenesis.

PURPOSE: To investigate the roles of a selective MMP-2 and -9 inhibitor (SB-3CT) in corneal inflammatory lymphangiogenesis. METHODS: The expression of MMP-2 and -9 in the cornea after suture inplacement, treated with SB-3CT or negative control, was detected by real-time polymerase chain reaction (PCR). Inflammatory corneal neovascularization (NV) was induced by corneal suture placement. Mice were treated with SB-3CT eye drops (twice daily for 1 week, 5 µL per drop; 50, 100, or 200 µM). The outgrowth of blood and lymphatic vessels, and macrophage recruitment were analyzed by immunofluorescence assay. The expressions of vascular endothelial growth factor-C (VEGF-C) and its receptor VEGFR-3 were tested by real-time PCR. RESULTS: MMP-2 and -9 expression were suppressed significantly by treatment with SB-3CT. The data demonstrated, for the first time, that SB-3CT strongly reduced corneal lymphangiogenesis and macrophage infiltration during inflammation. Furthermore, expressions of VEGF-C and its receptor VEGFR-3 were significantly inhibited by SB-3CT during corneal lymphangiogenesis. CONCLUSIONS: These novel findings indicated that blockade of MMP-2 and -9 could inhibit lymphangiogenesis. Further investigation of this factor may provide novel therapies for transplant rejection and other lymphatic disorders.

Exploring the Potential Mechanisms of Danshen for the Treatment of Ulcerative Colitis based on Serum Pharmacochemistry, Gene Expression Profiling, and Network Pharmacology: Regulation of Cell Apoptosis and Inflammatory Response.

BACKGROUND: As a traditional Chinese medicine, Danshen shows potential efficacy for treating ulcerative colitis (UC). However, the bioactive components and mode of action were unclear. AIM OF THIS STUDY: This paper uses a combination of network pharmacology, serum medicinal chemistry, and gene expression profiling to clarify its possible molecular mechanism of action and material basis. METHODS: Ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) was utilized to analyze the herbal components and metabolites from the serum of Danshen-treated mice. Gene expression profiles were applied to construct a database of Danshen action targets. Then, active ingredient-target-biological functional module networks were constructed to analyze the mechanism of action. Molecular docking has further confirmed the possibility of its components to the targets. RESULTS: As a result, 193 common targets between 1684 Danshen-related DEGs and 1492 UC targets were determined as the potential targets for Danshen in treatment with UC. Serum pharmacochemistry and target prediction showed that 22 components in serum acted on 777 targets. Intersection with common targets yielded 46 core targets, and an active ingredienttarget- biological functional module network was constructed for analysis. Network prediction and molecular docking results showed that the main action modules were inflammatory response and cell apoptosis, which mainly acted on targets SRC, RELA, HSP90AA1, CTNNB1, STAT3, and CASP3. The main components of Danshen intervention in UC were predicted to include Catechol, 3,9-Dimethoxypterocarpan, 8-Prenylnaringenin, Isoferulic acid, Salvianolic acid C, and Danshensu. CONCLUSION: The present study provides a scientific foundation for further explicating the mechanisms of Danshen against UC.

[A retrospective study of 22 years endoscopic follow-up in elderly patients with gastrointestinal submucosal tumors].

OBJECTIVE: To observe the occurrence characteristics, dynamic variations and potential risks of smaller gastrointestinal submucosal tumor (SMT) in elderly patients. METHODS: A total of 54 SMT patients were retrospectively recruited from January 1981 to September 2010. There were 51 males (94.4%) and 3 females (5.6%) with an average age of (74 ± 1) years. During each visit, all the relevant data were collected, including symptoms, number of lesion, lesion location, shape, size (maximum transverse diameter under endoscope or endoscopic ultrasonography (EUS), morphology of mucosa, frequency and duration of follow-ups, treatment and pathological results. And the data were analyzed to examine the characteristics of SMT in elderly patients and their dynamic variations. Further more, according to lesion diameter, they were divided into two groups: a diameter ≤ 1 cm (n = 36) and a diameter > 1 cm and ≤ 3 cm (n = 16). Then the change of two groups were observed and compared during the follow-ups. RESULTS: Two cases were not under surveillance after direct surgical resection. The other 52 patients received a follow-up of 22 years. Among them, 5 patients underwent surgical resection for fast-growing tumor and mucosal ulcer. And all their pathologic diagnoses were malignant. Only 1 patient (2.8%) in the diameter ≤ 1 cm group and 4 in the diameter > 1 cm and ≤ 3 cm group turned malignant at 6 years. But, among 4 patients, the shortest interval was merely 14 months. Therefore, compared with the diameter > 1 cm group, the diameter ≤ 1 cm group had a lower rate of malignancy (P < 0.05). CONCLUSIONS: The incidence of smaller SMT (especially diameter ≤ 1 cm) is high in elderly patients, but the malignant potential remains low. Therefore, for elderly patients whose diameters of SMT are no bigger than 3 cm and without obvious malignancy under endoscope or EUS, we may plan an appropriate surveillance interval based on the size of tumor during a long follow-up period.

Comparative Transcriptomic Assessment of Chemosensory Genes in Adult and Larval Olfactory Organs of Cnaphalocrocis medinalis.

The rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), is a notorious pest of rice in Asia. The larvae and adults of C. medinalis utilize specialized chemosensory systems to adapt to different environmental odors and physiological behaviors. However, the differences in chemosensory genes between the olfactory organs of these two different developmental stages remain unclear. Here, we conducted a transcriptome analysis of larvae heads, male antennae, and female antennae in C. medinalis and identified 131 putative chemosensory genes, including 32 OBPs (8 novel OBPs), 23 CSPs (2 novel CSPs), 55 ORs (17 novel ORs), 19 IRs (5 novel IRs) and 2 SNMPs. Comparisons between larvae and adults of C. medinalis by transcriptome and RT-qPCR analysis revealed that the number and expression of chemosensory genes in larval heads were less than that of adult antennae. Only 17 chemosensory genes (7 OBPs and 10 CSPs) were specifically or preferentially expressed in the larval heads, while a total of 101 chemosensory genes (21 OBPs, 9 CSPs, 51 ORs, 18 IRs, and 2 SNMPs) were specifically or preferentially expressed in adult antennae. Our study found differences in chemosensory gene expression between larvae and adults, suggesting their specialized functions at different developmental stages of C. medinalis. These results provide a theoretical basis for screening chemosensory genes as potential molecular targets and developing novel management strategies to control C. medinalis.

Effect of purine-rich box1 on proliferation of fibroblasts.

Fibroblasts are pleomorphic cells that have a multi-directional effect on organ morphogenesis, tissue homeostasis, and immune response. In fibrotic diseases, fibroblasts synthesize large amounts of extracellular matrix (ECM), leading to scarring and organ failure. Purine-rich box1 (PU.1) is a specific transcription factor of hematopoietic cell and belongs to the E26 transformation specificity (ETS) family. Recently, it was found that the transcription factor PU.1 is an important regulatory factor of the profibrotic gene expression program. TGF-ß had been proved to play an important role in many ocular tissue fibrosis diseases, and up-regulated the expression of PU.1 in fibroblasts producing ECM in a Smad-3 dependent manner. We explore the effect of PU.1 on fibrosis of different ocular tissues from this perspective. This article reviews the role of PU.1 and its effects on fibrosis of ocular tissue and other tissues.

Altered microbial community structure in PI3Kγ knockout mice with colitis impeding relief of inflammation: Establishment of new indices for intestinal microbial disorder.

Lipopolysaccharide stimulates the intestinal microbiome to activate phosphoinositide 3 kinase (PI3K) signaling via several pathways; however, the direct effect that PI3K has on the intestinal bacterial community remains unclear. Herein, we investigate changes in the colonic microbiome of colitis PI3Kγ-knockout (PI3Kγ-/-) mice. Additionally, the effect of anal administration of colonic irrigation fluid from control mice to those with colitis was examined. Microbial 16S rRNA genes from the colonic mucosa of PI3Kγ-/- and WT mice were sequenced using Illumina MiSeq platform, and colonic IgA, IL-2, IL-10, and IL-17A production was quantified by western blot analysis. Myeloperoxidase (MPO) activity was detected by absorbance via colorimetric analysis. From the results, two new indices were derived by dividing the bacterial community into invading taxa, common taxa, and vanishing taxa. These indices were used to estimate the degree of microbiome disorder in chronic experimental colitis models. PI3Kγ-/- mice showed slower remission of inflammation as assessed by the disease activity index，pathological score, IL-2, IL-17, IL-10, IgA expression and MPO activity. The unique and common taxa of wild-type and PI3Kγ-/- mice increased as colitis symptoms regressed. Continuous loss of commensal bacteria happened with the continuous invasion of exogenous bacteria in the intestinal mucosa of PI3Kγ--/- mice after colitis begin to aggravate. However, transplantation of normal intestinal microbiota to PI3Kγ-/- mice promoted remission of inflammation; while the microbial dysbiosis observed during PI3Kγ dysfunction aggravated the intestinal microbiome disorder and impeded colitis recovery. Thus, the PI3Kγ signaling pathway may regulate microbial community composition in the colon.

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.

Matrix metalloproteinase 14 participates in corneal lymphangiogenesis through the VEGF-C/VEGFR-3 signaling pathway.

The aim of the present study was to investigate the roles of matrix metalloproteinase 14 (MMP-14) in corneal inflammatory lymphangiogenesis. The expression of MMP-14 in vivo was detected by immunohistochemistry, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot assays, under various corneal conditions. pCMV-MMP-14 or empty pCMV vectors were injected into mouse corneal stroma, 3 days after suture placement in a standard suture-induced inflammatory corneal neovascularization assay. The outgrowth of blood and lymphatic vessels and macrophage recruitment were analyzed using immunofluorescence. The expression levels of vascular endothelial growth factor (VEGF) subtypes were tested by RT-qPCR. MMP-14 expression was upregulated significantly following various corneal injuries. The results demonstrated, for the first time, that MMP-14 strongly promotes corneal lymphangiogenesis and macrophage infiltration during inflammation. Furthermore, expression levels of VEGF-C and VEGF receptor-3, but not other VEGF components, were significantly upregulated by the intrastromal delivery of MMP-14 during corneal lymphangiogenesis. In conclusion, this study indicates that MMP-14 is critically involved in the processes of lymphangiogenesis. Inhibition of MMP-14 may provide a viable treatment for transplant rejection and other lymphatic disorders.

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.