Synthesis of high quality phosphorothioate oligonucleotides as antisense drugs. Use of I-linker in the elimination of 3'-terminal phosphorothioate monoesters

Detritylation of a 5'-O-DMT-2'-deoxyadenosine moiety attached to solid support under acidic condition leads to depurination during oligonucleotide synthesis. Deprotection followed by reversed phase HPLC purification leads to desired oligonucleotide contaminated with significant levels of 3'-terminal phosphorothiaote (3'-TPT) monoester (n-1)-mer. However, it is demonstrated that attachment of dA nucleoside through its exocyclic amino group to solid support leads to substantial reduction of 3'-TPT formation thereby improving the quality of oligonucleotide synthesized.     

Synthesis of High Quality Phosphorothioate Oligonucleotides as Antisense Drugs. Use of I-Linker in the Elimination of 3′-Terminal Phosphorothioate Monoesters

Abstract

Detritylation of a 5′-O-DMT-2′-deoxyadenosine moiety attached to solid support under acidic condition leads to depurination during oligonucleotide synthesis. Deprotection followed by reversed phase HPLC purification leads to desired oligonucleotide contaminated with significant levels of 3′-terminal phosphorothiaote (3′-TPT) monoester (n?1)-mer. However, it is demonstrated that attachment of dA nucleoside through its exocyclic amino group to solid support leads to substantial reduction of 3′-TPT formation thereby improving the quality of oligonucleotide synthesized.     

5,6-unsaturated hexofuranosyl glycosides and 5',6'-unsaturated hexofuranosyl nucleosides.

Methyl 5,6-dideoxy-2,3-O-isopropylidene-alpha-D-lyxo-hex-5-enofuranoside, prepared from methyl 2,3-O-isopropylidene-5,6-di-O-methylsulfonyl-alpha-D-mannofuranoside with sodium iodide in 2-butanone, was acetolyzed and the product coupled with 6-benzamidochloromercuripurine by the titanium tetrachloride method. Removal of the N-benzoyl group with pictic acid afforded 9-(2,3-di-O-acetyl-5,6-dideoxy-beta-D-xylo-hex-5-enofuranosyl)adenine. In a similar manner, methyl 5,6-dideoxy-2,3-O-isopropylidene-alpha-L-lyxo-hex-5-enofuranoside was prepared from L-mannose and converted into 9-(2,3-di-O-acetyl-5,6-dideoxy-beta-L-xylo-hex-5-enofuranosyl)adenine, further de-esterified to give the free nucleoside. 2,3:5,6-Di-O-isopropylidene-alpha-L-mannofuranosyl chloride, prepared from L-mannose, gave 9-(2,3-O-isopropylidene-alpha-L-mannofuranosyl)adenine, hydrolyzed into 9-alpha-L-mannofuranosyladenine. Treatment with methanesulfonyl chloride gave the 5',6'-dimethanesulfonate, which gave with sodium iodide in acetone the 5',6'-unsaturated nucleoside, further hydrolyzed into 9-(5,6-dideoxy-alpha-L-lyxo-hex-5-enofuranosyl)adenine.     

Intra- and intermolecular interactions influence the reactivity of RNA oligonucleotides

The transesterification of RNA oligonucleotides was studied over a wide pH range. The rate constants obtained indicate that, under neutral conditions, oligonucleotides with an adenosine moiety as the 5'-linked nucleoside can be up to 1000-fold more reactive than the reference oligonucleotide, a 13-mer oligo-U (1). Experiments with the modified oligonucleotide with N6,N6-dimethyladenosine (9) as the 5'-linked nucleoside moiety suggest that the exocyclic amino group is involved in the reaction, influencing the reactivity of the neighboring phosphodiester bond. In addition to such intramolecular interactions, weak intermolecular interactions most probably contribute to the reactivity.     

Enantiomeric forms of 9-(5-deoxy-beta-erythro-pent-4-enofuranosyl)adenine and a new preparation of 5-deoxy-D-lyxose.

