A rapid synthetic route to conformationally restricted [5,5]-bicyclic nucleoside-amino acid conjugates

A concise synthetic route to a novel class of conformationally rigid 3',4'-cis-fused bicyclic nucleoside derivatives has been developed. The synthetic strategy and approach involves initial synthesis of a key [5,5]-bicyclic 6-aminofurofuran-2-one scaffold, employing an L-serine derived aminobutenolide as a strategically functionalized chiral template. Subsequent utilization of the carbonyl functionality of the above bicyclic lactone toward nucleobase incorporation, and linking of the resident amine functionality with appropriately protected amino acids completed the syntheses of the target bicyclic nucleoside-amino acid conjugates. Following the above route, and utilizing a combination of easily available nucleobases (4) and amino acids (4) as the two diversity elements, combinatorial synthesis of a 16-member demonstration library of the title amino acid-linked nucleosides has been accomplished.     

De novo synthetic route to a combinatorial library of peptidyl nucleosides

A stereoselective synthetic route has been developed for the combinatorial synthesis of a structurally unique class of C-4' side chain modified peptide-linked nucleosides. The synthetic strategy and approach involves initial synthesis of a strategically functionalized amino butenolide template, utilizing L-serine as a chiral starting material. Subsequent transformation of the above lactone to C4' aminoalkyl substituted nucleosides, followed by the peptidic coupling of the C4' side chain amine with various amino acids completed the syntheses of the target peptidyl nucleosides. Employing the above route, and utilizing a combination of easily available nucleobases (4) and amino acids (6) as the two diversity elements, synthesis of a 24-member combinatorial library of the title peptide-linked nucleosides has been accomplished.     

Automated solid-phase synthesis of linear nitrogen-linked compounds

A synthetic library motif has been developed to create linear, nitrogen-linked compounds as screening libraries to target structured RNA for drug discovery. Scaffolds were created in situ from suitably protected bifunctional compounds linked together either by acyl or amine links. Acyl links were created from amino acids, which also introduce one degree of functionality. Amine links from the amino acid nitrogen were created from an N-protected amino alcohol via Fukuyama Mitsunobu alkylation. Each amine site can then be used for introducing functionality or extending the scaffold. This synthetic scheme can be used to create a wide variety of modified-backbone PNA in situ, as shown by the synthesis of a PNA-type monomer. The synthesis steps have been enabled on a 96-well parallel-array synthesizer for high-throughput synthesis. The present study represents a versatile synthetic approach to a wide variety of potential RNA-binding molecules.     

Design and synthesis of dinucleotide 5'-triphosphates with expanded functionality

We propose the new approach to the synthesis of 5'-triphosphate derivatives of natural and modified dinucleotides with expanded functionality. Our strategy includes the combination of the solution phase synthesis of necessary dimers using the wide range of nucleic acids chemistry methods and the subsequent introduction of the triphosphate residue. A number of the new potential substrates for the template dependent synthesis of nucleic acids with expanded functionality are obtained, namely, 5'-triphosphates of dinucleotides containing the functionally active groups in heterocyclic bases, in carbohydrate-phosphate backbone, and the groups mimicking the residues of natural amino acids. The abilities of the proposed synthetic route are also demonstrated by the synthesis of 5'-triphosphates of dinucleotides with modified carbohydrate-phosphate backbone.     

Synthesis and evaluation of glycosidase inhibitory activity of octahydro-2H-pyrido[1,2-a]pyrimidine and octahydro-imidazo[1,2-a]pyridine bicyclic diazasugars

An efficient chiron approach for the synthesis of bicyclic diazasugars 4a and 4b having both -CH(2)OH and -OH functionality at the same carbon atom (C-6) is reported. Thus, easily available alpha-D-xylo-pentodialdo-1,4-furanose 5, obtained from D-glucose, on aldol-crossed Cannizzaro reaction followed by hydrogenolysis afforded 7. The regio-selective beta- and alpha-sulfonylation of hydroxymethyl groups in 7 afforded 8a (beta-sulfonylation) and 11 (alpha-sulfonylation) in good yields. The cleavage of the 1,2-acetonide functionality, individually in 8a and 11, followed by reaction with ethylenediamine gave in situ formation of sugar aminals that undergo concomitant nucleophilic displacement of the sulfonyloxy group, by amino functionality, to give hitherto unknown bicyclic diazasugars 4a and 4b, respectively. The inhibitory potency of the earlier reported bicyclic diazasugars 3a,b and 4a,b was evaluated against alpha- and beta-glycosidases and they were found to be potent and specific against the beta-glycosidases with IC(50) and K(1) values in the micro molar range.     

