WO2021210409A1 - 核酸オリゴマーを含む組成物 - Google Patents

核酸オリゴマーを含む組成物 Download PDF

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WO2021210409A1
WO2021210409A1 PCT/JP2021/014017 JP2021014017W WO2021210409A1 WO 2021210409 A1 WO2021210409 A1 WO 2021210409A1 JP 2021014017 W JP2021014017 W JP 2021014017W WO 2021210409 A1 WO2021210409 A1 WO 2021210409A1
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nucleic acid
hydrogen atom
methionine
chch
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Japanese (ja)
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悠也 森山
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Sumitomo Chemical Co Ltd
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Sumitomo Chemical Co Ltd
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Priority to US17/996,117 priority Critical patent/US20230192755A1/en
Priority to KR1020227035338A priority patent/KR20220167282A/ko
Priority to CN202180028331.4A priority patent/CN115397831B/zh
Priority to JP2022515301A priority patent/JP7699581B2/ja
Priority to EP21789499.7A priority patent/EP4137501A4/en
Publication of WO2021210409A1 publication Critical patent/WO2021210409A1/ja
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Priority to US17/970,138 priority patent/US20230322842A1/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H1/00—Processes for the preparation of sugar derivatives
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C12N15/101—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
    • Y02P20/00—Technologies relating to chemical industry
    • Y02P20/50—Improvements relating to the production of bulk chemicals
    • Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Definitions

  • the present invention relates to a composition containing a nucleic acid oligomer. More specifically, the present invention relates to a composition comprising a nucleic acid oligomer containing a phosphorothioate.
  • nucleic acid oligomers In recent years, there has been increasing interest in the application of nucleic acid oligomers to the medical field. For example, antisense nucleic acids, aptamers, ribozymes, and nucleic acids that induce RNA interference (RNAi) such as siRNA are mentioned, and these are called nucleic acid drugs.
  • RNAi RNA interference
  • Nucleic acid oligomers are known to be synthesized by the solid phase synthesis method, and nucleic acid oligomers having a phosphorothioate bond are also known as useful compounds synthesized by the solid phase synthesis method (Patent Document 1).
  • Nucleic acid oligomers having a phosphorothioate bond may have a problem of stability in the manufacturing process.
  • An object of the present invention is to provide a stable composition containing a nucleic acid oligomer having a phosphorothioate bond, a method for producing the same, and an efficient method for producing the nucleic acid oligomer from the composition.
  • the present inventors obtained a crude product of a nucleic acid oligomer having a phosphorothioate bond produced by the phosphoroamideite method in the solid phase synthesis method by reverse phase chromatography treatment. It has been found that the composition obtained by mixing the nucleic acid oligomer to be obtained by mixing an alkylammonium salt, a water-soluble organic solvent, water, and an additive can be stabilized. Therefore, the present invention provides the composition, a method for producing the same, and an efficient method for producing a nucleic acid oligomer from the composition.
  • Equation (1) (During the ceremony, B C represents the same or different nucleobase independently, R independently represents a hydrogen atom, a fluorine atom, or an OQ group, which are the same or different from each other.
  • Q are each independently the same or different, a hydrogen atom, a methyl group, a 2-methoxyethyl group, 'a methylene group bonded to the carbon atom of position, 4 of ribose' 4 of ribose carbon atom of a represents a bond to have an ethylene group or a bond to have an ethylidene group and 4 'position carbon atom of ribose, X independently represents an oxygen atom or a sulfur atom, which is the same or different from each other. Y represents a protecting group for a hydrogen atom or a hydroxyl group.
  • G represents ammonium ion, alkylammonium ion, alkali metal ion, hydrogen ion or hydroxyalkylammonium ion.
  • n is the equation (2): It is an integer satisfying 15 ⁇ n (2).
  • Equation (3) R a (R c ) CH-L-CH (R d ) R b (3)
  • L represents -S- or -SS- R a and R b may be the same or different and independently substituted with a hydrogen atom or at least one group selected from the group consisting of Z 1 and Z 2 below, which is an alkyl of C1-6.
  • R 11 is an alkyl group of C1-6 that may be substituted with at least one group selected from the group consisting of amino and carboxyl groups, or at least one group selected from the group consisting of amino and carboxyl groups.
  • R 2 represents a C1-6 alkylimino group, which may be substituted with a protected carboxyl group, or -OR 20 (R 20 represents a hydrogen atom or carboxyl protecting group).
  • R c and R d are the same or different and independently represent a hydrogen atom or an alkyl group of C1-6.
