The designing strategies of graphene-based peroxidase mimetic materials

Natural enzymes have been praised highly as ideal catalysts, presumably owing to their remarkable advantages of high efficiency, high selectivity, and mild reaction conditions. The reports of chemical simulation and systematic synthesis of natural enzymes such as peroxidase (POD) are rare because of their complex biological structures. POD represents a large family of oxidoreductases and offers a wide range of applications in many fields of science. Recent advance in the fusion of nanomaterial, catalysis, and biochemistry has inspired the development of artificial enzymes implemented with desired catalytic features of natural enzymes. Herein, we review the redox chemistry of POD and compare its catalytic performance to graphene-based nanomaterials (G-NMs) as POD mimetic nanoenzymes bases on catalytic center, binding site, and carrier function. Based on the viewpoints of stereo chemistry and molecular kinetic and dynamics in heterogeneous system, we evaluate and compare the suitability of different NMs as artificial enzyme constituent. We propose that reevaluates design strategies of graphene-based peroxidase (G-POD) mimetic materials and emphasizes on their selectivity (role as catalytic center, binding site, or carrier) is of uttermost.     

Catalytic,theoretical, and biological investigation of an enzyme mimic model

Artificial catalyst studies were always stayed at the kinetics investigation level, in this work bioactivity of designed catalyst were shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications. The development of artificial enzymes is a continuous quest for the development of tailored catalysts with improved activity and stability. Understanding the catalytic mechanism is a replaceable step for catalytic studies and artificial enzyme mimics provide an alternative way for catalysis and a better understanding of catalytic pathways at the same time. Here we designed an artificial catalyst model by decorating peptide nanofibers with a covalently conjugated catalytic triad sequence. Owing to the self-assembling nature of the peptide amphiphiles, multiple action units can be presented on the surface for enhanced catalytic performance. The designed catalyst has shown an enzyme-like kinetics profile with a significant substrate affinity. The cooperative action in between catalytic triad amino acids has shown improved catalytic activity in comparison to only the histidine-containing control group. Histidine is an irreplaceable contributor to catalytic action and this is an additional reason for control group selection. This new method based on the self-assembly of covalently conjugated action units offers a new platform for enzyme investigations and their further applications. Artificial catalyst studies always stayed at the kinetics investigation level, in this work bioactivity of the designed catalyst was shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications.     

Engineering of biocatalysts - from evolution to creation

Enzymes are increasingly being used in an industrial setting as a cheap and environmentally-friendly alternative to chemical catalysts. In order to produce the ideal biocatalyst, natural enzymes often require optimization to increase their catalytic efficiencies and specificities under a particular range of reaction conditions. A number of enzyme engineering strategies are currently employed to modify biocatalysts, improving their suitability for large-scale industrial applications. These include various directed evolution techniques, semi-rational design techniques, and more recently, the de novo design of novel enzymes. Advances in mutant library design, high-throughput selection processes, and the introduction of powerful computer algorithms have all contributed to the current exponential growth of the field of enzyme engineering. This review article aims to present some of the currently employed strategies for enzyme engineering and attempts to highlight the most recent advances in methodology.     

Understanding enzyme catalysis by means of supramolecular artificial enzymes

Enzymes are biomacromolecules responsible for the abundant chemical biotransformations that sustain life. Recently, biochemists have discovered that multiple conformations and numerous parallel paths are involved during the processes catalyzed by enzymes. It is plausible that the entire macromolecular scaffold is involved in catalysis via cooperative motions that result in incredible catalytic efficiency. Moreover, some enzymes can very strongly bind the transition state with an association constant of up to 1024 M-1, suggesting that covalent bond formation is a possible process during the conversion of the transition state in enzyme catalysis, in addition to the concatenation of noncovalent interactions. Supramolecular chemistry provides fundamental knowledge about the relationships between the dynamic structures and functions of organized molecules. By tak-ing advantage of supramolecular concepts, numerous supramolecular enzyme mimics with complex and hierarchical structures have been designed and investigated. Through the study of supramolecular enzyme models, a great deal of information to aid our understanding of the mechanism of catalysis by natural enzymes has been acquired. With the development of supramolec-ular artificial enzymes, it is possible to replicate the features of natural enzymes with regards to their constitutional complexity and cooperative motions, and eventually decipher the conformation-based catalytic mystery of natural enzymes.     

