Nucleotides,Part LXVIII,Acetals as New 2′‐O‐Protecting Functions for the Synthesis of Oligoribonucleotides: Synthesis of Monomeric Building Units and Oligoribonucleotides

For the efficient synthesis of oligoribonucleotides by the 5′‐O‐(4,4′‐dimethoxytrityl) phosphoramidite approach, the 2′‐O‐[1‐(benzyloxy)ethyl]acetals 56 – 67 were investigated. Studies with the 2′‐O‐[1‐(benzyloxy)ethyl]‐5′‐O‐(dimethoxytrityl)ribonucleoside 3′‐phosphoramidites 56 – 59 gave, however, only reasonable results. The oligoribonucleotides obtained showed some impurities since the acid stabilities of the acetal and dimethoxytrityl functions are too close to guarantee a high selectivity. A combination of new acid‐labile protected 2′‐O‐protecting groups with the 2‐(4‐nitrophenyl)ethyl/[2‐(4‐nitrophenyl)ethoxy]carbonyl (npe/npeoc) strategy for base protection was more successful. The synthesis and physical properties of the monomeric building units and their intermediates 8 – 67 and the conditions for the automated generation of homo‐ and mixed oligoribonucleotides is described. The new 2′‐acetal protecting group could be cleaved off in a two step procedure and was designed for levelling their stability with regard to the attached nucleobase as well. Therefore, we used the 1‐{{3‐fluoro‐4‐{{[2‐(4‐nitrophenyl)ethoxy]carbonyl}oxy}benzyl}oxy}ethyl (fnebe) moiety for the protection of 2′‐OH of uridine, and for that of 2′‐OH of A, C, and G, the 1‐{{4‐{{[2‐(4‐nitrophenyl)ethoxy]carbonyl}oxy}benzyl}oxy}ethyl (nebe) residue. After selective deprotection by β‐elimination induced by a strong organic base like DBU, the remaining activated acetal was hydrolyzed under very mild acidic protic conditions, which reduced 2′‐3′ isomerization and chain cleavage. Also storage, handling, and purification of the chemically and enzymatically sensitive oligomers was simplified by this approach.     

Nucleosides. Part LI The 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) and 2-(2,4-dinitrophenyl)ethoxycarbonyl (dnpeoc) groups for protection of hydroxy functions in ribonucleosides and 2′ -deoxyribonucleosides

The Common 2′ -deoxypyrimidine and -purine nucleosides, thymidine ( 4 ), O⁴-[2-(4-nitrophenyl)ethyl]-thymidine ( 17 ), 2′-deoxy-N⁴-[2-(4-nitrophenyl)ethoxycarbonyl]cytidine ( 26 ), 2′-deoxy-N⁶-[2-(4-nitrophenyl)-ethoxycarbonyl]adenosine- 39 , and 2′-deoxy-N²-[2-(4-nitrophenyl)(ethoxycarbonyl]-O⁶-[2–4-nitrophenyl)ethyl]-guanosine ( 52 ) were further protected by the 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) and the 2-(2,4-dinitrophenyl)ethoxycarbonyl (dnpeoc) group at the OH functions of the sugar moiety to form new partially and fully blocked intermediates for nucleoside and nucleotide syntheses. The corresponding 5′-O-monomethoxytrityl derivatives 5 , 18 , 30 , 40 , and 56 were also used as starting material to synthesize some other intermediates which were not obtained by direct acylations. In the ribonucleoside series, the 5′ -O-monomethoxytrityl derivatives 14 , 36 , 49 , and 63 reacted with 2-(4-nitrophenyl) ethyl chloroformate ( 1 ) to the corresponding 2′,3′-bis-carbonates 15 , 37 , 50 , and 64 which were either detriylated to 16 , 38 , 51 , and 65 , respectively, or converted by 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) treatment to the 2′,3′-cyclic carbonates 66 – 69 . The newly synthesized compounds were characterized by elemental analyses and UV and ¹H-NMR spectra.     

