Stereoselective synthesis of new bicyclic N,O-iso-homonucleoside analogues

The synthesis of two new bicyclic nucleoside analogues is reported. These compounds are iso-homonucleoside and are synthesised through a 1,3-dipolar cycloaddition of an enantiopure cyclic nitrone to protected allyl acohol and subsequent introduction of thymine by a Mitsunobu reaction.     

An alpha-D-configured bicyclic nucleoside restricted in an E-type conformation: synthesis and parallel RNA recognition

An alpha-D-arabino configured bicyclic nucleoside strongly restricted in an E-type conformation by a 2'-3'-fused oxetane ring is synthesized. Several synthetic strategies toward the target compound are described, and the successful preparation from a D-xylose derivative is based on a ruthenium-mediated cleavage of a double bond, an S(N)2-inversion at the 2-position to give an arabino-configuration, nucleobase coupling, and finally ring closure to give the oxetane ring. The E-type conformation is confirmed by molecular modeling and NMR. The nucleoside is incorporated into short alpha-DNA sequences. In a mixed pyrimidine context, these recognize complementary parallel RNA-sequences with mainly increased affinity and complementary parallel DNA-sequences with decreased affinity. The present bicyclic analogue represents the first conformationally restricted alpha-DNA-analogue to improve nucleic acid recognition in mixmers with alpha-DNA monomers.     

Bicyclic nucleosides; stereoselective dihydroxylation and 2'-deoxygenation

A series of polyhydroxylated bicyclic nucleoside derivatives is approached applying stereoselective dihydroxylation reactions. Three out of four isomeric and protected products were obtained after the stereoselectivity of dihydroxylation has been completely inverted comparing a bicyclic nucleoside with a tricyclic furanose substrate. A corresponding 2'-deoxynucleoside derivative has been obtained after an optimized deoxygenation procedure.     

Preparation and antiviral properties of new acyclic, achiral nucleoside analogues: 1- or 9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases and 1- or 9-[2,3-dihydroxy-2-(hydroxymethyl)propyl]nucleobases

Acyclic, achiral nucleoside derivatives 1b-e of adenine, cytosine, 5-methylcytosine, and guanine, containing a 3-hydroxy-2-(hydroxymethyl)prop-1-enyl group on N-1 or N-9, have been prepared analogously to the previously described thymine derivative 1a. In contrast to the adenine and guanine derivatives, the cytosine derivative 9 was unstable, and was obtained in a low yield due to side reactions. These include cleavage of the propenyl group from the base, and the formation of a bicyclic compound. The thymine derivative, although stable under neutral conditions, likewise underwent a reversible cyclization reaction (Michael addition) in the presence of acids or bases. The 5-methylcytosine derivative was stable under neutral and basic conditions. Four other nucleoside derivatives 26a-d containing a 2,3-dihydroxy-2-(hydroxymethyl)propyl group on N-1 or N-9, three of which are new, have likewise been prepared. All compounds were evaluated as antiviral agents against HIV-1 and HSV-1 but were devoid of antiviral activity.     

Enantiopure Aminopyrans by a Lewis Acid Promoted Rearrangement of 1,2‐Oxazines: Versatile Building Blocks for Oligosaccharide and Sugar Amino Acid Mimetics

1,3‐Dioxolanyl‐substituted 1,2‐oxazines, such as syn‐ 1 and anti‐ 1 , rearrange under Lewis acidic conditions to provide bicyclic products 2 – 5 . Subsequent reductive transformations afforded enantiopure 3‐aminopyran derivatives such as 7 and 9 or their protected diastereomers 16 and 18 , which can be regarded as carbohydrate mimetics. An alternative sequence of transformations including selective oxidation of the primary hydroxyl groups in 21 and 24 led to two protected β‐amino acid derivatives with carbohydrate‐like backbone (sugar amino acids). Treatment of bicyclic ester 23 with samarium diiodide cleaved the N? O bond and furnished the unusual β‐lactam 27 in excellent yield. Alternatively, γ‐amino acid derivative 29 was efficiently prepared in a few steps. Fairly simple transformations gave azides 32 and 35 or alkyne 30 which are suitable substrates for the construction of oligosaccharide mimetics such as 34 by copper iodide catalyzed cycloadditions. With this report we demonstrate that enantiopure rearrangement products 2 – 5 are protected precursors of a variety of polyfunctionalized pyran derivatives with great potential for chemical biology.     

