Control of stereoselectivity in an enzymatic reaction by backdoor access

Utilization of glycosyltransferases as a seamless tool for synthesis and modification of the oligosaccharides-A review

Glycosyltransferases (GTs) catalyze the transfer of active monosaccharide donors to carbohydrates to create a wide range of oligosaccharide structures. GTs display strong regioselectivity and stereoselectivity in producing glycosidic bonds, making them extremely valuable in the in vitro synthesis of oligosaccharides. The synthesis of oligosaccharides by GTs often gives high yields; however, the enzyme activity may experience product inhibition. Additionally, the higher cost of nucleotide sugars limits the usage of GTs for oligosaccharide synthesis. In this review, we comprehensively discussed the structure and mechanism of GTs based on recent literature and the CAZY website data. To provide innovative ideas for the functional studies of GTs, we summarized several remarkable characteristics of GTs, including folding, substrate specificity, regioselectivity, donor sugar nucleotides, catalytic reversibility, and differences between GTs and GHs. In particular, we highlighted the recent advancements in multi-enzyme cascade reactions and co-immobilization of GTs, focusing on overcoming problems with product inhibition and cost issues. Finally, we presented various types of GT that have been successfully used for oligosaccharide synthesis. We concluded that there is still an opportunity for improvement in enzymatically produced oligosaccharide yield, and future research should focus on improving the yield and reducing the production cost.

Lipase and Its Unique Selectivity: A Mini-Review

Contrary to other solid catalysts, enzymes facilitate more sophisticated chemical reactions because most enzymes specifically interact with substrates and release selective products. Lipases (triacylglycerol hydrolase, EC 3.1.1.3), which can catalyze the cleavage and formation of various acyl compounds, are one of the best examples of enzymes with a unique substrate selectivity. There are already several commercialized lipases that have become important tools for various lipid-related studies, although there is still a need to discover novel lipases with unique substrate selectivity to facilitate more innovative reactions in human applications such as household care, cosmetics, foods, and pharmaceuticals. In this mini-review, we focus on concisely demonstrating not only the general information of lipases but also their substate selectivities: typoselectivity, regioselectivity, and stereoselectivity. We highlight the essential studies on selective lipases in terms of enzymology. Furthermore, we introduce several examples of analysis methodology and experimental requirements to determine each selectivity of lipases. This work would stress the importance of integrating our understanding of lipase chemistry to make further advances in the relevant fields.

Homogeneity of Supported Single-Atom Active Sites Boosting the Selective Catalytic Transformations

Selective conversion of specific functional groups to desired products is highly important but still challenging in industrial catalytic processes. The adsorption state of surface species is the key factor in modulating the conversion of functional groups, which is correspondingly determined by the uniformity of active sites. However, the non-identical number of metal atoms, geometric shape, and morphology of conventional nanometer-sized metal particles/clusters normally lead to the non-uniform active sites with diverse geometric configurations and local coordination environments, which causes the distinct adsorption states of surface species. Hence, it is highly desired to modulate the homogeneity of the active sites so that the catalytic transformations can be better confined to the desired direction. In this review, the construction strategies and characterization techniques of the uniform active sites that are atomically dispersed on various supports are examined. In particular, their unique behavior in boosting the catalytic performance in various chemical transformations is discussed, including selective hydrogenation, selective oxidation, Suzuki coupling, and other catalytic reactions. In addition, the dynamic evolution of the active sites under reaction conditions and the industrial utilization of the single-atom catalysts are highlighted. Finally, the current challenges and frontiers are identified, and the perspectives on this flourishing field is provided.

Stereochemical dominance in hierarchically formed helicates

The competition of different chiral ligands in the control of stereochemistry of hierarchically formed helical coordination compounds is investigated. It is found that sterically demanding chiral units can dominate the chiral induction of the helix even if they are present as a minor species. Hereby the relative strength of stereoinduction of different chiral units can be evaluated.

Lessons in Organic Fluorescent Probe Discovery

Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.

Application of Enzymes in Regioselective and Stereoselective Organic Reactions

Nowadays, biocatalysts have received much more attention in chemistry regarding their potential to enable high efficiency, high yield, and eco-friendly processes for a myriad of applications. Nature’s vast repository of catalysts has inspired synthetic chemists. Furthermore, the revolutionary technologies in bioengineering have provided the fast discovery and evolution of enzymes that empower chemical synthesis. This article attempts to deliver a comprehensive overview of the last two decades of investigation into enzymatic reactions and highlights the effective performance progress of bio-enzymes exploited in organic synthesis. Based on the types of enzymatic reactions and enzyme commission (E.C.) numbers, the enzymes discussed in the article are classified into oxidoreductases, transferases, hydrolases, and lyases. These applications should provide us with some insight into enzyme design strategies and molecular mechanisms.

