Design of peptides that form amyloid-like fibrils capturing amyloid beta1-42 peptides

Amyloid beta-peptide (Abeta) plays a critical role in Alzheimer's disease (AD). The monomeric state of Abeta can self-assemble into oligomers, protofibrils, and amyloid fibrils. Since the fibrils and soluble oligomers are believed to be responsible for AD, the construction of molecules capable of capturing these species could prove valuable as a means of detecting these potentially toxic species and of providing information pertinent for designing drugs effective against AD. To this aim, we have designed short peptides with various hydrophobicities based on the sequence of Abeta14-23, which is a critical region for amyloid fibril formation. The binding of the designed peptides to Abeta and the amplification of the formation of peptide amyloid-like fibrils coassembled with Abeta are elucidated. A fluorescence assay utilizing thioflavin T, known to bind specifically to amyloid fibrils, revealed that two designed peptides (LF and VF, with the leucine and valine residues, respectively, in the hydrophobic core region) could form amyloid-like fibrils effectively by using mature Abeta1-42 fibrils as nuclei. Peptide LF also coassembled with soluble Abeta oligomers into peptide fibrils. Various analyses, including immunostaining with gold nanoparticles, enzyme-linked immunosorbent assays, and size-exclusion chromatography, confirmed that the LF and VF peptides formed amyloid-like fibrils by capturing and incorporating Abeta1-42 aggregates into their peptide fibrils. In this system, small amounts of mature Abeta1-42 fibrils or soluble oligomers could be transformed into peptide fibrils and detected by amplifying the amyloid-like fibrils with the designed peptides.     

Aggregation of amyloid Aβ(1–40) peptide in perdeuterated 2,2,2‐trifluoroethanol caused by ultrasound sonication

Ultrasound sonication of protein and peptide solutions is routinely used in biochemical, biophysical, pharmaceutical and medical sciences to facilitate and accelerate dissolution of macromolecules in both aqueous and organic solvents. However, the impact of ultrasound waves on folding/unfolding of treated proteins, in particular, on aggregation kinetics of amyloidogenic peptides and proteins is not understood. In this work, effects of ultrasound sonication on the misfolding and aggregation behavior of the Alzheimer's Aβ_(1–40)‐peptide is studied by pulsed‐field gradient (PFG) spin–echo diffusion NMR and UV circular dichroism (CD) spectroscopy. Upon simple dissolution of Aβ_(1–40) in perdeuterated trifluoroethanol, CF₃‐CD₂‐OD (TFE‐d₃), the peptide is present in the solution as a stable monomer adopting α‐helical secondary structural motifs. The self‐diffusion coefficient of Aβ_(1–40) monomers in TFE‐d₃ was measured as 1.35 × 10^?10 m² s^?1, reflecting its monomeric character. However, upon ultrasonic sonication for less than 5 min, considerable populations of Aβ molecules (ca 40%) form large aggregates as reflected in diffusion coefficients smaller than 4.0 × 10^?13 m² s^?1. Sonication for longer times (up to 40 min in total) effectively reduces the fraction of these aggregates in ¹H PFG NMR spectra to ca 25%. Additionally, absorption below 230 nm increased significantly upon sonication treatment, an observation, which also clearly confirms the ongoing aggregation process of Aβ_(1–40) in TFE‐d₃. Surprisingly, upon ultrasound sonication only small changes in the peptide secondary structure were detected by CD: the peptide molecules mainly adopt α‐helical motifs in both monomers and aggregates formed upon sonication. Copyright © 2010 John Wiley & Sons, Ltd.     

Structural Modifications of cis‐Glycofused Benzopyran Compounds and Their Influence on the Binding to Amyloid‐β Peptide

A small library of glycofused tricyclic compounds with a central pyran ring chemically modified in the position para to the ring oxygen has been synthesised. The influence of the chemical modification on the structural conformation of the compounds and on their ability to bind Aβ peptide has been evaluated respectively using molecular mechanics (MM) and molecular dynamics (MD) simulations, and STD NMR spectroscopy. The introduction of particularly polar/charged groups leads to the loss of binding ability, without a significant change in the conformation, whilst other substitutions does not significantly affect either the structural conformation or the binding.     

