Genes adaptability and NOL6 protein inhibition studies of fabricated flavan-3-ols lead skeleton intended to treat breast carcinoma

Network pharmacology and AI in cancer research uncovering biomarkers and therapeutic targets for RALGDS mutations

The lack of target therapies is accountable for the higher mortality of various types of cancer. To address this issue, we selected a target mutated Kirsten rat sarcoma virus oncogene homologue, which plays a significant role in various cancers. Our study aims to identify selective biomarkers and develop diagnostic and therapeutic strategies for KRAS-associated genes using artificial intelligence. Initially, Genomic data, cancer epidemiology, proteomics network interactions, and omics enrichment were analyzed. Structured E-pharmacophore model aided in capturing the binding cavity using eraser algorithms and fabricating a new selective lead compound for the KRSA. The selective molecule was abridged inside the binding cavity and stability was validated through 100 ns molecular dynamics simulations. Epidemiological-neural network studies indicated KRAS mutations leads 40 types of cancer, exclusively pancreatic and colorectal cancers, with diploid and missense mutations as primary factors. Pathway analysis highlighted the involvement of the MAPK and RAS signaling pathways in cancer development and proteomics analysis identified RALGDS as a key protein. Protein-based pharmacophore analysis mapped the biologically active features such as donor, acceptor and aromatic ring with the designed ligands. The results of interaction interpretation illustrate that the amino acid Tyr566 formed an H-bond interaction with the amine group of the octyl ring system and 20 amino acids crafted to properly orient the molecule to fit inside the polar cavity of KRAS protein. The MMGBSA score of - 53.33 kcal/mol conformed to the well-configured binding with KRSA and realistic model simulation exposed the π-π, π-cationic and hydrophobic interactions stabilised the molecule inside the KRSA protein throughout 100 ns simulation. The study demonstrates the vitality of AI and network pharmacology to identify potential-target biomarkers for KRAS-associated genes, paving the way for improved cancer diagnostics and therapeutics.

NOL6 Promotes Tumor Progression by Facilitating Cancer Cell-Induced Platelet Aggregation and Angiogenesis in Breast Cancer

BACKGROUND

Breast cancer (BC) is a prevalent malignancy among women, and numerous investigations have reported that platelet aggregation may play a role in BC progression. Thus, identifying new targets for BC is essential. In this regard, we focused on nucleolar protein 6 (NOL6), located on chromosome 9p13, which is implicated in tumor development.

OBJECTIVE

To investigate NOL6 expression in BC, examine its role in platelet aggregation and angiogenesis, and elucidate the underlying mechanisms.

METHODS

Bioinformatic analyses, immunoblotting, and quantitative real-time polymerase chain reaction (qPCR) were performed to assess NOL6 expression in BC. Cell counting kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assays were conducted to determine the impact of NOL6 on BC cell proliferation. Immunostaining, enzyme-linked immunosorbent assay (ELISA), and flow cytometry (FCM) assays were utilized to analyze the effects of NOL6 on platelet aggregation. Tube formation and transwell assays were performed to examine angiogenesis and invasion, immunoblot assays were used to confirm the underlying mechanisms, and tumor growth assays in mice were conducted to validate the findings in vivo.

RESULTS

NOL6 was found to be highly expressed in BC and was associated with patient prognosis, platelet aggregation, and angiogenesis. Its knockdown inhibited BC cell proliferation and reduced platelet aggregation induced by BC cells. Additionally, NOL6 depletion impaired angiogenesis and migration of BC cells. In vivo studies confirmed that NOL6 promotes tumor growth. Mechanistically, NOL6 enhances the Twisted spiral transcription factor 1 (Twist1)/galectin-3 axis, contributing to BC progression.

CONCLUSIONS

NOL6 can promote tumor progression by facilitating platelet aggregation and angiogenesis in BC cells through the Twist1/galectin-3 axis.

