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

Abstract

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.

Figure 1

Method validation for MMPBSA free energy calculations of various Aβ peptides bound to the antibodies PFA1 and PFA2. The original PFA1, PFA2, and pE3-Aβ_3–8 crystal structures (PDB IDs: 2IPU, 2R0W, and 3EYS) served as the basis for constructing homology models for all the other bound peptide structures. Our calculated MMPBSA binding free energy values were compared to the experimental binding affinity values reported by Gardberg et al. for their entire data set. All free energy values are given in units of kcal/ mol.

Figure 2

Comparison of the binding pose for Aβ_2–7 peptide variants bound to PFA1. Three Aβ peptides are shown bound to PFA1: (A) Aβ_2–7, (B) Grip1, and (C) the Pos4 mutant. All three images were taken at the halfway point of the production portion of the MD simulation.

Figure 3

Electrostatic contacts for Aβ_1–8 bound to PFA1. A surface map of PFA1 is provided which shows the key electrostatic contacts made between the PFA1 antibody and charged residues in Aβ_1–8. The N-terminal aspartate residue (D1) on the Aβ peptide appears in the lower right corner of the figure. Negatively charged regions are depicted in red while positively charged regions are shown in blue. Coulombic Surface Coloring was used to depict electrostatic contacts on the antibody surface where the scale ranges from −10 kcal/mol·e (red, negative region) to 0 kcal/mol·e (white, neutral region) to 10 kcal/mol·e (blue, positive region).

Figure 4

Gantenerumab bound to both N-terminal and central Aβ peptides. Gantenerumab is shown bound to the Aβ peptide containing the N-terminal epitope (PDB ID: 5CSZ) in the first frame of the MD simulation in parts A and B. Structures C–F show the most stable central Aβ peptide bound to gantenerumab in the forward sequence (HHQKLVFFAEDV) across the gantenerumab antigen-combining site taken from the first frame (C and D), the middle frame (E), and the last frame (F) of the MD production run. In all structures, the N-terminus end of the peptide appears toward the bottom of the antigen-combining site while the C-terminus appears near the top. Coulombic Surface Coloring was used to depict electrostatic contacts on the antibody surface where the scale ranges from −10 kcal/mol·e (red, negative) to 0 kcal/mol·e (white, neutral) to 10 kcal/ mol·e (blue, positive). The residues on the peptide were colored as acidic (red), basic (blue), or neutral (white).

Figure 5

Crenezumab bound to both central and N-terminal Aβ peptides. Crenezumab is shown bound to the Aβ peptide containing the central epitope (PDB ID: 5VZY) in the first frame of the MD simulation in structures A and B. Structures C–F show the N-terminal Aβ peptide bound to crenezumab in the reverse sense (SDHRFEAD) across the crenezumab antigen-combining site as observed in the first frame (C and D), the middle frame (E), and the last frame (F) of the MD production run. In structures A and B, the N-terminus end of the peptide appears toward the bottom of the antigen-combining site while the C-terminus appears near the top. For C–F, the N-terminus end appears toward the upper left of the antigen-combining site while the C-terminus end appears toward the lower right of the antigen-combining site. Coulombic Surface Coloring was used to depict electrostatic contacts on the antibody surface where the scale ranges from −10 kcal/mol·e (red, negative region) to 0 kcal/mol·e (white, neutral region) to 10 kcal/mol·e (blue, positive region). The residues on the peptide were colored as acidic (red), basic (blue), or neutral (white).

Figure 6

Snapshots from the MD trajectories of pE3-Aβ_3–8 bound to wildtype and mutant forms of PFA1. The structures here are visualized as snapshots taken at 10, 30, and 50 ns during the production run of the MD simulation.

Figure 7

Snapshots from the MD trajectories of Aβ_1–8 and Aβ_2–7 bound to wildtype and mutant forms of PFA1. The structures here are visualized as snapshots taken at 10, 30, and 50 ns during the production run of the MD simulation.