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The low binding affinity of unmodified triplex-forming oligonucleotides (TFO) is the main drawback to their promising utilization in gene therapy. In the present study, we have synthesized DNA intercalator 5-(pyren-1-ylethynyl)indole Y, known as twisted intercalating nucleic acid (TINA), by a Cu-mediated Sonogashira palladium-catalyzed coupling reaction of 1-ethynylpyrene with 5-iodoindole at a high temperature under anaerobic conditions. Coupling with indole C-5 was far more preferable in obtaining stable TINA-indole than enamine site C-3, as neither hydration of the triple bond to ketones nor competitive Glaser-type homocoupling of acetylenes was observed. The insertion of the new TINA monomer Y as a bulge in the middle or at the 5'-end of the oligodeoxynucleotide sequence

Indole was conjugated to deoxyuridine either directly or via ethynyl linkage to synthesize two new DNA monomers. Due to the high reactivity of indole toward electrophilic substitution reactions, unwanted iodination was observed during the oxidation step with iodine oxidizer in automated DNA synthesizer leading to an additional oligonucleotide having extra 126 mass unit beside the desired oligonucleotide. On the other hand, using CSO oxidizer ensured the formation of the wanted oligonucleotide. Oligonucleotide synthesis was confirmed by MALDI-TOF-MS analysis. Polypyrimidine strands containing non-iodinated indole nucleoside were able to form parallel triplexes, antiparallel RNA and DNA duplexes. The thermal denaturation experiments showed higher triplex stabilization for 5-(5-indolylethynyl)-2′-deoxyuridine over 5-(5-indolyl)-2′-deoxyuridine as the triple bond allows twisting to put the indole into a proper position within the triplex encouraging better π-π stacking.

In pancreatic Panc-1 cancer cells, an increase of oxidative stress enhances the level of 7,8-dihydro-8-oxoguanine (8OG) more in the KRAS promoter region containing G4 motifs than in non-G4 motif G-rich genomic regions. We found that H2O2 stimulates the recruitment to the KRAS promoter of poly [ADP-ribose] polymerase 1 (PARP-1), which efficiently binds to local G4 structures. Upon binding to G4 DNA, PARP-1 undergoes auto PARylation and thus becomes negatively charged. In our view this should favor the recruitment to the KRAS promoter of MAZ and hnRNP A1, as these two nuclear factors, because of their isoelectric points &gt, 7, are cationic in nature under physiological conditions. This is indeed supported by pulldown assays which showed that PARP-1, MAZ, and hnRNP A1 form a multiprotein complex with an oligonucleotide mimicking the KRAS G4 structure. Our data suggest that an increase of oxidative stress in Panc-1 cells activates a ROS-G4-PARP-1 axis that stimulates the transcription of KRAS. This mechanism is confirmed by the finding that when PARP-1 is silenced by siRNA or auto PARylation is inhibited by Veliparib, the expression of KRAS is downregulated. When Panc-1 cells are treated with H2O2 instead, a strong up-regulation of KRAS transcription is observed.

Twisted intercalating nucleic acid (TINA) has the ability to stabilize Hoogsteen triplex formation. New oligonucleotides containing 3-(pyren-1-ylethynyl)indole as a DNA linked intercalator backbone have been added to the TINA family and their synthetic route has been devised. The indole ring, under acidic conditions, polarizes the triple bond in the intercalator and this makes hydration of the triple bond possible during the DNA synthesis and an oligonucleotide with 1-(indol-3-yl)-2-(pyren-1-yl)ethanone as the intercalator is formed. Insertion of the unhydrated and hydrated linker systems gave characteristic UV spectra comparable to its monomeric diols due to π-conjugated and isolated pyrene systems, respectively. Thermal denaturation profile at pH 6–7.2 showed excellent stabilization of the triplex upon insertion of 3-(pyren-1-ylethynyl)indole when compared to wild-type triplexes. The investigation includes fluorescence spectroscopic and molecular modeling studies.

