Combinatorial Chemistry & High Throughput Screening - Online First
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101 - 134 of 134 results
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The Anti-PEDV Effects and Mechanisms of Forsythia Essential Oil Based on Network Pharmacology and Experimental Validation
Authors: Ruiping Liang, Jianbo Guo, Kai Li, Xuan Wang, Xiaoxiao Ge, Jinhui Wang, Jing Sun, Chongbo Zhao, Huanxian Shi, Rongxia Qiao, Hongqing Zheng and Xiaofei ZhangAvailable online: 10 March 2025More LessObjectivePorcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae, is responsible for acute diarrhea, vomiting, and dehydration, which can lead to high mortality in neonatal piglets. Previous research has indicated the antiviral potential of forsythia essential oil (FEO); however, its active components and mechanisms of action remain inadequately defined. This study aims to investigate the antiviral effects of FEO and elucidate its potential mechanisms for treating PEDV.
MethodsThe primary components of FEO were identified using gas chromatography-mass spectrometry (GC/MS) in conjunction with the National Institute of Standards and Technology Standard Spectrum (NIST) Database. Network pharmacology and weighting coefficients were employed to determine the key signaling pathways associated with PEDV-related diseases. Molecular docking simulations were conducted to explore the interactions between the active ingredients and their corresponding targets. The safety profile of FEO was assessed through cell viability assays utilizing the CCK8 method. Subsequently, immunofluorescence assays (IFA) and reverse transcription-quantitative polymerase chain reaction (RT-Q-PCR) were performed to provide evidence of the anti-PEDV effects. Additionally, the viral replication cycle was analyzed to identify the stages at which FEO exerts its antiviral effects. Finally, key targets were validated through RT-Q-PCR to further investigate the anti-PEDV mechanisms of FEO.
ResultsThe IL-17 signaling pathway was identified as a critical pathway for the treatment of PEDV with FEO based on network pharmacology and weighting coefficient analyses. Furthermore, results from RT-Q-PCR and IFA demonstrated that FEO influenced the replication of PEDV during the attachment and internalization phases. Specifically, during the viral attachment phase, FEO significantly upregulated the expression of HSP90AA1 while downregulating MAPK14 expression, leading to a reduction in associated inflammatory factors. At the high dose of FEO, the expression of HSP90AA1 was higher than that of the model group by about 5-fold, and the expression of MAPK14 was lower than that of the model group by about 2-fold. Cell viability assay showed no significant cytotoxicity of FEO at 0.63 µL/mL, thus confirming its safety.
ConclusionThe findings of this study suggest that FEO possesses potential antiviral properties against PEDV. Its novel mechanisms of action warrant further investigation, which may contribute to the development of effective therapeutic strategies for managing PEDV infections.
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Computational Study for Preparation of Benzoimidazo[1,2-a]pyrimidines from Reaction of Benzaldehyde, Indanedione and 1H-benzo[d]imidazol-2-amine
Authors: Yas Zibaei, Leila Zare Fekri and Mohammad NikpassandAvailable online: 03 March 2025More LessBackgroundBenzoimidazo[1,2-a]pyrimidines are important compounds that have many useful effects in the body. They can help fight cancer, fungal infections, inflammation, and viruses. They can also help with various other health conditions. They can act as antineoplastic, antitubercular, parasitical activity, benzodiazepine receptor agonists, calcium channel blockers, potent P38 MAP kinase inhibitors, TIE-2 and/or VEGFR2 inhibitory activities, protein kinase inhibitors, and T cell activation. There are different methods to make the benzoimidazo[1,2-a]pyrimidines. Some of them dealth with the one-pot threecomponent condensation reactions of β-dicarbonyl compounds, aldehyde and 1H-benzo[d]imidazol-2-amine in the presence of catalyst. Although the synthesis of this group of compounds has been done before, and the products have been identified from the spectroscopic point of view, the kinetics and reaction mechanism have not been investigated. The strength of these calculations is that evaluation of the activation energy of various steps suggests possible mechanisms, probable mechanisms, and valuable synthetic intermediates.
MethodsIn this report, seven possible mechanisms for synthesizing the benzoimidazo[1,2-a]pyrimidines have been investigated using density functional theory (DFT) at the B3LYP/6-311G** level of theory. Each synthetic route involves condensation of the benzaldehyde, indanedione and 1H-benzo[d]imidazol-2-amine molecules to yield the proposed product. The calculations showed that the suggested method has six steps; its initiation step includes the Knoevenagel reaction between indanedione and aldehyde, and the rate determining state is dehydration in the fifth step.
ResultSix potential pathways for the reaction will occur. Then, we focused on the best pathway and studied it in detail. The ways that three chemicals-indanedione (R1), benzaldehyde (R2), and 1H-benzo[d]imidazol-2-amine (R3) react with each other were studied using ab-initio program by ChemBio3D, Gauss View, and Gaussian 09. The Density Functional Theory (DFT) using the B3LYP basis set was used to improve the arrangement of molecules involved in the three-part creation of a specific compound called 12-phenyl-5H-benzo[4,5]imidazo[1,2-a]indeno[1,2-d]pyrimidin-13(12H)-one (P).
ConclusionDuring the study of the six mechanisms, the proposed pathway 2 is the best mechanism for this reaction because its rate-determining step has the lowest activation energy value. This route consists of 6 steps, the fifth step of which is related to the conversion of IM4 to IM5 (relative ∆E: 109.80 Kj/mol), during which a dehydration reaction is performed, and this step occurs by passing through transition state TS5 (Total Energy (Hart./particles: -1194.747403).
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Dry Powder Inhaler of Sustained-Release Microspheres Containing Glycyrrhizin: Factorial Design and Optimization
Authors: Arpita Chakraborty, Riya Mahar and Nidhi NainwalAvailable online: 28 February 2025More LessBackgroundGlycyrrhizin is a saponin glycoside of the liquorice plant. It is commonly used to treat respiratory problems. Inhalable glycyrrhizin formulation in asthma can be a good alternative for widely used inhaled corticosteroids that exhibit side effects upon long-term use.
AimAsthma is a major and prevalent respiratory disease. However, the rate of drug development in this arena is quite slow, as indicated by merely four new drugs approved by the USFDA in the last 6 years for respiratory diseases.
ObjectiveWe herein propose to design and develop Glycyrrhizin-inhalable microspheres for the treatment of asthma.
MethodA 32 full factorial design was applied to show the effect of the two independent variables (polycaprolactone, and polyvinyl alcohol concentration) on each of the selected dependent variables (drug loading and entrapment efficiency).
ResultsThe optimized microspheres were spherical and 1-5 µm in size. The formulation showed a fine particle fraction of 78%, indicating that the powders were suitable for inhalation. The Drug loading and encapsulation efficiency of the optimized formulation were found to be 9.8% and 40.98%, respectively. The aerosolization study on the Anderson cascade impactor showed that deposition of particles of formulation blended with lactose was better than nonblended formulation and drug in the lungs.
ConclusionIn comparison to the pure drug, optimized formulation prolonged drug residency in the lung for more than 12 hrs after inhalation. Inhalable microparticles of glycyrrhizin provide sustained and prolonged drug release in the lungs along with protection of drugs against pulmonary degradation.
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Revealing the Mechanism of Buzhong Yiqi Tang in Ameliorating Autoimmune Thyroiditis via the Toll-like Receptor Pathway
Authors: Zhuo Zhao, Jiayun Li, Donglin Liu, Hao Gao, Zhe Jin, Zhimin Wang, Yiran Chen, Si Chen, Ziyu Liu and Xiao YangAvailable online: 28 February 2025More LessIntroductionEsophageal Squamous Cell Carcinoma (ESCC) remains a significant global health challenge, underscoring the urgent need for the development of innovative therapeutic approaches. Ranunculus ternatus Thunb., a traditional herb, exhibits potential anticancer properties, but its mechanisms against ESCC remain poorly understood. This study integrates network pharmacology and experimental validation to explore the therapeutic effects of the ethyl acetate extract of Ranunculus ternatus Thunb. (RTE).
