Synthesis of 2′-Deoxyisoguanosine 5′-Triphosphate and 2′-Deoxy-5-methylisocytidine 5′-Triphosphate

The syntheses of the 5′-triphosphates of 2′-deoxyisoguanosine (=p₃isoG_d) and 2′-deoxy-5-methylisocytidine (=p₃me⁵isoC_d), two new bases for the genetic alphabet, are described. The triphosphates were synthesized from the corresponding nucleosides using a transient-protection procedure. The introduction of a methyl group at the 5-position of 2′-deoxyisocytidine remarkably improved the stability of the triphosphate. Characterization of the triphosphates included enzymatic incorporation opposite the complementary base in a template oligonucleotide.     

Facile Synthesis of 2′-Deoxyisoguanosine and Related 2′,3′-Dideoxyribonucleosides

The 2′-deoxyisoguanosine ( 1 ) was synthesized by a two-step procedure from 2′-deoxyguanosine ( 5 ). Amination of silylated 2′-deoxyguanosine yielded 2-amino-2′-deoxyadenosine ( 6 ) which was subjected to selective deamination of the 2-NH₂ group resulting in compound 1 . Also 2′,3′-dideoxyisoguanosine ( 2 ) was prepared employing the photo-substitution of the 2-substituent of 2-chloro-2′,3′-dideoxyadenosine ( 4 ). The latter was synthesized by Barton deoxygenation from 2-chloro-2′-deoxyadenosine ( 3 ) or via glycosylation of 2,6-dichloropurine ( 12 ) with the lactol 13 . Compound 1 was less stable at the N-glycosylic bond than 2′-deoxyguanosine ( 5 ). The dideoxynucleoside 2 was deaminated by adenosine deaminase affording 2′,3′-dideoxyxanthosine ( 17 ).     

2′-Deoxyisoguanosine and Base-Modified Analogues: Chemical and Photochemical Synthesis

The synthesis of 2′-deoxyisoguanosine ( 2 ), and the pyrrolo[2,3-d]pyrimidine and pyrazolo[3,4-d]pyrimidine 2′-deoxyribonucleosides 3 and 4 is described. Condensation of the imidazole precursor 5 with benzoyl isocyanate followed by reaction with ammonia gave 2 . Its N(7) regioisomer was obtained from 6 . Compound 2 was also prepared by the photochemically induced conversion of 2-Chloro- and 2-bromopurine 2′-deoxyribofuranosides 9a and 10 , respectively, in aqueous solution, The photo reaction was further used for the synthesis of the compounds 3 and 4 starting with the amino-chloro-2′-deoxynucleosides 9b and 9c , respectively.     

Synthesis and Properties of 2′-Deoxy-1′,2′-seco-D-ribosyl (5′ → 3′)oligonucleotides (= 1′,2′-seco-DNA) containing adenine and thymine

Some 2′-deoxy-1′,2′-seco-D-ribosyl (5′→3′)oligonucleotides (= 1′,2′-seco-DNA), differing from natural DNA only by a bond scission between the centers C(1′) and C(2′), were synthesized and studied in order to compare their structure properties and pairing behavior with those of corresponding natural DNA and homo-DNA oligonucleotides (2′,3′-dideoxy-β-D-glucopyranosyl oligonucleotides). Starting from (?)-D-tartaric acid, 2′-deoxy-1′,2′-secoadenosine derivative 9a and 1′,2′-secothymidine ( 9b ) were obtained in pure crystalline form. Using the phosphoramidite variant of the phosphite-triester method, a dinucleotide monophosphate 1′,2′-seco-d(T₂) was synthesized in solution, while oligonucleotides 1′,2′-seco-d[(AT)₆], 1′,2′-seco-d(A₁₀) and 1′,2′-seco-d(T₁₀) were prepared on solid phase with either automated or manual techniques. Results of UV- and CD-spectroscopic as well as gel-electrophoretic studies indicated that neither adenine-thymine base pairing (as observed in natural DNA and homo-DNA), nor the adenine-adenine base pairing (as observed in homo-DNA) was effective in 1′,2′-seco-DNA, Furthermore, hybrid pairing was observed neither between 1′.2′-seco-DNA and natural DNA nor between 1′,2′-seco-DNA and homo-DNA.     

