Efficient Oligomerization of Aromatic Amino Acids Induced by Gaps in Four-Helix Bundles of DNA or RNA

The formation of peptides from amino acids is one of the processes associated with life. Because of the dominant role of translation in extant biology, peptide-forming processes that are RNA induced are of particular interest. We have previously reported the formation of phosphoramidate-linked peptido RNAs as the products of spontaneous condensation reactions between ribonucleotides and free amino acids in aqueous solution. We now asked whether four-helix bundle (4HB) DNA or RNA folding motifs with a single- or double-nucleotide gap next to a 5’-phosphate can act as reaction sites for phosphoramidate formation. For glycine, this was found to be the case, whereas phenylalanine and tryptophan showed accelerated formation of peptides without a covalent link to the nucleic acid. Free peptides with up to 11 tryptophan or phenylalanine residues were found in precipitates forming in the presence of gap-containing DNA or RNA 4HBs. Control experiments using motifs with just a nick or primer alone did not have the same effect. Because folded structures with a gap in a double helix are likely products of hybridization of strands formed in statistically controlled oligomerization reactions, our results are interesting in the context of prebiotic scenarios. Independent of a putative role in evolution, our findings suggest that for some aromatic amino acids an RNA-induced pathway for oligomerization exists that does not have a discernable link to translation.     

Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs

When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5′-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2′,3′-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3′-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5′-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8–99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3′-UUC-5′ as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.

The C-terminus of dipeptido dinucleotides reacts with the 3′-terminus of a primer strand in template directed fashion with a strong dependence on the structures of peptide and template.     

Diastereoselective conjugate addition to chiral alpha,beta-unsaturated carbonyl systems in aqueous media: an enantioselective entry to alpha- and gamma-hydroxy acids and alpha-amino acids

The stereoselectivity of the ultrasonically induced zinc--copper conjugate addition of iodides to chiral alpha,beta-unsaturated carbonyl systems under aqueous conditions was studied. Alkyl iodides add diastereoselectively to methylenedioxolanone 1 and methyleneoxazolidinone 2 to afford the 1,4-addition products in good yields (38-95 %) and with high diastereomeric excess (44-90 % de). The 1,4-addition to chiral gamma,delta-dioxolanyl-alpha,beta-unsaturated esters 3-5 also proceeds with good yields (51-99 %). The diastereoselectivity is dependent on the geometry of the olefin: the Z isomer 3 gives high diastereoselectivity, while the reactions with the E isomer 4 are nonstereoselective. The reaction proceeds with excellent chemoselectivity and allows the use of iodides bearing ester, hydroxy, and amino groups. Since the 1,4-addition products can be readily hydrolyzed, this methodology constitutes a novel entry for the enantioselective synthesis of alpha- and gamma-hydroxy acids and alpha-amino acids in aqueous media. The results obtained support the radical mechanism proposed by Luche, and represent one of the few examples of a radical stereoselective conjugate addition in aqueous medium.     

High Diastereoselection of a Dissymmetric Capsule by Chiral Guest Complexation

Encapsulation of chiral guests in the dissymmetric capsule 1?4 BF₄ formed diastereomeric supramolecular complexes G ? 1?4 BF₄ ( G : guest). When chiral guests 2 a – q were encapsulated within the dissymmetric space of the self‐assembled capsule 1?4 BF₄, circular dichroism (CD) was observed at the absorption bands that are characteristic of the π–π* transition of the bipyridine moiety of the capsule, which suggests that the P and M helicities of the capsule are biased by the chiral guest complexation. The P helicity of diastereomeric complex (S)‐ 2 l ? 1?4 BF₄ was determined to be predominant, based on CD exciton coupling theory and DFT calculations. The diastereoselectivity was highly influenced by the ester substituents, such that benzyl ester moieties were good for improving the diastereoselectivity. A diastereomeric excess of 98 % was achieved upon the complexation of 2 j . The relative enthalpic and entropic components for the distereoselectivity were obtained from a van’t Hoff plot. The enthalpic components were linearly correlated with the substituent Hammett parameters (σ_p⁺). The electron‐rich benzyl ester moieties generated donor–acceptor π–π stacking interactions with the bipyridine moiety, which resulted in a significant difference in energy between the predominant and subordinate diastereomeric complexes.     

