Benzothiazole‐Based Neutral Ratiometric Fluorescence Sensor for Amyloid Fibrils

Early detection of amyloid fibrils is very important for the timely diagnosis of several neurological diseases. Thioflavin‐T (ThT) is a gold standard fluorescent probe for amyloid fibrils and has been used for the last few decades. However, due to its positive charge, ThT is incapable of crossing the blood–brain barrier and cannot be used for in vivo imaging of fibrils. In the present work, we synthesized a neutral ThT derivative, 2‐[2’‐Me,4’‐(dimethylamino)phenyl]benzothiazole (2Me‐DABT), which showed a strong affinity towards the amyloid fibrils. On association with the amyloid fibrils, 2Me‐DABT not only showed a large increase in its emission intensity, but also, unlike ThT, a large blueshift in its emission spectrum was observed. Thus, unlike ThT, 2Me‐DABT is a potential candidate for the ratiometric sensor of the amyloid fibrils. Detailed photophysical properties of 2Me‐DABT in amyloid fibrils and different solvent media were studied to understand its sensory activity. Fluorescence resonance energy transfer (FRET) studies suggested that the sites of localization for ThT and 2Me‐DABT in amyloid fibrils are not same and their average distance of separation in amyloid fibrils was determined. The experimental data was nicely supported by molecular docking studies, which confirmed the binding of 2Me‐DABT in the inner core of the amyloid fibrils.     

Thioflavin T forms a non-fluorescent complex with α-helical poly-L-glutamic acid

Thioflavin T (ThT) is a molecular-rotor-type fluorophore reputed for the selective binding to amyloid fibrils. Using induced circular dichroism, here we show that ThT binds in an orderly manner to α-helical poly-L-glutamic acid (PLGA) implying that neither stacked β-sheets nor π-π stacking interactions are necessary for the binding between the dye and proteins.     

硫黄素T对淀粉样β-蛋白质40聚集成核动力学的双重影响

荧光染料硫黄素T常用于淀粉样纤维聚集过程的定性定量检测。虽然有研究表明,某些抑制淀粉样蛋白质聚集的小分子抑制剂会与硫黄素T相互作用,影响其测试结果。但硫黄素T如何影响淀粉样蛋白质的聚集成核动力学尚不清晰。本文以淀粉样β-蛋白质40 (Aβ40)为模型,系统研究了硫黄素T对Aβ40聚集成核的影响。研究发现：硫黄素T能够显著改变Aβ40的聚集成核动力学,且影响程度与硫黄素T的浓度密切相关。即在低浓度硫黄素T存在下,Aβ40成核速率的延迟时间先随着硫黄素T浓度的升高而缩短,后随着硫黄素T浓度的升高延迟时间反而延长。但延伸的速率却随硫黄素T浓度的升高而缓慢增大。另外,硫黄素T基本不会影响Aβ40的二级结构和纤维形态。同时,等温滴定微量热实验结果表明,硫黄素T结合Aβ40之间的主要作用力为疏水相互作用。据此,本研究提出硫黄素T对Aβ40聚集成核动力学的双重影响机理。这些结果有助于进一步了解硫黄素T与淀粉样蛋白质的作用特点,为今后硫黄素T在Aβ40聚集成核动力学实验中的使用提供参考。     

Towards Ratiometric Sensing of Amyloid Fibrils In Vitro

The aggregation of amyloid‐β peptide and its accumulation in the human brain has an important role in the etiology of Alzheimer’s disease. Thioflavin T has been widely used as a fluorescent marker for these amyloid aggregates. Nevertheless, its complex photophysical behavior, with strong wavelength dependencies of all its fluorescence properties, requires searching for new fluorescent probes. The use of 2‐(2′‐hydroxyphenyl)imidazo[4,5‐b]pyridine (HPIP), which shows two emission bands and a rich excited‐state behavior due to the existence of excited‐state intramolecular processes of proton transfer and charge transfer, is proposed. These properties result in a high sensitivity of HPIP fluorescence to its microenvironment and cause a large differential fluorescence enhancement of the two bands upon binding to aggregates of the amyloid‐β peptide. Based on this behavior, a very sensitive ratiometric method is established for the detection and quantification of amyloid fibrils, which can be combined with the monitoring of fluorescence anisotropy. The binding selectivity of HPIP is discussed on the basis of the apparent binding equilibrium constants of this probe to amyloid‐β (1–42) fibrils and to the nonfibrillar protein bovine serum albumin. Finally, an exhaustive comparison between HPIP and thioflavin T is presented to discuss the sensitivity and specificity of these probes to amyloid aggregates and the significant advantages of the HPIP dye for quantitative determinations.     

