Self-Assembly and Anti-Amyloid Cytotoxicity Activity of Amyloid beta Peptide Derivatives

Electrospinning of Self-Assembling Oligopeptides into Nanofiber Mats: The Impact of Peptide Composition and End Groups

Low-molecular-weight oligopeptides can be electrospun into nanofiber mats. However, the mechanism underlying their electrospinnability is not well-understood. In this study, we used solid-phase peptide synthesis to produce the oligopeptide FFKK, to which the aromatic end-capping groups naphthalene, pyrene, and tetraphenylporphyrin were attached. Nuclear magnetic resonance, circular dichroism, and electrospray ionization mass spectrometry were used to characterize the oligopeptide structures. We investigated the effect of end-caps and oligopeptide concentration on their self-assembly as well as on their electrospinnability in fluorinated solvents. All oligopeptides with aromatic end-caps were amenable to electrospinning. Attenuated total reflectance Fourier transform infrared spectroscopy and microrheology results support the hypothesis that at sufficiently high concentrations, the self-assembled structures interact strongly, which facilitates electrospinning. Moreover, the results from this fundamental study can be extended to nonpeptidic small molecules possessing strong intermolecular interactions.

Molecular Simulation of the Binding of Amyloid Beta to Apolipoprotein A-I in High-Density Lipoproteins

Disrupted clearance of amyloid beta (Aβ) from the brain enhances its aggregation and formation of amyloid plaques in Alzheimer's disease. The most abundant protein constituent of circulating high-density lipoprotein (HDL) particles, apoA-I, readily crosses the blood-brain barrier from periphery circulation, exhibits low-micromolar binding affinity for soluble, neurotoxic forms of Aβ, and modulates Aβ aggregation and toxicity in vitro. Its highly conserved N-terminal sequence, 42LNLKLLD48 ('LN'), has been proposed as a binding region for Aβ. However, high-resolution structural characterisation of the mechanism of HDL-Aβ interaction is very difficult to attain. Molecular dynamics simulations were conducted to investigate for the first time the interaction of Aβ and the 'LN' segment of apoA-I. Favourable binding of Aβ by HDLs was found to be driven by hydrophobic and hydrogen-bonding interactions predominantly between the 'LN' segment of apoA-I and Aβ. Preferential binding of Aβ may proceed in small, protein-rich HDLs whereby solvent-exposed hydrophobic 'LN' segments of apoA-I interact specifically with Aβ, stabilising it on the HDL surface in a possibly non-amyloidogenic conformation, facilitating effective Aβ clearance. These findings rationalise the potentially therapeutic role of HDLs in reducing Aβ aggregation and toxicity, and of peptide mimics of the apoA-I interacting region in blocking Aβ aggregation.

Co-Localized in Amyloid Plaques Cathepsin B as a Source of Peptide Analogs Potential Drug Candidates for Alzheimer's Disease

Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by extracellular amyloid plaques, predominantly consisting of amyloid-β (Aβ) peptides. The oligomeric form of Aβ is acknowledged as the most neurotoxic, propelling the pathological progression of AD. Interestingly, besides Aβ, other proteins are co-localized within amyloid plaques. Peptide analogs corresponding to the "aggregation-prone" regions (APRs) of these proteins could exhibit high-affinity binding to Aβ and significant inhibitory potential against the Aβ oligomerization process. The peptide analogs of co-localized protease, Cathepsin B, may act as such potent inhibitors. In silico studies on the complexes of the oligomeric state of Aβ and Cathepsin B peptide analogs were performed utilizing molecular docking and molecular dynamics simulations, revealing that these analogs disrupt the β-sheet-rich core of Aβ oligomers, a critical structural feature of their stability. Of the four peptide analogs evaluated, two demonstrated considerable potential by effectively destabilizing oligomers while maintaining low self-aggregation propensity, i.e., a crucial consideration for therapeutic safety. These findings point out the potential of APR-derived peptide analogs from co-localized proteins as innovative agents against AD, paving the way for further exploration in peptide-based therapeutic development.

Rotating magnetic field inhibits Aβ protein aggregation and alleviates cognitive impairment in Alzheimer's disease mice

Amyloid beta (Aβ) monomers aggregate to form fibrils and amyloid plaques, which are critical mechanisms in the pathogenesis of Alzheimer's disease (AD). Given the important role of Aβ1-42 aggregation in plaque formation, leading to brain lesions and cognitive impairment, numerous studies have aimed to reduce Aβ aggregation and slow AD progression. The diphenylalanine (FF) sequence is critical for amyloid aggregation, and magnetic fields can affect peptide alignment due to the diamagnetic anisotropy of aromatic rings. In this study, we examined the effects of a moderate-intensity rotating magnetic field (RMF) on Aβ aggregation and AD pathogenesis. Results indicated that the RMF directly inhibited Aβ amyloid fibril formation and reduced Aβ-induced cytotoxicity in neural cells in vitro. Using the AD mouse model APP/PS1, RMF restored motor abilities to healthy control levels and significantly alleviated cognitive impairments, including exploration and spatial and non-spatial memory abilities. Tissue examinations demonstrated that RMF reduced amyloid plaque accumulation, attenuated microglial activation, and reduced oxidative stress in the APP/PS1 mouse brain. These findings suggest that RMF holds considerable potential as a non-invasive, high-penetration physical approach for AD treatment.

