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.     

Nonspecific catalysis by protein surfaces

Catalytic antibodies are the best availablea llaround enzyme mimics. They provide a unique experimental approach and some special insights into general questions about catalysis by enzymes. They offer enantiospecific reactions and levels of substrate binding that compare well with typical enzyme reactions, but not—so far—comparable catalytic efficiency. We and others have used the Kemp elimination as a probe of catalytic efficiency in antibodies. We compare these reactions with nonspecific catalysis by other proteins, and with catalysis by enzymes. Several simple reactions are catalyzed by theserum albumins with Michaelis-Menten kinetics, and can be shown to involve substrate binding and catalysis by local functional groups. Here, we report the details of one investigation, which implicate known binding sites on the protein surface and discuss implications for catalyst design and efficiency.     

Enzyme Mimics: Advances and Applications

Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti‐biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.     

Supramolecular Coordination Cages for Asymmetric Catalysis

Inspired by the high efficiency and specificity of enzymes in living systems, the development of artificial catalysts intrinsic to the key features of enzyme has emerged as an active field. Recent advances in supramolecular chemistry have shown that supramolecular coordination cages, built from non-covalent coordination bonds, offer a diverse platform for enzyme mimics. Their inherent confined cavity, analogous to the binding pocket of an enzyme, and the facile tunability of building blocks are essential for substrate recognition, transition-state stabilization, and product release. In particular, the combination of chirality with supramolecular coordination cages will undoubtedly create an asymmetric microenvironment for promoting enantioselective transformation, thus providing not only a way to make synthetically useful asymmetric catalysts, but also a model to gain a better understanding for the fundamental principles of enzymatic catalysis in a chiral environment. The focus here is on recent progress of supramolecular coordination cages for asymmetric catalysis, and based on how supramolecular coordination cages function as reaction vessels, three approaches have been demonstrated. The aim of this review is to offer researchers general guidance and insight into the rational design of sophisticated cage containers for asymmetric catalysis.     

Promiscuous partitioning of a covalent intermediate common in the pentein superfamily

Many enzymes in the pentein superfamily use a transient covalent intermediate in their catalytic mechanisms. Here we trap and determine the structure of a stable covalent adduct that mimics this intermediate using a mutant dimethylarginine dimethylaminohydrolase and an alternative substrate. The interactions observed between the enzyme and trapped adduct suggest an altered angle of attack between the nucleophiles of the first and second half-reactions of normal catalysis. The stable covalent adduct is also capable of further reaction. Addition of imidazole rescues the original hydrolytic activity. Notably, addition of other amines instead yields substituted arginine products, which arise from partitioning of the intermediate into the evolutionarily related amidinotransferase reaction pathway. The enzyme provides both selectivity and catalysis for the amidinotransferase reaction, underscoring commonalities among the reaction pathways in this mechanistically diverse enzyme superfamily. The promiscuous partitioning of this intermediate may also help to illuminate the evolutionary history of these enzymes.     

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.     

Iminosugar glycosidase inhibitors: structural and thermodynamic dissection of the binding of isofagomine and 1-deoxynojirimycin to beta-glucosidases

The design and synthesis of transition-state mimics reflects the growing need both to understand enzymatic catalysis and to influence strategies for therapeutic intervention. Iminosugars are among the most potent inhibitors of glycosidases. Here, the binding of 1-deoxynojirimycin and (+)-isofagomine to the "family GH-1" beta-glucosidase of Thermotoga maritima is investigated by kinetic analysis, isothermal titration calorimetry, and X-ray crystallography. The binding of both of these iminosugar inhibitors is driven by a large and favorable enthalpy. The greater inhibitory power of isofagomine, relative to 1-deoxynojirimycin, however, resides in its significantly more favorable entropy; indeed the differing thermodynamic signatures of these inhibitors are further highlighted by the markedly different heat capacity values for binding. The pH dependence of catalysis and of inhibition suggests that the inhibitory species are protonated inhibitors bound to enzymes whose acid/base and nucleophile are ionized, while calorimetry indicates that one proton is released from the enzyme upon binding at the pH optimum of catalysis (pH 5.8). Given that these results contradict earlier proposals that the binding of racemic isofagomine to sweet almond beta-glucosidase was entropically driven (Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568), we reinvestigated the binding of 1-deoxynojirimycin and isofagomine to the sweet almond enzyme. Calorimetry confirms that the binding of isofagomine to sweet almond beta-glucosidases is, as observed for the T. maritima enzyme, driven by a large favorable enthalpy. The crystallographic structures of the native T. maritima beta-glucosidase, and its complexes with isofagomine and 1-deoxynojirimycin, all at approximately 2.1 A resolution, reveal that additional ordering of bound solvent may present an entropic penalty to 1-deoxynojirimycin binding that does not penalize isofagomine.     

