Network and modeling analysis of MAPK signaling cascade uncovers EGR1 regulation through ERK2 protein in breast cancer

The study explores the therapeutic relevance of Cardiac glycosides (CGs), including lanatoside C (LC), peruvoside (PS), and strophanthidin (STR) in treating breast cancer, using network pharmacology studies and bioinformatics approaches. Building on our prior in vitro studies and transcriptome profiling, we aimed to explore protein expression alterations influenced by the selected compounds in the present study. The methodology was structured and directed to delineate the active protein targets and their molecular mechanism of action in controlling cancer progression. Initially, we predicted the protein targets of individual compounds using SWISSTargetPrediction, and the results were compared with the differentially expressed genes from the transcriptome data acquired in the preliminary studies. The identified protein targets were further studied for their network relatedness and cross-verified by comparing their expression in cancer and normal patient data from TCGA using the UALCAN algorithm. Additionally, we aimed to identify the candidate biomarkers that potentially served as predictive or prognostic indicators in malignant breast cancer by conducting survival analysis of the crucial proteins using the GEPIA2 database. Overall, the analysis allowed us to understand the co-dependence expression between MAPK1 and EGR1 proteins, further emphasizing their clinical significance in cancer diagnosis and probable therapeutic outcomes. MD simulation studies further verified the most significant protein targets with their interaction scores and structural stability of the compounds, which showed higher structural stability around 300-ns trajectories for MAPK1 and EGR1 proteins. Finally, the pathway simulation studies, modeling on the MAPK/ERK signaling cascade, showed significant alteration in the biochemical parameters and stability of the system depending on the concentration of crucial proteins ERK2, also known as MAPK1 and EGR1 proteins in the pathway. These findings underscore the therapeutic potential of CGs and further highlight the significant role of identified proteins in targeting breast cancer.