Identification of ceruloplasmin-binding anticancer peptides linked to cancer cell reprogramming in colorectal cancer

Colorectal cancer (CRC) progression is strongly influenced by tumour-cell plasticity and dynamic transcriptional reprogramming, which contribute to heterogeneity, treatment resistance and metastatic progression. This study developed an integrated computational framework to identify anticancer peptides that interact with molecular candidates associated with CRC reprogramming. Experimentally reported colon/colorectal cancer-associated anticancer peptides were curated and filtered according to physicochemical stability, predicted toxicity and haemolytic potential. Single-cell RNA-sequencing data from GSE132465 were analysed using tumour-normal differential expression, reprogramming-related Hallmark signatures and weighted gene co-expression network analysis, followed by protein-protein interaction, functional enrichment, immune-infiltration and machine-learning analyses. Ceruloplasmin (CP) emerged as the strongest internally consensus-stable candidate, being selected by at least two machine-learning feature-ranking methods in 73.3% of bootstrap iterations, while its differential expression was independently supported in TCGA-COAD/READ. Twelve prioritised peptides were subsequently evaluated by interface-guided HADDOCK docking, and six leading complexes were subjected to three independent 100-ns molecular dynamics simulations. FLAK26VAM produced the most favourable HADDOCK score and the highest hydrogen-bond occupancy, whereas FLAK93B showed the most consistent overall post-docking profile, including lower structural deviation, greater conformational compactness and the most favourable MM/GBSA and MM/PBSA energy estimates. HAL-1/20, HAL-1/9 and FLAK50Q7 also showed favourable complementary structural characteristics. Free-energy landscape analysis further supported the presence of defined low-energy conformational states in the prioritised complexes. Collectively, these findings identify CP as an externally supported CRC-associated candidate and prioritise FLAK26VAM and FLAK93B as complementary lead peptide candidates, with FLAK93B showing the strongest overall support when dynamic stability and post-MD energetics are considered. Thus, this study provides an integrated computational framework that links CRC reprogramming biology with peptide-target prioritisation, highlighting ceruloplasmin and selected anticancer peptides as candidates for further experimental validation.