Search Results (298)

Background: Lung cancer has the highest morbidity and mortality of all tumors, and the development of TKI drugs targeting EGFR activating mutations has brought lung cancer treatment into the targeted era. In view of their low efficacy and susceptibility to drug resistance, there is an urgent need to find strategies to increase their efficacy and reduce the incidence of drug resistance. Methods: In this study, we examined the distribution and probability of EGFR mutations in non-small cell lung cancer patients in the cBioPortal database and compared the survival prognosis of patients with normal and abnormal EGFR, NSCLC patients treated with and without TKI, and NSCLC patients with different EGFR gene copy numbers. We established a mouse lung cancer model and examined the histomorphological characteristics of lung tissues via hematoxylin and eosin staining. Additionally, changes in the copy number of the EGFR gene and its protein expression levels were detected using RT-qPCR and Western blotting. Furthermore, we quantified the concentration of the EGFR protein using ELISA. Results: We found no significant advantage of EGFR-TKI therapy over first-line chemotherapeutic agents in patients with EGFR-abnormal NSCLC. The reason for this may be related to the abnormal EGFR gene copy number; the higher the copy number increases, the worse the survival prognosis of the patients. In molecular biology experiments, we demonstrated that ginsenoside Rg3 down-regulated the copy number of 18, 19, 20, and 21 exons and protein expression of EGFR in lung adenocarcinoma cells. The results of in vivo pharmacodynamic assays confirmed that sequential administration of ginsenoside Rg3 with TKI drugs could achieve a gainful complementary effect. Conclusions: Ginsenoside Rg3 down-regulates the copy number of EGFR important exons in EGFR-mutant cells of lung adenocarcinoma and reduces EGFR protein expression, thus providing a high gainful complementary effect in combination with EGFR-TKI. Full article

The relationship between protein structure and function is intrinsically interconnected, as the structure of a protein directly determines its functional properties. To investigate the effects of temperature and pressure on protein function, this study employed ethyl carbamate (EC) hydrolase as a model food enzyme and conducted molecular dynamics (MD) simulations under varying temperature and pressure levels to elucidate its structure–function relationship. By systematically analyzing the dynamic changes in root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bonding, catalytic pocket conformation, and packing density under different temperature and pressure conditions, we revealed the structural adaptability of EC hydrolase. Furthermore, we analyzed the characteristics of EC hydrolase using molecular dynamics simulations with temperature and pressure levels, as well as conformational bias-based computer-aided engineering, providing both theoretical and experimental foundation for the adaptability mechanisms of enzymes under extreme conditions. Full article

As consumer demand for quality fish products continues to rise, quality has become a key factor in market competition. Ecological aquaculture research is exploring various farming methods to balance high-quality demand with environmental protection. This study compared three aquaculture models—cage culture (CG), recirculating aquaculture (RAG), and rice–fish co-culture (RG)—by analyzing muscle quality (AOAC, GC-MS), intestinal microbiota (16S rRNA), and liver metabolism (LC-MS) to assess their effects on M. albus. In terms of muscle quality, the RG group showed increased levels of EPA and DHA, reduced muscle moisture and crude lipid content, and enhanced crude protein accumulation. The crude protein content was significantly higher in the RAG group than in the CG group (p < 0.05). The RG group also had the highest levels of total, essential, and umami amino acids, followed by the RAG and CG groups. In terms of intestinal microbiota, the RG group had the highest microbial diversity and stability, with increased abundance of Firmicutes and Bacteroidetes and decreased levels of Proteobacteria. Compared to the CG, the RAG group also showed increased microbial diversity and a reduction in pathogenic genera. Liver metabolomics analysis demonstrated that the RG group had significant advantages over the CG group in amino acid, lipid, and energy metabolism. The RAG group exhibited upregulation of glycerophospholipid metabolism and a decrease in oxidative stress marker levels. Overall, the RG group enhanced muscle quality and optimized intestinal and liver metabolism in M. albus. Full article