Secretomic changes of amyloid beta peptides on Alzheimer's disease related proteins in differentiated human SH-SY5Y neuroblastoma cells

Alzheimer's disease (AD) is a neurodegenerative disease that causes physical damage to neuronal connections, leading to brain atrophy. This disruption of synaptic connections results in mild to severe cognitive impairments. Unfortunately, no effective treatment is currently known to prevent or reverse the symptoms of AD. The aim of this study was to investigate the effects of three synthetic peptides, i.e., KLVFF, RGKLVFFGR and RIIGL, on an AD in vitro model represented by differentiated SH-SY5Y neuroblastoma cells exposed to retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). The results demonstrated that RIIGL peptide had the least significant cytotoxic activity to normal SH-SY5Y while exerting high cytotoxicity against the differentiated cells. The mechanism of RIIGL peptide in the differentiated SH-SY5Y was investigated based on changes in secretory proteins compared to another two peptides. A total of 380 proteins were identified, and five of them were significantly detected after treatment with RIIGL peptide. These secretory proteins were found to be related to microtubule-associated protein tau (MAPT) and amyloid-beta precursor protein (APP). RIIGL peptide acts on differentiated SH-SY5Y by regulating amyloid-beta formation, neuron apoptotic process, ceramide catabolic process, and oxidative phosphorylation and thus has the potentials to treat AD.

Enhancement of Aggregate Formation Through Aromatic Compound Adsorption in Elastin-like Peptide (FPGVG)5 Analogs

Elastin-like peptides (ELPs) exhibit temperature-dependent reversible self-assembly. Repetitive sequences derived from elastin, such as Val-Pro-Gly-Val-Gly (VPGVG), are essential for the self-assembly of ELPs. Previously, we developed (FPGVG)5 (F5), in which the first valine residue in the VPGVG sequence was replaced with phenylalanine, which showed strong self-aggregation ability. This suggests that interactions through the aromatic amino acid residues of ELPs could play an important role in self-assembly. In this study, we investigated the thermoresponsive behavior of F5 analogs in the presence of aromatic compounds. Turbidimetry, spectroscopy, and fluorescence measurements demonstrated that aromatic compounds interacted with F5 analogs below the transition temperature and enhanced the self-assembly ability of ELPs by stabilizing amyloid-like structures. Furthermore, quantitative high-performance liquid chromatography analyses showed that the F5 analogs could adsorb and remove hydrophobic aromatic compounds from aqueous solutions during aggregate formation. These results suggested that the F5 analogs can be applicable as scavengers of aromatic compounds.

Self-assembling tripeptide forming water-bound channels and hydrogels

D-Ser(tBu)-L-Phe-L-Trp is described as a self-assembling tripeptide that yields nanofibrillar hydrogels at physiological conditions (phosphate buffer at pH 7.4). The peptide is characterized by several spectroscopic methods, such as circular dichroism and fluorescence, oscillatory rheometry, and transmission electron microscopy. Single-crystal X-ray diffraction reveals supramolecular packing into water-bound channels and allows the visualization of the intermolecular interactions holding together peptide stacks.

APPI-Derived Cyclic Peptide Enhances Aβ42 Aggregation and Reduces Aβ42-Mediated Membrane Destabilization and Cytotoxicity

An amyloid precursor protein inhibitor (APPI) and amyloid beta 42 (Aβ42) are both subdomains of the human transmembrane amyloid precursor protein (APP). In the brains of patients with Alzheimer's disease (AD), Aβ42 oligomerizes into aggregates of various sizes, with intermediate, low-molecular-weight Aβ42 oligomers currently being held to be the species responsible for the most neurotoxic effects associated with the disease. Strategies to ameliorate the toxicity of these intermediate Aβ42 oligomeric species include the use of short, Aβ42-interacting peptides that either inhibit the formation of the Aβ42 oligomeric species or promote their conversion to high-molecular-weight aggregates. We therefore designed such an Aβ42-interacting peptide that is based on the β-hairpin amino acid sequence of the APPI, which exhibits high similarity to the β-sheet-like aggregation site of Aβ42. Upon tight binding of this 20-mer cyclic peptide to Aβ42 (in a 1:1 molar ratio), the formation of Aβ42 aggregates was enhanced, and consequently, Aβ42-mediated cell toxicity was ameliorated. We showed that in the presence of the cyclic peptide, interactions of Aβ42 with both plasma and mitochondrial membranes and with phospholipid vesicles that mimic these membranes were inhibited. Specifically, the cyclic peptide inhibited Aβ42-mediated mitochondrial membrane depolarization and reduced Aβ42-mediated apoptosis and cell death. We suggest that the cyclic peptide modulates Aβ42 aggregation by enhancing the formation of large aggregates─as opposed to low-molecular-weight intermediates─and as such has the potential for further development as an AD therapeutic.

