生物正交剪切反应及其应用

生物正交反应在化学生物学的研究中发挥着越来越重要的作用.传统的生物正交反应以新化学键生成的连接反应为主,其在实现生物分子的“标记”、“示踪”和“捕捉”等研究中发挥着重要作用.近年来,一类新兴的反应类型--以化学键断裂为基础的生物正交剪切反应逐渐发展起来,并在分子的“释放”、“激活”和“操控”等方面得到了越来越广泛的应用.本文首先重点介绍了生物正交剪切反应,总结了这些反应的特点、适用范围和已经实现的用途.随后通过具体的例子介绍了这些反应在化学生物学中的应用,包括小分子前药的激活、蛋白质功能的调控、细胞的工程化等.最后文章对生物正交剪切反应的发展趋势进行了展望.     

点击化学和生物正交化学中的化学基础概念和前沿思想——2022年诺贝尔化学奖浅析

2022年诺贝尔化学奖授予了Carolyn R. Bertozzi、Morten Meldal和K. Barry Sharpless三位科学家，以表彰他们开创了点击化学和生物正交化学。点击化学源于对有机合成方法学的改进，提供了一种在温和条件下高效快速地偶联化学分子的新方法。生物正交化学的开发则起始于生命体系中糖质生物大分子的特异性标记和成像，发展出一类不干扰生命体系且不受生命体系干扰的连接反应。二者殊途同归、异曲同工，成为了在化学、生物医药和材料科学等领域中应用最为广泛的一类化学反应。本文从点击化学与生物正交化学开发中所涉及的化学基础概念出发，对这两种方法的前沿思想进行简要探讨。     

生物模拟转氨反应在蛋白质修饰中的应用

作为化学生物学研究的重要方向,生物正交反应的发展与应用为生命科学研究提供了有力武器.利用生物正交反应,人们可以将合成分子与目标天然大分子在特定位点上实现特异性连接,进而达成诸如标记、定位、功能化、固定等一系列目标.生物模拟转氨反应及其衍生反应是一类特异性蛋白质N端修饰的生物正交反应,与天然蛋白侧链、C端的连接反应相互补充.由于该反应具有高效性、通用性、温和性及不需要引入突变或非天然氨基酸等优点,从发现以来已较为广泛地运用于蛋白质化学生物学的多个相关领域.在介绍其基本原理及反应优化的基础上,综述该类反应的发展及应用情况.     

基于非天然氨基酸的蛋白质生物正交标记

生物正交化学反应正日益成为在活体内对生物大分子进行特异标记的一种有效方法. 最近涌现出的一个突出的例子是将金属钯催化的碳碳偶联反应这一在有机合成领域具有里程碑意义的反应拓展到生物大分子的标记上. 在活细胞上进行生物正交反应的一个先决条件是需要将参与这类反应的正交官能团特异地引入到目标生物大分子当中. 遗传密码子拓展技术是将多种生物正交活性基团引入到蛋白质当中的一种先进的手段; 最近发展出的基于吡咯赖氨酸氨酰合成酶和tRNA的体系能够将携带有生物正交官能团的非天然氨基酸有效地引入到原核生物、真核生物, 甚至是动物体内的蛋白质上. 在这一展望中, 我们首先介绍在生物正交反应和遗传密码子拓展这两个领域内的研究前沿与进展. 接着我们将讨论将这些新发展的研究工具, 尤其是基于钯催化的生物正交反应和基于吡咯赖氨酸氨酰合成酶的遗传密码子拓展技术, 应用于标记和修饰哺乳动物细胞蛋白质上的优势和诱人前景. 生物相兼容性更好的正交反应和更为灵活的非天然氨基酸引入技术必将有力地增强和拓宽人们在活细胞环境下特异操纵蛋白质的能力.     

点击化学作为分子连接工具:机遇与挑战（英文）

2022年诺贝尔化学奖授予点击化学以及生物正交化学领域的三位科学家,显示了点击化学在当代合成领域的重要地位.点击化学本质是一类连接反应,旨在通过将不同单元分子高效地拼接在一起,最终得到具有特定结构与功能的分子.在传统有机化学中,碳碳键的合成通常具有较大难度,因为它们涉及较低的化学驱动力和较多的副反应.点击化学强调开发基于碳杂原子键的新型组合化学反应,并通过这些反应简单有效地获得多样性分子.点击化学的发展将科学家们从复杂、专业性强的有机合成中解放出来,使他们可以专注于分子功能的开发,一定程度拓宽了合成化学的应用范围.基于点击化学的优越性能,其在聚合物合成以及生物医学等领域表现出了非常广泛的应用前景.本文简要概述了几种涉及不同底物和催化剂类型的典型点击反应,并尝试解释这一领域背后的发展逻辑.此外,阐述了点击化学在现代科学,尤其是聚合物合成和生命科学等领域的应用,及其目前存在的局限性和未来可能的发展方向.点击反应的主要特征包括产率高、选择性好、副产物无害且易分离、反应条件简单、原料易得、符合原子经济性和应用范围广等.典型的点击化学包括亲核开环反应、环加成反应、保护基反应、碳碳多键加成反应和施...     

