Concise and efficient synthesis of 3′-O-triphosphates of 2′-deoxyadenosine and 2′-deoxycytidine

We describe concise and efficient synthesis of 2′-deoxyadenosine-3′-O-triphosphate (2′-d-3′-ATP) and 2′-deoxycytidine-3′-O-triphosphate (2′-d-3′-CTP) which are well known for their various biological applications. One-pot synthetic methodology was used to convert N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine into N⁶-Benzoyl-5′-O-levulinoyl-2′-deoxyadenosine-3′-O-triphosphate in 72% yield. One-step concurrent deprotection of N⁶-Benzoyl and 5′-O-levulinoyl groups using concentrated aqueous ammonia resulted in 2′-d-3′-ATP in 75% yield. The same synthetic strategy was successfully employed to convert N⁴-Benzoyl-5′-O-levulinoyl-2′-deoxycytidine into 2′-d-3′-CTP in 66% yield.     

Synthesis of 4-N-alkyl and ribose-modified AICAR analogues on solid support

Herein, we report the solid-phase synthesis of several 5-aminoimidazole-4-(N-alkyl)carboxamide-1-ribosides (4-N-alkyl AICARs) and the corresponding 2′,3′-secoriboside derivatives. The method uses the N-1-dinitrophenyl-inosine 5′-bonded to a solid support. This inosine derivative has the C-2 of the purine base strongly activated towards the attack of N-nucleophiles thus allowing the preparation of several N-1 alkylated inosine supports from which a small library of 4-N-alkyl AICAR derivatives has been synthesized. A set of new 4-N-alkyl AICA-2′,3′-secoriboside derivatives have also been obtained in high yields by solid-phase cleavage of the 2′,3′-ribose bond.     

Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNA, with S-type sugar conformation fixed by N-O linkage

We designed a novel 2′-O,5′-N bridged nucleic acid, 2′,5′-BNA^ON, whose sugar puckering was fixed to S-type conformation by an N-O linkage. A dimer unit formed from 2′,5′-BNA^ON-U and thymidine was synthesized via a coupling reaction between a protected 2′,5′-BNA^ON-U monomer and a thymidine derivative. Introduction of 2′,5′-BNA^ON-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2′,5′-BNA^ON-U-modified oligonucleotides against DNA or RNA complement were evaluated.     

Facile synthesis of 2′-O-cyanoethyluridine by ring-opening reaction of 2,2′-anhydrouridine with cyanoethyl trimethylsilyl ether in the presence of BF3·Et2O

In this Letter, a facile method for the synthesis of 2′-O-cyanoethyluridine, which is a key intermediate in the synthesis of fully and partially 2′-O-cyanoethylated oligoribonucleotides as well as unmodified oligoribonucleotides, was developed by the ring-opening reaction of 2,2′-anhydrouridine with 2-cyanoethyl trimethylsilyl ether in the presence of BF₃·Et₂O in dimethylacetamide. The 2′-O-cyanoethyluridine 3′-phosphoramidite derivative was converted into the 2′-O-cyanoethyl-4-N-acetylcytidine 3′-phosphoramidite derivative by a series of reactions involving displacement of the 4-(1H-1,2,4-triazol-1-yl)uridine derivative with ammonia followed by acetylation.     

Stepwise solid phase synthesis of uridylylated viral genome-linked peptides using uridylylated amino acid building blocks

The uridylylated amino acid building blocks 2-cyanoethyl-(N^α-9-fluorenylmethoxy-carbonyl-tyrosin-4-yl)-(2′,3′-di-O-acetyluridin-5′-yl) phosphate and 2-chlorophenyl-(N^α-fluorenyl-methoxycarbonyl-serin-3-yl)-(2′,3′-di-O-acetyluridin-5′-yl) phosphate have been used successfully in an on-line SPPS of the VPgpU from the polio, coxsackie and cowpea mosaic virus.     

A one-step synthesis of N-Fmoc-4-O-[O′,O″-di-tert-butyl-2-(2-fluoromalonyl)]-l-tyrosine from commercially available starting material

A one-step high yield synthesis from commercially available starting material is reported for the novel phosphotyrosyl mimetic, N^α-Fmoc-4-O-[O′,O″-di-tert-butyl-2-(2-fluoromalonyl)]-l-tyrosine. The conditions employed for this transformation may also be applicable for the direct electrophilic fluorination of other N^α-Fmoc-protected amino acids.     