The Syntheses of Pyrimido‐pyridazinone and Pyrrolidino‐pyrimidinone 2′‐Deoxynucleoside Derivatives

Nucleosides that have ambivalent tautomeric properties have value in a variety of nucleic‐acid hybridisation applications and as mutagenic agents. We describe here synthetic studies directed to stable derivatives based on N⁴‐aminocytosine. Treatment of the 5‐(chloroethyl)‐4‐(triazol‐1‐yl)pyrimidine‐nucleoside derivative 1 with benzylhydrazine leads to the formation of the 6,6‐bicyclic pyrimido‐pyridazin‐7‐one 6 , in addition to the 5,6‐bicyclic derivative 7 . The 6,6‐bicyclic benzyl derivative 6 was converted to its 5′‐triphosphate for studies with DNA polymerases. Reaction of the triazole 1 with hydrazine, followed by acetylation, led to the desired acetylated 6,6‐bicyclic derivative 12 . However, the latter compound undergoes acyl migration followed by ring contraction to the 5,6‐bicyclic compound 13 on treatment with base.     

Efficient photosensitized splitting of the thymine dimer/oxetane unit on its modifying beta-cyclodextrin by a binding electron donor

Two modified beta-cyclodextrins (beta-CDs) with a thymine dimer and a thymine oxetane adduct respectively, TD-CD and Ox-CD, have been prepared, and utilized to bind an electron-rich chromophore, indole or N,N-dimethylaniline (DMA), to form a supramolecular complex. We have examined the photosensitized splitting of the dimer/oxetane unit in TD-CD/Ox-CD by indole or DMA via an electron-transfer pathway, and observed high splitting efficiencies of the dimer/oxetane unit. On the basis of measurements of fluorescence spectra and splitting quantum yields, it is suggested that the splitting reaction occurs in a supramolecular complex by an inclusion interaction between the modified beta-CDs and DMA or indole. The back electron transfer, which leads low splitting efficiencies for the covalently-linked chromophore-dimer/oxetane compounds, is suppressed in the non-covalently-bound complex, and the mechanism has been discussed.     

Introduction of vinyl and hydroxymethyl functionalities at C-4 of glucose-derived substrates: synthesis of spirocyclic, bicyclic, and tricyclic nucleosides

Installing hydroxymethyl and hydroxyethyl substitutions at C-4 through vinylation and hydroboration-oxidation reactions of the C-4 bis-hydroxymethyl derivative of d-glucose based substrate, and inserting heteroatoms thereafter permitted formation of N-, O-, or S-heterocycles leading to [4,5]- or [5,5]-spirocycles and a bicyclo[3.3.0]octane product. Some of the spirocycles were converted to spironucleosides under Vorbruggen glycosidation reaction conditions. Similarly, the bicyclic product was elaborated to the corresponding bicyclic nucleoside as well as an unexpected tricyclic nucleoside.     

Serendipitously discovered diazomethane-mediated novel molecular rearrangements of norbornyl alpha-ketohemiketals

[reaction: see text] Unprecedented molecular rearrangements during diazomethane-mediated reaction of norbornyl alpha-ketohemiketals leading to novel molecular entities are presented. A dramatic change in the reaction outcome was noted for five- and six-membered alpha-ketohemiketals: the former predominantly furnished rearranged bicyclic products involving migration of the gamma-alkoxy group, and the latter furnished the oxetane derivative as the major product. Interestingly, six-membered O-methyl-ketal yielded a product arising from the migration of the vicinal alkoxy group.     

Nucleic acid secondary structures containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine

Oligodeoxynucleotides containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine were prepared by standard solid phase synthesis. The synthetic building block for incorporating the double-headed moiety was prepared from thymidine, which was stereoselectively converted to a protected 5'(S)-C-hydroxyethyl derivative and used to alkylate the additional thymine by a Mitsunobu reaction. The oligodeoxynucleotides were studied in different nucleic acid secondary structures: duplexes, bulged duplexes, three-way junctions and artificial DNA zipper motifs. The thermal stability of these complexes was studied, demonstrating an almost uniform thermal penalty of incorporating one double-headed nucleoside moiety into a duplex or a bulged duplex, comparable to the effects of the previously reported double-headed nucleoside 5'(S)-C-(thymin-1-yl)methylthymidine. The additional base showed only very small effects when incorporated into DNA or RNA three-way junctions. The various DNA zipper arrangements indicated that extending the linker from methylene to ethylene almost completely removed the selective minor groove base-base stacking interactions observed for the methylene linker in a (-3)-zipper, whereas interactions, although somewhat smaller, were observed for the ethylene linker in a (-4)-zipper motif.     

