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.     

Nucleotides. Part XLV. Synthesis of new (2′–5′)adenylate trimers,containing 5′-amino-5′-deoxyadenosine residues at the 5′-end of the oligoadenylate chain,and of its analogues,carrying a 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus

The 5′-amino-5′-deoxy-2′,3′-O-isopropylideneadenosine ( 4 ) was obtained in pure form from 2′,3′-O-isopropylideneadenosine ( 1 ), without isolation of intermediates 2 and 3 . The 2-(4-nitrophenyl)ethoxycarbonyl group was used for protection of the NH₂ functions of 4 (→7) . The selective introduction of the palmitoyl (= hexadecanoyl) group into the 5′-N-position of 4 was achieved by its treatment with palmitoyl chloride in MeCN in the presence of Et₃N (→ 5 ). The 3′-O-silyl derivatives 11 and 14 were isolated by column chromatography after treatment of the 2′,3′-O-deprotected compounds 8 and 9 , respectively, with (tert-butyl)dimethylsilyl chloride and 1H-imidazole in pyridine. The corresponding phosphoramidites 16 and 17 were synthesized from nucleosides 11 and 14 , respectively, and (cyanoethoxy)bis(diisopropylamino)phosphane in CH₂Cl₂. The trimeric (2′–5′)-linked adenylates 25 and 26 having the 5′-amino-5′-deoxyadenosine and 5′-deoxy-5′-(palmitoylamino)adenosine residue, respectively, at the 5′-end were prepared by the phosphoramidite method. Similarly, the corresponding 5′-amino derivatives 27 and 28 carrying the 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus, were obtained. The newly synthesized compounds were characterized by physical means. The synthesized trimers 25–28 were 3-, 15-, 25-, and 34-fold, respectively, more stable towards phosphodiesterase from Crotalus durissus than the trimer (2′–5′)ApApA.     

Nucleotides. Part XXXV. Synthesis of 3′-deoxyadenylyl-(2′–5′)-3′-deoxyadenyIyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines

Via the phosphotriester approach, new structural analogs of (2′–5′)oligoadenyiates, namely 3′-deoxyadenylyl-(2′–5′)-3′-dcoxyadenylyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines 18 – 21 , have been synthesized (see Scheme) which should preserve biological activity and show higher stability towards phosphodiesterases. The newly synthesized oligonucleotides 18 – 21 have been characterized by ¹H-NMR spectra, TLC, and HPLC analysis.     

Nucleotides. Part XLVI. The synthesis of phospholipid conjugates of antivirally active nucleosides by the improved phosphoramidite methodology

The application of the improved phosphoramidite strategy for the synthese of oligonucleotides using β-eliminating protecting groups to phospholipid chemistry offers the possibility to synthesize phospholipid conjugates of AZT ( 6 ) and cordycepin. The synthesis of 3′-azido-3′-deoxythymidine ( 6 ) was achieved by a new isolation procedure without chromatographic purification steps in an overall yield of 50%. Protected cordycepin ( = 3′-de-oxyadenosine) derivatives, the N⁶,2′-bis[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 12 ) and the N⁶,5′-bis[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 13 ) wre prepared by known methods and direct acylation of N⁶-[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 9 ), respectively. These protected nucleosides and the 3′-azido-3′-de-oxythymidine ( 6 ) reacted with newly synthesized and properly characterized lipid-phosphoramidites 21–25 , catalyzed by 1H-tetrazole, to the corresponding nucleoside-phospholipid conjugates 26–38 in high yield. The deprotection was accomplished via β-elimination with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in aprotic solvents to give analytically pure nucleoside-phospholipid diesters 39–51 as triethylammonium or sodium salts. The newly synthesized compounds were characterized by elemental analyses and UV and ¹H-NMR spectra.     

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 ).     

Nucleotides. Part XXVIII. Chemical syntheses of the 2′-5′-cordycepin-trimer core

The chemical synthesis of 3′-deoxyadenyly-(2′-5′)-3′-deoxyadenylyl-(2′-5′)-3′-deoxyadenosine ( 30 ; trimeric cordycepin) is described by three different routes using various protecting groups and applying the phosphotriester approach. The intermediates have been isolated and characterized by elemental analyses and spectroscopic means. High yields of 30 have been obtained on deprotection making this biologically very active compound available in preparative scale.     

Nucleotides. Part LXXV

The reactivity of the 2′‐deoxy‐N⁴‐(phenoxycarbonyl)cytidine derivatives 3 and 4 with aromatic amines was studied to form new types of urea derivatives (see 5 – 10 ). On the same basis, labeling of 3 and 4 with 5‐aminofluorescein ( 14 ) was achieved to give the conjugates 15 and 17 , respectively (Scheme 1). Treatment of 17 with 2‐(4‐nitrophenyl)ethanol in a Mitsunobu reaction led to double protection of the fluorescein moiety (→ 18 ) and desilylation yielded 19 . Dimethoxytritylation (→ 20 ) and subsequent phosphitylations afforded the new building blocks 21 and 22 . Synthesis of the fully protected trimer 28 was achieved by condensation of 21 with 23 to 26 which after detritylation (→ 27 ) was coupled with 25 to give 28 (Scheme 2). Deprotection of all blocking groups was performed with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) in one step to give 29 . The synthesis of the decamer 5′‐d(C^FluCCG GCC CGC)‐3′ ( 33 ) started from 30 which was attached to the solid support and then elongated with 31, 32 , and 22 at the 5′‐terminal end (C^Flu=deprotected phosphate derivative of 22 ). Hybridization with the complementary oligomer 5′‐d(G GGC CGG GCG)‐3′ ( 34 ) showed the influence of the fluorescein label on the stability of the duplex.     