Structural Comparison of Oligoribonucleotides and Their 2′-Deoxy-2′-fluoro Analogs by heteronuclear NMR spectroscopy

1-(2′-Deoxy-2′-fluororibofuranosyl)pyrimidines were synthesized and incorporated into an RNA oligonucleotide to give 5′-r[C_fGC_f(U_fU_fC_fG)GC_fG]-3′ (C_f: short form of C = 2′-deoxy-2′-fluorocytidine; U_f: short form of U = 2′-deoxy-2′-fluorouridine). The oligomer was investigated by means of UV, CD, and NMR spectroscopy to address the question of how F-labels can substitute ¹³C-labels in the ribose ring. Through-space (NOE) and through-bond (scalar couplings) experiments were performed that make use of the ameliorated chemical-shift dispersion induced by ¹⁹F as an alternative heteronucleus. A comparison of the structures of fluorinated vs. unmodified oligomer is given. It turns out that the fluorinated oligonucleotide exists in a 14:3 equilibrium between a hairpin and a duplex conformation, in contrast to the unmodified oligonucleotide which predominantly adopts the hairpin conformation. Furthermore, the fluorinated hairpin structure adopts two distinct conformations that differ in the sugar conformation of the U and C nucleoside units, as detected by the ¹⁹F-NMR chemical shifts. The role of the 2′-OH group as stabilizing element in RNA secondary structure is discussed.     

Synthesis,Base Pairing,and Structural Transitions of Oligodeoxyribonucleotides Containing 8-Aza-2′-deoxyguanosine

The synthesis of oligonucleotides containing 8-aza-2′-deoxyguanosine (z⁸G_d; 1 ) or its N⁸-regioisomer z⁸G_d^* ( 2 ) instead of 2′-deoxyguanosine (G_d) is described. For this purpose, the NH₂ group of 1 and 2 was protected with a (dimethylamino)methylidene residue (→ 5, 6 ), a 4,4′-dimethoxytrityl group was introduced at 5′-OH (→ 7, 8 ), and the phosphonates 3a and 4 as well as the phosphoramidite 3b were prepared. These building blocks were used in solid-phase oligonucleotide synthesis. The oligonucleotides were characterized by enzymatic hydrolysis and melting curves (T_m values). The thermodynamic data of the oligomers 12–15 indicate that duplexes were stabilized when 1 was replacing G_d. The aggregation of d(T-G-G-G-G-T) ( 18 ) was studied by RP 18 HPLC, gel electrophoresis and CD spectroscopy and compared with that of oligonucleotides containing an increasing number of z⁸G_d residues instead of G_d. Similarly to [d(C-G)]₃ ( 12a ), the hexamer d(C-z⁸G-C-z⁸G-C-G) ( 14 ) underwent salt-dependent B-Z transition.     

Oligonucleotides Containing Consecutive 2′-Deoxyisoguanosine Residues: Synthesis,duplexes with parallel chain orientation,and aggregation

The 2′-deoxyisoguanosine phosphonates 3a and 4a and the phosphoramidites 3b and 4b were prepared as building blocks for solid-phase oligonucleotide synthesis. The diphenylcarbamoyl (dpc) residue was introduced as 2-oxo protecting group which stabilizes the N-glycosylic bond against hydrolysis and prevents the molecule from side reactions. The dpc-protected building blocks 4a, b were employed in solid-phase synthesis and were found to be much more efficient than the unprotected compounds 3a, b. Oligonucleotides with alternating ( 11 ) or consecutive isoguanine residues ( 13–15 ) were synthesized. They form duplexes with parallel chain orientation. The aggregate d(T₄-iG₄-T₄) ( 15 ) containing four consecutive 2′-deoxyisoguanosine is shown to be a tetramer similar to that of d(T₄-G₄-T₄).     

Synthesis and Adenosine Deaminase Inhibitory Activity of 3′-Deoxy-1-deazaadenosines

New 1-deazapurine nucleosides were synthesized by coupling 2,6-dichloro-1-deaza-9H-purine (=5,7-dichloro-3H-imidazo[4,5-b]pyridine) with a 3-deoxyribose derivative by the acid-catalyzed fusion method. The condensation reaction gave an anomeric mixture of the N⁹-β-D - and N⁹-α-D -3′-deoxynucleosides, which were treated with methanolic ammonia at room temperature to obtain the deprotected derivatives. Reaction of the β-D -anomer with different amines gave 2-chloro-N⁶-substituted nucleosides, which were dechlorinated to give the corresponding 3′-deoxy-1-deazaadenosines. Biological studies on adenosine deaminase from calf intestine showed that the new compounds are inhibitors of the enzyme, the 3′-deoxy-1-deazaadenosine being the most potent one with a K_i of 2.6 μM .     