Neuroprotective Effect of NO-Delivery Dinitrosyl Iron Complexes (DNICs) on Amyloid Pathology in the Alzheimer's Disease Cell Model

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive impairment, memory loss, and behavioral deficits. β-amyloid1-42 (Aβ1-42) aggregation is a significant cause of the pathogenesis in AD. Despite the numerous types of research, the current treatment efficacy remains insufficient. Hence, a novel therapeutic strategy is required. Nitric oxide (NO) is a multifunctional gaseous molecule. NO displays a neuroprotective role in the central nervous system by inhibiting the Aβ aggregation and rescuing memory and learning deficit through the NO signaling pathway. Targeting the NO pathway might be a therapeutic option; however, NO has a limited half-life under the biological system. To address this issue, a biomimetic dinitrosyl iron complex [(NO)2Fe(μ-SCH2CH2COOH)2Fe(NO)2] (DNIC-COOH) that could stably deliver NO was explored in the current study. To determine whether DNIC-COOH exerts anti-AD efficacy, DNIC-COOH was added to neuron-like cells and primary cortical neurons along with Aβ1-42. This study found that DNIC-COOH protected neuronal cells from Aβ-induced cytotoxicity, potentiated neuronal functions, and facilitated Aβ1-42 degradation through the NO-sGC-cGMP-AKT-GSK3β-CREB/MMP-9 pathway.

Self-assembly of a peptide sequence, EKKE, composed of exclusively charged amino acids: Role of charge in morphology and lead binding

The self-assembly of peptides is influenced by their amino acid sequence and other factors including pH, charge, temperature, and solvent. Herein, we explore whether a four-residue sequence, EKKE, consisting of exclusively charged amino acids shows the propensity to form self-assembled ordered nanostructures and whether the overall charge plays any role in morphological and functional properties. From a combination of experimental data provided by Thioflavin T fluorescence, Congo red absorbance, circular dichroism spectroscopy, dynamic light scattering, field emission-scanning electron microscopy, atomic force microscopy, and confocal microscopy, it is clear that the all-polar peptide and charged EKKE sequence shows a pH-dependent tendency to form amyloid-like structures, and the self-assembled entities under acidic, basic and neutral conditions exhibit morphological variation. Additionally, the ability of the self-assembled amyloid nanostructures to bind to the toxic metal, lead (Pb²⁺ ), was demonstrated from the analysis of the ultraviolet absorbance and X-ray photoelectron spectroscopy data. The modulation at the sequence level for the amyloid-forming EKKE scaffold can further extend its potential role not only in the remediation of other toxic metals but also towards biomedical applications.

Chiral-engineered supraparticles: Emerging tools for drug delivery

The handedness of chiral-engineered supraparticles (CE-SPs) influences their interactions with cells and proteins, as evidenced by the increased penetration of breast, cervical, and myeloma cell membranes by d-chirality-coordinated SPs. Quartz crystal dissipation and isothermal titration calorimetry have been used to investigate such chiral-specific interactions. d-SPs are more thermodynamically stable compared with l-SPs in terms of their adhesion. Proteases and other endogenous proteins can be shielded by the opposite chirality of d-SPs, resulting in longer half-lives. Incorporating nanosystems with d-chirality increases uptake by cancer cells and prolongs in vivo stability, demonstrating the importance of chirality in biomaterials. Thus, as we discuss here, chiral nanosystems could enhance drug delivery systems, tumor markers, and biosensors, among other biomaterial-based technologies, by allowing for better control over their features.

An intelligent peptide recognizes and traps Mycobacterium tuberculosis to inhibit macrophage phagocytosis

Tuberculosis is a major public health concern worldwide, and it is a serious threat to human health for a long period. Macrophage phagocytosis of Mycobacterium tuberculosis (M. tuberculosis) is a crucial process for granuloma formation, which shelters the bacteria and gives them an opportunity for re-activation and spread. Herein, we report an intelligent anti-microbial peptide that can recognize and trap the M. tuberculosis, inhibiting the macrophage phagocytosis process. The peptide (Bis-Pyrene-KLVFF-WHSGTPH, in abbreviation as BFH) first self-assembles into nanoparticles, and then forms nanofibers upon recognizing and binding M. tuberculosis. Subsequently, BFH traps M. tuberculosis by the in situ formed nanofibrous networks and the trapped M. tuberculosis are unable to invade host cells (macrophages). The intelligent anti-microbial peptide can significantly inhibit the phagocytosis of M. tuberculosis by macrophages, thereby providing a favorable theoretical basis for inhibiting the formation of tuberculosis granulomas.

The Real-Time Validation of the Effectiveness of Third-Generation Hyperbranched Poly(ɛ-lysine) Dendrons-Modified KLVFF Sequences to Bind Amyloid-β1-42 Peptides Using an Optical Waveguide Light-Mode Spectroscopy System

The aggregation of cytotoxic amyloid peptides (Aβ_1-42) is widely recognised as the cause of brain tissue degeneration in Alzheimer's disease (AD). Indeed, evidence indicates that the deposition of cytotoxic Aβ_1-42 plaques formed through the gradual aggregation of Aβ_1-42 monomers into fibrils determines the onset of AD. Thus, distinct Aβ_1-42 inhibitors have been developed, and only recently, the use of short linear peptides has shown promising results by either preventing or reversing the process of Aβ_1-42 aggregation. Among them, the KLVFF peptide sequence, which interacts with the hydrophobic region of Aβ_16-20, has received widespread attention due to its ability to inhibit fibril formation of full-length Aβ_1-42. In this study, hyperbranched poly-L-lysine dendrons presenting sixteen KLVFF at their uppermost molecular branches were designed with the aim of providing the KLVFF sequence with a molecular scaffold able to increase its stability and of improving Aβ_1-42 fibril formation inhibitory effect. These high-purity branched KLVFF were used to functionalise the surface of the metal oxide chip of the optical waveguide lightmode spectroscopy sensor showing the more specific, accurate and rapid measurement of Aβ_1-42 than that detected by linear KLVFF peptides.

