Molecular mechanism of phosphorylation-mediated impacts on the conformation dynamics of ligand-bound BACE1 probed by Gaussian accelerated molecular dynamics

Alzheimer's disease (AD) is a chronic neurodegenerative disorder predominantly affecting the elderly population. The pathogenesis of AD involves the production of highly neurotoxic amyloid-β peptide 1-42 (Aβ_1-42) from the β-amyloid cleaving enzymes 1 (BACE1). Phosphorylation at the T259 site significantly influences the conformational dynamics of BACE1. Gaussian accelerated molecular dynamics (GaMD) simulations are combined with principal component analysis (PCA), hierarchical cluster analysis based on residue free energy decomposition, the molecular mechanics generalized Born surface area (MM-GBSA) method and solvation interaction energy (SIE) method to explore the effect of phosphorylation and binding with ZR7, ZQS, and ZRD on the conformation of BACE1. Phosphorylation and ligand binding lead to contact changes in key domains of the binding pocket. The results of PCA showed that PC1 and PC2 are responsible for the main state of BACE1, and pairing binding maintained the stability of the conformational state of BACE1. The analysis of free energy landscapes (FELs) showed that phosphorylation led to more disordered states of Flap (FP), F loop (FL) and other domains. Phosphorylation can induce a decrease in energy states compared with <i>apo</i> BACE1. The interaction network analysis results identified 11 hotspot residues, and phosphorylation had a significant effect on inhibitor-binding interactions. In summary, phosphorylation at T259 affects the conformation of BACE1 and its recognition of ligands and substrates. Therefore, these characteristics should be carefully considered when designing BACE1 inhibitors.