Some novel MC-1220 analogs were synthesized by condensation of 4,6-dichloro-N-methylpyrimidin-2-amine derivatives (1a,b and 15) and/or 4-chloro-6-methoxy-N,N,5-trimethylpyrimidin-2-amine (2a) with the sodium salt of 2,6-difluorophenylacetonitrile followed by treatment with aqueous sodium hydroxide in methanol, alkylation, reduction, halogenation, and/or acidic hydrolysis. All synthesized compounds were evaluated for their activity against HIV-1. The most active compound in this study was compound 7, which showed activity against HIV-1 comparable to that of MC-1220. The only difference in structure between compound 7 and MC-1220 is a fluoro atom instead of a CH3 group.

A facile and novel synthetic route to MC-1220 was achieved by condensation of 4,6-dichloro-N,N-5-trimethylpyrimidin-2-amine () with the sodium salt of 2,6-difluorophenylacetonitrile, followed by methylation and strong acidic hydrolysis. The prodrugs of MC-1220 were synthesized by reaction of chlorophosphoramidate derivatives () or α-acetobromoglucose with the sodium salt of MC-1220. The stability and anti-HIV-1 activity of phosphoramidate prodrugs turned out to be comparable to those of the parent drug MC-1220.

The phosphoramidites of DNA monomers of 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine (Y) and 7-(3-aminopropyn-1-yl)-8-aza-7-deazaadenine LNA (Z) are synthesized, and the thermal stability at pH 7.2 and 8.2 of anti-parallel triplexes modified with these two monomers is determined. When, the anti-parallel TFO strand was modified with Y with one or two insertions at the end of the TFO strand, the thermal stability was increased 1.2 °C and 3 °C at pH 7.2, respectively, whereas one insertion in the middle of the TFO strand decreased the thermal stability 1.4 °C compared to the wild type oligonucleotide. In order to be sure that the 3-aminopropyn-1-yl chain was contributing to the stability of the triplex, the nucleobase X without the aminopropynyl group was inserted in the same positions. In all cases the thermal stability was lower than the corresponding oligonucleotides carrying the 3-aminopropyn-1-yl chain, especially at the end of the TFO strand. On the other hand, the thermal stability of the anti-parallel triplex was dramatically decreased when the TFO strand was modified with the LNA monomer analog Z in the middle of the TFO strand (ΔTm = -9.1 °C). Also the thermal stability decreased about 6.1 °C when the TFO strand was modified with Z and the Watson-Crick strand with adenine-LNA (AL). The molecular modeling results showed that, in case of nucleobases Y and Z a hydrogen bond (1.69 and 1.72 Å, respectively) was formed between the protonated 3-aminopropyn-1-yl chain and one of the phosphate groups in Watson-Crick strand. Also, it was shown that the nucleobase Y made a good stacking and binding with the other nucleobases in the TFO and Watson-Crick duplex, respectively. In contrast, the nucleobase Z with LNA moiety was forced to twist out of plane of Watson-Crick base pair which is weakening the stacking interactions with the TFO nucleobases and the binding with the duplex part.

In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone. The insertion of anthraquinone was found to stabilize the i-motif structure when replacing any one of the positions of the central TAA loop and the thermal stabilities were typically higher than those previously found for i-motifs containing pyrene-modified uracilyl unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified with a double replacement by the 2,6-isomer into the TAA loops in the outer regions. The largest destabilization is observed for the 1,5-disubstituted anthraquinone linker upon the replacement of A18. CD curves of anthraquinone-modified variants imply no structural changes in all cases under potassium buffer conditions compared with those of the native i-motif. Molecular modeling studies explained the increased thermal stabilities of anthraquinone-modified i-motifs.