Supramolecular enzyme mimics by self-assembly

The development of supramolecular chemistry has led to a shift in the research focus from the structural design of supramolecules to developing functional systems, such as supramolecular enzyme models. The supramolecular enzyme mimics can be readily constructed by self-assembly which is an efficient strategy for generating highly-ordered structures with complex and hierarchical architectures to mimic the biopolymers. The study of supramolecular enzyme mimics has implications for understanding both the structure–function relationships of natural enzymes and the thermodynamic mechanism during catalysis. Additionally, they are potentially useful in many important applications, e.g., medicinal application and industrial biocatalysts and so on. This review is aimed at giving a brief overview of the synthesis of supramolecular enzyme mimics and their functions.     

Photooxidase‐Mimicking Nanovesicles with Superior Photocatalytic Activity and Stability Based on Amphiphilic Amino Acid and Phthalocyanine Co‐Assembly

Enzyme mimics have broad applications in catalysis and can assist elucidation of the catalytic mechanism of natural enzymes. However, challenges arise from the design of catalytic sites, the selection of host molecules, and their integration into active three‐dimensional structures. Herein, we describe the development of a photooxidase mimic by synergetic molecular self‐assembly. 9‐Fluorenylmethyloxycarbonyl‐l ‐histidine undergoes efficient co‐assembly with phthalocyanine into nanovesicles with tunable particle size and membrane thickness. The obtained nanovesicles can be used as catalysts for reactive‐oxygen‐mediated photosensitive oxidation with improved efficiency and stability. This work highlights the co‐assembly of simple building blocks into a supramolecular photocatalyst, which might give insight into possible evolutionary paths of photocatalytic membrane systems, and might allow facile transfer into photosensitive nanoreactors or artificial organelles.     

Reversing Chemoselectivity: Simultaneous Positive and Negative Catalysis by Chemically Equivalent Rims of a Cucurbit[7]uril Host

Enzyme catalysis has always been an inspiration and an unattainable goal for chemists due to features such as high specificity, selectivity, and efficiency. Here, we disclose a feature neither common in enzymes nor ever described for enzyme mimics, but one that could prove crucial for the catalytic performance of the latter, namely the ability to catalyze and inhibit two different reactions at the same time. Remarkably, this can be realized by two identical, spatially resolved catalytic sites. In the future, such a synchronized catalyst action could be used not only for controlling chemoselectivity, as in the present case, but also for regulating other types of chemical reactivity.     

High‐throughput droplet‐based microfluidics for directed evolution of enzymes

Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.     

When Nanozymes Meet Single‐Atom Catalysis

Nanomaterials with enzyme‐like activities, coined nanozymes, have been researched widely as they offer unparalleled advantages in terms of low cost, superior activity, and high stability. The complex structure and composition of nanozymes has led to extensive investigation of their catalytic sites at an atomic scale, and to an in‐depth understanding of the biocatalysis occurring. Single‐atom catalysts (SACs), characterized by atomically dispersed active sites, have provided opportunities for mimicking metalloprotease and for bridging the gap between natural enzymes and nanozymes. In this Minireview, we illustrate the unique properties of nanozymes and we discuss recent advances in the synthesis, characterization, and applications of SACs. Subsequently, we outline the impressive progress made in single‐atom nanozymes and we discuss their applications in sensing, degradation of organic pollutants, and in therapeutic roles. Finally, we present the major challenges and opportunities remaining for a successful marriage of nanozymes and SACs.     

Recent Advances of Metal-Organic Frameworks-based Nanozymes for Bio-applications

Artificial nanoenzymes with enzyme-like catalytic activity have gradually become an alternative to natural enzymes due to their low production cost, high stability, and good tolerance. In recent years, various enzyme mimics have emerged with the rapid development of nano-teclnology. Metal-organic frameworks(MOFs) are a novel class of porous inorganic-organic hybrid materials made from metal ions/clusters and organic ligands, and MOFs-based nanozymes show great prospect in biosensing, biocatalysis, biomedical imaging, and therapeutic applications, due to unique properties, such as high specific surface area, high porosity, tunable morphology, and excellent biocatalytic properties. In this paper, the recent progresses concerning MOFs-based nanozymes are systematically summarized, including the synthesis, design strategies and related applications, which are divided into two major categories, namely, MOFs structured nanoenzymes and MOFs composite structured nanoenzymes. Meanwhile, the applications of various classifications of MOFs research are introduced. At the end, current challenges and future perspectives of MOFs-based nanozymes are also discussed. It is highly expected that this review on this important area can provide a meaningful guidance for tumor therapy, biosensing and other aspects.     