Synthesis and properties of purine-type base-discriminating fluorescent (BDF) nucleosides: distinction of thymine by fluorescence-labeled deoxyadenosine derivatives

Novel base-discriminating fluorescent (BDF) nucleoside, 8-fluorescence-labeled adenosine derivative (^8PyA), was developed for the detection of thymine base on a target DNA. The BDF nucleoside was incorporated into oligodeoxynucleotides by post-synthetic modification. BDF probes containing ^8PyA selectively emit fluorescence only when the base opposite BDF nucleoside is thymine and act as effective reporter probes for homogeneous SNP typing.     

Catalytic Asymmetric Synthesis of the anti-COVID-19 Drug Remdesivir

The catalytic asymmetric synthesis of the anti-COVID-19 drug Remdesivir has been realized by the coupling of the P-racemic phosphoryl chloride with protected nucleoside GS441524. The chiral bicyclic imidazole catalyst used is crucial for the dynamic kinetic asymmetric transformation (DyKAT) to proceed smoothly with high reactivity and excellent stereoselectivity (96 % conv., 22:1 S_P:R_P). Mechanistic studies showed that this DyKAT is a first-order visual kinetic reaction dependent on the catalyst concentration. The unique chiral bicyclic imidazole skeleton and carbamate substituent of the catalyst are both required for the racemization process, involving the phosphoryl chloride, and subsequent stereodiscriminating step. A 10 gram scale reaction was also conducted with comparably excellent results, showing its potential for industrial application.     

Synthetic studies on ezomycins: stereoselective route to a thymine octosyl nucleoside derivative

The ezomycins are Streptomyces-derived antifungal natural products, belonging to the complex peptidyl nucleoside family of antibiotics. Employing D-serine as a chiral platform, we report herein a novel synthetic route to the bicyclic octosyl nucleoside core of the ezomycins. A key step in the sequence involved a stereoselective 6-exo-trig oxymercurationoxidation of a strategic delta-hydroxy alkene derivative, toward construction of the trans-fused furopyran ring system as present in the target products. In contrast to the known carbohydrate-based synthetic routes to the above furopyranyl fragment, the present amino acid chiral template approach is expected to offer a more flexible pathway toward potential SAR-targeted structural/stereochemical modifications of this central bicyclic nucleoside component of the ezomycins.     

Synthesis of a bicyclic analogue of AZT restricted in an unusual O4'-endo conformation.

The [3.2.0]bicyclic beta-nucleoside analogue 5 has been designed as a conformationally restricted analogue of the anti-HIV drug AZT. The synthesis of 5 as well as its alpha-anomer 29 is hereby described. The synthesis was accomplished from D-arabinose via a modified Corey-Link procedure stereoselectively incorporating the azide moiety as well as a methyl ester function. When the tert-butyldiphenylsilyl group was used as a permanent protecting group, a selective formation of an oxetane ring failed. When using the p-methoxyphenyl group as a permanent protecting group, 5 and 29 were efficiently obtained via a selective reduction of the ester, a nucleobase coupling followed by separation of the anomers and ring-closing procedures. The nucleoside 5 is conformationally restricted in an unusual O4'-endo (East) conformation, which is an intermediate between the North- and South-type conformations. Nevertheless, neither 5 nor 29 displayed any anti-HIV activity.     

Some 2′-Modified 4′-Thionucleosides via Sulfur Participation and Synthesis of Thio-Azt from 4′-Thiofuranoid 1,2-Glycal

ThioAZT 14 was synthesized in eight steps from D-arabinose derivative 4 via the new thiofuranoid 1,2-glycal, 5-O-Acetyl-1,2,4-trideoxy-1,4-epithio-3-O-p-toluenesulfonyl-D- threo -pent-1-enitol ( 8 ). Ribosylation of the thiosugar 6 with thymine afforded regioselectively the nucleoside 16 . Treatment of 16 with sodium azide in hot DMF gave, after spontaneous intramolecular displacment, the 2'-azido-xylo derivative 18 , which furnished the free nucleoside 19 on treatment with methanolic ammonia. Similarly, treatment of 16 with sodium ethylthiolate in boiling methanol led to inversion in configuration and gave, after several intramolecular displacments, via the sulfur participation, the 2',3'-diethylthiolate-ribo derivative 23 . Deblocking of 23 with methanolic ammonia afforded the free nuclaoside 24 .     