Methyl 5-deoxy-5-iodo-2,3-O-isopropylidene-beta-D-ribofuranoside (3) was obtained in three steps from D-ribose. Exchange of the isopropylidene group for benzoate groups and acetolysis gave 1-O-acetyl-2,3-di-O-benzoyl-5-deoxy-5-iodo-D-ribofuranose which was coupled with 6-benzamidochloromercuripurine by the titanium tetrachloride method to afford the blocked nucleoside. Treatment with 1,5-diazabicyclo[5.4.0]undec-5-ene in N,N-dimethylformamide and removal of the blocking groups have 9-(5-deoxy-beta-D-erythro-pent-4-enofuranosyl)adenine (9). A similar route starting from methyl 5-deoxy-5-iodo-2,3-O-isopropylidene-alpha-D-lyxofuranoside (14) afforded the enantiomeric nucleoside, 9-(5-deoxy-beta-L-erythro-pent-4-enofuranosyl)adenine (20). Methyl 2,3-O-isopropylidene-alpha-D-mannofuranoside was treated with sodium periodate and then with sodium borohydride to give methyl 2,3-O-isopropylidene-alpha-D-lyxofuranoside (11). Acid hydrolysis afforded D-lyxose. Tosylation of 11 gave methyl 2,3-O-isopropylidene-5-O-p-tolylsulfonyl-alpha dp-lyxofuranoside (12) which was converted into 14 with sodium iodide in acetone. Reduction of 12 gave methyl 5-deoxy-2,3-O-isopropylidene-alpha-D-lyxofuranoside which was hydrolyzed to give 5-deoxy-D-lyxose.     

Solvent effects on lipase-catalyzed esterification of glycerol and fatty acids

The lipase-catalyzed acylglycerol synthesis with fatty acids of different chain length is studied. Measured ester mole fractions at equilibrium are compared with calculated mole fractions. For these calculations the computer program TREP (Two-phase Reaction Equilibrium Prediction) is used. This program is based on the UNIFAC group contribution method and is developed for nondilute two-phase reaction systems.With one set of equilibrium constants, namely 1.3, 0.8, and 0.6 for monoester, diester, and triester synthesis, respectively, the equilibrium position of the reaction between glycerol and all saturated fatty acids with a chain length from 6 to 18 and oleic acid (cis-9-octadecenoic acid) can be calculated. Deviations, expressed as the ratio between calculated and measured ester mole fractions, usually were between 0.7 and 1.2. In the presence of solvents, the deviations of the monoester mole fractions were higher and rose up to 3. Without addition of a solvent, the ester mole fractions at equilibrium are dependent on the fatty acid chain length. With the short-chain hexanoic acid, the monoester mole fraction is the highest ester mole fraction, while for the long-chain oleic acid, the diester mole fraction is the highest one. The ester mole fractions become independent on the chain length of the fatty acid with a solvent added in a sufficient high concentration. Both reactions, with saturated and unsaturated C(18) fatty acids, lead to the same equilibrium position. The program TREP is found to make good predictions of the equilibrium amounts of ester and fatty acid. However, systematic deviations arise between measured and calculated amounts of water and glycerol in the organic phase. The calculated water and glycerol amounts are always lower than the measured ones. These deviations seem to be highest in nonpolar media and are probably due to deficiencies in the UNIFAC calculation method. Some preliminary experiments show the effect of the choice of solvent on the reaction rates. In polar solvents, the monoester production rate is enhances by a factor of 1.5 as compared to the reaction rate in a system without solvent. (c) 1993 John Wiley & Sons, Inc.     

Nucleoside phosphotransferase activity of human colon carcinoma cytosolic 5'-nucleotidase.

A cytosolic 5'-nucleotidase, acting preferentially on IMP and GMP, has been isolated from human colon carcinoma extracts. This enzyme activity catalyzes also the transfer of the phosphate group of 5'-nucleoside monophosphates (mainly, 5'-IMP, 5'-GMP, and their deoxycounterparts) to nucleosides (preferentially inosine and deoxyinosine, but also nucleoside analogs, such as 8-azaguanosine and 2',3'-dideoxyinosine). It has been proposed that the enzyme mechanism involves the formation of a phosphorylated enzyme as an intermediate which can transfer the phosphate group either to water or to the nucleoside. The enzyme is activated by some effectors, such as ATP and 2,3-diphosphoglycerate. Results indicate that the effect of these activators is mainly to favor the transfer of the phosphate of the phosphorylated intermediate to the nucleoside (i.e., the nucleoside phosphotransferase activity). This finding is in accordance with previous suggestions that cytosolic 5'-nucleotidase cannot be considered a pure catabolic enzyme.     