Recent progress in carbon-dots-based nanozymes for chemosensing and biomedical applications

Nanozymes are nanomaterials with enzyme-like activities that efficiently overcome the drawbacks of natural enzymes in biosensing, detection, and biomedical fields, and they are the most widely used artificial enzymes. Owing to their excellent catalytic characteristics, biocompatibility, and environmental favorability, carbon-dots-based (CDs) nanozymes have inspired a research upsurge. However, no review focusing on CDs nanozymes has been published, even though substantial advances have been achieved. Herein, the advances, catalytic activities, and applications of CDs nanozymes are highlighted and summarized. In addition, the critical issues and challenges of researching nanozymes are discussed. We hope that this review will broaden the horizons of nanozymes and CDs nanozymes, as well as promote their development.     

Dynamic Responsive Systems for Catalytic Function

Responsive systems have recently gained much interest in the scientific community in attempts to mimic dynamic functions in biological systems. One of the fascinating potential applications of responsive systems lies in catalysis. Inspired by nature, novel responsive catalytic systems have been built that show analogy with allosteric regulation of enzymes. The design of responsive catalytic systems allows control of catalytic activity and selectivity. In this Review, advances in the field over the last four decades are discussed and a comparison is made amongst the dynamic responsive systems based on the principles underlying their catalytic mechanisms. The catalyst systems are sorted according to the triggers used to achieve control of the catalytic activity and the distinct catalytic reactions illustrated.     

Advances in Single‐Atom Nanozymes Research†

Nanozymes with intrinsic enzyme‐like properties have attracted significant interest owing to their capability to address the limitations of traditional enzymes such as fragility, high cost and difficult mass production. However, the currently reported nanozymes are generally less active than natural enzymes. In recent years, with the rapid development of nanoscience and nanotechnology, single‐atom nanozymes (SAzymes) with well‐defined electronic and geometric structures have shown a promise to serve as direct surrogates of traditional enzymes by mimicking the highly evolved catalytic center of natural enzymes. In this review, we will introduce the enzymatic characteristics and recent advances of SAzymes, and summarize their significant applications from in vitro detection to in vivo monitoring and therapy.     

Chemoproteomic Evaluation of the Polyacetylene Callyspongynic Acid

Polyacetylenes are a class of alkyne‐containing natural products. Although potent bioactivities and thus possible applications as chemical probes have already been reported for some polyacetylenes, insights into the biological activities or molecular mode of action are still rather limited in most cases. To overcome this limitation, we describe the application of the polyacetylene callyspongynic acid in the development of an experimental roadmap for characterizing potential protein targets of alkyne‐containing natural products. To this end, we undertook the first chemical synthesis of callyspongynic acid. We then used in situ chemical proteomics methods to demonstrate extensive callyspongynic acid‐mediated chemical tagging of endoplasmic reticulum‐associated lipid‐metabolizing and modifying enzymes. We anticipate that an elucidation of protein targets of natural products may serve as an effective guide to the development of subsequent biological assays that aim to identify chemical phenotypes and bioactivities.     

环钯化合物在Heck反应中的应用研究

钯催化交叉偶联反应在化学工业、合成天然产物及生物活性物质中有着广泛的应用.催化剂体系是交叉偶联反应研究的核心.环钯化合物结构简单、性能稳定,在催化交叉偶联反应中具有高活性、高选择性,引起研究者们的极大关注,不断有新的环钯化合物被合成出来,其催化性能也得到了研究.本文综述了环钯化合物的合成方法及其在Heck反应中的应用.     

Capturing molecules with templated materials--analysis and rational design of molecularly imprinted polymers

The creation of synthetic tailor-made receptors capable of recognizing desired molecular targets with high affinity and selectivity is a persistent long-term goal for researchers in the fields of chemical, biological, and pharmaceutical research. Compared to biomacromolecular receptors, these synthetic receptors promise simplified production and processing, less costs, and more robust receptor architectures. During recent decades, molecularly imprinted polymers (MIPs) are widely considered mimics of natural molecular receptors suitable for a diversity of applications ranging from biomimetic sensors, to separations and biocatalysis.A remaining challenge for the next generation of MIPs is the synthesis of deliberately designed and highly efficient receptor architectures suitable for recognizing biologically relevant molecules, for which natural receptors are either not prevalent, or difficult to isolate and utilize. Hence, this review discusses recent advances in synthetic receptor technology for biomolecules (e.g. drugs, amino acids, steroids, proteins, entire cells, etc.) via molecular imprinting techniques. Surface imprinting methods and epitope imprinting approaches have been introduced for protein recognition at imprinted surfaces. Imprinting techniques in aqueous solution or organic-water co-solvents have been introduced avoiding denaturation of biomolecules during MIP synthesis. In addition, improved bioreactivity of entire enzyme or active site mimics generated by molecular imprinting will be highlighted. Finally, the emerging importance of molecular modeling and molecular dynamics studies detailing the intermolecular interactions between the template species, the porogenic solvent molecules, and the involved monomer and cross-linker in the pre-polymerization solution will be addressed yielding a rational approach toward next-generation MIP technology.     