A series of thalidomide and phthalimide ester analogs were efficiently synthesized from N-chloromethylthalidomide, N-chloromethylphthalimide, and N-(2-bromoethyl)phthalimide derivatives with various biologically important carboxylic acids. The synthesized compounds were purified and characterized by various chromatographic and spectroscopic techniques. The antitumor activity of all the synthesized compounds was screened against human liver and breast cancer cells, which showed that phthalimide ester 6a was the best cytotoxic compound against MCF7 cells, while all of the tested compounds showed a non-cytotoxic effect against HepG2 cells. Compounds 5a, 6a, and 7a possess immunosuppressant effect, while compounds 5c, 5d, 6c, 6d, 7c, and 7d showed an immunostimmulatory effect. Meanwhile, estimation of the binding affinity for all the synthesized compounds toward the vascular endothelial growth factor receptor (VEGFR) showed that compounds 5a, 5b, and 7d were the most potent inhibitors.

Synthesis An allopurinol locked nucleic acid (LNA) monomer was prepared by a novel strategy through C6 deamination of the corresponding 8-aza-7-bromo-7- deazaadenine LNA monomer with aqueous sodium hydroxide. An 8-aza-7-deazaadenine LNA monomer was also synthesized by a modification of the new synthetic pathway. N-Glycosylation at the 8-position was prevented by steric hindrance from the 7-bromo atom in the starting material 8-aza-7-bromo-7-deazaadenine. In the final step of the synthesis, the bromine was removed together with a benzyl protecting group by catalytic reduction with ammonium formate to give the required LNA monomers.

In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DSI). We thus report on the development of a clamp type of LNA ON—bisLNA—with capacity to bind and invade into supercoiled double-stranded DNA. The bisLNA links a triplex-forming, Hoogsteen-binding, targeting arm with a strand-invading Watson–Crick binding arm. Optimization was carried out by varying the number and location of LNA nucleotides and the length of the triplex-forming versus strand-invading arms. Single-strand regions in target duplex DNA were mapped using chemical probing. By combining design and increase in LNA content, it was possible to achieve a 100-fold increase in potency with 30% DSI at 450 nM using a bisLNA to plasmid ratio of only 21:1. Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes.

Three or four aromatic rings interconnected by acetylene bridges form a stiff conjugated system with sufficient conformational freedom to make it useful to link together the two strands of a DNA clamp. Upon targeting a ssDNA, the conformational flexibility allows better stacking of the linker to the underlying non-planar base triplet in the formed triplex. This type of triplexes has a substantially higher thermal melting temperature which can be further improved by inserting locked nucleic acids (LNAs) in the Hoogsteen part of the clamp. An extremely high sensitivity to mismatches is observed in an octamer triplex when placed in the middle of the sequence.

Two-pronged attack: We describe the maturation of a bivalent aptamer by a chemically driven two-step process. From an improved monovalent aptamer subdomain that had been modified by polycyclic aromatic hydrocarbons at individual positions, a mature bivalent variant with superior activities to its progenitor molecule was obtained through domain reassembly.

This paper describes the synthesis and the antiviral activities of dimeric compounds derived from homo and asymmetric combinations of N-1 propynyloxymethyl analogues 1a,b of MKC-442, an N-1 4-iodobenzyloxymethyl analogue of TNK-651 5, potent contraceptive norgestrel and AZT. They were obtained by Sonogashira reaction, ‘click' chemistry or Pd-catalyzed oxidative coupling. The iodo precursor 5 turned out as a potent compound against wild type and mutated HIV-1 virus. All dimeric compounds showed lower activity against HIV-1 than MKC-442, except the asymmetric dimer of AZT and 1a which showed an activity comparable to MKC-442.

Some novel MC-1220 analogs were synthesized by condensation of 4,6-dichloro-N-methylpyrimidin-2-amine derivatives (1a,b and 15) and/or 4-chloro-6-methoxy-N,N,5-trimethylpyrimidin-2-amine (2a) with the sodium salt of 2,6-difluorophenylacetonitrile followed by treatment with aqueous sodium hydroxide in methanol, alkylation, reduction, halogenation, and/or acidic hydrolysis. All synthesized compounds were evaluated for their activity against HIV-1. The most active compound in this study was compound 7, which showed activity against HIV-1 comparable to that of MC-1220. The only difference in structure between compound 7 and MC-1220 is a fluoro atom instead of a CH3 group.

