Michler’s Hydrol Blue: A Sensitive Probe for Amyloid Fibril Detection

The detection methods currently available for protein aggregation in neurological diseases

Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.

Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette

9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.

Design, Synthesis, and Characterization of Novel Styryl Dyes as Fluorescent Probes for Tau Aggregate Detection in Vitro and in Cells

A series of novel styryl dye derivatives incorporating indolium and quinolinium core structures were successfully synthesized to explore their interacting and binding capabilities with tau aggregates in vitro and in cells. The synthesized dyes exhibited enhanced fluorescence emission in viscous environments due to the rotatable bond confinement in the core structure. Dye 4, containing a quinolinium moeity and featuring two cationic sites, demonstrated a 28-fold increase in fluorescence emission upon binding to tau aggregates. This dye could also stain tau aggregates in living cells, confirmed by cell imaging using confocal fluorescence microscopy. A molecular docking study was conducted to provide additional visualization and support for binding interactions. This work offers novel and non-cytotoxic fluorescent probes with desirable photophysical properties, which could potentially be used for studying tau aggregates in living cells, prompting further development of new fluorescent probes for early Alzheimer's disease detection.

Controlling Peptide Function by Directed Assembly Formation: Mechanistic Insights Using Multiscale Modeling on an Antimicrobial Peptide-Drug-Membrane System

Owing to their potential applicability against multidrug-resistant bacteria, antimicrobial peptides (AMPs) or host defense peptides (HDPs) gain increased attention. Besides diverse immunomodulatory roles, their classical mechanism of action mostly involves membrane disruption of microbes. Notably, their unbalanced overexpression has also been associated with host cell cytotoxicity in various diseases. Relatedly, AMPs can be subject to aggregate formation, either via self-assembly or together with other compounds, which has demonstrated a modulation effect on their biological functions, thus highly relevant both for drug targeting projects and understanding their in vivo actions. However, the molecular aspects of the related assembly formation are not understood. Here, we focused in detail on an experimentally studied AMP-drug system, i.e., CM15-suramin, and performed all-atom and coarse-grain (CG) simulations. Results obtained for all systems were in close line with experimental observations and indicate that the CM15-suramin aggregation is an energetically favorable and dynamic process. In the presence of bilayers, the peptide-drug assembly formation was highly dependent on lipid composition, and peptide aggregates themselves were also capable of binding to the membranes. Interestingly, longer CG simulations with zwitterionic membranes indicated an intermediate state in the presence of both AMP-drug assemblies and monomeric peptides located on the membrane surface. In sharp contrast, larger AMP-drug aggregates could not be detected with a negatively charged membrane, rather the AMPs penetrated its surface in a monomeric form, in line with previous in vitro observations. Considering experimental and theoretical results, it is promoted that in biological systems, cationic AMPs may often form associates with anionic compounds in a reversible manner, resulting in lower bioactivity. This is only mildly affected by zwitterionic membranes; however, membranes with a negative charge strongly alter the energetic preference of AMP assemblies, resulting in the dissolution of the complexes into the membrane. The phenomenon observed here at a molecular level can be followed in several experimental systems studied recently, where peptides interact with food colors, drug molecules, or endogenous compounds, which strongly indicates that reversible associate formation is a general phenomenon for these complexes. These results are hoped to be exploited in novel therapeutic strategies aiming to use peptides as drug targets and control AMP bioactivity by directed assembly formation.

Fluorescent Probe for Selective Imaging of α-Synuclein Fibrils in Living Cells

Plaques of amyloid fibrils composed of neuronal protein α-synuclein are one of the hallmarks of Parkinson's disease, and their selective imaging is crucial to study the mechanism of its pathogenesis. However, the existing fluorescent probes for amyloids are efficient only in solution and tissue systems, and they are not selective enough for the visualization of amyloid fibrils in living cells. In this study, we present two molecular rotor-based probes RB1 and RB2. These thiazolium probes show affinity to α-synuclein fibrils and turn-on fluorescence response upon interactions. Because of its extended π-conjugation and high rotational degree of freedom, RB1 exhibits a 76 nm red-shift of absorption maxima and 112-fold fluorescence enhancement upon binding to amyloid fibrils. Owing to its strong binding affinity to α-synuclein fibrils, RB1 can selectively stain them in the cytoplasm of living HeLa and SH-SY5Y cells with high optical contrast. RB1 is a cell-permeable and noncytotoxic probe. Taken together, we have demonstrated that RB1 is an amyloid probe with an outstanding absorption red-shift that can be used for intracellular imaging of α-synuclein fibrils.