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.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Synthetic studies on pterin glycosides: the first synthesis of 2′-O-(α-d-glucopyranosyl)biopterin

l-Rhamnose was led, in a 14-step-sequence, to N²-(N,N-dimethylaminomethylene)-1′-O-(4-methoxybenzyl)-3-[2-(4-nitrophenyl)ethyl]biopterin (23), an appropriately protected precursor for 2′-O-glycosylation, while 4,6-di-O-acetyl-2,3-di-O-(4-methoxybenzyl)-α-d-glucopyranosyl bromide (32), a novel glycosyl donor, was efficiently prepared from d-glucose in 8 steps. The first synthesis of 2′-O-(α-d-glucopyranosyl)biopterin (2a) was achieved by treatment of the key intermediate 23 with 32 in the presence of silver triflate and tetramethylurea, followed by successive removal of the protecting groups.     

Rapid and high-yield solution-phase synthesis of DOTA-Tyr-octreotide and DOTA-Tyr-octreotate using unprotected DOTA

An improved method for the solution-phase derivatization of Tyr³-Lys⁵(Dde)-octreotide (TOC(Dde)) and Tyr³-Lys⁵(Dde)-octreotate (TATE(Dde)) with the macrocyclic chelator DOTA (1,4,7,10-tetraazacyclododecane-N′,N″,N?,N?-tetraacetic acid) has been developed. The fully protected parent peptides were assembled via solid-phase peptide synthesis (SPPS) using Fmoc-strategy. After cleavage from the solid support, disulfide bond formation was carried out using H₂O₂. Both TOC(Dde) and TATE(Dde) were successfully coupled with DOTA in the presence of NHS, EDCI and DIPEA in a water/DMF solvent system. Yields of the coupling reaction were >98% within only 2 h with no detectable formation of sideproducts. This method for the preparation of DOTATOC, DOTATATE and other DOTA-peptide conjugates is therefore a rapid and economic alternative to the currently used methods.     

Scalable synthesis of substituted 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH): useful for the preparation of crystalline 5′-O-DMPx-protected nucleosides

A convenient single-step synthesis of several 2,7-dimethyl-9-phenylxanthen-9-ol (DMPx-OH) analogs has been accomplished using a Friedel-Crafts reaction. Treatment of various DMPx-OH with unprotected 2′-O-methoxyethyl-ribonucleosides (MOE) in the presence of B(C₆F₅)_3, as a Lewis Acid catalyst, furnished 5′-O-protected derivatives of 2′-MOE-ribonucleosides in good yields. The deprotection of the DMPx groups was accomplished by acid hydrolysis under very mild conditions. Among the five DMPx analogs synthesized, the 2,7-dimethyl-9-(4-nitrophenyl)xanthene-9-yl group furnished crystalline products enabling non-chromatographic isolation of 5′-O-protetced nucleosides.     

Solid-phase synthesis of a type II′ β-turn peptido-mimetic library

The solid-phase synthesis of a dipeptide derived 2-amino-3-oxohexahydroindolizino[8,7-b]indole-5-carboxylate system (IBTM) is described. The IBTM moiety is formed via a solid-phase mediated Pictet-Spengler reaction of N-terminal tryptophan and the 4-{N-[1-(4,4-dimethyl-2,6-dioxocyclohexylidene)-3-methylbutyl]amino}benzyl (Dmab) ester of Fmoc protected aspartic acid β-aldehyde followed by γ-lactamization. This synthesis allows the regio- and stereoselective incorporation of a dipeptide surrogate of type II′ β-turns. The procedure is easily adaptable to combinatorial synthesis and a 576-member library was synthesized.     

Stereoselective synthesis of all stereoisomers of vicinal and distal bis(O-2-aminoethyl)-p-tert-butylthiacalix[4]arene

O,O″- and O,O′-bis(2-aminoethyl)-p-tert-butylthiacalix[4]arenes of anti conformation have been prepared by the reduction of the corresponding O,O″- and O,O′-bis(cyanomethyl) ethers. Their syn-O,O″- and O,O′-counterparts have been prepared by alternative routes via the Mitsunobu reaction of thiacalix[4]arene with N-(2-hydroxyethyl)phthalimide and the reduction of a O,O′-disiloxanediyl-bridged O″,O?-bis(cyanomethyl) ether of 1,2-alternate conformation, respectively. These products are expected to serve as useful precursors of highly elaborated synthetic receptors, including biscalixarenes.     

