Disruption of amyloid-derived peptide assemblies through the controlled induction of a beta-sheet to alpha-helix transformation: application of the switch concept

Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools

Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.

Mechanism of Spatial and Temporal Control in Precision Cyclic Vinyl Polymer Synthesis by Lewis Pair Polymerization

In typical cyclic polymer synthesis via ring‐closure, chain growth and cyclization events are competing with each other, thus affording cyclic polymers with uncontrolled molecular weight or ring size and high dispersity. Here we uncover a mechanism by which Lewis pair polymerization (LPP) operates on polar vinyl monomers that allows the control of where and when cyclization takes place, thereby achieving spatial and temporal control to afford precision cyclic vinyl polymers or block copolymers with predictable molecular weight and low dispersity (≈1.03). A combined experimental and theoretical study demonstrates that cyclization occurs only after all monomers have been consumed (when) via conjugate addition of the propagating chain end to the specific site of the initiating chain end (where), allowing the cyclic polymer formation steps to be regulated and executed with precision in space and time.

Secondary Structure-Dominated Layer-by-Layer Growth Mode of Protein Coatings

Benefiting from the luxury functions of proteins, protein coatings have been extended to various applications, including tissue engineering scaffolds, drug delivery, antimicrobials, sensing and diagnostic equipment, food packaging, etc. Fast construction of protein coatings is always interesting to materials science and significant to industrialization. Here, we report a layer-by-layer (LbL) multilayer-constructed coating of tannic acid (TA) and lysozyme (Lyz), in which the secondary conformations of Lyz dominate the growth rate of the TA/Lyz coating. As well characterized by various techniques (quartz crystal microbalance with dissipation (QCM-D), circular dichroism (CD) spectra, Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM), contact angle, etc.), TA-induced conformational transition of Lyz to α-helices occurs at pH 8 from other secondary structures (β-sheets, β-turns, and random coils), which leads to the very fast growth of TA/Lyz with a number of deposited bilayers, with thicknesses of more than 90 nm for six bilayers. In contrast to the leading conformation of α-helices at pH 8, Lyz displayed multiple conformations (α-helices, β-sheets, β-turns, and random coils) at pH 6, which resulted in coating thicknesses of less than 30 nm for six bilayers. By the addition of NaCl, Tween 20, and urea, we further confirmed that the secondary conformations of Lyz relied greatly on the interactions between TA and Lyz and dominated the growth rate of the multilayers. We believe that these findings will help to understand the transformation of secondary conformations by TA or other polyphenols and inspire a new route to quickly build protein coatings.

Coassembly-Induced Transformation of Dipeptide Amyloid-Like Structures into Stimuli-Responsive Supramolecular Materials

Conformational transition of proteins and peptides into highly stable, β-sheet-rich structures is observed in many amyloid-associated neurodegenerative disorders, yet the precise mechanism of amyloid formation at the molecular level remains poorly understood due to the complex molecular structures. Short peptides provide simplified models for studying the molecular basis of the assembly mechanism that governs β-sheet fibrillation processes underlying the formation and inhibition of amyloid-like structures. Herein, we report a supramolecular coassembly strategy for the inhibition and transformation of stable β-sheet-rich amyloid-derived dipeptide self-assemblies into adaptable secondary structural fibrillar assemblies by mixing with bipyridine derivatives. The interplay between the type and mixing ratio of bipyridine derivatives allowed the variable coassembly process with stimuli-responsive functional properties, studied by various experimental characterizations and computational methods. Furthermore, the resulting coassemblies showed functional redox- and photoresponsive properties, making them promising candidates for controllable drug release and fluorescent imprint. This work presents a coassembly strategy not only to explore the mechanism of amyloid-like structure formation and inhibition at the molecular level but also to manipulate amyloid-like structures into responsive supramolecular coassemblies for material science and biotechnology applications.