Michler's hydrol blue elucidates structural differences in prion strains

Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler's hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs.

Exploring the LDS 821 dye as a potential NIR probe for the two photon imaging of amyloid fibrils

We report a commercially available benzothiazolium based dye LDS 821 (Styryl 9M) as a near infrared fluorescent probe for the detection of lysozyme amyloid fibrils. Change in the photophysical properties of the dye with respect to the change in viscosity of the environment is investigated. Increment in fluorescence lifetime and quantum yield with increment in viscosity proves the dye as a molecular rotor. The dye, upon binding with lysozyme fibrils, exhibits a red shift in the absorption spectrum with increased quantum yield. Strong fluorescence emission near the biological window as compared with Thioflavin T makes the LDS 821 dye a potential probe for imaging amyloid fibrils in vivo. Molecular docking studies were carried out to understand the mode of interaction between the dye and amyloid fibrils. Nonlinear optical properties of the dye upon incorporation with amyloid fibrils were explored, and they show a sizeable enhancement in two photon absorption with an increase in the concentration of amyloid fibrils. The findings suggest that the nonlinear optical absorption of the LDS 821 dye can be used as an alternative marker for amyloid fibrils.

Interaction of antitubercular drug candidates with α1-acid glycoprotein produced in pulmonary granulomas

The intracellular pathogen Mycobacterium tuberculosis can survive and replicate within host macrophages. Among various immunomodulatory substances, macrophages also produce α₁-acid glycoprotein (AAG) which is secreted into the extracellular matrix of tuberculosis granulomas that represents a specific binding environment. Employing circular dichroism (CD) and UV/VIS absorption spectroscopic methods, we demonstrated and evaluated the AAG binding properties of novel antitubercular drug candidates developed against sensitive and multidrug-resistant strains of M. tuberculosis. As inferred from the CD spectroscopic data, these chemically diverse organic molecules are engulfed within the β-barrel of the protein either in a monomeric or dimeric form. Molecular docking simulations suggested the importance of H-bonds and ligand-aromatic residue π-π stacking interactions in stabilizing the drug molecules at the protein binding site. Based on the estimated K_d values (7-20 μM), AAG could be considered as the significant binding partner of the antitubercular agents studied herein. As such, it may affect the drug distribution and bioavailability not only in serum but also in macrophages and in the extracellular matrix of tuberculosis granulomas.

The New Application of UHPLC-DAD-TOF/MS in Identification of Inhibitors on β-Amyloid Fibrillation From Scutellaria baicalensis

Literary evidence depicts that aggregated β-amyloid (Aβ) leads to the pathogenesis of Alzheimer's disease (AD). Although many traditional Chinese medicines (TCMs) are effective in treating neurodegenerative diseases, there is no effective way for identifying active compounds from their complicated chemical compositions. Instead of using a traditional herbal separation method with low efficiency, we herein apply UHPLC-DAD-TOF/MS for the accurate identification of the active compounds that inhibit the fibrillation of Aβ (1-42), via an evaluation of the peak area of individual chemical components in chromatogram, after incubation with an Aβ peptide. Using the neuroprotective herbal plant Scutellaria baicalensis (SB) as a study model, the inhibitory effect on Aβ by its individual compounds, were validated using the thioflavin-T (ThT) fluorescence assay, biolayer interferometry analysis, dot immunoblotting and native gel electrophoresis after UHPLC-DAD-TOF/MS analysis. The viability of cells after Aβ (1-42) incubation was further evaluated using both the tetrazolium dye (MTT) assay and flow cytometry analysis. Thirteen major chemical components in SB were identified by UHPLC-DAD-TOF/MS after incubation with Aβ (1-42). The peak areas of two components from SB, baicalein and baicalin, were significantly reduced after incubation with Aβ (1-42), compared to compounds alone, without incubation with Aβ (1-42). Consistently, both compounds inhibited the formation of Aβ (1-42) fibrils and increased the viability of cells after Aβ (1-42) incubation. Based on the hypothesis that active chemical components have to possess binding affinity to Aβ (1-42) to inhibit its fibrillation, a new application using UHPLC-DAD-TOF/MS for accurate identification of inhibitors from herbal plants on Aβ (1-42) fibrillation was developed.

