α‑Helix Mimetics as Modulators of Aβ Self-Assembly

A key molecular species in Alzheimer’s disease (AD) is the Aβ₄₂ alloform of Aβ peptide, which is dominant in the amyloid plaques deposited in the brains of AD patients. Recent studies have decisively demonstrated that the prefibrillar soluble oligomers are the neurotoxic culprits and are associated with the pathology of AD. Nascent Aβ₄₂ is predominantly disordered but samples α-helical conformations covering residues 15–24 and 29–35 in the presence of micelles and structure-inducing solvents. In this report, a focused library of oligopyridylamide based α-helical mimetics was designed to target the central α-helix subdomain of Aβ (Aβ_13–26). A tripyridylamide, ADH-41, was identified as one of the most potent antagonists of Aβ fibrillation. Amyloid-assembly kinetics, transmission electron microscopy (TEM), and atomic force microscopy (AFM) show that ADH-41 wholly suppresses the aggregation of Aβ at a substoichiometric dose. Dot blot and ELISA assays demonstrate the inhibition of the putative neurotoxic Aβ oligomers. ADH-41 targets Aβ in a sequence and structure-specific manner, as it did not have any effect on the aggregation of islet amyloid polypeptide (IAPP), a peptide which shares sequence similarity with Aβ. Spectroscopic studies using NMR and CD confirm induction of α-helicity in Aβ mediated by ADH-41. Calorimetric and fluorescence titrations yielded binding affinity in the low micromolar range. ADH-41 was also effective at inhibiting the seed-catalyzed aggregation of Aβ probably by modulating the Aβ conformation into a fiber incompetent structure. Overall, we speculate that ADH-41 directs Aβ into off-pathway structures, and thereby alters various solution based functions of Aβ. Cell-based assays to assess the effect of ADH-41 on Aβ are underway and will be presented in due course

Noncovalent Template-Assisted Mimicry of Multiloop Protein Surfaces: Assembling Discontinuous and Functional Domains

We report here a novel noncovalent synthetic strategy for template-assembled <i>de novo</i> protein design. In this approach, a peptide was first conjugated with two oligoguanosine strands via click chemistry and the conjugates were then self-assembled in the presence of metal ions. G-quadruplex formation directs two peptide strands to assemble on one face of the scaffold and form an adjacent two loop surface. This approach can be used to rapidly prepare multiple two-loop structures with both homo- and heterosequences

Mimicry of a β‑Hairpin Turn by a Nonpeptidic Laterally Flexible Foldamer

The design and characterization of a proteomimetic foldamer that displays lateral flexibility endowed by intramolecular bifurcated hydrogen bonds is reported. The MAMBA scaffold, derived from <i>meta</i>-aminomethylbenzoic acid, adopts a serpentine conformation that mimics the side chain projection of all four residues in a β-hairpin turn

Tetracyanoresorcin[4]arene selectively recognises trimethyllysine and inhibits its enzyme-catalysed demethylation

<p><i>N</i>ε-methylation of lysine within proteins is a critical biological process that, among other roles, is involved in the control of gene expression. Compounds that recognise <i>N</i>ε-methylated lysine may therefore be useful probes for the study of the associated biological mechanisms and have therapeutic potential. Here, we show that tetracyanoresorcin[4]arene (<b><i>1</i></b>) selectively recognises <i>N</i>ε-trimethyllysine and binds to <i>N</i>ε-trimethyllysine within the context of a short peptide. Its binding properties compare favourably to a previously characterised <i>N</i>ε-trimethyllysine binder, <i>p</i>-sulfonatocalix[4]arene (<b><i>2</i></b>). We also show that both <b><i>1</i></b> and <b><i>2</i></b> inhibit the demethylation of <i>N</i>ε-trimethyllysine within a histone-derived peptide by the histone demethylase KDM4A.</p

Peptidomimetic-Based Multidomain Targeting Offers Critical Evaluation of Aβ Structure and Toxic Function

