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.     

Determining the Diastereoselectivity of the Formation of Dipeptidonucleotides by NMR Spectroscopy

Proteins are composed of l -amino acids, but nucleic acids and most oligosaccharides contain d -sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate-linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Here we report how the diastereoselectivity of the first peptide coupling of the peptido RNA pathway can be determined in situ by NMR spectroscopy. When a racemic mixture of an amino acid ester was allowed to react with an 5′-aminoacidyl nucleotide, diastereomeric ratios of up to 72 : 28 of the resulting dipeptido nucleotides were found by integration of ³¹P- or ¹H-NMR peaks. The highest diastereomeric excess was found for the homochiral coupling product d -Ser-d -Trp, phosphoramidate-linked to adenosine 5′-monophosphate with its d -ribose ring. When control reactions with an N-acetyl amino acid and valine methyl ester were run in organic solvent, the diastereoselectivity was found to be lower, with diastereomeric ratios≤62 : 38. The results from the exploratory study thus indicate that the ribonucleotide residue not only facilitates the coupling of lipophilic amino acids in aqueous medium but also the formation of a homochiral dipeptide. The methodology described here may be used to search for other stereoselective reactions that shed light on the origin of homochirality.     

Ribonucleotides and RNA Promote Peptide Chain Growth

All known forms of life use RNA‐mediated polypeptide synthesis to produce the proteins encoded in their genes. Because the principal parts of the translational machinery consist of RNA, it is likely that peptide synthesis was achieved early in the prebiotic evolution of an RNA‐dominated molecular world. How RNA attracted amino acids and then induced peptide formation in the absence of enzymes has been unclear. Herein, we show that covalent capture of an amino acid as a phosphoramidate favors peptide formation. Peptide coupling is a robust process that occurs with different condensation agents. Kinetics show that covalent capture can accelerate chain growth over oligomerization of the free amino acid by at least one order of magnitude, so that there is no need for enzymatic catalysis for peptide synthesis to begin. Peptide chain growth was also observed on phosphate‐terminated RNA strands. Peptide coupling promoted by ribonucleotides or ribonucleotide residues may have been an important transitional form of peptide synthesis that set in when amino acids were first captured by RNA.     

Mixed Anhydride Intermediates in the Reaction of 5(4H)‐Oxazolones with Phosphate Esters and Nucleotides

5(4H)‐Oxazolones can be formed through the activation of acylated α‐amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic‐phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono‐substituted phosphate group at the 3’‐ or 5’‐terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3’‐terminus are considered to be particularly relevant to the common prebiotic chemistry of α‐amino acids and nucleotides.     

Hydrogen‐bonding features in the 1:2 adduct of 4‐aminobenzoic acid and l‐proline

The title adduct, 4‐aminobenzoic acid–l ‐proline–water (1/2/1), C₇H₇NO₂·2C₅H₉NO₂·H₂O, contains two independent proline chains with a C(5) motif, each of the head‐to‐tail type and each held together by N—H...O hydrogen bonds, propagated parallel to the b and c axes of the unit cell. Thus, the proline residues aggregate parallel to the ac plane. 4‐Aminobenzoic acid (PABA) residues are arranged on both sides of the proline aggregate and are connected through water O atoms, which act as acceptors for PABA and as hydrogen‐bond donors to the amino acids. The characteristic features of PABA, viz. twisting of the carboxyl plane from the aromatic ring and the formation of a head‐to‐tail chain motif [C(8)] along the b axis, are observed. A distinct feature of the structure is that no proton transfer occurs between proline and PABA.     

How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water

Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5’‐monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two‐fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life‐like reaction systems in the absence of enzymes.     

Organocatalysts Derived from Unnatural α‐Amino Acids: Scope and Applications

The organocatalytic properties of unnatural α‐amino acids are reviewed. Post‐translational derivatives of natural α‐amino acids include 4‐hydroxy‐l ‐proline and 4‐amino‐l ‐proline scaffolds, and also proline homologues. The activity of synthetic unnatural α‐amino acid‐based organocatalysts, such as β‐alkyl alanines, alanine‐based phosphines, and tert‐leucine derivatives, are reviewed herein. The organocatalytic properties of unnatural monocyclic, bicyclic, and tricyclic proline derivatives are also reviewed. Several families of these organocatalysts permit the efficient and stereoselective synthesis of complex natural products. Most of the reviewed organocatalysts accelerate the reported reactions through covalent interactions that raise the HOMO (enamine intermediates) or lower the LUMO (iminium intermediates).     

