Binding mode of Thioflavin T in insulin amyloid fibrils

Cytotoxic Staphylococcus aureus PSMα3 inhibits the aggregation of human insulin in vitro

Phenol-soluble modulins (PSMs) are extracellular short amphipathic peptides secreted by the bacteria Staphylococcus aureus (S. aureus). They play an essential role in the bacterial lifecycle, biofilm formation, and stabilisation. From the PSM family, PSMα3 has been of special interest recently due to its cytotoxicity and highly stable α-helical conformation, which also remains in its amyloid fibrils. In particular, PSMα3 fibrils were shown to be composed of self-associating "sheets" of α-helices oriented perpendicular to the fibril axis, mimicking the architecture of canonical cross-β fibrils. Therefore, they were called cross-α-fibrils. PSMα3 was synthesised and verified for identity with wild-type sequences (S. aureus). Then, using several experimental techniques, we evaluated its propensity for in vitro aggregation. According to our findings, synthetic PSMα3 (which lacks the N-terminal formyl groups found in bacteria) does not form amyloid fibrils and maintains α-helical conformation in a soluble monomeric form for several days of incubation. We also evaluated the influence of PSMα3 on human insulin fibrillation in vitro, using a variety of experimental approaches in combination with computational molecular studies. First, it was shown that PSMα3 drastically inhibits the fibrillation of human insulin. The anti-fibrillation effect of PSMα3 was concentration-dependent and required a concentration ratio of PSMα3: insulin equal to or above 1 : 100. Molecular modelling revealed that PSMα3 most likely inhibits the production of insulin primary nuclei by competing for residues involved in its dimerization.

Electrostatic interactions mediated defibrillation of β-lactoglobulin fibrils using Keggin Polyoxometalates

The whey protein β-lactoglobulin (βLG) forms fibrils similar to the amyloid fibrils in the neurodegenerative diseases due to its higher predisposition of β-sheets. This study shed light on the understanding different inorganic Keggin polyoxometalates (POMs) interaction with the protein βLG fibrils. POMs such as Phosphomolybdic acid (PMA), silicomolybdic acid (SMA), tungstosilicic acid (TSA), and phosphotungstic acid (PTA) were used due to their inherent higher anionic charges. The interaction studies were monitored with fluorescence spectra and Thioflavin T assay for both the βLG monomers and the fibrils initially to elucidate the binding ability of the POMs. The binding of POMs and βLG is also demonstrated by molecular docking studies. Zeta potential studies showed the electrostatic mediated higher interactions of the POMs with the protein fibrils. Isothermal titration calorimetry (ITC) studies showed that the molybdenum containing POMs have higher affinity to the protein fibrils than the tungsten. This study could help understanding formation of food grade protein fibrils which have profound importance in food industries.

Thioflavin T indicates mitochondrial membrane potential in mammalian cells

The fluorescent benzothiazole dye thioflavin T (ThT) is widely used as a marker for protein aggregates, most commonly in the context of neurodegenerative disease research and diagnosis. Recently, this same dye was shown to indicate membrane potential in bacteria due to its cationic nature. This finding prompted a question whether ThT fluorescence is linked to the membrane potential in mammalian cells, which would be important for appropriate utilization of ThT in research and diagnosis. Here, we show that ThT localizes into the mitochondria of HeLa cells in a membrane-potential-dependent manner. Specifically, ThT colocalized in cells with the mitochondrial membrane potential indicator tetramethylrhodamine methyl ester (TMRM) and gave similar temporal responses as TMRM to treatment with a protonophore, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP). Additionally, we found that presence of ThT together with exposure to blue light (λ = 405 nm), but neither factor alone, caused depolarization of mitochondrial membrane potential. This additive effect of the concentration and blue light was recapitulated by a mathematical model implementing the potential-dependent distribution of ThT and its effect on mitochondrial membrane potential through photosensitization. These results show that ThT can act as a mitochondrial membrane potential indicator in mammalian cells, when used at low concentrations and with low blue light exposure. However, it causes dissipation of the mitochondrial membrane potential depending additively on its concentrations and blue light exposure. This conclusion motivates a re-evaluation of ThT's use at micromolar range in live-cell analyses and indicates that this dye can enable future studies on the potential connections between mitochondrial membrane potential dynamics and protein aggregation.

Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus

Recombinant core spidroin eADF4(C16) has received increasing attention due to its ability to form micro- and nano-structured scaffolds, which are based on nanofibrils with great potential for biomedical and biotechnological applications. Phosphate anions have been demonstrated to trigger the eADF4(C16) self-assembly into cross-beta fibrils. In the present work, we systematically addressed the effect of nine sodium anions, namely SO4 2- , HPO4 2- (Pi), F- , Cl- , Br- , NO3 - , I- , SCN- , and ClO4 - from the Hofmeister series on the in vitro self-assembly kinetics of eADF4(C16). We show that besides the phosphate anions, only kosmotropic anions such as sulfate and fluoride can initiate the eADF4(C16) fibril formation. Global analysis of the self-assembly kinetics, utilizing the platform AmyloFit, showed the nucleation-based mechanism with a major role of secondary nucleation, surprisingly independent of the type of the kosmotropic anion. The rate constant of the fibril elongation in mixtures of phosphate anions with other studied anions correlated with their kosmotropic or chaotropic position in the Hofmeister series. Our findings suggest an important role of anion hydration in the eADF4(C16) fibrillization process.