Amino Acid‐Specific,Ribonucleotide‐Promoted Peptide Formation in the Absence of Enzymes

Nucleic acids and polypeptides are at the heart of life. It is interesting to ask whether the monomers of these biopolymers possess intrinsic reactivity that favors oligomerization in the absence of enzymes. We have recently observed that covalently linked peptido RNA chains form when mixtures of monomers react in salt‐rich condensation buffer. Here, we report the results of a screen of the 20 proteinogenic amino acids and four ribonucleotides. None of the amino acids prevent phosphodiester formation, so all of them are compatible with genetic encoding through RNA chain growth. A reactivity landscape was found, in which peptide formation strongly depends on the structure of the amino acid, but less on the nucleobase. For example, proline gives ribonucleotide‐bound peptides most readily, tyrosine favors pyrophosphate and phosphodiester formation, and histidine gives phosphorimidazolides as dominant products. When proline and aspartic acid were allowed to compete for incorporation, only proline was found at the N‐terminus of peptido chains. The reactivity described here links two fundamental classes of biomolecules through reactions that occur without enzymes, but with amino acid specificity.     

Self-Replication of Oligonucleotides in Reverse Micelles

The coupling between the tri(deoxynucleotides) d[(MeO)C-G-Ap] ( 1 ) and d[(NH₂)T_d5′-C-G-] ( 2 ) to yield the phosphoramidate-linked (hexadeoxy-nucleotide) d[(MeO)C-G-Anh⁵′T_d5′-C-G] ( 3 ) was investigated both in aqueous solution and in reverse micelles constituted of CTAB (cetyl(trimethyl)ammonium bromide) in hexane/pentan-1-ol 9:1. No siginificant difference was found concerning the yield and the kinetics of the reaction in the two systems. The coupling between 1 and 2 was also carried out in the presence of the template d[(MeO)C-G-A-T-C-G] ( 4 ), an analogue of 3 , so as to reproduce the conditions of template-directed self replication. It was shown that the trinucleotide coupling in the presence of a template obeys the so-called square-root law both in H₂O and in reverse micelles. No significant difference of the time course of the reaction in H₂O and in reverse micelles was observed. This shows that self-replication of oligonucleotides occurs within geometrically bounded structures, which represents a step forward in the mimicking of minimal life processes.     

Diastereomeric excess upon cleavage and reformation of diastereomeric alkoxyamines

The thermal reactions of several TEMPO and DEPN (N-(2-methylpropan-2-yl)-N-(1-diethylphosphono-2,2-dimethylpropyl)-aminoxyl) based alkoxyamines were studied by means of (1)H and (31)P NMR spectroscopy aiming to distinguish the contributions of diastereoselective homolysis and coupling to the total equilibrium diastereomeric distribution. The TEMPO-based compounds reveal no diastereomeric excess while DEPN based compounds show a moderate excess both upon homolysis and coupling. The diastereomeric preference of homolysis for DEPN-(propionate-like) adducts does not depend on the ester group and it is mainly affected by the size of beta-substituents. The diastereoselective coupling is sensitive to the total recombination rate constant k(c) and diastereoselectivity increases with the decrease of k(c). Small diastereoselective coupling is found in the recombination of DEPN with sec-butyl isobutyrate radical, where no prochiral centers are formed upon cleavage of corresponding alkoxyamine.     

Amino Acid‐Specific,Ribonucleotide‐Promoted Peptide Formation in the Absence of Enzymes

Nucleic acids and polypeptides are at the heart of life. It is interesting to ask whether the monomers of these biopolymers possess intrinsic reactivity that favors oligomerization in the absence of enzymes. We have recently observed that covalently linked peptido RNA chains form when mixtures of monomers react in salt‐rich condensation buffer. Here, we report the results of a screen of the 20 proteinogenic amino acids and four ribonucleotides. None of the amino acids prevent phosphodiester formation, so all of them are compatible with genetic encoding through RNA chain growth. A reactivity landscape was found, in which peptide formation strongly depends on the structure of the amino acid, but less on the nucleobase. For example, proline gives ribonucleotide‐bound peptides most readily, tyrosine favors pyrophosphate and phosphodiester formation, and histidine gives phosphorimidazolides as dominant products. When proline and aspartic acid were allowed to compete for incorporation, only proline was found at the N‐terminus of peptido chains. The reactivity described here links two fundamental classes of biomolecules through reactions that occur without enzymes, but with amino acid specificity.     

