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.     

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.     

Irreversible Inhibition of IspG,a Target for the Development of New Antimicrobials,by a 2-Vinyl Analogue of its MEcPP Substrate

IspG (also called GcpE) is an oxygen-sensitive [4Fe-4S] enzyme catalyzing the penultimate step of the methylerythritol phosphate (MEP) pathway, a validated target for drug development. It converts 2-C-methyl-d -erythritol-2,4-cyclo-diphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl-1-diphosphate (HMBPP). The reaction, assimilated to a reductive dehydration, involves redox partners responsible for the formal transfer of two electrons to substrate MEcPP. The 2-vinyl analogue of MEcPP was designed to generate conjugated species during enzyme catalysis, with the aim of providing new reactive centers to be covalently trapped by neighboring amino acid residues. The synthesized substrate analogue displayed irreversible inhibition towards IspG. Furthermore, we have shown that electron transfer occurs prior to inhibition; this might designate conjugated intermediates as probable affinity tags through covalent interaction at the catalytic site. This is the first report of an irreversible inhibitor of the IspG metalloenzyme.     

A de novo designed peptide ligase: a mechanistic investigation.

A 33-residue de novo designed peptide ligase is reported which catalyzes the template-directed condensation of suitably activated short peptides with catalytic efficiencies in excess of 10(5) ([k(cat)/K(m)]/k(uncat)). The ligase peptide, derived from natural and designed alpha-helical coiled-coil proteins, presents a surface for substrate assembly via formation of a hydrophobic core at the peptide interface. Charged residues flanking the core provide additional binding specificity through electrostatic complementarity. Addition of the template to an equimolar fragment solution results in up to 4100-fold increases in initial reaction rates. Dramatic decreases in efficiency upon mutation of charged residues or increase in ionic strength establishes the importance of electrostatic recognition to ligase efficiency. Although most of the increase in reaction efficiency is due to entropic gain from binding of substrates in close proximity, mechanistic studies with altered substrates demonstrate that the system is highly sensitive to precise ordering at the point of ligation. Taken together these results represent the first example of a peptide catalyst with designed substrate binding sites which can significantly accelerate a bimolecular reaction and support the general viability of alpha-helical protein assemblies in artificial enzyme design.     

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.     

Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization.

BACKGROUND: EntF is a 142 kDa four domain (condensation-adenylation-peptidyl carrier protein-thioesterase) nonribosomal peptide synthetase (NRPS) enzyme that assembles the Escherichia coli N-acyl-serine trilactone siderophore enterobactin from serine, dihydroxybenzoate (DHB) and ATP with three other enzymes (EntB, EntD and EntE). To assess how EntF forms three ester linkages and cyclotrimerizes the covalent acyl enzyme DHB-Ser-S-PCP (peptidyl carrier protein) intermediate, we mutated residues of the proposed catalytic Ser-His-Asp triad of the thioesterase (TE) domain. RESULTS: The Ser1138-->Cys mutant (kcat decreased 1000-fold compared with wild-type EntF) releases both enterobactin (75%) and linear (DHB-Ser)2 dimer (25%) as products. The His 1271-->Ala mutant (kcat decreased 10,000-fold compared with wild-type EntF) releases only enterobactin, but accumulates both DHB-Ser-O-TE and (DHB-Ser)2-O-TE acyl enzyme intermediates. Electrospray ionization and Fourier transform mass spectrometry of proteolytic digests were used to analyze the intermediates. CONCLUSIONS: These results establish that the TE domain of EntF is both a cyclotrimerizing lactone synthetase and an elongation catalyst for ester-bond formation between covalently tethered DHB-Ser moieties, a new function for chain-termination TE domains found at the carboxyl termini of multimodular NRPSs and polyketide synthases.     

