Peptidyl-transferase ribozymes: trans reactions,structural characterization and ribosomal RNA-like features

Background: One of the most significant questions in understanding the origin of life concerns the order of appearance of DNA, RNA and protein during early biological evolution. If an ‘RNA world’ was a precursor to extant life, RNA must be able not only to catalyze RNA replication but also to direct peptide synthesis. Iterative Iterative RNA selection previously identified catalytic RNAs (ribozymes) that form amide bonds between RNA and an amino acid or between two amino acids.Results: We characterized peptidyl-transferase reactions catalyzed by two different families of ribozymes that use substrates that mimic A site and P site tRNAs. The family II ribozyme secondary structure was modeled using chemical modification, enzymatic digestion and mutational analysis. Two regions resemble the peptidyl-transferase region of 23S ribosomal RNA in sequence and structural context; these regions are important for peptide-bond formation. A shortened form of this ribozyme was engineered to catalyze intermolecular (‘trans’) peptide-bond formation, with the two amino-acid substrates binding through an attached AMP or oligonucleotide moiety.Conclusions: An in vitro-selected ribozyme can catalyze the same type of peptide-bond formation as a ribosome; the ribozyme resembles the ribosome because a very specific RNA structure is required for substrate binding and catalysis, and both amino acids are attached to nucleotides. It is intriguing that, although there are many different possible peptidyl-transferase ribozymes, the sequence and secondary structure of one is strikingly similar to the ‘helical wheel’ portion of 23S rRNA implicated in ribosomal peptidyl-transferase activity.     

Isolation of novel ribozymes that ligate AMP-activated RNA substrates

Background: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5′-5′-pyrophosphate ‘capped’ RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5′-monophosphate (AMP) may be a vestige of ‘RNA world’ catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated.Results: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10¹⁵ RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5′-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of ∼ 5 × 10⁵ over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3′-5′-phosphodiester bonds and were highly specific for activation by AMP at the ligation site.Conclusions: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.     

RNA enzymes with two small-molecule substrates

Background: The ‘RNA world’ hypothesis posits ancient organisms employing versatile catalysis by RNAs. In particular, such a metabolism would have required RNA catalysts that join small molecules. Such anabolic reactions now occur very widely, for example in phospholipid, terpene, amino acid and nucleotide synthetic pathways in modern organisms. Present RNA systems, however, do not perform such reactions using substrates that do not base pair. Here we ask whether this lack is a methodological artifact due to the practice of selection-amplification, or a fundamental property of active sites reconstructed within RNA structures.Results: Three rationally modified RNA enzymes, Iso6-G, Iso6-2G and Iso6-3G, catalyze the formation of (5′→5′) polyphosphate-linked oligonucleotides in trans. One of these, Iso6-G RNA, has a specific substrate site for a guanosine triphosphate, GTP, dGTP or ddGTP, and one nonspecific substrate site for a terminal-phosphate-containing small molecule. This ribozyme catalyzes multiple turnovers, proceeding at a constant rate. Guanosine specificity is probably not attributable to Watson-Crick base pairing.Conclusions: Ribozymes can readily bind multiple small-molecule substrates simultaneously and catalyze reactions that build up larger products, apparently independent of substrate-RNA Watson-Crick base pairing. RNA enzymes therefore parallel proteins, which often overcome the entropic difficulties of positioning multiple small substrates for catalysis of anabolic reactions. These results support the idea of a complex ancestral metabolism based on RNA catalysis.     

Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme

Background: RNA and DNA are polymers that lack the diversity of chemical functionalities that make proteins so suited to biological catalysis. All naturally occurring ribozymes (RNA catalysts) that catalyze the formation, transfer and hydrolysis of phosphodiesters require metal-ion cofactors for their catalytic activity. We wished to investigate whether, and to what extent, DNA molecules could catalyze the cleavage (by either hydrolysis or transesterification) of a ribonucleotide phosphodiester in the absence of divalent or higher-valent metal ions or, indeed, any other cofactors.Results: We performed in vitro selection and amplification experiments on a library of random-sequence DNA that incorporated a single ribonucleotide, a suitable site for cleavage. Following 12 cycles of selection and amplification, a ‘first generation’ of DNA enzymes (DNAzymes) cleaved their internal ribonucleotide phosphodiesters at rates ∼ 10⁷-fold faster than the spontaneous rate of cleavage of the dinucleotide ApA in the absence of divalent cations. Re-selection from a partially randomized DNA pool yielded ‘second generation’ DNAzymes that self-cleaved at rates of ∼ 0.01 min⁻¹ (a 10⁸-fold rate enhancement over the cleavage rate of ApA). The properties of these selected catalysts were different in key respects from those of metal-utilizing ribozymes and DNAzymes. The catalyzed cleavage took place in the presence of different chelators and ribonuclease inhibitors. Trace-metal analysis of the reaction buffer (containing very high purity reagents) by inductively coupled plasma-optical emission spectrophotometry indicated that divalent or higher-valent metal ions do not mediate catalysis by the DNAzymes.Conclusions: Our results indicate that, although ribozymes are sometimes regarded generically to be metalloenzymes, the nucleic acid components of ribozymes may play a substantial role in the overall catalysis. Given that metal cofactors increase the rate of catalysis by ribozymes only ∼ 10²−10³-fold above that of the DNAzyme described in this paper, it is conceivable that substrate positioning, transition-state stabilization or general acid/base catalysis by the nucleic acid components of ribozymes and DNAzymes may contribute significantly to their overall catalytic performance.     

Tilted amides in amino acid and peptide derivatives

Background: Amide bonds in peptides and proteins typically adopt planar cis or trans conformations. Conversions between cis and trans amide conformations are necessary for protein folding and for many other processes, but are difficult to achieve since they involve disruption of the planarity of the bond. As a first step to understanding cis-trans isomerization, we set out to synthesize and characterize peptides that mimic the tilted or twisted amide structures that are postulated to form the intermediate states in this process.Results: We have synthesized a model amino acid and four dipeptide derivatives containing a methyl-substituted aziridine residue. Single crystals of phenacyl (2R, 3R)-benzyloxycarbonyl-3-methyl-2-aziridinecarboxylate and phenacyl (2R, 3R)-acetyl-glycyl-3-methyl-2-aziridine-carboxylate were obtained. Using X-ray diffraction analysis, we determined that the amide nitrogens of the aziridine rings have tetrahedral sp³-like geometry with tilt angles in the range of 37–38°. The ¹³C-NMR spectra indicate that the amide carbonyl is dramatically shifted downfield as a consequence of the tilt.Conclusions: In peptides containing a substituted aziridine ring, the orbitals of the amide nitrogen are constrained into a tilted configuration. These peptides may mimic the transition state between cis and trans amide conformations. This technique thus provides a novel strategy for the study of isomerization and other biorecognition processes.     

Cross-metathesis of allyl halides with olefins bearing an α-alkoxy amide group

We have examined whether the allyl halide cross-metathesis reaction tolerates α-alkoxy amide groups. Ruthenium-based catalysts I-III did not catalyze the cross-metathesis of allyl halides in the presence of an α-alkoxy N,N-dimethylamide group to any appreciable extent, but the reaction could tolerate either a bulky N,N-diisopropylamide or Weinreb amide group. In particular, the Grubbs-Hoveyda-Blechert 2nd generation catalyst (III) efficiently catalyzed the cross-metathesis of allyl halides with olefins bearing a Weinreb amide group.     

Subtilisin-catalyzed religation of proteolyzed hen egg-white lysozyme: investigation of the role of disulfides

Background: The use of proteases to form, instead of break, peptide bonds has expanded the repertoire of techniques available for protein semisynthesis. Several groups have previously reported the use of proteases in aqueous-organic solvents to form single amide bonds within proteins, but low yields and lengthy reaction times make this an impractical approach to protein synthesis. We recently found that proteolyzed triose phosphate isomerase can be re-ligated rapidly and efficiently by subtilisin, in mixed aqueous-organic solvent systems.Results: We now report the use of subtilisin to resynthesize hen egg-white lysozyme from a mixture of its proteolyzed fragments in high yield and with rapid reaction times. This enzymatic religation can also be achieved after reduction of the four disulfide bonds present in lysozyme, with the same efficiency as that observed for the disulfide-containing proteolysis mixture.Conclusions: For egg-white lysozyme, the subtilisin religation reaction can be used to re-synthesize a proteolyzed protein even after reduction of disulfide bonds. The utility of this reaction in more generalized protein semisynthesis reactions is currently being explored.     

