Transient Substrate‐Induced Catalyst Formation in a Dynamic Molecular Network

In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion of the substrate, the network disassembles the catalyst. These results open up new opportunities for controlling catalysis in synthetic chemical systems.     

Designing for sustainability with biocatalytic and chemoenzymatic cascade processes

Cascade reactions have been widely recognized to cut costs, decrease solvent usage, and reduce cycle times in chemical processes. Recently, biocatalytic cascades have altered how we design synthetic routes to complex molecules to achieve sustainable commercial processes for pharmaceutical, agricultural, and fine chemical industries. With advancements in protein engineering and an increase in the number of enzyme classes available to chemists, industrial and academic groups alike have endeavored to expand the scope of biocatalysis from single reactions to multi-enzyme cascades to rapidly build complex molecular structures. Recent reports have drawn inspiration from biosynthetic pathways and have applied engineered enzymes to in vitro enzymatic cascades. Furthermore, combining transition-metal catalysis and enzymes in one-pot chemoenzymatic cascades likewise serves to broaden the scope of biocatalysis, enabling traditional chemical reactions to be performed under mild aqueous conditions. In this article, we review recent biocatalytic and chemoenzymatic cascades from 2019 to 2021.     

酶催化脂肪族聚酯的合成

脂肪族聚酯是一种可生物降解的新型高聚物,可通过化学催化、发酵和酶催化来合成.酶催化合成聚酯是一种新型的环境友好绿色化学技术,可以在温和条件下高效的合成聚酯,有着传统聚合方法难以比拟的优势.尤其是特种酶的应用,为传统方法难以合成的聚酯,开辟了一条新的合成途径.本文综述了脂肪酶催化缩聚、酯交换、内酯开环聚合等聚酯合成方法,并讨论了反应参数(如溶剂、温度、酶和单体的浓度)对反应的影响.     

Genetically Encodable Scaffolds for Optimizing Enzyme Function

Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.     

Enzymatic Reactions using Ionic Liquids for Green Sustainable Chemical Process; Stabilization and Activation of Lipases

The enzymatic reaction is highly respected from an environmentally-friendly point-of-view. Optimization of the reaction media and supporting materials of enzymes must be investigated in parallel with the effort to develop new enzymes. Lipases are frequently used for organic syntheses as synthetic tools even industry because of their acceptance of having a broad range of substrates, stability, and availability. We have investigated the possibility of ILs as both a solvent and activating or stabilization agent of enzymes, in particular, lipase as a model enzyme. ILs allowed recyclable use of a lipase and significant acceleration of transesterification, and also enhanced the stability and reaction activity of a lipase by immobilization through a lyophilization process. We discuss how we enhanced the enzyme capability using the IL engineering focusing on lipase-catalyzed reactions, i. e., realization of the recyclable use of an enzyme, how ILs mediated the enhanced reaction rate, and improved the stability of the enzyme.     

Analytical platforms for activity-based protein profiling--exploiting the versatility of chemistry for functional proteomics

The field of proteomics aims to develop and apply technologies for the characterization of protein function on a global scale. Toward this end, synthetic chemistry has played a major role by providing new reagents to profile segments of the proteome based on activity rather than abundance. Small molecule probes for activity-based protein profiling have been created for more than a dozen enzyme classes and used to discover several enzyme activities elevated in disease states. These innovations have inspired complementary advancements in analytical chemistry, where new platforms have been introduced to augment the information content achievable in chemical proteomics experiments. Here, we will review these analytical platforms and discuss how they have exploited the versatility of chemical probes to gain unprecedented insights into the function of proteins in biological samples of high complexity.     

The Schenck Ene Reaction: Diastereoselective Oxyfunctionalization with Singlet Oxygen in Synthetic Applications

Oxyfunctionalized molecules are principal building blocks in organic synthesis. In cellular processes highly efficient enzymes serve as selective catalysts for the formation of such synthetic units, for example the oxygenases oxyfunctionalize substrates by activating molecular oxygen. To date no comparable effective chemical oxidation system has been found. A useful photochemical process is the oxyfunctionalization of allylic substrates by sensitized photooxygenation, for which molecular oxygen and light serve as natural sources. This allylic oxidation of olefins by the ene reaction with singlet oxygen (Schenck reaction) figures as a highly versatile synthetic method. While the regioselectivity of this transformation has been studied for decades, only during the last years has attention focused on stereocontrol. Through these recent efforts it has become possible to control high stereoselectivity in the photooxygenation of organic substrates. This breakthrough has enhanced substantially the utility of singlet oxygen in diastereoselective synthesis.     

