Design, synthesis, and biological activities of 3-((4,6-diphenylpyrimidin-2-ylamino)methylene)-2,3-dihydrochromen-4-ones.

Novel (Z)-3-((4,6-diphenylpyrimidin-2-ylamino)methylene)-2,3-dihydrochromen-4-one derivatives were designed and synthesized to find chemotherapeutic agents. Derivative 9 was selected based on its clonogenicity against cancer cells and synthetic yield for further biological experiments. It showed decreases in aurora kinase A, B, and C phosphorylation from western blot analysis. Derivative 9 upregulated the expression of G1 cell cycle inhibitory proteins including p21 and p27, and G1 progressive cyclin D1, and downregulated G1-to-S progressive cyclins, resulting in cell cycle arrest at the G1/S boundary. It stimulated the cleavage of caspase-9, -3, -7, and poly (ADP-ribose) polymerase, resulting in triggering apoptosis through a caspase-dependent pathway. In addition, derivative 9 inhibited in vivo tumor growth in a syngeneic tumor implantation mouse model. The findings of this study suggest that derivative 9 can be considered as a lead compound for chemotherapeutic agents.

Mass spectrometric investigation of concentration-dependent effect of curcumin and oxidative stress on intracellular glutathione levels.

Herein, we investigated the correlation between curcumin and glutathione (GSH) levels in mammalian cells using gold nanoparticles (AuNPs) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). GSH exists in high concentration in the cytosol and acts as a major antioxidant and reducing agent in organisms. Previous studies showed that curcumin, a well-known antioxidant with anti-inflammatory, anti-proliferative, and anti-carcinogenic activities, affects GSH levels in mammalian cells. However, the correlation between their levels remains controversial and has not yet been completely elucidated. This study used our recent strategy of GSH quantification, where GSH in cell lysate is captured on maleimide groups of AuNPs and analyzed using MALDI-TOF MS with isotopomer GSH (GSH*)-conjugated AuNPs as an internal standard. The comparison between GSH and GSH* relative intensities allows the quantitation of GSH in cells. In this way, GSH levels in mammalian cells were investigated after incubation with curcumin at various concentrations with or without oxidative stress. We observed that intracellular GSH levels were affected by curcumin in a concentration-dependent manner with oxidative stress; GSH levels decrease at a lower curcumin concentration, which can be recovered at increased curcumin concentrations. We also found that the GSH level increased at all curcumin concentrations after a certain incubation time. We believe our strategy can be commonly used to determine GSH levels in cells that are treated differently with various exogenous stimulants like reactive oxygen species, biofunctional natural products, and drug candidates. Graphical abstract.

Mass spectrometric analysis of protein tyrosine nitration in aging and neurodegenerative diseases.

This review highlights the significance of protein tyrosine nitration (PTN) in signal transduction pathways, the progress achieved in analytical methods, and the implication of nitration in the cellular pathophysiology of aging and age-related neurodegenerative diseases. Although mass spectrometry of nitrated peptides has become a powerful tool for the characterization of nitrated peptides, the low stoichiometry of this modification clearly necessitates the use of affinity chromatography to enrich modified peptides. Analysis of nitropeptides involves identification of endogenous, intact modification as well as chemical conversion of the nitro group to a chemically reactive amine group and further modifications that enable affinity capture and enhance detectability by altering molecular properties. In this review, we focus on the recent progress in chemical derivatization of nitropeptides for enrichment and mass analysis, and for detection and quantification using various analytical tools. PTN participates in physiological processes, such as aging and neurodegenerative diseases. Accumulation of 3-nitrotyrosine has been found to occur during the aging process; this was identified through mass spectrometry. Further, there are several studies implicating the presence of nitrated tyrosine in age-related diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis.

Enhanced synthesis of antibody-functionalized gold nanoparticles for multiplexed exosome detection via mass signal amplification in LDI-TOF MS.