Nucleoside 5''-phosphordiamidates, synthesis and some properties.

A simple way of preparing nucleoside 5'-phosphordiamidate is described. The procedure is based on the ammonolysis of nucleoside 5'-phosphordichloridates by dilute aqueous ammonium hydroxide. The behaviour of nucleoside phosphordiamidates under acidic and alkaline conditions is also reported. Alkaline hydrolysis results in the formation of the parent nucleoside, whereas one amide group can be removed selectively by mild acid hydrolysis. This property of nucleoside phosphordiamidates served as a basis for the elaboration of a simple synthesis of nucleoside phosphoramidates starting from nucleosides.     

Distribution of branched-chain fatty acid in the skin surface lipid of laboratory animals

1. The distribution of the branched-chain fatty acid (BCFA) was studied in skin surface lipids of laboratory animals (rat, mouse, hamster and rabbit) and the experimental animal for the study of the metabolic fate of BCFA was chosen. 2. The monoester fraction resistant to microbial degradation was the index of which fatty acids were identified and the compositions were analyzed by capillary gas chromatography and mass spectrometry (GC-MS). 3. The contents of monoester fractions in rat, mouse, hamster and rabbit were 78.9, 15.9, 30.4 and 45.6% of the total skin surface lipid, respectively. 4. BCFAs were exclusively identified to be either iso- or anteiso-series type by means of mass spectrometry. 5. The sum of iso- and anteiso-acid was the highest in hamster comprising 53% in male and 38% in female of the monoester acid. 6. Sex related differences of BCFA concentration were not so evident in the other three species. 7. BCFA contents in the monoester fractions were as follows: rat 32%, mouse 25% and rabbit 3%. 8. Concentrations of iso-series fatty acid were consistently higher than that of anteiso-series type in all animals studied. 9. Abundance of 2-hydroxy fatty acid in the rabbit monoester fraction was noted for the first time. 10. Suitability of these laboratory animals for the study of BCFA metabolism was discussed.     

A novel universal linker for efficient synthesis of phosphorothioate oligonucleotides

A versatile and conformationally preorganized universal linker molecule is reported here for efficient synthesis of phosphorothioate oligonucleotides. With respect to nucleoside loaded support, comparable yield and quality based on ion-pair LC-MS are obtained for both deoxy and 2'-O-methoxyethyl modified phosphorothioate oligonucleotides. No 3'-phosphate or phosphorothioate monoester or any modification of universal molecule still attached to oligonucleotide was observed. [structure: see text]     

Enantioseparation of secondary alcohols by diastereoisomeric salt formation

A general method was found for the resolution of the racemic 1-phenyl-1-propanol (1) and 1-phenyl-2-propanol (2) with various resolving agents. Monoesters of the alcohols were prepared, which were then reacted with different chiral bases. Successful optical resolutions were achieved only with the maleic acid monoesters (3 and 6). Alcohol 1 has been resolved to >99% enantiomeric excess by diastereoisomeric salt formation via its maleic acid monoester (3) using cinchonidine (9) as resolving agent. Alcohol 2 has been obtained in 98% enantiomeric excess by diastereoisomeric salt formation via its the maleic acid monoester (6) using (+)-dehydroabietylamine (11) as resolving agent.     

Transition-state complex of the purine-specific nucleoside hydrolase of T. vivax: enzyme conformational changes and implications for catalysis

Nucleoside hydrolases cleave the N-glycosidic bond of ribonucleosides. Crystal structures of the purine-specific nucleoside hydrolase from Trypanosoma vivax have previously been solved in complex with inhibitors or a substrate. All these structures show the dimeric T. vivax nucleoside hydrolase with an "open" active site with a highly flexible loop (loop 2) in its vicinity. Here, we present the crystal structures of the T. vivax nucleoside hydrolase with both soaked (TvNH-ImmH(soak)) and co-crystallised (TvNH-ImmH(co)) transition-state inhibitor immucillin H (ImmH or (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol) to 2.1 A and 2.2 A resolution, respectively. In the co-crystallised structure, loop 2 is ordered and folds over the active site, establishing previously unobserved enzyme-inhibitor interactions. As such this structure presents the first complete picture of a purine-specific NH active site, including leaving group interactions. In the closed active site, a water channel of highly ordered water molecules leads out from the N7 of the nucleoside toward bulk solvent, while Trp260 approaches the nucleobase in a tight parallel stacking interaction. Together with mutagenesis results, this structure rules out a mechanism of leaving group activation by general acid catalysis, as proposed for base-aspecific nucleoside hydrolases. Instead, the structure is consistent with the previously proposed mechanism of leaving group protonation in the T. vivax nucleoside hydrolase where aromatic stacking with Trp260 and an intramolecular O5'-H8C hydrogen bond increase the pKa of the N7 sufficiently to allow protonation by solvent. A mechanism that couples loop closure to the positioning of active site residues is proposed based on a comparison of the soaked structure with the co-crystallized structure. Interestingly, the dimer interface area increases by 40% upon closure of loop 2, with loop 1 of one subunit interacting with loop 2 of the other subunit, suggesting a relationship between the dimeric form of the enzyme and its catalytic activity.     

