Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity

Real-Time Visualization of Embryonic Apoptosis Using a Near-Infrared Fluorogenic Probe for Embryo Development Evaluation

Developing an accurate and reliable detection technique for early embryonic apoptosis is of great significance for real-time monitoring and evaluation of embryonic development in living systems. Herein, we have rationally designed and synthesized a novel near-infrared (NIR) fluorogenic probe CGK(QSY21)DEVD-Cy5.5 for real-time imaging of embryonic apoptosis. This probe is constructed with a NIR dye Cy5.5, a fluorescence quencher QSY21, and a peptide substrate Asp-Glu-Val-Asp (DEVD) of the caspase-3 enzyme that is a key executor of cell apoptosis. The probe was initially nonfluorescent in aqueous solution but emitted strong NIR fluorescence upon specific cleavage by activated caspase-3 in a concentration-dependent manner. Taking advantage of this unique feature, this fluorogenic probe was for the first time used for real-time imaging of caspase-3 activity in apoptotic embryos. More notably, significant fluorescence enhancement was solely determined from the apoptotic embryos with the treatment of the probe both in vitro and in vivo, highly suggesting that this probe has great potential to monitor the apoptosis of embryos. We thus envision that this probe would provide a very useful means for real-time visualization and accurate evaluation of embryonic development in the future.

Fluorescence imaging of drug target proteins using chemical probes

Fluorescence imaging can provide valuable information on the expression, distribution, and activity of drug target proteins. Chemical probes are useful small-molecule tools for fluorescence imaging with high structural flexibility and biocompatibility. In this review, we briefly introduce two classes of fluorescent probes for the visualization of drug target proteins. Enzymatically activatable probes make use of the specific enzymatic transformations that generally produce a fluorogenic response upon reacting with target enzymes. Alternatively, specific imaging can be conferred with a ligand that drives the probes to target proteins, where the labeling relies on noncovalent binding, covalent inhibition, or traceless labeling by ligand-directed chemistry.

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Fluorescence imaging of drug target proteins is useful for studying their localization and interaction with drugs.

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Enzymatically activatable probes provide high-contrast imaging and a readout of enzyme activity.

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Targeted probes favor specific imaging of non-enzymatic proteins, and LD chemistry allows for traceless labeling.

Metabolic-Pathway-Oriented Screening Targeting S-Adenosyl-l-methionine Reveals the Epigenetic Remodeling Activities of Naturally Occurring Catechols

Methyl transfer reactions play important roles in many biological phenomena, wherein the methylation cofactor S-adenosyl-l-methionine (SAM) serves as the important currency to orchestrate those reactions. We have developed a fluorescent-probe-based high-throughput screening (HTS) system to search for the compounds that control cellular SAM levels. HTS with a drug repositioning library revealed the importance of catechol-O-methyltransferase (COMT) and its substrates in controlling the SAM concentrations and histone methylation levels in colorectal tumor cells.

PIMT-Mediated Protein Repair: Mechanism and Implications

Amino acids undergo many covalent modifications, but only few amino acid repair enzymes have been identified. Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PIMT), also known as L-isoaspartyl/D-aspartyl protein carboxyl methyltransferase (PCMT), methylates covalently modified isoaspartate (isoAsp) residues accumulated in proteins via Asn deamidation and Asp hydrolysis. This cytoplasmic reaction occurs through the formation of succinimide cyclical intermediate and generates either isoAsp or Asp from succinimide. Succinimide conversion into Asp is spontaneous, while isoAsp is restored by PIMT using S-adenosylmethionine as a methyl donor. PIMT transforms isoAsp into succinimide, thereby creating an opportunity for the later to be converted into Asp. Apart from normal cell physiology, formation of isoAsp in proteins is promoted by various stress conditions. The resulting isoAsp can form a kink or bend in the protein backbone thus making the protein conformationally and functionally distorted. Many PIMT-interacting proteins (proteins with isoAsp residues) have been reported in eukaryotes, but only few of them have been found in prokaryotes. Extensive studies in mice have shown the importance of PIMT in neurodegeneration. Detail elucidation of PIMT function can create a platform for addressing various disorders such as Alzheimer's disease and cancer.

