An Artificial Enzyme for Asymmetric Nitrocyclopropanation of α,β-Unsaturated Aldehydes - Design and Evolution

The introduction of an abiological catalytic group into the binding pocket of a protein host allows for the expansion of enzyme chemistries. Here, we report the generation of an artificial enzyme by genetic encoding of a non-canonical amino acid that contains a secondary amine side chain. The non-canonical amino acid and the binding pocket function synergistically to catalyze the asymmetric nitrocyclopropanation of α,β-unsaturated aldehydes by the iminium activation mechanism. The designer enzyme was evolved to an optimal variant that catalyzes the reaction in high yield with high diastereo- and enantioselectivity. This work demonstrates the application of genetic code expansion in enzyme design and expands the scope of enzyme-catalyzed abiological reactions.

Proteolytic polymer: polyacrylamides functionalized with amino acids cleave bovine and human serum albumins

Polyacrylamides with various compositions of serine, aspartic acid, and histidine, which are the amino acids involved in the catalytic triad of natural serine protease chymotrypsin, were synthesized and their protein cleavage activity was investigated. SDS-PAGE analysis showed that some of the synthesized ternary copolymers showed cleavage activity against bovine and human serum albumins. Polyacrylamides incorporating a single type of amino acid were also able to cleave the protein substrates. These homopolymers exhibited unique cleavage profiles and pH and temperature sensitivities that differed from those of α-chymotrypsin. The results indicate the potential of polymers functionalized with amino acids as proteolytic artificial enzymes.

Probing the effect of microenvironment on the enzyme-like behavior of catalytic peptide assemblies

As bridging species between short peptides and macromolecular proteins, peptide assemblies not only provide a supramolecular approach for the fabrication of controllable molecular machines with enzyme-like functions, but also a simplified model for understanding the catalytic mechanism of natural enzymes. In this study, we focused on probing the effect of microenvironment on the catalytic behavior of peptide assemblies. Upon simply replacing the X residue in Fmoc-FFXAH-CONH2, we realized the modulation of the microenvironment of the amyloid assemblies, which thus appeared esterase-like function with different catalytic abilities. The chemistry, structure and activity were analyzed to explore the principles that how the hydrophobic, charged, polar and chiral microenvironment deciding the catalytic behavior of the esterase mimic. In addition, we also presented the potential of the catalytic assemblies in the encapsulation, delivery and enzymatic metabolization of a mutual prodrug. This work sheds new insights for understanding the structure-function relationship of catalytic peptide assemblies and natural enzymes, and also provides a new avenue for the designing of artificial enzymes with better functions.

Precisely controlled and deeply penetrated micro-nano hybrid multifunctional motors with enhanced antibacterial activity against refractory biofilm infections

The biofilm resistance of microorganisms has severe economic and environmental implications, especially the contamination of facilities associated with human life, including medical implants, air-conditioning systems, water supply systems, and food-processing equipment, resulting in the prevalence of infectious diseases. Once bacteria form biofilms, their antibiotic resistance can increase by 10-1,000-fold, posing a great challenge to the treatment of related diseases. In order to overcome the contamination of bacterial biofilm, destroying the biofilm's matrix so as to solve the penetration depth dilemma of antibacterial agents is the most effective way. Here, a magnetically controlled multifunctional micromotor was developed by using H₂O₂ as the fuel and MnO₂ as the catalyst to treat bacterial biofilm infection. In the presence of H₂O₂, the as-prepared motors could be self-propelled by the generated oxygen microbubbles. Thereby, the remotely controlled motors could drill into the EPS of biofilm and disrupt them completely with the help of bubbles. Finally, the generated highly toxic •OH could efficiently kill the unprotected bacteria. This strategy combined the mechanical damage, highly toxic •OH, and precise magnetic guidance in one system, which could effectively eliminate biologically infectious fouling in microchannels within 10 min, possessing a wide range of practical application prospects especially in large scale and complex infection sites.