Nucleotides,Part LXVII,The 2‐Cyanoethyl and (2‐Cyanoethoxy)carbonyl Group for Base Protection in Nucleoside and Nucleotide Chemistry

The amino functions of the common 2′‐deoxyribo‐ and ribonucleosides were blocked by the (2‐cyanoethoxy)carbonyl group on treatment with 2‐cyanoethyl carbonochloridate ( 5 ) or 1‐[(2‐cyanoethoxy)carbonyl]‐3‐methyl‐1H‐imidazolium chloride ( 6 ) leading to 7 , 18 , 8 , 19 , 9 , and 20 . In 2′‐deoxyguanosine, the amide group was additionally blocked at the O⁶ position by the 2‐cyanoethyl (→ 27 ) and 2‐(4‐nitrophenyl)ethyl group (→ 31 , 32 ). Comparative kinetic studies regarding the cleavage of the ce/ceoc and npe/npeoc group by β‐elimination revealed valuable information about the ease and sequential deprotection of the various blocking groups at different sites of the nucleobases. Besides the 5′‐O‐(dimethoxytrityl)‐protected 3′‐(2‐cyanoethyl diisopropylphosphoramidites) 38 and 39 of N⁴‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxycytidine and N⁶‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxyadenosine, respectively, the N²‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxy‐O⁶‐[2‐(4‐nitrophenyl)ethyl]guanosine analog 40 is recommended as building block for oligo‐2′‐deoxyribonucleotide synthesis.     

Nucleosides. Part LIX. The 2-(4-nitrophenyl)ethylsulfonyl (Npes) Group: A New Type of Protection in Nucleoside Chemistry

The 2-(4-nitrophenyl)ethylsulfonyl (npes) group is developed as a new sugar OH-blocking group in the ribonucleoside series. Its cleavage can be performed in a β-eliminating process under aprotic conditions using 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) as the most effective base. Since sulfonates do not show acyl migration, partial protection of 1,2-cis-diol moieties is possible leading to new types of oligonucleotide building blocks. A series of Markiewicz-protected ribonucleosides 1–10 is converted into their 2′-O-[2-(4-nitrophenyl)ethylsulfonyl] derivatives 29–38 in which the 5′-O? Si bond can be cleaved by acid hydrolysis forming 39–45 . Subsequent monomethoxytritylation leads to 46–50 , and desilylation affords the 5′-O-(monomethoxytrityl)-2′-O-[2-(4-nitrophenyl)ethylsulfonyl]ribonucleosides 51–55 . Acid treatment to remove trityl groups do also not harm the npes group (→ 56–58 ). Unambiguous syntheses of fully blocked 2′-O-[2-(4-nitrophenyl)ethylsulfonyl]ribonucleosides 96–102 are achieved from the corresponding 3′-O-(tert-butyl)dimethylsilyl derivatives. Furthermore, various base-protected 5′-O-(monomethoxytrityl)- and 5′-O-(dimethoxytrityl)ribonucleosides, i.e. 59–77 , are treated directly with 2-(4-nitrophenyl)ethylsulfonyl chloride forming in all cases a mixture of the 2′,3′-di-O- and the two possible 2′- and 3′-O-monosulfonates 107–148 which can be separated into the pure components by chromatographic methods. The npes group is more labile towards DBU cleavage than the corresponding base-protecting 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) groups allowing selective deblocking which is of great synthetic potential.     

Nucleotides Part XL. Synthesis and Characterization of Modified 2′–5′ Adenylate Trimers–Potential Antiviral Agents

2′–5′ Adenylate trimers 41–44 carrying the (tert-butyl)dimethylsilyl (tbds) group at the 3′-OH position of various sugar moieties were synthesized via the phosphoramidite method. The use of the (tert-butyloxy)carbonyl (boc) and 2-(4-nitrophenyl)ethylsulfonyl (npes) groups for 2′-OH protection in neighbourhood to the 3′-O-tbds residue was compared during the synthesis of the target trimers. For other functional positions, the use of the 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) blocking groups were favoured.     

Nucleotides. Part LXXIX

Two series of new ribonucleoside 3′‐phosphoramidites (see 36 – 42 ) carrying the photolabile [2‐(2‐nitrophenyl)propoxy]carbonyl group at the 5′‐O‐position were synthesized and characterized as monomeric building blocks for photolithographic syntheses of RNA chips. Base protection was achieved in the well‐known manner by the 2‐(4‐nitrophenyl)ethyl (npe) and the [2‐(4‐nitrophenyl)ethoxy]carbonyl (npeoc) group. The carbohydrate moiety carried in addition the 2′‐O‐(tetrahydro‐4‐methoxy‐2H‐pyran‐4‐yl) group for blocking the 2′‐OH function.     

