Rana Abdullah Alghamdi

Alzheimer’s Disease (AD) is a multifactorial neurodegenerative disorder characterized by dysregulated kinase signaling, neuroinflammation, immune remodeling, and Blood–Brain Barrier (BBB) dysfunction. In this study, we applied an integrated systems pharmacology approach to investigate the therapeutic potential of resveratrol-derived phytochemicals in AD. Initially, nine structurally related stilbene derivatives were screened for Central Nervous System (CNS), drug-likeness, and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. Pterostilbene and desoxyrhapontigenin demonstrated superior lipophilicity, intestinal absorption, and predicted BBB permeability, prioritizing them for downstream analyses. Differential Gene Expression (DEG) analysis of the GSE85426 dataset identified 818 AD-associated genes, which were further explored using Weighted Gene Co-expression Network Analysis (WGCNA). Fourteen co-expression modules were constructed, with nine modules significantly correlated with the AD phenotype. Integrated overlap analysis combining compound targets, DEGs, curated AD databases, and WGCNA modules identified high-confidence therapeutic targets, highlighting Mitogen-Activated Protein Kinase (MAPK1) and MAPK3 as central hub genes. Functional enrichment analysis revealed dominant involvement of MAPK signaling, neurotrophin signaling, Toll-like receptor pathways, and synaptic vesicle regulation. Immune infiltration profiling demonstrated increased myeloid-associated signatures and subtle adaptive immune alterations in AD samples. Machine learning approaches, Support Vector Machine-Recursive Feature Elimination (SVM-RFE), Least Absolute Shrinkage and Selection Operator (LASSO), and Random Forest (RF), consistently identified Thymidine Phosphorylase (TYMP) as a robust peripheral biomarker candidate. Moreover, molecular docking demonstrated stable binding of resveratrol derivatives within a conserved hydrophobic pocket, with pterostilbene exhibiting the strongest binding affinity (−6.80 kcal/mol). Collectively, this multi-layered analysis suggests that resveratrol derivatives may exert therapeutic effects through coordinated modulation of kinase-driven signaling networks and neuroinflammatory pathways, supporting their potential as multi-target.

Colorectal cancer (CRC) progression involves complex mechanisms of invasion and metastasis. Claudin‑2 (CLDN2), a tight junction protein, has emerged as a key regulator paracellular permeability and its dysregulation is implicated in chronic inflammatory diseases and cancer. The present study aimed to determine the mechanisms by which CLDN2 deletion affects genes associated with motility and invasion of colon cancer cells. CRISPR/Cas9 was used to knock out CLDN2 in HCT116 cells. Subsequently, gene expression was analyzed using reverse transcription‑quantitative PCR and migratory capacity was assessed using wound healing assays. CLDN2 deletion led to the downregulation of genes associated with motility and metastasis, including zonula occludens‑1‑associated nucleic acid binding protein, N‑Myc downstream‑regulated gene 1, CLDN14, CLDN23, Bcl‑2, p53 and Bcl‑6, suggesting that CLDN2 supports pro‑migratory gene networks. These findings demonstrated that CLDN2 regulates metastatic gene expression in CRC. Although further mechanistic studies are warranted, the present study provided notable genetic and phenotypic evidence of the role of CLDN2 in promoting cancer cell migration and invasion, offering a potential foundation for future studies into its signaling interactions and therapeutic potential.

Alkaloids have garnered significant interest as potential anticancer agents. Vitamin D receptor (VDR) plays a role in preventing the progression of colorectal cancer (CRC) and may be a crucial mediator of the anticancer effects produced by certain alkaloids. The search for novel anticancer drugs that induce VDR expression and act through the VDR could improve the clinical outcomes of CRC patients. The anticancer and pro-apoptotic effects of coclaurine and reticuline were investigated using CRISPR/Cas9-edited VDR/knockout (KO) and wild-type (WT) CRC HCT116 cell lines. Western blotting, RT-qPCR, confocal microscopy, cell viability, scratch assays, and flow cytometry were employed to assess VDR expression and cellular localization, cell growth, wound-healing, cytotoxicity, apoptotic status, cell cycle progression, and VDR-mediated gene expression. Coclaurine and reticuline dose-dependently inhibited HCT116-WT cell viability, decreased wound-healing, and increased VDR nuclear localization and gene expression while downregulating the oncogenic genes SNAIL1 and SNAIL2. Both alkaloids induced late apoptosis in HCT116-WT cells, increased the cleavage of PARP and caspase-3, and upregulated Bax and TP53 while decreasing BCL-2. Both alkaloids caused HCT116-WT cell growth arrest in the S-phase, which is associated with cyclin A1 overexpression. Coclaurine and reticuline lost their anticancer effects in HCT116-VDR/KO cells. Docking studies revealed that both alkaloids occupied the VDR’s active site. These findings demonstrate that coclaurine and reticuline exert anti-CRC and pro-apoptotic activities via the VDR, suggesting them as natural therapeutic candidates. The use of in vivo CRC models is needed to validate the anticancer activities of coclaurine and reticuline.