The Anti-Aggregative Peptide KLVFF Mimics Aβ1-40 in the Modulation of Nicotinic Receptors: Implications for Peptide-Based Therapy

In recent years, the inhibition of beta-amyloid (Aβ) aggregation has emerged as a potential strategy for Alzheimer’s disease. KLVFF, a small peptide corresponding to the aminoacidic sequence 16-20 of Aβ, reduces Aβ fibrillation dose dependently. Therefore, the toxic and functional characterization of its brain activity is fundamental for clarifying its potential therapeutic role. Accordingly, we studied the modulatory role of KLVFF on the cholinergic receptors regulating dopamine and noradrenaline release in rat synaptosomes. Nicotinic receptors on dopaminergic nerve terminals in the nucleus acccumbens are inhibited by KLVFF, which closely resembles full-length Aβ1-40. Moreover, KLVFF entrapped in synaptosomes does not modify the nicotinic receptor’s function, suggesting that external binding to the receptor is required for its activity. The cholinergic agent desformylflustrabromine counteracts the KLVFF effect. Remarkably, muscarinic receptors on dopaminergic terminals and nicotinic receptors regulating noradrenaline release in the hippocampus are completely insensitive to KLVFF. Based on our findings, KLVFF mimics Aβ1-40 as a negative modulator of specific nicotinic receptor subtypes affecting dopamine transmission in the rat brain. Therefore, new pharmacological strategies using the anti-aggregative properties of KLVFF need to be evaluated for potential interference with nicotinic receptor-mediated transmission.

Macrocyclic Cavitand β-Cyclodextrin Inhibits the Alcohol-induced Trypsin Aggregation

Trypsin, the most abundant pancreatic protein, aids in protein digestion by hydrolysis and exhibits aggregation propensity in presence of alcohol which can further lead to pancreatitis and eventually pancreatic cancer. Herein, by several experimental and theoretical approaches, we unearth the inhibition of alcohol-induced aggregation of Trypsin by macrocyclic cavitand, β-cyclodextrin (β-CD). β-CD interacts with the native protein and shows inhibitory effect in a dose dependent manner. Moreover, the secondary structures and morphologies of Trypsin in presence of β-CD also clearly emphasize the inhibition of fibril formation. From Fluorescence Correlation Spectroscopy, we observed an enhancement in diffusion time of Nile Red with ~ 2.5 times increase in hydrodynamic radius, substantiating the presence of fibrillar structure. Trypsin also shows reduction in its functional activity due to alcohol-induced aggregation. Our simulation data reports the probable residues responsible for fibril formation which was validated by molecular docking studies.

Dipeptide self-assembly into water-channels and gel biomaterial

Dipeptides are convenient building blocks for supramolecular gel biomaterials that can be produced on a large scale at low cost and do not persist in the environment. In the case of unprotected sequences, hydrophobicity is a key requirement to enable gelation, with Phe-Phe standing out for its self-assembling ability. Conversely, more hydrophilic sequences such as homochiral dipeptides Phe-Val and Val-Phe neither fibrillate nor gel aqueous buffers and their crystal structures reveal amphipathic layers. In this work, we test emerging rules for the design of self-assembling dipeptides using heterochiral Phe-Val and Val-Phe. Each dipeptide is characterized by ¹H- and ¹³C-NMR, LC-MS, circular dichroism, infrared and Raman spectroscopies, rheology, electron microscopy, and single-crystal X-ray diffraction. In particular, D-Phe-L-Val is the first heterochiral dipeptide to self-assemble into supramolecular water-channels whose cavity is defined by four peptide molecules arranged head-to-tail. This minimalistic sequence is devoid of amyloid character as probed by thioflavin T fluorescence and it displays excellent biocompatibility in vitro. The dataset provided, through comparison with the literature, significantly advances the definition of molecular design rules for minimalistic unprotected dipeptides that self-assemble into water-channels and biocompatible gels, to assist with the future development of supramolecular biomaterials with fine control over nanomorphological features for a variety of applications.

Single-atom substitution enables supramolecular diversity from dipeptide building blocks

Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by ¹H- and ¹³C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.

Surface Modification of Curcumin Microemulsions by Coupling of KLVFF Peptide: A Prototype for Targeted Bifunctional Microemulsions

Curcumin is one of the most promising natural therapeutics for use against Alzheimer's disease. The major limitations of curcumin are its low oral bioavailability and difficulty in permeating the blood-brain barrier. Therefore, designing a delivery system of curcumin to overcome its limitations must be employed. KLVFF, a peptide known as an amyloid blocker, was used in this study as a targeting moiety to develop a targeted drug delivery system. A prototype of transnasal KLVFF conjugated microemulsions containing curcumin (KLVFF-Cur-ME) for the nose-to-brain delivery was fabricated. The KLVFF-Cur-ME was developed by a titration method. A conjugation of KLVFF was performed through a carbodiimide reaction, and the conjugation efficiency was confirmed by FTIR and DSC technique. KLVFD-Cur-ME was characterized for the drug content, globule size, zeta potential, and pH. A transparent and homogeneous KLVFF-Cur-ME is achieved with a drug content of 80.25% and a globule size of 76.1 ± 2.5 nm. The pH of KLVFF-Cur-ME is 5.33 ± 0.02, indicating non-irritation to nasal tissues. KLVFD-Cur-ME does not show nasal ciliotoxicity. An ex vivo diffusion study revealed that KLVFF-Cur-ME partitions the porcine nasal mucosa through diffusion, following the Higuchi model. This investigation demonstrates the successful synthesis of a bifunctional KLVFF-Cur-ME as a novel prototype to deliver anti-Aβ aggregation via an intranasal administration.