Biocompatible zeolite-dye composites with anti-amyloidogenic properties

One of the most attractive approaches in biomedicine and pharmacy is the application of multifunctional materials. The mesoporous structure of clinoptilolite (CZ) absorbs various types of substances and can be used as a model for studying the carriers for targeted drug delivery with controlled release. CZ-dye composites are fabricated by incorporation into clinoptilolite pores commonly used dyes, aluminum phthalocyanine, zinc porphine, and hypericin. We examined and compared the effect of pure dyes and CZ-dye composites on insulin amyloidogenesis. The formation of insulin amyloid fibrils and the disassembly of preformed fibrils is significantly affected by any of the three compounds, however, the strongest effect is observed for aluminum phthalocyanine indicating a structurally-dependent anti-amyloidogenic activity of the dyes. The incorporation of dyes into CZ particles resulted in enhanced anti-amyloidogenic activity in comparison to pure CZ particles. The cell metabolic activity, biocompatibility and fluorescence biodistribution of the dyes entrapped in the composites were tested in vitro (U87 MG cells) and in vivo in the quail chorioallantoic membrane model. Considering the photoactive properties of the dyes used, we assume their applicability in photodiagnostics and photodynamic therapy. It can also be expected that their anti-amyloidogenic potential can be enhanced by photodynamic effect.

Structural mechanism for specific binding of chemical compounds to amyloid fibrils

Amyloid fibril is an important pharmaceutical target for diagnostic and therapeutic treatment of neurodegenerative diseases. However, rational design of chemical compounds that interact with amyloid fibrils is unachievable due to the lack of mechanistic understanding of the ligand-fibril interaction. Here we used cryoelectron microscopy to survey the amyloid fibril-binding mechanism of a series of compounds including classic dyes, (pre)clinical imaging tracers and newly identified binders from high-throughput screening. We obtained clear densities of several compounds in complex with an α-synuclein fibril. These structures unveil the basic mechanism of the ligand-fibril interaction, which exhibits remarkable difference from the canonical ligand-protein interaction. In addition, we discovered a druggable pocket that is also conserved in the ex vivo α-synuclein fibrils from multiple system atrophy. Collectively, these findings expand our knowledge of protein-ligand interaction in the amyloid fibril state, which will enable rational design of amyloid binders in a medicinally beneficial way.

A highly sensitive hemicyanine-based near-infrared fluorescence sensor for detecting toxic amyloid aggregates in human serum

The development of an accurate and sensitive sensor for detecting amyloid plaques, which are responsible for many protein disorders like Alzheimer's disease, is crucial for early diagnosis. Recently, there has been a notable increase in the development of fluorescence probes that exhibit emission in the red region (>600 nm), aiming to effectively tackle the challenges encountered when working with complex biological matrices. In the current investigation, a hemicyanine-based probe, called LDS730, has been used for the sensing of amyloid fibrils, which belong to the Near-Infrared Fluorescence (NIRF) family of dyes. NIRF probes provide higher precision in detection, prevent photo-damage, and minimize the autofluorescence of biological specimens. The LDS730 sensor emits in the near-infrared region and shows a 110-fold increase in fluorescence turn-on emission when bound to insulin fibrils, making it a highly sensitive sensor. The sensor has an emission maximum of ~710 nm in a fibril-bound state, which shows a significant red shift along with a Stokes' shift of ~50 nm. The LDS730 sensor also displays excellent performance in the complicated human serum matrix, with a limit of detection (LOD) of 103 nM. Molecular docking calculations suggest that the most likely binding location of LDS730 in the fibrillar structure is the inner channels of amyloid fibrils along its long axis, and the sensor engages in several types of hydrophobic interactions with neighboring amino acid residues of the fibrillar structure. Overall, this new amyloid sensor has great potential for the early detection of amyloid plaques and for improving diagnostic accuracy.

An AIE-Active NIR Fluorescent Probe with Good Water Solubility for the Detection of Aβ1-42 Aggregates in Alzheimer's Disease

Alzheimer's disease (AD), an amyloid-related disease, seriously endangers the health of elderly individuals. According to current research, its main pathogenic factor is the amyloid protein, which is a kind of fibrillar aggregate formed by noncovalent self-assembly of proteins. Based on the characteristics of aggregation-induced emission (AIE), a bislactosyl-decorated tetraphenylethylene (TPE) molecule TMNL (TPE + malononitrile + lactose), bearing two malononitrile substituents, was designed and synthesized in this work. The amphiphilic TMNL could self-assemble into fluorescent organic nanoparticles (FONs) with near-infrared (NIR) fluorescence emission in physiological PBS (phosphate buffered saline), achieving excellent fluorescent enhancement (47-fold) upon its combination with Aβ_1-42 fibrils. TMNL was successfully applied to image Aβ_1-42 plaques in the brain tissue of AD transgenic mice, and due to the AIE properties of TMNL, no additional rinsing process was necessary. It is believed that the probe reported in this work should be useful for the sensitive detection and accurate localization mapping of Aβ_1-42 aggregates related to Alzheimer's disease.

Single-Molecule Orientation Imaging Reveals Two Distinct Binding Configurations on Amyloid Fibrils

Fluorescence readouts for an amyloid fibril sensor critically depend on its molecular interaction and local environment offered by the available structural motifs. Here we employ polarized points accumulation for imaging in nanoscale topography with intramolecular charge transfer probes transiently bound to amyloid fibrils to investigate the organization of fibril nanostructures and probe binding configurations. Besides the in-plane (θ ≈ 90°) mode for binding on the fibril surface parallel to the long fibril axis, we also observed a sizable population of over 60% out-of-plane (θ < 60°) dipoles for rotor probes experiencing a varying degree of orientational mobility. Highly confined dipoles exhibiting an out-of-plane configuration probably reflect tightly bound dipoles in the inner channel grooves, while the weakly bound ones on amyloid enjoy rotational flexibility. Our observation of an out-of-plane binding mode emphasizes the pivotal role played by the electron donor amino group toward fluorescence detection and hence the emergence of anchored probes alongside conventional groove binders.