分子印迹技术用于模拟酶及分子反应器的研究进展

分子印迹技术是制备特异性分子识别材料的新技术. 分子印迹聚合物(Molecularly-imprinted polymer, MIP)具有可同酶相媲美的选择性识别能力, 能够催化手性及区域选择性的反应, 是一种新型的分子反应器; 同时MIP具有良好的化学和物理稳定性, 因而在替代酶用于某些苛刻条件下的催化反应方面有良好的应用前景. 就近年来利用MIP模拟酶催化有机合成反应, 以及利用MIP作为分子反应器反面的研究进展进行了综述.     

Protocell Communication through the Eyes of Synthetic Organic Chemists

The bottom-up fabrication of synthetic cells (protocells) from molecules and materials, is a major challenge of modern chemistry. A significant breakthrough has been the engineering of protocells capable of chemical communication using bio-derived molecules and ex situ stabilised cell machineries. These, however, suffer from short shelf-lives, high costs, and require mild aqueous conditions. In this Concept Article we analyse the chemistry at the heart of protocell communication to highlight new opportunities for synthetic chemists in protocell engineering. Specifically, we (i) categorise the main bio-derived chemical communication machineries in enzyme cascades, DNA strand displacement, and gene-mediated communication; (ii) review the chemistries of these signal transduction machineries; and (iii) introduce new types of bio-inspired, fully synthetic artificial enzymes to replace their natural counterparts. Developing protocells that incorporate synthetic analogues of bio-derived signal transduction machineries will improve the robustness, stability, and versatility of protocells, and broaden their applications to highly strategic fields such as photocatalysis and fine chemicals production.     

Bioinspired catalysis at the crossroads between biology and chemistry: A remarkable example of an electrocatalytic material mimicking hydrogenases

There is an increasing need for new, efficient and cheap chemical catalysts, as part of the emerging “green” chemistry field. Living organisms provide a wealth of fascinating enzymes, with exceptional catalytic efficiencies and selectivities, which can be either directly exploited in biotechnological synthetic systems or imitated by chemists. The bioinspired catalysis approach exploits the basic chemical principles on which a biological enzyme active site is built in order to generate original functional analogs of this site. This is illustrated here with a molecular electrode material inspired from hydrogenases, metalloenzymes involved in hydrogen metabolism, and displaying exceptional electrocatalytic properties for hydrogen production and oxidation, thus with potential applications for electrolyzer and fuel cell technologies.     

Creating novel enzymes by applied molecular evolution

Recent molecular techniques have made it feasible to simulate evolutionary processes and apply in vitro selection to evolve enzymes with novel properties that may have potential benefits for medical and industrial applications. The characterization of such mutants has also provided new insights into how molecular structure determines enzyme function.     

Modulating the Biofunctionality of Metal–Organic-Framework-Encapsulated Enzymes through Controllable Embedding Patterns

Embedding an enzyme within a MOF as exoskeleton (enzyme@MOF) offers new opportunities to improve the inherent fragile nature of the enzyme, but also to impart novel biofunctionality to the MOF. Despite the remarkable stability achieved for MOF-embedded enzymes, embedding patterns and conversion of the enzymatic biofunctionality after entrapment by a MOF have only received limited attention. Herein, we reveal how embedding patterns affect the bioactivity of an enzyme encapsulated in ZIF-8. The enzyme@MOF can maintain high activity when the encapsulation process is driven by rapid enzyme-triggered nucleation of ZIF-8. When the encapsulation is driven by slow coprecipitation and the enzymes are not involved in the nucleation of ZIF-8, enzyme@MOF tends to be inactive owing to unfolding and competing coordination caused by the ligand, 2-methyl imidazole. These two embedding patterns can easily be controlled by chemical modification of the amino acids of the enzymes, modulating their biofunctionality.     

Halogenation in Fungi: What Do We Know and What Remains to Be Discovered?

In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.     

Enzyme activity and stability control by amphiphilic self-organizing systems in aqueous solutions

The interaction of surfactants with proteins in aqueous solutions has been the subject of many investigations to understand the interactions between membrane proteins and lipids, structurally similar to synthetic surfactants. The effect of surfactant on enzyme structure and activity is the result of chemically selective interactions that may be influenced both by the enzyme structure and by the chemistry of the surfactant. For many years, surfactants have been considered as non-specific denaturants of proteins, even if in the literature several of them are reported to enhance activity and/or stability of some enzymes: the detergent can interact with the enzyme and cause a conformational change to a more active form and/or stabilize its native folded structure. Although the surfactant head group seems to have a determining role, other structural features of the detergent are also important in influencing the catalytic properties of an enzyme, i.e. head group size and its hydrophobic/hydrophilic balance. Up to now it is very difficult to predict the molecular features of the surfactant and an extensive investigation on the relationship between the surfactant chemical structure and the catalytic properties of enzyme is still required.     

