Effect of excess water on the desilylation of oligoribonucleotides using tetrabutylammonium fluoride.

The most commonly available 2' hydroxyl protecting group used in the synthesis of oligoribonucleotides is the tert-butyldimethylsilyl moiety. This protecting group is generally cleaved with 1 M tetrabutylammonium fluoride (TBAF) in tetrahydrofuran (THF). The efficiency of this reaction was tested on ribonucleotidyldeoxythymidine dinucleotides (AT, CT, GT, and UT). We have found that the efficiency of desilylation of uridine and cytidine is greatly dependent on the water content of the TBAF reagent. Conversely, the water content of the TBAF reagent [up to 17% (w/w)] had no detectable effect on the rate of desilylation of adenosine and guanosine. It was concluded that for effective desilylation of pyrimidine nucleosides the water content of the TBAF reagent must be 5% or less, which is readily achieved using molecular sieves. TBAF dried in such a manner was shown to be effective in deprotecting an oligoribonucleotide containing both purine and pyrimidine residues.

A non-nucleotide-based linking method for the preparation of psoralen-derivatized methylphosphonate oligonucleotides.

A method is reported for conjugating an analog of 4'-(aminomethyl)-4,5',8- trimethylpsoralen to methylphophonate oligonucleotides. This method enables the psoralen moiety to be coupled to the phosphonate backbone between any two desired bases in a sequence. When hybridized to a target mRNA, the psoralen moiety can be directed toward a uridine base and, in turn, can undergo a photo-addition reaction with the target under UV irradiation at 365 nm. Several different non-nucleotide-based amino-linker reagents have been prepared for incorporation into methylphosphonate oligonucleotides by standard phosphonamidite chemistry. In addition, an N-hydroxysuccinimide activated ester analog of 4'-[(3-carboxypropionamido)methyl]-4,5',8- trimethylpsoralen has been synthesized for conjugation to the amino-linker moieties. Using this approach, we have prepared a number of psoralen-methylphosphonate-oligonucleotide conjugates which are complementary to the chimeric bcr/abl mRNA associated with chronic myelogenous leukemia. Solution hybridization studies with a 440-base subfragment of the bcr/abl RNA have shown that the psoralen moiety does not adversely affect duplex stability. Polyacrylamide gel electrophoresis analyses have demonstrated that the psoralen-oligonucleotide conjugates undergo photo-addition to the RNA in a sequence-specific manner. Optimal photo-addition occurs when the psoralen moiety is inserted adjacent to one or more adenine residues in the oligonucleotide sequence, particularly between adenine and thymine (5'-3'). This internal labeling approach greatly increases the number of potential target sites available for photo-cross-linking experiments.

Synthesis and biological properties of purine and pyrimidine 5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl analogues of AMP, GMP, IMP, and CMP.

Methyl 2,3-O-isopropylidene-D-ribofuranoside (1) was converted to 1-O-acetyl-5-bromo-5-deoxy-2,3-di-O-benzoyl-D-ribofuranose (6) in five steps with good yield. The Arbuzov condensation of compound 6 with triethyl phosphite resulted in the synthesis of 1-O-acetyl-2,3-di-O-benzoyl-5-deoxy-5-(diethoxyphosphinyl)-D-ribofuranos e (7). Compound 7 was used for direct glycosylation of both purine and pyrimidine bases. The glycosylation was accomplished with the dry silylated heterocyclic base in the presence of trimethylsilyl triflate. Deblocking of the glycosylation products gave exclusively the beta anomer of the 5'-phosphonate analogues of 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]adenine (13), 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]guanosin e (16), 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]hypoxant hine (17), and 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]cytosine (15), described here for the first time. The target compounds as well as their intermediates showed no in vitro antiviral or antitumor activity, although phosphorylation of 15 and 16 to di- and triphosphate analogues was demonstrated with use of isolated cellular enzymes.

Nucleoside imidodiphosphates synthesis and biological activities.

The synthesis of imidodiphosphate analogues of natural nucleoside 5'-diphosphates including adenosine 5'-imidodiphosphate (4a), guanosine 5'-imidodiphosphate (4b), 2'-deoxyadenosine 5'-imidodiphosphate (4c), and 2'-deoxy-guanosine 5'-imidodiphosphate (4d) has been accomplished for the first time. These compounds are the products of the reaction between nucleosides and trichloro [(dichlorophosphoryl)imido] phosphorane in trimethyl phosphate. Some of the major by-products of the reaction including 5'-deoxy-5'-chloro nucleosides are discussed. Compounds 4b, 4c, and 4d are potent inhibitors of ecto-5'-nucleotidase whereas compound 4a also active but less potent inhibitor. Compound 4b is the most potent inhibitor of phosphoribosyl pyrophosphate (PPRP) synthetase which follows by 4c, 4d and 4a. All of these compounds were more potent inhibitor of PPRP-synthetase than ADP or GDP. Ribavirin imidodiphosphate (4e) was also synthesized and tested for its inhibitory effect on ecto-5'-nucleotidase, PPRP-synthetase as well as IMP dehydrogenase. Compound 4e is the most potent inhibitor of IMP dehyrogenase but was a weak inhibitor of the other two enzymes. compound 4a, 4b, 4c and 4d are weak inhibitors of IMP dehydrogenase.

Synthesis of glycopyranosylphosphonate analogues of certain natural nucleoside diphosphate sugars as potential inhibitors of glycosyltransferases.