Native Design of Soluble, Aggregation-Resistant Bioactive Peptides: Chemical Evolution of Human Glucagon

Peptide-based therapeutics commonly suffer from biophysical properties that compromise pharmacology and medicinal use. Structural optimization of the primary sequence is the usual route to address such challenges while trying to maintain as much native character and avoiding introduction of any foreign element that might evoke an immunological response. Glucagon serves a seminal physiological role in buffering against hypoglycemia, but its low aqueous solubility, chemical instability, and propensity to self-aggregate severely complicate its medicinal use. Selective amide bond replacement with metastable ester bonds is a preferred approach to the preparation of peptides with biophysical properties that otherwise inhibit synthesis. We have recruited such chemistry in the design and development of unique glucagon prodrugs that have physical properties suitable for medicinal use and yet rapidly convert to native hormone upon exposure to slightly alkaline pH. These prodrugs demonstrate in vitro and in vivo pharmacology when formulated in physiological buffers that are nearly identical to native hormone when solubilized in conventional dilute hydrochloric acid. This approach provides the best of both worlds, where the pro-drug delivers chemical properties supportive of aqueous formulation and the native biological properties.

Medicinal Chemistry Focusing on Aggregation of Amyloid-β

The aggregation of peptides/proteins is intimately related to a number of human diseases. More than 20 have been identified which aggregate into fibrils containing extensive β-sheet structures, and species generated in the aggregation processes (i.e., oligomers and fibrils) contribute to disease development. Amyloid-β peptide (designated Aβ), related to Alzheimer's disease (AD), is the representative example. The intensive aggregation property of Aβ also leads to difficulty in its synthesis. To improve the synthetic problem, we developed an O-acyl isopeptide of Aβ1-42, in which the N-acyl linkage (amide bond) of Ser(26) was replaced with an O-acyl linkage (ester bond) at the side chain. The O-acyl isopeptide demonstrated markedly higher water-solubility than that of Aβ1-42, while it quickly converted to intact monomer Aβ1-42 via an O-to-N acyl rearrangement under physiological conditions. Inhibition of the pathogenic aggregation of Aβ1-42 might be a therapeutic strategy for curing AD. We succeeded in the rational design and identification of a small molecule aggregation inhibitor based on a pharmacophore motif obtained from cyclo[-Lys-Leu-Val-Phe-Phe-]. Moreover, the inhibition of Aβ aggregation was achieved via oxygenation (i.e., incorporation of oxygen atoms to Aβ) using an artificial catalyst. We identified a selective, cell-compatible photo-oxygenation catalyst of Aβ, a flavin catalyst attached to an Aβ-binding peptide, which markedly decreased the aggregation potency and neurotoxicity of Aβ.

Amyloid β derived switch-peptides as a tool for investigation of early events of aggregation: a combined experimental and theoretical approach

π → π stacking interaction takes place prior to aggregation as the early event of amyloid aggregation of amyloidogenic peptides.

Synthesis of O-acyl isopeptides

O-Acyl isopeptides, in which the N-acyl linkage on the hydroxyamino acid residue (e.g., Ser and Thr) is replaced with an O-acyl linkage, generally possess superior water-solubility to their corresponding native peptides, as well as other distinct physicochemical properties. In addition, O-acyl isopeptides can be rapidly converted into their corresponding native peptide under neutral aqueous conditions through an O-to-N acyl migration. By exploiting these characteristics, researchers have applied the O-acyl isopeptide method to various peptide-synthesis fields, such as the synthesis of aggregative peptides and convergent peptide synthesis. This O-acyl-isopeptide approach also serves as a means to control the biological function of the peptide in question. Herein, we report the synthesis of O-acyl isopeptides and some of their applications.

Formation of α-helical nanofibers by mixing β-structured and α-helical coiled coil peptides

The helical coiled coil is a well-studied folding motif that can be used for the design of nanometer-sized bioinspired fibrous structures with potential applications as functional materials. A two-component system of coiled coil based model peptides is investigated, which forms, under acidic conditions, uniform, hundreds of nanometers long, and ~2.6 nm thick trimeric α-helical fibers. In the absence of the other component and under the same solvent conditions, one model peptide forms β-sheet-rich amyloid fibrils and the other forms stable trimeric α-helical coiled coils, respectively. These observations reveal that the complementary interactions driving helical folding are much stronger here than those promoting the intermolecular β-sheet formation. The results of this study are important in the context of amyloid inhibition but also open up new avenues for the design of novel fibrous peptidic materials.