卡罗琳·露丝·贝尔托西——诺贝尔化学奖史上第八位女性得主

卡罗琳·露丝·贝尔托西因开创了生物正交化学而获得2022年诺贝尔化学奖,该反应使科学家能够在不破坏细胞正常化学功能的情况下探索细胞、跟踪生物过程并实现了多种应用,提高了人类探索生命运动的能力和医学药物治疗的发展水平。通过回顾贝尔托西的研究背景以及相关的科研历程,提出了重视自主研究能力,在实践探索中收获无限可能;关注跨学科知识生产,在交叉领域开拓学科前沿;发挥科研“她”力量,更加多元与开放包容的思考与启示。     

生物正交标记反应研究进展

对活体生物大分子进行特异性标记是一项具有挑战性的工作, 它要求这类化学反应能够在生理条件下高效特异地进行, 不会与生物体系中存在的各种活性物质发生副反应. 最近十几年开发的生物正交反应能够比较好地满足这些要求, 它们在生物分子标记方面的应用拓展了我们对细胞内生物体系的理解. 主要介绍那些应用广泛且可以用于活体细胞标记的生物正交反应. 重点介绍通过位点特异性引入生物正交官能团来进行选择性标记细胞内目标蛋白质的策略. 同时, 我们根据使用催化剂类型对这些生物正交反应进行分类, 并且列表比较它们的差异, 以便于研究者挑选合适的反应. 最后对生物正交反应的开发和进一步应用进行了展望.     

Glaser反应研究新进展

Glaser偶联反应是合成二炔化合物的重要反应,广泛应用于有机合成、材料化学等领域.介绍了近年来Glaser偶联反应中溶剂、氧化剂、底物等领域的研究新进展,指出Glaser偶联反应在不断加深其各方面绿色化研究的同时,多功能团底物的Glaser偶联反应与不对称的Glaser偶联反应也值得关注.     

线上线下混合式-六环节实验教学实践与探索——以化学生物学实验"基于生物正交反应的蛋白质标记"为例

化学生物学综合实验是针对化学生物学专业高年级本科生开设的一门衔接本科-硕士教学的综合性实验课程。本文以“基于生物正交反应的蛋白质标记”科研融合型实验为例,结合化学生物学学科特点,将实验教学内容模块化,探索设计线上线下混合式-六环节教学方式,应用于本科生综合实验教学。经实践取得良好的教学效果,为综合型实验课程教学提供了参考与借鉴。     

铜催化水相Ullmann类型偶联反应研究进展

铜催化的Ullmann类型交叉偶联反应是有机合成中重要的合成方法.与通常有机反应中采用的有机溶剂相比,利用自然界储量丰富、廉价、绿色环保的水作为有机反应介质更符合当前所倡导的"绿色"化学和低碳可持续发展的要求.综述了最近几年来水相铜催化的包括C—N,C—O,C—S和C—C等Ullmann类型交叉偶联反应的最新研究进展.     

Live Monitoring of Strain-Promoted Azide Alkyne Cycloadditions in Complex Reaction Environments by Inline ATR-IR Spectroscopy

The strain-promoted azide alkyne cycloaddition (SPAAC) is a powerful tool for forming covalent bonds between molecules even under physiological conditions, and therefore found broad application in fields ranging from biological chemistry and biomedical research to materials sciences. For many applications, knowledge about reaction kinetics of these ligations is of utmost importance. Kinetics are commonly assessed and studied by NMR measurements. However, these experiments are limited in terms of temperature and restricted to deuterated solvents. By using an inline ATR-IR probe we show that the cycloaddition of azides and alkynes can be monitored in aqueous and even complex biological fluids enabling the investigation of reaction kinetics in various solvents and even human blood plasma under controlled conditions in low reaction volumes.     