Synthesis and Characterization of Fluorinated Polyimide Derived from 3,3′‐Diisopropyl‐4,4′‐diaminodiphenyl‐3′′,4′′‐difluorophenylmethane

A novel aromatic diamine monomer, 3,3′‐diisopropyl‐4,4′‐diaminodiphenyl‐3′′,4′′‐difluorophenylmethane (PAFM), was successfully synthesized by coupling of 2‐isopropylaniline and 3,4‐difluorobenzaldehyde. The aromatic diamine was adopted to synthesize a series of fluorinated polyimides by polycondensation with various dianhydrides: pyromellitic dianhydride (PMDA), 3,3′,4,4′‐biphenyltetracarboxylic dianhydride (BPDA), 4,4′‐oxydiphthalic anhydride (ODPA) and 3,3′,4,4′‐benzophenone tetracarboxylic dianhydride (BTDA) via the conventional one‐step method. These polyimides presented excellent solubility in common organic solvents, such as N,N‐dimethylformamide (DMF), N,N‐dimethyl acetamide (DMAc), dimethyl sulfoxide (DMSO), N‐methyl‐2‐pyrrolidone (NMP), chloroform (CHCl₃), tetrahydrofuran (THF) and so on. The glass transition temperatures (T_g) of fluorinated polyimides were in the range of 260–306°C and the temperature at 10% weight loss in the range of 474–502°C. Their films showed the cut‐off wavelengths of 330–361 nm and higher than 80% transparency in a wavelength range of 385–463 nm. Moreover, polymer films exhibited low dielectric properties in the range of 2.76–2.96 at 1 MHz, as well as prominent mechanical properties with tensile strengths of 66.7–97.4 MPa, a tensile modulus of 1.7–2.1 GPa and elongation at break of 7.2%–12.9%. The polymer films also showed outstanding hydrophobicity with the contact angle in the range of 91.2°–97.9°.     

The Base-Pairing Properties of 7-Deaza-2′-deoxyisoguanosine and 2′-Deoxyisoguanosine in Oligonucleotide Duplexes with Parallel and Antiparallel Chain Orientation

Oligonucleotides with parallel (ps) or antiparallel (aps) chain orientation containing 7-deaza-2′-deoxyisoguanosine ( 1 ) or 2′-deoxyisoguanosine ( 2 ) were prepared. The phosphoramidite and phosphonate building blocks 3 – 6 were synthesized and used in solid-phase synthesis. The diphenylcarbamoyl (dpc) residue was used for the 2-oxo group protection and the isobutyryl (iBu=ib) residue for the amino function. Hybridization experiments were performed with oligonucleotides containing 7-deazaisoguanine or isoguanine. Regarding 7-deazapurine-containing oligonucleotides, the 7-deazaisoguanine⋅cytosine base pair was the strongest in ps-duplexes, while that of 7-deazaisoguanine⋅5-methylisocytosine was the most stable one in aps-DNA. Ambiguous base pairing of 7-deazaisoguanine with cytosine, 5-methylisocytosine, thymine, and guanine was observed in the case of aps-duplexes, whereas in ps-duplexes, the ambiguity was extended to adenine. The 7-deazaisoguanine-containing duplexes showed almost identical base-pair stabilities as those containing isoguanine. According to this, various base-pair motifs are proposed. The 7-deaza-2′-deoxyisoguanosine was found to be an effective substitute of 2′-deoxyisoguanosine.     

Synthesis of 2′-Deoxyisoinosine and Related 2′-Deoxyribonucleosides

Various 2-substituted purine and pyrrolo[2,3-d]pyrimidine 2′-deoxyribonucleosides with methylthio ( 13a ), chloro ( 13b ), methoxy ( 9b ), and oxo ( 2, 3 ) substituents at C(2) are prepared. They are obtained either via stereoselective nucleobase-anion glycosylation or by base transformation. A three-step synthesis of the unknown 2′-deoxyisoinosine ( 2 ) from 2′-deoxyguanosine ( 15 ) is described. Compound 2 as well as its 7-deazapurine derivative 3 exhibit strong fluorescence.     

Synthesis of 2′-amino-2′-deoxy-5-fluorocytidine

Acetylation of 2′-deoxy-5-fluoro-2′-trifluoroacetamidouridine with acetic anhydride in pyridine, followed by treatment with phosphorus pentasulfide in refluxing dioxane afforded 3′,5′-di-O-acetyl-2′-deoxy-5-fluoro-2′-trifluorothioacetamido-4-thiouridine ( 3 ). Treatment of 3 with methanolic sodium methoxide furnished 2′-deoxy-2′-trifluorothioacetamido-4-thiouridine ( 4 ), whereas its treatment with methanolic ammonia gave 2′-amino-2′-deoxy-5-fluorocytidine ( 5 ). An alternative approach for the preparation of this compound proceeding from 2′-trifluoroacetamidocytidine was unsuccessful, since the use of acetic anhydride in pyridine led to the replacement of the trifluoroacetyl function by an acetyl group, yielding an intermediate unsuitable for obtaining the target compound. The title compound was inactive at 1 × 10^?4 M concentration against HeLa and leukemia L1210 cells in vitro, but inhibited the in vitro growth of E. coli cells at a concentration of 1 × 10^?7 M. It was also found to be a substrate for CR/dCR deaminase partially purified from human liver, with a Km of 128 μM.     

