Efficient Base-Catalyzed Kemp Elimination in an Engineered Ancestral Enzyme

The routine generation of enzymes with completely new active sites is a major unsolved problem in protein engineering. Advances in this field have thus far been modest, perhaps due, at least in part, to the widespread use of modern natural proteins as scaffolds for de novo engineering. Most modern proteins are highly evolved and specialized and, consequently, difficult to repurpose for completely new functionalities. Conceivably, resurrected ancestral proteins with the biophysical properties that promote evolvability, such as high stability and conformational diversity, could provide better scaffolds for de novo enzyme generation. Kemp elimination, a non-natural reaction that provides a simple model of proton abstraction from carbon, has been extensively used as a benchmark in de novo enzyme engineering. Here, we present an engineered ancestral β-lactamase with a new active site that is capable of efficiently catalyzing Kemp elimination. The engineering of our Kemp eliminase involved minimalist design based on a single function-generating mutation, inclusion of an extra polypeptide segment at a position close to the de novo active site, and sharply focused, low-throughput library screening. Nevertheless, its catalytic parameters (k_cat/K_M~2·10⁵ M⁻¹ s⁻¹, k_cat~635 s⁻¹) compare favorably with the average modern natural enzyme and match the best proton-abstraction de novo Kemp eliminases that are reported in the literature. The general implications of our results for de novo enzyme engineering are discussed.     

Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases

Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high‐volume, low‐price sectors, such as polymers, to low‐volume, high‐price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas‐phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a “synthetic platform technology”. Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2‐arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.     

Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization

The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.     

C−H Amination via Nitrene Transfer Catalyzed by Mononuclear Non-Heme Iron-Dependent Enzymes

Expanding the reaction scope of natural metalloenzymes can provide new opportunities for biocatalysis. Mononuclear non-heme iron-dependent enzymes represent a large class of biological catalysts involved in the biosynthesis of natural products and catabolism of xenobiotics, among other processes. Here, we report that several members of this enzyme family, including Rieske dioxygenases as well as α-ketoglutarate-dependent dioxygenases and halogenases, are able to catalyze the intramolecular C−H amination of a sulfonyl azide substrate, thereby exhibiting a promiscuous nitrene transfer reactivity. One of these enzymes, naphthalene dioxygenase (NDO), was further engineered resulting in several active site variants that function as C−H aminases. Furthermore, this enzyme could be applied to execute this non-native transformation on a gram scale in a bioreactor, thus demonstrating its potential for synthetic applications. These studies highlight the functional versatility of non-heme iron-dependent enzymes and pave the way to their further investigation and development as promising biocatalysts for non-native metal-catalyzed transformations.     

Production of biodiesel by esterification of natural fatty acids over modified organoclay catalysts

Biodiesel has been produced by esterification of natural fatty acids with methanol in the presence of a modified bentonite with 1-benzyl-1H-benzimidazole-based Brønsted acidic ionic liquids as catalysts. The effect of reaction temperature, type and amount of catalyst, molar ratio and reaction time was investigated. The results showed that MB3B (bentonite modified with 3,3′-(butane-1,6-diyl)bis(6-sulfo-1-(4-sulfobenzyl)-1H-benzimidazolium) hydrogensulfate) has the highest catalytic activity and best recyclability under the optimized reaction conditions. Thus, this modified bentonite is able to catalyze the esterification of oleic acid to its methyl ester in 6 h with yields of more than 92%. The catalytic activity of MB3B for the esterification of natural other fatty acids and alcohols has also been studied.     

Systematic regulation of the enzymatic activity of phenylacetaldoxime dehydratase by exogenous ligands

Phenylacetaldoxime dehydratase from Bacillus sp. OxB-1 (OxdB) contains a heme that acts as the active site for the dehydration reaction of aldoxime. Ferrous heme is the active form, in which the heme is five coordinate with His282 as a proximal ligand. In this work, we evaluated the functional role of the proximal ligand for the catalytic properties of the enzyme by "the cavity mutant technique". The H282G mutant of OxdB lost enzymatic activity, although the heme, which was five coordinate with a water molecule (or OH-) as an axial ligand, existed in the protein matrix. The enzymatic activity was rescued by imidazole or pyridine derivatives that acted as the exogenous proximal ligand. By changing the electron-donation ability of the exogenous ligand with different substituents, the enzymatic activity could be regulated systematically. The stronger the electron-donation ability of the exogenous ligand, the higher was the restored enzymatic activity. Interestingly, H282G OxdB with 2-methyl imidazole showed a higher activity than the wild-type enzyme. Kinetic analyses revealed that the proximal His regulated not only the affinity of substrate binding to the heme but also the elimination of the OH group from the substrate.     

