Synthesis and hybridization affinity of oligodeoxyribonucleotides incorporating 4-N-(N-arylcarbamoyl)deoxycytidine derivatives

Modified oligodeoxynucleotides incorporating 4-N-(N-arylcarbamoyl)-dC derivatives 1a-c were synthesized. The ¹H NMR spectra of 1a-c suggest that the carbamoyl group forms an intramolecular hydrogen bond with the cytosine ring nitrogen atom so that formation of a Watson-Crick base pair with the complementary guanine base is inhibited. The hybridization properties of oligodeoxynucleotides containing 1a-c were investigated by use of T_m analysis. The hybridization properties of 4-N-(N-phenylcarbamoyl)-dC (1a) were similar to those of 4-N-(N-alkylcarbamoyl)-dC derivatives reported previously. In sharp contrast to 1a, it turned out that 4-N-(N-napht-1-yl) and (N-quionol-5-yl)-dC (1b,c) have a unique property as a universal base.     

Cyanuryl peptide nucleic acid: synthesis and DNA complexation properties

The synthesis of cyanuryl PNA monomer (CyaPNA) 6 was achieved by direct N-monoalkylation of cyanuric acid with N-(2-Boc-aminoethyl)-N′-(bromoacetyl)glycyl ethyl ester 4. Compound 6 was incorporated as a T-mimic into PNA oligomers and biophysical studies on their triplexes/duplex complexes with complementary DNA oligomers indicated unusual stabilization of PNA:DNA hybrids when the cyanuryl unit was located in the middle of the PNA oligomer.     

The Synthesis of Novel Iodinated Iminodiacetic Acid Analogues as Hepatobiliary Imaging Agents

Summary. The synthesis and characterization of N-[2-[[4-iodo-2,6-bis(1-methylethyl)phenyl]amino]-2-oxoethyl]-N-(carboxymethyl)glycine and N-[2-[(4-iodo-2,6-diethylphenyl)amino]-2-oxoethyl]-N-(carboxymethyl)glycine is presented, as well as a modified and improved synthesis of N-[2-[(2,4-diiodo-6-methylphenyl)amino]-2-oxoethyl]-N-(carboxymethyl)glycine. These compounds are new agents for hepatobiliary imaging.     

The Synthesis of Novel Iodinated Iminodiacetic Acid Analogues as Hepatobiliary Imaging Agents

The synthesis and characterization of N-[2-[[4-iodo-2,6-bis(1-methylethyl)phenyl]amino]-2-oxoethyl]-N-(carboxymethyl)glycine and N-[2-[(4-iodo-2,6-diethylphenyl)amino]-2-oxoethyl]-N-(carboxymethyl)glycine is presented, as well as a modified and improved synthesis of N-[2-[(2,4-diiodo-6-methylphenyl)amino]-2-oxoethyl]-N-(carboxymethyl)glycine. These compounds are new agents for hepatobiliary imaging.     

A general approach toward the synthesis of 8-acylamidopyrazolo[1,5-a]-1,3,5-triazines

An expedient synthesis of 8-acylamidopyrazolo[1,5-a]-1,3,5-triazines was developed by treating 8-amino-4-[N-(4-aminophenyl)-N-(methyl)amino]pyrazolo[1,5-a]-1,3,5-triazine with various acyl chlorides following by the displacement of the so-formed N-(methyl)-N-[4-(acylamido)phenyl]amino leaving group with various amines. Applications to high-throughput synthesis are suggested.     

Electrochemical detection of hybridization using peptide nucleic acids and methylene blue on self-assembled alkanethiol monolayer modified gold electrodes

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probes is presented. PNA probes were attached covalently through a competition of free amines on the guanine bases and also at the 5^′ end of the probe, using N-(3-dimethylamino)propyl)-N^′-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) onto a carboxylate terminated alkanethiol self-assembled monolayer (SAM) preformed on a gold electrode (AuE). The covalently immobilized probe could selectively hybridize with the target DNA to form a hybrid on the surface despite the bases being attached to the SAM. The changes in the peak currents of methylene blue (3,7-bis(dimethylamino)phenothiazin-5-ium chloride, MB), an electroactive label, were observed upon hybridization of probe with the target. Effective discrimination against point mutation was also obtained. Performance characteristics of the sensor are described, along with future prospects.     

