Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells

Abstract

Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small‐molecule probes to visualize the protein‐aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.

Biosensors for Studying Neuronal Proteostasis

“…In addition to folding sensors, specialized tools have been developed for probing the UPS system and autophagy (reviewed in Lindsten et al, 2003 ; Matilainen et al, 2016 ; Klionsky et al, 2021 ). Finally, sensors for monitoring certain chaperones and canonical stress responses such as the heat shock response or the unfolded protein response of the endoplasmic reticulum are also available (e.g., Batulan et al, 2003 ; Morley and Morimoto, 2004 ; van Oosten-Hawle et al, 2013 ; Kijima et al, 2018 ; Pereira et al, 2018 ; Miles and van Oosten-Hawle, 2020 ; Shen et al, 2021 ), but will not be discussed in detail here.…”

RNA‐Selective Small‐Molecule Ligands: Recent Advances in Live‐Cell Imaging and Drug Discovery

“…Over the last three years, more than a hundred review articles focusing on bioimaging and drug discovery related development with the use of fluorescent small molecule ligands have been published, indicating a significant progress and discovery on these hot research areas. Some most recently highlighted topics with the use of target-selective fluorescent ligands include cancer cell and tissue diagnosis, [2] imagingguided drug therapy, [3] disease biomarker identification, [4] ferroptosis investigations, [5] in vivo imaging, [6] plasma membrane staining, [7] cellular organelle imaging (targeting mitochondria, [8] lysosomes, [9] Golgi [10] and endoplasmic reticulum [11] ), enzymatic activity, [12] drug target proteins study, [13] visualization of ion dynamics, [14] reactive oxygen species, [15] biological hydrogen sulphide, [16] protein aggregation in live cells, [17] bacterial labelling and infection detection, [18] imaging of viscosity in living biosystems, [19] imaging of microenvironments [8b] and G-quadruplex structures of DNA and RNA in live cells. [20] Among these interesting research areas, the specific area of RNA-selective small molecule ligands in fluorescence live cell imaging and drug discovery is relatively underexplored at present.…”

Fluorogenic sensing of amorphous aggregates, amyloid fibers, and chaperone activity via a near‐infrared aggregation‐induced emission‐active probe

“…[ 13 ] In contrast, fluorescent probes offer several advantages, including robustness, high sensitivity, and cost‐effectiveness, making them an attractive avenue for protein aggregation research. [ 14,15 ]…”

“…[13] In contrast, fluorescent probes offer several advantages, including robustness, high sensitivity, and cost-effectiveness, making them an attractive avenue for protein aggregation research. [14,15] Currently, the primary emphasis of chemical probes lies in targeting amyloid fibers. This preference is motivated by the strong association of amyloid fibers with dozens of human diseases, as well as their well-defined cross βstrand structures, which are ideal for structure-based probe design.…”