Progress in the Development of non‐BET Bromodomain Chemical Probes

The bromodomain and extra terminal (BET) family of bromodomains have been the focus of extensive research, leading to the development of many potent, selective chemical probes and recent clinical assets. The profound biology associated with BET bromodomain inhibition has provided a convincing rationale for targeting bromodomains for the treatment of disease. However, the BET family represents just eight of the at least 56 human bromodomains identified to date. Until recently, there has been significantly less interest in non‐BET bromodomains, leaving a vast area of research and the majority of this new target class yet to be thoroughly investigated. It has been widely reported that several non‐BET bromodomain containing proteins are associated with various diseases including cancer and HIV. Therefore, the development of chemical probes for non‐BET bromodomains will facilitate elucidation of their precise biological roles and potentially lead to the development of new medicines. This review summarises the progress made towards the development of non‐BET bromodomain chemical probes to date. In addition, we highlight the potential for future work in this new and exciting area.     

Structural Analysis of Small‐Molecule Binding to the BAZ2A and BAZ2B Bromodomains

The bromodomain‐containing protein BAZ2A is a validated target in prostate cancer research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a similar binding site for their natural ligand, the acetylated lysine side chain. Here, we present an analysis of the binding modes of eight compounds belonging to three distinct chemical classes. For all compounds, the moiety mimicking the natural ligand engages in essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent‐exposed and adopts different orientations with different interactions in the two bromodomains. Some of these differences could be exploited for designing inhibitors with selectivity within the BAZ2 bromodomain subfamily.     

NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains

The complex biology associated with inhibition of bromodomain and extra‐terminal (BET) domains by chemical probes has attracted increasing attention, and there is a need to identify non‐BET bromodomain (BD) inhibitors. Several potent inhibitors of the BRD9 BD have recently been discovered, with anticancer and anti‐inflammation activity. However, its paralogue, BRD7 BD, remains unexploited. Here, we identified new chemotypes targeting BRD7 BD by using NMR fragment‐based screening. BRD7/9 BDs exhibit similar patterns of chemical‐shift perturbation upon the titration of hit compound 1 . The crystal structure revealed that 1 repels the Y222 group of BRD9 BD in a similar way to that for butyryllysine, but not acetyllysine and known inhibitors. Hit 1 induced less rearrangement of residue F161 of BRD9 BD than acetyllysine, butyryllysine, and crotonyllysine. Our study provides structural insight into a new generation of butyryllysine mimics for probing the function of BRD7/9 BD.     

Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex

Bromodomains represent an extensive family of evolutionarily conserved domains that are found in many chromatin-associated proteins such as histone acetyltransferases (HAT) and subunits of ATP-dependent chromatin-remodeling complexes. These domains are associated with acetylated lysine residues that bind both in vivo and in vitro; for example, they bind to the N-acetylated lysines of the histone tail of nucleosomes. In this report, we determined the structure of the bromodomain from human brahma-related gene 1 (BRG1) protein, a subunit of an ATP-dependent switching/sucrose nonfermenting (SWI/SNF) remodeling complex, and have also characterized its in vitro interaction with N-acetylated lysine peptides from histones. In addition to a typical all-alpha-helical fold that was observed in the bromodomains, we observed for the first time a small beta-sheet in the ZA loop region of the BRG1 protein. The BRG1 bromodomain exhibited binding, albeit weak, to acetylated peptides that were derived from histones H3 and H4. We have compared the acetyl-lysine binding sites of BRG1 bromodomain with the yGCN5 (general control of amino acid biosynthesis). By modeling the acetylated-lysine peptide into the BRG1 bromodomain structure, we were able to explain the weak binding of acetylated-lysine peptides to this bromodomain.     

