Isoxazolidine analogues of pseudouridine: a new class of modified nucleosides

Synthesis of 3-substituted isoxazolidin-4-ols using hydroboration-oxidation reactions of 4,5-unsubstituted 2,3-dihydroisoxazoles

Isoxazolidines represent a very important class of N/O-containing heterocycles used as the key intermediates in the synthesis of more complex cyclic and acyclic compounds, including various biologically active molecules. Here, we present a fast and highly stereoselective approach towards both C-3/4-cis and C-3/4-trans isomers of 3-substituted isoxazolidin-4-ols. The strategy relies on a highly regio- and trans-stereoselective hydroboration-oxidation reaction of the 4,5-unsubstituted 2,3-dihydroisoxazoles with basic hydrogen peroxide. The consecutive oxidation/reduction route, sequentially employing Dess-Martin periodinane and ʟ-selectride, is used for the inversion of the C-3/4-trans relative configuration of the isoxazolidine ring. The significance of the method lies in its variability and applicability to a concise synthesis of various 4-hydroxyisoxazolidines, starting from the readily available C-alkyl/aryl-nitrones. The resemblance to 3-hydroxypyrrolidines certainly makes the 4-hydroxyisoxazolidines important and valuable structural fragments in drug discovery.

1, 3-Dipolar cycloaddition reactions of selected 1,3-dipoles with 7-isopropylidenenorbornadiene and follow-up thermolytic cleavage: A computational study

The mechanism, regio-, stereo-, and enantio-selectivities of the 1,3-dipolar cycloaddition reactions of 7-isopropylidenenorbornadiene (DENBD) with nitrones and azides to form pharmaceutically relevant isoxazolidine and triazole analogues have been studied computationally at the M06/6-31G(d), 6-31G(d,p), 6-311G(d,p), 6-311++G(d,p) and M06-2X/6-31G(d) levels of theory. In the reactions of DENBD with phenyl nitrones, the cycloaddition steps have low activation barriers, with the highest being 16 kcal/mol; and the Diels-Alder cycloreversion steps have generally high barriers, with the lowest being 20 kcal/mol, suggesting that the isolable products in these reactions are the bicyclic isoxazolidine cycloadducts and not the thermolytic products. This is in contrast to the reactions of DENBD with phenyl azide where the isolable products are predicted to be the thermolytic products since the Diels-Alder cycloreversion steps had relatively lower activation barriers. Electron-donating substituents on the dipolarophile substrate favour attack of the nitrone on the least hindered side of the DENBD substrate while electron-withdrawing substituents on the dipolarophile substrate favour attack on the more hindered side of the DENBD, indicating that site-selectivity is affected by nature of substituents. Global reactivity indices calculations are in good agreement with the activation barriers obtained. Analysis of the electrophilic (P_K⁺) and nucleophilic (P_K^-) Parr functions at the reactive centres reveal that the cycloaddition occurs between atoms with the largest Mulliken and NBO atomic spin densities which agrees well with the energetic trends and the experimental product outcomes.

Quantum chemical studies on the mechanistic aspects of tandem sequential cycloaddition reactions of cyclooctatetraene with ester and nitrones

The mechanisms of the tandem sequential [4 + 2]/[3 + 2] and [3 + 2]/[4 + 2] cycloaddition sequences involving an ester, cyclooctatetraene (COTE), and cyclic and acyclic nitrones for the formation of a diverse range of isoxazolidine derivatives and other synthetic precursors are reported. A thorough exploration of the PES has characterized several regio-, stereo- and enantio-selective mechanistic channels involved in these reactions. A perturbation molecular orbital (PMO) analysis been employed to rationalize the results. It has also been found that the initial electrocyclic ring closure of the COTE is the rate-determining step in the tandem sequential [4 + 2]/[3 + 2] addition sequence. The thermolytic breakdown of the tandem adducts to subsequent monocyclic, bicyclic and tricyclic adducts occurs generally with very high activation barriers making it an inconvenient synthetic approach. The different reactivity of all the three double bonds present in the dipolarophile is reported. Finally, the mechanistic possibilities of [3 + 2]/[4 + 2] addition sequences involving the same reaction components in the case of cyclic and acyclic nitrones are explored extensively. The results suggest a novel and convenient routes for obtaining products of high selectivity with less energetic requirements. In some instances, new cycloadducts hitherto unreported are obtained.

Molecular modeling studies of pseudouridine isoxazolidinyl nucleoside analogues as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase

In this paper, we investigated the hypothesis that pseudouridine isoxazolidinyl nucleoside analogues could act as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase. This purpose was pursued using molecular modeling and in silico ADME-Tox profiling. From these studies emerged that the isoxazolidinyl derivative 1 5'-monophosphate can be effectively accommodated within the active site of the enzyme with a ligand efficiency higher than that of the natural substrate. In this context, the poor nucleofugality of the N-protonated isoxazolidine prevents or slows down, the first mechanistic step proposed for the degradation of the pseudouridine 5'-monophosphate glycosidase, leading to the enzyme inhibition. Finally, the results of the physicochemical and ADME-Tox informative analysis pointed out that compound 1 is weakly bounded to plasma protein, only moderately permeate the blood-brain barrier, and is non-carcinogen in rat and mouse. To the best of our knowledge, this is the first paper that introduces the possibility of inhibition of pseudouridine 5'-monophosphate glycosidase by a molecule that competing with the natural substrate hinders the glycosidic C-C bond cleavage.