In Vivo and In Vitro Monitoring of Amyloid Aggregation via BSA@FGQDs Multimodal Probe

Early detection of peptide aggregate intermediates is quite challenging because of their variable and complex nature as well as due to lack of reliable sensors for diagnosis. Herein, we report the detection of monomers and oligomers using specified fluorescence and a magnetic resonance imaging (MRI) multimodal probe based on bovine-serum-albumin-capped fluorine functionalized graphene quantum dots (BSA@FGQDs). This probe enables in vitro fluorescence-based monitoring of human islet amyloid polypeptide (hIAPP), insulin, and amyloid β_(1-42) (Aβ₄₂) monomers and oligomers during the fibrillogenesis dynamic. Up to 90% fluorescence quenching of BSA@FGQDs probe upon addition of amyloid monomers/oligomers was observed due to static quenching and nonradiative energy transfer. Moreover, the BSA@FGQDs probe shows 10 times higher signals in detecting amyloid intermediates and fibrils than that of conventional thioflavin dye. A negative Δ G° value (-36.21 kJ/mol) indicates spontaneous interaction of probe with the peptide. These interactions are hydrogen bonding and hydrophobic as proved by thermodynamic parameters. Visual binding clues of BSA@FGQDs with different morphological states of amyloid protein was achieved through electron microscopy. Furthermore, intravenous and intracranial injection of BSA@FGQDs probe in Alzheimer model mice brain enabled in vivo detection of amyloid plaques in live mice brain by ¹⁹F MRI through contrast enhancement. Our proposed probe not only effectively monitors in vitro fibrillation kinetics of number of amyloid proteins with higher sensitivity and specificity than thioflavin dye, but also, the presence of a ¹⁹F center makes BSA@FGQDs an effective probe as a noninvasive and nonradiative in vivo detection probe for amyloid plaques.

A sensitive probe for amyloid fibril detection with strong fluorescence and early response

We synthesized a new probe, 4-[2-(2-naphthyl)-(E)-ethenyl]-benzyl(triphenyl)phosphonium bromide (NEB), to detect the formation of amyloid fibrils of bovine insulin. The fluorescence intensity of NEB in the presence of insulin fibrils was 30 times higher than that before fibrillation, with the fluorescence quantum yield increased from 2.5% to 78%. In comparison with the commercially available probe, thioflavin T (ThT), NEB exhibits a 10 times stronger fluorescence and a shorter identification lag phase for detecting insulin fibrillation, indicating a higher sensitivity in detection of insulin oligomers and fibrils.

We synthesized a new probe, 4-[2-(2-naphthyl)-(E)-ethenyl]-benzyl(triphenyl)phosphonium bromide (NEB), to detect the formation of amyloid fibrils of bovine insulin.

N-Methyl Mesoporphyrin IX as an Effective Probe for Monitoring Alzheimer's Disease β-Amyloid Aggregation in Living Cells

Formation of amyloid fibrils by amyloid-β peptide (Aβ) is an important step in Alzheimer's disease (AD) progression. Screening and designing of new molecules which can monitor the amyloidosis process especially in cells are diagnostically and therapeutically important. Utilizing Thioflavin T (ThT), the commonly used amyloid dye, is the most standardized way to monitor amyloid. However, with the green fluorescence emission and small Stokes shift, the fluorescence of ThT can overlap with that arising from other intrinsic fluorescent components in the cells, making it not suitable for detection of protein aggregates in vivo. Therefore, it is urgent for developing amyloid probes with large Stokes shifts and red-shifted fluorescence emission to detect Aβ aggregates in cells. In this report, we found that N-methyl mesoporphyrin IX (NMM), a widely used G-quadruplex DNA specific fluorescent binder, can be an efficient probe for monitoring Aβ fibrillation in living cells. NMM is nonfluorescent in aqueous solution or monomeric Aβ environments. However, through stacking with the Aβ assemblies, NMM emits strong fluorescence. Furthermore, the large Stokes shift and stable photoluminescence make it an ideal probe for detecting Aβ aggregates in highly fluorescent environments and cell culture. Our results provide a new sight to design and screen new reagents for monitoring the diseases associated with protein conformational disorders.