Background: Obesity is characterized by a chronic state of low-grade inflammation. Investigating immune-critical genes and their biological functions in the adipose tissue of postmenopausal obese women is crucial for elucidating the underlying mechanisms of immune dysregulation associated with obesity. Methods: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE176171) datasets were obtained from the Gene Expression Omnibus (GEO). For microarray data analysis, weighted gene co-expression network analysis (WGCNA), protein–protein interaction network (PPI) analysis, and immune infiltration analysis (ssGSEA) were employed to identify obesity-related immune-critical genes. Subsequently, the candidate genes were validated using scRNA-seq data to explore their expression patterns at the single-cell level. Finally, the expression levels of these immune-critical genes were experimentally verified in adipose tissue from obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data through WGCNA, PPI and ssGSEA identified 16 obesity-related immune-critical genes, including IL7R, CD3E, CD2, CCR5, CD3D, MS4A1, TRAT1, SLAMF8, CCL3L1, SPP1, CCL5, IL2RG, CD3G, TLR8, ITK, and CCL3. Differential expression of SPP1, ITK and CCL5 was confirmed in scRNA-seq data, with ITK and CCL5 showing distinct expression patterns in natural killer (NK) cells. Furthermore, RT-qPCR analysis revealed upregulation of SPP1 and ITK in adipose tissue of obese zebrafish compared to lean controls. Conclusions: This study identifies SPP1, ITK and CCL5 as key immune hub genes in the adipose tissue of postmenopausal obese women, with NK cells playing a significant role in adipose tissue inflammation through the expression of these genes. These findings provide novel insights into potential therapeutic targets for the prevention and treatment of obesity in postmenopausal women. Full article

Background/Objectives: Pomegranate (Punica granatum) peel, often discarded as waste, contains abundant bioactive compounds such as polyphenols, vitamins, flavonoids, tannins, anthocyanins, and many more. This contributes to remarkable bioactivities, including anticancer, anti-inflammatory, antioxidant, antibacterial, and antifungal properties. Pancreatic cancer is a deadly cancer with a 9% survival rate. Its aggressiveness, invasiveness, quick metastasis, and poor prognosis significantly decrease the survival rate. Thus, we aim to explore pomegranate peel as a possible alternative medication for treating pancreatic cancer through virtual methods. Methods: Firstly, bioactive compounds were collected from multiple databases and screened for oral bioavailability (OB) ≥ 0.3 and drug likeness (DL) ≥ 0.18 scores. Simultaneously, network pharmacology was employed to extract the most probable targets for pancreatic cancer. Further computational analyses were performed, including molecular docking, molecular dynamics simulation, and in silico pharmacokinetics evaluation. Results: Consequently, the top 10 key targets from network analysis were AKT1, IL6, TNF, SRC, STAT3, EGFR, BCL2, HSP90AA1, HIF1A, and PTGS2. However, only AKT1, EGFR, BCL2, HSP90AA1, and PTGS2 exhibited strong binding affinities with pomegranate compounds, which are significantly declared in affected cells to enhance cancer progression. Outcomes from molecular dynamics simulations, particularly RMSD, RMSF, hydrogen bonding, and radius of gyration (Rg), confirmed stable interactions between 1-O-Galloyl-beta-D-glucose, epicatechin, phloridzin, and epicatechin gallate with respective target proteins. Conclusions: This suggests that pomegranate peels hold anticancer bioactive compounds for treating pancreatic cancer. Surprisingly, most compounds adhere to Lipinski’s and Pfizer’s rules and display no toxicity. However, as this study relies entirely on computational methods, experimental validation is necessary to confirm these findings and assess real-world efficacy and potential side effects. Full article

