Combinatorial chemistry & high throughput screening最新文献

Introduction: DNA microarray synthesis enables the large-scale and precise generation of DNA sequences for genomic research, data storage, and synthetic biology. However, the order of nucleotide addition significantly affects synthesis efficiency and accuracy. This study aims to model DNA microarray in situ synthesis as a traveling salesman problem (TSP) and to develop an optimized synthesis strategy.

Methods: A mathematical model for in situ microarray synthesis was established, and both greedy algorithms and a simulated annealing algorithm were applied to optimize the nucleotide addition order. The performance of these approaches was evaluated by comparing the number of synthesis cycles required at different sequence scales, ranging from 10 × 10 nt to 10000 × 120 nt arrays.

Results: The optimized synthesis schemes effectively reduced the total number of synthesis cycles. At the 10 × 10 nt scale, simulated annealing reduced cycles by 40.65% compared to the traditional scheme and by 8.52% compared to the greedy algorithm. At larger scales (100 × 100 nt to 10000 × 120 nt), cycle reductions ranged from 33.80% to 37.26%, with simulated annealing outperforming the greedy algorithm by 2.68% to 3.42%. These reductions translated into significant savings in synthesis time, reagent consumption, and overall cost.

Discussion: The simulated annealing-based optimization strategy demonstrates clear advantages in improving DNA microarray synthesis efficiency while reducing material usage and waste, thereby enhancing cost-effectiveness. Such improvements offer practical benefits for applications, including gene editing, drug development, and DNA data storage.

Introduction: The aim of this study was to investigate the potential mechanisms and therapeutic effects of Total Flavonoids of Drynaria roosii Nakaike (TFRD) on osteoporotic rats following ovariectomy, through modulation of the stromal cell-derived factor-1 (SDF-1)/CXC chemokine receptor 4 (CXCR4) axis.

Methods: Ovariectomized (OVX) osteoporotic rat models were established and treated with TFRD. The effects of TFRD on Bone Mineral Density (BMD), bone microarchitecture, and the expression of genes and proteins related to the SDF-1/CXCR4 axis in rat lumbar vertebrae were assessed using BMD measurement, bone histomorphology analysis, and molecular biology techniques.

Results: In the TFRD treatment group, lumbar spine BMD significantly increased, and trabecular structure improved. Further mechanistic studies revealed that TFRD regulated SDF-1 expression, thereby promoting its binding to the CXCR4 receptor and, in turn, enhancing migration, homing, and osteogenic differentiation of BMSCs. These changes ultimately led to increased bone formation and decreased bone resorption, improving symptoms of osteoporosis.

Discussion: This study provides novel insights into the molecular mechanism of TFRD gene therapy in OVX osteoporosis rats by elucidating its involvement through the SDF-1/CXCR4 axis and BMSCs-mediated osteogenic differentiation.

Conclusion: These findings serve as a solid experimental and theoretical foundation for developing new anti-osteoporosis drugs. Furthermore, due to its natural plant extract origin, TFRD shows promising clinical application potential and requires further comprehensive investigation.

Introduction: Endometriosis (EMs), a prevalent disorder characterized by pelvic pain and infertility, affects numerous bodily systems and markedly diminishes life quality. Yiqi Huoxue formula (YQHXF) has demonstrated promising therapeutic efficacy. However, its active substances and underlying mechanisms remain ambiguous.

Methods: An innovative methodological framework incorporating NP, transcriptomics, proteomics, and molecular biology was utilized to investigate the active components and mechanisms of YQHXF. A network pharmacological analysis was conducted to identify the targets, biological processes, and pathways associated with YQHXF's effects on EMs. Additionally, transcriptomics, proteomics, and molecular biology techniques were applied for further mechanistic exploration at both the gene and protein levels.

Results: The findings suggest that YQHXF prevents EMs by modulating critical cellular processes- proliferation, invasiveness, adhesion, and apoptosis-within ectopic endometrial cells. The integration of network pharmacology, multi-omics, and molecular biology confirmed that this regulation occurs via key targets (EGFR, AKT1, FOS, MAPK3, NFKB1) and associated pathways.