Bethe-Salpeter study of cationic dyes: Comparisons with ADC(2) and TD-DFT

We present a theoretical investigation of the excited-state properties of a large series of structurally diverse arylcarbonium derivatives that are known to be challenging for theoretical models. More specifically, we compare the pros and cons of TD-DFT (TD-M06-2X), ADC(2), and BSE/GW approaches for a large panel of compounds, using two different solvent models. Both 0-0 and vertical transition energies are considered and compared to the experimental values. All approaches reasonably reproduce the auxochromic and acidochromic shifts, although in most cases both TD-DFT and BSE/GW return larger correlation with experimental values than ADC(2) for these shifts. In contrast, the absolute transition energies obtained with ADC(2) tend to be closer to the measurements, TD-DFT using the M06-2X functional largely overestimating the experimental references (by ca. 0.5 eV), and BSE/GW providing intermediate values. In addition, we show that the selected solvent model has a significant impact on the results, the corrected linear-response approach providing larger transition energies than its linear-response counterpart.

Color in Bridge-Substituted Cyanines

Theories of color in cyanine dyes have evolved around the idea of a "resonance" of structures with distinct bonding and charge localization. Understanding the emergence of resonance models from the underlying many-electron problem remains a central issue for these systems. Here, the issue is addressed using a maximum-entropy approach to valence-bond representations of state-averaged complete-active space self-consistent field models. The approach allows calculation of energies and couplings of high-energy valence-bond structures that mediate superexchange couplings and chemical bonding. A series of valence-bond Hamiltonians for a series of bridge-substituted derivatives of Michler's hydrol blue (a monomethine cyanine) is presented. The Hamiltonians are approximated with a simple linear model parametrized by the Brown-Okamoto σ_p⁺ parameter of the bridge substituent. A quantitative lower bound on σ_p⁺, beyond which a resonant cyanine-like ground state will not exist, is presented. The large effective coupling in two-state resonance models emerges from superexchange associated with either covalent bonding or charge-carrier delocalization, with the former contribution significantly the stronger. The results provide ab initio justification for empirical diabatic-state models of methine optical response. They are of general interest for understanding the optoelectronic response in cyanines.

Dimeric binding of plant alkaloid ellipticine to human serum proteins

Induced exciton circular dichroism signals reveal the accommodation of a pair of ellipticine molecules to the subdomain IB of human serum albumin and the β-barrel of α₁-acid glycoprotein.

Valence-bond non-equilibrium solvation model for a twisting monomethine cyanine

We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localizations, there are two possible twisting pathways with different charge localizations in the excited state. For parameters corresponding to symmetric monomethines, the model predicts two low-energy twisting channels on the excited-state surface, which leads to a manifold of TICT states. For typical monomethines, twisting on the excited state surface will occur with a small barrier or no barrier. Changes in the solvation configuration can differentially stabilize TICT states in channels corresponding to different bonds, and that the position of a conical intersection between adiabatic states moves in response to solvation to stabilize either one channel or the other. There is a conical intersection seam that grows along the bottom of the excited-state potential with increasing solvent polarity. For monomethine cyanines with modest-sized terminal groups in moderately polar solution, the bottom of the excited-state potential surface is completely spanned by a conical intersection seam.

Development and application of methodology for rapid screening of potential amyloid probes

Herein, we demonstrate that it is possible to rapidly screen hydrophobic fluorescent aromatic molecules with regards to their properties as amyloid probes. By grinding the hydrophobic molecule with the amyloidogenic protein insulin, we obtained a water-soluble composite material. When this material is dissolved and exposed to conditions promoting amyloid formation, the protein aggregates into amyloid fibrils incorporating the hydrophobic molecule. As a result, changes in the fluorescence spectra of the hydrophobic molecule can be correlated to the formation of amyloid fibrils, and the suitability of the hydrophobic molecular skeleton as an amyloid probe can thus be assessed. As a result, we discovered two new amyloid probes, of which one is the well-known laser dye DCM. The grinding method can also be used for rapid preparation of novel composite materials between dyes and proteins, which can be used in materials science applications such as organic electronics and photonics.