Asymmetric synthesis of N-3 substituted phenoxypropyl piperidine benzimidazol-2-one derivatives, potent and selective NOP agonists

The asymmetric synthesis of the potent selective NOP agonist 2-(3-{1-[3-(5-methoxy-2-methyl-phenoxy)-4-methyl-pentyl]-piperidin-4-yl}-2-oxo-2,3-dihydro-benzimidazol-1-yl)-N-methyl-acetamide and analogues was developed. The key step, chiral reduction of methyl isobutyryl acetate, was achieved using a mild Noyori-type asymmetric hydrogenation.     

(2S,5R/2R,5S)-Aminoethylpipecolyl aepip-aegPNA chimera: synthesis and duplex/triplex stability

This article reports the design and facile synthesis of novel chiral six-membered PNA analogues (2S,5R/2R,5S)-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA IV that upon incorporation into standard aegPNA sequences effected stabilization of complexes with complementary target DNA. Substitution of aegPNA unit by the designed monomer at the C-terminus was more effective than substitution at N-terminus. The stabilizing behaviour improved with degree of substitution and was found to be dependent on their relative positions in the sequence. The six-membered piperidine ring in the design may freeze the rigid chair conformations and the relative stereochemistry of the substituents may in effect direct the complex formation with DNA/RNA by sequence-specific nucleobase recognition. In the present aepipPNA analogues, the l-trans stereochemical disposition of the substituents seems to lead to the favorable pre-organization of the PNA oligomers for complex formation with DNA. The results reported here further expand the repertoire of cyclic PNA analogues.     

Trimethylsilyl derivatives of N-Boc-cytosine and their effect on I2-mediated nucleosidation of O-MTM ethers

Mono- and bis(trimethylsilyl) derivatives of N⁴-Boc-cytosine were synthesized and characterized by ¹H NMR. Only the mono(trimethylsilyl)-N⁴-Boc-cytosine participates in the iodine-mediated nucleosidation of N-Fmoc-O-methylthiomethyl serine benzyl ester to produce the cytosine nucleoamino acid, while the bis(trimethylsilyl) derivative failed to give any product. A tentative mechanistic explanation is proposed.     

N7-DNA: Synthesis and Base Pairing of Oligonucleotides Containing N7-(2-Deoxy-β-D-erythro-pentofuranosyl)guanine (N7Gd)

The synthesis of oligonucleotides containing N⁷-(2-deoxy-β-D -erythro-pentofuranosyl)guanine (N⁷G_d; 1 ) is described. Compound 1 was prepared by nucleobase-anion glycosylation of 2-amino-6-methoxypurine ( 5 ) with 2-deoxy-3,5-di-O-(4-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 6 ) followed by detoluoylation and displacement of the MeO group ( 8→10→1 ). Upon base protection with the (dimethylamino)methylidene residue (→ 11 ) the 4,4-dimethoxytrityl group was introduced at OH? C(5′) (→ 12 ). The phosphonate 3 and the phosphoramidite 4 were prepared and used in solid-phase oligonucleotide synthesis. The self-complementary dodecamer d(N⁷G? C)₆ shows sigmoidal melting. The T_m of the duplex is 40°. This demonstrates that guanine residues linked via N(7) of purine to the phosphodiester backbone are able to undergo base pairing with cytosine.     