MethodsPotential targets of RTE and ESCC were screened using public databases. A Protein-Protein Interaction (PPI) network was constructed to identify key targets, followed by GO and KEGG pathway enrichment analyses. The predicted mechanisms were validated using in vitro assays, including cell proliferation analysis and western blot assay in ESCC cell lines.
ResultsNetwork pharmacology analysis identified 274 potential targets, with 14 key genes implicated in the therapeutic effects of RTE. GO analysis revealed significant involvement in the inflammatory response and apoptotic signaling pathways. KEGG pathway analysis highlighted the MAPK, Relaxin, and PI3K/Akt signaling pathways as critical mechanisms. In vitro experiments demonstrated that RTE significantly inhibited the proliferation of EC-109 and TE-13 cells by modulating the MAPK/ERK and PI3K/Akt pathways.
DiscussionThe study reveals that active compounds of RTE target MAPK/ERK and PI3K/Akt pathways, aligning with prior evidence. However, future studies should explore animal models to confirm efficacy.
ConclusionThis study provides a comprehensive understanding of the molecular mechanisms underlying the anticancer effects of RTE against ESCC. These findings underscore the potential of RTE as a promising natural compound for ESCC treatment.
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Agaricus blazei Murill Extract (FA-2-b-β) Induces Ferroptosis in Diffuse Large B-Cell Lymphoma via the Nrf2/HO-1 Pathway
Authors: Rong Li, Dan Huang, Along Wu and Yanqin SunAvailable online: 28 February 2025More LessIntroductionFerroptosis is a recently identified iron-dependent programmed cell death closely linked to the progression of diffuse large B-cell lymphoma (DLBCL). While studies have shown that FA-2-b-β extracted from Agaricus blazei Murill affects various malignancies, its specific role in modulating ferroptosis in DLBCL and the underlying mechanisms are not yet clear. Objectives: This study aims to elucidate the anticancer properties and mechanisms of FA-2-b-β in inducing ferroptosis in DLBCL cells.
MethodsThe cell counting kit 8 assay was carried out to evaluate the inhibition of cellular proliferation. Ferroptosis was evaluated using the ferrous colorimetric method, together with kits for measuring malondialdehyde (MDA), reduced glutathione (GSH), reactive oxygen species (ROS), western blotting, JC-1 assays, and transmission electron microscopy. Reverse transcription-quantitative polymerase chain reaction and western blot were conducted to determine whether FA-2-b-β affected nuclear factor erythroid 2- related factor 2 (Nrf2) and heme oxygenase 1 (HO-1).
ResultsFA-2-b-β induced ferroptosis in DLBCL cells by elevating the ROS and MDA levels, facilitating the accretion of Fe2+, diminishing GSH, upregulating the expression of PTGS2, and downregulating the expression of FTH1, SLC7A11, and GPX4. Furthermore, FA-2-b-β caused structural damage to mitochondria and diminished the mitochondrial membrane potential. The ferroptosis triggered by FA-2-b-β also led to the downregulation of Nrf2 and HO-1, thereby regulating the Nrf2/HO-1 pathway.
ConclusionFA-2-b-β suppressed DLBCL cell growth by inducing ferroptosis through the Nrf2/HO-1 pathway, making it an attractive potential therapeutic option.
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20D-Dynamic Representation of Protein Sequences Combined with K-means Clustering
Authors: Dorota Bielińska-Wąż, Piotr Wąż and Agata BłaczkowskaAvailable online: 26 February 2025More LessObjectiveThe objective of this research is to demonstrate that alignment-free bioinformatics approaches are effective tools for analyzing the similarity and dissimilarity of protein sequences. All numerical parameters representing sequences are expressed analytically, ensuring precision, clarity, and efficient processing, even for large datasets and long sequences. Additionally, a novel approach for identifying previously unknown virus strains is introduced.
MethodsA novel approach is proposed, integrating the unique features of our newly developed method, the 20D-Dynamic Representation of Protein Sequences, with the K-means clustering algorithm. The sequences are represented as clouds of material points in a 20-dimensional space (20D-dynamic graphs), with their spatial distribution being unique to each protein sequence. The numerical parameters, referred to as descriptors in molecular similarity theory, represent quantities characteristic of dynamic systems and serve as input data for the K-means clustering algorithm.
ResultsExamples of the application of the approach are presented, including projections of the 20D-dynamic graphs onto 3D spaces, which serve as a visual tool for comparing sequences. Additionally, cluster plots for the analyzed sequences are provided using the proposed method.
DiscussionCombining the 20D-Dynamic Representation of Protein Sequences with an unsupervised machine learning algorithm (K-means clustering) enhances its scalability. This approach is applicable to large datasets without restrictions on sequence length.
ConclusionIt has been demonstrated that the 20D-Dynamic Representation of Protein Sequences, combined with the K-means clustering algorithm, successfully classifies subtypes of influenza A virus strains.
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Identification of Mitochondrial-related Characteristic Biomarkers in Osteosarcoma using Bioinformatics and Machine Learning
Authors: Jingyi Hou, Yu Zhang, Ning Yang, Bin Chen, Chengbing Chang, Haipeng Gu, Yanqi Liu and Naiqiang ZhuAvailable online: 25 February 2025More LessBackground/AimsOsteosarcoma (OS), a malignant tumor originating in bone or cartilage, primarily affects children and adolescents. Notably, substantial alterations in mitochondrial energy metabolism have been observed in OS; however, the specific contribution of mitochondrial-related genes (MRGs) to OS pathogenesis and prognosis remains unclear. Herein, we identified novel diagnostic biomarkers associated with mitochondrial-related processes in OS via comprehensive bioinformatics analysis.
MethodsOS mRNA expression profiles were retrieved from GSE16088 and GSE19276 databases. Mitochondrial-related differentially expressed genes (MitoDEGs) were identified by integrating differentially expressed analysis with mitochondrial-localized genes. A protein-protein interaction network was constructed, and machine learning algorithms (LASSO regression analysis and SVM-RFE) identified characteristic MitoDEGs. Subsequently, immune cell infiltration, microenvironment analysis, and single-cell RNA sequencing (scRNA-seq) analyzed differences in characteristic MitoDEGs, and RT-PCR was used for in vitro verification of characteristic MitoDEGs.
ResultsMitoDEGs in OS were significantly enriched in the pathways associated with mitochondrial function and immune regulation. Two MitoDEGs, UCP2 and PRDX4, were identified via LASSO and SVM-RFE. Correlation analysis demonstrated a close association between UCP2 and PRDX4 expression levels and immune cell infiltration, particularly in CD8+ T and native CD4+ T cells, as observed in both immune cell and scRNA-seq analyses. Furthermore, RT-PCR confirmed the expression levels of UCP and PRDX4 at the cellular level, which was consistent with the bioinformatics results.
ConclusionThis study identified UCP2 and PRDX4 as characteristic MitoDEGs and potential diagnostic biomarkers for OS using machine learning algorithms. These findings provide novel insights into the clinical applications of these biomarkers for OS diagnosis.
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Evaluation of Carbamazepine and Gabapentin’s Safety and Efficacy in Trigeminal Neuralgia Treatment: A Systematic Review and Meta-Analysis
Authors: Yang Yan, Haitao Shang and Tao HanAvailable online: 24 February 2025More LessAimThis study aimed to assess the safety and effectiveness of carbamazepine in treating trigeminal neuralgia in contrast to gabapentin. Hence, a systematic review and meta-analysis of randomised controlled trials had been carried out.
MethodsThe relevant studies were searched in PubMed and filtered according to the inclusion and exclusion criteria. Independently, two reviewers chose the studies, evaluated the quality of the investigations, and retrieved the data. RevMan was used for analysis when the data were collected and entered into the data extraction sheet. In addition to heterogeneity, the overall estimate measures were computed as mean differences with a 95% confidence interval for continuous data and relative risk for dichotomous data. To investigate the impact of outliers on the result, a sensitivity analysis was performed. A funnel plot was used to qualitatively evaluate the publishing bias. A total of 1,650 participants from 19 randomised controlled trials were evaluated.
