Combinatorial Chemistry & High Throughput Screening - Volume 26, Issue 13, 2023

Rheumatoid arthritis (RA) is a chronic, destructive condition that affects and destroys the joints of the hand, fingers, and legs. Patients may forfeit the ability to conduct a normal lifestyle if neglected. The requirement for implementing data science to improve medical care and disease monitoring is emerging rapidly as a consequence of advancements in computational technologies. Machine learning (ML) is one of these approaches that has emerged to resolve complicated issues across various scientific disciplines. Based on enormous amounts of data, ML enables the formulation of standards and drafting of the assessment process for complex diseases. ML can be expected to be very beneficial in assessing the underlying interdependencies in the disease progression and development of RA. This could perhaps improve our comprehension of the disease, promote health stratification, optimize treatment interventions, and speculate prognosis and outcomes.

Gastric cancer is one of the most common and highest mortality rate cancers in the world. Exosomes are vesicles secreted by cells carrying different types of molecules, such as protein and RNA. Numerous studies have confirmed that exosomes are involved in various stages of the occurrence and development of gastric cancer and play an important role. With the gradual development, exosomes have been widely employed in the diagnosis and treatment of gastric cancer. In this review, we have provided a basic overview of exosome, and discussed the role of exosome in the occurrence, proliferation, invasion, metastasis, and drug resistance in gastric cancer. In addition, we have emphasized the bright development prospect of exosome in the diagnosis and treatment of gastric cancer. The data on the discovery, diagnosis, treatment, and prognosis of gastric cancer are not particularly optimistic, but the discovery of exosome, applied in diagnosis and treatment, provides a new and effective way to improve the survival rate of patients with gastric cancer.

Background: Nonalcoholic steatohepatitis (NASH) is a common liver injury which will develop into advanced fibrosis and cirrhosis. This study was designed to identify the different serum metabolites of NASH hamsters and predict the diagnosis biomarkers for NASH. Methods: Golden hamsters were randomly divided into a control group that received a normal diet and a NASH group that received a high-fat diet (HFD). After 12 weeks of feeding, the body and liver weight of the hamsters were monitored. Serum biochemical parameters and liver histopathological changes were analyzed. Moreover, an untargeted metabolomics analysis based on a GCTOF/ MS system was performed to identify the serum differential metabolites between the NASH and control groups. Results: The liver weight was increased in the NASH group, accompanied by significantly higher levels of serum TC, TG, ALT, AST, LDL-C, and lower HDL-C. HE, Masson, and oil red O staining showed the hepatocyte structure destroyed, lipid droplets accumulated, and fibers proliferated in the NASH group. Furthermore, 63 differential metabolites were identified by metabolomic analysis. Lipids and fatty acids were significantly up-regulated in the NASH group. The top 9 differential metabolites included cholesterol, methyl phosphate, taurine, alpha-tocopherol, aspartic acid, etc. Metabolites were mainly involved in amino acid metabolism (glycine, cysteine, taurine), spermine, fatty acid biosynthesis, urea cycle, bile acid metabolism pathways, etc. Conclusion: Metabonomics analysis identified 63 differential metabolites in the serum of NASH hamsters; among them, lipids and fatty acids had a key role and may be used as biomarkers for the early diagnosis of NASH.

Background: Cancer is the second leading cause of death in the world. Leukemia is a type of cancer that accounts for 31.5% of all cancers in children under the age of 15 in industrialized countries and 15.7% in developing countries. The inhibition of FMS-like tyrosine kinase 3 (FLT3) is a suitable approach for acute myeloid leukemia (AML) therapy as it is overexpressed in AML. Aim and Objective: This study intends to explore the natural constituents from the bark of Corypha utan Lamk., and assess their cytotoxicity on murine leukemia cell lines (P388) in addition to predicting their interaction with FLT3 as a studied target by computational methods. Methods: Compounds 1 and 2 were isolated from Corypha utan Lamk using the stepwise radial chromatography method. These compounds were assessed for their cytotoxicity against Artemia salina using the BSLT and P388 cells and the MTT assay. The docking simulation was employed to predict the possible interaction between triterpenoid and FLT3. Results: Isolation from the bark of C. utan Lamk. generated two triterpenoids, cycloartanol (1) and cycloartanone (2). Based on the in vitro and in silico studies, both compounds were found to have anticancer activity. The evaluation of cytotoxicity from this study reveals that cycloartanol (1) and cycloartanone (2) could inhibit P388 cell growth (IC50 value at 102.6 and 110.0 μg/mL, respectively). The binding energy of cycloartanone was -9.94 Kcal/mol with a Ki value of 0.051 μM, while the binding energy and Ki value of cycloartanol (1) were found to be 8.76 Kcal/mol and 0.38 μM, respectively. These compounds also demonstrate a stable interaction by forming hydrogen bonds with FLT3. Conclusion: Cycloartanol (1) and cycloartanone (2) exhibit potency as anticancer agents by inhibiting P388 cells in vitro and the FLT3 gene in silico.