On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy

Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.     

Fluorescent dyes in the context of DNA‐binding: The case of Thioflavin T

Thioflavin T (ThT) is a dye characterized by a strong fluorescence light‐up on binding to biosubstrates. Although this effect is known to be related to the inhibition of intramolecular torsion on excitation, the binding modes and their role in affecting photoinduced processes are by no means adequately understood. Here, a combined molecular dynamics and quantum chemical modeling is used to study the tuning of the photophysical properties of ThT when moving from solution to DNA binding. The binding mechanism of ThT to B‐DNA was found to be very complex as a result of an uncommon interplay between different binding modes, for example, monomer intercalation and external binding but also groove binding of the dimer. The detailed analysis of the relation between the different binding modes and the structural and electronic properties of ThT can be used to better understand the interaction with other biosubstrates.     

Guest Binding with Sulfated Cyclodextrins: Does the Size of Cavity Matter?

Sulfated cyclodextrins have recently emerged as potential candidates for producing host–induced guest aggregation with properties better than p-sulfonatocalixarenes that have previously shown numerous applications involving the phenomena of host-induced guest aggregation. In the class of sulfated cyclodextrins (SCD), sulfated β-cyclodextrin (β-SCD) remains the most extensively investigated host molecule. Although it is assumed that the host-induced guest aggregation is predominantly an outcome of interaction of the guest molecule with the charges on the exterior of SCD cavity, it has not been deciphered whether the variation in the cavity size will make a difference in the efficiency of host-induced guest-aggregation process. In this investigation, we present a systematic study of host–induced guest aggregation of a cationic molecular rotor dye, Thioflavin T (ThT) with three different sulfated cyclodextrin molecules, α-SCD, β-SCD and γ-SCD, which differ in their cavity size, using steady-state emission, ground-state absorption and time-resolved emission measurements. The obtained photophysical properties of ThT, upon interaction with different SCD molecules, indicate that the binding strength of ThT with different SCD molecules correlate with the cavity size of the host molecule, giving rise to the strongest complexation of ThT with the largest host molecule (γ-SCD). The binding affinity of ThT towards different host molecules has been supported by molecular docking calculations. The results obtained are further supported with the temperature and ionic strength dependent studies performed on the host-guest complex. Our results indicate that for host–induced guest aggregation, involving oppositely charged molecules, the size of the cavity also plays a crucial role beside the charge density on the exterior of host cavity.     

Solvent effect on excited state potential energy surfaces of Thioflavin T. Qualitatively different results by TDDFT and SA-2-CASSCF methods

Thioflavin T (ThT) is a viscosity-sensitive fluorescent dye and its emission intensity undergoes a significant enhancement upon binding to DNA or amyloid fibrils. This fluorescence light-up feature has been attributed earlier to restriction of structural rearrangements in the excited state that are coupled to an intramolecular charge transfer (ICT) reaction. In this work TDDFT (using B3LYP and CAM-B3LYP functionals) and SA-2-CASSCF calculations were carried out to obtain relaxed excited-state potential energy surfaces (PES) along twisting φ and wagging δ angles that describe mutual orientation of benzothiazole (BTZ) and dimethylaniline (DMA) fragments in ThT. For isolated ThT molecule both methods predict that during structural rearrangements of the initially excited Franck-Condon state, besides twisting along C C bond which connects BTZ and DMA fragments, a considerable wagging motion is expected to occur. Account for solvent effect using polarized continuum model showed qualitative differences in the excited state PES features calculated by SA-2-CASSCF and TDDFT methods. Single-reference TDDFT calculations failed to describe solvation of TICT state and predicted increase of its energy in more polar media.     

Quantum dot nanocrystals for in vivo molecular and cellular imaging

Semiconductor quantum dots (QD) are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. In comparison with organic dyes and fluorescent proteins, QD are emerging as a new class of fluorescent labels with improved brightness, resistance against photobleaching and multicolor fluorescence emission. These properties could improve the sensitivity of biological detection and imaging by at least 10- to 100-fold. Further development in high-quality near-infrared-emitting QD should allow ultrasensitive and multicolor imaging of molecular targets in deep tissue and living animals. Here, we discuss recent developments in QD synthesis and bioconjugation, applications in molecular and cellular imaging as well as promising directions for future research.     