Self-Assembly of DNA–Peptide Supermolecules: Coiled-Coil Peptide Structures Templated by d-DNA and l-DNA Triplexes Exhibit Chirality-Independent but Orientation-Dependent Stabilizing Cooperativity

DNA nanostructures have been designed and used in many different applications. However, the use of nucleic acid scaffolds to promote the self-assembly of artificial protein mimics is only starting to emerge. Herein five coiled-coil peptide structures were templated by the hybridization of a d -DNA triplex or its mirror-image counterpart, an l -DNA triplex. The self-assembly of the desired trimeric structures in solution was confirmed by gel electrophoresis and small-angle X-ray scattering, and the stabilizing synergy between the two domains was found to be chirality-independent but orientation-dependent. This is the first example of using a nucleic acid scaffold of l -DNA to template the formation of artificial protein mimics. The results may advance the emerging POC-based nanotechnology field by adding two extra dimensions, that is, chirality and polarity, to provide innovative molecular tools for rational design and bottom-up construction of artificial protein mimics, programmable materials and responsive nanodevices.     

De Novo Design,Synthesis and Characterisation of MP3, A New Catalytic Four‐Helix Bundle Hemeprotein

A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four‐helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix–loop–helix/heme/helix–loop–helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP‐like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix‐forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe^III–MP3 possesses peroxidase‐like activity comparable to R38A–hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic.     

Enzyme‐Responsive Multifunctional Magnetic Nanoparticles for Tumor Intracellular Drug Delivery and Imaging

Enzyme‐responsive, hybrid, magnetic silica nanoparticles have been employed for multifunctional applications in selective drug delivery and intracellular tumor imaging. In this study, doxorubicin (Dox)‐conjugated, enzyme‐cleavable peptide precursors were covalently tethered onto the surface of uniform silica‐coated magnetic nanoparticles through click chemistry. This enzyme‐responsive nanoparticle conjugate demonstrated highly efficient Dox release upon specific enzyme interactions in vitro. It also exhibits multiple functions in selective tumor intracellular drug delivery and imaging in the tumor cells with high cathepsin B expression, whereas it exhibited lower cytotoxicity towards other cells without enzyme expression.     

Polyfunctional Bis‐Lewis‐Acid‐/Bis‐Triazolium Catalysts for Stereoselective 1,4‐Additions of 2‐Oxindoles to Maleimides

Achieving enzyme‐like catalytic activity and stereoselectivity without the typically high substrate specificity of enzymes is a challenge in the development of artificial catalysts for asymmetric synthesis. Polyfunctional catalysts are considered to be a promising tool for achieving excellent catalytic efficiency. A polyfunctional catalyst system was developed, which incorporates two Lewis acidic/Brønsted basic cobalt centers in combination with triazolium moieties that are crucial for high reactivity and excellent stereoselectivity in the direct 1,4‐addition of oxindoles to maleimides. The catalyst is assembled through click chemistry and is readily recyclable through precipitation by making use of its charges. Kinetic studies support a cooperative mode of action. Diastereodivergency is achievable with either Boc‐protected or unprotected maleimide.     

Substrate mimetics in protease catalysis: characteristics,kinetics, and synthetic utility

This article reviews the latest developments in protease-catalyzed peptide synthesis focusing on the use of substrate mimetics. The substrate mimetics approach takes advantage of the characteristic of this novel type of substrates to direct the enzyme to recognize an alternative site on the acyl donor, i.e. the site-specific ester leaving group, mediating the acceptance of originally poorly reactive acyl moieties. At first the kinetics and catalytic mechanism of substrate mimetics-mediated reactions are discussed on the basis of hydrolysis, peptide synthesis, protein-ligand docking, and molecular dynamics studies. By the example of the Glu-specific V8 protease and the aromatic amino acid-specific chymotrypsin both the empirical and computer-aided design of specific substrate mimetics is described. The influence of the leaving group specifically recognized by the enzyme is also considered. The benefits of these artificial substrates over common acyl donor components are illustrated by selected synthesis reactions of small peptides, peptide isosteres, non-peptidic carboxylic acid amides, and the coupling of peptide fragments at non-specific ligation sites resulting in biologically active peptide products. Finally, this review focuses on critical syntheses that uses specific-amino acid-containing peptides as the reactants of ligation. Based on these, the restrictions of the substrate mimetics approach is critically discussed and techniques to their overcoming are presented.     

