A Comprehensive In Silico Study of the NDB-IL-24 Fusion Protein for Tumor Targeting: A Promising Anti-Cancer Therapeutic Candidate

Abstract

Background: Breast cancer remains a pervasive global health concern among women, with conventional therapies such as chemotherapeutic agents, radiography, and surgery lacking selectivity and causing undesirable side effects. In response to this challenge, fusion proteins are emerging as a promising avenue for targeted cancer therapy. This study aimed at in silico design of a chimeric protein by fusing the cell-penetrating peptide, nemo binding domain (NBD) peptide, with the cell-targeting peptide, interleukin 24 (IL-24), using linkers of varying lengths. The selected bifunctional peptide was investigated for its potential of enhanced anti-tumor activity through in silico methods. Methods: The 3D structure of the fusion peptide was initially modeled using I-TASSER (Iterative Threading Assembly Refinement) and AlphaFold2. The predicted structures underwent rigorous quality check and validation through Ramachandran plot analysis, ERRAT, and VERIFY 3D. The best model was refined, and physiochemical properties were evaluated. Subsequently, docking analysis was performed using ClusPro 2.0, and molecular dynamic simulations were performed using NAMD with VMD. Results: The results demonstrated a valid 3D structure with high model quality. The docked complex exhibited stability with 23 salt bridges, 17 hydrogen bonds, and 236 non-bonded contacts, suggesting a successful interaction of the fusion peptide with its potential receptor, thereby generating an apoptotic signal. Molecular dynamic simulations further confirmed the stability, flexibility, and functionality of the fusion protein, indicated by non-significant fluctuations in the generated graphs. Conclusion: In conclusion, our newly designed peptide holds promise as a potential drug candidate against breast cancer, warranting further evaluation through in vitro studies. Computational tools for designing such fusion proteins have proven valuable as an initial step preceding in vitro production.