An in vitro study on probable inhibition of cerebrovascular disease by salidroside as a potent small molecule against induction of protein amyloid fibrils and cytotoxicity

Protein aggregation and associated amyloid formation is linked with several harmful human pathophysiologies including Alzheimer's, Parkinson's, and cerebrovascular diseases. A potential approach for modulating and exploring amyloid fibrillization is the control of protein self-assembly. Herein, anti-aggregation effects of salidroside, its influence on the kinetics of amyloid fibrillization of Aβ_1-42 peptide and its cytotoxicity against cerebrovascular endothelial cells (bEnd.3) were assessed by using a wide range of spectroscopic and cellular techniques. The present outcome of Thioflavin T (ThT) and 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence, Congo red (CR), and circular dichroism (CD) analyses indicated that salidroside potentially inhibits protein fibril formation. The cellular studies inferred that salidroside protects bEnd.3 cells against Aβ_1-42 oligomers -triggered cytotoxicity through modulation of oxidative stress [reactive oxygen species (ROS), superoxide dismutase (SOD) and catalase (CAT) activities] and apoptosis (caspase-3 activity). Therefore, the data signifies the role of salidroside as a promising small molecule in inhibiting Aβ_1-42 aggregation and associated cerebrovascular endothelial cell toxicity. Hence, salidroside can serve as a potential inhibitor in the therapeutic advancement to combat cerebrovascular diseases.     

Self-assembly of tissue transglutaminase into amyloid-like fibrils using physiological concentration of Ca2+

Tissue transglutaminase (tTG or TG2) is a member of the transglutaminase family that catalyzes calcium dependent formation of isopeptide bonds. It has been shown that the expression of TG2 is elevated in neurodegenerative diseases such as Parkinson's, Huntington's, and Alzheimer's. We have investigated the self-assembly of TG2 in vitro. First, using software, hot spots, which are prone for aggregation, were identified in domain 2 of the enzyme. Next we expressed and purified recombinant TG2 and its truncated version that contains only the catalytic domain, and examined their amyloidogenic behavior in various conditions including different temperatures and pHs, in the presence of metal ions and Guanosine triphosphate (GTP). To analyze various stages leading to TG2 fibrillation, we employed various techniques including Thioflavin T (ThT) binding assay, Congo-Red, birefringence, Circular Dichroism (CD), 8-anilino-1-naphthalene sulfonic acid (ANS) binding, Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). Our results indicated that using low concentrations of Ca(2+), TG2 self-assembled into amyloid-like fibrils; this self-assembly occurred at the physiological temperature (37 °C) and at a higher temperature (57 °C). The truncated version of TG2 (domain 2) also forms amyloid-like fibrils only in the presence of Ca(2+). Because amyloid formation has occurred with domain 2 alone where no enzymatic activity was shown, self-cross-linking by the enzyme was ruled out as a mechanism of amyloid induction. The self-assembly of TG2 was not significant with magnesium and zinc ions, indicating specificity of the self-assembly for calcium ions. The calcium role in self-assembly of TG2 into amyloid may be extended to other proteins with similar biophysical properties to produce novel biomaterials.     

Single Molecule Characterization of Amyloid Oligomers

The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation.     

Polarity-active NIR probes with strong two-photon absorption and ultrahigh binding affinity of insulin amyloid fibrils

Amyloid fibrils are associated with many neurodegenerative diseases. In situ and in vivo visualization of amyloid fibrils is important for medical diagnostics and requires fluorescent probes with both excitation and emission wavelengths in the far-red and NIR region, and simultaneously with high binding-affinity to amyloid fibrils and the ability to cross the blood–brain barrier, which, however, remain a challenge. Here, we rationally design and synthesize an excellent polarity-sensitive two-photon excited NIR fluorophore (TZPI) based on a donor (D)–acceptor (A)-ion compound. The electron-rich carbazole group and the ionic pyridinium bromide group, linked by an electron-poor π-conjugated benzothiadiazole group, ensure strong near infrared (NIR) emission. Furthermore, the lipophilic carbazole together with the benzothiadiazole group facilitates docking of the probe in the hydrophobic domains of amyloid aggregates with the dissociation constant K_d = 20 nM and 13.5-fold higher binding affinity to insulin fibrils than the commercial probe ThT. On association with the amyloid fibrils, the tiny decrease in polarity leads to a large increase in its NIR emission intensity with an on–off ratio > 10; meanwhile, the TZPI probe exhibits a quantum yield of up to 30% and two-photon absorption cross-section values of up to 467.6 GM at 890 nm. Moreover, the application of TZPI in two-photon imaging is investigated. The ultrahigh binding affinity, the strong NIR emission, the good two-photon absorption properties, the high photo-stability, the appropriate molecular mass of 569 Da and the lipophilicity with log P = 1.66 ± 0.1 to cross the BBB make TZPI promising as an ideal candidate for detecting amyloid plaques in vivo.