Smart self-assembled hybrid hydrogel biomaterials

Hybrid biomaterials are systems created from components of at least two distinct classes of molecules, for example, synthetic macromolecules and proteins or peptide domains. The synergistic combination of two types of structures may produce new materials that possess unprecedented levels of structural organization and novel properties. This Review focuses on biorecognition-driven self-assembly of hybrid macromolecules into functional hydrogel biomaterials. First, basic rules that govern the secondary structure of peptides are discussed, and then approaches to the specific design of hybrid systems with tailor-made properties are evaluated, followed by a discussion on the similarity of design principles of biomaterials and macromolecular therapeutics. Finally, the future of the field is briefly outlined.

Chemical strategies for controlling protein folding and elucidating the molecular mechanisms of amyloid formation and toxicity

It has been more than a century since the first evidence linking the process of amyloid formation to the pathogenesis of Alzheimer's disease. During the last three decades in particular, increasing evidence from various sources (pathology, genetics, cell culture studies, biochemistry, and biophysics) continues to point to a central role for the pathogenesis of several incurable neurodegenerative and systemic diseases. This is in part driven by our improved understanding of the molecular mechanisms of protein misfolding and aggregation and the structural properties of the different aggregates in the amyloid pathway and the emergence of new tools and experimental approaches that permit better characterization of amyloid formation in vivo. Despite these advances, detailed mechanistic understanding of protein aggregation and amyloid formation in vitro and in vivo presents several challenges that remain to be addressed and several fundamental questions about the molecular and structural determinants of amyloid formation and toxicity and the mechanisms of amyloid-induced toxicity remain unanswered. To address this knowledge gap and technical challenges, there is a critical need for developing novel tools and experimental approaches that will not only permit the detection and monitoring of molecular events that underlie this process but also allow for the manipulation of these events in a spatial and temporal fashion both in and out of the cell. This review is primarily dedicated in highlighting recent results that illustrate how advances in chemistry and chemical biology have been and can be used to address some of the questions and technical challenges mentioned above. We believe that combining recent advances in the development of new fluorescent probes, imaging tools that enabled the visualization and tracking of molecular events with advances in organic synthesis, and novel approaches for protein synthesis and engineering provide unique opportunities to gain a molecular-level understanding of the process of amyloid formation. We hope that this review will stimulate further research in this area and catalyze increased collaboration at the interface of chemistry and biology to decipher the mechanisms and roles of protein folding, misfolding, and aggregation in health and disease.

Inhibition of amyloid aggregation by formation of helical assemblies

The formation of amyloid aggregates is responsible for a wide range of diseases, including Alzheimer's and Parkinson's disease. Although the amyloid-forming proteins have different structures and sequences, all undergo a conformational change to form amyloid aggregates that have a characteristic cross-β-structure. The mechanistic details of this process are poorly understood, but different strategies for the development of inhibitors of amyloid formation have been proposed. In most cases, chemically diverse compounds bind to an elongated form of the protein in a β-strand conformation and thereby exert their therapeutic effect. However, this approach could favor the formation of prefibrillar oligomeric species, which are thought to be toxic. Herein, we report an alternative approach in which a helical coiled-coil-based inhibitor peptide has been designed to engage a coiled-coil-based amyloid-forming model peptide in a stable coiled-coil arrangement, thereby preventing rearrangement into a β-sheet conformation and the subsequent formation of amyloid-like fibrils. Moreover, we show that the helix-forming peptide is able to disassemble mature amyloid-like fibrils.