We present a novel method for sensitive exosomal protein detection using organic matrix-free laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) and gold nanoparticles (AuNPs) functionalized with mass tags for signal amplification (Am-tags). Target exosomes were captured by specific antibodies on AuNPs and a biochip, where the antibody-presenting AuNPs (Ab/Am-tag@AuNPs) contained excess Am-tags. LDI-TOF MS analysis revealed the mass signal of Am-tags on Ab/Am-tag@AuNPs, indicating the presence of target exosomes. Thus, the target signal was amplified by a large number of Am-tags, resulting in enhanced sensitivity. We optimized the protocol to prepare stable Ab/Am-tag@AuNPs, focusing on parameters such as the concentration and ratio of thiol molecules for AuNP functionalization, suitable solvents for the coupling reaction, and amount of antibodies conjugated to the AuNPs. Subsequently, we evaluated the ability of our method to detect exosomes isolated from three cell lines, NIH3T3, MCF7, and HeLa, using an anti-Rab5 immobilized gold chip and anti-CD63/Am-tag@AuNPs with LDI-TOF MS analysis. Calibration curves constructed for the three cell lines showed a linear relationship with an excellent limit of detection. Finally, we emphasized the versatility of our method for the quantitative detection of exosomal proteins CD63 and mucin 1 (MUC1) using two types of Am-tags. LDI-TOF MS analysis revealed the presence of CD63 and MUC1 at different expression levels in HeLa and MCF7 cancer cells. Our findings clearly indicate the potential of Ab/Am-tag@AuNPs as a sensitive and reliable approach for identifying biomarkers in exosomes, providing valuable insights into their utility in biomedical research and clinical settings.

Preparation and evaluation of in situ photocleavable mass tags with facile mass variation for matrix-free laser desorption ionization mass spectrometry.

Mass tags have been used for the precise identification, quantification, and characterization of macrobiomolecules and small organic molecules. Existing research has not yet demonstrated the preparation of a series of trityl-based photocleavable mass tags (PMTs) with similar structures but different molecular weights and mass variability. Herein, we introduce the design and synthesis of trityl-based in situ PMTs that generate heterolytic photocleavable cationic species upon laser irradiation. Mass variation of the PMTs was achieved via a simple conjugation reaction in the final step of synthesis. We prepared a series of PMTs with similar structures but different molecular weights and performed organic matrix-free laser desorption/ionization mass spectrometry (LDI MS) analysis. The practical applicability of the PMTs was evaluated by conjugating PMTs to oligonucleotides and utilizing them for detecting specific oligonucleotide targets combined with a mass signal amplification strategy. Quantitative aspects were also evaluated to verify the capability of the mass tags for multiplexed detection and the quantification of targets. The LDI MS analysis clearly demonstrated in situ heterolytic photocleavage that formed trityl cation peaks with high S/N ratios and high sensitivity. We strongly believe that the developed mass tags and LDI MS are useful alternatives to conventional signal transduction methods used for biosensors, such as surface plasmon resonance, electrochemical redox, and fluorescence.

Preparation of gradient surfaces by using a simple chemical reaction and investigation of cell adhesion on a two-component gradient.

This article describes a simple method for the generation of multicomponent gradient surfaces on self-assembled monolayers (SAMs) on gold in a precise and predictable manner, by harnessing a chemical reaction on the monolayer, and their applications. A quinone derivative on a monolayer was converted to an amine through spontaneous intramolecular cyclization following first-order reaction kinetics. An amine gradient on the surface on a scale of centimeters was realized by modulating the exposure time of the quinone-presenting monolayer to the chemical reagent. The resulting amine was used as a chemical handle to attach various molecules to the monolayer with formation of multicomponent gradient surfaces. The effectiveness of this strategy was verified by cyclic voltammetry (CV), matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS), MS imaging, and contact-angle measurements. As a practical application, cell adhesion was investigated on RGD/PHSRN peptide/peptide gradient surfaces. Peptide PHSRN was found to synergistically enhance cell adhesion at the position where these two ligands are presented in equal amounts, while these peptide ligands were competitively involved in cell adhesion at other positions. This strategy of generating a gradient may be further expandable to the development of functional gradient surfaces of various molecules and materials, such as DNA, proteins, growth factors, and nanoparticles, and could therefore be useful in many fields of research and practical applications.