  • Re and R f are the same or different and may be independently substituted with a hydrogen atom, a C1-6 alkoxy-carbonyl group, a carboxyl group, or a C1-6 alkoxycarbonyl group or a carboxyl group, respectively.
  • R 1 represents a hydrogen atom, an amino protecting group, or 11 C (O) -R groups.
  • R 1 is hydrogen atom, benzoyl group, 4-methoxybenzoyl group, formyl group, acetyl group, propionyl group, butyryl group, isobutyryl group, phenylacetyl group, phenoxyacetyl group, 4-tert-butylphenoxyacetyl group, 4- Represents an isopropylphenoxyacetyl group, a benzyloxycarbonyl group, a 9-fluorenylmethyloxycarbonyl group, or 11 C (O) -R groups.
  • R 11 represents the alkyl group of C1-6 which may be substituted with at least one group selected from the group consisting of amino and carboxyl groups.
  • R 2 may be substituted with a carboxyl group that may be protected by a methyl group, a benzyl group, an allyl group and a tert-butyl group, an alkylimino group of C1-6, or -OR 20 groups
  • R 20 is , Represents a hydrogen atom, a methyl group, a benzyl group, an allyl group or a tert-butyl group
  • Composition R 20 is , Represents a hydrogen atom, a methyl group, a benzyl group, an ally
  • R 1 represents a hydrogen atom, a benzoyl group, a formyl group, an acetyl group, a benzyloxycarbonyl group and a 9-fluorenylmethyloxycarbonyl group, or a C (O) -R 11 group.
  • R 11 represents the alkyl group of C1-6 which may be substituted with at least one group selected from the group consisting of amino and carboxyl groups
  • R 2 is an alkylimino group of C1-6 that may be substituted with a carboxyl group that may be protected by a methyl group, or -OR 20 groups (R 20 represents a hydrogen atom or a methyl group).
  • Item 7 The composition according to any one of items 1 to 6 above, wherein the additive is at least one compound selected from the group consisting of lipoic acid, oxidized glutathione and methionine.
  • Item 8 The composition according to any one of items 1 to 7 above, wherein the alkylammonium salt is at least one alkylammonium salt selected from the group consisting of monoalkylammonium salts and dialkylammonium salts.
  • Item 9 The composition according to any one of items 1 to 8 above, wherein the water-soluble organic solvent is a water-soluble organic solvent selected from the group consisting of an alcohol-based water-soluble organic solvent and a nitrile-based water-soluble organic solvent.
  • the water-soluble organic solvent is a water-soluble organic solvent selected from the group consisting of an alcohol-based water-soluble organic solvent and a nitrile-based water-soluble organic solvent.
  • Item 10 The composition according to any one of items 1 to 9 above, wherein R is independently a hydroxy group or a methoxy group in the above formula (1).
  • Item 11 The composition according to any one of items 1 to 9 above, wherein R is a hydroxy group in the above formula (1).
  • a nucleic acid oligomer comprising mixing the composition according to any one of items 1 to 11 above with an organic solvent of C1-C4 having at least one oxygen atom to isolate the precipitated nucleic acid oligomer. Production method.
  • the present invention provides a stable composition containing a nucleic acid oligomer having a phosphorothioate bond, and an efficient method for producing the nucleic acid oligomer using the same.
  • FIG. 1 is a diagram showing an example of synthesis of a nucleic acid oligomer by the phosphoramidite method.
  • a composition characterized by being at least one compound selected from the group consisting of the compounds having the same will be described.
  • the nucleic acid is expressed by B C base (hereinafter, sometimes, referred to as the "base”.) May be natural or non-natural nucleobases. Examples of such non-natural nucleobases include modified analogs of natural or non-natural nucleobases.
  • Nucleobases typically include purine and pyrimidine compounds, eg, US Pat. No. 3,687,808, "Concise Encyclopedia Of Polymer Science And Engineering," pp. 858-859, Croschwitzer. Edited by Kroschwitz JI, John Willey & Sons, 1990, and English et al. (Engineering et al.), Angewandte Chemie, International Edition, 1991, 30 p.
  • the nucleobases disclosed in 613 are exemplified.