Recent advances of small-molecule fluorescent probes for detecting biological hydrogen sulfide

H₂S is well-known as a colorless,acidic gas,with a notoriously rotten-egg smell.It was recently revealed that H₂S is also an endogenous signaling molecule that has important biological functions,however,most of its physiology and pathology remains elusive.Therefore,the enthusiasm for H₂S research remains.Fluorescence imaging technology is an important tool for H₂S biology research.The development of fluorescence imaging technology has realized the study of H₂S in subcellular organelles,facilitated by the development of fluorescent probes.The probes reviewed in this paper were categorized according to their chemical mechanism of sensing and were divided into three groups:H₂S reducibility-based probes,H₂S nucleophilicity-based probes,and metal sulfide precipitation-based probes.The structure of the probes,their sensing mechanism,and imaging results have been discussed in detail.Moreover,we also introduced some probes for hydrogen polysulfides.     

Fluorescent probes and functional materials for biomedical applications

Due to their simplicity in preparation, sensitivity and selectivity, fluorescent probes have become the analytical tool of choice in a wide range of research and industrial fields, facilitating the rapid detection of chemical substances of interest as well as the study of important physiological and pathological processes at the cellular level. In addition, many long-wavelength fluorescent probes developed have also proven applicable for in vivo biomedical applications including fluorescence-guided disease diagnosis and theranostics (e.g., fluorogenic prodrugs). Impressive progresses have been made in the development of sensing agents and materials for the detection of ions, organic small molecules, and biomacromolecules including enzymes, DNAs/RNAs, lipids, and carbohydrates that play crucial roles in biological and disease-relevant events. Here, we highlight examples of fluorescent probes and functional materials for biological applications selected from the special issues “Fluorescent Probes” and “Molecular Sensors and Logic Gates” recently published in this journal, offering insights into the future development of powerful fluorescence-based chemical tools for basic biological studies and clinical translation.     

Chemical Tools for Studying the Biological Function of Glycolipids

Glycolipids play an important role in many biological processes and to this end, synthetic chemists have developed a variety of new techniques and “chemical tools” that allow for the study of glycolipids in vitro and in vivo. The types of probes prepared include fluorescent, radio‐labelled, biotinylated and photoreactive ones, as well as others based on liposomes, microarrays and other supramolecular constructs—each of which offers its own advantages, as is discussed. A number of more specialised probes, such as metabolically engineered glycolipids and photopolymerisable glycolipids, have also been prepared in order to investigate various processes including substrate specificities and binding interactions. The purpose of this review is to present the key approaches that can be used for the development of glycolipid probes, organised according to application, and also to discuss the limitations of such strategies, which include the nontrivial task of ensuring that the probe does not adversely influence the biological activity of the parent compound. On the whole, it is exciting to see what can be achieved through the development of chemical probes as tools to study biological processes, and it is envisioned that the reader will be inspired by the large number of superb studies highlighted here and will be encouraged to undertake further work in this research area.     

Recent Developments in Metal-Catalyzed Bio-orthogonal Reactions for Biomolecule Tagging

With the rapid advances in single-molecule and live-cell imaging studies to investigate biological problems, the role of chemical probes to monitor reactions in a live cell has considerably increased. However, selective labeling of a target protein or a specific residue is highly challenging due to the high complexity of the biological system. In particular, biological macromolecules (such as proteins, DNA, or RNA) share many functional groups that potentially cross-react with exogenous chemical probes. Thus, there are high demands for perfect biocompatible reactions utilizing biologically unavailable chemistry. Metal-catalyzed reactions have been extensively investigated as synthetic methodology studies, including initial attempts in applying the chemistry in aqueous solutions in vitro or even in biological conditions. Herein, the latest developments and progress in metal-catalyzed bio-orthogonal reactions for biomolecule labeling are summarized.     

Identifying Small‐Molecule Binding Sites for Epigenetic Proteins at Domain–Domain Interfaces

Epigenetics is a rapidly growing field in drug discovery. Of particular interest is the role of post‐translational modifications to histones and the proteins that read, write, and erase such modifications. The development of inhibitors for reader domains has focused on single domains. One of the major difficulties of designing inhibitors for reader domains is that, with the notable exception of bromodomains, they tend not to possess a well‐enclosed binding site amenable to small‐molecule inhibition. As many of the proteins in epigenetic regulation have multiple domains, there are opportunities for designing inhibitors that bind at a domain–domain interface which provide a more suitable interaction pocket. Examination of X‐ray structures of multiple domains involved in recognising and modifying post‐translational histone marks using the SiteMap algorithm identified potential binding sites at domain–domain interfaces. For the tandem plant homeodomain–bromodomain of SP100C, a potential inter‐domain site identified computationally was validated experimentally by the discovery of ligands by X‐ray crystallographic fragment screening.     