Ethynylglycine synthon from Garner’s aldehyde: a useful precursor for the synthesis of non-natural amino acids

Summary. The ethynylglycine synthon, namely (R)-2,2-dimethyl-3-(tert-butoxycarbonyl)-4-ethynyl-oxazolidine, can be obtained through the synthetic elaboration of naturally occurring serine. This compound has been exploited as a helpful and versatile non-racemic building block to be used for the design and synthesis of biologically important compounds, mainly non-natural α-amino acids. Taking advantage of the terminal acetylene moiety several synthetic applications can be designed. Metalation followed by trapping with electrophiles or Cu/Pd catalysed coupling with aromatic halogenides are shown to deliver useful precursors of ethynylglycine derivatives. Additions of bimetallic reagents like stannyl- or silylcuprates are useful entries for the regio- and stereoselective functionalization of the lateral chain, aimed at the synthesis of modified vinylglycine precursors.An overview of our recent work in the field will be given, and the use of ethynylglycine synthon in the synthesis of non-racemic saturated and unsaturated non-natural amino acids will be briefly reviewed.     

Synthesis of fluorine-containing bioisosteres corresponding to phosphoamino acids and dipeptide units

It has been shown that fluorinated analogues of naturally occurring biological active compounds including amino acids often exhibit unique physiological activity. Among wide varieties of fluorine-containing amino acids, nonhydrolyzable phosphoamino acids possessing a substituent of the difluoromethylene (CF(2)) unit for the phosphoryl ester oxygen are of value in the medicinal and biological fields. We have engaged in the synthesis of these classes of nonhydrolyzable phosphoamino acids corresponding to pTyr 3, pSer 4, and pThr 5 with their incorporation into peptides using newly developed deprotecting procedures. In this article, stereoselective synthesis of the CF(2)-substituted pThr mimetics and development of a two-step deprotecting methodology for the nonhydrolyzable analogues are reviewed. In the course of the above synthetic study, we found that gamma,gamma-difluoro-alpha,beta-enoates were reduced to gamma-fluoro-beta,gamma-enoates by organocopper reagents and then applied to the synthesis of (Z)-fluoroalkene dipeptide isosteres, which have served as potential dipeptide mimetics having structural as well as electrostatic similarity to the parent peptide bonds. Furthermore, mechanistic investigation of the organocopper-mediated reduction led us to development of a SmI(2)-mediated approach toward the synthesis of the fluoroalkene isosteres.     

Aromatic interactions with naphthylalanine in a β‐hairpin peptide

Stable peptides have been explored as epitope mimics for protein–protein and protein–nucleic acid interactions; however, presentation of a regular structure is critical. Aromatic interactions are ubiquitous and are competent at stabilizing a β‐hairpin fold. The greatest stabilization has been reported from pairs of tryptophan side chains. Naphthylalanine residues are often used as tryptophan replacements, but it is not clear if 1‐naphthylalanine or 2‐naphthylalanine is adequate at replicating the geometry and stability observed with tryptophan aromatic interactions. Herein, a 12‐residue peptide has been constructed with laterally disposed aromatic amino acids. A direct comparison is made between tryptophan and other bicyclic, unnatural amino acids. Significant stabilization is gained from all bicyclic amino acids; however, geometric analysis shows that only 1‐naphthylalanine adopts a similar edge to face geometry as tryptophan, whereas the 2‐naphthylalanine appears most similar to a substituted phenylalanine. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

3-Thiopropionic acid as a highly versatile multidetachable thioester resin linker

Summary This paper describes a practical new use of 3-mercaptopropionic acid as a highly versatile multidetachable linker for solid-phase synthesis. Our approach is based on the stability of the alkylthioester functionality to optimized Boc-SPPS protocols and HF treatment, as well as on the mild activation of the thioester functionality toward nucleophilic or reductive displacement. This allows several C-terminal modifications to be introduced into a synthetic molecule during the cleavage step. We have shown that unprotected peptides can be efficiently cleaved from a propyl thioester-polyethylene glycol-poly-(N,N-dimethylacrylamide) copolymer resin using a great variety of nucleophiles to give the corresponding C-terminally modified peptides (esters, thioesters, carboxylic acids, thioacids, amides, hydroxamic acids, hydrazides, alcohols). The nucleophilic cleavage reaction is both rapid and exceptionally clean in all the cases tested. Abbreviations: HBTU,N-[(1H-benzotriazol-1-yl)(dimethylamino)methylene]-N-methylmethanaminium hexafluorophosphateN-oxide); DIEA,N,N-diisopropylethylamine; DMF,N,N-dimethyl formamide; ES-MS, electrospray mass spectrometry; FAB-MS, fast atom bombardment mass spectrometry; HMBA, hydroxymethylbenzoic acid; HPLC, high performance liquid chromatography; PBS: phosphate buffer saline; PEGA, polyethylene glycolpoly-(N,N-dimethylacrylamide); TFA, trifluoroacetic acid; SPPS, solid-phase peptide synthesis. Standard IUPAC single and triple letter codes for amino acids are used throughout     