仿酶催化与绿色化学

仿酶催化是绿色化学研究中的一个重要课题。本文简要论述了仿酶催化研究的一些新进展,包括功能环糊精和桥联环糊精仿酶研究、双核铜酶的模拟、咪唑环番仿酶新体系、手性金属胶束体系以及新型手性口恶唑硼烷化学酶。     

酶复合催化剂原位合成新方法及生物催化应用

工业生物催化面临两大重要挑战,一是可工业应用的酶催化反应类型仍然比较有限,远少于化学催化剂,因此需要拓展酶催化的反应类型;二是酶在苛刻的工业催化反应条件下尤其是在高温、有机溶剂、不适宜的pH等环境下稳定性较差,因此需要提高工业酶催化剂的稳定性.研究者已经开发了很多方法,以解决这两方面难题,例如酶的定向进化、定点突变、酶的计算机从头设计和构建人工金属酶等.本文系统介绍了本课题组开发的酶复合催化剂原位合成方法及其生物催化应用,期望为解决工业生物催化的上述挑战提供新思路.原位合成是构建酶-无机晶体复合催化剂的一种简便、高效、普适的方法.酶-无机晶体复合物中,限域包埋使酶具有高于常规固定化酶的催化活性和稳定性.该方法可以简便拓展至其它多种类型的无机晶体材料,显著提高酶的稳定性.无机晶体的限域包埋对酶分子结构和性能有着重要影响,通过理性设计复合催化剂的结构,可实现对酶的活性、稳定性以及多酶反应级联效率的有效调控.本课题组采用分子模拟和实验相结合的方法阐释了多酶-无机晶体复合催化剂所驱动的级联反应效率提高的关键因素.通过调控原位合成中金属离子和有机配体的浓度,实现了酶分子在缺陷型甚至无定形载体中的包埋.在此基础上,深入探讨了缺陷对酶分子结构和催化活性的调控机制,为酶复合催化剂的理性设计提供了依据.同样基于原位合成方法,本课题组构建了酶-金属团簇复合催化剂,实现了温和条件下酶催化和金属催化的高效耦合和协同.以脂肪酶-钯团簇复合催化剂为例,阐明了酶-金属团簇复合催化剂中二者相互作用对酶分子结构和活性以及金属催化活性的影响机制,为酶催化和金属催化相融合的研究提供了重要基础.我们对这一领域存在的挑战和未来重要的研究方向也进行了讨论,希望本文可以从催化剂工程角度为高效酶催化剂的设计以及生物催化应用领域的拓展提供新思路,推动该领域发展.     

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.     

How much do enzymes really gain by restraining their reacting fragments?

The steric effect, exerted by enzymes on their reacting substrates, has been considered as a major factor in enzyme catalysis. In particular, it has been proposed that enzymes catalyze their reactions by pushing their reacting fragments to a catalytic configuration which is sometimes called near attack configuration (NAC). This work uses computer simulation approaches to determine the relative importance of the steric contribution to enzyme catalysis. The steric proposal is expressed in terms of well defined thermodynamic cycles that compare the reaction in the enzyme to the corresponding reaction in water. The S(N)2 reaction of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10, which was used in previous studies to support the strain concept is chosen as a test case for this proposal. The empirical valence bond (EVB) method provides the reaction potential surfaces in our studies. The reliability and efficiency of this method make it possible to obtain stable results for the steric free energy. Two independent strategies are used to evaluate the actual magnitude of the steric effect. The first applies restraints on the substrate coordinates in water in a way that mimics the steric effect of the protein active site. These restraints are then released and the free energy associated with the release process provides the desired estimate of the steric effect. The second approach eliminates the electrostatic interactions between the substrate and the surrounding in the enzyme and in water, and compares the corresponding reaction profiles. The difference between the resulting profiles provides a direct estimate of the nonelectrostatic contribution to catalysis and the corresponding steric effect. It is found that the nonelectrostatic contribution is about -0.7 kcal/mol while the full "apparent steric contribution" is about -2.2 kcal/mol. The apparent steric effect includes about -1.5 kcal/mol electrostatic contribution. The total electrostatic contribution is found to account for almost all the observed catalytic effect ( approximately -6.1 kcal/mol of the -6.8 calculated total catalytic effect). Thus, it is concluded that the steric effect is not the major source of the catalytic power of haloalkane dehalogenase. Furthermore, it is found that the largest component of the apparent steric effect is associated with the solvent reorganization energy. This solvent-induced effect is quite different from the traditional picture of balance between the repulsive interaction of the reactive fragments and the steric force of the protein.     