IEDDA: An Attractive Bioorthogonal Reaction for Biomedical Applications

The pretargeting strategy has recently emerged in order to overcome the limitations of direct targeting, mainly in the field of radioimmunotherapy (RIT). This strategy is directly dependent on chemical reactions, namely bioorthogonal reactions, which have been developed for their ability to occur under physiological conditions. The Staudinger ligation, the copper catalyzed azide-alkyne cycloaddition (CuAAC) and the strain-promoted [3 + 2] azide–alkyne cycloaddition (SPAAC) were the first bioorthogonal reactions introduced in the literature. However, due to their incomplete biocompatibility and slow kinetics, the inverse-electron demand Diels-Alder (IEDDA) reaction was advanced in 2008 by Blackman et al. as an optimal bioorthogonal reaction. The IEDDA is the fastest bioorthogonal reaction known so far. Its biocompatibility and ideal kinetics are very appealing for pretargeting applications. The use of a trans-cyclooctene (TCO) and a tetrazine (Tz) in the reaction encouraged researchers to study them deeply. It was found that both reagents are sensitive to acidic or basic conditions. Furthermore, TCO is photosensitive and can be isomerized to its cis-conformation via a radical catalyzed reaction. Unfortunately, the cis-conformer is significantly less reactive toward tetrazine than the trans-conformation. Therefore, extensive research has been carried out to optimize both click reagents and to employ the IEDDA bioorthogonal reaction in biomedical applications.     

Bioorthogonal Cycloadditions with Sub‐Millisecond Intermediates

Tetrazine‐ and sydnone‐based click reactions have emerged as important bioconjugation strategies with fast kinetics and N₂ or CO₂ as the only byproduct. Mechanistic studies of these reactions have focused on the initial rate‐determining cycloaddition steps. The subsequent N₂ or CO₂ release from the bicyclic intermediates has been approached mainly through computational studies, which have predicted lifetimes of femtoseconds. In the present study, bioorthogonal cycloadditions involving N₂ or CO₂ extrusion have been examined experimentally at the single‐molecule level by using a protein nanoreactor. At the resolution of this approach, the reactions appeared to occur in a single step, which places an upper limit on the lifetimes of the intermediates of about 80 μs, which is consistent with the computational work.     

Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide Probe

We report a lipid‐based strategy to visualize Golgi structure and dynamics at super‐resolution in live cells. The method is based on two novel reagents: a trans‐cyclooctene‐containing ceramide lipid (Cer‐TCO) and a highly reactive, tetrazine‐tagged near‐IR dye (SiR‐Tz). These reagents assemble via an extremely rapid “tetrazine‐click” reaction into Cer‐SiR, a highly photostable “vital dye” that enables prolonged live‐cell imaging of the Golgi apparatus by 3D confocal and STED microscopy. Cer‐SiR is nontoxic at concentrations as high as 2 μM and does not perturb the mobility of Golgi‐resident enzymes or the traffic of cargo from the endoplasmic reticulum through the Golgi and to the plasma membrane.     

Spatiotemporal Resolved Live Cell Membrane Tracking through Photo-click Reactions Enriched in Lipid Phase

A set of photo-switchable monopeptides derived from cis-β-dibenzodiazocine-l -alanine (cis-DBDAA) have been designed and synthesized, which are capable of photo-click reacting with diaryltetrazoles or diarylsydnones in a hydrophobic phospholipid bilayer environment. The DBDAA monopeptides include both a hydrophobic tail on C-terminal, providing high affinity toward lipid membrane, and a modularized functional moiety on N-terminal, enabling rapid optimization of the self-assembly strength to form multifunctional supramolecules. With the cis-DBDAA monopeptides photo-switched into trans-configuration, we were able to disrupt the supramolecular assembly through an efficient photo-click reaction across the lipid bilayer of liposomes. We reveal that the performance of the photo-click reactions between the monopeptides and photo-generated nitrile imine intermediates is significantly enhanced by enrichment of both reactants in the hydrophobic membrane lamel of liposomes. Enrichment of the DBDAA monopeptide in lipid phase serves as a convenient method to introduce bioorthogonal chemical handles on live cell membranes, which enables fluorescence labelling of single cell's membrane with high spatiotemporal resolution to facilitate the studies on cell membrane dynamics.     