ResultsThe meta-analysis revealed that the group receiving gabapentin therapy had a similar overall effective rate to the group receiving carbamazepine therapy (OR = 1.94, 95% CI 1.46, 2.57, P = 0.32). Additionally, our meta-analysis revealed that the group receiving gabapentin therapy witnessed a significantly lower risk of adverse reactions than the group receiving carbamazepine therapy (OR= 0.29, 95% CI 0.22, 0.387, P<0.00001).
ConclusionIn summary, the current trials comparing carbamazepine and gabapentin have had inadequate methodological quality. It is not possible to conclude that gabapentin is more effective than carbamazepine in terms of adverse effects based on the evidence that is currently available.
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UPLC-Q-TOF-MS, Network Pharmacology and Molecular Docking to Reveal the Antidepressant Mechanism of the Different Components of Medicinal and Edible Lilies (Lilium sp. pl)
Authors: Zhaoyang Tan, Linghe Huang, Yanqiu Tian, Sai Jiang, Zhi Wang, Hongping Long, Qiaozhen Tong, Shunxiang Li and Lin JiangAvailable online: 24 February 2025More LessBackground and ObjectivesTo explore the mechanism of action of the differential components of medicinal and edible lilies in treating depression by network pharmacology using UPLC-Q-TOF-MS technology.
MethodsThe chemical composition of medicinal and edible lilies was analyzed, screening for unique medicinal compounds. Searched for depression-related targets. Constructed PPI networks. Performed GO and KEGG analyses. Built a network of differential components, and conducted molecular docking. In addition, the contents of regaloside before and after lily processing were compared.
ResultsMedicinal lilies and edible lilies have 17 main differences, including regaloside B and regaloside E. There are 179 targets for actives, 2690 for antidepressants, and 98 intersected. Core targets (7) led to 238 GO processes and 107 KEGG pathways. The molecular docking results showed that 17 components, including regaloside B, regaloside E, (25R)-3β,17α-Dihydroxy-5α- spirostan-6-one 3-O-α-L- rhamnopyranosyl-(1→2)-β- D-glucopyranoside (Named: Lilium lancifolium saponin), etc. could act on 7 potential targets such as EGFR, HSP90AA1, STAT3, TNF, etc. to exert antidepressant effects.
ConclusionThis study employed a network pharmacology combined with a molecular docking approach to compare the active constituents of medicinal and edible lilies in antidepressants, and their pharmacological mechanisms, both theoretically and technically. The phytoconstituents were found to act mainly by inhibiting the inflammatory response in depression. Especially Lilium lancifolium saponin may have a close relationship with antidepressants. These results provide some justification for lilies in the treatment of depression.
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Exploring the Blueprint of Life: The Innovation in Antibody and Protein Design
Authors: Zhiwei Yang and Gerald H. LushingtonAvailable online: 20 February 2025More LessThe innovation in antibody and protein design highlights the transformation from empirical approaches to sophisticated strategies integrating computational methods and artificial intelligence (AI). Key principles, such as combinatorial, structure-based, consensus, and computational designs, have been pivotal in predicting structures from sequences (in silico design). Advances in tools, like AlphaFold and Rosetta suite, enable accurate structure prediction, facilitating the development of functional proteins and antibodies. However, challenges remain, including improving prediction accuracy, modeling flexible regions, understanding structural dynamics, and designing catalytic and binding sites. Despite these, the field promises groundbreaking advancements in biomedical sciences, enriching our understanding and serving human health and scientific discovery.
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Therapeutic Potential of Desert Truffles in the Management of Eye Infections: Demystifying the Fact
Available online: 10 February 2025More LessTruffle, an ascomycetous, hypogeous macrofungi, has long been recognized and valued for its therapeutic and dietary properties. Of late, a range of medicinal compounds, such as ergosterol, tuberoside anandamide, polysaccharides, and phenolics exhibiting anti-inflammatory, immunomodulatory, anticancer, antibacterial, and aphrodisiac properties have been identified in truffles. This review provides an update on contemporary truffle research with a focus on antimicrobial potentials and aims to draw the attention of researchers to exploit the therapeutic potential of truffles in the management of eye infections. The scholarly literature pertaining to the utilization of desert truffles in the management of ocular infections was systematically summarized and reviewed from multiple databases, including Scopus, Web of Science Core Collection, PubMed, and others. The essence of truffle is used as a remedy for trachoma and as an anti-inflammatory agent for ocular problems. The most probable inhibitory constituents are the fungal lectins, polysaccharides, and laccases. Truffle lectins possess the ability to identify and remove bacterial exopolysaccharides. In addition, the fungal polysaccharides affect the bacterial defensive systems. Conversely, laccases facilitate the process of oxidizing phenols, resulting in the release of superoxide anion radicals and the production of hydrogen peroxide. The application of desert truffles in addressing ocular issues has been clinically observed to be satisfactory. The existing literature clearly indicates a pressing need for further investigation into the translation of the antimicrobial properties of crude truffle extract into truffle-based pharmaceutical formulations for clinical application.
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Identification of NR4A2 as a Potential Predictive Biomarker for Atherosclerosis
Authors: Lebin Yuan, Ruru Bai, Xinhao Han and Jiajia XiangAvailable online: 10 February 2025More LessIntroduction/ObjectiveAtherosclerosis, a leading cause of death globally, is characterized by the buildup of immune cells and lipids in medium to large-sized arteries. However, its precise mechanism remains unclear. The purpose of this study is to explore innovative and reliable biomarkers as a viable approach for the identification and management of atherosclerosis.
MethodsThe atherosclerosis-related datasets GSE100927 and GSE66360 were retrieved from the Gene Expression Omnibus (GEO) database. The Limma package in the R programming language was utilized, applying the criteria of |logFC| > 1 and P < 0.05. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the 127 identified DEGs using R. Machine learning techniques were then applied to these data to explore and pinpoint potential biomarkers. The diagnostic potential of these markers was assessed via Receiver Operating Characteristic (ROC) curve analysis. Finally, western blot, real-time quantitative PCR (qRT-PCR), and immunohistochemistry (IHC) were employed to confirm the key biomarkers.
ResultsOur research indicated that a total of 127 DEGs linked to atherosclerosis were successfully identified. Through the application of machine learning methods, eight critical genes were highlighted. Among these, Nuclear Receptor Subfamily 4 Group A Member-2 (NR4A2) emerged as the most promising marker for further investigation. CIBERSORT analysis revealed that NR4A2 expression levels were significantly correlated with multiple immune cell types, including B cells, plasma cells, and macrophages. Additional validation experiments confirmed that NR4A2 expression was indeed elevated in atherosclerotic plaques, supporting its potential as a biomarker for atherosclerosis.
ConclusionOur study identified NR4A2 as a potential immune-related biomarker for the diagnosis and treatment of atherosclerosis.
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Causal Mediation Analysis of the Effect of Dietary Habits on Sleep Apnea Risk
Authors: Yingying-Li1, Liang Wu and Wendo- ChenAvailable online: 06 February 2025More LessObjectiveDiet is a modifiable factor that influences several chronic diseases, making lifelong dietary interventions critically important for reducing disease risk. Hence, this study aims to assess the potential causal relationship between diet and sleep apnea (SA).
MethodsWe analyzed genome-wide association study (GWAS) data from approximately 450,000 individuals, focusing on 8 dietary intakes and GWAS statistics for 249 metabolites from the UK Biobank. Sleep apnea-related phenotypic data from 16,761 participants were sourced from the FinnGen Biobank. Furthermore, we conducted a series of two-sample Mendelian Randomization (two-sample MR) to explore the causality between diet and SA. Sensitivity analyses were conducted to assess the robustness of the two-sample MR results, and reverse MR analysis was performed to examine potential reverse causality. Multivariate MR (MVMR) analysis and mediation effect estimation were employed to evaluate the mediating roles of metabolites.
ResultsTwo-sample MR analyses revealed significant causal associations between bread intake (OR=0.56, 95% CI 0.35–0.89, P =0.014), cheese intake (OR=0.67, 95% CI 0.50–0.89, P =0.006), and dried fruit intake (OR=0.61, 95% CI 0.39–0.95, P =0.029) with SA. Reverse MR analysis indicated a causal effect of SA on dried fruit intake (P < 0.05). Univariate MR analyses further identified significant causal effects of bread and cheese intakes on 2 and 32 metabolites, respectively (P < 0.05). Subsequent MVMR analysis demonstrated direct causal effects of bread and cheese intake on SA, independent of metabolite mediation (P < 0.05). Furthermore, the mediating effect of cheese intake on SA through glucose was estimated at 0.023 (90% CI 0.01–0.046), whereas other modeled mediation effects were not statistically significant.