Non‐natural Olefin Cyclopropanation Catalyzed by Diverse Cytochrome P450s and Other Hemoproteins

Recent work has shown that engineered variants of cytochrome P450_BM3 (CYP102A1) efficiently catalyze non‐natural reactions, including carbene and nitrene transfer reactions. Given the broad substrate range of natural P450 enzymes, we set out to explore if this diversity could be leveraged to generate a broad panel of new catalysts for olefin cyclopropanation (i.e., carbene transfer). Here, we took a step towards this goal by characterizing the carbene transfer activities of four new wild‐type P450s that have different native substrates. All four were active and exhibited a range of product selectivities in the model reaction: cyclopropanation of styrene by using ethyl diazoacetate (EDA). Previous work on P450_BM3 demonstrated that mutation of the axial coordinating cysteine, universally conserved among P450 enzymes, to a serine residue, increased activity for this non‐natural reaction. The equivalent mutation in the selected P450s was found to activate carbene transfer chemistry both in vitro and in vivo. Furthermore, serum albumins complexed with hemin were also found to be efficient in vitro cyclopropanation catalysts.     

天然油脂制备生物柴油新技术研究——油脂制备生物柴油的催化剂选择及优化组合

以不同油脂为原料制备生物柴油,对各类催化剂催化活性进行了研究;利用气相色谱及化学分析法,对各类催化剂进行了优化组合。结果表明,对于酸值低于10的油脂,碱性催化剂由于催化效果好,反应时间短,是首选的理想催化剂;而对于酸值高于10的油脂,无论酸性还是碱性催化剂,均难于在短时间内完成酯化反应。自配的NG催化剂,在质量分类(相对油脂质量)为0.1%,反应温度180℃,反应时间为2 h的条件下,反应转化率达到93%,有望作为亚临界状态下制备生物柴油理想的催化剂。     

Bifunctional asymmetric catalysis: cooperative Lewis acid/base systems

In the field of catalytic, asymmetric synthesis, there is a growing emphasis on multifunctional systems, in which multiple parts of a catalyst or multiple catalysts work together to promote a specific reaction. These efforts, in part, are result-driven, and they are also part of a movement toward emulating the efficiency and selectivity of nature's catalysts, enzymes. In this Account, we illustrate the importance of bifunctional catalytic methods, focusing on the cooperative action of Lewis acidic and Lewis basic catalysts by the simultaneous activation of both electrophilic and nucleophilic reaction partners. For our part, we have contributed three separate bifunctional methods that combine achiral Lewis acids with chiral cinchona alkaloid nucleophiles, for example, benzoylquinine (BQ), to catalyze highly enantioselective cycloaddition reactions between ketene enolates and various electrophiles. Each method requires a distinct Lewis acid to coordinate and activate the electrophile, which in turn increases the reaction rates and yields, without any detectable influence on the outstanding enantioselectivities inherent to these reactions. To place our results in perspective, many important contributions to this emerging field are highlighted and our own reports are chronicled.     

Design of Artificial Enzymes Bearing Several Active Centers: New Trends,Opportunities and Problems

Harnessing enzymes which possess several catalytic activities is a topic where intense research has been carried out, mainly coupled with the development of cascade reactions. This review tries to cover the different possibilities to reach this goal: enzymes with promiscuous activities, fusion enzymes, enzymes + metal catalysts (including metal nanoparticles or site-directed attached organometallic catalyst), enzymes bearing non-canonical amino acids + metal catalysts, design of enzymes bearing a second biological but artificial active center (plurizymes) by coupling enzyme modelling and directed mutagenesis and plurizymes that have been site directed modified in both or in just one active center with an irreversible inhibitor attached to an organometallic catalyst. Some examples of cascade reactions catalyzed by the enzymes bearing several catalytic activities are also described. Finally, some foreseen problems of the use of these multi-activity enzymes are described (mainly related to the balance of the catalytic activities, necessary in many instances, or the different operational stabilities of the different catalytic activities). The design of new multi-activity enzymes (e.g., plurizymes or modified plurizymes) seems to be a topic with unarguable interest, as this may link biological and non-biological activities to establish new combo-catalysis routes.     