Isolation and characterization of N6-succinyladenosine from human urine.

From the urines of colon carcinoma patients and normal subjects we have isolated a nucleoside in which an amino group of aspartic acid is attached to the six position of purine ribonucleoside. The structure, N6-succinyladenosine, N-(9-B-D-ribofuranosylpurin-6-yl)aspartic acid was assigned on the basis of spectral data, chemical degradation, and by synthesis. The ultraviolet and mass spectra, chromatographic and electrophoretic mobilities, and the chemical properties of the naturally occurring nucleoside were identical to those of the synthetic N6-succinyladenosine. In contrast to the methylated and hypermodified nucleosides which are products of RNA catabolism, this urinary nucleoside appears to be derived from adenylosuccinic acid, a key intermediate required in the biosynthesis of ubiquitous, natural purine nucleotide adenosine-5'-monophosphate (AMP).     

On-line clean-up by multidimensional liquid chromatography-electrospray ionization tandem mass spectrometry for high throughput quantification of primary and secondary phthalate metabolites in human urine

We developed a new and fast multidimensional on-line HPLC-method for the quantitative determination of the secondary, chain oxidized monoester metabolites of diethylhexylphthalate (DEHP), 5-hydroxy-mono-(2-ethylhexyl)-phthalate (5OH-MEHP) and 5-oxo-mono-(2-ethylhexyl)-phthalate (5oxo-MEHP) in urine samples from the general population. Also included in the method were the simple monoester metabolites of DEHP, dioctylphthalate (DOP), dibutylphthalate (DBP), butylbenzylphthalate (BBzP) and diethylphthalate (DEP). Except for enzymatic hydrolysis for deconjugation of the metabolites no further sample pre-treatment step is necessary. The phthalate metabolites are stripped from urinary matrix by on-line extraction on a restricted access material (LiChrospher((R)) ADS-8) precolumn, transferred in backflush-mode and chromatographically resolved by reversed-phase HPLC. Eluting metabolites are detected by ESI-tandem mass spectrometry in negative ionization mode and quantified by isotope dilution. Within a total run time of 25 min we can selectively and sensitively quantify seven urinary metabolites of six commonly occurring phthalate diesters including the controversial di(2-ethylhexyl)phthalate (DEHP). The detection limits for all analytes are in the low ppb range (0.5-2.0 microgram/l urine). First results on a small non-exposed group (n=8) ranged for 5OH-MEHP from 0.59 to 124 microgram/l, for 5oxo-MEHP from 相似文献   

Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase

The human mitochondrial deoxyribonucleotidase catalyzes the dephosphorylation of thymidine and deoxyuridine monophosphates and participates in the regulation of the dTTP pool in mitochondria. We present seven structures of the inactive D41N variant of this enzyme in complex with thymidine 3'-monophosphate, thymidine 5'-monophosphate, deoxyuridine 5'-monophosphate, uridine 5'-monophosphate, deoxyguanosine 5'-monophosphate, uridine 2'-monophosphate, and the 5'-monophosphate of the nucleoside analog 3'-deoxy 2'3'-didehydrothymidine, and we draw conclusions about the substrate specificity based on comparisons with enzyme activities. We show that the enzyme's specificity for the deoxyribo form of nucleoside 5'-monophosphates is due to Ile-133, Phe-49, and Phe-102, which surround the 2' position of the sugar and cause an energetically unfavorable environment for the 2'-hydroxyl group of ribonucleoside 5'-monophosphates. The close binding of the 3'-hydroxyl group of nucleoside 5'-monophosphates to the enzyme indicates that nucleoside analog drugs that are substituted with a bulky group at this position will not be good substrates for this enzyme.     