A polarity-active NIR probe based on the transformation from the CT state to the LE state for two-photon imaging of amyloid fibrils.     

硫黄素T与侧翼连接双链DNA的G-四链体高特异性作用

富G碱基的DNA序列在离子诱导下可形成G-四链体(G4),基于这一构型转化设计了大量的传感检测平台。其中的荧光检测平台是基于G4与荧光小分子的相互作用。但是,G4与荧光小分子的有效结合依赖于G4构型和体系中存在的离子种类和离子浓度,尤其是高Na⁺浓度(140 mmol·L^-1)。那么如何实现G4与荧光小分子普适性地有效结合,并不依赖于体系中的Na⁺和Na⁺浓度,是一个难题。在本研究中,以最简单的富G DNA序列凝血酶适体链TBA (thrombin binding aptamer)为例,在3’端和5’端分别增加10个碱基(TBA-10 bp),K⁺诱导TBA-10 bp形成K⁺稳定TBA (K⁺-TBA,G4)并衔接含有10个互补碱基对的双链DNA (K⁺-TBA-10 bp)。相较于K⁺-TBA,硫磺素T与K⁺-TBA-10 bp结合后的荧光强度增加了100倍,相互作用强度增加了1000倍,而且与体系中的Na⁺ (5-140 mmol·L^-1)无关。结合荧光光谱,紫外吸收光谱和圆二色光谱发现硫磺素T特异性的嵌合于K⁺-TBA和双链DNA衔接处的空腔内。有趣的是,这一结合模式不受G4构型的影响。该研究结果为研究G4与荧光小分子的有效结合提供了新视角,也为拓展G4在生物功能和生化检测领域的应用提供了实验依据。     

Binding Modes of Thioflavin T on the Surface of Amyloid Fibrils Studied by NMR

The mechanism for the interaction of thioflavin T (ThT) with amyloid fibrils at the molecular level is not known. Here, we used ¹H NMR spectroscopy to determine the binding mode of ThT on the surface of fibrils from lysozyme and insulin. Relayed rotating‐frame Overhauser enhancements in ThT were observed, indicating that the orientation of ThT is orthogonal to the fibril surface. Importantly, the assembly state of ThT on both surfaces is different. On the surface of insulin fibrils, ThT is oligomeric, as indicated by rapid ¹H spin‐lattice relaxation rate in the rotating frame (R_1ρ), presumably due to intermolecular dipole–dipole interactions between ThT molecules. In contrast, ThT on the surface of lysozyme fibrils is a monomer, as indicated by slower ¹H R_1ρ. These results shed new light into the mechanism for the enhancement of ThT fluorescence and may lead to more efficient detectors of amyloid assemblies, which have escaped detection by ThT in monomer form.     

Aβ-binding molecules: Possible application as imaging probes and as anti-aggregation agents

As amyloid β (Aβ) is at the centre of pathogenesis of Alzheimer's disease (AD), Aβ aggregate-specific probes for in vivo studies of Aβ are potentially important for the early diagnosis and the assessment of new treatment strategies in the AD brain by noninvasive imaging. Several series of compounds derived from Congo red (CR) and Thioflavin T (ThT) have been evaluated as potential probes for the Aβ imaging. They include a diversity of core structures contributing to their affinities to Aβ. Small-molecule inhibi- tors were known to inhibit the formation of Aβ oligomers and fibrils. This inhibition has to be performed in such a way that these inhibitors bind to Aβ in the binding channel where Aβ-binding probes should sit. Therefore, several of them were used as novel core structures to develop Aβ probes, with their de- rivatives exhibiting good Aβ affinities. This approach will facilitate the design of a variety of candidates for Aβ probe molecules and anti-aggregation-therapeutic drugs. Moreover, the finding of Aβ probes with diverse core structures recognized by binding sites on Aβs will likely provide a promising per- spective for the design of 99mTc-labeled probe-derived molecules.     