In-Cell Dual Drug Synthesis by Cancer-Targeting Palladium Catalysts

Transition metals have been successfully applied to catalyze non-natural chemical transformations within living cells, with the highly efficient labeling of subcellular components and the activation of prodrugs. In vivo applications, however, have been scarce, with a need for the specific cellular targeting of the active transition metals. Here, we show the design and application of cancer-targeting palladium catalysts, with their specific uptake in brain cancer (glioblastoma) cells, while maintaining their catalytic activity. In these cells, for the first time, two different anticancer agents were synthesized simultaneously intracellularly, by two totally different mechanisms (in situ synthesis and decaging), enhancing the therapeutic effect of the drugs. Tumor specificity of the catalysts together with their ability to perform simultaneous multiple bioorthogonal transformations will empower the application of in vivo transition metals for drug activation strategies.     

Chemoselectivity of Tertiary Azides in Strain-Promoted Alkyne-Azide Cycloadditions

The strain-promoted alkyne-azide cycloaddition (SPAAC) is the most commonly employed bioorthogonal reaction with applications in a broad range of fields. Over the years, several different cyclooctyne derivatives have been developed and investigated in regard to their reactivity in SPAAC reactions with azides. However, only a few studies examined the influence of structurally diverse azides on reaction kinetics. Herein, we report our investigations of the reactivity of primary, secondary, and tertiary azides with the cyclooctynes BCN and ADIBO applying experimental and computational methods. All azides show similar reaction rates with the sterically non-demanding cyclooctyne BCN. However, due to the increased steric demand of the dibenzocyclooctyne ADIBO, the reactivity of tertiary azides drops by several orders of magnitude in comparison to primary and secondary azides. We show that this chemoselective behavior of tertiary azides can be exploited to achieve semiorthogonal dual-labeling without the need for any catalyst using SPAAC exclusively.     

Double Strain‐Promoted Macrocyclization for the Rapid Selection of Cell‐Active Stapled Peptides

Peptide stapling is a method for designing macrocyclic alpha‐helical inhibitors of protein–protein interactions. However, obtaining a cell‐active inhibitor can require significant optimization. We report a novel stapling technique based on a double strain‐promoted azide–alkyne reaction, and exploit its biocompatibility to accelerate the discovery of cell‐active stapled peptides. As a proof of concept, MDM2‐binding peptides were stapled in parallel, directly in cell culture medium in 96‐well plates, and simultaneously evaluated in a p53 reporter assay. This in situ stapling/screening process gave an optimal candidate that showed improved proteolytic stability and nanomolar binding to MDM2 in subsequent biophysical assays. α‐Helicity was confirmed by a crystal structure of the MDM2‐peptide complex. This work introduces in situ stapling as a versatile biocompatible technique with many other potential high‐throughput biological applications.     

An Alkyne‐Appended,Click‐Ready PtII Complex with an Unusual Arrangement in the Solid State

To better understand the range of cellular interactions of Pt^II‐based chemotherapeutics, robust and efficient methods to track and analyze Pt targets are needed. A powerful approach is to functionalize Pt^II compounds with alkyne or azide moieties for post‐treatment conjugation through the azide–alkyne cycloaddition (click) reaction. Herein, we report an alkyne‐appended cis‐diamine Pt^II compound, cis‐[Pt(2‐(5‐hexynyl)amido‐1,3‐propanediamine)Cl₂] ( 1 ), the X‐ray crystal structure of which exhibits a combination of unusual radially distributed CH/π(C?C) interactions, Pt? Pt bonding, and NH:O/NH:Cl hydrogen bonds. In solution, 1 exhibits no Pt? alkyne interactions and binds readily to DNA. Subsequent click reactivity with nonfluorescent dansyl azide results in a 70‐fold fluorescence increase. This result demonstrates the potential for this new class of alkyne‐modified Pt compound for the comprehensive detection and isolation of Pt‐bound biomolecules.     

Site‐Selective Cysteine–Cyclooctyne Conjugation

We report a site‐selective cysteine–cyclooctyne conjugation reaction between a seven‐residue peptide tag (DBCO‐tag, Leu‐Cys‐Tyr‐Pro‐Trp‐Val‐Tyr) at the N or C terminus of a peptide or protein and various aza‐dibenzocyclooctyne (DBCO) reagents. Compared to a cysteine peptide control, the DBCO‐tag increases the rate of the thiol–yne reaction 220‐fold, thereby enabling selective conjugation of DBCO‐tag to DBCO‐linked fluorescent probes, affinity tags, and cytotoxic drug molecules. Fusion of DBCO‐tag with the protein of interest enables regioselective cysteine modification on proteins that contain multiple endogenous cysteines; these examples include green fluorescent protein and the antibody trastuzumab. This study demonstrates that short peptide tags can aid in accelerating bond‐forming reactions that are often slow to non‐existent in water.