ConclusionThe MR analysis in this study offers genetic evidence indicating that heightened genetic susceptibility to cheese and bread intake potentially reduces SA risk. These findings underscore and validate the significance of diet in preventing SA.
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Adaptability of Thermotoga Maritima's Glycolysis Pathway in Both Oxic and Anoxic Environments
Authors: Raja Lakhal, Manaf AlMatar and Tahani AlkalafAvailable online: 06 February 2025More LessBackgroundThe phylum Thermotogae is composed of five families: Fervidobacteriaceae, Thermatogaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae; one class: Thermotogae; and four orders: Kosmotogales, Petrotogales, and Mesoaciditogales. There are thirteen genera in all. The physical and metabolic characteristics of the Thermotogae species reflect the extreme heat from which they were separated. Thermotogae members have a broad spectrum of metabolic capacities, resulting in a pool of valuable chemicals with potential uses in many different sectors.
MethodA 1.5-liter operating capacity bioreactor with a 2.3-liter double-jacket glass volume was utilised to culture Thermotoga maritima in both oxic and anoxic conditions. In addition to temperature, pH, and redox potential, sensors that were installed within the fermentor monitored additional parameters. RNA extraction and cDNA synthesis A total of RNAs was extracted utilising Roche's High Pure RNA reagent. Analysis of glycolysis pathways in T. maritima was performed by NMR spectroscopy
ResultBased on NMR analysis, our findings demonstrate that T. maritima uses the EM route to metabolize 90% of glucose in anoxia and the ED pathway for 10%. On the other hand, T. maritima continues to employ the EM and ED glycolysis routes concurrently when exposed to extended oxidative stress; however, the ED pathway's contribution drops from 10% to around 5%.
ConclusionCompared to the EM route, the ED pathway has more strongly repressed transcripts that encode its unique enzymes.
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CD4+ Effector Memory T Cells Related Marker Gene Signatures in Osteoporosis and Aging: Insight From Single-Cell Analysis and Mendelian Randomization
Authors: Xiangwen Shi, Linmeng Tang, Mingjun Li, Yipeng Wu and Yongqing XuAvailable online: 04 February 2025More LessObjectiveWith the accelerated aging of the population, aging has emerged as a major risk factor for osteoporosis (OP). This study aims to investigate the relationship and shared molecular mechanisms between OP and aging through various genetic approaches.
MethodsSingle-cell data from the peripheral blood of osteoporosis patients, aging individuals, and healthy controls were integrated to analyze characteristic changes in cell subpopulations. Differentially expressed genes (DEGs) were then identified within core subpopulations, and Mendelian randomization (MR) analysis was employed to explore potential causal links between key genes and OP. Additionally, an OP model was established in rats, and mRNA levels of key genes were measured using RT-qPCR.
ResultsThrough the integration, filtering, and analysis of scRNA-seq data, an increased proportion of CD4+ effector memory T (CD4+ TEM) cells were identified in OP and aging samples, marking them as a core subpopulation. Differential expression analysis identified 49 DEGs, and further analysis through Mendelian Randomization (MR) identified three key genes (KLRB1, NR4A2, and S100A4) significantly associated with OP. Notably, the upregulation of KLRB1 and S100A4 may enhance the interactions within T cells and with other cell subgroups. At the same time, the downregulation of NR4A2 could impede communication between T cells and other cell subpopulations. The RT-qPCR results indicated that NR4A2 was significantly downregulated in the OP group.
ConclusionThis study conducted a comprehensive analysis of the potential link between OP and aging, identifying CD4+ TEM cells as the core cell subgroup in OP and aging samples. It further revealed the causal relationship between KLRB1, NR4A2, and S100A4 and the occurrence of OP. The upregulation of KLRB1 and S100A4 may contribute to OP pathogenesis by promoting interactions between CD4+ TEM cells and other cell subgroups, providing new insights for molecular targeting and immunotherapy of OP.
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A Comparative Chemoinformatics Analysis of Compounds Extracted from Nyctanthes Arbor-tristis
Authors: Nandini Sandeep Kotharkar, Sanket Bapat, Pranav Pathak and Renu VyasAvailable online: 02 February 2025More LessIntroductionNatural products are a rich source of diverse chemical compounds with interesting therapeutic properties. There is a need for in-depth investigation of this reservoir with in-silico tools to assert the molecular diversity with respect to clinical significance. Although studies have been reported on plants such as Nyctanthes arbor-tristis(NAT) and its medicinal importance. A comprehensive study on comparative analysis of all phyto-constituents has not been carried out.
Aimn the present work, we have carried out a comparative study of compounds obtained from the ethanolic extracts of various parts such as calyx, corolla, leaf, and bark of the NAT plant.
MethodsThe extracted compounds were characterized by LCMS and GCMS studies. This was further corroborated by the network analysis, docking, and dynamic simulation studies with validated anti-arthritic targets.
ResultsThe most significant observation from LCMS and GCMS was that the compounds from calyx and corolla were closer in chemical space to the anti-arthritic compounds. To further expand and explore chemical space, the common scaffolds were seeded to enumerate a virtual library. The virtual molecules were prioritized based on the drug-like, leadlike scores and docked against anti-arthritic targets to reveal identical interactions in the pocket region.
ConclusionThe comprehensive study will be of immense value to medicinal chemists for the rational synthesis of molecules as well as bioinformatics professionals for getting useful insight into identifying rich diverse molecules from plant sources.
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Forsythiaside A Ameliorates Inflammation by Regulating the Autophagy in Methotrexate-induced Intestinal Mucositis
Authors: Wuying Lang, Jiayi Zhang, Xuejun Xiao, Min Cheng, Xin Zheng, Haizhou Gong, Ihsan Ali, Yongping Zhao, Feng Jia, Zhe Wang, Jing Wang, Wei Li and Haihua ZhangAvailable online: 29 January 2025More LessBackgroundMethotrexate (MTX) effectively eliminates cancerous cells but can also cause inflammation intestinal, known as mucositis. Forsythiaside A (FTA) from Forsythia suspensa has shown promise in relieving mucositis by targeting the NLRP3 pathways. Since NLRP3 inflammasome activation is negatively regulated by autophagy, this study explores how FTA-mediated autophagy affects NLRP3 inflammasome in treating MTX-induced intestinal inflammation.
MethodsIntestinal mucositis was induced in rats with MTX. FTA's impact was assessed using HE staining and ELISA. The mechanism was studied using immunofluorescence, western blot, and ELISA.
ResultsFTA treatment resulted in reduced levels of D-lactic acid and diamine oxidase (DAO) in MTX-treated rats. Western blot and immunofluorescence analyses revealed up-regulation of Beclin-1 and LC3II/I, accumulation of LC3, and down-regulation of p62 expression levels in MTX-treated rats following 40 or 80 mg/kg FTA intervention. However, when the autophagy inhibitor 3-MA was used, the intestinal pathology was exacerbated, the inflammatory scores increased, and serum levels of TNF-α, IL-1β, and IL-18 were elevated. Western blotting indicated decreased LC3II/I expression, while NLRP3, cleaved caspase 1, and cleaved IL-1β expressions were upregulated.
ConclusionThese findings suggested that FTA alleviated MTX-treated intestinal mucositis by activating autophagy, which in turn inhibits the NLRP3 inflammasome.
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Predicting Polymerase Chain Reaction Success: Integrating the K-Word Order Model, Physicochemical Properties Modeling of Double Bases, and Support Vector Machine
Available online: 23 January 2025More LessIntroductionPolymerase Chain Reaction (PCR) has been a pivotal scientific technique since the twentieth century, and it is widely applied across various domains. Despite its ubiquity, challenges persist in efficiently amplifying specific DNA templates.