Fusion Enzymes Involved in Biosynthetic Tailoring Reactions in Fungi

Enzyme fusion, the fusion of enzymes with different domains to a single protein, has been widely recognized as a promising strategy in the development of biocatalysts. Nature has evolved gene fusion to combine different catalytic enzymes to function as a fusion enzyme, and this strategy is utilized in many natural product biosynthetic pathways. Owing to rapid advances in genome sequencing and biosynthetic pathway characterization, there is increasing interest in fusion enzymes from fungal biosynthetic pathways, particularly those involved in tailoring steps. This concept aims to provide an up-to-date overview of fusion enzymes that catalyze tailoring reactions in the biosynthesis of fungal secondary metabolites. Since fungal fusion enzymes are often associated with novel metabolites, this pioneering work may stimulate the exploration of the structural diversity of fungal natural products through genome mining of the untapped biosynthetic pathways involving fusion enzymes.     

非均相金属钯配体催化剂的研究进展

Suzuki-Miyaura反应是一类具有工业化应用前景的C-C键合成反应。反应多数是在均相金属钯配体催化剂催化下完成。均相催化具有催化效率高、产品选择性好等优点,但催化剂回收困难,增加了反应成本,限制了其应用。非均相金属钯配体催化剂是将均相金属钯配体催化剂固载到载体上,使其在不影响反应活性和选择性的同时,实现循环使用,已成为Suzuki-Miyau-ra反应的研究热点。对几年来以有序介孔材料MCM-41和SBA-15、无机载体SiO2和Al2O3、聚苯乙烯和聚乙二醇等合成材料以及天然高分子材料为载体,制备非均相金属钯配体催化剂的方法及其催化性能进行了综述。     

Proteolytic Antibodies

Catalytic activities are known to arise naturally in antibodies. Several naturally-occurring peptides, synthetic protease substrates, DNA, and esters are known to be cleaved by antibodies. There is increased production of antigen-specific catalytic antibodies in autoimmune disease. Polyreactive catalytic antibodies are present in unimmunized donors. Antibody light chains isolated from multiple myeloma patients frequently express proteolytic activity. Immunization protocols using as immunogens the ground state of a naturally-occurring polypeptide, anti-enzyme antibodies, or the enzyme itself are known to provoke catalytic antibody synthesis. Active site residues in the light chain subunit serve as the catalytic residues in a model antibody with peptide bond cleaving activity. A split-site model in which distinct amino acids serve as the essential catalytic residues and substrate ground-state recognition residues has been developed from mutagenesis studies. Engineering of the available antibodies could potentially generate improved catalysts. The possible mechanisms underlying proteolysis by natural antibodies and evolution of the catalytic activity are reviewed.     

Biohybrid Systems for Improved Bioinspired,Energy-Relevant Catalysis

Biomimetic catalysts, ranging from small-molecule metal complexes to supramolecular assembles, possess many exciting properties that could address salient challenges in industrial-scale manufacturing. Inspired by natural enzymes, these biohybrid catalytic systems demonstrate superior characteristics, including high activity, enantioselectivity, and enhanced aqueous solubility, over their fully synthetic counterparts. However, instability and limitations in the prediction of structure-function relationships are major drawbacks that often prevent the application of biomimetic catalysts outside of the laboratory. Despite these obstacles, recent advances in synthetic enzyme models have improved our understanding of complicated biological enzymatic processes and enabled the production of catalysts with increased efficiency. This review outlines important developments and future prospects for the design and application of bioinspired and biohybrid systems at multiple length scales for important, biologically relevant, clean energy transformations.     

过渡金属催化5-羟甲基糠醛合成2,5-呋喃二甲酸研究进展

随着绿色合成理念的不断提升,以具有高催化活性、高稳定性及价格低廉等优势的过渡金属催化剂代替强氧化剂和贵金属催化剂催化氧化5-羟甲基糠醛(HMF)制备精细化学品,逐渐成为研究者关注的焦点。本文综述了近年来廉价过渡金属基催化剂用于催化HMF氧化制备2,5-呋喃二甲酸(FDCA)的相关研究,对该领域的最新研究进行了叙述,重点介绍了锰基、铜基、铁/钴基、镍基及其他催化体系在HMF氧化反应中的应用,主要包括锰基金属氧化物、CuCl_(2)催化体系、Fe_(3)O_(4)-CoO_(x)的磁性催化体系等。此外,在介绍上述催化剂的基础上,还对廉价过渡金属基催化剂催化HMF氧化制备FDCA的发展前景进行了展望。     

