An affinity-based probe for the proteomic profiling of aspartic proteases

We have developed an affinity-based probe for the proteomic profiling of aspartic proteases. Our probe was shown to be selective towards aspartic proteases over other proteins. It was also shown that the strategy may be used to label selectively aspartic proteases in the presence of a large excess of other proteins, thus making it useful for future proteome profiling experiments.     

Biochemical reactions in metabolite-protein interaction

An update on the recently developed chemical proteomics called activity-based protein profiling (ABPP) has been reviewed. ABPP is able to identify proteins interacted either covalently or non-covalently with metabolites significantly, which will facilitate the characterization of specific metabolite regulating proteins in human disease progression.     

活性导向的化学探针在氨基酸反应活性表征中的应用进展

原创药物的研制得益于蛋白质新靶标的发现,而新靶标的发现依赖于高可信度、高通量的药物-蛋白质相互作用分析方法。蛋白质作为生命功能的执行者,其表达量、空间定位与结构差异直接影响药效的发挥。目前,超过85%的蛋白质尚被认为是无法成药的,主要原因是缺少药物分子靶向的空腔以及相应的反应活性位点。因此,基于蛋白质组学层次实现对氨基酸反应活性位点的表征成为原创共价靶向药物设计的关键,也是克服难以成药靶标蛋白问题的关键。近年来,质谱技术的飞速发展极大地推动了基于蛋白质组学技术的药物-靶蛋白相互作用研究。其中基于活性的蛋白质组分析(ABPP)策略是利用活性位点导向的化学探针分子在复杂样品中实现功能状态酶和药物靶标等蛋白质的检测。基于化学探针的开发和质谱定量技术的发展,ABPP技术在氨基酸反应活性表征研究中展现出重要的应用潜力,将助力于药物新靶标的发现和药物先导化合物的开发。ABPP策略主要基于蛋白质的活性特征进行富集,活性探针作为ABPP策略的核心,近年来取得了飞速进展。该文回顾了ABPP策略的发展历程,重点介绍基于广谱活性探针的ABPP技术在多种氨基酸反应活性筛选领域的研究进展,并对其在药物靶点发现中的应用前景进行展望。     

Fura-2荧光探针法检测细胞内La~(3+)

使用Fura - 2荧光探针技术 ,检测细胞内的镧离子浓度 [La3+]i 变化 ,研究其跨膜行为。结果显示 ,细胞外镧 [La3+]o(0 .1mmol/L)可使细胞内镧离子浓度增加 ,说明镧离子能够跨越小鼠心肌细胞膜 ,讨论了跨膜机理。     

Small molecule fluorescent probes of protein vicinal dithiols

The vicinal dithiol motif is widely present in proteins, and is critical for proteins' structures and functions.In recent years, a variety of fluorescent probes with high specificity and outstanding optical properties for sensing protein vicinal dithiols have been developed. In this review, we summarized the fluorescent probes of protein vicinal dithiols in literature. These probes are classified into four types based on their acceptor sites, i.e., biarsenical probes, monoarsenical probes, dimaleimide probes and diacrylate probes.Through analyzing the properties of different probes, we expect that this review would help readers further understand the structural factors of these probes and provide the design strategy for novel fluorescent probes with improved properties.     

Small molecule fluorescent probes of protein vicinal dithiols

Small molecule fluorescent probes that recognize and label protein vicinal dithiols have been summarized according to their different acceptor sites. This review will provide the purposeful design strategy of novel probes for detecting vicinal dithiols.     

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term “catalomics” defines an emerging ‘-omics’ field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.     

Development of activity-based probes with tunable specificity for protein tyrosine phosphatase subfamilies

Herein we describe the development of activity-based probes toward protein tyrosine phosphatase (PTP) subfamilies. A novel phosphotyrosine analog serving as the latent trapping unit has been designed and explored. It allows addition of various amino acid residues to its C- and N-termini to extend the recognition element. As a proof-of-concept, we have synthesized three tripeptide probes, which carry the phosphotyrosine analog in the middle position and a leucinamide residue at the C-terminus. The three tripeptide probes differed only in their N-terminal amino acid (Glu, Phe, and Lys). The labeling properties of these probes were determined and the results showed the newly synthesized probes could selectively label PTPs in an activity-dependent manner. In addition, the probes’ target specificity was also shown to be influenced by the amino acid residues flanking the phosphotyrosine analog.     

Synthesis of photoaffinity probes of tautomycin

Two types of photoaffinity probe, which possesses a benzophenone or a diazirine photophore on the 2-position of tautomycin, were prepared in order to prove the details of binding site to PP1. These photoaffinity probes were designed on the basis of the structure-activity relationship; thus, the diacid moiety is indispensable. The selective introduction of photolabeling units on the 2-position of tautomycin was achieved through the 2-oxime of tautomycin diacid.     

Semi-synthesis of Ubiquitin-propargylamide for identifying deubiquitinase targeting inhibitors

We report a novel semi-synthetic strategy to prepare Ub-PA in large-scale. Biochemical assays prove that semi-synthetic Ub-PA is an effective probe in identifying DUBs targeting inhibitors.     