Recent progress on immobilization of enzymes on molecular sieves for reactions in organic solvents

Enzymes exhibit high selectivity and reactivity under normal conditions but are sensitive to denaturation or inactivation by pH and temperature extremes, organic solvents, and detergents. To extend the use of these biocatalysts for practical applications, the technology of immobilization of enzymes on suitable supports was developed. Recently, these immobilized biomolecules have been widely used and a variety of immobilization supports have been studied. The majority of these supports cover diverse kinds of materials such as natural or synthetic polyhydroxylic matrives, porous in organic carriers, and all kinds of functional polymers. Microporous molecular sieve, zeolite, has attracted extensive interest in research because of its distinctive physical properties and geochemistry. Recently, with the discovery of a new family of mesoporous molecular sieves, MCM-41, this series of materials shows great potential for various applications. Molecular sieves involve such a series of materials that can discriminate between molecules, particularly on the basis of size. As support materials, they offer interesting properties, such as high surface areas, hydrophobic or hydrophilic behavior, and electrostatic interaction, as well as mechanical and chemical resistance, making them attractive for enzyme immobilization. In this article, different types of molecular sieves used in different immobilization methods including physical adsorption on zeolite, entrapment in mesoporous and macroporous MCM series, as well as chemically covalent binding to functionalized molecular sieves are reviewed. Key factors affecting the application of this biotechnology are discussed systematically, and immobilization mechanisms combined with newly developed techniques to elucidate the interactions between matrixes and enzyme molecules are also introduced.     

Modulating the Biofunctionality of Metal–Organic‐Framework‐Encapsulated Enzymes through Controllable Embedding Patterns

Embedding an enzyme within a MOF as exoskeleton (enzyme@MOF) offers new opportunities to improve the inherent fragile nature of the enzyme, but also to impart novel biofunctionality to the MOF. Despite the remarkable stability achieved for MOF‐embedded enzymes, embedding patterns and conversion of the enzymatic biofunctionality after entrapment by a MOF have only received limited attention. Herein, we reveal how embedding patterns affect the bioactivity of an enzyme encapsulated in ZIF‐8. The enzyme@MOF can maintain high activity when the encapsulation process is driven by rapid enzyme‐triggered nucleation of ZIF‐8. When the encapsulation is driven by slow coprecipitation and the enzymes are not involved in the nucleation of ZIF‐8, enzyme@MOF tends to be inactive owing to unfolding and competing coordination caused by the ligand, 2‐methyl imidazole. These two embedding patterns can easily be controlled by chemical modification of the amino acids of the enzymes, modulating their biofunctionality.     

Enzymes immobilized in mesoporous silica: A physical–chemical perspective

Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.     

In Vivo EPR Characterization of Semi‐Synthetic [FeFe] Hydrogenases

EPR spectroscopy reveals the formation of two different semi‐synthetic hydrogenases in vivo. [FeFe] hydrogenases are metalloenzymes that catalyze the interconversion of molecular hydrogen and protons. The reaction is catalyzed by the H‐cluster, consisting of a canonical iron–sulfur cluster and an organometallic [2Fe] subsite. It was recently shown that the enzyme can be reconstituted with synthetic cofactors mimicking the composition of the [2Fe] subsite, resulting in semi‐synthetic hydrogenases. Herein, we employ EPR spectroscopy to monitor the formation of two such semi‐synthetic enzymes in whole cells. The study provides the first spectroscopic characterization of semi‐synthetic hydrogenases in vivo, and the observation of two different oxidized states of the H‐cluster under intracellular conditions. Moreover, these findings underscore how synthetic chemistry can be a powerful tool for manipulation and examination of the hydrogenase enzyme under in vivo conditions.     

Current advances in microbial cell factories for lactate-based polyesters driven by lactate-polymerizing enzymes: Towards the further creation of new LA-based polyesters

Polylactic acid (PLA), a representative bio-based polyester, has been commonly synthesized via a multi-step by chemical process. The current modes of generating PLA involve microbial fermentation of starting material, lactic acid (LA), followed by chemical ring-opening polymerization. Recently, one-pot complete bioprocess for LA-based polyesters has been established as a microbial cell factory (MCF). The concept is a process conversion from the usual chemical factory to the MCF. This new challenge was triggered by discovery of an engineered LA-polymerizing enzyme (LPE). The LPE was found as one of the members of an extensive mutant library that has been created through the long-term evolutionary engineering study of natural biopolyester-synthesizing enzymes. Needless to say, a strategic method of getting the beneficial mutation in the enzyme is of the utmost importance and an essential step towards accomplishing the desired purpose, the acquisition of the LA-polymerizing activity in this case. In this review, the structures and properties of LPE-catalyzed polymerization products will be discussed as well as backgrounds on establishment of the MCFs for synthesis of LA-based polyesters. Also, experimental strategies for enrichment of the LA fraction will be proposed to further advance the prototype of MCF based on the related metabolic pathways.