Asymmetric Mannich-type reactions for the synthesis of aspartic acid derivatives from chiral N-tert-butanesulfinylimino esters

Addition of ketene acetals to sulfinimines derived from homochiral N-tert-butanesulfinamide using various Lewis acids furnishes derivatives of aspartic acid in diastereomeric ratios up to 97:3. Following an easy removal of the N-tert-butanesulfinyl chiral auxiliary, optical active beta-amino esters are obtained.     

Origins of opposite syn-anti diastereoselectivities in primary and secondary amino acid-catalyzed intermolecular aldol reactions involving unmodified alpha-hydroxyketones

The effects of different amino acid catalysts on the stereoselectivity of the direct intermolecular aldol reactions between alpha-hydroxyketones and isobutyraldehyde or 4-nitrobenzaldehyde have been studied with the aid of density functional theory methods. The transition states of the crucial C-C bond-forming step with the enamine intermediate addition to the aldehyde for the proline and threonine-catalyzed asymmetric aldol reactions are reported. B3LYP/6-31+G** calculations provide a good explanation for the opposite syn vs anti diastereoselectivity of these two kinds of amino acid catalysts (anti-selectivity for the secondary cyclic amino acids proline, syn-selectivity for the acyclic primary amino acids like threonine). Calculated and observed diastereomeric ratio and enantiomeric excess values are in good agreement.     

Highly diastereoselective mannich-type reactions of chiral N-acylhydrazones

The Lewis acid-mediated addition of silyl enolates to easily accessible homochiral N-acylhydrazones derived from 3-amino-2-oxazolidinones proceeded in yields up to 71% and diastereomeric ratios of 99:1. In most cases, optimal reaction conditions entailed the simple use of ZnCl(2) in acetonitrile at room temperature. Hydrazones derived from phenyl-, isopropyl-, and benzyl-substituted 2-oxazolidinones were examined in the reaction in terms of yield and diastereoselectivity. The facile SmI(2)-mediated N-N bond cleavage of the formed hydrazines was demonstrated yielding a beta-amino acid derivative. Hence, the overall reaction sequence constitutes an efficient asymmetric Mannich-type reaction. The sense of diastereoselectivity was explained by a preferential attack on the less shielded Si face of the chiral hydrazones and confirmed by means of X-ray crystallography.     

Asymmetric synthesis of α-mercapto-β-amino acid derivatives: application to the synthesis of polysubstituted thiomorpholines

Tandem conjugate addition of homochiral lithium N-benzyl-N-(α-methyl-p-methoxybenzyl)amide to tert-butyl cinnamate and enolate trapping with TsS^tBu proceeds with high diastereoselectivity to give a homochiral anti-α-tert-butylthio-β-amino ester. Stepwise deprotection gives the corresponding free α-tert-butylthio-β-amino acid without epimerisation. Tandem conjugate addition of homochiral lithium N-allyl-N-(α-methylbenzyl)amide to tert-butyl cinnamate and enolate trapping with TsS^tBu followed by conversion of the S-tert-butyl group to a disulphide, and reduction with Lalancette’s reagent generates polysubstituted thiomorpholine derivatives.     

Stereoselective synthesis of activated cyclopropanes with an α-pyridinium acetamide bearing an 8-phenylmenthyl group as the chiral auxiliary

The reaction between an α-pyridinium acetamide bearing an 8-phenylmenthyl group as the chiral auxiliary and β-substituted methylidenemalononitriles gave rise to trans-cyclopropanes with diastereomeric ratios of up to 98:2. For most of the reactions, the absolute stereochemistry of the major product was found to be opposite of that of the major products of the reaction of the corresponding ester series, which also utilized the 8-phenylmenthyl group.     