Oxidation Catalysis by Supported Gold Nano-Clusters

The historical notion regarding the inability of gold to catalyze reactions has been discarded in view of recent studies, which have clearly demonstrated the high catalytic efficiency of supported nano-gold catalysts. Although nano-Au catalysts are known to catalyze a variety of reactions, the major focus has been on CO oxidation catalysis. In this work we focus on the important aspects related to the CO oxidation reaction. Special emphasis is placed on the studies undertaken on model nano-Au systems as these studies have considerably enhanced the understanding of the oxidation process. Gold in a highly dispersed state can selectively oxidize CO in the presence of excess hydrogen (of tremendous interest to state-of-the-art low-temperature fuel cells); related studies are addressed in this review. The nano-gold catalysts have also been investigated for the direct vapor-phase oxidation of propylene to propylene oxide in the presence of molecular oxygen; these investigations are highlighted in this work.     

The direct catalytic asymmetric mannich reaction

The direct catalytic asymmetric addition of unmodified carbonyl compounds to preformed or in situ-generated imines has emerged as a promising new route to optically enriched alpha- and beta-amino acid derivatives, beta-lactams, and 1,2- and gamma-amino alcohols. The direct catalytic asymmetric Mannich reactions are mediated by small organometallic and organic amine catalysts that can achieve levels of selectivity similar to those possible with natural enzymes. The different small-molecule catalysts described here are complementary in their applications. They also complement each other in syn or anti selectivity of the direct asymmetric Mannich reaction. In this Account, we highlight the recent developments in and contributions to this research.     

联萘酚纳米孔道配位聚合物催化剂的研究进展

纳米多孔材料可用作催化剂、气体储存材料和光电子器件,是目前新型多孔材料的研究热点之一。手性联萘酚配体所修饰的催化剂是一种很优异的C2轴对称手性诱导源,可以催化各种α,β-不饱和羰基化合物,具有良好的催化活性和对映选择性。本文对由手性联萘酚类配体所修饰的小分子催化剂、聚合物负载的催化剂和自负载催化剂,在不饱和羰基化合物催化不对称环氧化反应中的应用进行了综述。本文介绍了对手性联萘酚纳米多孔配位聚合物的研究。     

Advancements in Heterogeneous Catalysis for Biodiesel Synthesis

Heterogeneous catalysts are promising for the transesterification reaction of vegetable oils to produce biodiesel and have been studied intensively over the last decade. Unlike the homogeneous catalysts, heterogeneous catalysts can be easily separated from reaction mixture and reused for many times. They are environmentally benign and could be easily operated in continuous processes. This review classifies the solid catalysts into two categories based on their catalytic temperature, i.e. high temperature catalysts and low temperature catalysts. The nature of the catalysts can be specified into solid bases and solid acids. Three aspects, catalyst activity, catalyst life and oil flexibility, will be reviewed. Two kinds of heterogeneous catalysts, reported by IFP Inc. and by WSU, respectively, show a high catalytic activity, long catalyst life and low leaching of catalyst components. These two catalysts also show ability to simultaneously catalyze esterification and transesterification, and can be used in half-refined or crude oil system which provide a potential for greatly decrease the feedstock cost.     

Evaluating the Catalytic Potential of a General RNA-Cleaving FANA Enzyme

The discovery of synthetic genetic polymers (XNAs) with catalytic activity demonstrates that natural genetic polymers are not unique in their ability to function as enzymes. However, all known examples of in vitro selected XNA enzymes function with lower activity than their natural counterparts, suggesting that XNAs might be limited in their ability to fold into structures with high catalytic activity. To explore this problem, we evaluated the catalytic potential of FANAzyme 12–7, an RNA-cleaving catalyst composed entirely of 2′-fluoroarabino nucleic acid (FANA) that was evolved to cleave RNA at a specific phosphodiester bond located between an unpaired guanine and a paired uracil in the substrate recognition arm. Here, we show that this activity extends to chimeric DNA substrates that contain a central riboguanosine (riboG) residue at the cleavage site. Surprisingly, FANAzyme 12–7 rivals known DNAzymes that were previously evolved to cleave chimeric DNA substrates under physiological conditions. These data provide convincing evidence that FANAzyme 12–7 maintains the catalytic potential of equivalent DNAzymes, which has important implications for the evolution of XNA catalysts and their contributions to future applications in synthetic biology.