Proline-based dipeptides with two amide units as organocatalyst for the asymmetric aldol reaction of cyclohexanone with aldehydes

A series of proline-based dipeptide organocatalysts with two amide units (1-16) have been developed and evaluated in the direct catalytic asymmetric aldol reactions of aldehydes with cyclohexanone. These catalysts showed good solubility in organic solvents compared with their corresponding carboxyl terminal dipeptides. The robust amide bond formation allowed structural modifications and fine tuning of catalyst properties by varying the stereo and electronic effects of the terminal amide to affect the ability of hydrogen bonding formation between the catalysts and the substrates. The reactions proceeded smoothly in high yields (up to 99%), enantioselectivities (up to 98% ee) and anti-diastereoselectivities (up to 99:1) in the presence of bifunctional organocatalyst 4 under the optimal reaction conditions.     

In vitro selection of self-cleaving DNAs

Background: Ribozymes catalyze an important set of chemical transformations in metabolism, and ‘engineered’ ribozymes have been made that catalyze a variety of additional reactions. The possibility that catalytic DNAs or ‘deoxyribozymes’ can be made has only recently been addressed. Specifically, it is unclear whether the absence of the 2′ hydroxyl renders DNA incapable of exhibiting efficient enzyme-like activity, making it impossible to discover natural or create artificial DNA biocatalysts.Results: We report the isolation by in vitro selection of two distinct classes of self-cleaving DNAs from a pool of random-sequence oligonucleotides. Individual catalysts from ‘class I’ require both Cu²⁺ and ascorbate to mediate oxidative self-cleavage. Individual catalysts from class II use Cu²⁺ as the sole cofactor. Further optimization of a class II individual by in vitro selection yielded new catalytic DNAs that facilitate Cu²⁺-dependent self-cleavage with rate enhancements exceeding 1000 000-fold relative to the uncatalyzed rate of DNA cleavage.Conclusions: Despite the absence of 2′ hydroxyls, single-stranded DNA can adopt structures that promote divalent-metal-dependent self-cleavage via an oxidative mechanism. These results suggest that an efficient DNA enzyme might be made to cleave DNA in a biological context.     

Catalytic Linkage Engineering of Covalent Organic Frameworks for the Oxygen Reduction Reaction

Metal-free covalent organic frameworks (COFs) have been employed to catalyze the oxygen reduction reaction (ORR). To achieve high activity and selectivity, various building blocks containing heteroatoms and groups linked by imine bonds were used to create catalytic COFs. However, the roles of linkages of COFs in ORR have not been investigated. In this work, the catalytic linkage engineering has been employed to modulate the catalytic behaviors. To create single catalytic sites while avoiding other possible catalytic sites, we synthesized COFs from benzene units linked by various bonds, such as imine, amide, azine, and oxazole bonds. Among these COFs, the oxazole-linkage in COFs enables to catalyze the ORR with the highest activity, which achieved a half-wave potential of 0.75 V and a limited current density of 5.5 mA cm⁻². Moreover, the oxazole-linked COF achieved a conversion frequency (TOF) value of 0.0133 S⁻¹, which were 1.9, 1.3, and 7.4-times that of azine-, amide- and imine-COFs, respectively. The theoretical calculation showed that the carbon atoms in oxazole linkages facilitated the formation of OOH* and promoted protonation of O* to form the OH*, thus advancing the catalytic activity. This work guides us on which linkages in COFs are suitable for ORR.     

Post-Synthesis Conversion of an Unstable Imine Cage to a Stable Cage with Amide Moieties Towards Selective Receptor for Fluoride

Synthesis of robust covalent macrocycles/cages via multiple amide-bond forming reaction is highly challenging and generally it needs multistep reactions. One-pot reaction of appropriate di-/tri-acyl chloride with a diamine generally results polymers or oligomers instead of discrete architectures. To overcome this limitation, a strategy is reported here using dynamic imine chemistry for facile construction of imine-based macrocycle and cage upon treatment of a diamine with di- and tri-aldehydes respectively, followed by post-synthesis one-step conversion of imine bonds to amides to form the desired robust macrocycle and cage containing multiple amide bonds. While the macrocycle was found to form aggregates in DMSO, the cage was intact without any aggregation. Six amide groups in the confined pocket of the cage made it an ideal receptor for selective binding of fluoride with very high selectivity (∼3 10³ fold) over chloride, and it was silent towards other halides, phosphate, and other oxyanions.     