Antioxidant colloids via heteroaggregation of cerium oxide nanoparticles and latex beads

Antioxidant colloids were developed via controlled heteroaggregation of cerium oxide nanoparticles (CeO₂ NPs) and sulfate-functionalized polystyrene latex (SL) beads. Positively charged CeO₂ NPs were directly immobilized onto SL particles of opposite surface charge via electrostatic attraction (SL/Ce composite), while negatively charged CeO₂ NPs were initially functionalized with poly(diallyldimethylammonium chloride) (PDADMAC) polyelectrolyte and then, aggregated with the SL particles (SPCe composite). The PDADMAC served to induce a charge reversal on CeO₂ NPs, while the SL support prevented nanoparticle aggregation under conditions, where the dispersions of bare CeO₂ NPs were unstable. Both SL/Ce and SPCe showed enhanced radical scavenging activity compared to bare CeO₂ NPs and were found to mimic peroxidase enzymes. The results demonstrate that SL beads are suitable supports to formulate CeO₂ particles and to achieve remarkable dispersion storage stability. The PDADMAC functionalization and immobilization of CeO₂ NPs neither compromised the peroxidase-like activity nor the radical scavenging potential. The obtained SL/Ce and SPCe artificial enzymes are foreseen to be excellent antioxidant agents in various applications in the biomedical, food, and cosmetic industries.

An artificial metalloprotein with metal-adaptive coordination sites and Ni-dependent quercetinase activity

Engineering non-native metal active sites into proteins using canonical amino acids offers many advantages but is hampered by significant challenges. The TIM barrel protein, imidazole glycerol phosphate synthase from the hyperthermophilic organism Thermotoga maritima (tHisF), is well-suited for the construction of artificial metalloenzymes by this approach. To this end, we have generated a tHisF variant (tHisF^EHH) with a Glu/His/His motif for metal ion coordination. Crystal structures of Zn^II:tHisF^EHH and Ni^II:tHisF^EHH reveal that both metal ions bind to the engineered histidines. However, the two metals bind at distinct sites with different geometries, demonstrating the adaptability of tHisF. Only Zn^II additionally ligates the Glu residue and adopts a tetrahedral geometry. The pseudo-octahedral Ni^II site comprises the two His and a native Ser residue. Ni^II:tHisF^EHH catalyzes the oxidative cleavage of the flavanols quercetin and myricetin, providing an unprecedented example of an artificial metalloprotein with quercetinase activity.

On paper synthesis of multifunctional CeO2 nanoparticles@Fe-MOF composite as a multi-enzyme cascade platform for multiplex colorimetric detection of glucose, fructose, sucrose, and maltose

This study reports an economical and portable point-of-care (POC) monitoring device based on artificial multi-enzyme cascade systems for multiple detection purposes. The device was made up of a disposable three dimensional microfluidic paper-based analytical device (3D μPAD) with multiple detection zones and a smartphone readout. On-paper synthesis of a multifunctional mimetic composite, based on the CeO₂ nanoparticles embedded in the amino-functionalized Fe metal-organic frameworks (CeO₂@NH₂-MIL-88B(Fe)), for cascade reactions was the main achievement of this work. The 3D μPAD was applied for simultaneous quantification of glucose, fructose, sucrose and maltose, and the detection process consisted of the enzymatic reaction of each sugar by anchored enzymes on the metal-organic frameworks (MOF) and successive oxidation of 3,3',5,5'-tetramethylbenzidine (TMB). Utilizing the new artificial mimicking system improved the color development uniformity and resulted in a reliable detection tool, with excellent detection limits in the range of 20-280 μM. It was directly applied to analyze the sugars levels of human total blood, urine, semen, honey and juice samples with the relative errors of less than 7.7% compared with the HPLC method. The cost-effective and easy-to-use μPAD has a great potential to be used in either medical diagnostics or the food industry. Also, it can be considered as a competitive POC method for patients in disadvantaged communities or emergencies.

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.

Enhancing promiscuous chemistries of a Schiff-base forming enzyme by divergent evolution

Directed evolution has emerged as a powerful technique for the rapid tailoring of enzymes toward particular synthetic demands, spawning a number of enzymes capable of complex chemical transformations. During random mutagenesis of a protein, changes in fitness must be assayed in order to quantify and understand the relative effect a given mutation has, and the assay employed must be carefully chosen to report directly on the transformation of interest. Here, we describe a series of medium-throughput screening techniques that have been utilized for the evolution and engineering of an artificial carboligase, RA95.5-8, resulting in improvement of catalytic efficiency of a number of promiscuous chemistries. The methods make use of common analytical chemistry equipment and low-cost materials, and may help inspire development of novel screening workflows for related transformations.