Identification of β-aminopyrrolidine containing peptides as β-amyloid aggregation inhibitors for Alzheimer's disease

Alzheimer's disease (AD) is caused by a series of events initiated by the production and aggregation of the amyloid β-protein (Aβ). In the early stages of the disease, Aβ is released in a soluble form then progressively forms oligomeric, multimeric, and fibrillar aggregates, triggering neurodegeneration. Thus, development of inhibitors that initiate reverse Aβ aggregation is thought to be a logical approach in treating AD. In this context, we developed β-aminopyrrolidine containing 12 mer peptide 3 which is very potent in inhibiting the Aβ aggregation and also reducing Aβ(42)-induced cytotoxicity.

Mechanism of Cellular Formation and In Vivo Seeding Effects of Hexameric β-Amyloid Assemblies

The β-amyloid peptide (Aβ) is found as amyloid fibrils in senile plaques, a typical hallmark of Alzheimer's disease (AD). However, intermediate soluble oligomers of Aβ are now recognized as initiators of the pathogenic cascade leading to AD. Studies using recombinant Aβ have shown that hexameric Aβ in particular acts as a critical nucleus for Aβ self-assembly. We recently isolated hexameric Aβ assemblies from a cellular model, and demonstrated their ability to enhance Aβ aggregation in vitro. Here, we report the presence of similar hexameric-like Aβ assemblies across several cellular models, including neuronal-like cell lines. In order to better understand how they are produced in a cellular context, we investigated the role of presenilin-1 (PS1) and presenilin-2 (PS2) in their formation. PS1 and PS2 are the catalytic subunits of the γ-secretase complex that generates Aβ. Using CRISPR-Cas9 to knockdown each of the two presenilins in neuronal-like cell lines, we observed a direct link between the PS2-dependent processing pathway and the release of hexameric-like Aβ assemblies in extracellular vesicles. Further, we assessed the contribution of hexameric Aβ to the development of amyloid pathology. We report the early presence of hexameric-like Aβ assemblies in both transgenic mice brains exhibiting human Aβ pathology and in the cerebrospinal fluid of AD patients, suggesting hexameric Aβ as a potential early AD biomarker. Finally, cell-derived hexameric Aβ was found to seed other human Aβ forms, resulting in the aggravation of amyloid deposition in vivo and neuronal toxicity in vitro.

Amyloidogenic Properties of Peptides Derived from the VHL Tumor Suppressor Protein

The von Hippel-Lindau tumor suppressor protein (pVHL) is involved in maintaining cellular oxygen homeostasis through the regulated degradation of HIF-α. The intrinsically disordered nature of pVHL makes it prone to aggregation that impairs its function, and this is further aggravated in mutant versions of the protein, thus promoting tumor development. By using in silico analysis, we predicted six peptide fragments from pVHL to be amyloidogenic. This was verified for two of the peptides by biophysical approaches, which demonstrated self-assembly and formation of β-sheet-rich aggregates, which, under transmission electron microscopy, atomic force microscopy, and X-ray diffraction, displayed typical fibrillar amyloid characteristics. These motifs may serve as proxies for exploring the nature of pVHL aggregation.

Contribution of the Commensal Microflora to the Immunological Homeostasis and the Importance of Immune-Related Drug Development for Clinical Applications

Not long ago, self-reactive immune activity was considered as pathological trait. A paradigm shift has now led to the recognition of autoimmune processes as part of natural maintenance of molecular homeostasis. The immune system is assigned further roles beneath the defense against pathogenic organisms. Regarding the humoral immune system, the investigation of natural autoantibodies that are frequently found in healthy individuals has led to further hypotheses involving natural autoimmunity in other processes as the clearing of cellular debris or decrease in inflammatory processes. However, their role and origin have not been entirely clarified, but accumulating evidence links their formation to immune reactions against the gut microbiome. Antibodies targeting highly conserved proteins of the commensal microflora are suggested to show self-reactive properties, following the paradigm of the molecular mimicry. Here, we discuss recent findings, which demonstrate potential links of the commensal microflora to the immunological homeostasis and highlight the possible implications for various diseases. Furthermore, specific components of the immune system, especially antibodies, have become a focus of attention for the medical management of various diseases and provide attractive treatment options in the future. Nevertheless, the development and optimization of such macromolecules still represents a very time-consuming task, shifting the need to more medical agents with simple structural properties and low manufacturing costs. Synthesizing only the biologically active sites of antibodies has become of great interest for the pharmaceutical industry and offers a wide range of therapeutic application areas as it will be discussed in the present review article.