Objective: Study the mechanism of ginsenoside Rg₁ in ameliorating hyperuricemia (HUA) induced by high-purine diet. Methods: Rats were randomly divided into groups, and the HUA model was established by administering a high-purine diet containing potassium oxonate combined with yeast. After the experiment, blood was collected via cardiac puncture, and the organ indices of the rats were calculated. Serum biochemical markers including aspartate aminotransferase (AST), alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), xanthine oxidase (XOD), creatinine (CREA), uric acid (UA), and blood urea nitrogen (BUN) were measured. Histopathological sections of the kidney and intestine were prepared. Western blot was used to assess the expression levels of intestinal occludin and zonula occludens-1 barrier proteins and key proteins in IL-17/NF-κB inflammatory pathways. After the experiment, fecal samples were collected from the rats. The gut microbiota of HUA-induced rats was analyzed via 16S rRNA sequencing, and the levels of short-chain fatty acids in the fecal samples were quantified using gas chromatography–mass spectrometry. Results: Ginsenoside Rg₁ significantly increased body weight and organ indexes as well as reduced serum levels of BUN, CREA, ALT, AST, XOD, and UA. Pathologic analysis showed that ginsenoside Rg₁ improved renal cell injury, glomerulosclerosis, and renal interstitial fibrosis while restoring intestinal barrier function. Ginsenoside Rg₁ down-regulated the expression of inflammatory proteins and up-regulated the levels of intestinal barrier proteins. The results of 16S rRNA sequencing showed that ginsenoside Rg₁ significantly increased the diversity index of gut microbiota and enhanced the number of beneficial bacteria in HUA rats. Short-chain fatty acids analysis demonstrated that ginsenoside Rg₁ markedly elevated the levels of acetate, propionate, butyrate, and valerate in HUA rats. Conclusions: Ginsenoside Rg₁ ameliorates and treats HUA by improving the composition of intestinal flora and inhibiting the IL-17/NF-κB signaling pathway to reduce inflammatory factors in the intestinal tract in HUA rats. Full article

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by rapid progression, high metastatic potential, and limited therapeutic options. Lysine-specific demethylase 1 (LSD1) has been identified as a promising epigenetic target in SCLC. RG6016 (ORY-1001) is a selective LSD1 inhibitor currently under clinical investigation for its antitumor activity. In this study, publicly available RNA-Seq datasets from SCLC patient-derived xenograft (PDX) models treated with RG6016 were reanalyzed using bioinformatic approaches. Differential gene expression analysis was conducted to identify genes responsive to LSD1 inhibition. Candidate genes showing significant downregulation were further evaluated by molecular docking to assess their potential interaction with RG6016. The analysis identified a set of differentially expressed genes following RG6016 treatment, including notable downregulation of MYC, UCHL1, and TSPAN8. In silico molecular docking revealed favorable docking poses between RG6016 and the proteins encoded by these genes, suggesting potential direct or indirect targeting. These findings support a broader mechanism of action for RG6016 beyond its known interaction with LSD1. This study demonstrates that RG6016 may exert its antitumor effects through the modulation of additional molecular targets such as MYC, UCHL1, and TSPAN8 in SCLC. The combined bioinformatic and molecular docking analyses provide new insights into the potential multi-target profile of RG6016 and indicate the need for further experimental validation. Full article

African Swine Fever Virus (ASFV) Topo II ATPase domain, resistant to conventional inhibitors (e.g., ICRF-187) due to M18/W19 steric clashes, was targeted via hierarchical virtual screening (Schrödinger) of the Chembridge library combined with MM/GBSA calculations. Five ligands (10012949, 40242484, 46712145, 15880207, and 33688815) showed high affinity, with 46712145 adopting symmetrical π–π stacking, hydrogen bonds, and alkyl interactions to bypass steric hindrance. Molecular dynamics simulations (100 ns) revealed ligand-induced flexibility, evidenced by elevated RMSD/Rg values versus the free protein. DCCM analysis highlighted enhanced anti-correlated motions between GHKL motifs and sensor domains in chain B/C, suggesting stabilization of a non-catalytic conformation to inhibit ATP hydrolysis. Free energy landscape (FEL) analysis showed 46712145 occupying a broad, shallow energy basin, enabling conformational adaptability, contrasting the narrow deep well of the free protein. This study proposes a symmetric ligand design strategy and conformational capture mechanism to block ATPase activity. Compound 46712145 demonstrates stable binding and dynamic regulation, providing a novel lead scaffold for anti-ASFV drug development. These findings establish a structural framework for combating ASFV through targeted ATPase inhibition. Full article

