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Oligonucleotide N3'-P5' thiophosphoramidates: their synthesis and use

a technology of thiophosphoramidates and oligonucleotides, applied in the field of oligonucleotides, can solve the problems of adversely affecting the pharmacological properties of some applications

Inactive Publication Date: 2007-02-15
GERON CORPORATION
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0013] The present invention also includes pharmaceutical compositions and kits including a polynucleotide having at least one N3′→P5′ thiophosphoramidate linkage, as described above. The inventive oligonucleotides are particularly useful in oral therapeutic applications based on hybridization, such as, antigene and antisense applications, including the inhibition of telomerase enzyme activity.

Problems solved by technology

Unfortunately, improvements in one property, such as nuclease resistance, often involve trade-offs against other properties, such as binding strength.
These features of the oligonucleotide phosphoramidates potentially adversely affect their pharmacological properties for some applications.

Method used

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  • Oligonucleotide N3'-P5' thiophosphoramidates: their synthesis and use
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  • Oligonucleotide N3'-P5' thiophosphoramidates: their synthesis and use

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example 1

General Methods

[0143]31P NMR spectra were obtained on a Varian 400 Mhz spectrometer. 31P NMR spectra were referenced against 85% aqueous phosphoric acid. Anion exchange HPLC was performed using a Dionex DX 500 Chromatography System, with a Pharmacia Bitotech Mono Q HR 5 / 5 or 10 / 16 ion exchange columns. Mass spectral analysis was performed by Mass Consortium, San Diego, Calif. MALDI-TOF analysis of oligonucleotides was obtained using a PerSpective Biosystems Voyager Elite mass spectrometer with delayed extraction. Thermal dissociation experiments were conducted on a Cary Bio 100 UV-Vis spectrometer.

[0144] All reactions were carried out in oven dried glassware under a nitrogen atmosphere unless otherwise stated. Commercially available DNA synthesis reagents were purchased from Glen Research (Sterling, Va.). Anhydrous pyridine, toluene, dichloromethane, diisopropylethyl amine, triethylamine, acetic anhydride, 1,2-dichloroethane, and dioxane were purchased from Aldrich (Milwaukee, Wis...

example 2

Synthesis of Arabino-fluorooligonucleotide N3′→P5′ Phosphoramidates

[0147] The solid phase synthesis of oligo-2′-arabino-fluoronucleotide N3′→P5′ phosphoramidates was based on the phosphoramidite transfer reaction employing the monomer building blocks—5′-(O-cyanoethyl-N,N′-diisopropylamino)-phosphoramidites of 3′-MMTr-protected-3′-amino-2′-ara-fluoro nucleosides. Preparation of the nucleoside monomers is depicted in Scheme 4.

[0148] Sugar precursor 1 (from Pfanstiehl) was converted into the α-1-bromo intermediate 2 with retention of sugar C-1 configuration. Compound 2 was then used, without isolation, for a SN2-type glycosylation reaction with silylated uracil and thymine bases, which resulted in formation of nucleosides 3. Stereo selectivity of the glycosylation reaction was quite high—more than 90% of the formed nucleoside 3 had the desired β-anomeric configuration, as was judged by 1H NMR analysis of the reaction mixture. The pure β-isomer of nucleoside 3 was isolated by crystal...

example 3

Synthesis of Oligonucleotide N3′→P5′ Thiophosphoramidates

[0149] Oligonucleotide N3′→P5′ thiophosphoramidates were prepared by the amidite transfer reaction on an ABI 394 synthesizer. The fully protected monomer building blocks were 3′-aminotrityl nucleoside-5′-(2-cyanoethyl-N,N-diisopropyl) phosphoramidite where nucleoside is 3′-deoxy-thymidine, 2′,3′-dideoxy-N2-isobutyryl-guanosine, 2′,3′-dideoxy-N6-benzoyl-adenosine or 2′,3′-dideoxy-N-benzoyl-cytidine. 5′-Succinyl-3′-aminotrityl-2′,3′-dideoxy nucleosides were coupled with an amino group containing long chain controlled pore glass (LCAA-CPG) and used as the solid support. The synthesis was performed in the direction of 5′ to 3′. The following protocol was used for the assembly of oligonucleotide N3′→P5′ thiophosphoramidates: (i) detritylation, 3% dichloroacetic acid in dichloromethane; (ii) coupling, 0.1 M phosphoramidite and 0.45 M tetrazole in acetonitrile, 25 sec; (iii) capping, isobutyric anhydride / 2,6-lutidine / THF 1 / 1 / 8 v / v / v...

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Abstract

Oligonucleotides with a novel sugar-phosphate backbone containing at least one internucleoside 3′-NHP(O)(S−)O-5′ linkage, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive thiophosphoramidate oligonucleotides were found to retain the high RNA binding affinity of the parent oligonucleotide N3′→P5′ phosphoramidates and to exhibit a much higher acid stability.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application is a continuation of U.S. Ser. No. 10 / 967,755, filed Oct. 18, 2004, allowed, which is a continuation of U.S. Ser. No. 10 / 463,076, filed Jun. 17, 2003, pending, which is a continuation of U.S. Ser. No. 09 / 657,445, filed Sep. 8, 2000, now U.S. Pat. No. 6,608,036; which claimed priority from U.S. Ser. No. 60 / 153,201, filed Sep. 10, 1999 and U.S. Ser. No. 60 / 160,444, filed Oct. 19, 1999. All of the above-referenced applications are incorporated herein by reference.FIELD OF THE INVENTION [0002] The present invention relates to oligonucleotides having a novel sugar-phosphate backbone containing internucleoside 3′-NHP(O)(S−)O-5′ linkages. More particularly, the present invention is directed to thiophosphoramidate oligonucleotide compositions, their use as diagnostic or therapeutic agents and methods for synthesizing thiophosphoramidate oligonucleotides. BACKGROUND OF THE INVENTION [0003] Nucleic acid polymer chemistry has play...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): A61K48/00C12Q1/68C07H21/02A61K31/7125C12N15/09A61P31/12A61P35/00A61P43/00C07H19/173C07H21/00C07H21/04C12N15/11C12N15/113
CPCC07H21/00C12N15/111C12N15/113C12N15/1137C12N2310/314C12N2320/51C12Q1/6832C12Y207/07049C07H1/06C12N2320/10C12N2320/50C12N2330/30C12Q1/6813A61P31/12A61P35/00A61P43/00A61K31/7088
Inventor GRYAZNOV, SERGEIPONGRACZ, KRISZTINAMATRAY, TRACY
Owner GERON CORPORATION
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