Different analogues of TMC120 derived from pyridazin-3(2H)-one rings were synthesized by coupling of 3,6-dichloropyridazine with arylacetonitriles, phenols and/or aniline derivative followed by hydrolysis and alkylation with different benzyl bromide derivatives.

6H-Indolo[2,3-b]quinoxaline was studied as a covalently bound heteroaromatic intercalator. Six monomers were synthesized and incorporated into DNA oligonucleotides. Through a study of linker length dependence it was concluded that the linker between the oligo and the intercalator must consist of at least five C atoms in order to stabilize a DNA duplex. An intercalator with a 2′-deoxy- d -riboside linker to the oligo could also stabilize a DNA/RNA duplex, while (S)-4-(6-methylindolo[2,3-b]quinoxalin-3-ylmethoxy)-butane-1,2-diol was able to stabilize both DNA/DNA, DNA/RNA and a DNA/LNA duplex. Mismatch studies revealed a huge sensitivity to the C–C mismatch at the 5′-site of the intercalator.

Inhibition assay. Pentaribonucleotides can bind to a DNA template strand near the transcription start site of an open complex (−4 to +1). 2′‐OMe‐Pentamers encompassing locked nucleic acids (TL, GL and AL) and intercalating nucleic acids (INA monomer P) exhibited enhanced inhibition compared to the unmodified pentamer.

Hexofuranosyl nucleosides are considered as conformationally restricted acyclic nucleosides using a furanose ring to link the diol backbone to the nucleobase. The phosphoramidite of 1-(2,3-dideoxy-beta-D-erythro-hexofuranosyl)thymine was synthesized from thymidine with formation of a new stereocentre at C-5' and the nucleoside was used in oligodeoxynucleotide (ODN) synthesis. Binding of mixed sequence ODNs towards complementary DNA and RNA showed decreased affinity compared to the wild-type oligos. Insertion in the middle of poly alphaT sequence led to stabilization of ODN/dA(14) duplexes at low ionic strength, but a decrease was observed in medium and high salt buffers compared to d(alphaT)(14)/dA(14). Both beta and alpha hexofuranosyl thymidines allowed cleavage of complementary mixed-sequence RNA by RNase H to the 3'-site of the modification in ODNs whereas a limited inhibition was detected from the 5'-site.

The synthesis and insertions of ( S )-1- O -(pyren-1-ylmethyl)glycerol into intercalating nucleic acids is described. Insertions of this S -isomer as a bulge lead to reduced binding affinity towards complementary ssDNA compared to intercalating nucleic acids possessing ( R )-1- O -(pyren-1-ylmethyl)glycerol in the same positions. Insertions of both ( R ) or ( S ) 1- O -(pyren-1-ylmethyl)glycerols as bulges into two complementary strands decreased the stability of the complex compared to dsDNA possessing the pyrene pseudo-nucleotide in one of the strands.

Furoannelated analogues 1-alkoxymethyl-7-phenyl-5, 7-dihydro-1H-furo[3, 4-d]-pyrimidine-2, 4-diones of Emivirine (3a, b) were synthesized from the primary alcohols 1-alkoxymethyl-6-benzyl-5-hydroxymethyl-1H-pyrimidine-2, 4-dione (5a, b) using a radical ring closure reaction with Pb(OAc)(4). These analogues are conformationally restricted in order to fix the aromatic substituent of Emivirine in nearly the same position as it is in the case when the complex of Emivirine is bound to HIV-1 RT. However, the anti HIV-1 activities of 3a, b were considerably lower than those of the lead Emivirine.