A class of α-amino acids-derived multifunctional amidophosphane precatalysts: application to the highly enantio- and diastereoselective silver(I)-catalyzed 1,3-dipolar cycloaddition reaction

A class of multifunctional amidophosphanes derived from chiral α-amino acids have been developed with two amide bonds, a tertiary amine and a phosphine. In combination with Ag(I) salts, these amidophosphanes have been demonstrated as highly efficient multifunctional catalysts in the asymmetric 1,3-dipolar cycloaddition of azomethine ylides as well as the three-component reaction of the α-iminoesters in situ generated. Under optimal conditions, highly functionalized endo-8 pyrrolidines were obtained with good to excellent yields (up to 99% yield) and enantioselectivities (up to 98% ee).     

Novel cyclic β-aminophosphonate derivatives as efficient organocatalysts for the asymmetric Michael addition reactions of ketones to nitrostyrenes

Three novel catalysts based upon cyclic β-aminophosphonate derivatives 1–3 were designed to catalyze the asymmetric Michael addition reactions of ketones to β-nitrostyrenes. Among the catalysts that have been prepared in this study, cyclic β-aminophosphonic acid monoethylester 3 showed the highest catalytic ability, giving the corresponding Michael adduct in good yields, high enantioselectivities (up to 92% ee), and high diastereoselectivities (syn:anti up to 95:5).     

Reactivite des epoxydes—IV: Mise en evidence de complexes HMPT-lithium lors de l'ouverture des epoxydes par les amidures de lithium—interet sur la plan synthetique

The study of the ratio $\text{|HMPT|}\text{|Amide|}$ effect on the percentage of α-elimination products during the opening of 3,4-epoxycyclooctene 1 with Et₂NLi leads to notice the formation of two complexes: HMPT, Li⁺ and 2HMPT, Li⁺. The α-elimination is entirely suppressed when the second complex is formed. With 5,6-epoxycyclo-octene 2 as a substrate, the study of the ratio $\text{|HMPT|}\text{|Amide|}$ effect on the β-elimination evidences the formation of a third complex: 4HMPT. Li⁺; up to a concentration of |HMPT| = 2|amide| β-elimination is still possible, but for |HMPT|=4|amide| γ-elimination is mainly observed. These conclusions have been applied to 3-allyl epoxy-cylooctane 3 reaction which is able to lead to α, β and γ-elimination.     

Hydrogen-bonding-induced oligoanthranilamide foldamers. Synthesis, characterization, and complexation for aliphatic ammonium ions

The self-assembly of a novel series of intramolecular hydrogen bonding-driven foldamers have been described. Five linear aromatic amide oligomers 1-5, which bear two to six repeating benzoyl amide subunits, respectively, have been prepared by continuous amide-coupling reactions. The existence of three-centered hydrogen bonds in the oligomers and consequently, the folding conformation of the oligomers in the solid state and solution have been proved by the X-ray analysis (for 2) and the ¹H NMR and IR experiments. Molecular modeling reveals a planar and rigid conformation for the oligomers and a cavity of 0.86 nm in diameter for 6-mer 5. Fluorescent and ¹H NMR experiments have demonstrated that the new aromatic oligo-amide foldamers can bind primary and secondary alkyl ammonium ions in chloroform and the associated binding constants have been determined. It is revealed that 5-mer 4 exhibits the largest binding ability. A face-to-face binding mode has been proposed for the complexes.     

Two-Metal Ion Catalysis in Enzymatic Acyl- and Phosphoryl-Transfer Reactions

Numerous studies, both in enzymatic and nonenzymatic catalysis, have been undertaken to understand the way by which metal ions, especially zinc ions, promote the hydrolysis of phosphate ester and amide bonds. Hydrolases containing one metal ion in the active site, termed mononuclear metallohydrolases, such as carboxypeptidase. A and thermolysin were among the first enzymes to have their structures unraveled by X-ray crystallography. In recent years an increasing number of metalloenzymes have been identified that use two or more adjacent metal ions in the catalysis of phosphoryl-transfer reactions (R-OPO₃ + R′-OH → R′-OPO₃ + R-OH; in the case of the phosphatase reaction R′-OH is a water molecule) and carbonyl-transfer reactions, for example, in peptidases or other amidases. These dinuclear metalloenzymes catalyze a great variety of these reactions, including hydrolytic cleavage of phosphomono-, -di- and -triester bonds, phosphoanhydride bonds as well as of peptide bonds or urea. In addition, the formation of the phosphodiester bond of RNA and DNA by polymerases is catalyzed by a two-metal ion mechanism. A remarkable diversity is also seen in the structures of the active sites of these di- and trinuclear metalloenzymes, even for enzymes that catalyze very similar reactions. The determination of the structure of a substrate, product, stable intermediate, or a reaction coordinate analogue compound bound to an active or inactivated enzyme is a powerful approach to investigate mechanistic details of enzyme action. Such studies have been applied to several of the metalloenzymes reviewed in this article; together with many other biochemical studies they provide a growing body of information on how the two (or more) metal ions cooperate to achieve efficient catalysis.     