Investigating the toxicity of malachite green and copper sulfate in brine shrimp: In-vivo and computational study

Colour is crucial for enhancing the appetizing value and consumer acceptance of food products. The commonly used food colourants and food preservatives such as Malachite Green (MG) and Copper Sulfate (CS) can cause severe health problems. This study investigates the toxicity of these food-grade colourants through acute exposure using in vivo cytotoxicity using the brine shrimp model including 3D surface analysis (3DSA) and in-silico studies Brine shrimp were treated with various concentrations of MG and CS. The cytotoxic effect was confirmed by brine shrimp lethality assay and 3DSA. Molecular docking and Molecular Dynamic simulation were done using hAChE binding cavity. Results showed that concentrations (2.5-10 µg/ml) of MG and CS significantly decreased locomotor behaviour within 1 h, while higher concentrations (10-100 µg/ml) caused high mortality rates. Morphological studies revealed that there is a significant reduction (p<0.05) in shrimp length treated with MG and CS. The 3DSA indicates that there is an inappropriate surface of the shrimp morphology. Interestingly, MG-treated shrimps had shown significant inhibition of AChE in homogenates, indicating cholinergic nerve-mediated toxicity. Computational studies showed MG confined active binding with human acetylcholinesterase (hAChE), with a binding energy MMGBSA of -51.3 kcal/mol. MD simulation confirmed reversible binding stability inside the hAChE pocket. It can be concluded that acute exposure to brine shrimps with MG and CS exhibited cytotoxicity as evidenced by the increase in mortality of the shrimps. This study further warrants the investigation of MG and CS residues from commonly used fruits and vegetables and their putative toxic effect using in-vivo studies.

Exploring acetylation-related gene markers in polycystic ovary syndrome: insights into pathogenesis and diagnostic potential using machine learning

OBJECTIVE

Polycystic ovary syndrome (PCOS) is a prevalent cause of menstrual irregularities and infertility in women, impacting quality of life. Despite advancements, current understanding of PCOS pathogenesis and treatment remains limited. This study uses machine learning-based data mining to identify acetylation-related genetic markers associated with PCOS, aiming to enhance diagnostic precision and therapeutic efficacy.

METHODS

Advanced machine learning techniques were used to improve the precision of key gene identification and reveal their biological mechanisms. Validation on an independent dataset (GSE48301) confirmed their diagnostic value, assessed through ROC curves and nomograms for PCOS risk prediction. Molecular mechanisms of acetylation-related gene regulation in PCOS were further examined through clustering, immune-environmental, and gene network analyses.

RESULTS

Our analysis identified 15 key acetylation-regulated genes differentially expressed in PCOS, including SGF29, NOL6, KLF15, and INO80D, which are relevant to PCOS pathogenesis. ROC curve analyses on training and validation datasets confirmed the model's high diagnostic accuracy. Additionally, these genes were associated with immune cell infiltration, offering insights into the inflammatory aspect of PCOS.

CONCLUSION

The identified acetylation gene markers offer novel insights into the molecular mechanisms underlying PCOS and hold promise for enhancing the development of precise diagnostic and therapeutic strategies.

Role of MARK2 in the nervous system and cancer

Microtubule-Affinity Regulating Kinase 2 (MARK2), a member of the serine/threonine protein kinase family, phosphorylates microtubule-associated proteins, playing a crucial role in cancer and neurodegenerative diseases. This kinase regulates multiple signaling pathways, including the WNT, PI3K/AKT/mTOR (PAM), and NF-κB pathways, potentially linking it to cancer and the nervous system. As a crucial regulator of the PI3K/AKT/mTOR pathway, the loss of MARK2 inhibits the growth and metastasis of cancer cells. MARK2 is involved in the excessive phosphorylation of tau, thus influencing neurodegeneration. Therefore, MARK2 emerges as a promising drug target for the treatment of cancer and neurodegenerative diseases. Despite its significance, the development of inhibitors for MARK2 remains limited. In this review, we aim to present detailed information on the structural features of MARK2 and its role in various signaling pathways associated with cancer and neurodegenerative diseases. Additionally, we further characterize the therapeutic potential of MARK2 in neurodegenerative diseases and cancer, and hope to facilitate basic research on MARK2 and the development of inhibitors targeting MARK2.