Identification of Compounds that Selectively Stabilize Specific G‐Quadruplex Structures by Using a Thioflavin T‐Displacement Assay as a Tool

Small molecules are used in the G‐quadruplex (G4) research field in vivo and in vitro, and there are increasing demands for ligands that selectively stabilize different G4 structures. Thioflavin T (ThT) emits an enhanced fluorescence signal when binding to G4 structures. Herein, we show that ThT can be competitively displaced by the binding of small molecules to G4 structures and develop a ThT‐displacement high‐throughput screening assay to find novel and selective G4‐binding compounds. We screened approximately 28 000 compounds by using three different G4 structures and identified eight novel G4 binders. Analysis of the structural conformation and stability of the G4 structures in presence of these compounds demonstrated that the four compounds enhance the thermal stabilization of the structures without affecting their structural conformation. In addition, all four compounds also increased the G4‐structure block of DNA synthesis by Taq DNA polymerase. Also, two of these compounds showed selectivity between certain Schizosaccharomyces pombe G4 structures, thus suggesting that these compounds or their analogues can be used as selective tools for G4 DNA studies.     

基于ThT荧光寿命检测蛋清溶菌酶蛋白寡聚体

采用时间分辨荧光技术, 检测了不同形态蛋白聚集体的荧光染料硫磺素T(ThT)荧光寿命. 利用蛋清溶菌酶体外制备了蛋白聚集体; 采用透射电子显微镜(TEM)及ThT稳态荧光检测了结合蛋白纤维生长的动力学曲线, 确定其形成寡聚体及纤维样聚集体的特征和时间. 通过时间相关单光子计数(TCSPC)技术测定了蛋清溶菌酶单体、 寡聚体和淀粉样纤维的ThT荧光寿命曲线, 并拟合、 计算其荧光寿命. 根据圆二色谱(CD)分析结果推测聚集体的结构不同导致其与ThT的结合状态不同, 从而影响ThT荧光寿命. 结果表明, 通过测定ThT荧光寿命可以区分蛋白单体、 寡聚体和纤维样聚集体, 并监测蛋白寡聚体的形成, 为后续病理蛋白聚集过程中形成寡聚体物质的监测提供了研究基础.     

Thioflavin T hydroxylation at basic pH and its effect on amyloid fibril detection

The fluorescent dye thioflavin T (ThT) is commonly used for in situ amyloid fibril detection. In this work, we focused on the spectroscopic properties and chemical stability of ThT in aqueous solution as a function of pH, temperature, and dye concentration. A reversible hydroxylation process occurs in alkaline solutions, which was characterized using a combination of UV-vis absorption spectroscopy, proton NMR, and density functional theory (DFT). On the basis of these studies, we propose a chemical structure for the hydroxylated form. Finally, by means of fluorescence spectroscopy, ThT hydroxylation effects on in situ amyloid detection have been investigated, providing new insights on the efficiency of the ThT assay for quantitative fibril evaluation at basic pH.     

Harnessing Intramolecular Rotation To Enhance Two‐photon Imaging of Aβ Plaques through Minimizing Background Fluorescence

The aggregation of amyloid beta (Aβ) proteins in senile plaques is a critical event during the development of Alzheimer's disease, and the postmortem detection of Aβ‐rich proteinaceous deposits through fluorescent staining remains one of the most robust diagnostic tools. In animal models, fluorescence imaging can be employed to follow the progression of the disease, and among the different imaging methods, two‐photon microscopy (TPM) has emerged as one of the most powerful. To date, several near‐infrared‐emissive two‐photon dyes with a high affinity for Aβ fibrils have been developed, but there has often been a tradeoff between excellent two‐photon cross‐sections and large fluorescence signal‐to‐background ratios. In the current work, we introduced a twisted intramolecular charge state (TICT)‐based de‐excitation pathway, which results in a remarkable fluorescence increase of around 167‐fold in the presence of Aβ fibrils, while maintaining an excellent two‐photon cross section, thereby enabling high‐contrast ex vivo and in vivo TPM imaging. Overall, the results suggest that adopting TICT de‐excitation in two‐photon fluorophores may represent a general method to overcome the tradeoff between probe brightness and signal‐to‐background ratio.