Multifunctional Photo-Cross-Linking Probes: From Target Protein Searching to Imaging Applications.

Despite advances in genome sequencing technology, the complete molecular interaction networks reflecting the biological functions of gene products have not been fully elucidated due to the lack of robust molecular interactome profiling techniques. Traditionally, molecular interactions have been investigated in vitro by measuring their affinity. However, such a reductionist approach comes with throughput constraints and does not depict an intact living cell environment. Therefore, molecular interactions in live cells must be captured to minimize false-positive results. The photo-cross-linking technique is a promising tool because the production of a temporally controlled reactive functional group can be induced using light exposure. Photoaffinity labeling is used in biochemistry and medicinal chemistry for bioconjugation, including drug and antibody conjugation, target protein identification of bioactive compounds, and fluorescent labeling of target proteins. This Account summarizes recent advances in multifunctional photo-cross-linkers for drug target identification and bioimaging. In addition to our group's contributions, we reviewed the most notable examples from the last few decades to provide a comprehensive overview of how this field is evolving. Based on cross-linking chemistry, photo-cross-linkers are classified as either (i) reactive intermediate-generating or (ii) electrophile-generating. Reactive intermediates generating photoaffinity tags have been extensively modified to target a molecule of interest using aryl azide, benzophenone, diazirine, diazo, and acyl silanes. These species are highly reactive and can form covalent bonds, irrespective of residue. Their short lifetime is ideal for the instant capture and labeling of biomolecules. Recently, photocaged electrophiles have been investigated to take advantage of their residue selectivity and relatively high yield for adduct formation with tetrazole, nitrobenzyl alcohol, o-nitrophenylethylene, pyrone, and pyrimidone. Multifunctional photo-cross-linkers for two parallel practical applications have been developed using both classes of photoactivatable groups. Unbiased target interactome profiling of small-molecule drugs requires a challenging structure-activity relationship study (SAR) step to retain the nature or biological activity of the lead compound, which led to the design of a multifunctional "minimalist tag" comprising a bio-orthogonal handle, a photoaffinity labeling group, and functional groups to load target molecules. In contrast, fluorogenic photo-cross-linking is advantageous for bioimaging because it does not require an additional bio-orthogonal reaction to introduce a fluorophore to the minimalist tag. Our group has made progress on minimalist tags and fluorogenic photo-cross-linkers through fruitful collaborations with other groups. The current range of photoactivation reactions and applications demonstrate that photoaffinity tags can be improved. We expect exciting days in the rational design of new multifunctional photo-cross-linkers, particularly clinically interesting versions used in photodynamic or photothermal therapy.

Orthogonally-tunable and ER-targeting fluorophores detect avian influenza virus early infection.

Cell-based assays can monitor virus infection at a single-cell level with high sensitivity and cost-efficiency. For this purpose, it is crucial to develop molecular probes that respond selectively to physiological changes in live cells. We report stimuli-responsive light-emitters built on a T-shaped benzimidazole platform, and consecutive borylation reactions to produce a library of homologs displaying systematic changes in fluorescence quantum yield and environmental sensitivity. We find that certain fluorophores localize selectively at the endoplasmic reticulum, and interact with proteins involved in the stress signaling pathways. Notably, the mono-borylated compound responds selectively to the stress conditions by enhancing fluorescence, and detects avian influenza virus infection at the single-cell level. Our findings demonstrate the unprecedented practical utility of the stress-responsive molecular probes to differentiate cellular states for early diagnosis.

Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection.

Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation. Using photo-activated electrophile generating probes, we successfully revealed under-represented host cell response factors using an avian influenza virus infection model.

Correction: Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection.

Correction for 'Temporal control of protein labeling by a photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection' by Nicholas Asiimwe et al., Chem. Commun., 2022, https://doi.org/10.1039/d2cc04091c.

Kidney-Targeted Cytosolic Delivery of siRNA Using a Small-Sized Mirror DNA Tetrahedron for Enhanced Potency.

A proper intracellular delivery method with target tissue specificity is critical to utilize the full potential of therapeutic molecules including siRNAs while minimizing their side effects. Herein, we prepare four small-sized DNA tetrahedrons (sTds) by self-assembly of different sugar backbone-modified oligonucleotides and screened them to develop a platform for kidney-targeted cytosolic delivery of siRNA. An in vivo biodistribution study revealed the kidney-specific accumulation of mirror DNA tetrahedron (L-sTd). Low opsonization of L-sTd in serum appeared to avoid liver clearance and keep its size small enough to be filtered through the glomerular basement membrane (GBM). After GBM filtration, L-sTd could be delivered into tubular cells by endocytosis. The kidney preference and the tubular cell uptake property of the mirror DNA nanostructure could be successfully harnessed for kidney-targeted intracellular delivery of p53 siRNA to treat acute kidney injury (AKI) in mice. Therefore, L-sTd could be a promising platform for kidney-targeted cytosolic delivery of siRNA to treat renal diseases.