Ultrasensitive detection of microRNAs using nanoengineered micro gold shells and laser desorption/ionization time-of-flight MS.

We report on a simple, fast, and highly sensitive method that allows femtomolar detection of microRNAs (miRNAs) without the need of polymerase chain reaction using a nanoengineered micro gold shell (µAuS) and laser desorption/ionization time-of-flight (LDI-TOF) mass spectrometry (MS). Target miRNAs are selectively captured by a chemically decorated gold chip and a µAuS, which carries with it a large number of small molecules, termed amplification tags (Am-tags). Subsequent LDI-TOF MS analysis allows a highly amplified mass signal of Am-tags for the presence of target miRNAs in a sample, resulting in ultrasensitive detection.

Self-assembled monolayers with dynamicity stemming from (bio)chemical conversions: from construction to application.

Surfaces with "dynamicity" whereby surface properties can be modulated by an external stimulus on user demand have been actively exploited for the past decade. These switchable surfaces with dynamic properties are widely used for a number of applications such as micro/nanoarrays, biomolecule immobilization, basic cell studies, and tissue engineering on a variety of materials. This minireview highlights the dynamic control of surface properties on self-assembled monolayers and focuses on dynamicity that stems from (bio)chemical conversions achieved by electrical potentials, photoillumination, chemical reagents, enzymes, and pH.

Analysis of the biochemical role of Lys-11 in polyubiquitin chain formation using quantitative mass spectrometry.

RATIONALE: Protein ubiquitination plays a critical role in regulating many cellular events, such as protein localization and stability, cellular signal transduction and DNA repair. Recent studies have shown that polyubiquitin (polyUb) chains elongate through heterogeneous isopeptide linkages to K11, K29, K48 and K63. In this study we have investigated the usage of isopeptide linkages of polyUb chains in different molecular weight regions by using quantitative mass spectrometry. METHODS: Recombinant Chfr protein was autoubiquitinated by E1 enzyme, E2 enzyme UbcH5 and ubiquitin (WT Ub, K11R Ub, K48R Ub and K63R Ub) in vitro, and different molecular weight regions of ubiquitinated Chfr were then subjected to liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) following sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and in-gel digestion. RESULTS: Absolute QUantitative Analysis (AQUA) of polyUb chain formation with wild-type (WT) and point mutants of ubiquitin was performed, and the results suggested that the K11 polyUb chain was most frequently used in the high ubiquitin conjugates of WT Ub. Furthermore, the extent of polyUb chain formation with K11R Ub was decreased about 10-fold compared to polyUb chain formation with WT Ub through the entire molecular weight region. The present study suggests that the linkage through K11 plays crucial roles in polyUb chain formation. CONCLUSIONS: Topologies of polyUb chains in the low and high Ub conjugates were studied using mass spectrometry. K48 and K63 were the primary ubiquitination sites of the low molecular weight Ub conjugates, whereas K11 was the critical site of polyUb chain formation in high molecular weight Ub conjugates.

Efficient Analysis of Small Molecules via Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (LDI-TOF MS) Using Gold Nanoshells with Nanogaps.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a commonly used technique for analyzing large biomolecules. However, the utilization of organic matrices limits the small-molecule analysis because of the interferences in the low-mass region and the reproducibility issues. To overcome these limitations, a surface-assisted laser desorption/ionization (SALDI), which utilizes nanostructured metallic surfaces, has been developed. Herein, a novel approach for SALDI-MS was proposed using silica@gold core-shell hybrid materials with a nanogap-rich shell (SiO2@Au NGS), which is an emerging material due to its excellent heat-generating capabilities. The gold shell thickness was controlled by adjusting the concentration of gold precursor for the growth of gold nanoparticles. SALDI-MS measurements were performed on a layer formed by drop-casting a mixture of SiO2@Au NGS and analytes. At the optimized process, the gold shell thickness was observed to be 17.2 nm, which showed the highest absorbance. Based on the enhanced SALDI capability, SiO2@Au NGS was utilized to detect various small molecules, including amino acids, sugars, and flavonoids, and the ionization softness was confirmed with a survival yield upon fragmentation. The limits of detection, reproducibility, and salt tolerance of SiO2@Au NGS demonstrate its potential as an effective and reliable SALDI material for small-molecule analyses.