Background and Objective: β-elemene is a plant-derived drug with broad-spectrum anticancer activity. Studies have found that β-elemene can inhibit tumor cell proliferation, induce tumor cell apoptosis, and resist tumor cell migration and invasion. Esophageal cancer is a common digestive tract malignant tumor. Progress has been made in the treatment of esophageal cancer, including the use of β-elemene, but the mechanism of anti-migration is unclear. PI3K/Akt/NF- ΚB/MMP9 signaling pathway is involved in the regulation of tumor cell proliferation, migration, extracellular matrix(ECM), and basement membrane(BM) degradation. This study aims to investigate the effect of β-elemene on the migration of esophageal squamous cell carcinoma (ESCC) and its related mechanisms by bioinformatics, network pharmacology, and molecular docking methods. Methods: In this study, the differentially expressed genes (DEGs) of ESCC were screened through GeneCards and BATMAN-TCM databases combined with the Gene Expression Omnibus (GEO) database (GSE17351). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to identify the functions and related pathways of the genes. The protein-protein interaction (PPI) network of these DEGs was constructed with the STRING database. Five hub genes were screened by CytoHubba plug-in Cytoscape according to the principle of degree value and the expressions of which were validated by the UALCAN database from the Cancer Genome Atlas (TCGA). The hub gene with the strongest binding energy was identified by molecular docking. A wound healing assay was subjected to assess the migration ability. RT-PCR was used to detect the content of migration-related mRNA. Western blotting was performed to examine the expression rates of Akt, NF-ΚB, and MMP9 in ESCC tissues by β-elemene and SC79. Results: 71 target genes were obtained which were mainly involved in biological processes such as epidermal development and extracellular matrix decomposition. In addition, critical pathways, including PI3K/AKT signaling pathway and focal adhesion, were verified to be subject to β-elemene regulation. It exhibited marked binding affinity between β-elemene and MMP9 with an excellent docking score of -6.56 kcal/mol. The expression levels of Akt, NF-ΚB, and MMP9 in ESCC tissues were significantly upregulated compared to normal tissues. Western blot detection demonstrated that β-elemene specifically reduced the phosphorylation level of Akt, and its downstream target molecule NF-ΚB, thus resulting in reduced levels of their target proteins, including MMP9 in ESCC. A wound healing assay showed β-elemene inhibited the migration of ESCC cells. RT-PCR results found that the mRNA expression of Akt, NF-ΚB, and MMP9 in the β-elemene group was significantly lower than that in the control group. However, the application of SC79 partially reversed the effect of β-elemene. Conclusion: In summary, our study suggests that the anti-tumor migration effect of β-elemene on ESCC is associated with the inhibition of PI3K/Akt/NF-ΚB/MMP9 signalling pathway, and it provides a theoretical reference for further rational clinical application.

