Reduction of an aldehyde by a NADH/Zn2+ -dependent redox active ribozyme

We report here the ability of an alcohol dehydrogenase (ADH) ribozyme to reduce a benzaldehyde. While the ribozyme was initially evolved in vitro based on the activity for the NAD+-dependent oxidation of the benzyl alcohol, we found that this ADH ribozyme is also capable of reducing the aldehyde in the presence of NADH and Zn2+. The rate acceleration gained by ribozyme catalysis was more than 6 orders of magnitude larger than the spontaneous reaction. Although the reversibility of phosphordiester and acyl transfer reactions catalyzed by ribozymes was known, that of other chemical reactions has not been well established. This study has demonstrated the reversibility of a hydride transfer chemistry catalyzed by the ADH ribozyme. Most interestingly, the ribozyme shares many features with the protein ADHs, e.g., reversibility and NADH/Zn2+ dependence.     

Analysis on a cooperative pathway involving multiple cations in hammerhead reactions

The hammerhead ribozyme reaction is more complex than might have been expected, perhaps because of the flexibility of RNA, which would have enhanced the potential of RNA during evolution of and in the RNA world. Divalent Mg(2+) ions can increase the rate of the ribozyme-catalyzed reaction by approximately 10(9)-fold as compared to the background rate under standard conditions. However, the role of Mg(2+) ions is controversial since the reaction can proceed in the presence of high concentrations of monovalent ions, such as Li(+), Na(+), and NH(4)(+) ions, in the absence of divalent ions. We thus carried out ribozyme reactions under various conditions, and we obtained parameters that explain the experimental data. On the basis of the analysis, we propose a new pathway in the hammerhead ribozyme reaction in which divalent metal ions and monovalent ions act cooperatively.     

The cooperative effect of a hydroxyl and carboxyl group on the catalytic ability of novel β-homoproline derivatives on direct asymmetric aldol reactions

Novel β-homoproline derivatives, 2-hydroxy-2-(pyrrolidin-2-yl)acetic acids (R,S)- and (S,S)-1a-d, were synthesized. All of the prepared compounds were used as organocatalysts in the direct asymmetric aldol reaction of 4-nitrobenzaldehyde with several ketones. Among these catalysts, (R)-2-hydroxy-2-((S)-pyrrolidin-2-yl)acetic acid (R,S)-1a showed good catalytic ability in the formation of aldol product 13 (up to 69% ee, 95% yield), which was similar to the results catalyzed by l-proline (71% ee, 96% yield). Relatively low yields and low enantioselectivities were observed in aldol reactions catalyzed by (S,S)-1a, for example, 13 was obtained in 55% yield and 13% ee. The aldol reaction catalyzed by the methyl-protected carboxylic acid 1b and esters 1c,d produced much lower chemical yields and enantioselectivities during the formation of 13. The cooperative effect of the (R)-configured hydroxyl group and the carboxyl group was found to play an important role in inducing enantioselectivity in the aldol reaction. Relatively high diastereoselectivities (anti:syn = 85:15) and enantioselectivity (anti, 83% ee) were observed in the aldol reactions of 4-nitrobenzaldehyde with cyclohexanone, which was catalyzed by (R,S)-1a.     

Enantioselective organocatalytic aldol reaction using small organic molecules

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Enantioselective reactions catalyzed by small organic molecules (asymmetric organocatalysis) are a comparatively new and popular segment in the area of contemporary research in asymmetric synthesis. The great synthetic utility of the aldol reaction for the formation of C–C bonds has geared up for a hard battle for research in this area resulting in a rapid evolution of tremendous highly enantioselective chiral catalysts. This review emphasizes asymmetric direct aldol reactions catalyzed by small enantioenriched organic molecules, particularly those involving enamine catalysis through primary and secondary amines. We have made significant efforts to include several important contributions from different groups in this area.     

Promiscuous catalysis by the tetrahymena group I ribozyme

Catalytic promiscuity, the ability of an enzyme to catalyze alternative reactions, has been suggested to have played an important role in the evolution of new catalytic activities in protein enzymes. Similarly, promiscuous activities may have been advantageous in an earlier RNA world. The Tetrahymena Group I ribozyme naturally catalyzes the site-specific guanosine attack on an anionic phosphate diester and has been shown to also catalyze aminoacyl transfer to water, albeit with a small rate acceleration (<10-fold). This inefficient catalysis could be due to the differences in charge and/or geometry requirements for the two reactions. Herein, we describe a new promiscuous activity of this ribozyme, the site-specific guanosine attack on a neutral phosphonate diester. This alternative substrate lacks the negative charge at the reaction center but, in contrast to the aminoacyl substrate, can undergo nucleophilic attack with the same geometry as the natural substrate. Our results show that the neutral phosphonate reaction is catalyzed about 1 x 106-fold, substantially better than the acyl transfer but far below the normal anionic substrate. We conclude that both charge and geometry are important factors for catalysis of the normal reaction and that promiscuous catalytic activities of ribozymes could have been created or enhanced by reorienting and swapping RNA domains.     