Quantification of proteins on gold nanoparticles by combining MALDI-TOF MS and proteolysis.

Protein-coated nanoparticles have been used in many studies, including those related to drug delivery, disease diagnosis, therapeutics, and bioassays. The number and density of proteins on the particles' surface are important parameters that need to be calculable in most applications. While quantification methods for two-dimensional surface-bound proteins are commonly found, only a few methods for the quantification of proteins on three-dimensional surfaces such as nanoparticles have been reported. In this paper, we report on a new method of quantifying proteins on nanoparticles using matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS). In this method, the nanoparticle-bound proteins are digested by trypsin and the resulting peptide fragments are analyzed by MALDI-TOF MS after the addition of an isotope-labeled internal standard (IS) which has the same sequence as a reference peptide of the surface-bound protein. Comparing the mass intensities between the reference peptide and the IS allows the absolute quantification of proteins on nanoparticles, because they have the same molecular milieu. As a model system, gold nanoparticles were examined using bovine serum albumin (BSA) as a coating protein. We believe that our strategy will be a useful tool that can provide researchers with quantitative information about the proteins on surfaces of three-dimensional materials.

On-demand electrochemical activation of the click reaction on self-assembled monolayers on gold presenting masked acetylene groups.

We report on a new surface modification method for grafting a "dynamic" property for on-demand activation of the click reaction. Our approach utilizes the acetylene group masked with dicobalt hexacarbonyl, Co(2)(CO)(6), which is not reactive toward the click reaction. Electrochemical treatment reveals the acetylene group on the selected region, which is then used as a chemical handle for surface functionalization via the click reaction with an azide-containing molecule. Electrochemical and chemical conversions on the surface were verified by cyclic voltammetry, X-ray photoelectron spectroscopy, and fluorescence spectroscopy. We have demonstrated immobilization of an azide-modified RGD peptide and promotion of cell adhesion/migration to the region of electrochemical induction.

Selective enrichment and mass spectrometric identification of nitrated peptides using fluorinated carbon tags.

Protein tyrosine nitration (PTN) is a post-translational modification that is related to several acute or chronic diseases. PTN introduces a nitro group in the ortho position of the phenolic hydroxyl group of tyrosine residues. PTN has been shown to be involved in the pathogenesis of inflammatory responses, cancers, and neurodegenerative and age-related disorders. Furthermore, it has been proposed that PTN regulates signal cascades related to nitric oxide (NO·) production and NO-mediated processes. Although nitrated proteins as markers of oxidative stress are confirmed by immunological assays in various affected cells or tissues, it is not known how many different types of proteins in living cells are nitrated. Since protein nitration is a low-abundance post-translational modification, development of an effective enrichment method for nitrated proteins is needed to detect nitrated peptides or proteins from the limited amount of pathophysiological samples. In the present study, we developed an enrichment method using specific chemical tagging. Nitroproteome profiling using chemical tagging and mass spectrometry was validated by model proteins. Furthermore, we successfully identified numerous nitrated proteins from the Huh7 human hepatoma cell line.

Role of ginseng in the neurovascular unit of neuroinflammatory diseases focused on the blood-brain barrier.

Ginseng has long been considered as an herbal medicine. Recent data suggest that ginseng has anti-inflammatory properties and can improve learning- and memory-related function in the central nervous system (CNS) following the development of CNS neuroinflammatory diseases such as Alzheimer's disease, cerebral ischemia, and other neurological disorders. In this review, we discuss the role of ginseng in the neurovascular unit, which is composed of endothelial cells surrounded by astrocytes, pericytes, microglia, neural stem cells, oligodendrocytes, and neurons, especially their blood-brain barrier maintenance, anti-inflammatory effects and regenerative functions. In addition, cell-cell communication enhanced by ginseng may be attributed to regeneration via induction of neurogenesis and angiogenesis in CNS diseases. Thus, ginseng may have therapeutic potential to exert cognitive improvement in neuroinflammatory diseases such as stroke, traumatic brain injury, multiple sclerosis, Parkinson's disease, and Alzheimer's disease.

