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.     

Enzyme Activity by Design: An Artificial Rhodium Hydroformylase for Linear Aldehydes

Artificial metalloenzymes (ArMs) are hybrid catalysts that offer a unique opportunity to combine the superior performance of natural protein structures with the unnatural reactivity of transition‐metal catalytic centers. Therefore, they provide the prospect of highly selective and active catalytic chemical conversions for which natural enzymes are unavailable. Herein, we show how by rationally combining robust site‐specific phosphine bioconjugation methods and a lipid‐binding protein (SCP‐2L), an artificial rhodium hydroformylase was developed that displays remarkable activities and selectivities for the biphasic production of long‐chain linear aldehydes under benign aqueous conditions. Overall, this study demonstrates that judiciously chosen protein‐binding scaffolds can be adapted to obtain metalloenzymes that provide the reactivity of the introduced metal center combined with specifically intended product selectivity.     

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating‐associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6‐helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg²⁺; whereas Na⁺ switches it to the expanded state, as revealed by MD simulations, small‐angle X‐ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure–function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications.     

Deciphering a Nanocarbon‐Based Artificial Peroxidase: Chemical Identification of the Catalytically Active and Substrate‐Binding Sites on Graphene Quantum Dots

The design and construction of efficient artificial enzymes is highly desirable. Recent studies have demonstrated that a series of carbon nanomaterials possess intrinsic peroxidase activity. Among them, graphene quantum dots (GQDs) have a high enzymatic activity. However, the catalytic mechanism remains unclear. Therefore, in this report, we chose to decipher their peroxidase activity. By selectively deactivating the ketonic carbonyl, carboxylic, or hydroxy groups and investigating the catalytic activities of these GQD derivatives, we obtained evidence that the ? C?O groups were the catalytically active sites, whereas the O?C? O? groups acted as substrate‐binding sites, and ? C? OH groups can inhibit the activity. These results were corroborated by theoretical studies. This work should not only enhance our understanding of nanocarbon‐based artificial enzymes, but also facilitate the design and construction of other types of target‐specific artificial enzymes.     

Modification of Cyclodextrins for Use as Artificial Enzymes

The magical powers of enzymes have been attributed to their ability to bind specific substrates and catalyze reactions of the bound substrate. Artificial enzymes synthetically mimic the binding and the catalytic site to produce molecules that are not only smaller in size but also potentially have similar activity to the real enzymes. The main objective of our research is to create artificial redox enzymes by using cyclodextrins as binding sites and attaching flavin derivatives as the catalytic site. We have developed a strategy to attach a catalytic site to cyclodextrin exclusively at the 2-, 3- or the 6-position. The evaluation of the artificial enzyme in which flavin is attached to the 2-position gives a 647-fold acceleration factor. Although this is modest compared to those of real enzymes (which can have acceleration factors of a trillion), the artificial enzymes allow us to understand the elements that contribute to the incredible catalytic power of enzymes.     

Polymeric Heterogeneous Catalysts of Transition‐Metal Oxides: Surface Characterization,Physicomechanical Properties,and Catalytic Activity

We investigate the physicomechanical properties of polymeric heterogeneous catalysts of transition‐metal oxides, specifically, the specific surface area, elongation at break, breaking strength, specific electrical resistance, and volume resistivity. Digital microscopy, Fourier‐transform infrared spectroscopy, X‐ray diffraction, scanning electron microscopy, and energy‐dispersive analysis are used to study the surfaces of the catalysts. The experimental results show that polymeric heterogeneous catalysts of transition‐metal oxides exhibit high stability and can maintain their catalytic activity under extreme reaction conditions for long‐term use. The oxidation mechanism of sulfur‐containing compounds in the presence of polymeric heterogeneous catalysts of transition‐metal oxides is confirmed. Microstructural characterization of the catalysts is performed by using X‐ray computed tomography. The activity of various catalysts in the oxidation of sulfur‐containing compounds is determined. We demonstrate the potential application of polymeric heterogeneous catalysts of transition‐metal oxides in industrial wastewater treatment.     

A Thermophilic Tetramolecular G‐Quadruplex/Hemin DNAzyme

The quadruplex‐based DNAzyme system is one of the most useful artificial enzymes or catalysts; their unique properties make them reliable alternatives to proteins for performing catalytic transformation. The first prototype of a thermally stable DNAzyme system is presented. This thermophilic DNAzyme is capable of oxidizing substrates at high temperatures (up to 95 °C) and long reaction times (up to 18 h at 75 °C). The catalytic activity of the DNAzymes were investigated with the standard peroxidase‐mimicking oxidation of 2,2′‐azino‐bis(3‐ethylbenzothiozoline‐6‐sulfonic acid) (ABTS) by H₂O₂. The step‐by‐step design of this unique heat‐activated G‐quadruplex/hemin catalyst, including the modification of adenines at both ends of G‐tracts, the choice of cation, and its concentration for DNAzyme stabilization, is described. This work investigates thoroughly the molecular basis of these catalytic properties and provides an example of an industrially relevant application.     