Conformational preference of bicyclic β-amino acid dipeptides

Bridged bicyclic amino acids have high potential applicability as self-organized, conformationally constrained synthetic building blocks that do not require assistance from hydrogen bond formation. We systematically investigated the intrinsic conformational propensities of dipeptides of bridged bicyclic β-amino acids by means of accelerated molecular dynamics simulation and density functional theory (DFT) calculations in methanol, chloroform, and water. While the main-chain conformation, represented by φ and θ values, is fixed by the nature of the bicyclic ring structure, rotation of the C-terminal carbonyl group (ψ) is also restricted, converging to one or two minima. In endo-type dipeptides, in which the two N- and C-terminal amides are spatially close to each other, the C-terminal amide plane is placed horizontally. In exo-type dipeptides, in which the two amides are on opposite sides of the ring plane, the C-terminal carbonyl group can take two types of positions: either parallel/antiparallel with the N-terminal carbonyl or beneath the bicyclic ring, forcing the amide NHMe moiety to lie outside of the ring. We also examined the cis-trans preference of model bicyclic amides. Although the parent amides exhibit cis-trans equilibrium without any preference, addition of a methyl group on one of the bridgehead positions tips the equilibrium towards trans.     

Primate relaxin: Synthesis of gorilla and rhesus monkey relaxins

The synthesis of the hormone relaxin from the speciesGorilla gorilla (gorilla) andMacaca mulatta (rhesus monkey) has been achieved. Each of the two chains which constitute the peptide structures was assembled separately, the A-chains (24 amino acids) by the Boc-polystyrene solid-phase procedure and the B-chains (29 and 28 amino acids) by the Fmoc-polyamide (gorilla) and the Boc-polystyrene (rhesus monkey) solid-phase methods. After cleavage from the solid supports, the separate chains were purified to a high degree of homogeneity. Oxidative combination of the respective A- and B-chains in solution at highpH afforded the synthetic relaxins in low overall yield. Chemical and physiochemical characterization of the products confirmed both their purity and their conformational similarity to the human hormone. The synthetic gorilla and rhesus monkey relaxins were both found to possess potent chronotropic and inotropic activity in the isolated rat cardiac atrium assay.     

Recent synthesis of aminophosphonic acids as potential biological importance

Aminophosphonic acids are an important group of medicinal compounds, and their synthesis has been a focus of considerable attention in synthetic organic chemistry as well as medicinal chemistry. Although the phosphonic and carboxylic acid groups differ considerably with respect to shape, size, and acidity, α-aminophosphonic acids are considered to be structural analogues of the corresponding amino acids and the transition state mimics peptide hydrolysis. This review summarizes recent developments in the synthesis, characterization and biological activity of α-aminophosphonic acid and N-analogues. An account of both uses will be presented, emphasizing one of the potential future developments, and some implications in medicinal chemistry are also disclosed. In addition, a brief account on the characterization of N-(phosphonomethyl) glycine derivatives will be presented.     

A chiron approach towards the synthesis of 3-hydroxy lysine and its derivatives

A general and efficient route towards the synthesis of three derivatives of structurally and functionally important amino acid, lysine is reported. Chemoselective reduction of aldehydic functionality in C-3-azido conjugated aldehyde 4, under Luche condition, is the key step in the synthetic sequence. The lysine derivative, (2S,3R)-2,6-diazido-3-hydroxy-hex-4-ene-oic acid 9 could be used to prepare switch peptide using Staudinger reaction, while the unprotected (2S,3R)-2,6-diamino-3-hydroxy-hexanoic acid hydrochloride 10 is a proven reaction intermediate towards the synthesis of natural product (?)-Balanol.     

Development of Defined, Minimal, and Complete Media for the Growth of Hyphomicrobium neptunium

A complete synthetic medium containing 15 amino acids, a minimal synthetic medium (GAMS) containing 4 amino acids, and a supplemented minimal medium (GAMS + calcium pantothenate) have been developed for the cultivation of Hyphomicrobium neptunium ATCC 15444. Depending on the complexity of the synthetic media, generation times were approximately 2 to 3 times longer, and maximum cell densities were 0.3 to 0.9 log₁₀ lower than in ZoBell marine broth 2216. The fates of ¹⁴C-labeled amino acids in GAMS were monitored. Results suggested that H. neptunium was auxotrophic for methionine, utilized glutamic acid as a primary energy source, and readily anabolized and catabolized serine and aspartic acid. Individual amino acid concentrations above 125 mM induced prolonged lag periods, whereas only methionine was not growth limiting at a concentration as low as 2 mM.     