A doubly signal-amplified DNA detection method based on pre-complexed [Ru(bpy)3]2+-doped silica nanoparticles.

Easy detection: The target DNA in a 10-100 aM range can be detected by pre-complexed nanoparticles without additional amplification or target labeling. The [Ru(bpy)(3)](2+)-doped silica nanoparticles are hybridized to form a complex with highly enhanced sensitivity (see scheme). This method will be a significant improvement over conventional microarray/fluorescence readout systems.

Mass spectrometric analysis of acid-assisted photochemical release of the trimethyl lock system on the monolayers on gold.

We report the acid-assisted photolysis of the trimethyl lock system which has long been harnessed for a variety of applications such as drug delivery, cellular imaging, enzyme activity assays, and surface patterning. By mass spectrometric analysis, we found that photoinduced intramolecular cyclization and the ensuing release of the pendant groups of the trimethyl lock on the self-assembled monolayers proceeded cleanly in the presence of HCl, to give a high yield.

Organic matrix-free imaging mass spectrometry.

Mass spectrometry (MS) is an ideal tool for analyzing multiple types of (bio)molecular information simultaneously in complex biological systems. In addition, MS provides structural information on targets, and can easily discriminate between true analytes and background. Therefore, imaging mass spectrometry (IMS) enables not only visualization of tissues to give positional information on targets but also allows for molecular analysis of targets by affording the molecular weights. Matrixassisted laser desorption/ionization-time of flight (MALDI-TOF) MS is particularly effective and is generally used for IMS. However, the requirement for an organic matrix raises several limitations that get in the way of accurate and reliable images and hampers imaging of small molecules such as drugs and their metabolites. To overcome these problems, various organic matrix-free LDI IMS systems have been developed, mostly utilizing nanostructured surfaces and inorganic nanoparticles as an alternative to the organic matrix. This minireview highlights and focuses on the progress in organic matrix-free LDI IMS and briefly discusses the use of other IMS techniques such as desorption electrospray ionization, laser ablation electrospray ionization, and secondary ion mass spectrometry. [BMB Reports 2020; 53(7): 349-356].

Chemical approach for specific enrichment and mass analysis of nitrated peptides.

The analysis and detection of 3-nitrotyrosine are biologically and clinically important because protein tyrosine nitration is known to be involved in a number of biological phenomena such as cellular signal transduction, pathogenesis of inflammatory responses, and age-related disorders. However, the main obstacles in the study are low abundance of nitrated species and lack of efficient enrichment methods. Here in, we suggest a new chemical approach to analyze nitrated peptides using mass spectrometry by incorporating specific tagging groups in the peptides through simple chemical transformations. Nitro groups on tyrosine side chains of nitrated peptides were subjected to reduction to give rise to amine which was further converted to metal-chelating motif. Mass analyses verified that Ni(2+)-NTA magnetic agarose beads selectively captured and isolated the modified peptides, i.e., nitrated peptides, by strong and specific metal chelating interactions. We further demonstrated the utility of our approach by detection of nitrated peptides in complex samples such as tryptic peptide mixtures of bovine serum albumin (BSA) and a HeLa cell lysate.

In vitro solubility, stability and permeability of novel quercetin-amino acid conjugates.

In order to discover a quercetin prodrug with improved bioavailability, we synthesized nine quercetin-amion acid conjugates and estimated their pharmacokinetic properties including water solubility, stability against chemical or enzymatic hydrolysis, and cell permeability. Among the synthesized quercetin prodrugs, quercetin-glutamic acid conjugate Qu-E (4g/5g) showed remarkable increases in water solubility, stability, and cell permeability compared with quercetin, which warrants further development as a quercetin prodrug.