Rehmannia glutinosa (RG), a fundamental herb in traditional Chinese medicine belonging to the Orobanchaceae family, has been widely used for centuries due to its diverse therapeutic properties, including promoting blood circulation, enhancing immunity, managing diabetes, reducing inflammation, and supporting kidney function. Despite its traditional significance, scientific studies on RG’s therapeutic mechanisms remain limited, and its underlying pharmacological pathways are not extensively elucidated. This study employed network pharmacology and molecular docking to identify RG’s active compounds and investigate their therapeutic potential in allergy, anemia, diabetes, and menopause. From an initial pool of 122 compounds, 50 bioactive compounds were screened based on bioavailability and drug-likeness, resulting in 40 active compounds and 11 target proteins closely associated with these conditions. Key active compounds identified included iridoid glycosides (rehmaglutin A, B, C, D, jioglutin A, B, C, jioglutolide) and other bioactive molecules such as caffeic acid, geraniol, 5-hydroxytryptamine, melatonin, and rhodioloside. Molecular docking technology was employed to verify the stable binding of target proteins with active compounds. Protein–protein interaction (PPI) analysis revealed that RG’s core target proteins are central to pathways regulating inflammation, cell survival, apoptosis, and immune response. Enrichment analyses demonstrated that RG’s target proteins intersect significantly with pathways including the AGE-RAGE signaling pathway in diabetic complications, IL-17, HIF-1 signaling, and neuroactive ligand-receptor interactions, all of which are essential in managing diabetes and menopause symptoms. These findings underscore RG’s multi-target therapeutic potential, particularly in modulating immunity, metabolism, and inflammation. This study highlights RG’s potential as a therapeutic agent and provides a framework for future research to further elucidate its mechanisms and support the development of targeted drugs based on RG’s active compounds. Full article

Both hepatitis B virus (HBV), an hepadnavirus with a DNA genome, and hepatitis A virus (HAV), a picornavirus, require the TRAMP-like host ZCCHC14-TENT4 complex for efficient replication. However, whereas HBV requires the nucleotidyltransferase activity of TENT4 to extend and stabilize the 3′ poly(A) tails of mRNA transcribed from its genome, the role played by TENT4 in HAV replication is uncertain. HAV proteins are synthesized directly from its genomic RNA, which possesses a 3′ poly(A) tail, with its length and composition presumably maintained by 3D^pol-catalyzed RNA transcription during its replicative cycle. Using nanopore long-read sequencing of RNA from infected cells, we confirm here that the length of the HAV 3′ poly(A) tail is not altered by treating infected cells with RG7834, a small molecule TENT4 inhibitor with potent anti-HAV activity. Despite this, TENT4 catalytic activity is essential for HAV replication. Surprisingly, nanopore sequencing revealed a low abundance of HAV subgenomic RNAs (hsRNAs) that extend from the 5′ end of the genome to a site within the 5′ untranslated RNA (5′UTR) immediately downstream of a stem-loop to which the ZCCHC14-TENT4 complex is recruited. These hsRNAs are polyadenylated, and their abundance is sharply reduced by RG7834 treatment, implying they are likely products of TENT4. Similar subgenomic RNAs were not identified in poliovirus-infected cells. hsRNAs are present not only in HAV-infected cell culture but also in the liver of HAV-infected mice, where they represent 1–3% of all HAV transcripts, suggesting their physiological relevance. However, transfecting exogenous hsRNA into TENT4-depleted cells failed to rescue HAV replication, leaving the functional role of hsRNA unresolved. These findings reveal a novel picornaviral subgenomic RNA species while highlighting mechanistic differences in the manner in which HAV and HBV exploit the host ZCCHC4-TENT4 complex for their replication. Full article

