Computational investigation of Amyloid Precursor Protein Familial Mutants and their interaction with F-spondin in Alzheimer’s Disease

Alzheimer's disease (AD) is a neurodegenerative disease and represents the most common form of dementia, characterized by a progressive deterioration of memory and cognitive functions. It mainly affects the elderly population (late onset) but can also occur at a younger age (early onset), especially in the presence of genetic mutations. According to the amyloid hypothesis, a central role is played by the amyloid precursor protein (APP), which is cleaved by β- and γ-secretase through the amyloidogenic pathway, generating the Amyloid Beta (Aβ) protein, in particular Aβ42, a form more prone to aggregation and neurotoxic. Familial APP mutations, such as the Swedish (KM670/671NL), Iowa (D694N) and Iberian (I716F) mutations, alter APP processing, favoring the pathological accumulation of Aβ. A possible strategy to counteract this mechanism is the use of ligands capable of binding to APP and preventing the initial cleavage by β-secretase. In this context, F-spondin has proven to be a potential natural inhibitor: it interacts with the extracellular E2 domain of APP and negatively regulates its amyloidogenic processing. In this thesis, computational molecular modeling methods were used to study the interactions between different variants of the APP protein and the F-Spondin protein, with the aim of investigating the molecular mechanisms involved in AD. Starting from the amino acid sequences obtained from the UniProt database, AlphaFold Server was employed to predict the three-dimensional structure of APP, its mutated variants (Swedish, Iowa and Iberian) and the F-spondin segment with reelin and spondin domains. To improve their stability and optimize their conformation, preliminary molecular dynamics (MD) simulations were performed on all protein models. Molecular Docking was then performed, via the ClusPro server, between F-spondin and each APP variant, generating four distinct molecular complexes: wild-type APP/F-spondin, Swedish APP (KM670/671NL)/F-spondin, Iowa APP (D694N)/F-spondin and Iberian APP (I716F)/F-spondin. The four complexes were subjected to molecular dynamics simulations. A comparative analysis was then conducted by examining the global stability (RMSD), the system’s flexibility (RMSF), and the interface stability between the two proteins in each complex, based on the number of hydrogen bonds and the contact surface. Finally, the binding free energy was estimated to assess the binding affinity across the different complexes.