Acceptor Specificity Observed with Crude Preparation of Nucleoside Phosphotransferases

The acceptor specificities of bacterial nucleoside phosphotransferase were further investigated by phosphorylating various kinds of nucleoside analogues. The bacteria belonging to A group(5′-nucleotide former) specifically phosphorylated the primary alcohol at 5′-position of nucleosides and their analogues, such as adenine xyloside, psicofuranine and pseudouridine, while the others belonging to B group (3′(2′)-nucleotide former) the secondary alcohol at 3′(2′)-position. The phosphorylation at 5′-primary alcohol with the bacteria belonging to A group, however, was prohibited mainly by phosphoryl-or amino-radical at 3′-position, as observed in the case of 3′-nucleotide or amino-nucleoside (or puromycin), depending on the steric conformation around the 3′-position of acceptor. Besides, both types of nucleoside phosphotransferases were also able to phosphorylate nucleoside having a C-C-linkage between base and sugar moieties.     

Synthesis of 9-fluorenemethyl boranophosphonodiphosphate via an H-phosphonate approach

9-Fluorenemethyl boranophosphonate 6 and its boranophosphonodiphosphate 7 were synthesized via an H-phosphonate approach. The method is efficient for the synthesis of acyclic compounds 6 & 7, and can be explored for the synthesis of nucleoside 5'-deoxy boranophosphonodiphosphate.     

5-Phosphoribosyl 1-pyrophosphate synthetase converts the acyclic nucleoside phosphonates 9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine and 9-(2-phosphonylmethoxyethyl)adenine directly to their antivirally active diphosphate derivatives.

The acyclic nucleoside phosphonates 9-(3-hydroxy-2-phosphonylmethoxypropyl)adenine (HPMPA) and 9-(2-phosphonylmethoxyethyl)adenine (PMEA) are potent inhibitors of DNA viruses and retroviruses, respectively. Unlike nucleoside triphosphates, the metabolically active (diphosphorylated) forms of HPMPA and PMEA (designated HPMPApp and PMEApp) are synthesized in a reversible reaction in which the pyrophosphate group of 5-phosphoribosyl 1-pyrophosphate (PRPP) is directly transferred to HPMPA and PMEA by purified PRPP synthetase. In this respect, PRPP synthetase does not act stereospecifically in that it recognizes both the S-enantiomer and the R-enantiomer of HPMPA as substrate. PRPP synthetase also recognizes other acyclic adenine and 2,6-diaminopurine riboside phosphonates as a substrate. It is now imperative to evaluate the potential role of PRPP synthetase, as activating enzyme, in the antiviral action of this type of molecules in intact cells.     

Synthesis and in vitro cytostatic activity of 1,2- and 1,3-diacylglycerophosphates of clofarabine

The conjugates of anticancer nucleoside clofarabine [2-chloro-9-(2-deoxy-2-fluoro-β-d-arabinofuranosyl)adenine] with 1,2- and 1,3-diacylglycerophosphates have been prepared by the phosphoramidite method using a combination of 1,1,3,3-tetraisopropyldisiloxane-1,3-diyl protecting group for the sugar moiety of the nucleoside and 2-cyanoethyl protection for the phosphate fragment. Some of the synthesized conjugates exhibited cytostatic activity against HL-60, A-549, MCF-7, and HeLa tumor cell lines.     

Bicyclic nucleoside analogues from D-glucose: synthesis of chiral as well as racemic 1,4-dioxepane ring-fused derivatives

The dioxepanofuranose derivatives 4 and 12, obtained through the cyclization of the 3-(2-hydroxyethyl) ether of a D-xylo-pentodialdose derivative, were appropriately functionalized and elaborated to the first examples of the new class of 3'-O and 5'-O-bicyclic nucleoside analogues 9, 10, and 14 with a fused seven-membered ring. Reactions carried out through the intermediacy of the D-xylo-pentodialdose derivative 5 yielded racemic products, while prior protection of the 4-formyl group (as in 7) before deprotection of the 1,2-hydroxyl groups led to optically active analogues.