Prevention of insulin fibrillation by biocompatible choline-amino acid based ionic liquids: Biophysical insights

We have synthesized biocompatible ionic liquids (ILs) with choline as cation and amino acids as anions to explore their potential towards prevention of fibrillation in insulin and the obtain corresponding mechanistic insights. This has been achieved by examining the effect of these ILs on insulin at the nucleation, elongation and maturation stages of the fibrillation process. A combination of high sensitivity isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) have been employed along with spectroscopy and microscopy to evaluate interaction of the ILs at each stage of fibrillation quantitatively. Choline glycinate is observed to provide maximum stabilization to insulin compared to that provided by choline prolinate, choline leucinate, and choline valinate. This increased thermal stabilization has direct correlation with the extent of reduction in the fibrillation of insulin by ILs determined using Thioflavin T and 8-anilinonaphthalene sulfonate based fluorescence assays. ITC has permitted understanding nature of interaction of the ILs with the protein at different fibrillation stages in terms of standard molar enthalpy of interaction whereas DSC has enabled understanding the extent of reduction in thermal stability of the protein at these stages. These ILs are able to completely inhibit formation of insulin aggregates at a concentration of 50 mM. Stabilization of proteins by ILs could be explained based on involvement of preferential hydration process. The work provides biocompatible IL based approach in achieving stability and prevention of fibrillation in insulin.

Mechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids

Amyloid aggregation of protein is linked to many neurodegenerative diseases. Identification of small molecules capable of targeting amyloidogenic proteins has gained significant importance. Introduction of hydrophobic and hydrogen bonding interactions through site-specific binding of small molecular ligand to protein can effectively modulate the protein aggregation pathway. Here, we investigate the possible roles of three different bile acids, cholic acid (CA), taurocholic acid (TCA), and lithocholic acid (LCA) with varying hydrophobic and hydrogen bonding properties in inhibiting protein fibrillation. Bile acids are an important class of steroid compounds that are synthesized in the liver from cholesterol. Increasing evidence suggests that altered taurine transport, cholesterol metabolism, and bile acid synthesis have strong implications in Alzheimer's disease. We find that the hydrophilic bile acids, CA and TCA (taurine conjugated form of CA), are substantially more efficient inhibitors of lysozyme fibrillation than the most hydrophobic secondary bile acid LCA. Although LCA binds more strongly with the protein and masks the Trp residues more prominently through hydrophobic interactions, the lesser extent of hydrogen bonding interactions at the active site has made LCA a relatively weaker inhibitor of HEWL aggregation than CA and TCA. The introduction of a greater number of hydrogen bonding channels by CA and TCA with several key amino acid residues which are prone to form oligomers and fibrils has weakened the protein's internal hydrogen bonding capabilities for undergoing amyloid aggregation.

Synthesis of benzylidene-indandione derivatives as quantification of amyloid fibrils

The formation of amyloid fibrils due to its association with fatal diseases, including Alzheimer's, has been investigated by many researchers. These common diseases, mostly become verified when it is too late to be treated. Currently, no cure is available for neurodegenerative diseases, and the process of diagnosing amyloid fibrils in the early stages, while there are fewer amyloid fibrils, has become an issue of interest. To do so, determining new probes with the highest binding affinity to the lowest number of amyloid fibrils is necessary. In this study, we proposed to employ new synthesized benzylidene-indandione derivatives as amyloid fibrils fluorescent detection probes. Native soluble proteins of insulin, bovine serum albumin (BSA), BSA amorphous aggregation, and insulin amyloid fibrils were used to evaluate our compounds' specificity to the amyloid structure. While ten synthesized compounds were examined individually, four of them including 3d, 3g, 3i, and 3j showed a high binding affinity with selectivity and specificity to amyloid fibrils, and their binding properties were also confirmed with in silico analysis. The drug-likeness prediction results for selected compounds by Swiss ADME server shows a satisfactory percentage of blood-brain barrier (BBB) permeability and gastrointestinal (GI) absorption for the compounds 3g, 3i, and 3j. More evaluation is needed to determine all properties of compounds in vitro and in vivo.

Electroabsorption and Stark Fluorescence Spectroscopies of Thioflavin T

Thioflavin T (ThT) is a typical fluorescent marker for detecting the formation of amyloid fibrils, because its fluorescence intensity increases by more than 2 orders of magnitude upon complexation with the fibrils. Strong electrostatic fields on protein surfaces are known to be a significant factor in chemical reactions and biological functions. Therefore, ThT bound to amyloid fibrils must experience strong electric fields. This study employed electroabsorption and Stark fluorescence spectroscopies to clarify the effects of external electric fields on the photophysics of ThT. The absorption spectrum shows two bands ascribed to locally excited (LE) and charge transfer (CT) states. Coupling between the LE and CT states is enhanced in the presence of an external electric field, resulting in fluorescence quenching. The electric field strength of the amyloid fibril surface was inferred from the fluorescence quenching efficiency of ThT.

Dual Role of a Fluorescent Small Molecule as a Sensor and Inhibitor of Protein Fibrillation

Ordered fibrillar aggregates of proteins, called amyloids, are prevalent in several diseases like Alzheimer's, Parkinson's, and Type II diabetes. The key challenge in the treatment of such diseases is the early detection of protein fibrillation and its effective inhibition using extrinsic agents. Thus, molecules that can both detect and inhibit protein fibril formation have great diagnostic and therapeutic utility. Using insulin as a model protein, we report the dual action of an isoquinoline based molecule, named MK14 which detects and prevents insulin fibrillation. Dose dependent inhibition of insulin fibrillation by MK14 gave an IC₅₀ value of 9 μM, and mechanistic investigations suggested that MK14 prevented the elongation of fibrils by interacting with pre-fibrillar intermediates. The fluorescence of MK14 enhanced upon binding to fibrils of insulin as well as those of α-synuclein, the protein involved in Parkinson's disease. MK14 is an environmentally sensitive fluorophore, which could also detect amorphous aggregates of insulin. The dual nature of MK14 as an inhibitor and detector of protein fibrillation makes it an attractive lead compound for monitoring and disrupting protein amyloidogenesis.

Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1-42) Amyloid Fibrils

Alzheimer's disease is a neurodegenerative disorder associated with the deposition of misfolded aggregates of the amyloid-β protein (Aβ). Aβ(1-42) is one of the most aggregation-prone components in senile plaques of AD patients. We demonstrated that relatively homogeneous Aβ(1-42) fibrils with one predominant fold visible in solid-state NMR spectra can be obtained at acidic pH. The structure of these fibrils differs remarkably from some other polymorphs obtained at neutral pH. In particular, the entire N-terminal region is part of the rigid fibril core. Here, we investigate the effects of a pH shift on the stability and the fold of these fibrils at higher pH values. Fibril bundling at neutral pH values renders cryo-EM studies impractical, but solid-state NMR spectroscopy, molecular dynamics simulations, and biophysical methods provide residue-specific structural information under these conditions. The LS-fold of the Aβ(1-42) fibrils does not change over the complete pH range from pH 2 to pH 7; in particular, the N-terminus remains part of the fibril core. We observe changes in the protonation state of charged residues starting from pH 5 on a residue-specific level. The deprotonation of the C-terminal carboxyl group of A42 in the intermolecular salt bridge with D1 and K28 is slow on the NMR time scale, with a local pK_a of 5.4, and local conformations of the involved residues are affected by deprotonation of A42. Thus, we demonstrate that this fibril form is stable at physiological pH values.

The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism: A Methodological Approach

The amyloidophilic dyes thioflavin T and Congo red are small, yet powerful, molecules that allow the in vitro and in vivo detection of amyloid fibrils in protein solutions. Even though Congo red and thioflavin T binding assays are widespread techniques for unveiling amyloid fibers and are gradually replacing the more demanding X-ray diffraction method, handling samples containing amyloid fibrils is still challenging and can lead to false-positive/negative results. Here we describe a relatively straightforward procedure of preparing hen egg-white lysozyme amyloid fibrils in different buffer solutions and their detection with thioflavin T and Congo red, supported by an indispensable method for determining the secondary structure of proteins - circular dichroism.

Tuning the surface charge of phospholipid bilayers inhibits insulin fibrilization

The interactions between proteins and materials, in particular lipid bilayers, have been studied extensively for their relevance in diseases and for the formulation of protein-based therapeutics and vaccines. However, the precise rules by which material properties induce favorable or unfavorable structural states in biomolecules are incompletely understood, and as a result, the rational design of materials remains challenging. Here, we investigated the influence of lipid bilayers (in the form of small unilamellar vesicles) on the formation of insulin amyloid fibrils using a fibril-specific assay (thioflavin T), polyacrylamide gel electrophoresis, and circular dichroism spectroscopy. Lipid bilayers composed of equal mixtures of cationic and anionic lipids effectively inhibited fibril formation and stabilized insulin in its native conformation. However, other lipid bilayer compositions failed to inhibit fibril formation or even destabilized insulin, exacerbating fibrilization and/or non-amyloid aggregation. Our findings suggest that electrostatic interactions with lipid bilayers can play a critical role in stabilizing or destabilizing insulin, and preventing the conversion of insulin to its amyloidogenic, disease-associated state.

Sensing lysozyme fibrils by salicylaldimine substituted BODIPY dyes - A correlation with molecular structure

Quick and efficient detection of protein fibrils has enormous impact on the diagnosis and treatment of amyloid related neurological diseases. Among several methods, fluorescence based techniques have garnered most importance in the detection of amyloid fibrils due to its high sensitivity and extreme simplicity. Among other classes of molecular probes, BODIPY derivatives have been employed extensively for the detection of amyloid fibrils. However, there are very few studies on the relationship between the molecular structure of BODIPY dyes and their amyloid sensing activity. Here in a BODIPY based salicylaldimine Schiff base and its corresponding boron complex have been evaluated for their ability to sense amyloid fibrils from hen-egg white lysozyme using steady state and time-resolved spectroscopic techniques. Both dyes show fluorescence enhancement as well as increase in their excited state lifetime upon their binding with lysozyme fibrils. However, the BODIPY derivative which shows more emission enhancement in fibrillar solution has much lower affinity towards amyloid fibrils as compared to other derivative. This contrasting behaviour in the emission enhancement and binding affinity has been explained on the basis of differences in their photophysical properties in water and amyloid fibril originating from the difference in their molecular structure. Such correlation between the amyloid sensitivity and the molecular structure of the probe can open up a new strategy for designing new efficient amyloid probes.

The intriguing dose-dependent effect of selected amphiphilic compounds on insulin amyloid aggregation: Focus on a cholesterol-based detergent, Chobimalt

The amyloidogenic self-assembly of many peptides and proteins largely depends on external conditions. Among amyloid-prone proteins, insulin attracts attention because of its physiological and therapeutic importance. In the present work, the amyloid aggregation of insulin is studied in the presence of cholesterol-based detergent, Chobimalt. The strategy to elucidate the Chobimalt-induced effect on insulin fibrillogenesis is based on performing the concentration- and time-dependent analysis using a combination of different experimental techniques, such as ThT fluorescence assay, CD, AFM, SANS, and SAXS. While at the lowest Chobimalt concentration (0.1 µM; insulin to Chobimalt molar ratio of 1:0.004) the formation of insulin fibrils was not affected, the gradual increase of Chobimalt concentration (up to 100 µM; molar ratio of 1:4) led to a significant increase in ThT fluorescence, and the maximal ThT fluorescence was 3-4-fold higher than the control insulin fibril’s ThT fluorescence intensity. Kinetic studies confirm the dose-dependent experimental results. Depending on the concentration of Chobimalt, either (i) no effect is observed, or (ii) significantly, ∼10-times prolonged lag-phases accompanied by the substantial, ∼ 3-fold higher relative ThT fluorescence intensities at the steady-state phase are recorded. In addition, at certain concentrations of Chobimalt, changes in the elongation-phase are noticed. An increase in the Chobimalt concentrations also triggers the formation of insulin fibrils with sharply altered morphological appearance. The fibrils appear to be more flexible and wavy-like with a tendency to form circles. SANS and SAXS data also revealed the morphology changes of amyloid fibrils in the presence of Chobimalt. Amyloid aggregation requires the formation of unfolded intermediates, which subsequently generate amyloidogenic nuclei. We hypothesize that the different morphology of the formed insulin fibrils is the result of the gradual binding of Chobimalt to different binding sites on unfolded insulin. A similar explanation and the existence of such binding sites with different binding energies was shown previously for the nonionic detergent. Thus, the data also emphasize the importance of a protein partially-unfolded state which undergoes the process of fibrils formation; i.e., certain experimental conditions or the presence of additives may dramatically change not only kinetics but also the morphology of fibrillar aggregates.