Simultaneous Chain‐Growth and Step‐Growth Polymerization—A New Route to Cyclic Polymers

Reinvestigation of numerous ring‐opening polymerizations by means of MALDI‐TOF mass spectrometry has evidenced that cyclic polymers were formed as the only reaction products or, at least, in large fractions. This finding is ascribed to the intermediate formation of difunctional chains having active end groups that can react with each other. Due to the low concentration of these difunctional chains cyclization is favored over chain extension according to the Ruggli–Ziegler dilution principle. A polymerization mechanism which usually favors the formation of cyclic polymers is the zwitterionic polymerization, but an exception from this rule is known. The following classes of monomers were discussed: α‐amino acid, N‐carboxyanhydrides (oxazolidine‐2,5‐diones), dithiolane‐2,4‐diones, 5,5‐dimethyl‐1,3,2‐dioxathiolan‐4‐one‐2‐oxide, salicylic acid O‐carboxyanhydride, L ‐lactide and D ,L ‐lactide, hexamethyl cyclotrisiloxane, and macrocyclic dithiocarbamates.

     

Wet and Functional Adhesives from One‐Step Aqueous Self‐Assembly of Natural Amino Acids and Polyoxometalates

Sessile organisms have undergone long‐term evolution to develop the unique ability by positioning themselves on wet solid surface through secreting adhesive proteins. The present study reveals that natural amino acid monomers can also exhibit similar adhesion capacity. This kind of biomimetic adhesives were created by the one‐step aqueous assembly of basic amino acids with assistance of anionic polyoxometalates. The polyoxometalates not only serve as multivalent scaffold to initiate the supramolecular cross‐linking of amino acid molecules, but also function as a redox component, bestowing the wet adhesives with electrochromic features.     

Liquid chromatographic resolution of proline and pipecolic acid derivatives on chiral stationary phases based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid

Two liquid chromatographic chiral stationary phases based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid were applied to the resolution of the amide derivatives of cyclic α‐amino acids including proline and pipecolic acid. Among the five amide derivatives of proline, aniline amide was resolved best on the first chiral stationary phase, which contains two N–H tethering amide groups, with the separation factor of 1.31 and the resolution of 2.60, and on the second chiral stationary phase, which contains two N–CH₃ tethering amide groups, with the separation factor of 1.57 and the resolution of 5.50. Among the five amide derivatives of pipecolic acid, 2‐naphthyl amide was resolved best on the first chiral stationary phase with the separation factor of 1.30 and the resolution of 1.75, but 1‐naphthylmethyl amide was resolved best on the second chiral stationary phase with the separation factor of 1.30 and the resolution of 2.26. In general, the second chiral stationary phase was found to be better than the first chiral stationary phase in the resolution of the amide derivatives of cyclic α‐amino acids. In this study, the second chiral stationary phase was first demonstrated to be useful for the resolution of secondary amino compounds.     

Facile synthesis of well‐defined pH‐liable Schiff‐base‐type photosensitive polymers via visible‐light‐activated ambient temperature RAFT polymerization

Inspired by the structure character and photosensitive molecular mechanism of natural rhodopsin or bacteriorhodopsin, a novel pH‐liable photosensitive polymer whose chromophores directly bind with Schiff base linkages was designed. Accordingly, 2‐((3‐phenylallylidene)amino)ethyl methacrylate (PAAEMA), 2‐((3‐(4‐fluorophenyl)allylidene)amino)ethyl methacrylate (FPAAEMA), and 2‐((3‐(4‐methoxyphenyl)allylidene)amino)ethyl methacrylate (MPAAEMA) monomers were synthesized. These monomers were polymerized upon irradiating with mild visible light at ambient temperature. The results indicate that Schiff base linkages of these monomers are stable under such mild polymerizing conditions, and the weak absorption of dithioester functionalities in the visible wave range leads to a rapid and well‐controlled RAFT polymerization. The polymerization rate slows down but initialization period significantly shortens on increasing the feed molar ratio of monomer. The pendant electron‐withdrawing‐group‐substituted chromophore improves the reactivity of monomer, but electron‐donating‐group‐substituted chromophore significantly inactivates monomer. Glycidyl methacrylate (GMA) may well incorporate in this polymer via RAFT random copolymerization of PAAEMA and GMA monomers due to the comparable reactivity ratios of this monomer pair. PolyMPAAEMA exhibits reversible fluorescence emitting or quenching upon deprotonating or protonating the Schiff base linkages. This fluorescence behavior may be of interest in the fabrication of pH‐responsive photosensors, light modulators, or actuators. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6668–6681, 2009     