MethodWhile PCR experimental procedures have garnered significant attention, the analysis of the DNA template, which is the experiment's focal point, has been notably overlooked. This study addresses the uncertainty surrounding the amplification of DNA fragments using conventional Taq DNA polymerase-based PCR protocols. The imperative need to characterize DNA templates and devise a reliable method for predicting PCR success is underscored.
ResultIn this study, we formulate a 72-dimensional feature vector representing a DNA template through the utilization of k-word order and modeling of physicochemical properties of double bases. Subsequently, a Support Vector Machine (SVM) model is employed to assess PCR results.
ConclusionA jackknife cross-validation test is used to evaluate the anticipated success rates, resulting in an overall accuracy of 95.77%. Sensitivity, specificity, and Matthew's Correlation Coefficient (MCC) stand at 95.75%, 95.79%, and 0.915, respectively.
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Investigation of the Mechanism of Pachyman against Gout Arthritis with Network Pharmacology Analysis and Verification In Vivo
Authors: Qing-xin Kong, Wei-ping Xu, Cheng Fan, Bi-Lin Liu, Li-Ping Reng and Qiao RuanAvailable online: 22 January 2025More LessPurposePachyman, derived from Poria cocos, has been used to treat gouty arthritis (GA) for thousands of years, although its precise role and mechanisms remain unclear. Herein, we investigate the therapeutic effects of pachyman on GA and explore their underlying mechanisms.
MethodsNetwork pharmacology and experimental methods were employed to investigate the therapeutic mechanisms of pachyman against GA. The protein-protein interaction network of shared targets between pachyman and gout was constructed. Furthermore, we elucidated the functions and mechanisms of pachyman against GA. Subsequently, we validated the predicted mechanisms from an experiment on rats.
ResultsThe treatment of GA with pachyman primarily related to tumor necrosis factor (TNF), matrix metalloproteinases (MMP), and relaxation factor signaling pathways. In the experimental validation, pachyman were found to regulate the expression of IL-1β, TNF-α, TGF-β, superoxide dismutase, and glutathione peroxidase of hyperuricemic rats.
ConclusionThese collective findings suggest that pachyman holds promise as an alternative treatment for GA.
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Mechanisms of the Compound of Magnoliae Flos and Xanthii Fructus Essential Oils for the Treatment of Allergic Rhinitis based on the Integration of Network Pharmacology, Molecular Docking, and Animal Experiment
Authors: Tao Lu, Yuqin Yang, Zhenlin Yang, Ziyi Liu, Miao Li, Ziman Lu, Ting Gong and Jincheng ZhangAvailable online: 22 January 2025More LessAim and ObjectiveMagnoliae Flos (Chinese name: Xin-Yi) and Xanthii Fructus (Chinese name: Cang-Er-Zi) are Chinese herbal medicines and have been used to treat allergic rhinitis (AR). However, the therapeutic effect, active ingredients, and probable processes of a compound of Magnoliae Flos and Xanthii Fructus in the form of essential oils (CMFXFEO) in treating AR have not been reported. This study aims to determine the efficacy of the CMFXFEO on ovalbumin (OVA)-induced AR in a rat model and to use network pharmacology and molecular docking to reveal the hub genes, biological functions, and signaling pathways of CMFXFEO against AR.
MethodsAnimal experiments were applied to validate the role of CMFXFEO in the treatment of AR. 20 rats were randomly divided into four groups: control group (CON, n=5), positive control group (AR, n=5), CMFXFEO-treated group (AR+CMFXFEO, n=5), and budesonide-treated group (AR+Budesonide, n=5). Rats were stimulated with OVA to induce AR. Symptom scores assessment and histo-pathomorphological evaluation was performed. The serum level of OVA-specific immunoglobulin (Ig) E was measured. Gas Chromatograph-Mass Spectrometer analysis (GC-MS) was used to identify the monomer chemical composition of CMFXFEO. The target genes of CMFXFEO were obtained by using PubChem and SwissTargetPrediction databases. The target genes of AR were screened using GeneCards, DisGeNET, and OMIM databases. The target genes were intersected using the venny2.1 website to obtain the potential therapeutic targets of CMFXFEO for treating AR and to construct the PPI network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal associated signaling pathways. The Sybyl tool was used to dock the CMFXFEO with key therapeutic targets molecularly.
ResultsIntranasal CMFXFEO administration significantly suppressed the allergic symptoms, reduced the inflammatory cell infiltration, and the serum level of OVA-specific immunoglobulin (Ig) E. The main components of CMFXFEO obtained through the GC-MS analysis, listed as γ-terpinene (9.4908%), limonene (7.2693%), menthol (7.1821%), β-pinene (7.1190%), β-caryophyllene (7.0396%), eucalyptol (6.1367%), linalool(5.9686%), eugenol (5.0776%). A total of 398 CMFXFEO targets and 488 AR-related targets were screened, of which 42 were common targets. The GO and KEGG pathway analyses unveiled that CMFXFEO were strongly associated with several signaling pathways, including the AGE-RAGE signaling pathway, TNF signaling pathway, and Chemokine signaling pathway. PPI network construction screened six hub genes as therapeutic targets, including STAT3, IL1B, TLR4, PTGS2, ICAM1, and VCAM1. The molecular docking verification indicated that CMFXFEO have good binding activity with therapeutic targets, and β-Pinene’s docking ability with TLR4 is particularly prominent.
ConclusionThe anti-inflammatory and anti-allergic effects of CMFXFEO are to inhibit the infiltration of inflammatory cells in the OVA-induced AR rat model. The results of the network pharmacology and molecular docking deduced that the CMFXFEO may have the potential to treat AR by multiple pathways through relieving inflammatory, anti-oxidative stress response, and modulating the immune system.
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Herbal Mucoadhesive Gels for Canker Sores: Analysis of Physicochemical Properties, Efficacy, and Safety
Available online: 20 January 2025More LessAimThe goal of this research was to formulate mucoadhesive gels using hydroglyceric extracts of Cistus creticus L. and Inula viscosa (L.) Aiton, either separately or in combination, utilizes carboxymethyl cellulose and detects their physicochemical characteristics and safety for oromucosal cells and antimicrobial (antibacterial, antifungal, and antiviral) efficacy to assess their performance.
MethodsUsing LC-HRMS, the extracts of C. creticus and I. viscosa were examined. Evaluations were conducted on the formulations' viscosity, cytotoxicity-cell proliferation controls, texture, antibacterial activity, pH, and organoleptic properties. The minimal inhibitory concentrations and microbroth dilution tests were used to assess the effectiveness of the formulations.
ResultsThe pH, organoleptic, and physical characteristics of each formulation have been determined to be appropriate. The research results demonstrated that I. viscosa contributed antiviral efficacy to the formulations linked to dose-dependent activities against all examined mouth pathogens, whereas C. creticus provided antibacterial and antifungal efficacy. The formulation containing C. creticus extract alone was the most cytotoxic, whereas the formulation including I. viscosa extract alone was the least cytotoxic against gingival fibroblast cells, according to the findings of tests on cell proliferation and cytotoxicity.
ConclusionThe formulation contained a 32% 1:1 mixture of I. viscosa and C. creticus hydroglyceric extracts was detected as safe with acceptable cytotoxicity along with antibacterial and antiviral effectiveness, were encouraging for future investigations.
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Transcriptome-Based Analysis of the Oxidative Response of Thermotoga maritima to the O2 Stress
Authors: Raja Lakhal, Manaf AlMatar, Tahani Alkalaf and Osman AlbarriAvailable online: 16 January 2025More LessBackgroundThermotoga maritima is an anaerobic hyperthermophilic eubacterium isolated from geothermally heated maritime surfaces. It can grow at temperatures up to 80 degrees Celsius.
MethodsA 2.3-L bioreactor was specifically designed to cultivate hyperthermophilic bacteria under carefully regulated pH, redox potential, temperature, and dissolved O2.
ResultsUsing this bioreactor, which was adjusted at 80°C and pH 7.0, it was found that Thermotoga maritima demonstrated continued growth even after being exposed to oxygen for an extended period. Transcription studies revealed that following prolonged oxygen exposure, the genes encoding ROS-scavenging systems, alkyl hydroperoxide reductase (ahp), thioredoxin-dependent thiol peroxidase (bcp 2), and, to a lesser extent, neelaredoxin (nlr), were upregulated/overexpressed. When oxygen was available, the metabolism of glucose was diverted to make lactate rather than acetate.