Efficient functional molecule incorporation method to functionalized peptide nucleic acid (PNA): use in synthesis of labeled PNA oligomers

A novel efficient synthetic method for a functionalized PNA (peptide nucleic acid) is described, in which a functional molecule is incorporated in place of a nucleobase. Novel ω-AA-^BocPNA-OH (20-24, AA=amino acid) were designed as PNA precursor monomer units into which functional molecules could be incorporated efficiently. Compounds 20-24 reacted quantitatively with OSu (N-hydroxysuccinimidyl) active ester derivatives and isothiocyanate derivatives of commercial functional molecules to give target functionalized PNA monomer units 25-53. Various types of functionalized PNA monomer units could be efficiently incorporated into multiple predetermined positions in a PNA oligomer by SPPS (solid phase peptide synthesis) in the same way as for the four A(Cbz), G(Cbz), C(Cbz), and T PNA monomer units.     

Stereoselective synthesis of protected (2S,3S)-N-methyl-5-hydroxyisoleucine, a component of halipeptins

The stereocontrolled synthesis of the protected (2S,3S)-N-methyl-5-hydroxyisoleucine, a component of halipeptins A and B with potent anti-inflammatory activity, has been achieved. The key steps include (i) installation of a double bond to bicyclic lactam 4 using N-tert-butyl phenylsulfinimidoyl chloride, (ii) highly exo-selective Michael reaction with lithium dimethylcuprate in the presence of chlorotrimethylsilane, and (iii) Ru-catalyzed oxidative deprotection of N,O-benzylidene acetal to the acid anhydride.     

A novel synthetic route for the total synthesis of (±)-uleine

In this study, a new synthetic route for the total synthesis of (±)-uleine is described. The important step in the synthesis of this alkaloid consists of an intramolecular cyclization of the D ring of the azocino[4,3-b]indole skeleton. Reduction of (N-methyl){3-β-ethyl-4-oxo-2,3,4,9-tetrahydrospiro[1H-carbazole-1,2′(1,3)dithiolane]-2-yl}-2-acetamide with borane yielded the corresponding (N-methyl){3-β-ethyl-4-hydroxy-2,3,4,9-tetrahydrospiro[1H-carbazole-1,2′(1,3)dithiolane]-2-yl}-2-acetamide, which underwent acid-catalyzed ring closure to produce azocino[4,3-b]indole core. Finally, the synthesis of (±)-uleine was completed through several steps from the azocino[4,3-b]indole core.     

Chimeric peptide nucleic acids incorporating (2S,5R)-aminoethyl pipecolyl units: synthesis and DNA binding studies

The design and facile synthesis of a novel chiral six-membered PNA analogue (2S,5R )-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA, that upon incorporation into PNA sequences effected stabilization of complexes with target complementary DNA. This is the first example where a six membered-PNA is shown to be capable of forming stable complexes with DNA and further expands the repertoire of cyclic PNA analogues.     

Efficient access to novel hexahydro-chromene and tetrahydro-pyrano[2,3-d]pyrimidine-annulated benzo-δ-sultones via a domino Knöevenagel-hetero-Diels-Alder reaction in water

An efficient catalyst-free, diastereosective synthesis of novel hexahydro-chromene and tetrahydro-pyrano[2,3-d]pyrimidine-annulated benzo-δ-sultones is described. A number of 2-formyl-4-phenyl (E)-2-phenylethenesulfonates were synthesized and underwent a one-pot domino Knöevenagel-hetero-Diels-Alder reaction, respectively, with dimedone and N,N-dimethylbarbituric acid in water, affording the desired products in moderate to excellent yields.     

Synthesis of New 1,2,3,4-Tetrahydroisoquinoline Derivatives. 2-(2,3,3-Trimethyl-1,2,3,4-tetrahydroisoquinolin-1-yl)anilines

A four-step procedure has been developed for the synthesis of new 2-(2,3,3-trimethyl-1,2,3,4-tetrahydroisoquinolin-1-yl)anilines by acylation of 2-(3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)anilines at the amino group with isobutyryl chloride, reduction of the endocyclic C=N bond in N-[2-(3,3-dimethyl-3,4-dihydroisoquinolin-1-yl)phenyl]isobutyramides, N-alkylation of N-[2-(3,3-dimethyl-1,2,3,4-tetrahydroisoquinolin-1-yl)phenyl]isobutyramides to N-[2-(2,3,3-trimethyl-1,2,3,4-tetrahydroisoquinolin-1-yl)phenyl]isobutyramides, and acid hydrolysis of the latter.     