An amphiphilic small molecule drives insulin aggregation inhibition and amyloid disintegration

The aggregation of proteins into ordered fibrillar structures called amyloids, and their disintegration represent major unsolved problems that limit the therapeutic applications of several proteins. For example, insulin, commonly used for the treatment of diabetes, is susceptible to amyloid formation upon exposure to non-physiological conditions, resulting in a loss of its biological activity. Here, we report a novel amphiphilic molecule called PAD-S, which acts as a chemical chaperone and completely inhibits fibrillation of insulin and its biosimilars. Mechanistic investigations and molecular docking lead to the conclusion that PAD-S binds to key hydrophobic regions of native insulin, thereby preventing its self-assembly. PAD-S treated insulin was biologically active as indicated by its ability to phosphorylate Akt, a protein in the insulin signalling pathway. PAD-S is non-toxic and protects cells from insulin amyloid induced cytotoxicity. The high aqueous solubility and easy synthetic accessibility of PAD-S facilitates its potential use in commercial insulin formulations. Notably, PAD-S successfully disintegrated preformed insulin fibrils to non-toxic smaller fragments. Since the structural and mechanistic features of amyloids are common to several human pathologies, the understanding of the amyloid disaggregation activity of PAD-S will inform the development of small molecule disaggregators for other amyloids.

Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates

Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.

Dual Functional Amphiphilic Sugar-Coated AIE-Active Fluorescent Organic Nanoparticles for the Monitoring and Inhibition of Insulin Amyloid Fibrillation Based on Carbohydrate-Protein Interactions

Amyloid-related diseases, such as Alzheimer's disease, are all considered to be related to the deposition of amyloid fibrils in the body. Insulin is a protein hormone that easily undergoes aggregation...

Fatty Acid-Based Polymeric Micelles to Ameliorate Amyloidogenic Disorders

To develop anti-amyloidogenic inhibitors for ameliorating the treatment of diabetes, herein, we have synthesized amphiphilic block copolymers with side-chain fatty acid (FA) moieties via reversible addition fragmentation chain-transfer (RAFT) polymerization....

In Silico study of Rosmarinic Acid Derivatives as Novel Insulin Fibril Inhibitors

The self-assembly of human insulin (HI) plays a crucial role in regulating amyloid fibrils. Therefore, it is a significant problem for the medical management of diabetes therapy and these findings have led us to investigate the amyloid formation and its inhibition. Few potential inhibitors have been identified to inhibit amyloid fibrils. Rosmarinic acid (RA) is one of the things that inhibits amyloid formation completely by increasing the resistivity of the amyloidogenic insulin (dimer) protein to thermal unfolding. Here, we choose different tested derivative compounds for designing amyloid inhibitors by substituting various functional groups of RA. These derivative compounds were subjected to in silico studies to determine the best drug candidates. In comparison to RA, 14 molecules have higher binding affinity and interactions with the target receptor. After frontier molecular orbitals study, ADME and toxicity analysis, the eight best compounds may act as the best inhibitors. The stability of the docked complexes was visualized by molecular dynamics (MD) simulations. This finding opens a new proposal to explore future studies with these best compounds to increase the thermal stability of the insulin dimers.

Luminescent imaging of insulin amyloid aggregation using a sensitive ruthenium-based probe in the red region

A sensitive and selective strategy to identify insulin fibrils remains a challenge for researchers in amyloid protein research. Thus, it is critical to detect, in vitro, the species generated during amyloid aggregation, particularly the fibrillar species. Here we demonstrate that the luminescent complex cis-[Ru(phen)₂(3,4Apy)₂]²⁺ (RuApy; phen = 1,10-phenanthroline; 3,4Apy = 3,4-diaminopyridine) is a rapid, low-cost alternative to in vitro detection of fibrillar insulin, using conventional optical techniques. The RuApy complex displays emission intensity enhancement at 655 nm when associated with insulin, which enables imaging of the conformational changes of the protein's self-aggregation. The complex shows high sensitivity to fibrillar insulin with a limit of detection of 0.85 μM and binding affinity of 12.40 ± 1.84 μM which is comparable to those of Thioflavin T and Congo red, with the advantage of minimizing background fluorescence, absorption of light by biomolecules, and light scattering from physiologic salts in the medium.

Patented AIE materials for biomedical applications

In recent years aggregation induced emission (AIE) concept has attracted researcher's interest worldwide. Several organic building blocks are developed as AIE materials. This chapter discusses the patented AIE material and their utilization related in biological, medicinal and biotechnology fields. It is demonstrated that AIE chromophores such as tetraphenylethylene (TPE) as well as other AIE building blocks became important fluorescent emissive bioactive materials. Such emissive materials are widely employed as bioprobes for the detection of mitochondria, cellular imaging and tracking, protein carrier detection of S-phase DNA, detection of d-glucose, visualization of cancer treatment, drug screening, image-guided therapy, bacterial imaging, photodynamic therapy and drug screening. Such AIE materials upon imaging in cellular environment displays significant enhancement of fluorescence emission. Such patented AIE chromophores has a great potential for bioimaging and biomedical applications. In this chapter we compile some patented representative examples to explore their bioimaging/medicinal imaging applications since lot of new inventions are reported every day.