Objective: This study aimed to investigate the active components and mechanism of action of rosemary volatile oil for treating Alzheimer's disease (AD) using network pharmacology. Methods: We obtained the constituents of the rosemary volatile oil by searching Chinese herbal systemic pharmacological databases and analytical platforms and constructed the constituent-target networks by predicting and screening the action targets of the rosemary volatile oil constituents using SwissTargetPrediction, metaTarFisher, and Pubchem. We obtained the AD-related targets using the Genecards, OMIM, and DisGeNET databases and constructed the protein-protein interaction networks (PPI) using the STRING database in Venny 2.1.0 graph to identify the cross-targets by screening the core-acting targets. Cytoscape 3.8.2 software was used to construct a componenttarget- pathway network to screen the potential active components of the rosemary volatile oil for the treatment of AD and predict the mechanism of action of the rosemary volatile oil for the treatment of AD in combination with existing pharmacological studies. We performed a gene ontology (GO) biological process and a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the targets of the rosemary volatile oil for the treatment of AD using R language and molecular docking using Discovery Studio 4.0 software to validate their biological activities. Results: A network constructed using gas chromatography-mass spectrometry (GC-MS) analysis identified 26 potentially active ingredients in the rosemary volatile oil. We retrieved a total of 10762 AD targets from Genecards and other databases. Our GO enrichment analysis yielded 39 entries (P < 0.05), including 14 entries for biological processes, five entries for cellular composition, and 20 entries for molecular function. A total of 14 entries (P < 0.05) were then enriched in the KEGG pathway that primarily involved the IL-17 signaling pathway and the AGE-RAGE pathway. Conclusion: The active components of rosemary volatile oil had good inhibition of the inflammatory response. This study provides a reference and guidance for the in-depth study on rosemary volatile oil for the treatment of AD.

Background: The role of the lncRNA-miRNA-mRNA competing endogenous RNA network in human colorectal cancer remains largely unknown, and accurate prognostics still elude us. This study aimed to identify differentially expressed mRNAs and lncRNAs between tumor and normal samples, delineate their interactions and find reliable biomarkers. Material and Methods: We downloaded the RNA sequencing profiles and clinical information of 624 CRC patients from The Cancer Genome Atlas database. After expression difference analysis and interaction prediction, we identified 37 miRNAs, 5 lncRNAs, and 93 mRNAs to construct the ceRNA network (|log2 Fold Change| > 1, P-value < 0.05), and assessed relationships between them and clinical characteristics by t-test, Spearman correlation analysis, and Kaplan-Meier curve analysis. Besides, we validated PIGR and CD3D protein expression by immunohistochemistry staining. Results: PIGR and CD3D mRNAs showed a negative correlation with tumor stage and their protein levels were lower in tumor tissues than in normal tissues. By survival analysis, MYC, F2RL2, and GINS2 positively correlated with the overall survival of CRC patients. Conclusion: Our study provides a novel comprehension of lncRNA-related ceRNA network in CRC and candidate molecules that serve as potential biomarkers of tumor stage and patient survival.

Background and Aim: To explore the possible mechanism of Dachaihu Decoction (DCHD) in the treatment of AP, and use in vivo experiments to verify. Methods: The targets and active ingredients of DCHD in the treatment of AP were obtained through network pharmacology, and the preliminary verification was carried out by molecular docking. Caerulein was used to develop the AP rat model. H staining was performed to observe variations in pancreatic tissue. Western blot and RT-qPCR were conducted to evaluate the associated proteins and mRNA. Results: The network pharmacology and molecular docking results showed that the key targets (EGFR, TNF, SRC, VEGFA and CTNNB1) and key active components (beta-sitosterol, stigmasterol, baicalein, quercetin, and kaempferol) of DCHD in the treatment of AP had good binding. H&E staining revealed that rat pancreatic tissues considerably damaged post caerulein intervention, and it has also been suggested that DCHD ameliorates damage to pancreatic tissue. Simultaneously, EGFR, TNF, SRC, VEGFA protein, and mRNA expression levels were increased in the model group compared to the blank group (P < 0.01), whereas CTNNB1 expression was found to be decreased in the model group (P < 0.01). Compared with the model group, the protein expression levels of EGFR, TNF, SRC, and VEGFA in the treatment group were down-regulated (P < 0.01), and CTNNB1 was up-regulated (P < 0.05). Conclusion: DCHD protects pancreatic tissues and improves symptoms in AP rats by upregulating CTNNB1 protein and mRNA while inhibiting EGFR, TNF, SRC, and VEGFA protein and mRNA expression.

