Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking...

Area of Science:

• Biochemistry
• Neuroscience
• Drug Discovery

Background:

• Memapsin 2 (BACE) is a beta-secretase involved in beta-amyloid peptide production, a key factor in Alzheimer's disease pathogenesis.
• The precise protonation states of catalytic aspartic acid residues (Asp32 and Asp228) in BACE are critical for its enzymatic activity but remain ambiguous.
• Understanding these protonation states is essential for developing effective BACE inhibitors.

Purpose of the Study:

• To determine the preferred protonation state of the Asp diad in Memapsin 2 (BACE) using molecular dynamics simulations.
• To elucidate the role of Asp32 and Asp228 in binding with potent inhibitors.
• To provide insights for structure-based design of novel BACE inhibitors.

Main Methods:

• Two independent molecular dynamics (MD) simulations of BACE in complex with the inhibitor OM99-2.
• Analysis of hydrogen bond formation and stability between the inhibitor and active site residues.
• Docking experiments with a novel potent inhibitor to assess energetic and structural features.

Main Results:

• MD simulations indicate that Asp32 is neutral and Asp228 is ionized to maintain a strong hydrogen bond with the inhibitor's hydroxyl group.
• This protonation state is energetically and structurally favored, consistent with X-ray crystal structures.
• Docking studies corroborate the findings, suggesting Asp228 acts as the primary hydrogen bond acceptor.

Conclusions:

• The study suggests Asp228, rather than Asp32, serves as the key hydrogen bond acceptor for BACE inhibitors.
• This finding has significant implications for the structure-based design and discovery of new Alzheimer's disease therapeutics targeting BACE.
• Clarifying the protonation states of BACE active site residues is crucial for optimizing inhibitor efficacy.