Efficient synthesis of 5′-O(N)-carbamyl and -polycarbamyl nucleosides

A simple and efficient method for the preparation of 5′-O(N)-carbamyl and 5′-O(N)-polycarbamyl nucleoside derivatives is reported. The method consisted of treatment of 2′,3′-O-protected purine (Ado, Ino) or pyrimidine nucleosides (Thd, Urd) with trichloroacetylisocyanate, followed by cleavage of the trichloroacetyl moiety by silica-gel promoted methanolysis during column chromatography. Iterative application of this method gave mono, di, and tricarbamyl derivatives in good to excellent yields (ave = 80%).     

Phosphoramidite building blocks for efficient incorporation of 2′-O-aminoethoxy(and propoxy)methyl nucleosides into oligonucleotides

A simple and efficient method for the preparation of eight phosphoramidite building blocks for incorporation of 2′-O-(2-aminoethoxymethyl)ribonucleosides and 2′-O-(3-aminopropoxymethyl)ribonucleosides into synthetic oligonucleotides has been developed. The synthetic routes are maximally convergent and provide sufficient amounts of phosphoramidites for several solid-phase synthesis coupling reactions. Using acyclic derivatives 17a,b the overall yields of phosphoramidites 2 and 3 were increased up to 50% for pyrimidine nucleosides and up to 30% for purine derivatives with substantial decrease of total reaction steps. The 2′-O-substituent was found to be stable during oligonucleotide synthesis. The resulting oligonucleotides are of particular interest for post-synthetic functionalization and conjugation.     

Syntheses of 2′-C-amidoalkyl and 2′-C-cyanoalkyl containing oligodeoxyribonucleotides and assessment of their hybridisation affinity for complementary DNA and RNA

Oligodeoxynucleotides containing 2′-C-branched nucleosides with an amide or nitrile appended to either a one or two carbon alkyl chain have been synthesised. The phosphoramidites of the 2′-C-modified nucleosides were prepared and incorporated into the oligonucleotides using automated DNA synthesis. The duplex stability with complementary RNA and DNA was measured by UV melting experiments, in order to assess whether the amide/nitrile function could induce any duplex stability without the presence of the 2′-oxygen. The duplex stabilities of the oligonucleotides containing the 2′-C-modifications were decreased in the absence of the 2′-oxygen.     

Straightforward synthesis of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes via 2′,3′-O-orthoester group elimination: a simple route to 3′,4′-didehydronucleosides

Straightforward, high-yielding syntheses of 3′-deoxy-3′,4′-didehydronucleoside-5′-aldehydes and 3′-deoxy-3′,4′-didehydronucleosides starting from 2′,3′-O-orthoester derivatives of ribonucleosides are described.     

Synthesis and hybridization properties of 2′-O-(tetrazol-5-yl)ethyl-modified oligonucleotides

2′-O-(1H-Tetrazol-5-yl)ethyladenosine was synthesized using 2′-O-cyanoethyladenosine derivative as a key intermediate. The 2′-O-(1H-tetrazol-5-yl)ethyl modifications exhibited intriguing properties such as the change in the structure of the tetrazole residue between a protonated and a deprotonated form. The T_m experiments of various oligodeoxynucleotides having a 2′-O-(1H-tetrazol-5-yl)ethyl-modified adenosine showed reduced hybridization affinity in comparison to the unmodified oligonucleotides toward their complementary oligodeoxynucleotides. The mechanism of the reduced hybridization affinity was discussed on the basis of the structure and the physicochemical properties of the tetrazole moiety.     

New and efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides

A short, efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides 1 has been developed through the diastereoselective addition of methylmagnesium bromide or methyllithium to an intermediate tert-butylsulfinimide.     

Convenient synthesis of N-isobutyryl-2′-O-methyl guanosine by efficient alkylation of O-trimethylsilylethyl-3′,5′-di-tert-butylsilanediyl guanosine

We present a novel route for the synthesis of N²-isobutyryl-2′-O-methyl guanosine, introducing 3′,5′-di-tert-butylsilyl and O⁶-trimethylsilylethyl groups as efficient protections during the 2′-O-methylation step with NaH/CH₃I. These protections were then removed simultaneously in a single step with TBAF. The eight-step synthesis is easy to perform, employing convenient commercially available reagents; crude mixtures are of satisfying purity, so only three chromatography purifications were required. Title compound was obtained in 25% overall yield from guanosine.     

Spiro-sulfamidate and sulfate nucleosides via 2′ and 3′-C-branched-chain sugars and nucleosides

C-branched-chain sugars and nucleosides were obtained by organocatalysis from ulose derivatives. After a reduction step, the corresponding 1,3-diol was derivatized into 3′-spiro-sulfamidates and unexpected sulfates by treatment with a Burgess reagent. Deprotection of the Boc-derivatives was carried out while preserving the cyclic sulfate. An example of ring opening of the cyclic sulfate derivative with sodium azide leading to the corresponding 3′-C-azidoalkyl branched-chain nucleosides is given.     

A simple route for the synthesis of 3,3,3′,3′-tetramethyl-2,3,3′,4′-tetrahydro-1H,1′H-[4,9′-bixanthene]-1,1′(2′H,9′H)-dione and its derivatives catalyzed by Mn and other transition metal cations

A simple and efficient unusual coupling reaction of 9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one and its derivatives was accomplished in the presence of Mn²⁺, Cu²⁺, Cd²⁺, Hg²⁺, Fe³, or La³⁺. The structure elucidation was accomplished by IR, ¹H NMR, ¹³C NMR, X-ray crystallography, UV-Visible and elemental analysis. A reaction mechanism is proposed.     