Background: The limited efficacy of chemotherapy and immunotherapy for pancreatic cancer is thought to be largely influenced by the surrounding cancer microenvironment. The hypoxic microenvironment caused by insufficient local blood supply is very important. However, the method to assess the level of hypoxia in the microenvironment of pancreatic cancer (PC) remains unclear. Methods: In our research, we downloaded transcriptomic and clinicopathological data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A prognostic model was developed using univariate and multivariate Cox regression. The ConsensuClusterPlus R package was used to consistently cluster PC samples through unsupervised clustering. Gene set variation analysis (GSVA) was performed to identify the different functional phenotypes. The CIBERSORT evaluated the infiltration status of immune cells. qRT128;PCR was performed to detect the expression of genes in PC cells and tissues. Results: A preliminary risk model was developed to reflect the hypoxic environment of pancreatic cancer. We found that a high hypoxia risk score indicated poor long-term survival and the presence of an immunosuppressive microenvironment. In addition, based on prognostic hypoxia-related genes, 177 PC samples were divided into two subtypes. Compared with cluster 2, cluster 1 was defined as the "hypoxic subgroup". The infiltration of CD8 T cells, activated memory CD4 T cells, naive B cells, memory B cells, plasma cells, and neutrophils were lower in cluster 1, suggesting that there was significant immunosuppression in cluster 1. Beyond that, we constructed a ceRNA regulatory network composed of differentially expressed lncRNA, miRNA, and mRNA. LSAMPAS1/ hsa-miR-129-5p/S100A2 has been identified as a key ceRNA network that regulates the hypoxic environment and the prognosis of PC. Notably, in our study, qRT-PCR revealed the relative expression of LSAMP-AS1 and S100A2 was significantly upregulated in PC cells and tissue. Conclusion: The hypoxia-related prognostic risk model and core ceRNA network established in our study will provide a new perspective for exploring the carcinogenic mechanism and potential therapeutic targets of pancreatic cancer.

Objective: To evaluate the effect of Sancao Lichang decoction as traditional Chinese medicine on diarrhea-predominant irritable bowel syndrome (IBS-D) and TLR4/MyD88/NF-ΚB pathway. Background: Traditional Chinese medicine has made significant progress in preventing and treating irritable bowel syndrome, and its efficacy has been validated by clinical practice. Sancao Lichang decoction is an empirical prescription developed by professor Tang Decai that has been used for many years to treat chronic diarrhoea with good curative effec. Still, its mechanism of action on IBS-D is unknown. Methods: The study sample of Fifty SD rats was randomly divided into a blank group, model group, low-dose group, medium-dose group, and high-dose group (n = 10). The IBS-D rat models were established by restraining stress method and acetic acid enema. After different treatments, defecation frequency, fecal water content (FWC), serum IL-6 and TNF-α contents, and protein level of TLR4/MyD88/NF-ΚB in colon tissues were detected separately. Results: The indexes of rats in each group were significantly different. The increase in body weight in the medium-dose and high-dose groups was significantly higher than that in the model group (p < 0.05). Compared with the model group, the medium and high dose groups had lower diarrhea frequency, FWC, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) (p < 0.05). The expression levels of TLR4, MyD88, and NF-ΚB protein in the colon of the three groups treated with Sancao-Lichan decoction were significantly lower than those in the model group (p < 0.01). After different treatments, the colonic mucosa of rats in each group was stained with HE, which proved that the structural damage of colonic mucosa was improved after treatment with Sancao Lichang decoction, and the improvement effect was dose-dependent. Conclusion: Sancao Lichang decoction may reduce IBS-D by inhibiting TLR4/MyD88/NF-ΚB pathway, inhibiting the inflammatory response, and improving intestinal mucosal barrier function.