The activity of Escherichia coli cyclopropane fatty acid synthase depends on the presence of bicarbonate

Cyclopropane fatty acid (CFA) synthases catalyze the formation of cyclopropane rings on isolated and unactivated olefinic bonds within various fatty acids; the methylene carbon is derived from the activated methyl group of (S)-adenosylmethionine. The E. coli enzyme is the prototype for this class of enzymes, which include the cyclopropane mycolic acid (CMA) synthases, which are potential targets for the design of antituberculosis agents. Crystal structures of several CMA synthases have recently been solved, and electron density attributed to a bicarbonate ion was found in or near the active site. Because a functional assay for CMA synthases has not been developed, the relevance of the bicarbonate ion has not been established. CFA synthase is 30-35% identical to the CMA synthases that have been analyzed structurally, suggesting that the mechanisms of these enzymes are conserved. In this work, we show that indeed the activity of CFA synthase requires bicarbonate, and that it is inhibited by borate, a planar trigonal molecule that mimics the structure of bicarbonate. We also show that substitutions of the conserved amino acids that act as ligands to the bicarbonate ion based on the structure of CMA synthases result in drastic losses in the activity of the protein.     

Cross-metathesis of allyl halides with olefins bearing amide and ester groups

An investigation was conducted to determine whether the cross-metathesis (CM) of allyl halides tolerates amide groups. The results show that the ruthenium-based complexes I–III serve as poor catalysts for the CM of allyl halides with olefins that contain an N,N-dimethylamide group. In contrast, the Grubbs–Hoveyda–Blechert second generation catalyst (III) efficiently promotes these processes with olefins bearing a Weinreb amide group. Lastly, a reinvestigation of the ester group tolerance of the allyl halide CM with unsaturated esters demonstrated that III serves as an efficient catalyst for these reactions.     

Anion receptors with viologen molecular scaffold

We have designed and synthesized new anion receptors 1²⁺ and 2²⁺. These receptors interact with anions through hydrogen bonds and charge transfer complex depending on the basicity of anion. Therefore, anions with weak basicity such as chloride, bromide, and hydrogen sulfate bound to the receptors 1²⁺ and 2²⁺ only through hydrogen bonds while anions with strong basicity such as fluoride, acetate and dihydrogen phosphate bound to the receptors 1²⁺ and 2²⁺ only through charge transfer interactions at UV–vis titration condition (20 μM). However, in more concentrated ¹H NMR titration condition (2 mM), 1²⁺ and 2²⁺ decomposed to form the product one of their amide arm is eliminated. As charge transfer complexes showed colorimetric response, they turned out to be efficient naked eye detector for anions with strong basicity such as fluoride, acetate, and dihydrogen phosphate.     

Conformational properties and chiroptical spectra of lactams and thiolactams with 2-azabicyclo[2.2.1]heptane, 2- and 3-azabicyclo[3.2.1]octane skeletons

The CD spectra of several bicyclic lactams and thiolactams were measured in different solvents. The concentration dependence of the spectra observed in hydrocarbon solvents was attributed to shifts in the equilibrium between monomer and hydrogen-bonded dimer forms. The CD of some compounds is characterized by unusually strong Cotton effects resulting from non-planarity of the amide bonds due to internal strain of the bicyclic skeletons. The X-ray crystallographic structures of 2a,c, 3b,d and 4a,b showed different degrees of distortion of the amide or thioamide moieties from planarity, which causes inherent chirality of the chromophores and profoundly affects the Cotton effect sign and magnitude. This distortion also restricts application of the sector rules for prediction of the n–π^* CD sign, since they can be used only for compounds with planar chromophores.