酶的分子仿生研究进展

回顾了近几十年来印迹高分子和有机团簇对酶的仿生发展历程，总结了目前的 研究现状，探讨了电子效应和空间效应（柔性空间效应）对仿对酶在催化过程中实 现类似酶的识别和诱导契合的影响，并展望了酶的仿生发展趋势。     

Vanadium in Asymmetric Synthesis: Emerging Concepts in Catalyst Design and Applications

In recent years vanadium catalysis has been extended to a range of different and even complementary directions in asymmetric synthesis. Inspired by nature’s way to activate both substrate and reagent in many cases, the design of efficient bifunctional and dinuclear vanadium catalysts has been achieved. Furthermore, vanadium catalysis has been an early field in which “hybrid catalysts” have been studied in detail by incorporation of oxovanadium complexes into proteins, thus giving artificial enzymes. In addition, a high compatibility of vanadium with proteins enabled the use of vanadium chemocatalysts for combinations with enzyme catalysis in one‐pot, thus leading to dynamic kinetic resolutions. In this contribution, these three concepts of vanadium catalysis opening up new perspectives for asymmetric synthesis are reviewed.     

分子印迹聚合物的设计合成

分子印迹法是制备对特定分子（印迹分子）具有识别选择性的聚合物的技术,近年来,分子印迹法制得的聚合物在分离,分析,免疫测定,催化、模拟酶及生物传感器等方面的应用引起人们的广泛关系。本文介绍了分子印迹技术的基本原理,对分子印迹聚合物合成研究的最新进展进行了综述,评述了各种制备方法的优缺点,拽出了合成技术未来的发展方向。     

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.     

A carbon nanotube structured biomimetic catalyst for polysaccharide degradation

A unique artificial catalyst that mimics the structure of active sites in real enzymes using functionalized carbon nanotubes is presented. This concept will allow for the potential construction of a library of biomimetic catalysts for enzyme active centers, for which the structure-catalysis relationships are well defined.     

Enzyme catalysis in organic solvents: a promising field for optical biosensing

The ability of enzymes to work in non-aqueous media offers new and almost unexploited possibilities for the development of new optical biosensors. The advantages of performing biocatalytic reactions in non-aqueous media are discussed in relation to their possible application in optical biosensor design. Attention is focused on the factors that influence enzymatic catalysis in organic solvents, including the role of enzyme-associated water, criteria for solvent selection and the alteration of enzyme specificity. Recent examples of relevant applications and future prospects of organic-phase optical biosensing are discussed.     

Chemoenzymatic Cascades Combining Biocatalysis and Transition Metal Catalysis for Asymmetric Synthesis

The combination of catalytic methods provides multiple advantages in organic synthesis, allowing access to diverse organic molecules in a straightforward manner. Merging metal and enzyme catalysis is currently receiving great attention due to the possibility to assemble metal catalysis in C−C coupling, olefin metathesis, hydration and other reactions with the exquisite stereospecificity displayed by enzymes. Thus, this minireview is organized based on the action of the metal species (Pd, Ru, Au, Ir, Fe…) in combination with different enzymes. Special attention will be paid to the design of sequential processes and concurrent cascades, presenting solutions such as the use of surfactants or compartmentalization strategies for those cases where incompatibilities could hamper the overall process.     

Role of protein dynamics in reaction rate enhancement by enzymes

An integrated view of protein structure, dynamics, and function is emerging, where proteins are considered as dynamically active assemblies and internal motions are closely linked to function such as enzyme catalysis. Further, the motion of solvent bound to external regions of protein impacts internal motions and, therefore, protein function. Recently, we discovered a network of protein vibrations in enzyme cyclophilin A, coupled to its catalytic activity of peptidyl-prolyl cis-trans isomerization. Detailed studies suggest that this network, extending from surface regions to active site, is a conserved part of enzyme structure and has a role in promoting catalysis. In this report, theoretical investigations of concerted conformational fluctuations occurring on microsecond and longer time scales within the discovered network are presented. Using a new technique, kinetic energy was added to protein vibrational modes corresponding to conformational fluctuations in the network. The results reveal that protein dynamics promotes catalysis by altering transition state barrier crossing behavior of reaction trajectories. An increase in transmission coefficient and number of productive trajectories with increasing amounts of kinetic energy in vibrational modes is observed. Variations in active site enzyme-substrate interactions near transition state are found to be correlated with barrier recrossings. Simulations also showed that energy transferred from first solvation shell to surface residues impacts catalysis through network fluctuations. The detailed characterization of network presented here indicates that protein dynamics plays a role in rate enhancement by enzymes. Therefore, coupled networks in enzymes have wide implications in understanding allostericity and cooperative effects, as well as protein engineering and drug design.     

Hydrolytische Spaltung von Nucleinsäuren-vom Enzymmechanismus zum Enzymmodell

Detailed knowledge of enzyme mechanisms has previously led to the design of „enzyme mimetics”︁, small synthetic compounds that use the same principles of catalysis as enzymes but need a less complicated framework than proteins. The development of enzyme mimetics for the hydrolysis of RNA is of special interest because of their potential use as drugs in gene therapy. Field development from the first active compounds discovered in the late 80s to the application of highly specific artificial RNases in vitro is described.