In-Silico and Computational Active Site-Driven Design and Characterization of Beta-NGF-Aβ Fusion Protein as a Novel and Targeted Alzheimer's Disease Therapy

The targeted delivery of therapeutic chimeric molecules significantly enhances pharmacological efficiency by triggering strong cellular uptake and prolonging the duration of systemic circulation. Purposeful molecular design incorporating specific chimeric protein-receptor interactions is an essential aspect of understanding biological mechanisms and precision modeling of molecular complexes. In this study, a detailed in-silico analysis was performed on a chimeric fusion protein designed to target Alzheimer's disease. The fusion protein was created using the amino acid sequences retrieved from the beta-NGF, Nerve Growth Factor protein and the A beta peptide, with a rigid linker in place that ensures structural integrity. Its physicochemical characterization was predicted using ProtParam along with the evaluation of its secondary and tertiary structures, while its potential toxicity and allergenicity were analyzed through online analytical tools. The structural integrity of the fusion protein was evaluated through Rampage and ERRAT analyses, resulting in an ERRAT quality factor of 85 and indicating that 98.6% of the residues were placed within favored regions as suggested by the corresponding Ramachandran plot. Docking experiments were conducted using the HDOCK Server, followed by molecular simulations with the OpenMM engine, employing the AMBER force field for evaluation. The quality, validity, interaction analysis and stability of the fusion protein reveal that it indeed represents a functional molecular entity. The fact that the beta-NGF-A beta fusion gene is cloned and expressed in a suitable prokaryotic system may indicate that this is a very promising candidate for novel therapeutic approaches that target Alzheimer's disease.