Amyloid-like Self-Assembly of a Hydrophobic Cell-Penetrating Peptide and Its Use as a Carrier for Nucleic Acids

Cell-penetrating peptides (CPPs) are a topical subject potentially exploitable for creating nanotherapeutics for the delivery of bioactive loads. These compounds are often classified into three major categories according to their physicochemical characteristics: cationic, amphiphilic, and hydrophobic. Among them, the group of hydrophobic CPPs has received increasing attention in recent years due to toxicity concerns posed by highly cationic CPPs. The hexapeptide PFVYLI (P, proline; F, phenylalanine; V, valine; Y, tyrosine; L, leucine; and I, isoleucine), a fragment derived from the C-terminal portion of α1-antitrypsin, is a prototypal example of hydrophobic CPP. This sequence shows reduced cytotoxicity and a capacity of nuclear localization, and its small size readily hints at its suitability as a building block to construct nanostructured materials. In this study, we examine the self-assembling properties of PFVYLI and investigate its ability to form noncovalent complexes with nucleic acids. By using a combination of biophysical tools including synchrotron small-angle X-ray scattering and atomic force microscopy-based infrared spectroscopy, we discovered that this CPP self-assembles into discrete nanofibrils with remarkable amyloidogenic features. Over the course of days, these fibrils coalesce into rodlike crystals that easily reach the micrometer range. Despite lacking cationic residues in the composition, PFVYLI forms noncovalent complexes with nucleic acids that retain β-sheet pairing found in amyloid aggregates. In vitro vectorization experiments performed with double-stranded DNA fragments indicate that complexes promote the internalization of nucleic acids, revealing that tropism toward cell membranes is preserved upon complexation. On the other hand, transfection assays with splice-correction oligonucleotides (SCOs) for luciferase expression show limited bioactivity across a narrow concentration window, suggesting that the propensity to form amyloidogenic aggregates may trigger endosomal entrapment. We anticipate that the findings presented here open perspectives for using this archetypical hydrophobic CPP in the fabrication of nanostructured scaffolds, which potentially integrate properties of amyloids and translocation capabilities of CPPs.

A Mechanism for the Inhibition of Tau Neurotoxicity: Studies with Artificial Membranes, Isolated Mitochondria, and Intact Cells

It is currently believed that molecular agents that specifically bind to and neutralize the toxic proteins/peptides, amyloid β (Aβ42), tau, and the tau-derived peptide PHF6, hold the key to attenuating the progression of Alzheimer's disease (AD). We thus tested our previously developed nonaggregating Aβ42 double mutant (Aβ42_DM) as a multispecific binder for three AD-associated molecules, wild-type Aβ42, the tau_K174Q mutant, and a synthetic PHF6 peptide. Aβ42_DM acted as a functional inhibitor of these molecules in in vitro assays and in neuronal cell-based models of AD. The double mutant bound both cytotoxic tau_K174Q and synthetic PHF6 and protected neuronal cells from the accumulation of tau in cell lysates and mitochondria. Aβ42_DM also reduced toxic intracellular levels of calcium and the overall cell toxicity induced by overexpressed tau, synthetic PHF6, Aβ42, or a combination of PHF6and Aβ42. Aβ42_DM inhibited PHF6-induced overall mitochondrial dysfunction: In particular, Aβ42_DM inhibited PHF6-induced damage to submitochondrial particles (SMPs) and suppressed PHF6-induced elevation of the ζ-potential of inverted SMPs (proxy for the inner mitochondrial membrane, IMM). PHF6 reduced the lipid fluidity of cardiolipin/DOPC vesicles (that mimic the IMM) but not DOPC (which mimics the outer mitochondrial membrane), and this effect was inhibited by Aβ42_DM. This inhibition may be explained by the conformational changes in PHF6 induced by Aβ42_DM in solution and in membrane mimetics. On this basis, the paper presents a mechanistic explanation for the inhibitory activity of Aβ42_DM against Aβ42- and tau-induced membrane permeability and cell toxicity and provides confirmatory evidence for its protective function in neuronal cells.

Tau/Aβ chimera peptides: A Thioflavin-T and MALDI-TOF study of Aβ amyloidosis in the presence of Cu(II) or Zn(II) ions and total lipid brain extract (TLBE) vesicles

Currently, Alzheimer's Disease (AD) is a complex neurodegenerative condition, with limited therapeutic options. Several factors, like Amyloid β (Aβ) aggregation, tau protein hyperphosphorylation, bio-metals dyshomeostasis and oxidative stress contribute to AD pathogenesis. These pathogenic processes might occur in the aqueous phase but also on neuronal membranes. Thus, investigating the connection between Aβ and biomembranes, becomes important for unveiling the molecular mechanism underlying Aβ amyloidosis as a critical event in AD pathology. In this work, the interaction of two peptides, made up with hybrid sequences from Tau protein 9-16 (EVMEDHAG) or 26-33 (QGGYTMHQ) N-terminal domain and Aβ_16-20 (KLVFF) hydrophobic region, with full length Aβ40 or Aβ42 peptides is reported. The studied "chimera" peptides Ac-EVMEDHAGKLVFF-NH₂ (τ_9-16-KL) and Ac-QGGYTMHQKLVFF-NH₂ (τ_26-33-KL) are endowed with Aβ recognition and metal ion interaction capabilities provided by the tau or Aβ sequences, respectively. These peptides were characterized in previous study along with their metal dependent interaction and amyloidogenesis, either in the presence or absence of metal ion and artificial membranes made up with Total Lipid Brain Extract (TLBE) components, (Sciacca et al., 2020). In the present paper, the ability of the two peptides to inhibit Aβ aggregation is studied using composite experimental conditions including aqueous solution, the presence of metal ions (Cu or Zn), the presence of lipid vesicles mimicking neuronal membranes as well as the co-presence of metals and TLBE artificial membranes. We used Thioflavine-T (ThT) fluorescence or MALDI-TOF spectrometry analysis of Aβ limited proteolysis to respectively monitor the Aβ aggregation kinetic or validation of the Aβ interacting regions. We demonstrate that τ_9-16-KL and τ_26-33-KL peptides differently affect Aβ aggregation kinetics, with the tau sequence playing a crucial role. The results are discussed in terms of chimera's peptides hydrophobicity and electrostatic driven interactions at the aqueous/membrane interface.

Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer

We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.

Self-Assembly of Block Heterochiral Peptides into Helical Tapes

Patterned substitution of d-amino acids into the primary sequences of self-assembling peptides influences molecular-level packing and supramolecular morphology. We report that block heterochiral analogs of the model amphipathic peptide KFE8 (Ac-FKFEFKFE-NH2), composed of two FKFE repeat motifs with opposite chirality, assemble into helical tapes with dimensions greatly exceeding those of their fibrillar homochiral counterparts. At sufficient concentrations, these tapes form hydrogels with reduced storage moduli but retain the shear-thinning behavior and consistent mechanical recovery of the homochiral analogs. Varying the identity of charged residues (FRFEFRFE and FRFDFRFD) produced similarly sized nonhelical tapes, while a peptide with nonenantiomeric l- and d-blocks (FKFEFRFD) formed helical tapes closely resembling those of the heterochiral KFE8 analogs. A proposed energy-minimized model suggests that a kink at the interface between l- and d-blocks leads to the assembly of flat monolayers with nonidentical surfaces that display alternating stacks of hydrophobic and charged groups.

Tandem-Homodimer of a β-Sheet-Forming Short Peptide Inhibits Random-to-β Structural Transition of Its Original Monomer

There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.

Engineering Nanogels for Drug Delivery to Pathogenic Fungi Aspergillus fumigatus by Tuning Polymer Amphiphilicity

Invasive aspergillosis is a serious threat to immunodeficient and critically ill patients caused mainly by the fungus Aspergillus fumigatus. Here, poly(glycidol)-based nanogels (NGs) are proposed as delivery vehicles for antifungal agents for sustained drug release. NGs are formed by simple self-assembly of random copolymers, followed by oxidative cross-linking of thiol functionalities. We investigate the impact of copolymer amphiphilicity on NG interaction with mature fungal hyphae in order to select the optimal drug delivery system for model antifungal drug amphotericin B. The results show that drug-loaded NGs decrease minimal inhibitory concentration (MIC) for around four times and slow down the fungal biofilm synthesis at concentrations lower than MIC. Our results suggest that amphiphilicity of nanoparticle's polymer matrix is an important factor in understanding the action of nanocarriers toward fungal cells and should be considered in the development of nanoparticle-based antifungal therapy.

Peptide-induced RAFT polymerization via an amyloid-β17-20-based chain transfer agent

We here describe the synthesis of a novel peptide/polymer-conjugate, embedding the amyloid-β (Aβ) protein core sequence Leu-Val-Phe-Phe (LVFF, Aβ17-20) via RAFT polymerization. Based on a novel chain transfer-agent, the "grafting-from" approach effectively generates the well-defined peptide-polymer conjugates with appreciably high monomer conversion rate, resulting in mechanically stiffer peptide-functional cross-linked polymeric hydrogels.

Seeding and Growth of β-Amyloid Aggregates upon Interaction with Neuronal Cell Membranes

In recent years, the prevalence of amyloid neurodegenerative diseases such as Alzheimer's disease (AD) has significantly increased in developed countries due to increased life expectancy. This amyloid disease is characterized by the presence of accumulations and deposits of β-amyloid peptide (Aβ) in neuronal tissue, leading to the formation of oligomers, fibers, and plaques. First, oligomeric intermediates that arise during the aggregation process are currently thought to be primarily responsible for cytotoxicity in cells. This work aims to provide further insights into the mechanisms of cytotoxicity by studying the interaction of Aβ aggregates with Neuro-2a (N2a) neuronal cells and the effects caused by this interaction. For this purpose, we have exploited the advantages of advanced, multidimensional fluorescence microscopy techniques to determine whether different types of Aβ are involved in higher rates of cellular toxicity, and we measured the cellular stress caused by such aggregates by using a fluorogenic intracellular biothiol sensor. Stress provoked by the peptide is evident by N2a cells generating high levels of biothiols as a defense mechanism. In our study, we demonstrate that Aβ aggregates act as seeds for aggregate growth upon interacting with the cellular membrane, which results in cell permeability and damage and induces lysis. In parallel, these damaged cells undergo a significant increase in intracellular biothiol levels.

Targeting self-assembly peptide for inhibiting breast tumor progression and metastasis

The ubiquitous interactions between tumor cells and the surrounding microenvironment contribute to tumor metastasis, interrupting these communications has, therefore, a great potential for antimetastasis therapy. Here, we describe an in situ self-assembly strategy that limits direct contact between tumor cells and the tumor microenvironment (TME). In this strategy, the Lys-Leu-Val-Phe-Phe (KLVFF) peptide motifs are targeted to the tumor by hyaluronic acid (HA) functionalized liposomes and spontaneously undergo self-assembly to form nanofibers with a net-like structure wrapping around tumor cells. The fibrous nanostructures bury the membrane protrusions and thus hinder the migration and invasion of tumor cells, especially the transmigration through the fenestrated endothelium. The nanofibril coatings on tumor cells significantly block tumor cells induced platelet aggregation in vitro and prevent the adhesion of platelet around circulating tumor cells (CTCs) in vivo, thus limit the pro-metastasis effect of platelets and prevent the early metastasis. Furthermore, the nano-nets stably retain in the primary tumor site for over 72 h and effectively prevent the activation of intratumoral platelet, which suppress tumor progression and the spontaneous lung metastasis in 4T1 breast cancer mice model. Our study paves a promising avenue to combat tumor metastasis by regulating the interactions between tumor cells and the TME.