Cyclization versus oligomerization of SP- and RP-5′-OH-N-benzoyl-2′-deoxycytidine-3′-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)s

The S_P-isomer of 5′-OH-N⁴-benzoyl-2′-deoxycytidine-3′-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) undergoes DBU-promoted intramolecular cyclization providing as a sole product S_P-deoxycytidine cyclic 3′,5′-O,O-phosphorothioate. Unexpectedly, the R_P-counterpart yields a mixture of products consisting of R_P-deoxycytidine cyclic 3′,5′-O,O-phosphorothioate and macrocyclic oligo(deoxycytidine phosphorothioate)s. The results of molecular modeling indicate that the dychotomy observed for the R_P substrate may result from remarkably higher energy of the corresponding transition states, caused by the presence of bulky ‘spiro’ pentamethylene substituent at the position C4 in the oxathiaphospholane ring.     

Efficient synthesis of tetramethylsulfonylguanidines between a free sulfonamide group and HBTU

The reaction of a sulfonamide moiety with HBTU (O-(1H-benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate) during amide coupling, leading to the formation of tetramethylsulfonylguanidines, is described. Optimised conditions showed that HBTU was as a convenient agent for the synthesis of tetramethylsulfonylguanidines, in basic conditions. A panel of diverse sulfonamides was used to demonstrate the scope of this procedure.     

An efficient convergent synthesis of adenosine-5′-N-alkyluronamides

Herein we report an efficient synthesis of adenosine-5′-N-alkyluronamides in which an enzyme-mediated deacetylation reaction is a key to the selective modification of the 5′-N-position, prior to coupling the ribose and purine components via a microwave-assisted Vorbrüggen coupling. This approach provides access to highly functionalised adenosines with 2- and N⁶-substitutents, which can be incorporated before or after the ribose-coupling step. In all cases the microwave-assisted Vorbrüggen coupling conditions afforded anomerically pure purine ribosides in good to excellent yields.     

New approach to preparation of N-acylphosphoramido(thio)(seleno)ates

N-[2-(X)-1,3,2-Oxathiaphospholane] derivatives (X = S, Se, O) of carboxamides were prepared and their DBU-assisted reaction with alcohols led to the corresponding O-alkyl-N-acylphosphoramido(thio)(seleno)ates. Their structures were confirmed by MS analysis and ¹H and ³¹P NMR spectroscopy. Independently N-acylphosphoramidoselenoates were converted to N-acylphosphoramidates by treatment with tert-butylperoxytrimethylsilane. The oxathiaphospholane approach was also applied to the synthesis of derivatives having N-prolylphosphoramido(thio)(seleno)ate linkages on the 5′-OH group of AMP.     

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.     

Solid-phase synthesis of O-sulfated glycopeptide by the benzyl-protected glycan strategy

To expand the repertoire of our benzyl-protection strategy for solid-phase glycopeptide synthesis, an O-sulfated glycopeptide was chosen as the synthetic target. Trisaccharyl serine derivatives (Galβ1-4-GlcNAcβ1-2-Manα1-3-Ser) carrying (4-methoxyphenyl)methyl (MPM) groups at either 3-O or 6-O of the Gal residue were prepared through three stereoselective glycosylations. Cleavage of MPM followed by reaction with Me₃N·SO₃ efficiently afforded 3-O- and 6-O-sulfo-glycoserines, respectively. A preliminary debenzylation study using the sulfated glycoserines revealed that the sulfate groups persisted under ‘low-acidity TfOH’ conditions, when using a limited amount of TfOH and extending the reaction period. The 3-O-sulfo-glycoserine was then introduced into an icosapeptide modeled after an α-dystroglycan fragment by a combination of automated and manual solid-phase peptide synthesis procedures. The synthesized glycopeptide was successfully debenzylated by the low-acidity TfOH cocktail with slight damage to the sulfate functionality.     

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%).