A Multiple Multicomponent Approach to Chimeric Peptide–Peptoid Podands

The success of multi‐armed, peptide‐based receptors in supramolecular chemistry traditionally is not only based on the sequence but equally on an appropriate positioning of various peptidic chains to create a multivalent array of binding elements. As a faster, more versatile and alternative access toward (pseudo)peptidic receptors, a new approach based on multiple Ugi four‐component reactions (Ugi‐4CR) is proposed as a means of simultaneously incorporating several binding and catalytic elements into organizing scaffolds. By employing α‐amino acids either as the amino or acid components of the Ugi‐4CRs, this multiple multicomponent process allows for the one‐pot assembly of podands bearing chimeric peptide–peptoid chains as appended arms. Tripodal, bowl‐shaped, and concave polyfunctional skeletons are employed as topologically varied platforms for positioning the multiple peptidic chains formed by Ugi‐4CRs. In a similar approach, steroidal building blocks with several axially‐oriented isocyano groups are synthesized and utilized to align the chimeric chains with conformational constrains, thus providing an alternative to the classical peptido‐steroidal receptors. The branched and hybrid peptide–peptoid appendages allow new possibilities for both rational design and combinatorial production of synthetic receptors. The concept is also expandable to other multicomponent reactions.     

Basic Amino Acid Conjugates of 1,2‐Diselenan‐4‐amine with Protein Disulfide Isomerase‐like Functions as a Manipulator of Protein Quality Control

Protein disulfide isomerase (PDI) can assist immature proteins to correctly fold by controlling cysteinyl disulfide (SS)‐relating reactions (i. e., SS‐formation, SS‐cleavage, and SS‐isomerization). PDI controls protein quality by suppressing protein aggregation, as well as functions as an oxidative folding catalyst. Following the amino acid sequence of the active center in PDI, basic amino acid conjugates of 1,2‐diselenan‐4‐amine ( 1 ), which show oxidoreductase‐ and isomerase‐like activities for SS‐relating reactions, were designed as a novel PDI model compound. By conjugating the amino acids, the diselenide reduction potential of compound 1 was significantly increased, causing improvement of the catalytic activities for all SS‐relating reactions. Furthermore, these compounds, especially histidine‐conjugated one, remarkably suppressed protein aggregation even at low concertation (0.3 mM～). Thus, it was demonstrated that the conjugation of basic amino acids into 1 simultaneously achieves the enhancement of the redox reactivity and the capability to suppress protein aggregation.     

Chemical cross‐linking with NHS esters: a systematic study on amino acid reactivities

Structure elucidation of tertiary or quaternary protein structures by chemical cross‐linking and mass spectrometry (MS) has recently gained importance. To locate the cross‐linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N‐hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross‐linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the α‐NH₂‐group of the N‐terminus or the ε‐NH₂‐group of lysine. As soon as additional cross‐linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type‐1 cross‐link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd.     

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.     

Chiral discrimination of β‐3‐homo‐amino acids using the kinetic method

Chiral discrimination of seven enantiomeric pairs of β‐3‐homo‐amino acids was studied by using the kinetic method and trimeric metal‐bound complexes, with natural and unnatural α‐amino acids as chiral reference compounds and divalent metal ions (Cu²⁺ and Ni²⁺) as the center ions. The β‐3‐homo‐amino acids were selected for this study because, first of all, chiral discrimination of β‐amino acids has not been extensively studied by mass spectrometry. Moreover, these β‐3‐homo‐amino acids studied have different aromatic side chains. Thus, the emphasis was to study the effect of the side chain (electron density of the phenyl ring, as well as the difference between phenyl and benzyl side chains) for the chiral discrimination. The results showed that by the proper choice of a metal ion and a chiral reference compound, all seven enantiomeric pairs of β‐3‐homo‐amino acids could be differentiated. Moreover, it was noted that the β‐3‐homo‐amino acids with benzyl side chains provided higher enantioselectivity than the corresponding phenyl ones. However, increasing or decreasing the electron density of the aromatic ring by different substituents in both the phenyl and benzyl side chains had practically no role for chiral discrimination of β‐3‐homo‐amino acids studied. When copper was used as the central metal, the phenyl side chain containing reference molecules (S)‐2‐amino‐2‐phenylacetic acid (L ‐Phg) and (S)‐2‐amino‐2‐(4‐hydroxyphenyl)‐acetic acid (L ‐4′‐OHPhg) gave rise to an additional copper‐reduced dimeric fragment ion, [Cu^I(ref)(A)]⁺. The inclusion of this ion improved noticeably the enantioselectivity values obtained. Copyright © 2010 John Wiley & Sons, Ltd.     