A novel entry to 2′-O-aminopropyl modified nucleosides amenable for further modifications

2′-O-aminopropyl modified 4,6-difluoro-substituted benzimidazole nucleosides were synthesized in a two-step synthesis via Michael reaction and a Raney-nickel catalyzed reduction in high yields. These building blocks were used as a starting point for the conjugation of different carboxylic acids to enhance the lipophilicity or cationic character of oligonucleotides when used in biological assays or medical applications.     

Synthesis of 2′-O,3′-O bicyclic adenosine analogues using ring closing metathesis

The synthesis of 2′-O,3′-O bicyclic adenosine derivatives is presented as the first examples of a new family of 13-membered ring bicyclic nucleoside analogues. Cyclisation was achieved through ring closing metathesis (RCM) on a diene intermediate using Grubbs’ catalyst. The Z and E isomers were purified and characterised.     

Highly diastereoselective chemoenzymatic synthesis of (2′R)- and (2′S)-2′-deoxy[2′-H]guanosines

In an effort to develop an efficient synthetic method of highly diastereoselective (2′R)- and (2′S)-2′-deoxy[2′-²H]guanosines, chemoenzymatic conversion was investigated. The synthesis of (2′R > 98% de)-2′-deoxy[2′-²H]guanosine was achieved by biological transdeoxyribosylation using (2′R > 98% de)-2′-deoxy[2′-²H]uridine, 2,6-diaminopurine, and Enterobacter aerogenes AJ-11125, followed by treatment with adenosine deaminase. (2′S > 98% de)-2′-Deoxy[2′-²H]guanosine was synthesized from (2′S > 98% de)-2′-deoxy[2′-²H]uridine and 2,6-diaminopurine using thymidine phosphorylase and purine nucleoside phosphorylase instead of E. aerogenes AJ-11125.     

Synthesis of (3′R,5′S)-3′-hydroxycotinine using 1,3-dipolar cycloaddition of a nitrone

To synthesize (3′R,5′S)-3′-hydroxycotinine [(+)-1], the main metabolite of nicotine (2), cycloaddition of C-(3-pyridyl)nitrones 3a, 3c, and 15 with (2R)- and (2S)-N-(acryloyl)bornane-10,2-sultam [(2R)- and (2S)-8] was examined. Among them, l-gulose-derived nitrone 15 underwent stereoselective cycloaddition with (2S)-8 to afford cycloadduct 16, which was elaborated to (+)-1.     

A convenient, large-scale synthesis of 4′-carboxamido N-Boc-2′,6′-dimethyl-l-phenylalanines

A large-scale synthesis of a series of 4′-carboxamido N-Boc-2′,6′-dimethyl-l-phenylalanines is described. This method features mild reaction conditions and high chemical yields from commercially available N-Boc-2′,6′-dimethyl-l-tyrosine methyl ester.     

Regioselective monobromination of (E)-1-(2′-hydroxy-4′,6′-dimethoxyphenyl)-3-aryl-2-propen-1-ones using bromodimethylsulfonium bromide and synthesis of 8-bromoflavones and 7-bromoaurones

A wide variety of monobrominated compounds 2a-l have been prepared in good yields from (E)-1-(2′-hydroxy-4′,6′-dimethoxyphenyl)-3-aryl-2-propen-1-ones (1a-l) through regioselective ring bromination using 1.5 equiv of bromodimethylsulfonium bromide (BDMS) at room temperature. Similarly, some of the 2′-hydroxychalcones can be converted directly into tribromides 3 or dibromides 4 by employing 4.0 equiv of BDMS under different reaction conditions which in turn can be transformed into 8-bromoflavones and 7-bromoaurones on treatment with 0.2 M ethanolic KOH solution. Mild reaction conditions, good yields and no chromatographic separation are some of the salient features of the present protocol.     

Diastereoselective synthesis of 1-alkyl-2,4,6-trioxoperhydropyrimidine-5-spiro-3′-(1′,2′,3′,4′-tetrahydroquinolines)

Knoevenagel products formed by the condensation of N-monoalkyl barbituric acids with o-tert-amino benzaldehydes undergo tert-amino effect reactions (T-reactions) yielding 1-alkyl-2,4,6-trioxoperhydropyrimidine-5-spiro-3′-(1′,2′,3′,4′-tetrahydroquinoline) derivatives as a mixture of (S^∗,S^∗)- and (S^∗,R^∗)-diastereomers. Mostly, the major diastereomer has the S^∗,S^∗-configuration. According to X-ray diffraction data in the solid form and NOE data in solution, diastereoselectivity of the T-reactions can be associated with the structure of the Knoevenagel products whose conformation is fixed by the strong intramolecular C-H?π interaction.     

Improved synthesis of N-alkyl substituted dithieno[3,2-b:2′,3′-d]pyrroles

A new, convergent and improved synthetic method to prepare N-alkyl substituted dithienopyrroles is described. The procedure consists of a Pd-catalyzed amination of 3,3′-dibromo-2,2′-bithiophene. The reaction conditions were optimized, which makes this method applicable to prepare these molecules easily in high yields and on a large scale.     

A simple and stereodivergent strategy for the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides exploiting (Z)-but-2-en-1,4-diol and (R)-2,3-cyclohexylideneglyceraldehyde

Barbier type additions of allylic bromide 4, derived from (Z)-but-2-en-1,4-diol 2 to (R)-2,3-cyclohexylideneglyceraldehyde 1 were performed through mediation with Zn employing Luche’s procedure and also with low valent Cu, Co, and Fe which were produced via bimetal redox strategy in THF to afford 5c,d as the major products. From these, 5a,b were prepared following an oxidation-reduction protocol. Compound 5c was exploited as a representative starting material to develop a simple and inexpensive strategy toward the synthesis of 3′-C-branched 2′,3′-dideoxynucleosides having stereodiversity at 3′- and 4′-positions.