Decoding the Roles of Amyloid-β (1–42)’s Key Oligomerization Domains toward Designing Epitope-Specific Aggregation Inhibitors

Abstract

Fibrillar amyloid aggregates are the pathological hallmarks of multiple neurodegenerative diseases. The amyloid-β (1–42) protein, in particular, is a major component of senile plaques in the brains of patients with Alzheimer’s disease and a primary target for disease treatment. Determining the essential domains of amyloid-β (1–42) that facilitate its oligomerization is critical for the development of aggregation inhibitors as potential therapeutic agents. In this study, we identified three key hydrophobic sites (17LVF19, 32IGL34, and 41IA42) on amyloid-β (1–42) and investigated their involvement in the self-assembly process of the protein. Based on these findings, we designed candidate inhibitor peptides of amyloid-β (1–42) aggregation. Using the designed peptides, we characterized the roles of the three hydrophobic regions during amyloid-β (1–42) fibrillar aggregation and monitored the consequent effects on its aggregation property and structural conversion. Furthermore, we used an amyloid-β (1–42) double point mutant (I41N/A42N) to examine the interactions between the two C-terminal end residues with the two hydrophobic regions and their roles in amyloid self-assembly. Our results indicate that interchain interactions in the central hydrophobic region (17LVF19) of amyloid-β (1–42) are important for fibrillar aggregation, and its interaction with other domains is associated with the accessibility of the central hydrophobic region for initiating the oligomerization process. Our study provides mechanistic insights into the self-assembly of amyloid-β (1–42) and highlights key structural domains that facilitate this process. Our results can be further applied toward improving the rational design of candidate amyloid-β (1–42) aggregation inhibitors.

IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules

“…Recently, Im et al used IM-MS to explore the Aβ42 domains that are important for oligomerization and identified the hydrophobic sequences L 17 VF 19 in the central hydrophobic core and I 32 GL 34 and I 41 A 42 at the C-terminal region as controlling the oligomerization process, 51 in agreement with many previous studies demonstrating the importance of these regions in Aβ self-assembly.…”

Small Molecules N-Phenylbenzofuran-2-carboxamide and N-Phenylbenzo[b]thiophene-2-carboxamide Promote Beta-Amyloid (Aβ42) Aggregation and Mitigate Neurotoxicity

“…This provides the molecular basis for the fibril to grow both in length and in thickness. Two hydrophobic domains within the amino acid sequence of Aβ42 were identified, KLVFFA and IGLMVGGVVIA, respectively. These regions are involved in initiating the aggregation process. , The conformations of hydrophobic surfaces are complementary, which promotes their interaction and aggregation.…”

“…The cross-β spine structure of Aβ42 fibrils constrains small molecules to move between fibril chains due to the tight packing. In the Aβ42 fibril assembly, the top-ranked binding poses of 7a (CDOCKER energy −14.66 kcal/mol, CDOCKER interaction energy −21.61 kcal/mol) and 7b (CDOCKER energy −9.77 kcal/mol, CDOCKER interaction energy −20.15 kcal/mol) were mainly interacting in the KLVFFA region (Figure A,C). In 7a , the benzofuran ring underwent pi-alkyl interactions with chain C: Ala21 (distance <5.0 Å), and C: Val18 (distance <5.0 Å) (Figure A,B).…”

“…In terms of the research progress related to understanding the mechanisms of the amyloid cascade, Aβ toxicity, and development of anti-Aβ-based therapeutic strategies, literature surveys from the last two decades show that most of the research has focused on the design and development of diverse classes of small molecules and peptides that act as direct inhibitors of Aβ aggregation and their application as potential chemical tools to study AD. ,− The molecular mechanisms of their anti-Aβ activity includes binding to (i) Aβ monomers or oligomers or fibrils; (ii) modulation of the aggregation kinetics to reduce or prevent Aβ aggregation; and (iii) remodeling the misfolding pathways to promote the formation of less toxic Aβ aggregates/fibrils. ,− In contrast, there is a lack of literature on the design and development of molecules that can promote Aβ fibrillogenesis. The availability of novel chemical tools that are capable of promoting Aβ aggregation and fibrillogenesis would enable researchers in the field to (i) study the complex molecular processes involved in the formation of various Aβ aggregates such as dimers, trimers, tetramers, pentamers, hexamers, oligomers, protofibrils, and fibrils; (ii) understand the molecular mechanisms of aggregation kinetics during Aβ fibrillogenesis; (iii) study the mechanisms of Aβ remodeling; and (iv) design novel Aβ aggregation “modulators” instead of “inhibitors” as potential therapeutics.…”

Generation and study of antibodies against two triangular trimers derived from Aβ

“…To gain insights into the structures of Aβ oligomers, researchers have prepared Aβ oligomers in vitro from synthetic or recombinantly expressed Aβ and then used low‐resolution biophysical techniques, such as transmission electron microscopy, atomic force microscopy, gel electrophoresis, circular dichroism spectroscopy, infrared spectroscopy, and small‐angle x‐ray scattering to characterize the structures of these oligomers. [ 6–14 ] These in vitro‐prepared Aβ oligomers have then been used as antigens to create antibodies, which are used as probes to correlate the structures of the oligomers prepared in vitro with oligomers in the brain. [ 15–21 ] While this “top‐down” approach has yielded valuable insights into the conformations and structures of Aβ oligomers that form in the brain, the Aβ antigens used to generate many of these antibodies contain heterogenous oligomers with structurally undefined epitopes; thus, the structural insights obtained from this approach are limited.…”