Conjugate addition of lithium N-tert-butyldimethylsilyloxy-N-(α-methylbenzyl)amide: asymmetric synthesis of β-trisubstituted amino acids

Conjugate addition of the homochiral ammonia equivalent lithium N-tert-butyldimethylsilyloxy-N-(α-methylbenzyl)amide to a range of α,β-unsaturated esters gives the corresponding β-amino esters in moderate to good levels of diastereoselectivity. O-Desilylation and cyclisation furnishes homochiral isoxazolidin-5-ones in >99:1 dr after purification. Sequential alkylation of these templates proceeds to give the corresponding 3,4-anti-disubstituted and 3,4,4-trisubstituted derivatives as single diastereoisomers after purification. The first alkylation occurs with high levels of diastereoselectivity on the face of the enolate anti to the C(3)-substituent, whereas the facial selectivity of the second alkylation is governed by a chiral relay effect, which depends upon the relative steric bulk of both the C(3)- and C(4)-substituents. Subsequent hydrogenolysis promotes cleavage of both the N-α-methylbenzyl group and the N-O bond within the isoxazolidin-5-one ring in one pot to give the corresponding β^2,2,3-trisubstituted amino acids directly.     

α-Chymotrypsin-catalyzed peptide synthesis in frozen aqueous solution using N-protected amino acid carbamoylmethyl esters as acyl donors

A kinetically controlled peptide synthesis catalyzed by α-chymotrypsin was performed in frozen aqueous solution (ice, −24 °C). The yield of the peptide was significantly improved by the use of the carbamoylmethyl (Cam) ester as the acyl donor instead of the conventional ethyl ester. The peptide yield increased up to ca. 90% when N-benzyloxycarbonyl (CBZ)-Phe-OCam and H-Phe-NH₂ were used as the acyl donor and nucleophile, respectively. Such an improvement of the peptide yield in ice was also observed in the coupling of other CBZ-amino acid Cam esters as acyl donors. Furthermore, this approach was applied to the synthesis of peptides containing d-amino acids. The peptides such as CBZ-d-Phe-Phe-NH₂, CBZ-Phe-d-Phe-NH₂ and CBZ-d-Phe-d-Phe-NH₂ were also obtained in excellent to moderate yields in ice. A high diastereoselectivity towards the l–l peptide was observed when the racemic amino acid Cam ester was used as the acyl donor in ice.     

α-Amino esters as nucleophiles in diastereoselective palladium catalysed allylic substitution reactions

Allylic acetates undergo palladium catalysed allylic substitution with amino ester nucleophiles. Using enantiomerically pure α-amino esters, the substitution products are obtained with moderate diastereoselectivity (up to 85:15: 70% d.e.). The reactions could also be performed using an enantiomerically pure ligand, which was found to exert a stronger influence over the stereochemical outcome.     

Peptide Chirality Sensing by a Cyclodextrin–Polythiophene Conjugate

A new cyclodextrin–polythiophene conjugate ( CDPT ) has been prepared by attaching permethyl-α-cyclodextrins to polythiophene (PT) through a hexamethylene tether. Circular dichroism spectral examination of CDPT revealed that only a weak positive Cotton effect (Δε=0.1 M ⁻¹ cm⁻¹) was induced at the main band of the PT in dimethyl sulfoxide and similarly weak bisignate signals in pure and aqueous methanol solutions, which indicates that the α-cyclodextrins appended to PT with a long tether are ineffective in inducing a homochiral structure in the PT backbone. Nevertheless, enantiomeric amino acids and dipeptides added to an aqueous methanolic solution of CDPT caused chirality-dependent hypochromic changes in the UV/Vis spectra, which enabled us to sense these species and quantitatively determine the enantioselectivity by observing the difference in absorbance upon interaction with pairs of enantiomers. Enantiomeric d,d /l,l -dipeptide pairs rather than D /L -amino acid pairs were better differentiated in general, the highest dd /ll selectivity of 13.7 being observed for Phe-Phe.     