Lysozyme Fibrils Alter the Mechanism of Insulin Amyloid Aggregation

Protein aggregation into amyloid fibrils is linked to multiple disorders. The understanding of how natively non-harmful proteins convert to these highly cytotoxic amyloid aggregates is still not sufficient, with new ideas and hypotheses being presented each year. Recently it has been shown that more than one type of protein aggregates may co-exist in the affected tissue of patients suffering from amyloid-related disorders, sparking the idea that amyloid aggregates formed by one protein may induce another protein’s fibrillization. In this work, we examine the effect that lysozyme fibrils have on insulin amyloid aggregation. We show that not only do lysozyme fibrils affect insulin nucleation, but they also alter the mechanism of its aggregation.

Exploring the occurrence of thioflavin-T-positive insulin amyloid aggregation intermediates

The aggregation of proteins is considered to be the main cause of several neurodegenerative diseases. Despite much progress in amyloid research, the process of fibrillization is still not fully understood, which is one of the main reasons why there are still very few effective treatments available. When the aggregation of insulin, a model amyloidogenic protein, is tracked using thioflavin-T (ThT), an amyloid specific dye, there is an anomalous occurrence of double-sigmoidal aggregation kinetics. Such an event is likely related to the formation of ThT-positive intermediates, which may affect the outcome of both aggregation kinetic data, as well as final fibril structure. In this work we explore insulin fibrillization under conditions, where both normal and double-sigmoidal kinetics are observed and show that, despite their dye-binding properties and random occurrence, the ThT-positive intermediates do not significantly alter the overall aggregation process.

Effect of Ionic Strength on Thioflavin-T Affinity to Amyloid Fibrils and Its Fluorescence Intensity

The formation of amyloid fibrils is linked to multiple neurodegenerative disorders, including Alzheimer’s and Parkinson’s disease. Despite years of research and countless studies on the topic of such aggregate formation, as well as their resulting structure, the current knowledge is still fairly limited. One of the main aspects prohibiting effective aggregation tracking is the environment’s effect on amyloid-specific dyes, namely thioflavin-T (ThT). Currently, there are only a few studies hinting at ionic strength being one of the factors that modulate the dye’s binding affinity and fluorescence intensity. In this work we explore this effect under a range of ionic strength conditions, using insulin, lysozyme, mouse prion protein, and α-synuclein fibrils. We show that ionic strength is an extremely important factor affecting both the binding affinity, as well as the fluorescence intensity of ThT.

Identifying Insulin Fibril Conformational Differences by Thioflavin-T Binding Characteristics

Amyloidogenic protein aggregation into highly structured fibrils is linked to more than 30 amyloidoses, including several neurodegenerative disorders. Despite significant progress in trying to understand the process of amyloid formation, there is still no cure or effective treatment available. A number of studies involving potential anti-amyloid compounds rely on the use of a fluorescent probe—thioflavin-T—to track the appearance, growth, or disassembly of these cytotoxic aggregates. Despite the wide application of this dye molecule, its interaction with amyloid fibrils is still poorly understood. Recent reports have shown it may possess distinct binding modes and fluorescence intensities based on the conformation of the examined fibrils. In this work, we generate insulin fibrils under four different conditions and attempt to identify distinct conformations using both classic methods, such as atomic force microscopy and Fourier-transform infrared spectroscopy, as well as their ThT binding ability and fluorescence quantum yield. We show that there is a significant variance of ThT fluorescence quantum yields, excitation/emission maxima positions, and binding modes between distinct insulin fibril conformations.

Molecular Interaction of Protein-Pigment C-Phycocyanin with Bovine Serum Albumin in a Gomphosis Structure Inhibiting Amyloid Formation

Accumulation of amyloid fibrils in organisms accompanies many diseases. Natural extracts offer an alternative strategy to control the process with potentially fewer side effects. In this study, the inhibition of C-phycocyanin from Spirulina sp. on amyloid formation of bovine serum albumin (BSA) during a 21-day incubation was investigated using fluorescence and circular dichroism (CD), and mechanisms were explored via kinetic fitting and molecular docking. C-phycocyanin (0-50 µg/mL) hindered the amyloid formation process of BSA with increased half-lives (12.43-17.73 days) based on fluorescence intensity. A kinetic model was built and showed that the k₁ decreased from 1.820 × 10^-2 d^-1 to 2.62 × 10^-3 d^-1 with the increase of C-phycocyanin, while k₂ showed no changes, indicating that the inhibition of BSA fibrillation by C-phycocyanin occurred in a spontaneous process instead of self-catalyzed one. CD results show that C-phycocyanin inhibited conformational conversion (α-helices and β-sheets) of BSA from day 6 to day 18. Molecular docking suggested that C-phycocyanin may hinder BSA fibrillation by hydrogen-bonding > 6 of 27 α-helices of BSA in a gomphosis-like structure, but the unblocked BSA α-helices might follow the self-catalytic process subsequently.