Nucleotides. Part XXXI. Modified Oligomeric 2′–5′ A Analogues: Synthesis of 2′–5′ oligonucleotides with 9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine and 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)adenine as modified nucleosides

A series of new 2′–5′ oligonucleotides carrying the 9-(3′-azido-3′deoxy-β-D-xylofuranosyl)adenine moiety as a building block has been synthesized via the phosphotriester method. The use of the 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) blocking groups for phosphate, amino, and hydroxy protection guaranteed straightforward syntheses in high yields and easy deblocking lo form the 2′–5′ trimers 21 , 22 , and 25 and the tetramer 23 . Catalytic reduction of the azido groups in [9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine]2′-yl-[2′-(O^p-ammonio)→ 5′]-[9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenin]-2′-yl-[2′-(O^p-ammonio)→ 5′]-9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine ( 21 ) led to the corresponding 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)-adenine 2′–5′ trimer 26 in which the two internucleotidic linkages are formally neutralized by intramolecular betaine formation.     

Improved Synthesis of Oligodeoxyribonucleotides by Solid-Phase Phosphotriester Method Utilizing O6-[2-(p-Nitrophenyl)ethyl]-2′-deoxyguanosine Derivatives

The synthesis of oligodeoxyribonucleotides on a cross-linked polystyrene solid support utilizing stable mono- and dinucleotide phosphotriester building blocks is presented. The use of O⁶[2-(p-nitrophenyl)ethyl]-2′-deoxyguanosine derivatives yields cleaner DNA fragments by suppressing side reactions. Modifications improving the phosphotriester methodology are presented. The purification methods and analysis of synthetic oligodeoxyribonucleotides are described.     

Nucleotides,Part LX,Synthesis and Characterization of New 2′-O-Methylriboside 3′-O-Phosphoramidites Useful for the Solid-Phase Synthesis of 2′-O-Methyloligoribonucleotides

A series of new 2′-O-methylribonucleoside 3′-O-[2-(4-nitrophenyl)ethyl dialkylphosphoramidites] 27 – 31 , 33 – 38 , 40 – 44 , and 45 – 50 were synthesized and their stability and reactivity compared in automated oligonucleotide synthesis with the standard 2′-O-methylribonucleoside 3′-O-(β-cyanoethyl diisopropylphosphoramidites) 32 , 39 , 45 , and 51 , respectively. The 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) groups were used for the protection of the base moieties.     

Nucleotides,Part LXIX,Synthesis of Phosphoramidite Building Blocks of Isoxanthopterin N8‐(2′‐Deoxy‐β‐D‐ribonucleosides): New Fluorescence Markers for Oligonucleotide Synthesis

The chemical synthesis of isoxanthopterin and 6‐phenylisoxanthopterin N⁸‐(2′‐deoxy‐β‐D ‐ribofuranosyl nucleosides) is described as well as their conversion into suitably protected 3′‐phosphoramidite building blocks to be used as marker molecules for DNA synthesis. Applying the npe/npeoc (=2‐(4‐nitrophenyl)ethyl/[2‐(4‐nitrophenyl)ethoxy]carbonyl) strategy, we used the new building blocks in the preparation of oligonucleotides by an automated solid‐support approach. The hybridization properties of a series of labelled oligomers were studied by UV‐melting techniques. It was found that the newly synthesized markers only slightly interfered with the abilities of the labelled oligomers to form stable duplexes with complementary oligonucleotides.     

Nucleosides. Part LXI. A Simple Procedure for the Monomethylation of Protected and Unprotected Ribonucleosides in the 2′-O- and 3′-O-Position Using Diazomethane and the Catalyst Stannous Chloride

Intensive studies on the diazomethane methylation of the common ribonucleosides uridine, cytidine, adenosine, and guanosine and its derivatives were performed to obtain preferentially the 2′-O-methyl isomers. Methylation of 5′-O-(monomethoxytrityl)-N²-(4-nitrophenyl)ethoxycarbonyl-O⁶-[2-(4-nitrophenyl)ethyl]-guanosine ( 1 ) with diazomethane resulted in an almost quantitative yield of the 2′- and 3′-O-methyl isomers which could be separated by simple silica-gel flash chromatography (Scheme 1). Adenosine, cytidine, and uridine were methylated with diazomethane with and without protection of the 5′ -O-position by a mono- or dimethoxytrityl group and the aglycone moiety of adenosine and cytidine by the 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) group (Schemes 2–4). Attempts to increase the formation of the 2′-O-methyl isomer as much as possible were based upon various solvents, temperatures, catalysts, and concentration of the catalysts during the methylation reaction.     