The synthesis of alpha-D-glucopyranosyl-, alpha-D-galactopyranosyl-, and alpha-D-mannopyranosylphosphonate is described. Condensation of tris(trimethylsilyl) phosphite with 2,3,4,6-tetrakis-O-(phenylmethyl)-1-O-acetyl-alpha-D-glucopyranose generated 2,3,4,6-tetrakis-O-(phenylmethyl)-alpha-D-glucopyranosylphosphonic acetic anhydride (13). The benzyl blocking groups were removed by catalytic hydrogenation, and the anhydride bond was cleaved by alkaline hydrolysis to obtain alpha-D-glucopyranosylphosphonate (15). alpha-D-Galactopyranosylphosphonate (17) and alpha-D-mannopyranosylphosphonate (19) were also similarly synthesized. The anomeric configuration of 15 was assigned by single-crystal X-ray analysis, and the structural assignments of 17 and 19 were made on the basis of comparative NMR spectral studies. Compound 15 was then coupled with adenosine 5'-phosphoric di-n-butylphosphinothioic anhydride in dry pyridine to give adenosine 5'-phosphoric alpha-D-glucopyranosylphosphonic anhydride (23). Similarly, uridine 5'-phosphoric alpha-D-galactopyranosylphosphonic anhydride (24) and guanosine 5'-phosphoric alpha-D-mannopyranosylphosphonic anhydride (25) were synthesized from 17 and 19, respectively. With ovalbumin as an acceptor for [3H]galactose, provided by UDP-[3H]galactose, only uridine 5'-phosphoric alpha-D-galactopyranosylphosphonic anhydride (24) was shown to inhibit glycoprotein beta-D-galactosyltransferase (EC 2.4.1.38), with an apparent Ki equal to 165 microM. Even though these ionic compounds hardly penetrate the cell membrane, preliminary in vitro antitumor screening shows that compounds 23 and 25 are slightly active against human B-lymphoblastic leukemia and human T-lymphoblastic leukemia. None of these compounds show any antiviral activity.

Synthesis of certain nucleoside methylenediphosphonate sugars as potential inhibitors of glycosyltransferases.

The synthesis of alpha-D-glucopyranosyl 1-(methylenediphosphonate) (11), alpha-D-galactopyranosyl 1-(methylenediphosphonate) (14), and alpha-D-mannopyranosyl 1-(methylenediphosphonate) (17) has been accomplished. [(Di-phenoxyphosphinyl)methyl]phosphonic acid (diphenyl-MDP) (5), synthesized by two different procedures, was fused with beta-D-glucopyranose pentaacetate followed by catalytic hydrogenation to give 2,3,4,6-tetra-O-acetyl-alpha-D-glucopyranosyl methylenediphosphonate (glucose-MDP) (10). The anomeric configuration of 10 was assigned on the basis of NMR spectral studies. Condensation of 10 with 2',3'-di-O-acetyladenosine was accomplished by using 1-(mesitylene-2-sulfonyl)-3-nitro-1,2,4-triazole (MSNT) as coupling agent, and removal of the blocking groups gave adenosine 5'-[(alpha-D-glucopyranosylhydroxyphosphinyl)methyl]phosphonate (20). Uridine 5'-[(alpha-D-galactopyranosylhydroxyphosphinyl)methyl] phosphonate (23) and guanosine 5'-[(alpha-D-mannopyranosylhydroxyphosphinyl)methyl]phosphonate (26) were similarly prepared. Using a specific glycoprotein galactosyltransferase (EC 2.4.1.38) assay, uridine 5'-[(alpha-D-galactopyranosylhydroxyphosphinyl)methyl]phosphonate (23) demonstrated competitive inhibition with an apparent Ki of 97 microM. The adenosine analogue did not inhibit the enzyme. None of the above compounds show any in vitro antitumor or antiviral activity. Such specific inhibitors of glycosyltransferases may serve as specific probes to study various glycosyltransferases that might be involved in the process of metastasis.

Synthesis and antiviral activity of certain nucleoside 5'-phosphonoformate derivatives.

(Ethoxycarbonyl)phosphonic dichloride (3) was synthesized by chlorination of bis(trimethylsilyl) (ethoxycarbonyl)phosphonate with thionyl chloride. Adenosine 5'-(ethoxycarbonyl)phosphonate (4), guanosine 5'-(ethoxycarbonyl)phosphonate (5), 2'-deoxyadenosine 5'-(ethoxycarbonyl)phosphonate (18) and 2'-deoxyguanosine 5'-(ethoxycarbonyl)phosphonate (19) were synthesized by coupling of compound 3 with adenosine, guanosine, 2'-deoxyadenosine, and 2'-deoxyguanosine, respectively. Alkaline treatment of 4, 5, 18, and 19 gave the corresponding adenosine 5'-(hydroxycarbonyl)phosphonate (14), guanosine 5'-(hydroxycarbonyl) phosphonate (15), 2'-deoxyadenosine 5'-(hydroxycarbonyl)phosphonate (20), and 2'-deoxyguanosine 5'-(hydroxycarbonyl) phosphonate (21). Treatment of 4 and 5 with methanolic ammonia resulted in the production of adenosine 5'-(aminocarbonyl)phosphonate (12) and guanosine 5'-(aminocarbonyl)phosphonate (13), respectively. The nucleotide analogue 20 exhibited the most potent antiviral activity of this group of nucleotide tested in vitro and was most active against herpes viruses especially HSV-2. The nucleotide analogue 21 had lower, but significant, activity against HSV-2. All of the compounds tested were nontoxic to confluent Vero cells at concentrations as high as 5000 microM.