1-(2,3-Dideoxy-3-amino-alpha-D-arabino-hexofuranosyl)thymine is considered as a conformationally restricted acyclic nucleoside using the furanose ring to link the diol backbone to the nucleobase. The appropriately substituted phosphoramidites were synthesised via 1-(5,6-di-O-acetyl-2,3-dideoxy-3-phthalimido-alpha-D-arabino-hexofuranosyl)thymine and used in oligodeoxynucleotide (ODN) synthesis. However, the binding affinity of the mixed ODNs towards complementary DNA and RNA was decreased compared to the wild-type oligos. The decrease was smaller when the monomer was inserted near the end of the sequence. The insertions into an alpha T sequence or in a beta T sequence gave nearly the same dropping in melting temperature per modification which indicates that the new nucleotide modifications behave both as alpha and beta nucleotides.

Fluorescence and hybridization specificity is reported for intercalating nucleic acids (INAs), which are here oligodeoxynucleotides (ODNs) synthesized with insertions using (S)-1-[bis(4-methoxyphenyl)(phenyl)methoxy]-3-[(pyren-1-yl)methoxy]propan-2-ol phosphoramidites. It is shown that an INA with two insertions placed as next-nearest neighbors can be used for discrimination between nucleic acids and their single-point mutants. Quenching of an excimer band at 480 nm is observed upon hybridizing to a complementary sequence, whereas the excimer band is present when the nucleobase pair between the two pyrene moieties is mismatched. It is the first example of a solution based on fluorescence detection of single-point mutants that uses excimer formation and does not rely on stringent hybridization conditions. Furthermore, it is shown that INAs with pyrene insertions retain their sequence specificity in thermal melting.

alpha-Aminoketone hydrochlorides 2a-d were synthesized by Dakin-West reaction from L-phenylalanine and L-cyclohexylalanine followed by hydrolysis in acidic medium. Treatment of 2a-d with aqueous potassium thiocyanate afforded 1, 3-imidazole-2-thiones 3a-d which were alkylated with methyl iodide to give 2-methylsulfanyl-1H-imidazoles 4a-d with 4-benzyl/4-cyclohexylmethyl and 5-ethyl/5-isopropyl substituents. Coupling of 4a-d with ethoxymethyl chloride or benzyloxymethyl chloride furnished N-1 5a-d and N-3 6a-h alkylated products. The synthesised compounds were tested for their activity against HIV-1. The most active compounds have a cyclohexylmethyl group in the 5-position of 6 and showed an activity against HIV-1 comparable to the activity of Nevirapine.

Deprotected compounds 1 and 9 were allowed to react with 4,4'-dimethoxytrityl chloride in pyridine to give 5'-O-DMT nucleosides 2 and 10. The 3'-phosphoramidites 4 and 11 were incorporated into oligodeoxynucleosides (ODNs). The hybridization properties of the modified ODNs with their complementary DNA strands were studied. Interesting results were obtained when 11 was inserted as a bulged nucleoside into TWAs, duplexes, and triplexes.

New S-DABOs with a long alkylating S-alkyl substituent showing antiretroviral activity against HIV-1 in the micromolar range were prepared from 5,6-disubstituted 4-oxo-2-thiopyrimidines and 1,7-dibromo-3,5-dioxaheptane. The analogues with an ethyl group in position 5 also showed activity in the micromolar range against a Tyr/8/Cys mutant strain of HIV-1. The S-DABO analogues showing activity against the HIV-1 RT mutant strain were transformed to the N-3 and N-1 ring closed 7-oxo-pyrimidino-1,3,5-oxathiazepines which surprisingly all showed activity against HIV-1 in the micromolar range, as well as against a Tyr/8/Cys mutant strain of HIV-1. Some analogues of S-DABO with a thien-2-ylmethyl residue in position 6 were synthesized and tested against HIV-1 wild type, but they showed less or comparable activities to those of the corresponding 6-benzyl analogues.

Ethoxymethylenemalononitrile and bis(methylthio)methylenemalononitrile were condensed with hydrazine hydrate to yield 5-aminopyrazole-4-carbonitrile (3a) and 5-amino-3-methylthiopyrazole-4-carbonitrile (3b), respectively. These compounds were treated with nitrous acid and coupled with different secondary amines to yield the triazenopyrazoles 4a–j. 5-(3,3-Diethyl-1-triazeno)pyrazole-4-carbonitrile (4c) was transferred into its two regioisomeric 2-deoxyribose nucleosides 5a,b which were subsequently hydrolyzed with H2O2/OH− to give the corresponding carboxamides 6a,b. All synthesized compounds were tested for biological activity against HIV-1 and herpes simplex virus, but only 4c showed moderate activity against HIV-1 with ED 50=32μM.