Early detection of prion protein aggregation with a fluorescent pentameric oligothiophene probe using spectral confocal microscopy

Misfolding of the prion protein (PrP) and templating of its pathological conformation onto cognate proteins causes a number of lethal disorders of central nervous system in humans and animals, such as Creutzfeldt-Jacob disease, chronic wasting disease and bovine spongiform encephalopathy. Structural rearrangement of PrP^C into PrP^Sc promotes aggregation of misfolded proteins into β-sheet-rich fibrils, which can be visualized by conformationally sensitive fluorescent probes. Early detection of prion misfolding and deposition might provide useful insights into its pathophysiology. Pentameric formyl thiophene acetic acid (pFTAA) is a novel amyloid probe that was shown to sensitively detect various misfolded proteins, including PrP. Here, we compared sensitivity of pFTAA staining and spectral microscopy with conventional methods of prion detection in mouse brains infected with mouse-adapted 22L prions. pFTAA bound to prion deposits in mouse brain sections exhibited a red-shifted fluorescence emission spectrum, which quantitatively increased with disease progression. Small prion deposits were detected as early as 50 days post-inoculation, well before appearance of clinical signs. Moreover, we detected significant spectral shifts in the greater brain parenchyma as early as 25 days post-inoculation, rivaling the most sensitive conventional method (real-time quaking-induced conversion). These results showcase the potential of pFTAA staining combined with spectral imaging for screening of prion-infected tissue. Not only does this method have comparable sensitivity to established techniques, it is faster and technically simpler. Finally, this readout provides valuable information about the spatial distribution of prion aggregates across tissue in the earliest stages of infection, potentially providing valuable pathophysiological insight into prion transmission.

Fluorescence Lifetime and Intensity of Thioflavin T as Reporters of Different Fibrillation Stages: Insights Obtained from Fluorescence Up-Conversion and Particle Size Distribution Measurements

Thioflavin T (ThT) assay is extensively used for studying fibrillation kinetics in vitro. However, the differences in the time course of ThT fluorescence intensity and lifetime and other physical parameters of the system, such as particle size distribution, raise questions about the correct interpretation of the aggregation kinetics. In this work, we focused on the investigation of the mechanisms, which underlay the difference in sensitivity of ThT fluorescence intensity and lifetime to the formation of protein aggregates during fibrillation by the example of insulin and during binding to globular proteins. The assessment of aggregate sizes and heterogeneity was performed using dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). Using the sub-nanosecond resolution measurements, it was shown that the ThT lifetime is sensitive to the appearance of as much as a few percent of ThT bound to the high-affinity sites that occur simultaneously with an abrupt increase of the average particle size, particles concentration, and size heterogeneity. The discrepancy between ThT fluorescence intensity and a lifetime can be explained as the consequence of a ThT molecule fraction with ultrafast decay and weak fluorescence. These ThT molecules can only be detected using time-resolved fluorescence measurements in the sub-picosecond time domain. The presence of a bound ThT subpopulation with similar photophysical properties was also demonstrated for globular proteins that were attributed to non-specifically bound ThT molecules with a non-rigid microenvironment.

High-resolution structure of a partially folded insulin aggregation intermediate

Insulin has long been served as a model for protein aggregation, both due to the importance of aggregation in the manufacture of insulin and because the structural biology of insulin has been extensively characterized. Despite intensive study, details about the initial triggers for aggregation have remained elusive at the molecular level. We show here that at acidic pH, the aggregation of insulin is likely initiated by a partially folded monomeric intermediate. High-resolution structures of the partially folded intermediate show that it is coarsely similar to the initial monomeric structure but differs in subtle details-the A chain helices on the receptor interface are more disordered and the B chain helix is displaced from the C-terminal A chain helix when compared to the stable monomer. The result of these movements is the creation of a hydrophobic cavity in the center of the protein that may serve as nucleation site for oligomer formation. Knowledge of this transition may aid in the engineering of insulin variants that retain the favorable pharamacokinetic properties of monomeric insulin but are more resistant to aggregation.

Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T

Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP_8-37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 k _B T, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 k _B T). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.

Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching

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Method enables investigation of amyloid-β oligomer stoichiometry without requiring extrinsic fluorescent probes.

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Uses single-molecule stepwise photobleaching in vitro.

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Unveils heterogeneity within populations of oligomers.

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Assays oligomer-induced dysregulation of intracellular Ca²⁺ homeostasis in living cells.

A major hallmark of Alzheimer’s disease is the misfolding and aggregation of the amyloid- β peptide (Aβ). While early research pointed towards large fibrillar- and plaque-like aggregates as being the most toxic species, recent evidence now implicates small soluble Aβ oligomers as being orders of magnitude more harmful. Techniques capable of characterizing oligomer stoichiometry and assembly are thus critical for a deeper understanding of the earliest stages of neurodegeneration and for rationally testing next-generation oligomer inhibitors. While the fluorescence response of extrinsic fluorescent probes such as Thioflavin-T have become workhorse tools for characterizing large Aβ aggregates in solution, it is widely accepted that these methods suffer from many important drawbacks, including an insensitivity to oligomeric species. Here, we integrate several biophysics techniques to gain new insight into oligomer formation at the single-molecule level. We showcase single-molecule stepwise photobleaching of fluorescent dye molecules as a powerful method to bypass many of the traditional limitations, and provide a step-by-step guide to implementing the technique in vitro. By collecting fluorescence emission from single Aβ(1–42) peptides labelled at the N-terminal position with HiLyte Fluor 555 via wide-field total internal reflection fluorescence (TIRF) imaging, we demonstrate how to characterize the number of peptides per single immobile oligomer and reveal heterogeneity within sample populations. Importantly, fluorescence emerging from Aβ oligomers cannot be easily investigated using diffraction-limited optical microscopy tools. To assay oligomer activity, we also demonstrate the implementation of another biophysical method involving the ratiometric imaging of Fura-2-AM loaded cells which quantifies the rate of oligomer-induced dysregulation of intracellular Ca²⁺ homeostasis. We anticipate that the integrated single-molecule biophysics approaches highlighted here will develop further and in principle may be extended to the investigation of other protein aggregation systems under controlled experimental conditions.

Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42)

Binding modes for the amyloid-β(1-42) fibril fluorescent dyes thioflavin T and Congo red were predicted by molecular dynamics simulations and binding free energy calculations. Both probes bind on the fibril surface to primarily hydrophobic grooves, with their long axis oriented almost parallel to the fibril axis. The computed binding affinities are in agreement with experimental values. The binding modes also explain observables from previous structural studies and, thus, provide a starting point for the systematic search and design of novel molecules, which may improve in vitro diagnostics for Alzheimer's disease.