Dual-channel surface plasmon resonance monitoring of intracellular levels of the p53-MDM2 complex and caspase-3 induced by MDM2 antagonist Nutlin-3

MDM2 can mediate the degradation of tumor suppressor p53 through an autoregulatory feedback loop, in which MDM2 abolishes wild-type p53 function and accelerates malignant transformation. However, the incorporation of MDM2 antagonist Nutlin-3 could reactivate the transcriptional activity of p53, up-regulate caspase-3, and induce apoptosis. In this work, the simultaneous and label-free monitoring of p53-MDM2 complex and caspase-3 levels in cancer cells before and after Nutlin-3 treatment was conducted using dual-channel surface plasmon resonance (SPR). The p53-MDM2 complex was captured in one fluidic channel covered with consensus double-stranded (ds)-DNA, while the other channel was pre-immobilized with caspase-3-specific biotinylated DEVD-containing peptides. To amplify the SPR signals, the attachment of streptavidin (SA)-conjugated anti-MDM2 antibody in both channels was achieved. The signal diversity before and after Nutlin-3 treatment is indicative of the difference in the levels of the intracellular p53-MDM2 complex and caspase-3. The limit of detection for p53-MDM2 and caspase-3 down to 4.54 pM and 0.03 ng mL^-1, respectively, was attained. Upon treatment with Nutlin-3, MCF-7 cancer cells with wild-type p53 showed decreased expression of the p53-MDM2 complex and an increased caspase-3 level, while MDA-MB-231 cancer cells with mutant p53 exhibited an elevated caspase-3 level and unchanged p53-MDM2 complex expression. The apoptosis of MCF-7 and MDA-MB-231 cancer cells upon Nutlin-3 treatment follows a p53-dependent and a p53-independent pathway, respectively. The proposed method is sensitive, selective and label-free, holding great promise for assaying intracellular p53-MDM2 complex and caspase-3 levels and differentiating Nutlin-3-mediated p53-dependent or p53-independent apoptotic pathways.

Fluorogenic probes for disease-relevant enzymes

Traditional biochemical methods for enzyme detection are mainly based on antibody-based immunoassays, which lack the ability to monitor the spatiotemporal distribution and, in particular, the in situ activity of enzymes in live cells and in vivo. In this review, we comprehensively summarize recent progress that has been made in the development of small-molecule as well as material-based fluorogenic probes for sensitive detection of the activities of enzymes that are related to a number of human diseases. The principles utilized to design these probes as well as their applications are reviewed. Specific attention is given to fluorogenic probes that have been developed for analysis of the activities of enzymes including oxidases and reductases, those that act on biomacromolecules including DNAs, proteins/peptides/amino acids, carbohydrates and lipids, and those that are responsible for translational modifications. We envision that this review will serve as an ideal reference for practitioners as well as beginners in relevant research fields.

Design strategy for serine hydroxymethyltransferase probes based on retro-aldol-type reaction

Serine hydroxymethyltransferase (SHMT) is an enzyme that catalyzes the reaction that converts serine to glycine. It plays an important role in one-carbon metabolism. Recently, SHMT has been shown to be associated with various diseases. Therefore, SHMT has attracted attention as a biomarker and drug target. However, the development of molecular probes responsive to SHMT has not yet been realized. This is because SHMT catalyzes an essential yet simple reaction; thus, the substrates that can be accepted into the active site of SHMT are limited. Here, we focus on the SHMT-catalyzed retro-aldol reaction rather than the canonical serine-glycine conversion and succeed in developing fluorescent and 19F NMR molecular probes. Taking advantage of the facile and direct detection of SHMT, the developed fluorescent probe is used in the high-throughput screening for human SHMT inhibitors, and two hit compounds are obtained.

Potential of Enzymomics Methodologies to Characterize Disease-Related Protein Functions

Enzymatic functions are often altered during disease onset and progression, and therefore chemical-biological studies, which utilize chemical knowledge to discover novel protein functions, are often employed to find proteins with functions closely related to disease phenotypes. Such studies are known as forward chemical-biological approaches and form part of the emerging field of enzymomics (omics of enzymes). This review provides an overview of methodologies available for discovering and characterizing disease-related alterations of enzymatic functions and prospects for the future.

Design of modular dual enzyme-responsive peptides

Dual enzyme-responsive peptides were synthesized by masking the ɛ-amine of lysine with various enzyme substrates. Enzymatic cleavage of these sequences unmasked the ɛ-amine, allowing for further digestion by a second enzyme, which was monitored colorimetrically. This modular peptide design should provide substrates for a large combination of clinically relevant enzymes.

Fluorescence detection of serum albumin with a turnover-based sensor utilizing Kemp elimination reaction

The Kemp elimination reaction is a well-known chemical reaction that is facilitated on a protein surface microenvironment, and in particular is highly accelerated in a unique binding pocket of serum albumin. We have designed and synthesized a fluorescently activatable coumarin derivative with a benzisoxazole scaffold to enable monitoring of the Kemp elimination reaction in terms of fluorescence change for the first time. We show that this fluorescent sensor can sensitively and selectively quantitate serum albumin in blood samples. It also works in a dry-chemistry format.