Reaction of methyl 5-tert-butyldiphenylsilyl-2,3-dideoxy-3-iodo-D-threo-pentofuranoside (3) with silylated 5-alkoxymethyluracils 2a–c using trimethylsilyl trifluoromethanesulfonate as a catalyst afforded the α nucleosides 4a–c and the β nucleosides 5a–c. The corresponding 3′,4′- and 4′,5′-didehydro nucleosides 6–9 were prepared in an elimination reaction by treating the iodo nucleosides 4a–c or 5a–c with 10 equivalents of sodium methoxide in methanol under reflux. The deprotected 3′-azido nucleosides 10a–c and 11a–c of the AZT type as well as the 4′,5′-didehydro nucleosides 7a–c and 9a–c were prepared by treating 4a–c and 5a–c, respectively, with sodium azide and subsequently with tetrabutylammonium fluoride.

A series of thalidomide and phthalimide ester analogs were efficiently synthesized from N-chloromethylthalidomide, N-chloromethylphthalimide, and N-(2-bromoethyl)phthalimide derivatives with various biologically important carboxylic acids. The synthesized compounds were purified and characterized by various chromatographic and spectroscopic techniques. The antitumor activity of all the synthesized compounds was screened against human liver and breast cancer cells, which showed that phthalimide ester 6a was the best cytotoxic compound against MCF7 cells, while all of the tested compounds showed a non-cytotoxic effect against HepG2 cells. Compounds 5a, 6a, and 7a possess immunosuppressant effect, while compounds 5c, 5d, 6c, 6d, 7c, and 7d showed an immunostimmulatory effect. Meanwhile, estimation of the binding affinity for all the synthesized compounds toward the vascular endothelial growth factor receptor (VEGFR) showed that compounds 5a, 5b, and 7d were the most potent inhibitors.

The synthesis of two new phosphoramidite building blocks for the incorporation of 5-(pyren-1-yl)uracilyl unlocked nucleic acid (UNA) monomers into oligonucleotides has been developed. Monomers containing a pyrene-modified nucleobase component were found to destabilize an i-motif structure at pH 5.2, both under molecular crowding and noncrowding conditions. The presence of the pyrene-modified UNA monomers in DNA strands led to decreases in the thermal stabilities of DNA*/DNA and DNA*/RNA duplexes, but these duplexes' thermal stabilities were better than those of duplexes containing unmodified UNA monomers. Pyrene-modified UNA monomers incorporated in bulges were able to stabilize DNA*/DNA duplexes due to intercalation of the pyrene moiety into the duplexes. Steady-state fluorescence emission studies of oligonucleotides containing pyrene-modified UNA monomers revealed decreases in fluorescence intensities upon hybridization to DNA or RNA. Efficient quenching of fluorescence of pyrene-modified UNA monomers was observed after formation of i-motif structures at pH 5.2. The stabilizing/destabilizing effect of pyrene-modified nucleic acids might be useful for designing antisense oligonucleotides and hybridization probes.

A T∗T dimer with ∗ representing a 2′-OCH2CH2NHC(O)-4′ linkage connecting two nucleoside units was prepared by condensation of (S)-1-[2-(2-aminoethoxy)-3-(4,4′-dimethoxytrityloxy)propyl]thymine with 1,2-dideoxy-1-thyminyl-β-D-erythro-pento-furanuronic acid. The T∗T dimer was incorporated in oligodeoxynucleotides and investigated for hybridization to DNA.