The prevailing hypothesis stipulates that the preamyloid oligomers of Aβ are the main culprits associated with the onset and progression of Alzheimer’s disease (AD), which has prompted efforts to search for therapeutic agents with the ability to inhibit Aβ oligomerization and amyloidogenesis. However, clinical progress is impeded by the limited structural information about the neurotoxic oligomers. To address this issue, we have adopted a synthetic approach, where a library of oligopyridylamide-based small molecules was tested against various microscopic events implicated in the self-assembly of Aβ. Two oligopyridylamides bind to different domains of Aβ and affect distinct microscopic events in Aβ self-assembly. The study lays the foundations for a dual recognition strategy to simultaneously target different domains of Aβ for further improvement in antiamyloidogenic activity. The data demonstrate that one of the most effective oligopyridylamides forms a high affinity complex with Aβ, which sustains the compound’s activity in cellular milieu. The oligopyridylamide was able to rescue cells when introduced 24 h after the incubation of Aβ. The rescue of Aβ toxicity is potentially a consequence of the colocalization of the oligopyridylamide with Aβ. The synthetic tools utilized here provide a straightforward strategic framework to identify a range of potent antagonists of Aβ-mediated toxic functions. This approach could be a powerful route to the design of candidate drugs for various amyloid diseases that have so far proven to be “untargetable”

Foldamer-Mediated Structural Rearrangement Attenuates Aβ Oligomerization and Cytotoxicity

The conversion of the native random coil amyloid beta (Aβ) into amyloid fibers is thought to be a key event in the progression of Alzheimer’s disease (AD). A significant body of evidence suggests that the highly dynamic Aβ oligomers are the main causal agent associated with the onset of AD. Among many potential therapeutic approaches, one is the modulation of Aβ conformation into off-pathway structures to avoid the formation of the putative neurotoxic Aβ oligomers. A library of oligoquinolines was screened to identify antagonists of Aβ oligomerization, amyloid formation, and cytotoxicity. A dianionic tetraquinoline, denoted as <b>5</b>, was one of the most potent antagonists of Aβ fibrillation. Biophysical assays including amyloid kinetics, dot blot, ELISA, and TEM show that <b>5</b> effectively inhibits both Aβ oligomerization and fibrillation. The antagonist activity of <b>5</b> toward Aβ aggregation diminishes with sequence and positional changes in the surface functionalities. <b>5</b> binds to the central discordant α-helical region and induces a unique α-helical conformation in Aβ. Interestingly, <b>5</b> adjusts its conformation to optimize the antagonist activity against Aβ. <b>5</b> effectively rescues neuroblastoma cells from Aβ-mediated cytotoxicity and antagonizes fibrillation and cytotoxicity pathways of secondary nucleation induced by seeding. <b>5</b> is also equally effective in inhibiting preformed oligomer-mediated processes. Collectively, <b>5</b> induces strong secondary structure in Aβ and inhibits its functions including oligomerization, fibrillation, and cytotoxicity

Quantifying Intrinsic Ion-Driven Conformational Changes in Diphenylacetylene Supramolecular Switches with Cryogenic Ion Vibrational Spectroscopy

We report how two flexible diphenylacetylene (DPA) derivatives distort to accommodate both cationic and anionic partners in the binary X^±·DPA series with X = TMA⁺ (tetramethylammonium), Na⁺, Cl^–, Br^–, and I^–. This is accomplished through theoretical analysis of X^±·DPA·2D₂ vibrational spectra, acquired by predissociation of the weakly bound D₂ adducts formed in a 10 K ion trap. DPA binds the weakly coordinating TMA⁺ ion with an arrangement similar to that of the neutral compound, whereas the smaller Na⁺ ion breaks all intramolecular H-bonds yielding a structure akin to the transition state for interconversion of the two conformations in neutral DPA. Halides coordinate to the urea NH donors in a bidentate H-bonded configuration analogous to the single intramolecular H-bonded motif identified at high chloride concentrations in solution. Three positions of the “switch” are thus identified in the intrinsic ion accommodation profile that differ by the number of intramolecular H-bonds (0, 1, or 2) at play