Synthesis of 5-aminoisoxazolines from N-allyl compounds and nitrile oxides via tandem isomerization-1,3-dipolar cycloaddition

A new strategy for the synthesis of derivatives of 5-aminoisoxazolines via tandem catalytic isomerization (of N-allyl systems to N-(1-propenyl) systems)—1,3-dipolar cycloaddition (of a stable nitrile oxide to N-(1-propenyl) systems) is presented. Rhodium and ruthenium complexes, Verkade’s superbase, and 18-crown-6/KOH system were used for the syntheses of the N-(1-propenyl) systems. 4-P-substituted isoxazoline was also synthesized via cycloaddition of diphenyl(1-propenyl)phosphine (prepared via isomerization of allyldiphenylphosphine) to 2,6-dichlorobenzonitrile oxide. All cycloadditions were regioselective but not stereoselective and not concerted. Cycloaddition to all N-(1-propenyl) systems yielded 5-N-substituted isoxazolines, but cycloaddition to P-(1-propenyl) system lead to the formation of a 4-P-regioisomer. This difference in regioselectivity is predicted by opposite FMO reactivity indices calculated for model compounds: N-(1-propenyl)amine and N-(1-propenyl)phosphine.     

Total synthesis and structure revision of petrobactin

The total synthesis and the revised structural assignment of petrobactin, a siderophore isolated from the marine bacterium Marinobacter hydrocarbonoclasticus, is reported. The key step in the synthesis involved condensation of N¹-(2,3-dibenzoyloxybenzoyl)-N⁴-benzylspermidine with 1,3-di-(p-nitrophenyl)-2-tert-butyl citrate. Proton NMR spectra of the synthesized product compared with those reported for the natural product revealed that the compound did not contain 2,3-dihydroxybenzoyl moieties as published; instead, the splitting pattern suggested 3,4-dihydroxybenzoyl fragments. The 3,4-dihydroxybenzoyl analogue was accessed via a similar route; the proton and carbon-13 NMR spectra of this compound were consistent with those reported for natural petrobactin.     

Straightforward, racemization-free synthesis of peptides with fairly to very bulky di- and trisubstituted glycines

Several fully protected tri- and pentapeptides containing a central symmetrical α,α-dialkyl glycine residue, with the alkyl group varying from methyl or ethyl to benzyl, were synthesized in good yields by a strategy based on the Ugi-Passerini reaction. Each Ugi-Passerini adduct was selectively cleaved and the product submitted to an assisted N,N′-dicyclohehylcarbodiimide coupling to an amino acid or dipeptide ester, respectively. Tripeptides as the above but containing a 4-methoxybenzyl group at the nitrogen atom of the central residue were also synthesized in fair to good yields by N-[(1H-benzotriazol-1-yl)-(dimethylamino)methylene]-N-methylmethanaminium hexafluorophosphate N-oxide assisted couplings. The results reported here show that our strategy is appropriate for routine synthesis of peptides incorporating these moieties.     

Synthesis of N-linked glycan derived from Gram-negative bacterium, Campylobacter jejuni

Recent research has revealed the presence of asparagine (Asn)-linked (N-linked) glycoproteins in certain prokaryotes. In this paper, we describe the chemical synthesis of a novel N-glycan derived from Campylobacter jejuni, a heptasaccharide composed of Asn-linked bacillosamine (Bac), repeating GalNAc, and branching Glc, namely GalNAc-α(1,4)-GalNAc-α(1,4)-[Glc-β(1,3)-]GalNAc-α(1,4)-GalNAc-α(1,4)-GalNAc-α(1,3)-Bac. The synthesis started from a Bac-acceptor, which was consecutively glycosylated with 4-O-pentafluoropropionyl (PFP) protected donors to give heptasaccharide. Reduction of azide groups was followed by debenzylation to complete the synthesis of the target oligosaccharide.