The effect of terminal groups and halogenation of KLVFF peptide on its activity as an inhibitor of β-amyloid aggregation

The aggregation of Aβ peptide into amyloid fibrils in the brain is associated with Alzheimer's disease (AD). Inhibition of Aβ aggregation seemed a potential treatment for AD. It was previously shown that a short fragment of Aβ peptide (KLVFF, 16-20) bound Aβ inhibited its aggregation. In this work, using KLVFF peptide, we synthesized two peptide families and then evaluated their inhibitory capacities by conventional assays such as thioflavin T (ThT) fluorescence spectroscopy, turbidity measurement, and the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS). The effect of peptide terminal groups on its inhibitory activity was first studied. Subsequently, the influence of halogenated amino acids on peptide anti-aggregation properties was investigated. We found that iodinated peptide with amine in the N and amide in the C termini, respectively, was the best inhibitor of Aβ fibers formation. Halogenated peptides seemed to decrease the number of Aβ fibrils; however, they did not reduce Aβ cytotoxicity. The data obtained in this work seemed promising in developing potential peptide drugs for treatment of AD.

Identification of a Novel Multifunctional Ligand for Simultaneous Inhibition of Amyloid-Beta (Aβ42) and Chelation of Zinc Metal Ion

Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn²⁺ chelating domain, derived from rapeseed meal, merge with a linker. The multifunctionality of the ligand was evaluated using a comprehensive set of MD simulations spanning up to 3.2 μs including Aβ relaxation, ligand-Zn²⁺ bilateral interaction, and, more importantly, ligand-Zn²⁺-Aβ₄₂ trilateral interactions. Analysis of the results strongly indicated that the bifunctional ligand can chelate zinc metal ion and avoid Aβ aggregation simultaneously. The present study illustrated that the proposed ligand has considerable hydrophobic interactions and hydrogen bonding with monomeric Aβ in the presence of zinc metal ion. Therefore, in light of these considerable interactions and contacts, the α-helical structure of Aβ has been enhanced, while the β-sheet formation is prevented and the α-helix native structure is protected. Furthermore, the analysis of interactions between Aβ and ligand-zinc complex revealed that the zinc metal ion is coordinated to Met13, the ending residue of the ligand and merely one residue in Aβ. The results have proven the previous experimental and theoretical findings in the literature about Aβ interactions with zinc metal ion and also Aβ interactions with the first domain of the proposed ligand. Moreover, the current research has evaluated the chelation using MD simulation and linear interaction energy (LIE) methods, and the result has been satisfactorily verified with previous experimental and theoretical (DFT) studies.

Rapid Growth of Acetylated Aβ(16-20) into Macroscopic Crystals

Aberrant assembly of the amyloid-β (Aβ) is responsible for the development of Alzheimer's disease, but can also be exploited to obtain highly functional biomaterials. The short Aβ fragment, KLVFF (Aβ_16-20), is crucial for Aβ assembly and considered to be an Aβ aggregation inhibitor. Here, we show that acetylation of KLVFF turns it into an extremely fast self-assembling molecule, reaching macroscopic ( i.e., mm) size in seconds. We show that KLVFF is metastable and that the self-assembly can be directed toward a crystalline or fibrillar phase simply through chemical modification, via acetylation or amidation of the peptide. Amidated KLVFF can form amyloid fibrils; we observed folding events of such fibrils occurring in as little as 60 ms. The ability of single KLVFF molecules to rapidly assemble as highly ordered macroscopic structures makes it a promising candidate for applications as a rapid-forming templating material.

The Conformation and Aggregation of Proline-Rich Surfactant-Like Peptides

The secondary structure of proline-rich surfactant-like peptides is examined for the first time and is found to be influenced by charged end groups in peptides P₆K, P₆E, and KP₆E and an equimolar mixture of P₆K and P₆E. The peptides exhibit a conformational transition from unordered to polyproline II (PPII) above a critical concentration, detected from circular dichroism (CD) measurements and unexpectedly from fluorescence dye probe measurements. Isothermal titration calorimetry (ITC) measurements provided the Gibbs energies of hydration of P₆K and P₆E, which correspond essentially to the hydration energies of the terminal charged residues. A detailed analysis of peptide conformation for these peptides was performed using density functional theory calculations, and this was used as a basis for hybrid quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations. Quantum mechanics simulations in implicit water show both peptides (and their 1:1 mixture) exhibit PPII conformations. However, hybrid QM/MM MD simulations suggest that some deviations from this conformation are present for P₆K and P₆E in peptide bonds close to the charged residue, whereas in the 1:1 mixture a PPII structure is observed. Finally, aggregation of the peptides was investigated using replica exchange molecular dynamics simulations. These reveal a tendency for the average aggregate size (as measured by the radius of gyration) to increase with increasing temperature, which is especially marked for P₆K, although the fraction of the most populated clusters is larger for P₆E.

Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology

Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.