Mapping the Landscape of Potentially Primordial Informational Oligomers: (3′→2′)‐D‐Phosphoglyceric Acid Linked Acyclic Oligonucleotides Tagged with 2,4‐Disubstituted 5‐Aminopyrimidines as Recognition Elements

The (3′→2′)‐phosphodiester glyceric acid backbone containing an acyclic oligomer tagged with 2,4‐disubstituted pyrimidines as alternative recognition elements have been synthesized. Strong cross‐pairing of a 2,4‐dioxo‐5‐aminopyrimidine hexamer, rivaling locked nucleic acid (LNA) and peptide nucleic acid (PNA), with complementary adenine‐containing DNA and RNA sequences was observed. The corresponding 2,4‐diamino‐ and 2‐amino‐4‐oxo‐5‐aminopyrimidine‐tagged oligomers were synthesized, but difficulties in deprotection, purification, and isolation thwarted further investigations. The acyclic phosphate backbone structure of the protected oligomer seems to be prone to an eliminative degradation owing to the acidic hydrogen at the 2′‐position—an arrangement that renders the oligomer vulnerable to the conditions used for the removal of the protecting groups on the heterocyclic recognition element. However, the free oligomers seem to be stable under the conditions investigated.     

Determination of 4‐hydroxyproline‐2‐epimerase activity by capillary electrophoresis: A stereoselective platform for inhibitor screening of amino acid isomerases

Isomerases involved in the metabolism of D /L ‐amino acids represent promising therapeutic targets for treatment of disease. Herein, we report a tunable platform for the assessment of enzymatic kinetics involving amino acid isomerization by CE that offers improved selectivity and sensitivity over traditional methods. Enzyme activity and competition assays were evaluated for various hydroxyproline diastereoisomers, proline enantiomers and their structural analogs using 4‐hydroxyproline‐2‐epimerase as a model system. In this work, pyrrole 2‐carboxylic acid was found to be a selective inhibitor of 4‐hydroxyproline‐2‐epimerase with a half‐maximal inhibition concentration of (2.3±0.1) mM. Reliable methods for unambiguous characterization of amino acid isomerases are required for the screening of novel inhibitors with epimerase and/or racemase activity.     

Adding a Functional Handle to Nature′s Building Blocks: The Asymmetric Synthesis of β‐Hydroxy‐α‐Amino Acids

β‐Hydroxy‐α‐amino acids are not only used by synthetic chemists but are also found in natural products, many of which show anti‐microbial or anti‐cancer properties. Over the past 30 years, chemists have searched for many asymmetric routes to these useful building blocks. Initial attempts to synthesize these compounds utilized chiral auxiliaries and the reactions of glycine equivalents with aldehydes to form two stereocenters in one step. Other methods with the formation of specific intermediates or that were aimed at a specific amino acid have also been investigated. Asymmetric hydrogenation by dynamic kinetic resolution has emerged as a high‐yielding method for the synthesis of an array of modified amino acids with good stereoselectivity. More recently, amino‐acid functionalization and multicomponent reactions have increased the atom economy and simplified many long and difficult routes. In this Focus Review, many of the elegant syntheses of these compounds are explored. The applications of β‐hydroxy‐α‐amino acids in natural‐product synthesis are also mentioned.     

The Role of a Dipeptide Outer‐Coordination Sphere on H2‐Production Catalysts: Influence on Catalytic Rates and Electron Transfer

The outer‐coordination sphere of enzymes acts to fine‐tune the active site reactivity and control catalytic rates, suggesting that incorporation of analogous structural elements into molecular catalysts may be necessary to achieve rates comparable to those observed in enzyme systems at low overpotentials. In this work, we evaluate the effect of an amino acid and dipeptide outer‐coordination sphere on [Ni(P^Ph₂N^Ph‐R₂)₂]²⁺ hydrogen production catalysts. A series of 12 new complexes containing non‐natural amino acids or dipeptides was prepared to test the effects of positioning, size, polarity and aromaticity on catalytic activity. The non‐natural amino acid was either 3‐(meta‐ or para‐aminophenyl)propionic acid terminated as an acid, an ester or an amide. Dipeptides consisted of one of the non‐natural amino acids coupled to one of four amino acid esters: alanine, serine, phenylalanine or tyrosine. All of the catalysts are active for hydrogen production, with rates averaging ～1000 s^?1, 40 % faster than the unmodified catalyst. Structure and polarity of the aliphatic or aromatic side chains of the C‐terminal peptide do not strongly influence rates. However, the presence of an amide bond increases rates, suggesting a role for the amide in assisting catalysis. Overpotentials were lower with substituents at the N‐phenyl meta position. This is consistent with slower electron transfer in the less compact, para‐substituted complexes, as shown in digital simulations of catalyst cyclic voltammograms and computational modeling of the complexes. Combining the current results with insights from previous results, we propose a mechanism for the role of the amino acid and dipeptide based outer‐coordination sphere in molecular hydrogen production catalysts.