High anisotropy of flow-aligned bicellar membrane systems

In recent years, multi-lipid bicellar systems have emerged as promising membrane models. The fast orientational diffusion and magnetic alignability made these systems very attractive for NMR investigations. However, their alignment was so far achieved with a strong magnetic field, which limited their use with other methods that require macroscopic orientation. Recently, it was shown that bicelles could be aligned also by shear flow in a Couette flow cell, making it applicable to structural and biophysical studies by polarized light spectroscopy. Considering the sensitivity of this lipid system to small variations in composition and physicochemical parameters, efficient use of such a flow-cell method with coupled techniques will critically depend on the detailed understanding of how the lipid systems behave under flow conditions. In the present study we have characterized the flow alignment behavior of the commonly used dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine (DMPC/DHPC) bicelle system, for various temperatures, lipid compositions, and lipid concentrations. We conclude that at optimal flow conditions the selected bicellar systems can produce the most efficient flow alignment out of any lipid systems used so far. The highest degree of orientation of DMPC/DHPC samples is noticed in a narrow temperature interval, at a practical temperature around 25 °C, most likely in the phase transition region characterized by maximum sample viscosity. The change of macroscopic orientation factor as function of the above conditions is now described in detail. The increase in macroscopic alignment observed for bicelles will most likely allow recording of higher resolution spectra on membrane systems, which provide deeper structural insight and analysis into properties of biomolecules interacting with solution phase lipid membranes.

In situ monitoring Alzheimer's disease β-amyloid aggregation and screening of Aβ inhibitors using a perylene probe

A cationic perylene tetracarboxylic acid diimide derivative (1) is employed as a probe for in situ monitoring of Aβ aggregation and screening Aβ inhibitors. The assay is based on the fluorescence change through the aggregation of compound 1 following Aβ assembly. Importantly, this probe, compared with the well known amyloid-staining compound thioflavin T (ThT), is more sensitive to Aβ oligomer, which is highly toxic and plays a crucial role in the early stages of Alzheimer's disease.

Dye-binding assays for evaluation of the effects of small molecule inhibitors on amyloid (aβ) self-assembly

Dye-binding assays, such as those utilizing Congo red and thioflavin T, are among the most widely used tools to probe the aggregation of amyloidogenic biomolecules and for the evaluation of small molecule inhibitors of amyloid aggregation and fibrillization. A number of recent reports have indicated that these dye-binding assays could be prone to false positive effects when assessing inhibitors' potential toward Aβ peptides, species involved in Alzheimer's disease. Specifically, this review focuses on the application of thioflavin T for determining the efficiency of small molecule inhibitors of Aβ aggregation and addresses potential reasons that might be associated with the false positive effects in an effort to increase reliability of dye-binding assays.

A three-state effective Hamiltonian for symmetric cationic diarylmethanes

We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states. The diabatic states can be identified with the bonding structures in classical resonance-theoretic models of cyanine dyes. We identify diabatic states with opposing charge and bond-order localization, analogous to the classical resonance structures, and a third state with charge on the bridge. While the left- and right-charged structures are similar for all dyes, the structure of the bridge-charged diabatic state, and the Hamiltonian matrix elements connected to it, change significantly across the series. The change is correlated with an inversion of the sign of the charge carrier on the bridge, which changes from an electron pair to a hole as the series is traversed.

Spectral properties and orientation of voltage-sensitive dyes in lipid membranes

Voltage-sensitive dyes are frequently used for probing variations in the electric potential across cell membranes. The dyes respond by changing their spectral properties: measured as shifts of wavelength of absorption or emission maxima or as changes of absorption or fluorescence intensity. Although such probes have been studied and used for decades, the mechanism behind their voltage sensitivity is still obscure. We ask whether the voltage response is due to electrochromism as a result of direct field interaction on the chromophore or to solvatochromism, which is the focus of this study, as result of changed environment or molecular alignment in the membrane. The spectral properties of three styryl dyes, di-4-ANEPPS, di-8-ANEPPS, and RH421, were investigated in solvents of varying polarity and in model membranes using spectroscopy. Using quantum mechanical calculations, the spectral dependence of monomer and dimer ANEPPS on solvent properties was modeled. Also, the kinetics of binding to lipid membranes and the binding geometry of the probe molecules were found relevant to address. The spectral properties of all three probes were found to be highly sensitive to the local environment, and the probes are oriented nearly parallel with the membrane normal. Slow binding kinetics and scattering in absorption spectra indicate, especially for di-8-ANEPPS, involvement of aggregation. On the basis of the experimental spectra and time-dependent density functional theory calculations, we find that aggregate formation may contribute to the blue-shifts seen for the dyes in decanol and when bound to membrane models. In conclusion, solvatochromic and other intermolecular interactions effects also need to be included when considering electrochromic response voltage-sensitive dyes.