Protein ubiquitination and formation of polyubiquitin chains without ATP,E1 and E2 enzymes

Studying protein ubiquitination is difficult due to the complexity of the E1–E2–E3 ubiquitination cascade. Here we report the discovery that C-terminal ubiquitin thioesters can undergo direct transthiolation with the catalytic cysteine of the model HECT E3 ubiquitin ligase Rsp5 to form a catalytically active Rsp5∼ubiquitin thioester (Rsp5∼Ub). The resulting Rsp5∼Ub undergoes efficient autoubiquitination, ubiquitinates protein substrates, and synthesizes polyubiquitin chains with native Ub isopeptide linkage specificity. Since the developed chemical system bypasses the need for ATP, E1 and E2 enzymes while maintaining the native HECT E3 mechanism, we named it “Bypassing System” (ByS). Importantly, ByS provides direct evidence that E2 enzymes are dispensable for K63 specific isopeptide bond formation between ubiquitin molecules by Rsp5 in vitro. Additionally, six other E3 enzymes including Nedd4-1, Nedd4-2, Itch, and Wwp1 HECT ligases, along with Parkin and HHARI RBR ligases processed Ub thioesters under ByS reaction conditions. These findings provide general mechanistic insights on protein ubiquitination, and offer new strategies for assay development to discover pharmacological modulators of E3 enzymes.     

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5‐4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non‐physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.     

A Cofactor‐Substrate‐Based Supramolecular Fluorescent Probe for the Ultrafast Detection of Nitroreductase under Hypoxic Conditions

Identifying the location and expression levels of enzymes under hypoxic conditions in cancer cells is vital in early‐stage cancer diagnosis and monitoring. By encapsulating a fluorescent substrate, L‐NO₂ , within the NADH mimic‐containing metal–organic capsule Zn‐ MPB , we developed a cofactor‐substrate‐based supramolecular luminescent probe for ultrafast detection of hypoxia‐related enzymes in solution in vitro and in vivo. The host–guest structure fuses the coenzyme and substrate into one supramolecular probe to avoid control by NADH, switching the catalytic process of nitroreductase from a double‐substrate mechanism to a single‐substrate one. This probe promotes enzyme efficiency by altering the substrate catalytic process and enhances the electron transfer efficiency through an intra‐molecular pathway with increased activity. The enzyme content and fluorescence intensity showed a linear relationship and equilibrium was obtained in seconds, showing potential for early tumor diagnosis, biomimetic catalysis, and prodrug activation.     

Plasmonic heterogeneous catalysis for organic transformations

Plasmonic catalysis has been recognised as a promising alternative to many conventional thermal catalytic processes in organic synthesis. In addition to their high activity in fine chemical synthesis, plasmonic photocatalysts are also able to maintain control of selectivity under mild conditions by utilising visible-light as an energy source. This review provides an overview of the recent advances in organic transformations with plasmonic metal nanostructures, including selective reduction, selective oxidation, cross-coupling and addition reactions. We also summarize the photocatalysts and catalytic mechanisms involving surface plasmon resonance. Finally, control of reaction pathway and strategies for tailoring product selectivity in fine chemical synthesis are discussed.     

Switchable Hydrolase Based on Reversible Formation of Supramolecular Catalytic Site Using a Self‐Assembling Peptide

The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH‐switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH‐responsive peptide. The peptide exhibits a conformational transition from random coil to β‐sheet by changing the pH from acidic to alkaline. The β‐sheet self‐assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity. Catalytic activity can be reversible switched by pH‐induced assembly/disassembly of the fibrils into random coils. At higher concentrations, the peptide forms a hydrogel which is also catalytically active and maintains its reversible (de‐)activation.     

In Situ Cyclization of Native Proteins: Structure‐Based Design of a Bicyclic Enzyme

Increased tolerance of enzymes towards thermal and chemical stress is required for many applications and can be achieved by macrocyclization of the enzyme resulting in the stabilizing of its tertiary structure. Thus far, macrocyclization approaches utilize a very limited structural diversity, which complicates the design process. Herein, we report an approach that enables cyclization through the installation of modular crosslinks into native proteins composed entirely of proteinogenic amino acids. Our stabilization procedure involves the introduction of three surface‐exposed cysteine residues, which are reacted with a triselectrophile, resulting in the in situ cyclization of the protein (INCYPRO). A bicyclic version of sortase A was designed that exhibits increased tolerance towards thermal as well as chemical denaturation, and proved to be efficient in protein labeling under denaturing conditions. In addition, we applied INCYPRO to the KIX domain, resulting in up to 24 °C increased thermal stability.     