Recent advances in the development of activatable multifunctional probes for in vivo imaging of caspase-3

Caspases are a family of proteases that play critical roles in controlling inflammation and cell death.Apoptosis is a caspase-3 mainly controlled behavior to avoid inflammation and damage to surrounding cells,whereas anomalistic cell apoptosis may be associated with many diseases.The detection and imaging of caspase-3 will be of great significance in evaluating the early therapeutic effect of tumors.Developing smart fluorescent probes may be helpful for the visualization of the rapeutic effect compared with "always on" probes.Thus,more and more works toward activatable fluorescent probes for caspase-3 imaging have been reported.In addition,multifunctional probes have also been designed to further improve the imaging of caspase-3.Herein,this review systematically summarized the representative wo rk of caspase-3 from the perspective of molecular design that it will play a guiding role in the design of probes that respond to caspase-3.Also,challenges and perspectives toward the field for imaging of cell apoptosis(caspase-3) are also discussed.     

Design,synthesis, and evaluation,derivatives of the fat-accumulation inhibitor ternatin: toward ternatin molecular probes

Ternatin, a cyclic heptapeptide derived from mushroom, strongly inhibits fat accumulation in 3T3-L1 adipocytes. However, its mechanism of action remains unclear. In this Letter, we designed, synthesized, and evaluated its derivatives for use as molecular probes to isolate its target protein. Finally, we successfully established a pair of ternatin molecular probes.     

萘酰亚胺类荧光分子探针的研究进展

荧光分子探针作为一种有效的金属离子检测手段,不仅使用方便,而且具有高灵敏度,高选择性等突出的优点.作者综述了萘酰亚胺类荧光分子探针的最新研究进展;指出萘酰亚胺化合物具有独特的荧光化学性质(如荧光量子产率高、荧光发射波长适中、斯托克斯位移大、光稳定性好、结构易于修饰等),因此被广泛应用于荧光探针研究领域,并且在合成、离子识别、检测及细胞成像等方面不断取得新的应用.     

多肽荧光探针在蛋白质检测中的应用

荧光探针法是痕量蛋白质检测的重要方法,其中多肽荧光探针得到了广泛的应用.本文综述了3种主要类型多肽荧光探针,即单荧光标记探针、双荧光标记探针和与其他材料形成复合物的探针的结构特点、检测原理以及不同类型多肽荧光探针在蛋白质定性、定量检测和酶活性测定等方面的应用,并对多肽荧光探针的未来发展方向进行了展望.     

Voronoi-based detection of pockets in proteins defined by large and small probes

The function of enzymatic proteins is given by their ability to bind specific small molecules into their active sites. These sites can often be found in pockets on a hypothetical boundary between the protein and its environment. Detection, analysis, and visualization of pockets find its use in protein engineering and drug discovery. Many definitions of pockets and algorithms for their computation have been proposed. Kawabata and Go defined them as the regions of empty space into which a small spherical probe can enter but a large probe cannot and developed programs that can compute their approximate shape. In this article, this definition was slightly modified in order to capture the existence of large internal holes, and a Voronoi-based method for the computation of the exact shape of these modified regions is introduced. The method first puts a finite number of large probes on the protein exterior surface and then, considering both large probes and atomic balls as obstacles for the small probe, the method computes the exact shape of the regions for the small probe. This is all achieved with Voronoi diagrams, which help with the safe navigation of spherical probes among spherical obstacles. Detected regions are internally represented as graphs of vertices and edges describing possible movements of the center of the small probe on Voronoi edges. The surface bounding each region is obtained from this representation and used for visualization, volume estimation, and comparison with other approaches. © 2019 Wiley Periodicals, Inc.     

Synthesis of the second generation photoaffinity probes of tautomycin

Five photoaffinity probes of tautomycin, which possess an aromatic azide with linker attached to the 2-position of tautomycin, were prepared in order to study the binding site of tautomycin with protein phosphatase 1γ. The photoaffinity probes were synthesized by selectively introducing the photolabeling units onto the 2-position of tautomycin by using oxime chemistry.     

New 1,3,5-triphenyl-2-pyrazoline-containing 3-hydroxychromones as highly solvatofluorochromic ratiometric polarity probes

Two novel 1,3,5-triphenyl-2-pyrazoline moiety containing derivatives of 3-hydroxychromone were synthesized and studied by ¹H NMR, absorption and fluorescence spectroscopy. The prospects of practical application of these compounds exhibiting high solvatofluorochromism into analytical chemistry and biophysics as effective ratiometric polarity probes were discussed proceeding from the data on their fluorescent properties.     

Microarray of DNA probes on carboxylate functional beads surface

The microarray of DNA probes with 5′-NH₂ and 5′-Tex/3′-NH₂ modified terminus on 10 μm carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is characterized in the present paper. It was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentration of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.     

Fluorescent probes for microdetermination of inorganic phosphates and biophosphates

This review covers the progress made in the development of fluorescent probes for inorganic and organic phosphates that are of significance in biosciences. Such probes need to work at physiological pH and at room temperature. The various modes of interactions between probe and phosphate species are discussed, not the least with the aim to assist in the design of more selective probes for which there is a substantial need. Correspondence: Otto S. Wolfbeis, Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany     

Microarray of DNA probes on carboxylate functional beads surface

The microarray of DNA probes with 5' -NH2 and 5' -Tex/3' -NH2 modified terminus on 10 um carboxylate functional beads surface in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) is characterized in the preseni paper. it was found that the microarray capacity of DNA probes on the beads surface depends on the pH of the aqueous solution, the concentra-tion of DNA probe and the total surface area of the beads. On optimal conditions, the minimum distance of 20 mer single-stranded DNA probe microarrayed on beads surface is about 14 nm, while that of 20 mer double-stranded DNA probes is about 27 nm. If the probe length increases from 20 mer to 35 mer, its microarray density decreases correspondingly. Mechanism study shows that the binding mode of DNA probes on the beads surface is nearly parallel to the beads surface.