Contemporaneous Dual Catalysis: Aldol Products from Non‐Carbonyl Substrates

The aldol reaction represents an important class of atom‐economic carbon–carbon bond‐forming reactions vital to modern organic synthesis. Despite the attention this reaction has received, issues related to chemo‐ and regioselectivity as well as reactivity of readily enolizable electrophiles remain. To help overcome these limitations, a new direct approach toward aldol products that does not rely upon carbonyl substrates is described. This approach employs room‐temperature contemporaneous lanthanum/vanadium dual catalysis, whereby a vanadium‐catalyzed 1,3‐transposition of allenols is coupled with a lanthanum‐catalyzed Meinwald rearrangement of epoxides in situ to directly form aldol products.     

Catalytic Asymmetric Mannich Reactions with Fluorinated Aromatic Ketones: Efficient Access to Chiral β‐Fluoroamines

Reported herein is a Zn/Prophenol‐catalyzed Mannich reaction using fluorinated aromatic ketones as nucleophilic partners for the direct enantio‐ and diastereoselective construction of β‐fluoroamine motifs featuring a fluorinated tetrasubstituted carbon. The reaction can be run on a gram scale with a low catalyst loading without impacting its efficiency. Moreover, a related aldol reaction was also developed. Together, these reactions provide a new approach for the preparation of pharmaceutically relevant products possessing tetrasubstituted C? F centers.     

Studies on Direct Stereoselective Aldol Reactions in Aqueous Media

The direct aldol reaction of 4‐nitrobenzaldehyde catalyzed by NaHCO₃, with three different ketones, Zn? proline, NaHCO₃/Zn? proline, and L ‐proline/Zn? proline in aqueous media, was studied to explore the selectivity of this environmentally benign type of reaction. Amazingly, NaHCO₃ proper was found to be an efficient catalyst for the selective synthesis of β‐hydroxy ketones, showing good regio‐ and diastereoselectivity, with all reactions being completed within 9 h. Cyclopentanone and cyclohexanone were found to give rise to reversed diastereoisomer ratios, the syn and anti isomers being the major products, respectively – an unprecedented result. Also, the observed syn diastereoselectivity of aldol reactions catalyzed by L ‐proline and Zn? proline is remarkable. The corresponding condensation products 7 and 8 were characterized by ¹H‐NMR and single‐crystal X‐ray analyses. Finally, a chelate‐ vs. nonchelate‐type transition state is proposed to account for the differential diastereoselectivities.     

Pyrrolidine as an efficient organocatalyst for direct aldol reaction of trifluoroacetaldehyde ethyl hemiacetal with ketones

Pyrrolidine-catalyzed aldol reaction of trifluoroacetaldehyde ethyl hemiacetal (1) with ketones or aldehydes was described. In the presence of 20 mol % of pyrrolidine, the reaction proceeded smoothly at room temperature to afford the aldol products in good to excellent yields (up to 95%). Pyrrolidine showed a much higher catalytic activity than piperidine in the reaction with less reactive ketones. GC analysis clearly indicated that the catalyst and the enamine intermediates were kept at extremely low concentration during the reaction. Based on these observations, we suggested that formation of the enamine would be a rate-determining step for the catalytic aldol reaction. In addition, the asymmetric aldol reaction of 1 with cyclohexanone catalyzed by l-proline derivatives was also discussed.     

Construction of polyheterocyclic spirotetrahydrothiophene derivatives via sulfa-Michael/aldol cascade reaction

A series of polyheterocyclic spirotetrahydrothiophene derivatives were obtained in moderate to excellent yields via a catalyst-free sulfa-Michael/aldol cascade reaction of chalcones 1 and commercially available 1,4-dithiane-2,5-diol 2 under mild conditions. We also present the first asymmetric sulfa-Michael/aldol cascade reaction of chalcones 1 and commercially available 1,4-dithiane-2,5-diol 2 with moderate to good enantioselectivities catalyzed by readily available chiral phase-transfer catalysts (PTCs).     