Targeted Degradation of Transcription Coactivator SRC-1 through the N-Degron Pathway.

Aberrantly elevated steroid receptor coactivator-1 (SRC-1) expression and activity are strongly correlated with cancer progression and metastasis. Here we report, for the first time, the development of a proteolysis targeting chimera (PROTAC) that is composed of a selective SRC-1 binder linked to a specific ligand for UBR box, a unique class of E3 ligases recognizing N-degrons. We showed that the bifunctional molecule efficiently and selectively induced the degradation of SRC-1 in cells through the N-degron pathway. Importantly, given the ubiquitous expression of the UBR protein in most cells, PROTACs targeting the UBR box could degrade a protein of interest regardless of cell types. We also showed that the SRC-1 degrader significantly suppressed cancer cell invasion and migration in vitro and in vivo. Together, these results demonstrate that the SRC-1 degrader can be an invaluable chemical tool in the studies of SRC-1 functions. Moreover, our findings suggest PROTACs based on the N-degron pathway as a widely useful strategy to degrade disease-relevant proteins.

Activity-Based Probes for the High Temperature Requirement A Serine Proteases.

The high temperature requirement A (HTRA) family of serine proteases mediates protein quality control. These proteins process misfolded proteins in several diseases including Alzheimer's disease (AD) and Parkinson's disease (PD). While their structures and activation mechanisms have been studied, the precise details of the regulation of their activity under physiological conditions have not been completely elucidated, partly due to the lack of suitable chemical probes. In the present study, we developed novel activity-based probes (ABPs) targeting the HTRAs and demonstrated their utility in the monitoring and quantification of changes in enzyme activity in live cells. Using our probes, we found the activity of HTRA1 to be highly elevated in an AD-like cell-based model. We also observed the active HTRA2 in live cells by using a mitochondrion-targeted probe. We believe that our probes can serve as a useful tool to study the role of human HTRAs in neurodegenerative diseases.

Structural homogeneity and mass density of bulk metallic glasses revealed by their rough surfaces and ultra-small angle neutron scattering (USANS).

The ultra-small angle neutron scattering (USANS) measures the microscale structure of heterogeneity and the scattering from rough surfaces with small scattering volumes can be neglected. But this is not true in amorphous alloys. The small angle scattering from such surfaces is not negligible, regardless of scattering volume. However, we demonstrate that the unwanted rough surfaces can be utilized to determine the homogeneity and mass density of amorphous metallic glasses using the USANS and surface neutron contrast matching technique. The power law scattering of the homogeneous Cu50Zr50 amorphous alloy disappeared under the surface contrast-matched environment, a mixture of hydrogenated/deuterated ethanol having low surface tension against the metallic alloys, indicating that the scattering originated not from its internal structure but from the rough surface. This confirms the structural homogeneity not only at the atomic level but also on a larger scale of micrometer. On the other hand, the crystallized Cu50Zr50 alloy showed strong power-law scattering under the matching environment due to the structural heterogeneity inside the alloy. This technique can apply to the bulk samples when the transmission is high enough not causing multiple scattering that is easily detected with USANS and when the surface roughness is dominant source of scattering.

Pulsed Current Activated Synthesis and Consolidation of Nanostructured Ti-TiC Composite and Its Mechanical Properties.

Ti and CNT powders were milled by high energy ball milling. The milled powders were then simultaneously synthesized and consolidated using pulsed current activated sintering (PCAS) within one minute under the applied pressure of 80 MPa. The advantage of this process is not only rapid densification to near theoretical density but also to prevent grain growth in nano-structured materials The milling did not induce any reaction between the constituent powders. Meanwhile, PCAS of the Ti-CNT mixture produced a Ti-TiC composite according to the reaction (Ti + 0.06CNT --> 0.94Ti+0.06TiC, Ti+0.12CNT --> 0.88Ti+0.12TiC). Highly dense nanocrystalline Ti-TiC compos- ites with a relative density of up to 99.5% were obtained within one minute. The hardness and fracture toughness of the dense Ti-6mole% TiC and Ti-12 mole% TiC produced by PCAS were also investigated.