Mapping the binding site topology of amyloid protein aggregates using multivalent ligands

Sanna, Elena; Rodrigues, Margarida; Fagan, Steven G.; Chisholm, Timothy S; Kulenkampff, Klara; Klenerman, David; Spillantini, Maria Grazia; Aigbirhio, Franklin I.; Hunter, Christopher A.

doi:10.1039/d1sc01263k

Cited by 7 publications

(11 citation statements)

References 34 publications

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“…This type of molecule has just recently been reported as a superior protein ligand for disease diagnosis with a high binding affinity due to its effective molarity effect. 31,32 Although we did not examine whether our MSdyads acted as such ligands, we unexpectedly found that in a high concentration solution, MS-dyads form aggregates showing optical properties characteristic of excitons spreading over multiple molecules. Their green fluorescence is intense even at 10 −1 M without aggregation-caused quenching.…”

Section: ■ Introductionmentioning

confidence: 89%

Supramolecular Complexation and Collective Optical Properties Induced by Linking Two Methyl Salicylates via a σ-Bridge

et al. 2022

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Supramolecular complexes or polymers, formed by noncovalent intermolecular forces such as π–π and dipole–dipole interactions, have the potential to render collective optical properties brought about by excitons spreading over multiple molecules, as seen in J-aggregates. In this respect, molecules with a large π-system and dipole moment are advantageous. However, we report here that methyl salicyate (MS) dyad-type molecules, synthesized by connection of two MSs via a σ-bridge, are effective for forming stable aggregates with collective optical properties. The self-association of MS-dyads occurs in a CHCl3 solution at a high concentration of over 10–2 M, which is recognized by the appearance of an absorption band (λmax = 464 nm) bathochromically shifted beyond 8300 cm–1 from the band in the dilute solution (λmax = 334 nm). Upon excitation of this band, an intense green fluorescence is observed without aggregation-caused quenching. The absorption and fluorescence bands, both of which have well-resolved vibronic progressions, are in a near-mirror image relationship, yielding a small Stokes shift of 600 cm–1. A reasonable explanation for these characteristic optical properties is provided from theoretical considerations on the aggregate model constructed based on the results of single-crystal X-ray analysis. The 1H NMR measurements suggest that unconnected MSs also form aggregates at high concentrations, although the absorption measurements do not provide any evidence for this. It is thus presumed that the connection of MSs stabilizes the MS stacking structure of the aggregates, leading to the generation of an excited state delocalized over multiple molecules.

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Section: ■ Introductionmentioning

confidence: 89%

Supramolecular Complexation and Collective Optical Properties Induced by Linking Two Methyl Salicylates via a σ-Bridge

et al. 2022

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“…We first compiled a data set of experimentally determined dissociation constants for ligand binding to Aβ(1–42) fibrils. − ...…”

Section: Resultsmentioning

confidence: 99%

Discovery of High-Affinity Amyloid Ligands Using a Ligand-Based Virtual Screening Pipeline

2023

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Fibrillar protein aggregates are characteristic of neurodegenerative diseases but represent difficult targets for ligand design, because limited structural information about the binding sites is available. Ligand-based virtual screening has been used to develop a computational method for the selection of new ligands for Aβ(1–42) fibrils, and five new ligands have been experimentally confirmed as nanomolar affinity binders. A database of ligands for Aβ(1–42) fibrils was assembled from the literature and used to train models for the prediction of dissociation constants based on chemical structure. The virtual screening pipeline consists of three steps: a molecular property filter based on charge, molecular weight, and logP; a machine learning model based on simple chemical descriptors; and machine learning models that use field points as a 3D description of shape and surface properties in the Forge software. The three-step pipeline was used to virtually screen 698 million compounds from the ZINC15 database. From the top 100 compounds with the highest predicted affinities, 46 compounds were experimentally investigated by using a thioflavin T fluorescence displacement assay. Five new Aβ(1–42) ligands with dissociation constants in the range 20–600 nM and novel structures were identified, demonstrating the power of this ligand-based approach for discovering new structurally unique, high-affinity amyloid ligands. The experimental hit rate using this virtual screening approach was 10.9%.