ConclusionBased on the O/R ratio of 1.0 in anaerobiosis and 1.67 in the presence of O2, we may conclude that Thermotoga maritima is capable of semi-oxidative metabolism.
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Artificial Intelligence in Computer-Aided Drug Design (CADD) Tools for the Finding of Potent Biologically Active Small Molecules: Traditional to Modern Approach
Available online: 15 January 2025More LessComputer-Aided Drug Design (CADD) entails designing molecules that could potentially interact with a specific biomolecular target and promising their potential binding. The stereo-arrangement and stereo-selectivity of small molecules (SMs)--based chemotherapeutic agents significantly influence their therapeutic potential and enhance their therapeutic advantages. CADD has been a well-established field for decades, but recent years have observed a significant shift toward acceptance of computational approaches in both academia and the pharmaceutical industry. Recently, artificial intelligence (AI), bioinformatics, and data science have played a significant role in drug discovery to accelerate the development of effective treatments, reduce expenses, and eliminate the need for animal testing. This shift can be attributed to the availability of extensive data on molecular properties, binding to therapeutic targets, and their 3D structures. Increasing interest from legislators, pharmaceutical companies, and academic and industrial scientists is evidence that AI is reshaping the drug discovery industry. To achieve success in drug discovery, it is necessary to optimize pharmacodynamic, pharmacokinetic, and clinical outcome-related properties. Moreover, the advent of on-demand virtual libraries containing billions of drug-like SMs, coupled with abundant computing capacities, has further facilitated this transition. To fully capitalize on these resources, rapid computational methods are needed for effective ligand screening. This includes structure-based virtual screening (SBVS) of vast chemical spaces, aided by fast iterative screening approaches. At the same time, advances in deep learning (DL) predictions of ligand properties and target activities have become very helpful, as they no longer need information about the structure of the receptor. This study examines recent progress in the drug discovery and development (DDD) approach, their potential to reshape the entire DDD process, and the challenges they face. This review examines the role of artificial intelligence as a fundamental component in drug discovery, particularly focusing on small molecules. It also discusses how AI-driven approaches can expedite the identification of diverse, potent, target-specific, and drug-like ligands for protein targets. This advancement has the potential to make drug discovery more efficient and cost-effective, ultimately facilitating the development of safer and more effective therapeutics.
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Mechanism Analysis of the Effect of Cordycepin on Colorectal Cancer via Network Pharmacology and Experiment
Authors: Ya Chen, Peng Wang, Mingzhu Zhang, Hao Yang and Beibei LiangAvailable online: 14 January 2025More LessObjectiveColorectal Cancer (CRC) has attracted much attention due to its high mortality and morbidity. Cordycepin, also known as 3'-deoxyadenosine (3'-dA), exhibits many biological functions, including antibacterial, anti-inflammatory, antiviral, anti-tumor, and immunomodulatory effects. It has been proven to show anticancer activity in both laboratory research studies and living organisms. However, the molecular mechanism of the effect of cordycepin on CRC remains unclear.
MethodsThe genes associated with cordycepin and colorectal cancer have been identified by comparing the toxicogenomics database (CTD) and GeneCards database. The common genes between cordycepin and CRC have been identified using the Venny tool. The Protein-protein Interaction (PPI) network has been drawn using the STRING database. GO and KEGG enrichment analyses of the intersecting genes have been followed by experimental validation, both in vitro and in vivo.
Results24 drug targets have been screened using the CTD database and 1490 disease targets have been obtained from the GeneCards database and GO and KEGG analyses. The effect of cordycepin on the proliferation of SW480 cells has been assessed using CCK-8. The related results have indicated cordycepin to inhibit the proliferation of SW480 cells, promote apoptosis, and activate the p53 signal pathway. The findings obtained from in vivo experiments have been found to be consistent with those obtained from in vitro studies.
ConclusionOur findings have elucidated an effective way to search for cordycepin’s potential mechanism of effect on CRC therapy by employing the network pharmacology and experiment. We have predicted that cordycepin can inhibit tumor growth by regulating the apoptosis pathway. This study has offered valuable insights into the potential mechanism of the effect of cordycepin on CRC and provided a theoretical basis for further validation of its clinical application.
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Mechanism Study on the Regulation of Th1/Th2 in the Treatment of Idiopathic Membranous Nephropathy by Shengyang Yiwei Decoction
Authors: Yuan Wu, Xue-Qin Zhang, Heng-Tong An, Shuai-Jie Wang, Ya-Yun Zhao and Zhi-Qiang ChenAvailable online: 13 January 2025More LessBackgroundShengyang Yiwei Decoction showed efficacy in idiopathic membranous nephropathy treatment, and this study aimed to assess the underlying molecular mechanisms.
MethodsRats with passive Heymann nephritis were divided into the model group, the Shengyang Yiwei Decoction group, the JAK2 inhibitor group, and the STAT3 inhibitor group. Healthy rats served as the normal control. 24-hour urinary protein excretion, IgG deposition, renal histopathology, the expression levels of synaptopodin, nephrin, podocalyxin, interferon-γ, interleukin-4, T-box expressed in T cells, GATA binding protein-3, and relevant pathway proteins were measured.
ResultsWithin the model group, a notable elevation in the 24-h urinary protein level was observed, accompanied by evident IgG deposition, increased glomerular volume, eosinophilic deposits, diminished expression of podocyte marker proteins, and a discernible imbalance in Th1/Th2 cellular immunity. Conversely, in Shengyang Yiwei Decoction and both inhibitor groups, enhancements were observed across the aforementioned indexes.
ConclusionShengyang Yiwei Decoction may reduce glomerular podocyte injury through the suppression of the JAK2/STAT3 signaling pathway and modulation of the Th1/Th2 immune balance.
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The Anaphylactic and Anti-allergenic Properties of Shuanghuanglian: A Review
Authors: Xin Jiang, Ji Li, Xiaohui Yao and Hao DingAvailable online: 13 January 2025More LessShuanghuanglian (SHL) and its primary constituents have demonstrated protective effects against allergenic diseases. This review examines the anaphylactic and anti-allergenic activities of SHL and its constituents. We also discuss potential avenues for future research, particularly regarding the expansion of the clinical applications of SHL formulations (oral or nebulized) for the treatment of allergenic disorders.
For this review, we searched the PubMed, Web of Science, and China National Knowledge Infrastructure databases for relevant publications. Additionally, details of the essential active components and target genes of SHL were obtained from the Traditional Chinese Medicine Systems Pharmacology database (TCMSP), and information on allergy-related genes was collected from the GeneCards and Online Mendelian Inheritance in Man(OMIM) databases. Lists of both the SHL target and disease-related genes were imported into the ‘Draw Venn Diagram’ tool on the website (http://bioinformatics.psb.ugen /web tools/Venn/). A protein–protein interaction network for SHL and disease targets was constructed with reference to the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the potential pathways were identified based on Kyoto Encyclopaedia of Genes and Genome enrichment analyses.
The allergenic reactions induced by SHL injection (intravenous) and its main constituents (intraperitoneal or intravenous injection) have been verified in animal experiments. Furthermore, the protective effects of SHL injection (intraperitoneal) and its individual Chinese herb components (intragastric administration), namely, Flos Lonicerae, Radix Scutellariae, and Fructus Forsythiae, as well as their main constituents (intraperitoneal or intragastric administration), have been verified in asthma, rhinitis, atopic dermatitis, and both IgE- and non-IgE-mediated systemic allergic responses. The network pharmacology analysis revealed that the therapeutic effects of SHL might be primarily mediated through the regulation of the IL-17 and TNF-α signalling pathways and Th17 cell differentiation.
Accumulated research data provide a theoretical basis for the clinical application of SHL (via extravascular routes) in the treatment of allergenic diseases.