  • purine bases such as adenine, isoguanine, xanthine, hypoxanthine and guanine
  • pyrimidine bases such as cytosine, uracil and thymine
  • nucleic acid base represented by B C for example, 2-amino-adenine, 2-aminopurine, amino derivatives such as 2,6-diaminopurine; 5-methyl uracil, 5-methylcytosine, 7-methylguanine , 6-Methylpurine, 2-propylpurine and other alkyl derivatives; 5-halouracil and 5-halocitosin; 5-propynyluracil and 5-propynylcitosine; 6-azauracil, 6-azacitosine and 6-azatimine; 5-uracil (pseudo) Uracil), 4-thiouracil, 5- (2-aminopropyl) uracil, 5-aminoallyl uracil; 8-haloxation, amination, thiolation, thioalkylation, hydroxylation and other 8-substituted purines; 5-tri Fluoromethylated and other 5-substituted pyrimidines; 6-aza
  • R represents an OQ group, Q 'methylene group bonded to the carbon atom of position, 4 of ribose' is 4 ribose ethylene group bonded to the carbon atom of position or carbon atom 4 'position of the ribose,
  • the structure is represented by the structures of LNA-1, LNA-2 and LNA-3 represented by the following formula (3).
  • B c represents the nucleobase as described above.
  • the protecting group for the hydroxyl group represented by Y can be used without particular limitation as long as it can function as a protecting group in the amidite method.
  • a widely known protecting group used for an amidite compound is widely used. Can be used.
  • the hydroxyl-protecting group represented by Y is preferably the following group.
  • R 1 , R 2 and R 3 independently represent the same or different hydrogen or alkoxy groups.
  • alkoxy group examples include a methoxy group.
  • the chain length of the nucleic acid oligomer of the formula (1) is n ⁇ 15.
  • n ⁇ 200 is exemplified.
  • at least one of n Xs may be a sulfur atom, and all Xs may be sulfur atoms.
  • the nucleic acid oligomer of the formula (1) may be, for example, a DNA or RNA oligomer, or one in which these oligomers contain a non-natural nucleobase.
  • the nucleic acid oligomer is typically a single-stranded DNA or RNA oligomer.
  • the substituent R is preferably a hydroxy group or a methoxy group independently of each other.
  • RNA which is a nucleic acid oligomer of the formula (1) in which the substituent R is independently a hydroxy group or a methoxy group is preferable. More specifically, a nucleic acid oligomer containing both a nucleotide in which the substituent R is a hydroxy group and a nucleotide in which the substituent R is a methoxy group is preferable.
  • the concentration of the nucleic acid oligomer in the composition is usually 0.05 mg / mL to 5 mg / mL, preferably 0.05 mg / mL to 1 mg / mL, and more preferably 0.1 mg / mL to 0. It is 5 mg / mL.
  • a monoalkylammonium salt, a dialkylammonium salt and a trialkylammonium salt are usually used, preferably a monoalkylammonium salt and a dialkylammonium salt, and more preferably a dialkylammonium salt.
  • the monoalkylamine forming the monoalkylammonium salt preferably has 3 to 10 carbon atoms, more preferably 4 to 6 carbon atoms, and even more preferably hexylamine.
  • the number of carbon atoms of the dialkylamine forming the dialkylammonium salt is preferably 4 to 10, and more preferably 5 to 9.
  • a preferred dialkylamine is dibutylamine.
  • the trialkylamine forming the trialkylammonium salt preferably has 6 to 12 carbon atoms, more preferably 6 to 9 carbon atoms, and specifically, triethylamine is exemplified.
  • Examples of the acid forming the monoalkylammonium salt, dialkylammonium salt and trialkylammonium salt include carbonic acid, acetic acid, formic acid, trifluoroacetic acid and propionic acid.
  • the concentration of the ammonium salt is usually 1 to 200 mM, preferably 5 to 150 mM, and more preferably 20 to 100 mM.
  • water-soluble solvent examples include alcohol-based organic solvents and nitrile-based organic solvents.
  • the amount of the alcohol-based organic solvent in the composition is usually 0 to 20%, preferably 0 to 15%, and more preferably 0% to 10%.
  • the eluent fraction obtained by reverse phase column chromatography usually contains water, a water-soluble solvent (for example, an alcohol-based organic solvent, a nitrile-based organic solvent), an alkylammonium salt, and a nucleic acid oligomer of the formula (1). included.
  • the amount of the nitrile-based organic solvent in the eluent is usually 10 to 70%, preferably 20 to 60%, more preferably 30 to 50% (all% represents mass%). .).
  • the amount of water may be an amount that is balanced so as to satisfy the concentration range of the above components, and is usually 90% to 30%, preferably 80% to 40%, and more preferably 70%. ⁇ 40%.
  • the protecting group for the amino group represented by R 1 is not particularly limited, and a known protecting group can be used.
  • Specific protective groups include, for example, a benzoyl group, a 4-methoxybenzoyl group, a formyl group, an acetyl group, a propionyl group, a butyryl group, an isobutyryl group, a phenylacetyl group, a phenoxyacetyl group, and a 4-tert-butylphenoxyacetyl group.