氟离子荧光探针的研究进展

氟离子是电负性最强、离子半径最小的阴离子,是一个强路易斯碱,在化学、生物学、医学和军事等方面都具有重要作用。适量的氟化物摄入人体可以预防龋齿、治疗骨质疏松症,但是过量的摄入会导致氟斑牙、氟骨症、尿石症以及癌症等疾病,因此氟离子的识别与检测具有重要意义。化学荧光探针具有选择性好、灵敏度高、方便快捷、成本低廉等优点,近年来化学研究者设计合成了大量的氟离子荧光探针。根据识别机理不同,氟离子荧光探针主要划分为3种:氢键型、路易斯酸受体型、氢键和路易斯酸混合型。综述了近年来不同类型的氟离子荧光探针的研究进展,总结了氢键型和路易斯酸型氟离子荧光探针的优缺点,对未来氟离子荧光探针的研究方向进行了展望。     

Nanoparticulate Photoluminescent Probes for Bioimaging: Small Molecules and Polymers

Recent interest in research on photoluminescent molecules due to their unique properties has played an important role in advancing the bioimaging field. In particular, small molecules and organic dots as probes have great potential for the achievement of bioimaging because of their desirable properties. In this review, we provide an introduction of probes consisting of fluorescent small molecules and polymers that emit light across the ultraviolet and near-infrared wavelength ranges, along with a brief summary of the most recent techniques for bioimaging. Since photoluminescence probes emitting light in different ranges have different goals and targets, their respective strategies also differ. Diverse and novel strategies using photoluminescence probes against targets have gradually been introduced in the related literature. Among recent papers (published within the last 5 years) on the topic, we here concentrate on the photophysical properties and strategies for the design of molecular probes, with key examples of in vivo photoluminescence research for practical applications. More in-depth studies on these probes will provide key insights into how to control the molecular structure and size/shape of organic probes for expanded bioimaging research and applications.     

反应型HClO/ClO-荧光探针的研究进展

次氯酸/次氯酸根是活性氧化物中重要的信号分子，在生物医药和环境安全等方面发挥着重要作用。反应型荧光探针基于出色的灵敏度、实时成像和生物兼容性好等特点，广泛应用于HClO/ClO^-的检测。本文评述了近5年反应型HClO/ClO^-荧光探针的研究进展，包括反应型HClO/ClO^-荧光探针的设计策略和识别机理，并从HClO/ClO^-引发的反应机理角度（碳碳双键的反应、硫族化合物的反应、醛肟基团的反应、腙/席夫碱的反应、酰肼/磺酰肼的反应、N,N-二甲基硫代氨基甲酸酯的反应和苯硼酸/硼酸酯的反应）概述了反应型HClO/ClO^-荧光探针的特点和实际应用，指出反应型HClO/ClO^-荧光探针的发展方向是合成性能优异的识别基团，构建选择性好、水溶性好、低荧光背景、光化学性能稳定和生物毒性低的反应型近红外HClO/ClO^-荧光探针，实现对生物体内外HClO/ClO^-的可视化检测及机理探索。     

Synergistically integrated nanoparticles as multimodal probes for nanobiotechnology