Atomic engineering of single-atom nanozymes for enzyme-like catalysis

Enzyme mimics, especially nanozymes, play a crucial role in replacing natural enzymes for diverse applications related to bioanalysis, therapeutics and other enzyme-like catalysis. Nanozymes are catalytic nanomaterials with enzyme-like properties, which currently face formidable challenges with respect to their intricate structure, properties and mechanism in comparison with enzymes. The latest emergence of single-atom nanozymes (SAzymes) undoubtedly promoted the nanozyme technologies to the atomic level and provided new opportunities to break through their inherent limitations. In this perspective, we discuss key aspects of SAzymes, including the advantages of the single-site structure, and the derived synergetic enhancements of enzyme-like activity, catalytic selectivity and the mechanism, as well as the superiority in biological and catalytic applications, and then highlight challenges that SAzymes face and provide relevant guidelines from our point of view for the rational design and extensive applications of SAzymes, so that SAzyme may achieve its full potential as the next-generation nanozyme.

Single-atom nanozymes with definite active centers, high catalytic activities and enzyme-like selectivities promote the nanozyme research entering a new period of atomic level.     

化学基元组学与药物创新

化学基元组学（chemomics）是与化学信息学、生物信息学、合成化学等学科相关的交叉学科．生物系统从内源性小分子（天然砌块）出发,通过酶催化的化学反应序列制造天然产物．生物系统通过化学反应和天然砌块向目标天然产物“砌入”一组原子,这样的一组原子称为化学基元（chemoyl）．化学基元组（chemome）是生物组织中所含有的化学基元的全体．化学基元组学研究各种化学基元的结构、组装与演化的基本规律．在生存压力和繁衍需求的驱动下,生物系统已经进化出有效手段来合成天然产物以应付环境的变化,并产生了丰富多彩的生物和化学多样性．近年来,人们意识到药物创新的瓶颈之一是药物筛选资源的日益枯竭．化学基元组学可以解决这个瓶颈问题,它通过揭示生物系统制备化学多样性的规律,发展仿生合成方法制备类天然化合物库（quasi natural product libraries）以供药物筛选．本文综述了化学基元组学的主要研究内容及其在药物创新各领域中的潜在应用．     

Chemomics and drug innovation

Chemomics is an interdisciplinary study using approaches from chemoinformatics,bioinformatics,synthetic chemistry,and other related disciplines.Biological systems make natural products from endogenous small molecules (natural product building blocks) through a sequence of enzyme catalytic reactions.For each reaction,the natural product building blocks may contribute a group of atoms to the target natural product.We describe this group of atoms as a chemoyl.A chemome is the complete set of chemoyls in an organism.Chemomics studies chemomes and the principles of natural product syntheses and evolutions.Driven by survival and reproductive demands,biological systems have developed effective protocols to synthesize natural products in order to respond to environmental changes;this results in biological and chemical diversity.In recent years,it has been realized that one of the bottlenecks in drug discovery is the lack of chemical resources for drug screening.Chemomics may solve this problem by revealing the rules governing the creation of chemical diversity in biological systems,and by developing biomimetic synthesis approaches to make quasi natural product libraries for drug screening.This treatise introduces chemomics and outlines its contents and potential applications in the fields of drug innovation.     

Effect of Additives on the Selectivity and Reactivity of Enzymes

Enzymes have been widely used as efficient, eco‐friendly, and biodegradable catalysts in organic chemistry due to their mild reaction conditions and high selectivity and efficiency. In recent years, the catalytic promiscuity of many enzymes in unnatural reactions has been revealed and studied by chemists and biochemists, which has expanded the application potential of enzymes. To enhance the selectivity and activity of enzymes in their natural or promiscuous reactions, many methods have been recommended, such as protein engineering, process engineering, and media engineering. Among them, the additive approach is very attractive because of its simplicity to use and high efficiency. In this paper, we will review the recent developments about the applications of additives to improve the catalytic performances of enzymes in their natural and promiscuous reactions. These additives include water, organic bases, water mimics, cosolvents, crown ethers, salts, surfactants, and some particular molecular additives.