2-O-Ethyluracil and 2-O-ethylthymine were silylated with 1,1,1,3,3,3-hexamethyldisilazane and condensed in the presence ofTMS triflate with 2,3-dideoxy-3-fluoro-D-erythro-pentofuranoside, 3-azido-2,3-dideoxy-D-erythro-pentofuranoside, and 2,3-dideoxy-3-phthalimido-β-D-erythro-pentofuranose derivatives to give the corresponding 2-O-ethyl nucleosides. Deprotection with saturated methanolic ammonia afforded the 2′,3′-dideoxy-3′-fluoro-2-O-ethyluridines, whereas 3′-azido-2′,3′-dideoxy-3-O-ethyluridine was obtained by deprotection with tetrabutylammonium fluoride in tetrahydrofuran. 3′-Amino-2′,3′-dideoxy-3-O-ethyluridine could be obtained only by treatment of the corresponding 3′-azido nucleoside with triphenylphosphine in pyridine. 3′-Deoxy-2-O-ethyl-3′-fluorothymidine (6b) showed moderate activity against HIV-1.

1-(2-Deoxy-3,5-bis-O-(4-methylbenzoyl)-D-erythro-pentofuranosyl)-5-formyluracil (4) was synthesized from 5-formyluracil and an appropriate methyl glycoside and condensed with 2-thiohydantoin (5a) and its corresponding 3-phenyl derivative5b to give 5-[1-(2-deoxy-3,5-bis-O-(4-methylbenzoyl)-D-erythro-pentofuranosyl)uracil-5-ylmethylene]-2-thiohydantoins7a and7b, respectively, in 65–70% yield. They were deprotected with sodium methoxide in methanol to give both anomers of the free nucleosides. In a different route 5-formyluracil (1) was condensed with5b and subsequently with an appropriate methyl glycoside to give7b.

3′-Amino and 5′-amino derivatives of hydantoin 2′-deoxynucleosides have been prepared from the corresponding 3′-phthalimido and 5′-azido nucleosides, respectively, which in turn were prepared by condensation of appropriate sugars with 5-benzylidenehydantoin. The amino nucleosides were tested for their potential activity against HIV and HSV.

Hydantoin nucleosides were synthesized from a protected methyl 2-deoxy-D-ribofuranoside in a Friedel-Crafts catalyzed silyl-Hilbert-Johnson reaction as modified by Vorbruggen. Atypical byproduts are accounted for by assuming the initial step being a ring opening of the sugar to give an acyclic glycos-1-yl cation

Raman spectra were obtained for two different samples of alumina. One is usually used as a support for hydro-treating catalysts in heterogeneous catalysis and the other was synthesized in the laboratory. Different excitation wavelengths were used: 457.9, 488.0, 514.5, 647.1 and 1064 nm. The commercially available alumina showed an intense broad background with excitation in the near-infrared region, whereas no significant background was observed with visible excitation. The synthetic alumina showed a broad background band with laser excitation in the visible region. It is shown that the appearance of these backgrounds is not due to fluorescent impurities (e.g. iron, chromium or organic compounds). Tentative explanations of the spectral features are provided in terms of density of states (alumina A) or bulk hydroxyl groups (alumina B).

Methyl 3-azido-5-O-tert-butyldiphenylsilyl-2,3-dideoxy-D-erythro-furanosi de (3) was coupled with silylated 5-hydroxymethyluracil (1a) and its C1-C6 alkyl ethers 1b-g to give the corresponding protected nucleosides 4a-g which were deprotected with Bu4NF to afford 3-azido nucleosides 5a-g and 6a-g. The alpha-anomers 6f,g show moderate activity against HIV. No significant activity against HSV-1 was found for the compounds 5 and 6.