A series of MOF/Ce-based nanozymes with dual enzyme-like activity disrupting biofilms and hindering recolonization of bacteria

Notorious bacterial biofilms are becoming severe threats to public health worldwide. As the important component in biofilm extracellular polymeric substances (EPS), extracellular DNA (eDNA) has been manifested to connect different EPS components and bacteria together, leading biofilms hard to eliminate. Herein a series of MOF/Ce-based nanozymes with deoxyribonuclease (DNase) and peroxidase mimetic activities have been designed and synthesized for combating biofilms. The cerium (IV) complexes (DNase mimics) are capable of hydrolyzing eDNA and disrupting established biofilms, while the MOF with peroxidase-like activity can kill bacteria exposed in dispersed biofilms in the presence of H₂O₂. This can avoid the recolonization of bacteria and recurrence of biofilms. Given the fact that single-modal antibacterial agent is difficult to drastically eradicate biofilms, the marriage of two kinds of nanozymes is a rational strategy to acquire enhanced performance in combating biofilms. Besides, the utilization of nanozymes circumvents drawbacks of natural enzymes which are costly and vulnerable. Further studies have demonstrated that this kind of artificial enzyme with dual enzyme-mimetic activities can penetrate the biofilms, and inhibit bacterial biofilm formation intensively. Consistently, in vivo anti-biofilm application in treating subcutaneous abscess exhibits commendable wound healing and admirable bactericidal effect. To the best of our knowledge, it is the first time to devise an integrated nanozyme based on the peroxidase-like activity of MOF to eliminate biofilms and kill bacteria on site. This work may promote the application of MOF in the antibacterial field.

A multicolorimetric assay for rapid detection of Listeria monocytogenes based on the etching of gold nanorods

Listeria monocytogenes (L. monocytogenes) is one of the most common food-borne pathogens. The authors describe a sensitive and reliable multicolorimetric assay for L. monocytogenes using a sensing system based on TMB²⁺ etching of gold nanorods. Apt-MNP was used as the capture probe, and IgY-BSA-MnO₂ NPs was chosen as an oxidase-like nano-artificial enzyme to oxidize TMB to generate TMB²⁺. Under the optimized conditions, the longitudinal shift of localized surface plasmon resonances had a linear correlation with the L. monocytogenes concentration in the range between 10 to 10⁶ cfu mL^-1. Meanwhile, the sensing system can generate vivid color responses as colorful as a rainbow, and the limit of detection is as low as 10 cfu mL^-1 at a glance. Recoveries ranging from 97.4 to 101.3% are found when analyzing spiked food samples without pre-enrichment. In our perception, it shows promise in rapid instrumental and on-site visual detection of L. monocytogenes.

Catalytic degradation of organophosphorous nerve agent simulants by polymer beads@graphene oxide with organophosphorus hydrolase-like activity based on rational design of functional bimetallic nuclear ligand

The degradation of organophosphorous nerve agents is of primary concern due to the severe toxicity of these agents. Based on the active center of organophosphorus hydrolase (OPH), a bimetallic nuclear ligand, (5-vinyl-1,3-phenylene)bis(di(1H-imidazol-2-yl) methanol) (VPIM), was designed and synthesized, which contains four imidazole groups to mimic the four histidines at OPH active center. By grafting VPIM on graphene oxide (GO) surface via polymerization, the VPIM-polymer beads@GO was produced. The obtained OPH mimics has an impressive activity in dephosphorylation reactions (turnover frequency (TOF) towards paraoxon: 2.3 s^-1). The synergistic catalytic effect of the bimetallic Zn²⁺ nuclear center and carboxyl groups on surface of GO possibly contributes to the high hydrolysis on organophosphate substrate. Thus, a biomimetic catalyst for efficient degradation of some organophosphorous nerve agent simulants, such as paraoxon and chlorpyrifos, was prepared by constructing catalytic active sites. The proposed mechanism and general synthetic strategy open new avenues for the engineering of functional GOs for biomimetic catalysts.