Discussion: This study employed an integrated approach combining transcriptomics, proteomics, and molecular biology to analyze the effects of YQHXF on EMs. A total of 180 direct targets, 128 indirect targets, and 19 pathways related to YQHXF's anti-EMs effects were preliminarily identified. Based on these findings, it is proposed that YQHXF potentially achieves its remedial outcomes by influencing the proliferation, invasiveness, adhesion, and apoptosis of ectopic endometrial cells through the regulation of EGFR, AKT1, FOS, MAPK3, and NFKB1.

Conclusion: The findings suggest that YQHXF prevents EMs by regulating critical cellular processes, including the proliferation, invasiveness, adhesion, and apoptosis of ectopic endometrial cells.

Introduction: Shikonin, a traditional Chinese medicine monomer, exhibits potential anticancer activity. An expanding body of literature indicates that targeting ferroptosis signaling pathways can elicit antitumor effects in HCC. However, it remains unclear whether shikonin inhibits HCC by inducing ferroptosis. This study aimed to verify the anticancer effect of shikonin on HepG2 cells and elucidate its underlying mechanisms and specific therapeutic targets through an integrative approach combining network pharmacology, bioinformatics, and experimental validation.

Methods: HCC, shikonin targets, and ferroptosis-related genes were retrieved from public databases and their intersection genes were identified. PPI network and enrichment analysis were used to identify them, and "cellular response to metal ion" was a highly enriched GO biological process. Molecular docking was conducted to evaluate the binding affinity between shikonin and candidate targets, followed by in vitro validation. We also constructed a prognostic nomogram via multivariate Cox regression to estimate 1-, 3-, and 5-year overall survival.

Results: We obtained a total of 12 intersecting genes. AURKA, identified as a hub gene, showed direct binding to shikonin via molecular docking, pointing to its therapeutic targeting potential for shikonin in HCC. Validation experiments showed shikonin induced ferroptosis and inhibited proliferation in HepG2 cells, accompanied by AURKA downregulation at both mRNA and protein levels. After prognostic model construction, validation experiments confirmed that the nomogram accurately predicted survival outcomes in HCC patients.

Discussion: This study explores the therapeutic potential of shikonin in inducing ferroptosis for treating hepatocellular carcinoma (HCC). Through network pharmacology, molecular docking, and in vitro assays, AURKA was identified as a key target, demonstrating that shikonin inhibits HCC cell proliferation by triggering ferroptosis, which suggests a promising ferroptosis-based treatment strategy for HCC.

Conclusion: Together, shikonin exerts significant antitumor effects on HepG2 cells, and the underlying mechanism may involve targeting AURKA to induce ferroptosis.

Cyclin-Dependent Kinases (CDKs) are proteins that help control the cell cycle. They are considered potential targets for cancer treatment because they are often found at higher levels in cancer tissues than in normal tissues, and their presence is linked to survival rates in many cancer types. Cyclin- Dependent Kinase 1 (CDK1) is crucial for cell division and growth in cancer, as it significantly influences cell cycle progression through complexes formed with cyclins. Tumor growth can occur when CDK1 is deregulated, as its activation and phosphorylation of substrates are crucial for tumor development. Various small molecules that inhibit CDK1 have been developed and tested in preclinical studies, and some have progressed to human clinical trials. By inhibiting CDK1 activity, these drugs prevent it from changing other proteins and controlling the growth of cancer cells. Our study uses the STRING database, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Ontology (GO) analysis to reveal that CDK1 interacts with many proteins involved in cancer pathways. However, developing the best CDK1 inhibitors is challenging due to selectivity, potency, and cost, which are influenced by CDK1's structure and interactions with other proteins. This review explores the structure, function, regulation, mechanisms, and expression of CDK1, its crystal structure with various ligands, interactions with other proteins, and potential applications of CDK1 inhibitors. Future research, such as combination medicines, CRISPR, nanotechnology, and AI-driven methods and tools, should highlight their practical applications and provide a guide for efficient CDK1 discovery and drug development. Thus, this review emphasizes the significance of CDK1 targeting in cancer therapy, the difficulties in identifying potent inhibitors, and the ongoing research to enhance cancer treatment results by focusing on CDK1.

