Computational Design Of A Peptide Candidate Targeting NOTCH1 And PI3K/AKT Signaling Pathways In Cancer: A Coarse-Grained Molecular Dynamics Simulation Study.

The PI3K/AKT and NOTCH1 signaling pathways are key regulators of tumor progression, proliferation, survival, and metastasis in numerous cancers, making them attractive targets for peptide-based anticancer therapies. Dermaseptin-B2 is a well-characterized anticancer peptide known to modulate the PI3K/AKT signaling pathway; however, its therapeutic application may be limited by suboptimal cellular uptake. In contrast, Magainin-2 exhibits strong membrane-interacting and cell-penetrating properties and has been widely employed in the development of hybrid bioactive peptides to enhance membrane permeability and intracellular delivery. In this study, a peptide library was constructed from truncated fragments of Dermaseptin-B2 and Magainin-2 to identify hybrid peptides targeting the PI3K/AKT and NOTCH1 signaling pathways. A five-amino-acid anticancer motif derived from Dermaseptin-B2 was fused to a ten-amino-acid membrane-active fragment of Magainin-2 to improve cellular penetration. Subsequently, three rational amino acid substitutions were introduced into the lead peptide (MD3)-lysine replacing phenylalanine, histidine replacing glycine, and valine replacing serine-to enhance anticancer activity, optimize cell penetration, and reduce potential toxicity. Molecular docking analyses demonstrated favorable binding of MD3 to proteins involved in the PI3K/AKT and NOTCH1 signaling pathways. Molecular dynamics simulations, including RMSD, RMSF, and radius of gyration analyses, confirmed the structural stability of the peptide-protein complexes throughout the simulation period. Binding free-energy calculations using the MM-PBSA method indicated thermodynamically favorable interactions between MD3 and its target proteins. Furthermore, analyses of hydrogen-bond distance and angle distributions supported the formation of stable, geometrically favorable intermolecular interactions. Coarse-grained membrane simulations further demonstrated the efficient membrane-penetrating capability of MD3 in a DOPS-DOPC lipid bilayer model. Collectively, these findings identify MD3 as a promising multifunctional hybrid peptide that targets multiple cancer-associated signaling pathways and exhibits favorable membrane penetration and structural stability, highlighting its potential as a candidate for future peptide-based anticancer therapeutics.