Aims: This study aimed to evaluate the underlying pharmacological mechanisms of Apatinib anti-bladder cancer via network pharmacology and experimental verification. Methods: Network pharmacology was used to screen the possible signaling pathways of Apatinib in bladder cancer, and the most likely pathway was selected for in vitro validation. CCK-8 and colony formation assay were used to detect the effect of Apatinib on the proliferation of bladder cancer cells. Hoechst staining and flow cytometry detected apoptosis of bladder cancer cells induced by Apatinib. Western blot was performed to distinguish the effect of Apatinib on the expression levels of key targets. Results: Apatinib can affect many signaling pathways and the correlation of the PI3K-AKT signaling pathway was the greatest. In vitro experiments showed that Apatinib could inhibit bladder cancer cell proliferation, induce apoptosis, and up-regulate the expression of apoptosisrelated proteins Cleaved-PARP and down-regulate the expression of Bcl-2. Furthermore, Apatinib could decrease the protein expression of VEGFR2, P-VEGFR2, P-PI3K and P-AKT. Conclusions: Apatinib could promote apoptosis of bladder cancer cells by inhibiting the VEGFR2- PI3K-AKT signaling pathway.

Objective: This study aimed to investigate the therapeutic effect of Specnuezhenide on myelosuppression induced by chemotherapy and clarify its mechanism. Methods: In this study, we measured peripheral blood cells, thymus index, spleen index, bone marrow nucleated cells (BMNCs), and the number of cell colonies counted in vitro by hematopoietic progenitor cells (HPCs) to determine the effect of SPN on cyclophosphamide (CTX)-induced myelosuppression. The alterations in the expression of relevant proteins, the cell cycle, and cytokines associated with hematopoietic cells were examined to better understand how it works. Results: In the cyclophosphamide-induced mouse model, our study discovered that SPN can increase the number of peripheral blood cells and BMNCs after treatment, increase the thymus index and decrease the spleen index, and promote the proliferation and differentiation of HPCs. SPN can improve the production of cultured colonies in vitro, reduce the level of hematopoietic factors in vivo, regulate the proportion of G0/G1 phase cells, and promote the normal growth and development of cells. SPN can increase the expression levels of key proteins MEK and p-ERK in the MAPK signaling pathway, which may be one of the important mechanisms for improving myelosuppression. Conclusion: SPN can enhance the hematological and immunological functions of myelosuppressionmice, and it is hypothesized that SPN is extremely helpful to the hematopoietic and immune functions of tumor patients following chemotherapy. SPN might be used to treat myelosuppression. Additionally, high doses of SPN have a stronger therapeutic effect than low levels of SPN.

Introduction: Diabetic osteoporosis (DOP) is a widespread public health problem. The flavonoids of Rhizoma Drynariae (RDF) have a clear preventive and therapeutic effect on osteoporosis (OP), but it is not yet clear whether RDF has an anti-DOP and whether its mechanism is related to the activation of the BMP2/Smad signaling pathway. The current study aimed to study this effect of RDF in DOP rats and the possible involvement of the BMP2/Smad signaling pathway activation. Methods: Following intragastric administration of RDF for 12 weeks, the body weight, blood glucose, and the bone histopathological changes detected by hematoxylin-eosin (H) and calcein staining were monitored, while bone parameters were regularly assessed from observations made by micro-CT. At the end of the experiment, the expression of Bmp2, Bmpr1a, Runx2, and Smad4/5 genes was detected by real-time PCR (RT-PCR). Meanwhile, western blotting or immunohistochemical staining monitored the protein expressions of BMP2, RUNX2, and SMAD5 in the bone. Results: The results firstly indicated that RDF significantly alleviated the signs and symptoms of DOP, which manifested as improved body weight and blood glucose. As obtained from the results of histopathology and micro-CT, RDF could promote the formation of bone trabeculae and alter several the bone microstructure parameters, including an increase in the bone volume/total volume (BV/TV), connective density (Conn-Dens), and trabecular bone number (Tb.N), as well as a decrease in the trabecular spacing (Tb.Sp). The western blotting analysis and RT-PCR results also confirmed that RDF could markedly increase the mRNA expression levels of Bmp2, Bmpr1α, Smad4, Runx2, and Smad5 in the bone, as well as the corresponding protein expression levels of BMP2, RUNX2, and SMAD5. These results reveal that RDF can activate the BMP2/Smad signaling pathway, thus promoting bone remodeling in DOP rats. Conclusion: RDF can increase bone trabeculae and bone mineral density by promoting bone formation and inhibiting bone absorption, thereby playing a role in improving DOP. This effect is related to the regulation of the BMP2/Smad signaling pathway.