Introduction: Shikonin (SKN) is known for its anti-inflammatory effects; however, the molecular mechanisms underlying its therapeutic action in rheumatoid arthritis (RA) remain unclear. This study aimed to investigate the anti-inflammatory effects of SKN in RA using an integrative approach combining network pharmacology and experimental validation.

Methods: Potential targets for SKN and RA were identified using multiple databases and network pharmacology approaches. The overlapping targets were subsequently analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Meanwhile, a protein-protein interaction (PPI) network was constructed to screen for core targets. Molecular docking was performed to evaluate binding affinities between SKN and the core targets. In vitro, the effects of SKN on RA fibroblast-like synoviocytes (RA-FLSs) were assessed using MTT assays, ELISA, qRT-PCR, and Western blot analyses.

Results: We identified 194 potential targets for SKN and 942 targets associated with RA. Among these, 87 overlapping targets were considered potential targets of SKN against RA and were primarily involved in cytokine-mediated signaling pathways, regulation of inflammatory responses, and the PI3K-AKT and NF-κB signaling pathways. Nine core targets-AKT1, BCL2, CCL2, EGF, INS, MMP9, NFκB1, TNF, and TP53-were screened through protein-protein interaction (PPI) network analysis. Molecular docking revealed stable binding affinities between SKN and all nine core targets (< -5 kcal/mol). In vitro, SKN significantly inhibited RA fibroblast-like synoviocyte (RA-FLS) proliferation and reduced the production of IL-17, IL-8, TNF-α, MMP3, and MMP9 in a dose-dependent manner. Furthermore, SKN downregulated the mRNA expression of most core targets and suppressed the PI3K-AKT and NF-κB signaling pathways.

Discussion: This article offers a methodological framework for the future development of natural products with anti-RA properties, while also incorporating data and insights from recent studies on biologics and JAK inhibitors in RA treatment, to enhance the evidence base for SKN's role in managing RA. We believe that our research provides novel insights into the therapeutic potential of SKN for RA.

Conclusion: SKN has shown potential as a therapeutic agent for RA by acting on multiple core targets and signaling pathways.

Background: Damp retention in the middle-jiao syndrome (DRMS), a common manifestation in Traditional Chinese Medicine (TCM), results from stagnation of damp pathogens in the middle jiao and impaired transport of food and fluids. Given the complex pathogenesis of DRMS, this study aimed to investigate its biological mechanisms using an advanced analytical approach.

Methods: A DRMS rat model was established based on three etiological factors: dietary disorders, depletion of vital qi, and excessive external dampness. Model validity was assessed via small intestinal carbon propulsion rate and histopathological examination. Urine metabolomics, using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS), systematically characterized metabolic profile changes and potential biomarkers.

Results: DRMS rats exhibited significantly reduced small intestinal propulsion, along with varying degrees of edema, disorganized tissue structures, and inflammatory cell infiltration in gastric, renal, and small intestinal tissues. Metabolomic analysis identified 52 differential metabolites as potential DRMS biomarkers, primarily involved in phenylalanine, tyrosine, and tryptophan biosynthesis, phenylalanine and tyrosine metabolism, the citrate cycle, and cysteine and methionine metabolism pathways. Metabolic correlation networks further validated the model's accuracy.

Discussion: The identified metabolites and pathways provide insight into the mechanisms underlying DRMS, complement existing TCM research, and offer a foundation for further studies. However, the findings are currently limited to the rat model and require human validation.

Conclusions: This study successfully established a DRMS animal model under clinically relevant TCM conditions and demonstrated the utility of metabolomics in elucidating DRMS mechanisms, providing experimental evidence for TCM syndrome characterization and advancing understanding of its etiology.

Objective: Lingguizhugan Decoction (LGZGD), a traditional Chinese herbal prescription with recognized efficacy in heart failure, has an unclear mechanism against cardiac hypertrophy. This study investigated its protective effects against angiotensin II (Ang II)-induced cardiac hypertrophy and the role of the LITAF signaling pathway.

Methods: An in vivo mouse model of cardiac hypertrophy was established via continuous Ang II infusion. LGZGD was administered, and its effects on cardiac function, hypertrophy markers, and pathway proteins were evaluated using echocardiography, histopathology, and molecular techniques. In vitro, H9c2 cardiomyocytes were treated with Ang II to induce hypertrophy; LGZGD-containing serum was applied to assess the impacts on cell size, hypertrophic markers, and signaling pathways. LITAF expression in H9c2 cells was silenced via siRNA to validate its role in LGZGD-mediated anti-hypertrophy.