Alkaloids of the flora of Siberia and Altai: XX. Synthesis of 5-aryl(hetaryl)-substituted anthranilic acid esters

Cross-coupling of methyl 2-acetylamino-5-bromobenzoate and 5′-bromolappaconitine with aryl-, furyl-, pyridyl-, and 5-acetylthiophen-2-ylboronic acids or 1-(2-fluoroquinolin-3-yl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane gave the corresponding 5-aryl(hetaryl)-substituted anthranilic acid derivatives. The use of the two-phase toluene-water system as reaction medium and addition of tetrabutylammonium bromide allows the cross-coupling to be accomplished under mild conditions. The catalytic system Pd(dba)₂-AsPh₃ was found to be efficient in the cross-coupling of methyl 2-acetylamino-5-bromobenzoate with furyl- and pyridylboronic acids, whereas the system Pd(OAc)₂-(o-Tol)₃P ensured good results in the reactions of 5′-bromolappaconitine with hetarylboronic acids. Facile esterification at the C⁸-OH and C⁹-OH groups of the aconitane skeleton was observed in the reactions of 5′-bromolappaconitine and 5′-phenyllappaconitine with phenylboronic acid. 5′-Bromo-8,9-O-(phenylboranediyl)lappaconitine under the Suzuki reaction conditions underwent hydrolysis of the boronic ester moiety with formation of the cross-coupling product of 5′-bromolappaconitine with phenylboronic acid.     

(3+3)-Cyclocondensation of the enantiopure and racemic forms of trans-1,2-diaminocyclohexane with terephthaldehyde. Formation of diastereomeric molecular triangles and their stereoselective solid-state stacking into microporous chiral columns

The non-templated reaction of both the homochiral as well as the racemic form of trans-1,2-diaminocyclohexane with terephthaldehyde affords (3+3)-cyclocondensed molecular triangles in practically quantitative yields. The configuration of the diastereomeric products resulting in the individual reactions has been determined by ¹H and ¹³C NMR spectroscopy. Unambiguous proof has been obtained by X-ray crystal structure analysis of both alternative diastereomers, revealing also a stereoselective stacking of the triangles into microporous chiral columns.     

Pyranosyl-RNA: chiroselective self-assembly of base sequences by ligative oligomerization of tetra nucleotide-2′,3′-cyclophosphates (with a commentary concerning the origin of biomolecular homochirality)

Background: Why did Nature choose furanosyl-RNA and not pyranosyl-RNA as her molecular genetic system? An experimental approach to this problem is the systematic comparison of the two isomeric oligonucleotide systems with respect to the chemical properties that are fundamental to the biological role of RNA, such as base pairing and nonenzymic replication. Pyranosyl-RNA has been found to be not only a stronger, but also a more selective pairing system than natural RNA; both form hairpin structures with comparable ease. Base sequences of pyranosyl-RNA can be copied by template-controlled replicatioe ligation of short activated oligomers (e.g. tetramer-2′,3′-cyclophosphates) under mild and potentially natural conditions. The copying proceeds with high regio-selectivity as well as chiroselectivity: homochiral template sequences mediate the formation of the correct (4′→2′)-phosphodiester junction between homochiral tetramer units provided they have the same sense of chirality as the template. How could homochiral template sequences assemble themselves in the first place?Results: Higher oligomers of pyranosyl-RNA can self-assemble in dilute solutions under mild conditions by ligative oligomerization of tetramer-2′,3′-cyclophosphates containing hemi self-complementary base sequences. The only side reaction that effectively competes with ligation is hydrolytic deactivation of 2′,3′-cyclophosphate end groups. The ligation reaction is highly chiroselective; it is slower by at least two orders of magnitude when one of the (d)-ribopyranosyl units of a homochiral (d)-tetramer-2′,3′-cyclophosphate is replaced by a corresponding (l)-unit, except when the (l)-unit is at the 4′ end of the tetramer and carries a purine, when the oligomerization rate can be ∼ 10% of that shown for a homochiral isomer. The oligomerization of homochiral tetramers is not, or only weakly, inhibited by the presence of the non-oligomerizing diastereomers.Conclusions: Available data on the chiroselective self-directed oligomerization of tetramer-2′,3′-cyclophosphates allow us to extrapolate that sets of tetramers with different but mutually fitting base sequences can be expected to co-oligomerize stochastically and generate sequence libraries consisting of predominantly homochiral (d)- and (l)-oligomers, starting from the racemic mixture of tetramers containing all possible diastereomers. Such a capability of an oligonucleotide system deserves special attention in the context of the problem of the origin of biomolecular homochirality: breaking molecular mirror symmetry by de-racemization is an intrinsic property of such a system whenever the constitutional complexity of the products of co-oligomerization exceeds a critical level.