3-Thiopropionic acid as a highly versatile multidetachable thioester resin linker

This paper describes a practical new use of3-mercaptopropionic acid as a highly versatilemultidetachable linker for solid-phase synthesis. Ourapproach is based on the stability of thealkylthioester functionality to optimized Boc-SPPSprotocols and HF treatment, as well as on the mildactivation of the thioester functionality towardnucleophilic or reductive displacement. This allowsseveral C-terminal modifications to be introduced intoa synthetic molecule during the cleavage step. We haveshown that unprotected peptides can be efficientlycleaved from a propyl thioester-polyethyleneglycol-poly-(N,N-dimethylacrylamide) copolymerresin using a great variety of nucleophiles to givethe corresponding C-terminally modified peptides(esters, thioesters, carboxylic acids, thioacids,amides, hydroxamic acids, hydrazides, alcohols). Thenucleophilic cleavage reaction is both rapid andexceptionally clean in all the cases tested.     

Synthesis of photoswitchable amino acids based on azobenzene chromophores: building blocks with potential for photoresponsive biomaterials

Three novel derivatives of azobenzene substituted amino acids have been synthesized. The compounds may serve as photoswitchable building blocks in the synthesis of bicyclic peptides or peptide strands interconnected with a photoisomerizable group.     

Synthesis of α-trifluoromethyl α-amino acids with aromatic, heteroaromatic and ferrocenyl subunits in the side chain

Summary. 5-Benzyloxy-4-trifluoromethyl-1,3-oxazoles, obtained from 5-fluoro-4-trifluoromethyloxazoles and benzyl alcohols, are capable for rearrangements. A 1,3 shift of a benzyl group is the key step of a new general route toward α-trifluoromethyl substituted aromatic and heteroaromatic amino acids, demonstrating that 5-fluoro-4-trifluoromethyl-1,3-oxazole is a synthetic Tfm-Gly equivalent. On reaction with benzpinacol partially fluorinated oxazoles are transformed into bis(trifluoromethyl) substituted 2,5-diamino adipic acid and N-benzoyl-2-benzhydryl-3,3,3-trifluoroalanine.     

Solution and solid-phase synthesis of potent inhibitors of hepatitis C virus NS3 proteinase

A versatile route for the synthesis of homochiral alpha-ketoamide analogues of amino acids is described. Incorporation of this functionality into peptide sequences using either solution or solid-phase chemistry resulted in potent inhibitors of the Hepatitis C Virus NS3 proteinase.     

Protein Synthesis in Plant Microsomal System

An active microsomal system from 48-h germinating seeds of Vigna sinensis (L.) Savi has now been developed. It can incorporate amino acids into protein under both in vitro and in vivo conditions, provided dithiothreitol (a protective reagent for SH groups) and phenylthiourea (an inhibitor of phenol oxidase) are present in the buffer system for extraction; and provided the assay mixture contains added dithiothreitol. The system consists of microsomes or ribosomes, tRNA or pH 5 fraction and 20 natural amino acids, ATP and an ATP-generating system and GTP with requirement for Mg ions. The cell fractions possess aminoacyl-RNA synthetase activity as indicated by the aminoacylhydroxamate formation. Microsomal synthesis is stimulated by exogenous tRNA from Escheriehia coli or rat liver and sensitive to various inhibitors such as cyclo-heximide, chloramphenicol, fusidic acid. The ribosomal transfer reaction has absolute dependence on the microsomal wash, on the crude enzyme from the same participate source, and on a synthetic messenger. It is greatly suppressed by fusidic acid and by cycloheximide.     

Selenotyrosine and related phenylalanine derivatives.

A new series of Se-substituted phenylalanine derivatives has been synthesized having the para position of the phenyl ring substituted by selenocyanate (-SeCN), seleninic acid (-SeO(2)H), or selenol (-SeH) functional groups. The starting material for synthesis was 4'-aminophenylalanine, which is readily available in DL- or L- forms. Selenium was incorporated into the ring by reacting the unprotected amino acid with nitrous acid, followed by reaction of the diazotized aromatic amine with potassium selenocyanate at pH 4-5 to give phenylalanine selenocyanate. The selenocyanate derivative was converted to the selenol directly by reduction with sodium borohydride, or oxidized to the seleninic acid, which was then reduced to the selenol. Alkylation of the selenol ('selenotyrosine') gave the selenoether derivatives of phenylalanine [(Phe-SeR), R=methyl or allyl], and air oxidation of the selenol gave the diselenide. Mild oxidation of the selenoether 4'-(MeSe)Phe with peroxide gave the selenoxide derivative, 4'-[Se(O)Me]. Because of their stability and useful redox properties, aromatic selenoamino acids can be used as synthetic analogues to increase chemical functionality in proteins or peptides, and have potential pharmaceutical or nutritional applications. The possibility that aromatic selenoamino acids could be formed metabolically through reactions of reactive selenium intermediates with aromatic amino acid residues is discussed.