Results: LGZGD improved cardiac function, reduced cardiomyocyte size, and downregulated hypertrophic markers. It also upregulated LITAF protein expression and suppressed the phosphorylation of ASK1, JNK1/2, and p38 MAPK. LGZGD-containing serum inhibited Ang IIinduced H9c2 hypertrophy via activating LITAF and inhibiting the ASK1-JNK/p38 pathway. LITAF silencing reversed these anti-hypertrophic effects, confirming its pivotal role in mediating LGZGD's protective action.

Discussion: LGZGD alleviates cardiac hypertrophy by activating LITAF and inhibiting the ASK1-JNK/p38 pathway, identifying key therapeutic targets of this formula. These findings advance understanding of LITAF's non-inflammatory cardiovascular protective roles and provide insights into multi-target strategies for cardiac hypertrophy.

Conclusion: LGZGD attenuates Ang II-induced cardiac hypertrophy by activating the LITAF pathway and inhibiting the ASK1-JNK/p38 signaling cascade.

Introduction: This study aims to assess the therapeutic mechanisms of Zishen Yutai Pills (ZYP) in treating recurrent spontaneous abortion (RSA) using network pharmacology analysis and in vitro validation of the molecular pathways relating to angiogenesis.

Methods: An online database screening-based strategy was applied for chemical constituent and target screening-based strategy was applied for chemical constituent and target collection, as well as target prediction. Network pharmacological analysis was conducted using protein-protein interaction data. Molecular docking was further employed to validate the active components of ZYP and the central target proteins. The tube formation assay was conducted in human umbilical vein endothelial cells (HUVECs) with the intervention of active constituents in ZYP. The expression of vascular endothelial growth factor A (VEGFA) and protein kinase B (AKT1) in HUVECs was also quantified by Western Blot (WB).

Results: Network pharmacological analysis revealed 283 target genes by ZYP in the treatment of RSA. Through protein-protein interaction (PPI) and topological analyses, a total of 57 key targets were identified as exerting central roles. Molecular docking proved that quercetin, β-carotene, resveratrol, and atractylenolide I had strong binding to AKT1 and VEGFA. Elevated levels of AKT1 and VEGFA protein expression were observed in WB analysis following intervention with the active ingredient.

Discussion: The findings suggest that ZYP may ameliorate RSA by promoting angiogenesis at the maternal-fetal interface. Key active compounds were predicted to act via the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway, as demonstrated by molecular docking and cell-based assays.

Conclusion: This study illuminates the comprehensive therapeutic effects of ZYP in RSA treatment, providing a foundation for its further exploration.

Introduction: Chan-Hou-Kang-Gao (CHKG) is a classical traditional Chinese medicine (TCM) formula widely used to promote uterine involution and manage postpartum hemorrhage (PPH). However, the pharmacological basis and molecular mechanisms of CHKG in treating PPH remain largely unclear.

Methods: Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was employed to systematically identify the chemical constituents of CHKG. Network pharmacology was used to predict active compounds, potential targets, and relevant signaling pathways. Protein-protein interaction (PPI) analysis and molecular docking were performed to validate the interactions between key compounds and therapeutic targets.

Results: A total of 173 compounds were identified in CHKG, including flavonoids, triterpenoids, and phenolic acids. Integration with public databases revealed 67 common targets shared between CHKG-related compounds and PPH-related genes. Enrichment analysis suggested that CHKG may modulate pathways involved in inflammation, immune regulation, and vascular function. TNF, IL6, and PTGS2 were identified as potential key targets. Molecular docking and molecular dynamics (MD) simulations indicated stable binding of ursolic acid, asiatic acid, and kaempferol to these proteins.

Conclusions: This study provides a systems-level prediction of the mechanisms by which CHKG may exert therapeutic effects in PPH, particularly via inflammation- and coagulationrelated pathways. These findings generate mechanistic hypotheses; however, further in vitro or in vivo experimental validation is required to confirm bioactivity and clinical relevance.