Nucleotides. Part XLIII. Solid-phase synthesis of oligoribonucleotides using the 2-dansylethoxycarbonyl (  2-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}ethoxycarbonyl; dnseoc) group for 5′-hydroxy protection

A new efficient method for solid-phase synthesis of oligoribonucleotides via the phosphoramidite approach is described. The combination of the base-labile 2-dansylethoxycarbonyl (Dnseoc) group for 5′-OH protection with the acid-labile tetrahydro-4-methoxy-2H-pyran-4-yl (Thmp) group as 2′-OH blocking group is orthogonal regarding cleavage reactions and fulfills the requirements of an automated synthesis in an excellent manner if the phosphoramidite function carries the N,N-diethyl-O-[2-(4-nitrophenyl)ethyl] substitution.     

Nucleotides Part LI. Synthesis and biological activities of (2′-5′)adenylate trimer conjugates with 2′-terminal 3′-O(ω-hydroxyalkyl) and 3′-O-(ω-carboxyalkyl) spacers

An efficient strategy for the synthesis of (2′-5′)adenylate trimer conjugates with 2′-terminal 3′-O-(ω-hydroxyalkyl) and 3′-O-(ω-carboxyalkyl) spacers is reported. Npeoc-protected adenosine building blocks 37--40 for phosphoramidite chemistry carrying a 3′-O-[11-(levulinoyloxy)undecyl], 3′-O-{2-[2-(levulinoyloxy)ethoxy]ethyl}, 3′-O-[5-(2-cyanoethoxycarbonyl)pentyl], and 3′-O-{5-[(9H-fluoren-9-ylmethoxy)carbonyl]pentyl} moiety, respectively, were prepared (npeoc = 2-(4-nitrophenyl)ethoxycarbonyl). Condensation with the cordycepin (3′-deoxyadenosine) dimer 1 led to the corresponding trimers 42, 43, 47 , and 48. Whereas the levulinoyl (lev) and 9H-fluoren-9-ylmethyl (fm) blocking groups could be cleaved off selectively from the trimers 42, 43 , and 48 yielding the intermediates 44, 45 , and 49 for the synthesis of the 3′-O-(ω-hydroxyalkyl)trimers 53, 54 and the cholesterol conjugates 59--61 , the 2-cyanoethyl (ce) protecting group of 47 , however, could not be removed in a similar manner from the carboxy function. Trimer 47 served as precursor for the preparation of the trimer 55 with a terminal 3′-O-(5-carboxypentyl)adenosine moiety. The metabolically stable 3′-O-alkyl-(2′--5′)A derivatives were tested regarding inhibition of HIV-1 syncytia formation and HIV-1 RT activity. Only the conjugate 59 showed significant effects, whereas the trimers 53--55 and the conjugates 60 and 61 were less potent inhibitors, even at 100-fold larger concentrations.     

Reaction of 2-{[2-(ethenyloxy)ethoxy]methyl}oxirane with oxazolidin-2-ones

Reactions of 2-{[2-(ethenyloxy)ethoxy]methyl}oxirane with N-unsubstituted oxazolidin-2-ones give mixtures of isomeric 3-{3-[2-(ethenyloxy)ethoxy]-2-hydroxypropyl}- and 5-{[2-(ethenyloxy)ethoxy]- methyl}-3-(2-hydroxyalkyl)oxazolidin-2-ones. If the initial oxazolidin-2-one contains two alkyl groups on C⁴, 3-{3-[2-(ethenyloxy)ethoxy]-2-hydroxypropyl}oxazolidin-2-ones are selectively formed.     

Nucleotides. Part LXXII

The synthesis of various N‐methylated nucleosides (m⁶A, m³C, m⁴C, m³U) is described. These minor nucleosides can be obtained by simple methylation with diazomethane of [2‐(4‐nitrophenyl)ethoxy]carbonyl(npeoc)‐protected nucleosides. These methylated compounds are easily further derivatized to fit into the scheme of the [2‐(dansyl)ethoxy]carbonyl (dnseoc) approach for RNA synthesis (dansyl=[5‐(dimethylamino)naphthalen‐1‐yl]sulfonyl). Various oligoribonucleotides containing N⁶‐methyladenosine were synthesized, underlining the usefulness of the dnseoc approach, especially for the synthesis of natural tRNA‐derived oligoribonucleotide sequences.     