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“…The above results reveal a mechanism wherein the flexible linker creates a well-defined dye aggregate with specific orientations and distinct photophysical properties. First, the chemical scaffold of multivalent ligand containing a flexible linker might be favorable for guaranteeing the probes in the fluorescence-off state with a minimized background before binding to Aβ 42 deposition due to rapid nonradiative decay via intramolecular charge transfer (ICT), which can be inhibited in the rigid environment within Aβ 42 aggregates to turn on fluorescence. − Second, different from monovalent ligand with a single binding site, two ligands moieties linked together with a distinct orientation and distance might lead to enhancement in the overall affinity, because the binding of the first headgroup at one side will bring the second headgroup into mutual proximity with another binding site, which increases effective molarity. , Third, the lipophilicity of the D-π- A scaffold and flexible linker can be well balanced to well regulate the aggregated behavior in vivo and guarantee BBB penetrability. , Taken together, our strategy could facile develop a simple and multipronged approach that elaborated the homodimer enjoys AIE-active NIR emission, excellent photostability, high S/N ratio, low interference from autofluorescence, high binding affinity and selectivity, and good BBB penetrability during the binding to Aβ 42 aggregates, which might satisfy the demand for the detection of Aβ 42 deposits both in vitro and in vivo, as illustrated in Scheme . It should be pointed out that the imaging performance of stilbazolium homodimer is not outstanding as compared with many probes reported in the literature, , while the flexible bivalent approach does significantly improve the comprehensive performance of stilbazolium monomer probes.…”

Section: Resultsmentioning

confidence: 99%

“…First, the chemical scaffold of multivalent ligand containing a flexible linker might be favorable for guaranteeing the probes in the fluorescence-off state with a minimized background before binding to Aβ 42 deposition due to rapid nonradiative decay via intramolecular charge transfer (ICT), which can be inhibited in the rigid environment within Aβ 42 aggregates to turn on fluorescence. 41−43 Second, different from monovalent ligand with a single binding site, two ligands moieties linked together with a distinct orientation and distance might lead to enhancement in the overall affinity, 44 because the binding of the first headgroup at one side will bring the second headgroup into mutual proximity with another binding site, which increases effective molarity. 45,46 Third, the lipophilicity of the D-π-A scaffold and flexible linker can be well balanced to well regulate the aggregated behavior in vivo and guarantee BBB penetrability.…”

Section: ■ Introductionmentioning

confidence: 99%

A Flexible Bivalent Approach to Comprehensively Improve the Performances of Stilbazolium Dyes as Amyloid-β Fluorescent Probes

Zhuang,

Zhou,

Chen

et al. 2023

ACS Appl. Mater. Interfaces

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Exploring new ways to reconstruct the structure and function of inappropriate organic fluorophores for improving amyloid-β (Aβ) fluorescent imaging performance is desired for precise detection and early diagnosis of Alzheimer's disease (AD). With stilbazolium dyes as examples, here, we present a multipronged approach to comprehensively improved the Aβ fluorescent imaging performance through a flexible bivalent method, where a flexible carbon chain was introduced to link two monomers to form a homodimer. Our results reveal a mechanism wherein the flexible linker creates a well-defined probe with specific orientations and distinct photophysical properties. Applying this approach in combination with theoretical simulation, the homodimers exhibited a comprehensive improvement of the Aβ fluorescent imaging performance of the dye monomers, including better photostability and higher signal-to-noise (S/N) ratio, higher "off−on" near-infrared fluorescence (NIRF) response sensitivity, higher specificity and affinity to Aβ deposits, and more reasonable lipophilicity for blood−brain barrier (BBB) penetrability. The results demonstrate that flexible homodimers offer a multipronged approach to obtaining high-performance NIRF imaging reagents for the detection of Aβ deposits both in vitro and in vivo.

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Mapping the binding site topology of amyloid protein aggregates using multivalent ligands

Abstract: Multivalent ligands offer a powerful approach to obtain high affinity reagents to bind the aggregates that form in neurodegenerative disease. Selectivity for different proteins was achieved by using different linkers to connect the head groups.

Cited by 7 publications

References 34 publications

Supramolecular Complexation and Collective Optical Properties Induced by Linking Two Methyl Salicylates via a σ-Bridge

Supramolecular Complexation and Collective Optical Properties Induced by Linking Two Methyl Salicylates via a σ-Bridge

Discovery of High-Affinity Amyloid Ligands Using a Ligand-Based Virtual Screening Pipeline

A Flexible Bivalent Approach to Comprehensively Improve the Performances of Stilbazolium Dyes as Amyloid-β Fluorescent Probes

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