Gram scale production of 1-azido-β-d-glucose via enzyme catalysis for the synthesis of 1,2,3-triazole-glucosides

The production of analytical amounts of azido sugars is used as a means of verifying catalytic acid/base mutations of retaining glycosidase, but application of this process to preparative synthesis has not been reported. The catalytic acid/base mutant of Thermoanaerobacterium xylanolyticus GH116 β-glucosidase, TxGH116D593A, catalyzed the gram scale production of 1-azido-β-d-glucose (1) from p-nitropheyl-β-d-glucopyranoside (pNPGlc) and azide via a transglucosylation reaction. Overnight reaction of the enzyme with pNPGlc and NaN₃ in aqueous MES buffer (pH 5.5) at 55 °C produced 1 (3.27 g), which was isolated as a white foamy solid in 96% yield. This 1 was successfully utilized for the synthesis of fifteen 1,2,3-triazole-β-d-glucosyl derivatives (2–16) containing a variety of functional groups, via click chemistry.

The retaining β-glucosidase acid/base mutant TxGH116D593A catalyzed the production of 1-azido-β-d-glucose for synthesis of 15 1,2,3-triazole β-glucosyl derivatives.

Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes

The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.

The effect of host structure on the selectivity and mechanism of supramolecular catalysis of Prins cyclizations

The effect of host structure on the selectivity and mechanism of intramolecular Prins reactions is evaluated using K12Ga4L6 tetrahedral catalysts. The host structure was varied by modifying the structure of the chelating moieties and the size of the aromatic spacers. While variation in chelator substituents was generally observed to affect changes in rate but not selectivity, changing the host spacer afforded differences in efficiency and product diastereoselectivity. An extremely high number of turnovers (up to 840) was observed. Maximum rate accelerations were measured to be on the order of 105, which numbers among the largest magnitudes of transition state stabilization measured with a synthetic host-catalyst. Host/guest size effects were observed to play an important role in host-mediated enantioselectivity.

Next-generation sequencing reveals how RNA catalysts evolve from random space

Catalytic RNAs are attractive objects for studying molecular evolution. To understand how RNA libraries can evolve from randomness toward highly active catalysts, we analyze the original samples that led to the discovery of Diels-Alderase ribozymes by next-generation sequencing. Known structure-activity relationships are used to correlate abundance with catalytic performance. We find that efficient catalysts arose not just from selection for reactivity among the members of the starting library, but from improvement of less potent precursors by mutations. We observe changes in the ribozyme population in response to increasing selection pressure. Surprisingly, even after many rounds of enrichment, the libraries are highly diverse, suggesting that potential catalysts are more abundant in random space than generally thought. To highlight the use of next-generation sequencing as a tool for in vitro selections, we also apply this technique to a recent, less characterized ribozyme selection. Making use of the correlation between sequence evolution and catalytic activity, we predict mutations that improve ribozyme activity and validate them biochemically. Our study reveals principles underlying ribozyme in vitro selections and provides guidelines to render future selections more efficient, as well as to predict the conservation of key structural elements, allowing the rational improvement of catalysts.

Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme

Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.

DNA as a versatile chemical component for catalysis, encoding, and stereocontrol

DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.

Catalytic DNA (deoxyribozymes) for synthetic applications-current abilities and future prospects

The discovery of naturally occurring catalytic RNA (RNA enzymes, or ribozymes) in the 1980s immediately revised the view of RNA as a passive messenger that solely carries information from DNA to proteins. Because DNA and RNA differ only by the absence or presence of a 2'-hydroxyl group on each ribose ring of the polymer, the question of 'catalytic DNA?' arises. Although no natural DNA catalysts have been reported, since 1994 many artificial DNA enzymes, or 'deoxyribozymes', have been described. Deoxyribozymes offer insight into the mechanisms of natural and artificial ribozymes. DNA enzymes are also used as tools for in vitro and in vivo biochemistry, and they are key components of analytical sensors. This review focuses primarily on catalytic DNA for synthetic applications. Broadly defined, deoxyribozymes may have the greatest potential for catalyzing reactions in which the high selectivities of 'enzymes' are advantageous relative to traditional small-molecule catalysts. Although the scope of DNA-catalyzed synthesis is currently limited in most cases to oligonucleotide substrates, recent efforts have began to expand this frontier in promising new directions.

Probing the active site of a diels-alderase ribozyme by photoaffinity cross-linking

The active site of a Diels-Alderase ribozyme is located in solution by photoaffinity cross-linking using a productlike azidobenzyl probe. Two key nucleotides are identified that contact the Diels-Alder product in a conformation-dependent fashion. The design of such probes does not require knowledge of the three-dimensional structure of the ribozyme, and the technique yields both static and dynamic structural information. This work establishes photoaffinity cross-linking as an empirical approach that is applied here for the first time to an artificial ribozyme.

Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing

In ribozyme catalysis, metal ions are generally known to make structural andor mechanistic contributions. The catalytic activity of a previously described Diels-Alderase ribozyme was found to depend on the concentration of divalent metal ions, and crystallographic data revealed multiple binding sites. Here, we elucidate the interactions of this ribozyme with divalent metal ions in solution using electron paramagnetic resonance (EPR) spectroscopy. Manganese ion titrations revealed five high-affinity Mn(2+) binding sites with an upper K(d) of 0.6+/-0.2 muM. In order to characterize each binding site individually, EPR-silent Cd(2+) ions were used to saturate the other binding sites. This cadmium-induced EPR silencing showed that the Mn(2+) binding sites possess different affinities. In addition, these binding sites could be assigned to three different types, including innersphere, outersphere, and a Mn(2+) dimer. Based on simulations, the Mn(2+)-Mn(2+) distance within the dimer was found to be approximately 6 A, which is in good agreement with crystallographic data. The EPR-spectroscopic characterization reveals no structural changes upon addition of a Diels-Alder product, supporting the concept of a preorganized catalytic pocket in the Diels-Alder ribozyme and the structural role of these ions.

Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis

Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.

Diels−Alder Ribozyme Catalysis: A Computational Approach

A computational comparison of the Diels-Alder reaction of a maleimide and an anthracene in water and the active site of the ribozyme Diels-Alderase is reported. During the course of the catalyzed reaction, the maleimide is held in the hydrophobic pocket while the anthracene approaches to the maleimide through the back passage of the active site. The active site is so narrow that the anthracene has to adopt a tilted approach angle toward maleimide. The conformation of the active site changes marginally at different states of the reaction. Active site dynamics contribution to catalysis has been ruled out. The active site stabilizes the product more than the transition state (TS). The reaction coordinates of the ribozyme reaction in TS, RC1-CD1 and RC4-CD2, are 2.35 and 2.33 A, respectively, compared to 2.37 and 2.36 A in water. The approach angle of anthracene toward maleimide is twisted by 18 degrees in the TS structure of ribozyme reaction while no twisted angle is found in TS of the reaction in water. The free energy barriers for reactions in both ribozyme and water were obtained by umbrella sampling combined with SCCDFTB/MM. The calculated free energy barriers for the ribozyme and water reactions are in good agreement with the experimental values. As expected, Mulliken charges of the atoms involved in the ribozyme reaction change in a similar manner as that of the reaction in water. The proficiency of the Diels-Alder ribozyme reaction originates from the active site holding the two reactants in reactive conformations, in which the reacting atoms are brought together in van der Waals distances and reactants approach to each other at an appropriate angle.

DNA and RNA induced enantioselectivity in chemical synthesis

One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer by nucleotide templated synthesis, enantioselective catalysis by RNA/DNAzymes and DNA-based asymmetric catalysis. In this article the concepts behind these strategies as well as the important achievements in this field will be discussed.

Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes

Allosteric mechanisms are widely used in nature to control the rates of enzymatic reactions, but little is known about RNA catalysts controlled by these principles. The only natural allosteric ribozyme reported to date catalyzes an RNA cleavage reaction, and so do almost all artificial systems. RNA has, however, been shown to accelerate a much wider range of chemical reactions. Here we report that RNA catalysts for organic reactions can be put under the stringent control of effector molecules by straight-forward rational design. This approach uses known RNA sequences with catalytic and ligand-binding properties, and exploits weakly conserved sequence elements and available structural information to induce the formation of alternative, catalytically inactive structures. The potential and general applicability is demonstrated by the design of three different systems in which the rate of a catalytic carbon–carbon bond forming reaction is positively regulated up to 2100-fold by theophylline, tobramycin and a specific mRNA sequence, respectively. Although smaller in size than a tRNA, all three ribozymes show typical features of allosteric metabolic enzymes, namely high rate acceleration and tight allosteric regulation. Not only do these findings demonstrate RNA's power as a catalyst, but also highlight on RNA's capabilities as signaling components in regulatory networks.

Universal initiator nucleotides for the enzymatic synthesis of 5'-amino- and 5'-thiol-modified RNA

We report the chemical synthesis of 5'-amino- and 5'-thiol-hexaethylene glycol guanosine nucleotides and their enzymatic incorporation into RNA, followed by chemical modifications at their nucleophilic ends. By using two similar routes, the conjugates of guanosine-5'-monophosphate and hexaethylene glycol with attached reactive groups (SH or NH(2)) were synthesized using phosphoramidite chemistry, and characterized by MALDI TOF mass spectrometry. These initiator molecules were efficiently incorporated into RNA at the 5'-end by run-off transcription using T7 RNA polymerase. The potential of these RNA conjugates for a broad reaction range with electrophiles is shown here, thereby enabling their use for diverse biochemical applications.