Nucleotides,Part LXIII,New 2-(4-Nitrophenyl)ethyl(Npe)- and 2-(4-Nitrophenyl)ethoxycarbonyl(Npeoc)-Protected 2′-Deoxyribonucleosides and Their 3′-Phosphoramidites – Versatile Building Blocks for Oligonucleotide Synthesis

A series of new base-protected and 5′-O-(4-monomethoxytrityl)- or 5′-O-(4,4′-dimethoxytrityl)-substituted 3′-(2-cyanoethyl diisopropylphosphoramidites) and 3′-[2-(4-nitrophenyl)ethyl diisopropylphosphoramidites] 52 – 66 and 67 – 82 , respectively, are prepared as potential building blocks for oligonucleotide synthesis (see Scheme). Thus, 3′,5′-di-O-acyl- and N ²,3′-O,5′-O-triacyl-2′-deoxyguanosines can easily be converted into the corresponding O⁶-alkyl derivatives 6 , 8 , 10 , 12 , 14 , and 16 by a Mitsunobu reaction using the appropriate alcohol. Mild hydrolysis removes the acyl groups from the sugar moiety (→ 9 , 11 , 13 , 15 , and 19 (via 18 ), resp.) which can then be tritylated (→ 38 – 42 ) and phosphitylated (→ 57 – 61 ) in the usual manner. N ²-[2-(4-nitrophenyl)ethoxycarbonyl]-substituted and N ²-[2-(4-nitrophenyl)ethoxycarbonyl]-O⁶-[2-(4-nitrophenyl)ethyl]-substituted 2′-deoxyguanosines 5 and 7 , respectively, are synthesized as new starting materials for tritylation (→ 28 , 35 , and 37 ) and phosphitylation (→ 54 , 56 , 70 , and 78 ). Various O⁴-alkylthymidines (see 20 – 24 ) are also converted to their 5′-O-dimethoxytrityl derivatives (see 43 – 47) and the corresponding phosphoramidites (see 62 – 66 and 79 – 82 ).     

1-[18F]Fluoroethyleneglycol-2-nitroimidazoles, a new class of potential hypoxia PET markers

Summary 1-[2-(2-Fluoroethoxy)ethyl]-2-1H-nitroimidazole (3a), 1-{2-[2-(2-fluoroethoxy)ethoxy]ethyl}-2-1H-nitroimidazole (3b) and 1-(2-{2-[2-(2-fluoroethoxy)ethoxy]ethoxy}ethyl)-2-1H-nitroimidazole (3c) were synthesized in a two step sequence.Coupling the ditosylate of di-, tri- or tetraethylene glycol with 2-nitroimidazole followed by fluoride substitution afforded the reference compounds in high yield and¹⁸F labeling gave the corresponding markers in 70-82% radiochemical yield.     

Nucleotides. Part XXVII Bis[2-(p-nitrophenyl)ethyl] Phosphorochloridate,a New Versatile Phosphorylating Agent in Nucleotide Chemistry

A new, versatile phosphorylating agent, bis[2-(p-nitrophenyl)ethyl] phosphorochloridate ( 3 ), has been prepared and is used for 3′- and/or 5′-phosphorylations of nucleosides. The resulting bis[2-(p-nitrophenyl)ethyl] phosphotriesters are versatile synthons in oligonucleotide synthesis leading finally to 3′- and/or 5′-terminated monophosphates in excellent yields.     

Halogenation of [2-(trimethylsilyl)ethoxy]methyl (SEM) protected 2,2′-Bi-H-imidazole

2,2′-Bi-1H-imidazole, when protected with the [2-(trimethylsilyl)ethoxy]methyl (SEM) blocking group, on treatment with N-bromosuccinimide or N-chlorosuccinimide yields predominantly the monohalogenated derivatives 4a and 4b. The [2-(trimethylsilyl)ethoxy]methyl group is subsequently removed to yield pure mono-halo-2,2′-bi-H-imidazoles 2 .