Model studies of the (6-4) photoproduct photoreactivation: efficient photosensitized splitting of thymine oxetane units by covalently linked tryptophan in high polarity solvents

Three covalently linked tryptophan-thymine oxetane compounds used as a model of the (6-4) photolyase-substrate complex have been prepared. Under 290 nm light, efficient splitting of the thymine oxetane with aromatic carbonyl compounds gives the thymine monomer and the corresponding carbonyl compounds by the covalently linked tryptophan via an intramolecular electron transfer, and exhibits a strong solvent dependence: the quantum yield (Phi) is ca. 0.1 in dioxane, and near 0.3 in water. Electron transfer from the excited tryptophan residue to the oxetane unit is the origin of fluorescence quenching of the tryptophan residue, and is more efficient in strong polar solvents. The splitting efficiency of the oxetane radical anion within the tryptophan.+-oxetane.- species is also solvent-dependent, ranging from ca. 0.2 in dioxane to near 0.35 in water. Thus, the back electron transfer reaction in the charge-separated species would be suppressed in water, but is still a main factor causing low splitting efficiencies in the tryptophan-oxetane systems. In contrast to the tryptophan-oxetane system, fast nonradiation processes are the main causes of low efficiency in the flavin-oxetane system. Hence, nonradiative processes of the excited FADH-, rather than electron transfer to oxetane, may be an important factor for the low repair efficiency of (6-4) photolyase.     

(6-4)-photolyase activity requires a charge shift reaction

A model compound containing a thymine oxetane moiety linked to a flavin chromophore was investigated regarding (6-4)-photolyase activity. The need for a charge shift reaction was demonstrated by a detailed pH-dependent kinetic analysis.     

Internally Protected Amino Sugar Equivalents from Enantiopure 1,2‐Oxazines: Synthesis of Variably Configured Carbohydrates with C‐Branched Amino Sugar Units

A stereodivergent synthesis of differently configured C2‐branched 4‐amino sugar derivatives was accomplished. The Lewis acid mediated rearrangement of phenylthio‐substituted 1,2‐oxazines delivered glycosyl donor equivalents that can directly be employed in glycosidation reactions. Treatment with methanol provided internally protected amino sugar equivalents that have been transformed into the stereoisomeric methyl glycosides 28 , ent‐ 28 , 29 , ent‐ 29 and 34 in two simple reductive steps. Reaction with natural carbohydrates or bicyclic amino sugar precursors allowed the synthesis of homo‐oligomeric di‐ and trisaccharides 44 , 46 and 47 or a hybrid trisaccharide 51 with natural carbohydrates. Access to a bivalent amino sugar derivative 54 was accomplished by reaction of rearrangement product 10 with 1,5‐pentanediol. Alternatively, when a protected L ‐serine derivative was employed as glycosyl acceptor, the glycosylated amino acid 60 was efficiently prepared in few steps. In this report we describe the synthesis of unusual amino sugar building blocks from enantiopure 1,2‐oxazines that can be attached to natural carbohydrates or natural product aglycons to produce new natural product analogues with potential applications in medicinal chemistry.     

A Paterno-Büchi approach to the synthesis of merrilactone A

A six-step approach to the tetracyclic core of merrilactone A is described that uses an intramolecular Paterno-Büchi photoaddition to install the key oxetane ring. Irradiation of bicyclic enone 16, constructed through cyclopentenone alkylation followed by a domino oxy-/carbopalladation reaction, produces the tetracyclic oxetane 17 in excellent yield, having the core carbon skeleton of the target compound merrilactone A. [reaction: see text]     

Characterization of novel nucleoside analogs by electrospray ionization mass spectra

In this paper, we synthesized a novel nucleoside analog by coupling thymine with dimethyl dicarboxylate biphenyl (DDB). The structure of the target compound was determined using 1H nuclear magnetic resonance (NMR) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). The fragmentation pathways were studied in details through ESI-MS/MS. By comparing with unsubstituted nucleosides, such as AZT, MCI, d4T and DDI, it was found that the nucleoside analog coupled with DDB would not yield the daughter ions corresponding to the fragments of the nucleoside base and arabinofuranose analogs, but would lose a neutral molecule HF and DDB easily. However, the unsubstituted nucleosides could lightly yield the fragment ions of the nucleoside base and sugar ring. Hence, electrospray ionization mass spectrometry combined with tandem mass spectrometry (MS/MS) provides a convenient method to recognize the substituted and unsubstituted nucleosides.