Structure, function and biological relevance of prolyl oligopeptidase

A group of serine peptidases, the prolyl oligopeptidase family, cannot hydrolyze proteins and peptides containing more than 30 residues. The crystal structure of prolyl oligopeptidase (POP) has shown that the enzyme is composed of a peptidase domain with an alpha/beta hydrolase fold and a seven-bladed beta-propeller domain. This domain covers the catalytic triad and excludes large, structured peptides from the active site. The mechanism of substrate selection has been reviewed, along with the binding mode of the substrate and the catalytic mechanism, which differ from that of the classical serine peptidases in several features. POP is essentially a cytosolic enzyme and has been shown to be involved in a number of biological processes, but its precise function is still unknown. Many reports addressed experimentally the possible role of POP in cognitive and psychiatric processes, its involvement in the inositol phosphate signaling pathway, and its ability to metabolize bioactive peptides. Inhibitors were designed to reveal the cellular functions of POP and to treat neurological disorders. Other studies concerned the cellular localization of POP, its presumed interaction with the cytoskeletal elements, and its involvement in peptide/protein transport/secretion processes. The possible role of POP in Alzheimer disease is an intriguing issue, which is still debated. Recently, recombinant bacterial POPs have been investigated as potential therapeutics for celiac sprue, an autoimmune disease of small intestine caused by the intake of gluten proteins.     

Photocatalytic Hydrogen Generation by Vesicle-Embedded [FeFe]Hydrogenase Mimics: A Mechanistic Study

Artificial photosynthesis—the direct photochemical generation of hydrogen from water—is a promising but scientifically challenging future technology. Because nature employs membranes for photodriven reactions, the aim of this work is to elucidate the effect of membranes on artificial photocatalysis. To do so, a combination of electrochemistry, photocatalysis, and time-resolved spectroscopy on vesicle-embedded [FeFe]hydrogenase mimics, driven by a ruthenium tris-2,2′-bipyridine photosensitizer, is reported. The membrane effects encountered can be summarized as follows: the presence of vesicles steers the reactivity of the [FeFe]-benzodithiolate catalyst towards disproportionation, instead of protonation, due to membrane characteristics, such as providing a constant local effective pH, and concentrating and organizing species inside the membrane. The maximum turnover number is limited by photodegradation of the resting state in the catalytic cycle. Understanding these fundamental productive and destructive pathways in complex photochemical systems allows progress towards the development of efficient artificial leaves.     

Steroid Cyclophanes as Artificial Cell-surface Receptors. Molecular Recognition and its Consequence in Signal Transduction Behavior

Steroid cyclophanes, bearing four bile acid moieties covalently placed on a tetraazaparacyclophane skeleton, were designed and synthesized as artificial cell-surface receptors. Guest-binding behavior of the steroid cyclophanes embedded in a bilayer membrane formed with a synthetic peptide lipid was clarified by means of fluorescence and circular dichroism spectroscopy. We found that the steroid cyclophane effectively bound aromatic guests in both bilayer membranes and aqueous solution. In addition, copper(II) ions acted as a guest species for the steroid cyclophane and a competitive inhibitor toward a NADH-dependent lactate dehydrogenase (LDH). On these grounds, we constituted a supramolecular assembly as an artificial signaling system in combination with the steroid cyclophane, a cationic peptide lipid, and LDH. As a consequence, the steroid cyclophane acted as an effective artificial cell-surface receptor being capable of transmitting an external signal to the enzyme in collaboration with copper(II) ions as a signal transmitter.     