Amino Acids Catalyzed Direct Aldol Reactions in Aqueous Micelles

Since the discovery of its roles as a good small-organic-molecule catalyst in intramolecular aldol reactions, pro line has drawn considerable attention in synthetic chemistry due to its similarity to the type-Ⅰ aldolases. Recently,List and others have reported some new direct asymmetric intermolecular reactions catalyzed by proline, including aldol, Mannich, Michael, and other analogous reactions. Except for two recent examples, [1,2] proline catalyzed aldol reactions in aqueous micelles have not been reported, nor have other amino acids as organocatalysts in directly catalyzing aldol reaction been reported. Herein we wish to present our recent results regarding environmentally be nign direct aldol reactions catalyzed by amino acids including proline, histidine and arginine in aqueous media.     

Direct catalytic asymmetric aldol reaction of hydroxyketones: asymmetric Zn catalysis with a Et(2)Zn/linked-BINOL complex

Full details of our newly developed catalyses with asymmetric zinc complexes as mimics of class II zinc-containing aldolase are described. A Et(2)Zn/(S,S)-linked-BINOL complex was developed and successfully applied to direct catalytic asymmetric aldol reactions of hydroxyketones. A Et(2)Zn/(S,S)-linked-BINOL 1 = 2/1 system was initially developed, which efficiently promoted the direct aldol reaction of 2-hydroxy-2'-methoxyacetophenone (7d). Using 1 mol % of (S,S)-linked-BINOL 1 and 2 mol % of Et(2)Zn, we obtained 1,2-dihydroxyketones syn-selectively in high yield (up to 95%), good diastereomeric ratio (up to 97/3), and excellent enantiomeric excess (up to 99%). Mechanistic investigation of Et(2)Zn/(S,S)-linked-BINOL 1, including X-ray analysis, NMR analysis, cold spray ionization mass spectrometry (CSI-MS) analysis, and kinetic studies, provided new insight into the active oligomeric Zn/(S,S)-linked-BINOL 1/ketone 7d active species. On the basis of mechanistic investigations, a modified second generation Et(2)Zn/(S,S)-linked-BINOL 1 = 4/1 with molecular sieves 3A (MS 3A) system was developed as a much more effective catalyst system for the direct aldol reaction. As little as 0.1 mol % of (S,S)-linked-BINOL 1 and 0.4 mol % of Et(2)Zn promoted the direct aldol reaction smoothly, using only 1.1 equiv of 7d as a donor (substrate/ligand = 1000). This is the most efficient, in terms of catalyst loading, asymmetric catalyst for the direct catalytic asymmetric aldol reaction. Moreover, the Et(2)Zn/(S,S)-linked-BINOL 1 = 4/1 system was effective in the direct catalytic asymmetric aldol reaction of 2-hydroxy-2'-methoxypropiophenone (12), which afforded a chiral tetrasubstituted carbon center (tert-alcohol) in good yield (up to 97%) and ee (up to 97%), albeit in modest syn-selectivity. Newly developed (S,S)-sulfur-linked-BINOL 2 was also effective in the direct aldol reaction of 12. The Et(2)Zn/(S,S)-sulfur-linked-BINOL 2 = 4/1 system gave aldol adducts anti-selectively in good ee (up to 93%). Transformations of the aldol adducts into synthetically versatile intermediates were also described.     

Direct asymmetric aldol condensation catalyzed by aziridine semicarbazide zinc(II) complexes

Previously obtained semicarbazides derived from N-triphenylmethyl-aziridine-2-carbohydrazide were explored as ligands in Zn(II) catalyzed diastereo- and enantioselective direct aldol reactions. Complexes of aziridine-semicarbazides with Zn(II) were efficient catalysts in reactions of acetone and hydroxyacetone with NO₂-substituted aromatic aldehydes in the presence of water.     

Enantioselective Aldol Reactions Catalyzed by Chiral Phosphine Oxides

The development of enantioselective aldol reactions catalyzed by chiral phosphine oxides is described. The aldol reactions presented herein do not require the prior preparation of the masked enol ethers from carbonyl compounds as aldol donors. The reactions proceed through a trichlorosilyl enol ether intermediate, formed in situ from carbonyl compounds, which then acts as the aldol donor. Phosphine oxides activate the trichlorosilyl enol ethers to afford the aldol adducts with high stereoselectivities. This procedure was used to realize a directed cross‐aldol reaction between ketones and two types of double aldol reactions (a reaction at one/two α position(s) of a carbonyl group) with high diastereo‐ and enantioselectivities.     

