Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies

Alzheimer's disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (Aβ) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing. Introducing rational mutations into anti-Aβ antibodies to increase their effectiveness is a way forward, but the path to take is unclear. In this study, we demonstrate the use of computational fragment-based docking and MMPBSA binding free energy calculations in the analysis of anti-Aβ antibodies for rational drug design efforts. Our fragment-based docking method successfully predicts the emergence of the common EFRH epitope. MD simulations coupled with MMPBSA binding free energy calculations are used to analyze scenarios described in prior studies, and we computationally introduce rational mutations into PFA1 to predict mutations that can improve its binding affinity toward the pE3-Aβ_3-8 form of Aβ. Two out of our four proposed mutations are predicted to stabilize binding. Our study demonstrates that a computational approach may lead to an improved drug candidate for AD in the future.