Cyclodextrin‐supported palladium complex: A highly active and recoverable catalyst for Suzuki–Miyaura cross‐coupling reaction in aqueous medium

A water‐soluble, cyclodextrin‐supported palladium complex (DACH‐Pd‐β‐CD) catalytic system was designed and synthesized, which can efficiently catalyze Suzuki–Miyaura cross‐coupling reactions between aryl halides and arylboronic acid in water under mild conditions. The catalyst was successfully characterized using the methods of transmission electron microscopy, energy‐dispersive X‐ray spectrometry, X‐ray diffraction, thermogravimetric analysis, and Fourier transform infrared and NMR spectroscopies. Furthermore, the catalyst can be easily separated from the reaction mixture and still maintain high catalytic activity after ten cycles. No leaching of palladium into the reaction solution occurred. The advantages of green solvent (water), short reaction times (2–6 h), low catalyst loading (0.001 mol%), excellent yields (up to 99%) and reusability of the catalyst mean it will have potential applications in green chemical synthesis.     

Prebiotic Cell Membranes that Survive Extreme Environmental Pressure Conditions

Attractive candidates for compartmentalizing prebiotic cells are membranes comprised of single‐chain fatty acids. It is generally believed that life may have originated in the depth of the protoocean, that is, under high hydrostatic pressure conditions, but the structure and physical–chemical properties of prebiotic membranes under such conditions have not yet been explored. We report the temperature‐ and pressure‐dependent properties of membranes composed of prebiotically highly‐plausible lipids and demonstrate that prebiotic membranes could not only withstand extreme temperatures, but also serve as robust models of protocells operating in extreme pressure environments. We show that pressure not only increases the stability of vesicular systems but also limits their flexibility and permeability to solutes, while still keeping the membrane in an overall fluid‐like and thus functional state.     

Enzyme Shielding in an Enzyme‐thin and Soft Organosilica Layer

The fragile nature of most enzymes is a major hindrance to their use in industrial processes. Herein, we describe a synthetic chemical strategy to produce hybrid organic/inorganic nanobiocatalysts; it exploits the self‐assembly of silane building blocks at the surface of enzymes to grow an organosilica layer, of controlled thickness, that fully shields the enzyme. Remarkably, the enzyme triggers a rearrangement of this organosilica layer into a significantly soft structure. We demonstrate that this change in stiffness correlates with the biocatalytic turnover rate, and that the organosilica layer shields the enzyme in a soft environment with a markedly enhanced resistance to denaturing stresses.     

Directed Evolution of an Artificial Imine Reductase

Artificial metalloenzymes, resulting from incorporation of a metal cofactor within a host protein, have received increasing attention in the last decade. The directed evolution is presented of an artificial transfer hydrogenase (ATHase) based on the biotin‐streptavidin technology using a straightforward procedure allowing screening in cell‐free extracts. Two streptavidin isoforms were yielded with improved catalytic activity and selectivity for the reduction of cyclic imines. The evolved ATHases were stable under biphasic catalytic conditions. The X‐ray structure analysis reveals that introducing bulky residues within the active site results in flexibility changes of the cofactor, thus increasing exposure of the metal to the protein surface and leading to a reversal of enantioselectivity. This hypothesis was confirmed by a multiscale approach based mostly on molecular dynamics and protein–ligand dockings.     

Synthesis and characterization of hyperbranched polyimides with good organosolubility and thermal properties based on a new triamine and conventional dianhydrides

A triamine monomer, 1,3,5‐tris(4‐aminophenoxy)benzene (TAPOB), was synthesized from phloroglucinol and 4‐chloronitrobenzene, and it was successfully polymerized into soluble hyperbranched polyimides (HB PIs) with commercially available dianhydrides: 4,4′‐(hexafluoroisopropylidene)diphthalic anhydride (6FDA), 4,4′‐oxydiphthalic anhydride (ODPA), and 3,3′,4,4′‐benzophenonetetracarboxylic dianhydride (BTDA). Different monomer addition methods and different monomer molar ratios resulted in HB PIs with amino or anhydride end groups. From ¹H NMR spectra, the degrees of branching of the amino‐terminated polymers were estimated to be 0.65, 0.62, and 0.67 for 6FDA–TAPOB, ODPA–TAPOB, and BTDA–TAPOB, respectively. All polymers showed good thermal properties with 10% weight‐loss temperatures (T₁₀'s) above 505 °C and glass‐transition temperatures (T_g's) of 208–282 °C for various dianhydrides. The anhydride‐terminated HB PIs showed lower T₁₀ and T_g values than their amino‐terminated counterparts. The chemical conversion of the terminal amino or anhydride groups of the 6FDA‐based polyimides into an aromatic imido structure improved their thermal stability, decreased their T_g, and improved their solubility. The HB PIs had moderate molecular weights with broad distributions. The 6FDA‐based HB PIs exhibited good solubility even in common low‐boiling‐point solvents such as chloroform, tetrahydrofuran, and acetone. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3804–3814, 2002