Dentin Phosphoprotein Mimetic Peptide Nanofibers Promote Biomineralization

Dentin phosphoprotein (DPP) is a major component of the dentin matrix playing crucial role in hydroxyapatite deposition during bone mineralization, making it a prime candidate for the design of novel materials for bone and tooth regeneration. The bioactivity of DPP‐derived proteins is controlled by the phosphorylation and dephosphorylation of the serine residues. Here an enzyme‐responsive peptide nanofiber system inducing biomineralization is demonstrated. It closely emulates the structural and functional properties of DPP and facilitates apatite‐like mineral deposition. The DPP‐mimetic peptide molecules self‐assemble through dephosphorylation by alkaline phosphatase (ALP), an enzyme participating in tooth and bone matrix mineralization. Nanofiber network formation is also induced through addition of calcium ions. The gelation process following nanofiber formation produces a mineralized extracellular matrix like material, where scaffold properties and phosphate groups promote mineralization. It is demonstrated that the DPP‐mimetic peptide nanofiber networks can be used for apatite‐like mineral deposition for bone regeneration.     

糖簇分子和糖树状分子及其生物学活性

糖簇分子和糖树状分子是近年来发展起来的一类新型糖缀合物,其目的是模拟天然存在的“多元效应”。本文主要综述了目前已知糖簇分子和糖树状分子所具有的生物活性及其潜在的应用领域。     

Elastin-Hyaluronan Bioconjugate as Bioactive Component in Electrospun Scaffolds

Hyaluronic acid or hyaluronan (HA) and elastin-inspired peptides (EL) have been widely recognized as bioinspired materials useful in biomedical applications. The aim of the present work is the production of electrospun scaffolds as wound dressing materials which would benefit from synergic action of the bioactivity of elastin peptides and the regenerative properties of hyaluronic acid. Taking advantage of thiol-ene chemistry, a bioactive elastin peptide was successfully conjugated to methacrylated hyaluronic acid (MAHA) and electrospun together with poly-D,L -lactide (PDLLA). To the best of our knowledge, limited reports on peptide-conjugated hyaluronic acid were described in literature, and none of these was employed for the production of electrospun scaffolds. The conformational studies carried out by Circular Dichroism (CD) on the bioconjugated compound confirmed the preservation of secondary structure of the peptide after conjugation while Scanning Electron Microscopy (SEM) revealed the supramolecular structure of the electrospun scaffolds. Overall, the study demonstrates that the bioconjugation of hyaluronic acid with the elastin peptide improved the electrospinning processability with improved characteristics in terms of morphology of the final scaffolds.     

Influence of the charge relay effect on the silanol condensation reaction as a model for silica biomineralization

The catalytic effect of various sequential peptides for silica biomineralization has been studied. In peptide sequence design, lysine (K) and histidine (H) were selected as the standard amino acids and aspartic acid (D) was selected to promote the charge relay effects, such as in the enzyme active site. Therefore, homopolypeptides (K(10) and H(10)), block polypeptides (K(5)D(5) and H(5)D(5)), and alternate polypeptides [(KD)(5) and (HD)(5)] were designed, and the dehydration reaction ability of trimethylethoxysilane was investigated as a quantitative model of silica mineralization. The catalytic activity per basic residue of alternate polypeptide was the highest because of the charge relay effects at the surface of the peptide. In silica mineralization using tetraethoxysilane, spherical silica particles were obtained, and their size is related to the catalytic activities of the peptides in the model systems. From these results, the effect of the functional group combination by the peptide sequence design enables the control of the efficiency of mineralization and preparation of specific inorganic materials.     

Diverse Approaches for Enantioselective C−H Functionalization Reactions Using Group 9 CpxMIII Catalysts

Transition-metal-catalyzed C−H functionalization reactions with Cp*M^III catalysts (M=Co, Rh, Ir) have found a wide variety of applications in organic synthesis. Albeit the intrinsic difficulties in achieving catalytic stereocontrol using these catalysts due to their lack of additional coordination sites for external chiral ligands and the conformational flexibility of the Cp ligand, catalytic enantioselective C−H functionalization reactions using the Group 9 metal triad with Cp-type ligands have been intensively studied since 2012. In this minireview, the progress in these reactions according to the type of the chiral catalyst used are summarized and discussed. The development of chiral Cp^x ligands the metal complexes thereof, artificial metalloenzymes, chiral carboxylate-assisted enantioselective C−H activations, enantioselective alkylations assisted by chiral carboxylic acids or chiral sulfonates, and chiral transient directing groups are discussed.     

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.