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Bushen Daozhuo Granules Alleviate Chronic Non-Bacterial Prostatitis in Rats through p38 MAPK and Akt Signaling Pathways Based on Tandem Mass Tag-Based Quantitative Proteomics and Network Pharmacology Analyses
Authors: Dalin Sun, Yuanyuan Liu, Dong Xing, Dandan Wang, Bin Cai, Zhian Tang, Qinglin Hu, Wenjun Ma and Baofang JinAvailable online: 13 January 2025More LessIntroductionThe traditional Chinese medicine formula, Bushen Daozhuo Granules (BSDZG), is used to treat chronic non-bacterial prostatitis (CNP) clinically. However, its mechanism of action is unclear. The aim of our study was to determine the effect of BSDZG on CNP and its underlying mechanisms.
MethodsMale Wistar rats were randomly assigned to control, CNP, and BSDZG groups. CNP was induced using purified prostaglandin solution and Freund's complete adjuvant, after which the BSDZG group received 1.54 g/kg/d of BSDZG for 30 days. Prostate tissues were used to determine apoptosis and inflammatory cytokines. The herb-composition-target network and functional signaling pathways were built using a network pharmacology approach, which was also confirmed in vivo.
ResultsTreatment with BSDZG significantly alleviated the histopathological lesions, inflammation, and apoptosis in the prostate of CNP rats. The herb-composition-target network comprising 42 active compounds and 32 targets of 11 herbs was illustrated, and KEGG pathways analysis identified the Akt and MAPK pathways as related to the effects of BSDZG. Phosphorylation of p38 MAPK, NF-кB, and Bax expression was significantly enhanced and phosphorylated Akt and Bcl-2 levels were decreased in CNP rats, which could be reversed by BSDZG.
ConclusionThis study presented for the first time that BSDZG effectively alleviated CNP symptoms in rats and elucidated the underlying mechanisms mediated by the Akt and MAPK pathways, providing the theoretical basis for the clinical use and promotion of BSDZG.
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TSPOAP1-AS1: A Novel Biomarker for the Prognosis and Therapeutic Target in Cervical Cancer
Authors: Jinyuan Li, Zhen Ye, Yuhong Gan, Dongbing Li and Yibiao ChenAvailable online: 13 January 2025More LessBackgroundTSPOAP1 antisense RNA 1 (TSPOAP1-AS1) is a long non-coding RNA (lncRNA) that has received widespread attention in oncology research in recent years. Its role and mechanism in some cancers have gradually been revealed. However, it is not clear what role TSPOAP1-AS1 plays in cervical cancer (CESC).
ObjectiveIn this study, bioinformatic analysis and experimental validation were carried out to investigate the relationship between TSPOAP1-AS1 and CESC.
MethodsThe relationships between clinical characteristics in patients with CESC, TSPOAP1-AS1 expression, prognostic factors, regulation network, and immune infiltration of TSPOAP1-AS1 were evaluated using statistics and The Cancer Genome Atlas database. Real-Time Quantitative Reverse Transcription PCR was used to test TSPOAP1-AS1, miR-17-5p, and AGFG2 expression in CESC cell lines.
ResultsCESC patients exhibited markedly reduced expression of TSPOAP1-AS1. There was a significant correlation between low expression of TSPOAP1-AS1 in CESC patients and the clinical stage (p < 0.05), weight (p < 0.05), and BMI (p < 0.05). Lower expression of TSPOAP1-AS1 in patients with CESC was associated with poorer overall survival (OS) (p = 0.014) and disease-specific survival (DSS) (p = 0.030). There was also an independent correlation between high expression of TSPOAP1-AS1 (p = 0.036) and DSS in patients with CESC. TSPOAP1-AS1 was involved in the ribosome, oxidative phosphorylation, antigen processing and presentation, cell adhesion molecules (CAMs), the chemokine signaling pathway, neuroactive ligand-receptor interaction, and primary immunodeficiencies. The infiltration of immune cells and the expression of TSPOAP1-AS1 were found to be correlated. A ceRNA network of TSPOAP1-AS1/miR-17-5p/AGFG2 was constructed in CESC. In CESC, a ceRNA network involving TSPOAP1-AS1/miR-17-5p/AGFG2 was successfully established. When comparing CESC cell lines with HcerEpic, the expression of TSPOAP1-AS1 and AGFG2 decreased significantly, and the expression of miR-17-5p increased significantly.
ConclusionIn CESC patients, low expression of TSPOAP1-AS1 was associated with poor survival and immune infiltration. It may be effective to use TSPOAP1-AS1 as a biomarker of prognosis and therapeutic target in CESC.
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Causal Association between Arm Fat, Left Leg Fat, and Trunk Fat Masses and Risk of Polycystic Ovarian Syndrome: A Mendelian Randomization Study
Authors: Yuhan Zhang, Wei Zhou, Qiong Su and Qi ChenAvailable online: 09 January 2025More LessBackgroundObservational studies have reported that arm fat, left leg fat, and trunk fat masses have different effects on polycystic ovarian syndrome (PCOS). However, the causal relationship between them remains unknown.
Materials and MethodsA two-sample Mendelian randomization (MR) study was conducted by utilizing pooled data from the largest Genome-Wide Association Study (GWAS). Random effect inverse variance weighted (IVW) method, weighted median (WM), and MR-Egger regression analysis were the main statistical methods utilized. Finally, a sensitivity assessment was conducted. Cochran’s Q test was used to analyze heterogeneity, whereas MR-Egger regression (intercept term) was used to analyze horizontal pleiotropy. The leave-one-out analysis was performed to assess if MR estimates were impacted by a single nucleotide polymorphism (SNP) exhibiting significant horizontal pleiotropy.
ResultsThis study discovered a significant positive correlation between left leg fat mass, arm fat mass, and trunk fat mass and genetic factors of PCOS (odds ratio (OR): 4.452, confidence interval (CI): 2.740−7.232, p < 0.001, OR: 3.321, CI: 2.248−4.907, p < 0.001, and OR: 2.518, CI: 1.722−3.682, p < 0.001, respectively).
ConclusionThis study indicates that arm fat, left leg fat, and trunk fat masses may be genetically correlated with PCOS.
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Unveiling the Interplay between Dopamine-like Molecules and Β-Amyloid Peptide: A Combined Molecular Dynamic and DFT Approach
Available online: 02 January 2025More LessAimsThis study aims explore the impact of catechol, dopamine, and L-DOPA on the stability and toxicity of β-amyloid peptides, which play a key role in the neurodegenerative process of Alzheimer's disease, to assess their potential as therapeutic agents.
BackgroundAlzheimer's disease is marked by the aggregation of β-amyloid peptides, which contribute to neurodegeneration. Exploring how various compounds interact with β-amyloid peptides can offer valuable insights into potential therapeutic strategies.
ObjectiveThe objective of this research is to explore the interaction mechanisms of catechol, dopamine, and L-DOPA with β-amyloid peptides and assess their impact on peptide stability and aggregation.
MethodThis study employs molecular dynamics simulations combined with density functional theory to investigate the interactions between β-amyloid and the three compounds. It evaluates changes in peptide stability and salt bridge lengths and performs electronic structure analyses using the Electron Localization Function (ELF) and Harmonic Oscillator Model of Aromaticity (HOMA).
ResultsThe findings reveal that β-amyloid stability decreases significantly when interacting with dopamine and L-DOPA compared to catechol. All three compounds inhibit β-amyloid, with dopamine and L-DOPA showing stronger effects. Catechol primarily interacts through hydrophobic interactions, while dopamine and L-DOPA also form hydrogen bonds with β-amyloid. Electronic structure analysis shows catechol has higher electron localization and anti-aromatic character, affecting its interactions differently than dopamine and L-DOPA. A decrease in the HOMO-LUMO gap from catechol to L-DOPA to dopamine indicates increasing reactivity towards β-amyloid.
ConclusionDopamine and L-DOPA more effectively disrupt β-amyloid aggregation than catechol, likely due to additional hydrogen bonding and increased electronic reactivity. These insights are crucial for developing therapeutic strategies targeting β-amyloid aggregation in Alzheimer's disease, emphasizing the importance of molecular interactions in modulating peptide stability and toxicity.
The study also provides a comparative analysis of the electronic properties and interaction dynamics of the compounds, which can guide future research in the design of β-amyloid inhibitors. The utilization of advanced simulation techniques underscores the potential for computational methods in understanding complex biological interactions and developing novel therapeutic agents. Furthermore, the insights into the differential effects of hydrophobic interactions versus hydrogen bonding offer valuable information for the synthesis of new compounds aimed at mitigating β-amyloid toxicity.