This study aimed to evaluate the heritability (h²) estimates of some important udder conformation traits, their relationship to each other and with production, and their phenotypic and genetic trends over a 10-year period in relatively high-yielding Holstein-Friesian cows. A total of 15,032 cows from six herds in Hungary were tested for milk (MY), butterfat (FY), and protein (PY) production yields over 305 days in first lactation. In addition, their udder conformation was scored for udder attachment (FU), rear udder height (RUH), central ligament (CL), udder depth (UD), front teat placement (FTP), and udder texture (UT) on a 1–9 linear udder score scale. REML and BLUP single-step animal model and linear regression model were used for data analysis and estimation. The production traits of the cows were quite reasonable, with 10,179.4 kg milk, 380.3 kg fat, and 333.1 kg protein in a standard lactation of 305 days. The scores of the udder conformation traits (5.4 to 6.1) were slightly above the mean of 5 on a linear scale of 1–9. The h² for MY, FY, and PY were obtained from 0.30 to 0.35, while those for udder traits were from 0.22 to 0.41. Phenotypic (r_p) and genetic (r_g) correlations for the relationship between production and udder conformation were weak or negligible (ranged from −0.33 to +0.15). Most of the associations between different udder traits were generally weak, but moderate positive correlations were observed between FU and UD (r_p = 0.42, r_g = 0.50 or 0.57), and between FU and UT (r_p= 0.36, r_g = 0.33 or 0.35). There were increasing genetic trends in the milk production (b = 2.2 to 16.5), but the studied udder conformation traits did not change over time (b = 0.00 to 0.03). In our study, despite an increase in milk yield over the studied ten-year period, udder conformation traits did not change. Therefore, considering that udder conformation scores were slightly above average and that udder traits were included in the selection index, we believe that it may be necessary to reconsider the udder conformation scoring system and its inclusion in the selection index. Full article

This study investigated whether ginsenoside Rg₁ (G-Rg₁) alleviated acute gouty arthritis (AGA) in rats by modulating the TLR4/NLRP3 pathway and neutrophil extracellular trap (NET) formation. Rats were orally administered G-Rg₁ or colchicine (Col) for 7 days, and monosodium urate (MSU) was injected into the ankle joints on day 5 to induce AGA. Joint swelling, histopathology (HE staining), and serum markers (MPO, NE, MPO-DNA, IL-6, IL-1β; ELISA) were assessed at the baseline and 6–36 h post-modeling. Western blot and immunofluorescence analyzed the NET-related and TLR4/NLRP3 pathway proteins in synovial tissue. G-Rg₁ significantly reduced ankle swelling and synovial inflammation compared with the AGA group, lowered the serum IL-6, IL-1β, MPO, NE, and MPO-DNA levels, and suppressed NET-associated protein expression. Mechanistically, G-Rg₁ downregulated TLR4/NLRP3 pathway activation in synovial tissue. These findings suggest that G-Rg₁ mitigates AGA by inhibiting TLR4/NLRP3 signaling, thereby reducing inflammatory cytokine release and NET formation. Full article

Background/Objectives: Ginseng has been a traditional remedy for centuries, known for its diverse benefits such as anti-inflammation, antioxidant, bactericidal, fungicidal antidiabetic, and anticancer effects. This study employs a network pharmacology approach with molecular dynamics simulation to investigate the potential mechanisms through which ginseng-derived compounds control hypertension. Methods: The total of 70 bioactive compounds were identified from the literature and classified as ginsenosides, which fall under Protopanaxadiol-type ginsenosides, Protopanaxatriol-type ginsenosides, and Ocotillol-type saponins. The target proteins related to hypertension were collected from the drug bank, and interactions between proteins network were examined using STRING 12.0 and Cytoscape 3.10.1. Bioinformatics tools were used to analyze the biological enrichment of genes. The core targets extracted through network pharmacology were subjected to molecular docking studies. Similarly, the docking score below −6.0 kcal/mol was further visualized by performing molecular dynamics simulation to see the binding affinity between the complexes. Finally, pharmacokinetics and toxicity of the compounds were evaluated using computational tools. Results: Molecular docking and simulation results revealed that Floralquinquenoside C, Ginsenoside Rg6, Notoginsenoside T1, and Floralquinquenoside B exhibited strong binding and stability with Angiotensin-converting enzyme (ACE) and Carbonic Anhydrase-I (CA-I), which alters the renin–angiotensin system, calcium signaling pathway, adrenergic signaling in cardiomyocytes, c-GMP-PKG signaling pathway, etc., to regulate high blood pressure. Conclusions: The results show that the phytochemicals from ginseng could act as potential candidates for the management of hypertension, which may help minimize the side effects caused by synthetic anti-hypertensive drugs available on the market. Full article