From polyesters to polyamides via O-N acyl migration: an original multi-transfer reaction

A new strategy for the synthesis of polyamides from polyesters of hydroxyl-containing amino acids using a multi O-N acyl transfer reaction was developed. This original approach allowed the synthesis of three generations of polymers from the same starting monomer. The polymerization of N-benzyloxycarbonyl-serine and its γ-homologated derivative provided the Z-protected polyesters; then the water-soluble polycationic polyesters were obtained by removal of the Z-protecting group; and finally the polyamides were obtained by a base-induced multi O-N acyl transfer, both in aqueous or organic medium. The key step transfer reaction was monitored by the disappearance and appearance of characteristic NMR proton signals and IR bands of polyesters and polyamides.

Click Peptide concept: o-acyl isopeptide of islet amyloid polypeptide as a nonaggregative precursor molecule

The O-acyl isopeptide (1) of islet amyloid polypeptide (IAPP), which contains an ester moiety at both Ala8-Thr9 and Ser19-Ser20, was prepared by sequential segment condensation based on the O-acyl isopeptide method. Isopeptide 1 possessed nonaggregative properties, retaining its random coil structure under the acidic conditions; this suggests that the insertion of the O-acyl isopeptide structures in IAPP suppressed aggregation of the molecule. As a result of the rapid O-to-N acyl shift of 1 under neutral pH, in situ-formed IAPP adopted a random-coil structure at the start of the experiment, and then underwent conformational change to α-helix/β-sheet mixed structures as well as aggregation. The click peptide strategy with the nonaggregative precursor molecule 1 could be a useful experimental tool to identify the functions of IAPP, by overcoming the handling difficulties that arise from IAPP's intense and uncontrollable self-assembling nature.

Dueling post-translational modifications trigger folding and unfolding of a beta-hairpin peptide

Protein post-translational modifications (PTMs) are used in nature as a means of turning on or off a myriad of biological events. Methylation of lysine and phosphorylation of serine are important PTMs in the histone code found to modulate chromatin packing, which in turn affects gene expression. The design of peptides that fold into secondary structures can help to further our understanding of complex protein interactions. Here we report the design of the Trpswitch peptide sequence that folds into a moderately stable beta-hairpin structure in aqueous solution and show that the stability of the structure can be tuned by incorporation of dimethyllysine or phosphoserine. Dimethylated Trpswitch results in an increase in beta-hairpin stability, while phosphorylated Trpswitch is unstructured at neutral pH. When both modifications are incorporated into Trpswitch, a less stable beta-hairpin structure is observed. This system provides a model to demonstrate how multiple PTMs may work in concert or against each other to influence structure.

Synthesis and conformation of an analog of the helix-loop-helix domain of the Id1 protein containing the O-acyl iso-prolyl-seryl switch motif

Synthetic peptides reproducing the helix-loop-helix (HLH) domains of the Id proteins fold into highly stable helix bundles upon self-association. Recently, we have shown that the replacement of the dipeptide Val-Ser at the loop-helix-2 junction with the corresponding O-acyl iso-dipeptide leads to a completely unfolded state that only refolds after intramolecular O --> N acyl migration. Herein, we report on an Id HLH analog based on the substitution of the Pro-Ser motif at the helix-1-loop junction with the corresponding O-acyl iso-dipeptide. This analog has been successfully synthesized by solid-phase Fmoc chemistry upon suppression of DKP formation. No secondary structure could be detected for the O-acyl iso-peptide before its conversion into the native form by O --> N acyl shift. These results show that the loop-helix junctions are determinant for the folded/unfolded state of the Id HLH domain. Further, despite the high risk of DKP formation, peptides containing O-acyl iso-Pro-Ser/Thr units are synthetically accessible by Fmoc chemistry.