Novel RNA catalysts for the Michael reaction

BACKGROUND: In vitro selected ribozymes with nucleotide synthase, peptide and carbon-carbon bond forming activity provide insight into possible scenarios on how chemical transformations may have been catalyzed before protein enzymes had evolved. Metabolic pathways based on ribozymes may have existed at an early stage of evolution. RESULTS: We have isolated a novel ribozyme that mediates Michael-adduct formation at a Michael-acceptor substrate, similar to the rate-limiting step of the mechanistic sequence of thymidylate synthase. The kinetic characterization of this catalyst revealed a rate enhancement by a factor of approximately 10(5). The ribozyme shows substrate specificity and can act as an intermolecular catalyst which transfers the Michael-donor substrate onto an external 20-mer RNA oligonucleotide containing the Michael-acceptor system. CONCLUSION: The ribozyme described here is the first example of a catalytic RNA with Michael-adduct forming activity which represents a key mechanistic step in metabolic pathways and other biochemical reactions. Therefore, previously unforeseen RNA-evolution pathways can be considered, for example the formation of dTMP from dUMP. The substrate specificity of this ribozyme may also render it useful in organic syntheses.     

Kinetic Analysis of the Divergence of Reaction Pathways in the Chiral Lewis Base Promoted Aldol Additions of Trichlorosilyl Enol Ethers: A Rapid‐Injection NMR Study

The aldol addition reaction of trichlorosilyl enol ethers and aldehydes with and without chiral Lewis base catalysts has been kinetically analyzed. The uncatalyzed reactions display classic first‐order dependence on each component. The reactions catalyzed by bulky chiral phosphoramide 5 were examined by ReactIR and exhibited first‐order dependence on the catalyst. To examine the kinetic behavior of the reaction catalyzed by phosphoramide 4 , a Rapid‐Injection (RI) NMR apparatus was constructed and employed to allow rapid in‐situ mixing and monitoring of the reaction course. The aldol addition catalyzed by 4 displayed second‐order dependence on phosphoramide, thus providing direct evidence that two catalyzed pathways (with complimentary stereochemical consequences) exist that depend on phosphoramide structure and concentration. Arrhenius activation parameters for all three reactions showed striking characteristics of negligible enthalpies and extremely high entropies of activation. Comparison of these values was precluded by the existence of complex preequilibria in the catalyzed process.     

Catalyzed and spontaneous reactions on ribozyme ribose

The RNA world hypothesis requires that early translation be catalyzed by RNA enzymes. Here we show that a five-nucleotide RNA enzyme, reacting with a tetranucleotide substrate and elevated PheAMP, forms aminoacyl- and peptidyl-RNAs RNA-Phe through RNA-Phe(5). A second series of products is formed from RNA-Phe diesters, after trans migration of phenylalanine from the 2'- to the 3'-hydroxyl group of the substrate RNA, followed by reaminoacylation of the 2'-OH. While the ribozyme is required for initial attachment of phenylalanine to an RNA substrate, as well as reacylation (and thus for formation of all products), further extension into RNA-peptides appears to be an uncatalyzed, but RNA-stimulated reaction. The ribozyme readily turns over at high PheAMP and GCCU concentrations. Thus, GUGGC/GCCU comprises a true RNA enzyme. We define Michaelis-Menten parameters plus and minus divalent magnesium and characterize ca. 20 molecular species of aminoacyl-, peptidyl-, dipeptidyl-, and mixed peptidyl/aminoacyl-RNAs.     

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.     

Zinc(II)‐Catalyzed Intermolecular Hydrative Aldol Reactions of 2‐En‐1‐ynamides with Aldehydes and Water to form Branched Aldol Products Regio‐ and Stereoselectively

This work describes zinc(II)‐catalyzed hydrative aldol reactions of 2‐en‐1‐ynamides with aldehydes and water to afford branched aldol products regio‐ and stereoselectively. The anti and syn selectivity can be modulated by the sizes of sulfonamides to yield E‐ and Z‐configured zinc(II) dienolates selectively. This new reaction leads to enantiopure aldol products by using a cheap chiral sulfonamide. The mechanistic analysis reveals that the sulfonamide amides of the substrates can trap a released proton to generate dual acidic sites to activate a carbonyl allylation reaction.