Current biomedical imaging techniques including magnetic resonance imaging (MRI), positron emission tomography (PET), and computed X-ray tomography (CT) are vital in the diagnosis of various diseases. Each imaging modality has its own merits and disadvantages, and a single technique does not possess all the required capabilities for comprehensive imaging. Therefore, multimodal imaging methods are quickly becoming important tools for state-of-the-art biomedical research and clinical diagnostics and therapeutics. In this Account, we will discuss synergistically integrated nanoparticle probes, which will be an essential tool in multimodal imaging technology. When inorganic nanoparticles are introduced into biological systems, their extremely small size and their exceptional physical and chemical properties make them useful probes for biological diagnostics. Nanoparticle probes can endow imaging techniques with enhanced signal sensitivity, better spatial resolution, and the ability to relay information about biological systems at the molecular and cellular levels. Simple magnetic nanoparticles function as MRI contrast enhancement probes. These magnetic nanoparticles can then serve as a core platform for the addition of other functional moieties including fluorescence tags, radionuclides, and other biomolecules for multimodal imaging, gene delivery, and cellular trafficking. For example, MRI-optical dual-modal probes composed of a fluorescent dye-doped silica (DySiO(2)) core surrounded by magnetic nanoparticles can macroscopically detect neuroblastoma cancer cells via MRI along with subcellular information via fluorescence imaging. Magnetic nanoparticles can also be coupled to radionuclides ((124)I) to construct MRI-PET dual-modal probes. Such probes can accurately detect lymph nodes (LNs), which are critical for assessing cancer metastasis. In vivo MRI/PET images can clearly identify small (approximately 3 mm) LNs along with precise anatomical information. Systems using multicomponent nanoparticles modified with biomolecules can also monitor gene expression and other markers in cell therapeutics studies. We have used hybrid stem cell-magnetic nanoparticle probes with MRI to monitor in vivo stem cell trafficking. MRI with hybrid probes of magnetic nanoparticles and adenovirus can detect target cells and can monitor gene delivery and the expression of green fluorescent proteins optically. Each component of such multimodal probes complements the other modalities, and their synergistic materials properties ultimately provide more accurate information in in vitro and in vivo biological systems.     

提高钾长石转化率的实验室研究

采用物理法，生物法和化学示对提高钾长石的利用率进行了实验室研究，结果表明：煅烧法和生物法对钾长石中钾的有效性转化有积极作用，但效果不显著。化学法可使大部分难溶性钾转变有效性钾，具有一定的工业意义。     

Activity-based protein profiling: new developments and directions in functional proteomics

Proteomic screening has become increasingly insightful with the availability of novel analytical tools and technologies. Detailed analysis and integration of the profound datasets attained from comprehensive profiling studies are enabling researchers to dig deeper into the foundations of genomic and proteomic networks, towards a clearer understanding of the intricate cellular circuitries they manifest. The major difficulty often lies in correlating the patho/physiological state presented with the underlying biological mechanisms; therefore, identification of causal variants as therapeutic targets is extremely important. Herein, we will describe methods that address this challenge through activity-based protein profiling, which applies chemical probes to the comparison and monitoring of protein dynamics across complex proteomes. Over recent years such activity-based probes have been creatively augmented with applications in gel-based separations, microarrays and in vivo imaging. These developments offer a newfound ability to characterise and differentiate cells, tissues and proteomes through activity-dependent signatures; this has expanded the scope and impact of activity-based probes in biomedical research.     

反应激活型酶荧光探针的研究进展

酶在维持生物体内稳态与生命活动的正常运行方面发挥着举足轻重的作用。某些特定酶含量及活性的异常与人类重大疾病的发生与发展密切相关。因此,生物体内特定酶的实时原位检测及可视化成像具有重要的意义。化学荧光探针具有选择性好、灵敏度高及高时空分辨率可视化成像等优点,近年来研究者设计合成了大量的可用于生物体系内酶识别与可视化成像的荧光探针。目前识别酶的荧光探针主要有两类：（1）基于酶对荧光探针分子中酶抑制剂基团的识别引起探针荧光信号的变化;（2）基于酶对荧光探针特异性催化反应来实现识别前后荧光信号的激活,称为反应激活型酶荧光探针。对反应激活型酶荧光探针的设计策略及4种重大疾病相关的生物标志酶（单胺氧化酶、β-半乳糖苷酶、硝基还原酶、γ-谷氨酰转肽酶）的识别可视化荧光探针研究进展进行了综述,对未来酶识别荧光探针的研究方向进行了展望。     

Synthetic Approaches of Epoxysuccinate Chemical Probes

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.