The iodide4(α) or7 synthesized in three steps from 2-deoxy-D-ribose1, has been subjected to a number of nucleophilic substitution reactions producing the 3-benzoylthio-, 3-methylthio- and the 3-thiocyanato-2,3-dideoxy-D-erythro-pentofuranosides8,13 and15, respectively, in addition to the disulfide17 of their 3-mercapto analogue. Subjecting the thiobenzoate8 to the Friedel-Crafts catalyzed silyl Hilbert Johnson reaction in conjunction with the silylated nucleobases of uracil, thymine and N4-isobutyrylcytosine9a–c resulted in the isolation of the 2′,3′-dideoxy-3′-mercapto nucleosides11 and their disulfides12 subsequent to deprotection. The 2,3-dideoxy-3-methylthio-pentofuranoside13 afforded both anomers of the 2′,3′-dideoxy-3′-methylthio nucleosides19 and20 under similar conditions. The first known example of a coupling directly on a 2,3-didehydro-2,3-dideoxyfuranose is presented. 2′,3′-Dideoxy-3′-mercaptocytidine showed protection against HIV-1 in MT-4 cells with ED50=20 µM.

The condensation of 5'-O-protected 3'-O-(2-aminoethyl)thymidine with 1,2-dideoxy-1-thyminyl-beta-D-erythro-pentofuranuronic acid gives a T*T dimer with * representing a 3'-OCH2CH2NHC(O)-4' linkage connecting the two pentofuranosyl moieties. The incorporation of this dimer in oligonucleotide sequences show only moderately lowered Tm values when hybridized with a complementary DNA relative to the unmodified DNA duplex. Consistently, no looped-out or bubble-type structure could be detected in DNA duplexes with an internal T*T module. Moreover, the 5-atom carboxamide linker causes complete stop on DNA polymerization and on exonuclease III degradation.

Uracil (8) was substituted in a Mannich reaction to give the 5-substituted dialkylamino-methyluracils11a–f in 65–85% yield. Compounds11a–f were silylated with hexamethyldisilazane and coupled with 2,3-dideoxy-3-fluoro-D-erythro-pentofuranoside4 and 3-azido-2,3-dideoxy-D-erythro-pentofuranoside7 to give the corresponding 3′-fluoro-2′,3′-dideoxynucleosides13a–f and 3′-azido-2′,3′-dideoxy nucleosides16d, f, respectively, by using trimethylsilyl trifluoromethanesulfonate as a catalyst. Deprotection of the 5-O-(4-phenylbenzoyl) protected nucleosides13a–f and16d, f with saturated methanolic ammonia and separation by chromatography yielded the new derivatives of 2′,3′-dideoxy-3′-fluorouridines14a–f and15a–f and 2′,3′-dideoxy-3′-azidouridines17d, f and18d, f.

Mercuric catalyzed hydrolysis of acetylatedL-rhamnal1 gave the α,β-unsaturated aldehyde2. 1,2,4-Triazole was coupled, in a Michael type addition reaction, to2 at C-3 in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) to give, after acetylation at the anomeric center, an anomeric mixture of 1,5-di-O-acetyl-3-(1,2,4-triazol-1-yl)-2,3,6-trideoxy-L-arabino-hexofuranose (3). Reaction of3 with silylated 2,4-dihydroxypyrimidines4 in the presence of trimethylsilyl triflate as catalyst followed by deprotection with 33% methylamine in absolute ethanol afforded the corresponding nucleosides7 and8.

Condensation of L- and D-3′-amino-2′,3′-dideoxynucleosides 2–5 with N-BOC-protected aminoacids 6 and 13 using dicyclohexylcarbodiimide and N-hydroxysuccinimide in DMF is reported to give the N-BOC-protected acylamino aminonucleosides 7–9 and 14 in 51–81% yield. After deprotection using trifluoroacetic acid the corresponding unprotected new analogues of puromucin 10–12 and 15 were obtained in 43–56% yield. These compounds did not show any significant antiviral activity using HIV (stain HTLV-III B)-infected MT-4 cells as target system.

Fetal neocortical tissue was grafted into neocortical lesion cavities made in newborn rats. After two weeks survival,in vitrobinding of[H3]- estradiol to cytosolic preparations provided evidence of estrogen receptors within the transplants. The observed high levels correspond to previous work demonstrating elevated estrogen receptor levels during the first postnatal week in the rat cerebral cortex.