Molecular mechanics simulations aimed at understanding the effects of amyloid precursor protein mutations on Alzheimer's disease pathogenesis

Alzheimer's disease (AD), the most common cause of dementia in older adults, despite decades of research, drug candidates and clinical trials, it remains a challenging condition, both from a biological and clinical perspective. Apart from palliative drugs, which only slow symptoms, there is no approved reversal therapy: the impact of AD is enormous on healthcare systems, and it is projected to grow with a progressively ageing population. While most of AD cases are idiopathic, i.e. without a clear causative factor, the production and following the accumulation of aberrant amyloid beta peptides in patients’ brains are considered as cornerstones of the disease and linked to the complex biochemical cascade, which is believed to start with excessive APP proteolytic cleavage by beta secretase (BACE1) enzyme. In 2012, a mutation at site 673 (alanine to threonine) in the amyloid precursor protein (APP) was found in an Icelandic population sample; carriers of this mutation have fivefold lower risk of AD and a reduction in amyloid beta production was observed. However, a precise mechanistic explanation of its neuroprotective effect is still lacking, with evidence pointing to inferior affinity of mutated APP-BACE1 or different amyloid oligomers behavior. The A673V and the double Swedish mutations are conversely associated with early onset AD and thought to enhance cleavage by BACE1. The aim of this M.Sc. thesis is therefore to study the APP-BACE1 complex using molecular docking and dynamics simulations: analysis of contact probabilities and type of interactions; residue fluctuations; and estimation of binding affinities via MM-GBSA method will be performed to characterize the behavior of mutated APP fragments in association with BACE1.