Exploiting biocatalysis in peptide self-assembly

This review article covers recent developments in the use of enzyme-catalyzed reactions to control molecular self-assembly (SA), an area that merges the advantages of biocatalysis with soft materials self-assembly. This approach is attractive because it combines biological (chemo-, regio-, and enantio-) selectivity with the versatility of bottom up nanofabrication through dynamic SA. We define enzyme-assisted SA (e-SA) as the production of molecular building blocks from nonassembling precursors via enzymatic catalysis, where molecular building blocks form ordered structures via noncovalent interactions. The molecular design of SA precursors is discussed in terms of three key components related to (i) enzyme recognition, (ii) molecular switching mechanisms, and (iii) supramolecular interactions that underpin SA. This is followed by a discussion of a number of unique features of these systems, including spatiotemporal control of nucleation and structure growth, the possibility of controlling mechanical properties and the defect correcting and component selecting capabilities of systems that operate under thermodynamic control. Applications in biomedicine (biosensing, controlled release, matrices for wound healing, controlling cell fate by gelation) and bio(nano)technology (biocatalysts immobilization, nanofabrication, templating, and intracellular imaging) are discussed. Overall, e-SA allows for unprecedented control over SA processes and provides a step forward toward production of nanostructures of higher complexity and with fewer defects as desired for next generation nanomaterials.

"Click peptide": pH-triggered in situ production and aggregation of monomer Abeta1-42

The intense and uncontrollable self-assembling nature of amyloid beta peptide (Abeta) 1-42 is known to cause difficulties in preparing monomeric Abeta1-42; this results in irreproducible or discrepant study outcomes. Herein, we report novel features of a pH click peptide of Abeta1-42 that was designed to overcome these problems. The click peptide is a water-soluble precursor peptide of Abeta1-42 with an O-acyl isopeptide structure between the Gly25-Ser26 sequence. The click peptide adopts and retains a monomeric, random coil state under acidic conditions. Upon change to neutral pH (pH click), the click peptide converts to Abeta1-42 promptly (t(1/2) approximately 10 s) and quantitatively through an O-to-N intramolecular acyl migration. As a result of this quick and irreversible conversion, monomer Abeta1-42 with a random coil structure is produced in situ. Moreover, the oligomerization, amyloid fibril formation and conformational changes of the produced Abeta1-42 can be observed over time. This click peptide strategy should provide a reliable experimental system to investigate the pathological role of Abeta1-42 in Alzheimer's disease.

O-acyl isopeptide method: efficient synthesis of isopeptide segment and application to racemization-free segment condensation

We report the establishment of the O-acyl isopeptide method-based racemization-free segment condensation reaction toward future chemical protein synthesis. Peptide segments containing C-terminal O-acyl Ser/Thr residues were successfully synthesized by use of a lower nucleophilic base cocktail for Fmoc removal, and then coupled to an amino group of a peptide-resin without side reactions or epimerization. We also succeeded in performing the segment condensation in a sequential manner and in solution phase conditions as well.

Switching from the unfolded to the folded state of the helix-loop-helix domain of the Id proteins based on the O-acyl isopeptide method

The inhibitors of DNA binding and cell differentiation Id1-4 are helix-loop-helix (HLH) proteins that negatively regulate DNA transcription by forming inactive dimers with ubiquitous and tissue-specific bHLH proteins, including E47 and MyoD, respectively. Their highly conserved HLH domains are essential for heterodimerization, but can also self-associate to highly stable, alpha-helix-rich structures at low micromolar peptide concentrations. Here, we show that the introduction of an O-acyl isodipeptide unit involving the putative N-cap serine residue of the C-terminal helix completely abrogates the propensity of the Id HLH analogue for any secondary and tertiary structure, resulting in a random coil, as shown by CD measurements in nonbuffered aqueous solutions. However, the HLH fold reappears as soon as an O-->N intramolecular acyl migration, which occurs spontaneously under physiological conditions, restores the native N-cap serine residue. These results show that changes addressing the N-terminus of the C-terminal helix can dramatically influence the HLH structure, and suggest that local interactions at the junction between the loop and the C-terminal helix might be crucial during the HLH folding process. Furthermore, the present study contributes to the evaluation of the O-acyl isodipeptide unit as a powerful tool to introduce a conformational switch into peptides.