Four-electron, three-orbital model for the low-energy electronic structure of cationic diarylmethanes: notes on a "Pauling Point"

We examine a four-electron, three-orbital complete active space self-consistent field (SA-CASSCF) and multistate multireference perturbation theory (MS-MRPT2) model of the electronic structure associated with the two lowest-lying electronic excitations of a series of cationic diarylmethanes related to Michler's Hydrol Blue. These dyes are of interest because of the sensitivity of their excited-state dynamics to environmental influence in biological and other condensed phases. We show that the model corresponds to an easily understandable physical approximation where the dye electronic structure is mapped onto the π-electron system of an allyl anion. We show that reported trends in solution-state absorbance bands and transition dipole moments associated with the first two electronic excitations can be described within reasonable accuracy by the model. We also show, for Michler's Hydrol Blue, that the four-electron, three-orbital model provides a more balanced description of the electronic difference densities associated with electronic excitation calculated with the full π-electron space than can be achieved with active space models intermediate between these limits. The valence excitation energies predicted by the model are not sensitive to the underlying basis set, so that considerable computational savings may be possible by using split-valence basis sets with a limited number of polarization functions. We conclude that the model meets the criteria for a "Pauling Point": a point where the cancellation of large errors leads to physically balanced model, and where further elaboration degrades, rather than improves, the quality of description. We advocate that this Pauling Point be exploited in condensed-phase dynamical models where the computational overhead associated with the electronic structure must kept to a minimum (for example, nonadiabatic dynamics simulations coupled to QM/MM environmental models).

Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics

Amyloid fibrillation of proteins is associated with a great variety of pathologic conditions. Development of new molecules that can monitor amyloidosis kinetics and inhibit fibril formation is of great diagnostic and therapeutic value. In this work, we have developed a biocompatible molecule that functions as an ex situ monitor and an in situ inhibitor for protein fibrillation, using insulin as a model protein. 1,2-Bis[4-(3-sulfonatopropoxyl)phenyl]-1,2-diphenylethene salt (BSPOTPE) is nonemissive when it is dissolved with native insulin in an incubation buffer but starts to fluoresce when it is mixed with preformed insulin fibril, enabling ex situ monitoring of amyloidogenesis kinetics and high-contrast fluorescence imaging of protein fibrils. Premixing BSPOTPE with insulin, on the other hand, inhibits the nucleation process and impedes the protofibril formation. Increasing the dose of BSPOTPE boosts its inhibitory potency. Theoretical modeling using molecular dynamics simulations and docking reveals that BSPOTPE is prone to binding to partially unfolded insulin through hydrophobic interaction of the phenyl rings of BSPOTPE with the exposed hydrophobic residues of insulin. Such binding is assumed to have stabilized the partially unfolded insulin and obstructed the formation of the critical oligomeric species in the protein fibrillogenesis process.

Electronic Structure Underlying Colour Differences Between Diarylmethane Dyes and their Azomethine Analogues

We show that multireference perturbation theory based on a four-electron, three-orbital state-averaged complete active space self-consistent field model can reproduce the shift in colour between diarylmethane dyes and their corresponding azomethine analogues. We relate the azomethine shift to changes in the electronic structure, through an examination of the relative changes in the state-averaged one-electron Hamiltonian (Fock) and surprisal matrices that characterise the analogous self-consistent field solutions.

Probing small molecule binding to amyloid fibrils

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.

Ligand polarizability contributes to tau fibril binding affinity

Whole brain imaging of tau-bearing neurofibrillary lesions has the potential to improve the premortem diagnosis and staging of Alzheimer's disease. Diverse compounds with high affinity for tau aggregates have been reported from high-throughput screens, but the affinity driving features common among them have not been determined. To identify these features, analogs of compounds discovered by high-throughput screening, including phenothiazine, triarylmethine, benzothiazole, and oxindole derivatives, were tested for their ability to displace fluorescent thioflavin dyes from filaments made from recombinant tau protein or authentic paired helical filaments purified from Alzheimer's disease tissue. When representative members of all scaffolds were assayed, the rank order of binding affinity determined for synthetic and authentic filaments correlated strongly, indicating that synthetic filaments have predictive utility for ligand development. Within individual scaffold families, binding affinity was found to correlate with compound polarizability, consistent with a role for dispersion forces in mediating ligand binding. Overall, the data indicate that polarizability is an important commonality among structurally diverse tau binding ligands, and that affinity for tau aggregates can be maximized by integrating formal assessment of this parameter into ligand discovery efforts.