The Regulator of G Protein Signaling 14 (RGS14) knockout (KO) mouse is a model of healthful longevity, i.e., its lifespan is prolonged and demonstrates enhanced exercise performance and protection against heart disease and hypertension. In this investigation, we found the RGS14 KO mouse is also protected against obesity and glucose intolerance by promoting a low white adipose tissue (WAT) phenotype with increased brown adipose tissue (BAT). This was confirmed by lower body weight, lower white adipocyte size, increased metabolism and improved glucose tolerance and insulin sensitivity. Upon examination of the white adipose tissue, RGS14 KO exhibited increased expression of “beiging” genes as well as significant increase in Uncoupling protein-1 (UCP-1) expression. The mechanism behind this protection was due to its unique brown adipose tissue. This was determined by BAT transplantation, which led to a reversal of phenotype, such that RGS14 BAT recipients developed protection similar to intact RGS14 KO mice, and the RGS14 KO BAT donors lost their protection. Thus, two novel mechanisms mediating obesity and glucose intolerance were found, i.e., inhibition of RGS14 and its BAT. Full article

Non-Small Cell Lung Cancer (NSCLC) is the most typical kind of lung cancer. Chemotherapy, radiation therapy, and other traditional cancer therapies are ineffective. Advancements in understanding cancer’s molecular causes have led to targeted therapies, such as those addressing NTRK gene fusions in NSCLC. Several machine-learning techniques were used in our work, including k-Nearest Neighbors (kNN), Support Vector Machine (SVM), Random Forest (RF), and Naive Bayes (NB). As a result, the RF model outperformed the other studied machine-learning methods, achieving an astonishing 93.12% accuracy for both training as well as testing datasets, and it was employed to screen 9000 chemicals, resulting in the discovery of 65 putative NTRK potential inhibitors. The active sites of NTRK proteins were then docked with these 65 active chemicals. Our findings show that Gancaonin X, 5-hydroxy-2-(4-methoxyphenyl)-8,8-dimethyl-2,3-dihydropyrano[2,3-h]chromen-4-one, (2S)-7-[[(2R)-3,3-dimethyloxiran-2-yl]methoxy]-5-hydroxy-2-phenyl-2,3-dihydrochromen-4-one, (2S)-5-hydroxy-2-(4-methoxyphenyl)-8,8-dimethyl-2,3-dihydropyrano[2,3-h]chromen-4-one, and methyl 2-(methylamino)-5-[(3S)-1,2,3,9-tetrahydropyrrolo[2,1-b]quinazolin-3-yl]benzoate establish strong interactions inside the binding region of NTRK, as a result of which stable complexes are formed. This study employs 100 ns molecular dynamics simulations to investigate the dynamic behavior of phytochemical-NTRK complexes, revealing stable interactions through RMSD, RMSF, Rg, and SASA analyses. The detailed examination of protein–ligand interactions provides crucial atomic-level insights, enhancing our understanding of potential neurotrophic receptor kinase-targeted therapeutic strategies. This highlights their significant ability as NTRK antagonists, giving novel treatment options for NSCLC therapy. To summarize, the application of machine learning in combination with virtual screening in this study not only can discover new NSCLC therapeutics but also highlight new computer approaches in the field of drug discovery. Full article