Colchicine models: Synthesis and Antitubulin Activity of 2′-Monosubstituted and 2′, 5-Disubstituted 2,3,4,4′-Tetramethoxy-1,1′-biphenyls. Synthesis of 4,4′, 5′, 6′-tetramethoxy-1,1′-biphenyl-2,3′-dicarboxylic acid

Reductive amination of 2,3,4,4′-tetramethoxtybiphenyl-2-carbaldehyde ( 4 ) with MeNH₂ afforded methylamine 5 (Scheme 1), Hydroxymethylation of amine 8 , prepared similarly from 4 by reductive amination with benzylamine followed by N-methylation, afforded alcohol 12 which was converted the 5-methyl-substituted methylamine 14 by conventional chemical reactions (Scheme 2), Methylamine 14 was also obtained from ester 16 after hydroxymethylation to alcohol 17 and conventional manipulation of alcohol and ester functions (Scheme 2). Both amines 5 and 14 as well as the 2′, 5-dimethyl-substituted biphenyl 26 prepared from the dialdehyde 25 by a Wolff-Kishner reduction, did not show noteworthy activity in the tubulin binding assay or as inhibitors of tubulin polymerization (Table). However, the 2′ethyl-substituted biphebyl 11 prepared from 4 by reaction with MeLi followed by dehyderation and catalytic reduction of styrene 10 (Scheme 1) showed appreciable activity in both assays, coming close to that of known phenyltropolone models. The X-ray analysis of 14 ·HCl and 11 showed significant difference in the orientation of the rings with respect to one another (Fig.).     

Nucleosides 4: Synthesis of 2′,3′-Didehydro-2′,3′-dideoxydoridosine and 2′,3′-Dideoxydoridosine as Potential Antihypertensive Agents

To measure the hydrophobic character of the ribose moiety of doridosine on the adenosine receptors, 2′,3′-didehydro-2′,3′-dideoxydoridosine (2) and 2′,3′-dideoxydoridosine (3) were prepared. Initial treatment of doridosine with N,N-dimethylformamide diethylacetal, and subsequently with tert-butyldimethylsilyl chloride gave 5. Compound 5 was then reacted with 1,1′-thiocarbonyldiimidazole and the resulting thionocarbonate 6 was heated with triethyl phosphite at 135°C to afford 7. Treatment of compound 7 with tetrabutylammonium fluoride and methanolic ammonia furnished compound 2 in good yield. Compound 2 was subjected to catalytic hydrogenation affording compound 3 in 85% yield.     

Synthesis and Conformational Analysis of 2′-Deoxy-2′-(3-methoxybenzamido)adenosine,a rational-designed inhibitor of trypanosomal glyceraldehyde phosphate dehydrogenase (GAPDH)

A series of 2′-benzamido-2′-deoxyadenosine analogues were synthesized in an effort to find new lead structures for the treatment of sleeping sickness. The 2′-deoxy-2′-(3-methoxybenzamido)adenosine ( 1h ) was proved to be a selective inhibitor of the parasite glyceraldehyde 3-phosphate dehydrogenase which confirms the modeling studies. The solution-state conformation of 2′-(thiophene-2-carboxamido) analogue 1d demonstrates a 2′-endo conformation, an orientation of the thiophene ring under the ribose moiety, and the base part occupying a ‘syn’/‘anti’ equilibrium.     

Synthesis of various 5-substituted 2′-deoxy-3′-5′-di-O-acetyluridines

The Pd(0)-catalyzed coupling reaction of β-5-iodo-2′-deoxy-3′,5′-di-O-acetyluridine with various heteroaryltrimethylstannyl compounds gave the corresponding β-5-heteroaryl-2′-deoxy-3′,5′-di-O-acetyluridines in moderate yields. This direct coupling approach for nucleosides represented an interesting alternative to the 5-heteroaryl functionalization of pyrimidines followed by the Hilbert-Johnson glycosylation reaction which often yields mixtures of the α and β anomers.