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 LXXI

A new labelling technique attaching fluorescein via a carbamoyl linker directly to the amino groups of the nucleobases was developed. The amino groups were first converted to the phenoxycarbonyl derivatives (→ 10, 15, 19, 58 ), which reacted under mild conditions with 5‐aminofluorescein to give the corresponding N‐[(fluorescein‐5‐ylamino)carbonyl] derivatives (→ 11 – 14, 16, 17, 20, 59, 60 ). The introduction of the 5‐aminofluorescein residue into properly protected adenylyl‐adenosine dimers (→ 39, 40 ) and trimer (→ 50 ) worked well, and final deprotection of these uniformly blocked precursors led on treatment with DBU (1,8‐diazabicyclo[5.4.0]undec‐7‐ene), in one step to dimer 41 and trimer 51 . Synthesis of an appropriately protected monomeric phosphoramidite building block (→ 75 ) was more difficult, since introduction of the 2‐(4‐nitrophenyl)ethyl residue into the fluorescein moiety in 59 led mainly to trisubstitution to give 61 including the urea function. Formation of the adenylyl dimer 66 and trimer 67 proceeded in the usual manner by phosphoramidite chemistry; however, deprotection of 67 with DBU was incomplete since the O‐alkyl group at the urea moiety was found to be very stable. Finally, the appropriate phosphoramidite building block 75 could be synthesized by the sequence 59 → 72 → 73 → 74 → 75 . The phosphoramidite 75 was used for the synthesis of dimer 77 and trimer 79 by solution chemistry, as well as for that of various oligonucleotides by the machine‐aided approach on solid support carrying the fluorophore at different positions of the chain (→ 84 – 87 ). The attachment of the fluorescein fluorophor via a short carbamoyl linker onto the 6‐amino group of 2′‐deoxyadenosine enables such molecules to function very well in fluorescence‐polarization experiments.     

Nucleotides. Part LV. Synthesis and application of a novel linker for solid-phase synthesis of modified oligonucleotides

Various bifunctional amino-protecting groups such as the phthaloyl, succinyl, and glutaryl group were investigated as potential linker molecules for attachment to solid-support materials. Pentane-1,3,5-tricarboxylic acid 1,3-anhydride ( 16 ) offered the best properties and reacted with the amino groups of differently sugar-protected adenosine (see 20 and 22 ), cytidine (see 29 ), and guanosine derivatives (see 32 ) to the corresponding 2-(2-carboxyethyl)glutaryl derivatives 23 , 24 , 30 , and 33 . The usefulness of the new linker-type molecules was demonstrated by the solid-support synthesis of the potentially antivirally active 3′-deoxyadenylyl-(2′–5′)-2′-adenylic acid 2′-{2-[(adenin-9-yl)methoxy]ethyl} ester ( 38 ) starting from the 2′-end with N⁶,N⁶-[2-(2-carboxyethyl)glutaryl]-9-{{2-[(4,4′-dimethoxytrityl)ethoxy]methyl}adenine ( 12 ).     

Synthesis and properties of 3′-deoxyadenylate trimer dA2′p5′A2′p5′A

The trimeric 3′-deoxyadenylyl-(2′→5′)-3′-deoxyadenylyl-(2′→5′)-3′-deoxyadenosine ($\text{1}$$\text{2}$) was synthesized via the phosphotriester approach starting from cordycepine ($\text{1}$). Various physical data have been determined and compared with those of the ribo-A2′p5′A2′p5′A analog.     

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.     

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. XXXII. Synthesis of 2′–5′ Connected oligonucleotides. Prodrugs for antiviral and antitumoral nucleosides

The cytotoxically and antivirally active compounds bvU_d ( 1 ), flU_d ( 4 ), acyclovir ( 7 ), and A_a ( 12 ) have chemically been combined with the appropriately protected (2′–5′)diadenylate 20 by the phosphotriester approach to give the 2′–5′ oligonucleotide trimers 21 – 24 . The deprotection of the various blocking groups by chemical means afforded the 2′–5′ trimers 25 – 28 , which can be regarded as new type of a potential prodrug form delivering nucleotides to the targets inside cells. In an analogous series of reactions, 9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine was coupled with 7 to the 2′–5′ trimer 31 . The antiviral screening of the oligonucleotides 25–27 and 31 showed biological activities closely related to the parent nucleosides, possibly indicating their release by enzymatic cleavage of the oligomers.     

Semisynthesis of 3′(2′)‐O‐(Aminoacyl)‐tRNA Derivatives as Ribosomal Substrate

An efficient synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated pCpA derivatives is described, which could lead to the production of (aminoacyl)‐tRNAs following T4 RNA ligase mediated ligation. The tetrahydrofuranyl (thf) group was used as a permanent protective group for the 2′‐OH of the cytidine moiety which can be removed during the purification of the 3′(2′)‐O‐aminoacylated‐pCpA. This approach allowed for a general synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated oligonucleotides. The fully protected pCpA 14 was synthesized by phosphoramidite chemistry and treated with NH₃ solution to remove the 2‐cyanoethyl and benzoyl groups (→ 15 ; Schemes 1 and 2). The 2′‐O‐thf‐protected‐pCpA 15 was coupled with α‐amino acid cyanomethyl esters, and the products 20a – c were deprotected and purified with AcOH buffer to afford 3′(2′)‐O‐aminoacylated pCpA 21a – c in high yields. The 3′(2′)‐O‐aminoacylated pCpA were efficiently ligated with tRNA(? CA) to yield (aminoacyl)‐tRNA which was an active substrate for the ribosome.