Background: Colon cancer progression heavily relies on intricate mechanisms of invasion, metastasis, and migration. Tight junction protein Cldn2 has emerged as a potential regulator of these processes. This study aimed to elucidate the molecular mechanisms linking Clan2 deletion to gene expression changes related to motility, invasion, and metastasis in colon caner. Methods: CRISPR/Cas9-mediated knockout of human Cldn2 in HCT116 cells was conducted, and the resulting cells were compared to the wild-type cells using real-time PCR to analyze the expression of genes associated with invasion and metastasis. Results: Cldn2-KO resulted in a widespread downregulation of genes linked to motility, invasion, and metastasis, including ZONAB, NDRG1, Cldn14, Cldn23, Bcl2, , P53, and BCL-6. These findings suggest a potential regulatory role of Cldn2 in the expression of these genes, influencing colon cancer cell migration and spread. Conclusion: This study identified Claudin-2 as a crucial regulator of genes involved in colorectal cancer metastasis. Downregulation of these genes upon Claudin-2 deletion suggests its inhibitory role in cancer cell motility and invasion. Further investigation into the specific downstream signaling pathways mediated by Claudin-2 could pave the way for novel therapeutic strategies targeting metastasis inhibition.

Background: Colon cancer is a serious global health concern caused by genetic variability and abnormal signaling pathways, such as the epidermal growth factor receptor (EGFR) axis. Although EGFR is a well-known therapeutic target in colorectal cancer, its expression pattern and function in colon cancer are context dependent. Methods: This study used an integrated in silico technique that included transcriptome analysis, pathway enrichment, molecular docking, pharmacophore modeling, virtual screening, ADMET profiling, and molecular dynamics (MD) simulation to find and assess new small-molecule EGFR inhibitors. Results: TCGA data showed downregulated EGFR expression in colon cancer tissues, with no significant patient survival association. KEGG pathway analysis revealed EGFR's central role in oncogenic pathways like PI3K-Akt and MAPK. Molecular docking identified Encorafenib as a strong EGFR binder, serving as a template for pharmacophore generation. Virtual screening of ZINC database compounds identified ZINC103239230 as a top hit. ZINC103239230, a promising candidate for further development, demonstrated favorable ADMET properties and formed a stable complex with EGFR in a 100 ns MD simulation, indicating its potential as a therapeutic target in colon cancer. This strategy holds promises for accelerating drug development, reducing resistance, and promoting oncology customized treatment.

The claudin multigene family is associated with various aberrant physiological and cellular signaling pathways. However, the association of claudins with survival prognosis, signaling pathways, and diagnostic efficacy in colon cancer remains poorly understood.Methods: Through the effective utilization of various bioinformatics methods, including differential gene expression analysis, gene set enrichment analysis protein-protein interaction (PPI) network analysis, survival analysis, single sample gene set enrichment analysis (ssGSEA), mutational variance analysis, and identifying receiver operating characteristic curve of claudins in The Cancer Genome Atlas colon adenocarcinoma (COAD).Results: We found that: CLDN2, CLDN1, CLDN14, CLDN16, CLDN18, CLDN9, CLDN12, and CLDN6 are elevated in COAD. In contrast, the CLDN8, CLDN23, CLDN5, CLDN11, CLDN7, and CLDN15 are downregulated in COAD. By analyzing the public datasets GSE15781 and GSE50760 from NCBI-GEO (https://www.ncbi.nlm.nih.gov/geo/), we have confirmed that CLDN1, CLDN2, and CLDN14 are significantly upregulated and CLDN8 and CLDN23 are significantly downregulated in normal colon, colon adenocarcinoma tumor, and liver metastasis of colon adenocarcinoma tissues from human samples. Various claudins are mutated and found to be associated with diagnostic efficacy in COAD.Conclusion: The claudin gene family is associated with prognosis, immune regulation, signaling pathway regulations, and diagnosis of COAD. These findings may provide new molecular insight into claudins in the treatment of colon cancer.