Isoxazolidine: A Privileged Scaffold for Organic and Medicinal Chemistry

The isoxazolidine ring represents one of the privileged structures in medicinal chemistry, and there have been an increasing number of studies on isoxazolidine and isoxazolidine-containing compounds. Optimization of the 1,3-dipolar cycloaddition (1,3-DC), original methods including electrophilic or palladium-mediated cyclization of unsaturated hydroxylamine, has been developed to obtain isoxazolidines. Novel reactions involving the isoxazolidine ring have been highlighted to accomplish total synthesis or to obtain bioactive compounds, one of the most significant examples being probably the thermic ring contraction applied to the total synthesis of (±)-Gelsemoxonine. The unique isoxazolidine scaffold also exhibits an impressive potential as a mimic of nucleosides, carbohydrates, PNA, amino acids, and steroid analogs. This review aims to be a comprehensive and general summary of the different isoxazolidine syntheses, their use as starting building blocks for the preparation of natural compounds, and their main biological activities.

Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles

Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts.

Synthesis and biological properties of 5-(1H-1,2,3-triazol-4-yl)isoxazolidines: a new class of C-nucleosides

A novel series of C-nucleosides, featuring the presence of a 1,2,3-triazole ring linked to an isoxazolidine system, has been designed as mimetics of the pyrimidine nucleobases. An antiproliferative effect was observed for compounds 17a and 17b: the growth inhibitory effect reaches the 50% in HepG2 and HT-29 cells and increases up to 56% in the SH-SY5Y cell line after 72 h of incubation at a 100 µM concentration.

Enantiomerically pure phosphonated carbocyclic 2'-oxa-3'-azanucleosides: synthesis and biological evaluation

Starting from enantiomeric pure 1-[(3S,5R)- and 1-[(3R,5S)-3-(hydroxymethyl)-2-methylisoxazolidin-5-yl]-5-methylpyrimidine-2,4(1H,3H)-diones (-)7a and (+)7b, obtained by lipase-catalyzed resolution, pure diethyl{[(3S,5R)-2-methyl-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)isoxazolidin-3-yl]methyl}phosphonate (-)12a and diethyl{[(3R,5S)-2-methyl-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)isoxazolidin-3-yl]methyl}phosphonate (+)12b have been synthesized. The obtained compounds showed no cytotoxic activity versus the U937 cell line in comparison with AZT, and were poorly able to inhibit HIV infection in vitro.

A top–down approach to crystal engineering of a racemic Δ2-isoxazoline

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top–down approach to be a useful tool for crystal engineering.

Microwave-assisted syntheses of nucleosides and their precursors

In recent decades, nucleosides analogs have been the cornerstone in the treatment of various diseases, such as AIDS, herpes and hepatitis. More than 40 modified nucleosides are officially approved by the US FDA and represent the major compound class for inhibition of viral replication. By comparison with traditional conditions, microwave irradiation offers a powerful tool that can increase yields and decrease reaction time, with simple manipulation and an environmentally friendly way. Here, we report the latest progress in nucleoside synthesis using microwave irradiation.

Hydrophilic modifications in peptide nucleic acid — Synthesis and properties of PNA possessing 5-hydroxymethyluracil and 5-hydroxymethylcytosine

We have investigated the chemistry for the incorporation of C5-hydroxymethyl-uracil and -cytosine in peptide nucleic acid (PNA) and the subsequent effect of this modification on PNA hybridization behavior. Largely based on literature precedent, we prepared a peptide nucleic acid monomer, possessing 5-hydroxymethyuracil, which was compatible with Fmoc-based oligopeptide synthesis. An improved, large-scale synthesis of 5-hydroxymethylcytosine was developed, as a starting point for the synthesis of a monomer containing this nucleobase. In each case, the hydroxyl group was blocked as a t-butyldiphenylsilyl ether, and the exocyclic amino group of cytosine was additionally blocked with the benzoyl-group. The modified monomers were incorporated into isolated positions in the oligomer sequence using standard protocols. The modified oligomers showed that the 5-hydroxymethyl group is compatible with triplex and duplex formation.Key words: peptide nucleic acid, hydroxymethyluracil, hydroxymethylcytosine, modified nucleobase, hybridization.

Zinc(II) Triflate-Controlled 1,3-Dipolar Cycloadditions of C-(2-Thiazolyl)nitrones: Application to the Synthesis of a Novel Isoxazolidinyl Analogue of Tiazofurin

[reaction: see text] The cycloaddition reaction between C-(2-thiazolyl) nitrones and allylic alcohol takes place with complete exo selectivity when the reactions are carried out in the presence of 1 equiv of zinc triflate. The rate of the reaction is increased enormously under microwave irradiation. The use of a chiral dipolarophile allowed application of the methodology to the synthesis of a hitherto unknown enantiomerically pure isoxazolidinyl analogue of the C-nucleoside tiazofurin.

A divergent chemoenzymatic route to an intermediate for nucleoside analogues

Two regioisomeric isoxazoline monoacetates 1 and 2 were synthesized from the corresponding diacetate 3 via PPL or PLE catalyzed hydrolysis. With both the enzymes, the initial regioselectivity (approximately 3-4:1) was offset by an intramolecular acyl transfer. In addition to a non-enzymatic catalysis for the acyl transfer, preliminary experiments do suggest a definite but minor role of enzyme for this intramolecular acyl transfer. Compounds 1 and 2 may serve as intermediates for nucleoside analogues.