Molecular Details of a Salt Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis

Insulin, a simple polypeptide hormone with huge biological importance, has long been known to self-assemble in vitro and form amyloid-like fibrillar aggregates. Utilizing high-resolution NMR, Raman spectroscopy, and computational analysis, we demonstrate that the fluctuation of the carboxyl terminal (C-ter) residues of the insulin B-chain plays a key role in the growth phase of insulin aggregation. By comparing the insulin sourced from bovine, human, and the modified glargine (GI), we observed reduced aggregation propensity in the GI variant, resulting from two additional Arg residues at its C-ter. NMR analysis showed atomic contacts and residue-specific interactions, particularly the salt bridge and H-bond formed among the C-ter residues Arg31^B, Lys29^B, and Glu4^A. These inter-residue interactions were reflected in strong nuclear Overhauser effects among Arg31^BδH-Glu4^AδH and Lys29^BδHs-Glu4^AδH in GI, as well as the associated downfield chemical shift of several A-chain amino terminal (N-ter) residues. The two additional Arg residues of GI, Arg31^B and Arg32^B, enhanced the stability of the GI native structure by strengthening the Arg31^B, Lys29^B, and Glu4^A salt bridge, thus reducing extensive thermal distortion and fluctuation of the terminal residues. The high stability of the salt bridge retards tertiary collapse, a crucial biochemical event for oligomerization and subsequent fibril formation. Circular dichroism and Raman spectroscopic measurement also suggest slow structural distortion in the early phase of the aggregation of GI because of the restricted mobility of the C-ter residues as explained by NMR. In addition, the structural and dynamic parameters derived from molecular dynamics simulations of insulin variants highlight the role of residue-specific contacts in aggregation and amyloid-like fibril formation.

Probing the Nongeneralized Amyloid Inhibitory Mechanism of Hydrophobic Chaperone

Increasing prevalence of protein misfolding disorders urges the search for effective therapies. Although several antiaggregation molecules have been identified, their molecular process of aggregation and clinical trials are underway. The present study is focused on the mechanism through which phenyl butyrate (PB), a chemical chaperone, triggers inhibition of human serum albumin (HSA) fibrillation. Turbidity and Rayleigh light scattering (RLS) measurements reveal the marked presence of aggregates in HSA that were confirmed as amyloid fibrils by thioflavin T (ThT) and Congo red (CR) and were subsequently inhibited by PB in a dose dependent manner. ThT fluorescence kinetics reveals a decrease in the apparent rate constant, K_app, in the presence of PB without triggering a lag phase in HSA suggesting PB's interference with the elongation phase. Dynamic light scattering (DLS) results display a reduction in the aggregate size in the presence of PB. Isothermal titration calorimetry (ITC) data reveals strong binding of PB at site II both at 25 °C (K_b ≈ 1.94 × 10⁵ M^-1) and 65 °C (K_b ≈ 2.90 × 10⁴ M^-1), mediated by hydrogen bonding. Overall, our finding establishes that PB stabilizes partially unfolded HSA molecules through hydrogen bonding, thereby preventing establishment of hydrogen bonds between them and hindering their progression into amyloid fibrils. This is in contrast to its chaperone effect manifested with other proteins.

Concentration-dependent polymorphism of insulin amyloid fibrils

Protein aggregation into highly structured fibrils has long been associated with several neurodegenerative disorders, such as Alzheimer's or Parkinson's disease. Polymorphism of amyloid fibrils increases the complexity of disease mechanisms and may be one of the reasons for the slow progress in drug research. Here we report protein concentration as another factor leading to polymorphism of insulin amyloid fibrils. Moreover, our data suggests that insulin amyloid conformation can self-replicate only via elongation, while seed-induced nucleation will lead to environment-defined conformation of fibrils. As similar observations were already described for a couple of other amyloid proteins, we suggest it to be a generic mechanism for self-replication of different amyloid fibril conformations.

Amyloid Protein-Induced Supramolecular Self-Assembly of Water-Soluble Platinum(II) Complexes: A Luminescence Assay for Amyloid Fibrillation Detection and Inhibitor Screening

Amyloid fibrillation has been acknowledged as a hallmark of a number of neurodegenerative ailments such as Alzheimer's disease. Accordingly, efficient detection of amyloid fibrillation will allow for great advances in the field of biomedical applications as well as in achieving early medical diagnosis. In this work, a luminescence assay for the sensitive and specific detection of amyloid fibrillation was developed by using platinum(II) complexes as sensing platforms. Supramolecular self-assembly of platinum(II) complexes was induced upon addition of amyloid, leading to alterations in the spectroscopic and luminescence properties of the complexes. As compared to fluorescent dyes, luminescent platinum(II) complexes exhibit attractive large Stokes shifts, phosphorescence lifetimes in the microsecond to submicrosecond regime, and low-energy red emission after aggregation, which are advantageous to biological imaging. At the same time, the platinum(II) complex adopted herein was found to have high photostability, high selectivity and specificity, and low cytotoxicity. The proposed design is the very first approach to detect amyloid fibrillation through the supramolecular self-assembly of luminescent platinum(II) complexes.

Additional Thioflavin-T Binding Mode in Insulin Fibril Inner Core Region

Amyloidogenic protein aggregation into fibrils is linked to several neurodegenerative disorders, such as Alzheimer's or Parkinson's disease. An amyloid specific fluorescent dye thioflavin-T (ThT) is often used to track the formation of these fibrils in vitro. Despite its wide application, it is still unknown how many types of ThT binding modes to amyloids exist, with multiple studies indicating varying numbers. In this work, we examine the binding of ThT to insulin fibrils generated at pH 2.4 and reveal a possible inner core binding mode which is not accessible to the dye molecule after aggregation occurs.