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Nanomaterials for Temporomandibular Joint Osteoarthritis Therapy: A Mini-Review
Authors: Lulu Chen and Chengcheng LiaoAvailable online: 02 January 2025More LessOsteoarthritis, particularly temporomandibular joint (TMJ) osteoarthritis (OA), poses significant challenges in diagnosis and treatment. Recent studies suggest that nanomaterials hold considerable promise in treating TMJ-OA, showing validated efficacy in animal models. However, further research is required to ensure their long-term safety within the TMJ-OA environment. Nanomaterials can facilitate drug delivery and encapsulate functional cells and extracellular vesicles, offering new avenues for exploration. This paper reviews the current research status of nanomaterials in TMJ-OA treatment, including drug delivery, anti-inflammatory, lubricating and buffering, antioxidant, tissue regeneration, scaffold, and stimuli-responsive nanomaterials. Additionally, the paper explores the development and future prospects of nanomaterials in TMJ-OA treatment, highlighting their unique contributions and aiming to provide new perspectives and solutions for unexplored areas.
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Ferroptosis-related Biotargets and Network Mechanisms of Maslinic Acid Against Myocardial Ischemia-reperfusion Injury: An Integrated Bioinformatic and Experimental Approach
Authors: Qi Li, Guiyuan He, Rujie Zheng, Chunlei Liu, Che Wang, Zhihao Liu, Zhuqing Li and Chengzhi LuAvailable online: 02 January 2025More LessBackgroundMaslinic acid (MA), a pentacyclic triterpenoid compound derived from leaves and fruits of Olea europaea, bears multi-pharmacological properties. Our previous studies found that MA exerted a cardioprotective effect by modulating oxidative stress, inflammation, and apoptosis during myocardial ischemia-reperfusion injury (MIRI). Nevertheless, data regarding the anti-ferroptosis effects of MA on MI/RI remains unidentified.
Aim of the StudyThis study aimed to explore the effects of MA on ferroptosis induced by MI/RI, with a focus on elucidating the underlying mechanisms through an integrated approach of network pharmacology and experimental validation.
Materials and MethodsSeveral public databases and a protein-protein interaction (PPI) network were used to identify the core targets shared by MI/RI, ferroptosis, and MA. The molecular function, cell component, biological process, and potential signaling pathways of core genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Subsequently, molecular docking and in vitro experiments were carried out to further validate network pharmacology results.
ResultsA total of 21 unique intersection genes were obtained as potential targets of MA in treating MI/RI-induced ferroptosis. The 10 hub genes with the highest interaction scores were identified from PPI analysis. GO and KEGG enrichment showed the contribution of the core genes to pharmacological actions and mechanisms in MA treatment of MI/RI, especially the ferroptosis-related signaling pathways. Additionally, MA docked well with ranked core targets, including MAPK, MTOR, STAT3, PTGS2, and MDM2. Subsequently, in vitro experiments revealed that MA notably alleviated oxidative damage, reduced ferrous iron overload and ferroptosis, and regulated the expression of ferroptosis-related genes (GPX4, PTGS2, and ACSL4) in erastin-induced H9c2 cells. Meanwhile, MA could significantly reduce phosphorylation of MAPK (ERK1/2) levels in H9c2 cells.
ConclusionBy utilizing network pharmacology and experimental data, our study revealed the correlation between MA and ferroptosis following MI/RI, and concluded that MA might protect against MI/RI by reducing ferroptosis through the ERK1/2 signaling pathway. This finding offered fresh insights into the pharmacological mechanisms of MA against MI/RI.
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Sanggenol L Alleviates Rotenone-induced Parkinson's Disease and Inhibits Mitochondrial Complex I by Apoptosis Via P13K/AKT/mTOR Signalling
Authors: Nan Zhao, Menghai Wu, Periyannan Velu, Annamalai Vijayalakshmi and Jianbin ZhangAvailable online: 13 December 2024More LessBackgroundParkinson’s disease (PD) is the age-associated, second most advanced neurodegenerative illness. Rotenone is an extensively used pesticide to study PD pathology and inhibits mitochondrial complex I. Reports indicate that rotenone exerts neurotoxicity by its capability to produce reactive oxygen species (ROS), which eventually leads to neuronal apoptosis.
ObjectiveSanggenol L (SL) is an eminent flavonoid present in the Morus alba root bark, which exhibits neuroprotective, anticancer, and antioxidant properties. Materials and Methods: Hence, we assessed the neuroprotective activity of SL (5 and 10 µM/ml) on rotenone-stimulated SK-N-SH neuroblastoma cells and elucidated the effect of the P13K/AKT/mTOR signalling.
ResultsThe anti-PD action of SL on proliferation, oxidative stress (OS), intracellular ROS, apoptosis, Bax, cleaved Caspase-12, -9, -3, and Cyt-c, Bcl-2 and P13K/AKT/mTOR signaling was determined by MTT assay, biochemical analysis, DCFDA, AO/EB staining and western blot. It was found that SL (5 and 10 µM/ml) reduced rotenone-triggered OS, ROS levels, and apoptosis in a concentration-related way. SL alleviates Bax, cleaved caspase-12, -9, -3, and Cyt-c, while reducing Bcl-2. Furthermore, SL safer mitochondria by increase MMP and suppresses phosphorylation of P13k/AKT/mTOR pathway, thereby regulating apoptotic signalling.
ConclusionOur findings indicate that SL showed protective effects against rotenone-induced OS, mitochondrial complex-I in neuronal cell damage, which suggests that SL might potentially serve as an anti-PD remedial candidate for PD treatment.
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Astaxanthin Alleviates Chronic Prostatitis via the ERK1/2 Signaling Pathway: Evidence from Network Pharmacology and Experimental Validation
Authors: Yifu Liu, Liang Huang, Zhicheng Zhang, Qiqi Zhu, Ping Xi, Ting Sun and Binbin GongAvailable online: 09 October 2024More LessBackgroundAstaxanthin (AST) has been widely recognized for its therapeutic potential in chronic inflammatory ailments. This study investigates the therapeutic efficacy and underlying mechanisms of AST in the management of chronic prostatitis (CP).
MethodsMale Sprague-Dawley (SD) rats were randomly divided into control, complete Freund's adjuvant (CFA), and CFA + AST groups. CFA was used to induce the CP model, and saline was used for the control group. Inflammation of the prostate was detected 28 days after oral administration of AST. qRT-PCR and ELISA were used to detect pro-inflammatory factors in RWPE-1 and WPMY-1 cells. Potential targets of AST for CP were explored by network pharmacology, and related proteins were detected by Western blotting.
ResultsOral administration of AST alleviated the increase in prostate stroma and reduced inflammatory cell infiltration in CP rats. The IC50 of AST-treated RWPE-1 and WPMY-1 cells for 48 h were 171 and 212.1 μM, respectively. AST pretreatment reduced IL-6 and IL-8 expression in these cells. PPI network, GO, and KEGG enrichment analyses suggested that the anti-inflammatory effect of AST was associated with the ERK1/2 pathway. Western blotting showed that AST inhibited ERK1/2 phosphorylation. In addition, AST and ERK1/2 pathway inhibitors (U0126) synergistically inhibited LPS-induced inflammation in prostate cells.
ConclusionOur study identified the potential of AST in the treatment of CP. However, subsequent randomized controlled trials are needed to validate its clinical efficacy.
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Label-Free Detection of Biomolecular Interactions Using BioLayer Interferometry for Kinetic Characterization
Authors: Joy Concepcion, Krista Witte, Charles Wartchow, Sae Choo, Danfeng Yao, Henrik Persson, Jing Wei, Pu Li, Bettina Heidecker, Weilei Ma, Ram Varma, Lian-She Zhao, Donald Perillat, Greg Carricato, Michael Recknor, Kevin Du, Huddee Ho, Tim Ellis, Juan Gamez, Michael Howes, Janette Phi-Wilson, Scott Lockard, Robert Zuk and Hong Tan
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