Integrated Molecular Docking and Gene Expression Analyses Suggest a Potential Interaction Between Diphtheria Toxin and Bcl‐2 in HT‐29 Colorectal Cancer Cells

Diphtheria toxin (DT) has been reported to exhibit cytotoxic effects in several cancer models; however, the molecular mechanisms underlying its apoptotic activity remain incompletely understood. In our previous study, DT was shown to induce cytotoxic and apoptotic responses in HT-29 colorectal cancer cells, characterized by the upregulation of pro-apoptotic genes and suppression of anti-apoptotic signaling. Building on these findings, the present study aimed to explore the potential molecular context underlying DT-induced transcriptional alterations using computational and bioinformatic approaches. Molecular protein-protein docking was performed to evaluate the possible interaction between DT and the anti-apoptotic protein Bcl-2. In parallel, previously obtained qRT-PCR gene expression data from HT-29 cells were reanalyzed to assess coordinated transcriptional responses associated with DT exposure. Network analysis using the STRING database indicated that DT-responsive genes form a functionally connected interaction network associated with apoptosis, cellular stress responses, and cell-cycle regulation. Principal component analysis and hierarchical clustering confirmed consistent differences in gene expression patterns between treated and control samples. Docking results suggested a potential interaction between DT and the BH3-binding groove of Bcl-2, supported by hydrogen bonding and hydrophobic contacts. Pathway enrichment analyses further linked the analyzed genes to apoptosis-related pathways, including FoxO and p53 signaling. Collectively, these findings provide an integrated framework suggesting that DT-induced cytotoxicity in HT-29 cells may involve coordinated transcriptional responses and potential structural interaction with Bcl-2, highlighting regulatory networks associated with apoptosis, cellular stress, and cell-cycle control.