Construction of Artificial Enzymes on a Virus Surface

Combination of artificial enzyme design and self-assembly strategies leads to a novel way to construct supramolecular enzymes. To address this challenge, auxotrophic expression systems show great potential because they can introduce nonnatural catalytic groups into the subunits of protein assemblies. Among nonnatural amino acids, selenocysteine is the catalytic group of glutathione peroxidase (GPx). With the aid of computer simulation, we have incorporated selenocysteine into natural protein assemblies such as tobacco mosaic virus (TMV) and ferritin by cysteine auxotrophic technology, resulting in the conversion of TMV and ferritin into supramolecular enzymes.

The first protection-free synthesis of magnetic bifunctional l-proline as a highly active and versatile artificial enzyme: Synthesis of imidazole derivatives

l-Proline is a bifunctional versatile organocatalyst that could promote a variety of useful transformations. Some passive and dynamic interactions between this simple amino acid and different substrates, which are necessary to enzymatic reactions, have given it "the simplest enzyme" title. Herein we presented the first report on the synthesis of magnetic bifunctional l-proline as an artificial enzyme without requiring any protection/deprotection steps according to an operationally simple process. This magnetic nano-biocatalyst is a promising catalyst that in a case study was successfully applied for the synthesis of 2,4,5-trisubstituted and 1,2,4,5-tetrasubstituted imidazoles in the 70-99% and 60-90% yields respectively, which it could be extended to the variety of l-proline-based organic transformations. The synergic effect of bifunctional l-proline shell as catalytic active site and magnetite nanoparticles core, which could function as protein mimics endow it high efficiency, versatility, recoverability, reusability and good turnover frequency, which are necessary characters for artificial enzymes' designing.

Remarkable reactivity of alkoxide/acetato-bridged binuclear copper(II) complex as artificial carboxylesterase

Bromo-containing binuclear Schiff base copper(II) complex, Cu₂L(OAc), with an alkoxo/acetato-bridged moiety was employed as a model of carboxylesterases to promote the hydrolytic cleavage of p-nitrophenyl picolinate (PNPP). Furthermore, the reactivity of a mononuclear complex (CuHL) was evaluated for comparing it with that of binuclear one. The results reveal that the as-prepared binuclear Cu₂L(OAc) efficiently accelerated the hydrolysis of PNPP, giving rise to excess four orders of magnitude rate enhancement in contrast to the un-catalyzed reaction. Cu₂L(OAc) represented an enzyme-like bell-shaped pH-responsive kinetic behavior. Moreover, the binuclear one is more reactive than its mononuclear analogue (CuHL) by two orders of magnitude. The total efficiency of Cu₂L(OAc) is about 61-fold than that of its mononuclear analogue, CuHL. In addition, a contrast experiment reveals that binuclear Cu₂L(OAc) displayed good activity in the hydrolysis of PNPP as well another active ester, i.e., S-2-benzothiazolyl 2-amino-alpha-(methoxyimino)-4-thiazolethiolacetate (AE-active ester). Noteworthyly, it was found that mononuclear one inspired more obvious rate enhancement in the hydrolysis of AE-active ester relative to PNPP hydrolysis. The estimated pK _a1 of bound water on the binuclear Cu₂L(OAc) using second derivative method (SDM) is relatively smaller than that for CuHL by a gap of about 0.8 pK unit, which facilitates the hydrolysis of PNPP. Four orders of magnitude rate enhancement was observed for the catalytic hydrolysis of p-nitrophenyl picolinate (PNPP) by one μ-alkoxide/acetato-bridged binuclear copper(II) complex under physiological conditions. Substrate specificity of the resulting binuclear complexes was observed for the hydrolysis of PNPP and AE-active ester.

Establishing catalytic activity on an artificial (βα)8-barrel protein designed from identical half-barrels

It has been postulated that the ubiquitous (βα)8-barrel enzyme fold has evolved by duplication and fusion of an ancestral (βα)4-half-barrel. We have previously reconstructed this process in the laboratory by fusing two copies of the C-terminal half-barrel HisF-C of imidazole glycerol phosphate synthase (HisF). The resulting construct HisF-CC was stepwise stabilized to Sym1 and Sym2, which are extremely robust but catalytically inert proteins. Here, we report on the generation of a circular permutant of Sym2 and the establishment of a sugar isomerization reaction on its scaffold. Our results demonstrate that duplication and mutagenesis of (βα)4-half-barrels can readily lead to a stable and catalytically active (βα)8-barrel enzyme.