A rare occurrence of a β‐turn in an amyloid βA4 peptide

The fragment β(25–35) of the amyloid β‐peptide, like its parent βA4, has shown neurotrophic and late neurotoxic activities in cultured cells. The 3D structure of this important peptide was examined by ¹H and ¹³C 2D‐NMR and MD simulations in DMSO‐d₆ and water. The NMR parameters of chemical shift, ³J(N,Hα) coupling constants, temperature coefficients of NH chemical shifts and the pattern of intra and inter‐residue NOEs were used to deduce the structures. In DMSO‐d₆, the peptide was found to take up a type I β‐turn around the C‐terminal residues Ile⁸–Gly⁹–Leu¹⁰–Met¹¹, whereas in water at pH 5.5, it adopts a random coil conformation. This is only the second report of a β‐turn in the β‐amyloid class of peptides. The solution structures generated using restrained molecular dynamics were refined by MARDIGRAS to an R factor of 0.33 in the case of DMSO‐d₆ and to 0.56 for water. Copyright © 2002 John Wiley & Sons, Ltd.     

Understanding Amyloid‐β Oligomerization at the Molecular Level: The Role of the Fibril Surface

The aggregation of the amyloid β‐peptide into fibrils is a complex process that involves mechanisms such as primary and secondary nucleation, fibril elongation and fibril fragmentation. Some of these processes generate neurotoxic Aβ oligomers, which are involved in the development of Alzheimer's disease. Recent experimental studies have emphasized the role of the fibril as a catalytic surface for the production of highly toxic oligomers during secondary nucleation. By using molecular dynamics simulations, we show that it is the hydrophobic fibril region that causes the structural changes required for catalyzing the formation of β‐sheet‐rich Aβ1‐42 oligomers on the fibril surface. These results reveal, for the first time, the molecular basis of the secondary nucleation pathway.     

Characterizing Methyl‐Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using 13Cmethyl‐DEST and Lifetime Line Broadening

Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced ¹⁵N dark‐state exchange saturation transfer (DEST) and ¹⁵N lifetime line‐broadening to study solution backbone dynamics and position‐specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2–80 MDa) protofibrillar Aβ aggregates. Here we use ¹³C_methyl DEST and lifetime line‐broadening to probe the interactions and dynamics of methyl‐bearing side chains in the Aβ‐protofibril‐bound state. We show that all methyl groups of Aβ40 populate direct‐contact bound states with a very fast effective transverse relaxation rate, indicative of side‐chain‐mediated direct binding to the protofibril surface. The data are consistent with position‐specific enhancements of ¹³C_methyl‐${R{{{\rm tethered}\hfill \atop 2\hfill}}}$ values in tethered states, providing further insights into the structural ensemble of the protofibril‐bound state.     

Rationally Designed CeNP@MnMoS4 Core‐Shell Nanoparticles for Modulating Multiple Facets of Alzheimer's Disease

Alzheimer's disease (AD) is a complicated multifactorial syndrome. Lessons have been learned through failed clinical trials that targeting multiple key pathways of the AD pathogenesis is necessary to halt the disease progression. Here, we construct core‐shell nanoparticles (CeNP@MnMoS₄) targeting multiple key pathways of the AD pathogenesis, including elimination of toxic metal ions, decrease of oxidative stress, and promotion of neurite outgrowth. The SOD activity and copper removal capacity of CeNP@MnMoS₄‐n (n represents the number of layers of MnMoS₄, n=1–5) was investigated in vitro. We found that CeNP@MnMoS₄‐3 made an excellent balance between SOD activity and copper removal capacity. The effect of CeNP@MnMoS₄‐3 on Cu²⁺‐induced Aβ aggregation was studied by gel electrophoresis, transmission electron microscope (TEM), and atomic force microscopy (AFM). Compared with MnMoS₄ or CeNP alone, a synergistic effect was observed. Moreover, CeNP@MnMoS₄‐3 promoted neurite outgrowth in a dose‐dependent manner. Taken together, the results reported in this work show the potential of new multifunctional core‐shell nanoparticles as AD therapeutics.     

A Hot‐Segment‐Based Approach for the Design of Cross‐Amyloid Interaction Surface Mimics as Inhibitors of Amyloid Self‐Assembly

The design of inhibitors of protein–protein interactions mediating amyloid self‐assembly is a major challenge mainly due to the dynamic nature of the involved structures and interfaces. Interactions of amyloidogenic polypeptides with other proteins are important modulators of self‐assembly. Here we present a hot‐segment‐linking approach to design a series of mimics of the IAPP cross‐amyloid interaction surface with Aβ (ISMs) as nanomolar inhibitors of amyloidogenesis and cytotoxicity of Aβ, IAPP, or both polypeptides. The nature of the linker determines ISM structure and inhibitory function including both potency and target selectivity. Importantly, ISMs effectively suppress both self‐ and cross‐seeded IAPP self‐assembly. Our results provide a novel class of highly potent peptide leads for targeting protein aggregation in Alzheimer’s disease, type 2 diabetes, or both diseases and a chemical approach to inhibit amyloid self‐assembly and pathogenic interactions of other proteins as well.