  • Preferred protecting groups include benzoyl groups, formyl groups, benzyloxycarbonyl groups, and 9-fluorenylmethyloxycarbonyl groups.
  • R 11 Represented by R 11, as the at least one alkyl group of C1-6 which may be substituted with a group selected from the group consisting of amino and carboxyl groups, for example, (CH 2) 2 CH ( NH 2)
  • the (COOH) group is exemplified, and examples of the phenyl group which may be substituted with at least one group selected from the group consisting of an amino group and a carboxyl group include a phenyl group, an aminophenyl group, a carboxyphenyl group and the like.
  • Preferred R 11 is a C1-6 alkyl group (eg, (CH 2 ) 2 CH (NH 2 ) (COOH) group which may be substituted with at least one group selected from the group consisting of amino and carboxyl groups.
  • Z 1 and Z 2 as the COR 2 group, a COOH group and a COOR 20 group are exemplified, and the protective group of the carboxyl group represented by R 20 is not particularly limited, and a known protective group may be used. Examples of such a protective group include a methyl group, a benzyl group, an allyl group and a tert-butyl group.
  • carboxyl group which may be optionally substituted C1-6 alkyl imino group represented by R 2, for example, methylimino group, ethylimino group, propylimino group, butylimino group, Penchiruimino group, And hexylumino groups, or groups in which these groups are substituted with a carboxyl group, which may be protected by a methyl group, a benzyl group, an allyl group, or a tert-butyl group, are exemplified.
  • the alkylimino group of C1-6 which may be protected by a methyl group or substituted with a carboxyl group, is preferable, and for example, the NHCH 2 CO 2 H group is exemplified as a preferable group.
  • Specific examples of the additive represented by the formula (3) include methionine, oxidized glutathione, N-formylmethionine, N-acetyl-DL-methionine, N-benzoyl-DL-methionine, and N-carbobenzoxine.
  • the definition of the compound represented by the formula (4) will be described.
  • the group represented by R e and R f as the C1-6 alkyl group or alkyl portion of which constitutes the alkoxycarbonyl groups and C1-6 alkyl groups C1-6, methyl group, ethyl group, propyl Examples include groups, isobutyl groups, n-butyl groups, pentyl groups and hexyl groups.
  • a hydrogen atom, a carboxyl group, or an alkyl group of C1-6 is preferable.
  • Specific examples of the group represented by Re or R f include a carboxyl group, an isobutyl group, (CH 2 ) 4 CO 2 H, and CO 2 C 2 H 5 .
  • CH 2 , (CH 3 ) C N, CH 2 NH, CH 2 OCH 2 and CH 2 COCH 2 .
  • Specific examples of the compound represented by the formula (4) include ⁇ -lipoic acid, thiazolidine-2-carboxylic acid, 2-isobutyl-4,5-dimethyl-3-thiazolin (isomer mixture) and the like. Will be done.
  • additives are usually used as a solution of an aqueous solution or a water-soluble organic solvent.
  • the concentration of the additive is usually 0.1 ⁇ M to 100 mM, preferably 1 mM to 10 mM.
  • the crude product of the nucleic acid oligomer of the formula (1) synthesized by the solid-phase synthesis method is usually reversed using a mobile phase containing an alkylammonium salt, a water-soluble organic solvent, and water. It is obtained by adding the above-mentioned additive to the column eluate obtained by the phase column chromatography treatment.
  • the composition of the present invention may be prepared as an elution fraction of reverse phase column chromatography by using a mobile phase containing the additive in advance.
  • the elution fraction obtained by reverse phase column chromatography is selected and collected by analyzing the composition by UV absorption at a wavelength of 260 nm under the chromatographic conditions generally used for separation and analysis of nucleic acids. From the collected fraction, a nucleic acid oligomer having a predetermined amount of phosphorothioate bond, which is a purified product, is obtained.
  • the analysis method for example, the method described in a non-patent document (Handbook of Analysis of Oligonucleotides and Related Products, CRC Press) can be used.
  • any one or more selected from, for example, a phenyl group, an alkyl group having 1 to 20 carbon atoms, and a cyanopropyl group as the silica or polymer which becomes a hydrophobic stationary phase is used.
  • Fixed silica or polymer is exemplified.
  • the silica or polymer as such a filler for example, one having a particle size of 2 ⁇ m or more or 5 ⁇ m or more is used.
  • the mobile phase of the reverse phase column chromatography includes, for example, a mobile phase containing an aqueous solution of an ammonium salt having a concentration and pH as described above and the water-soluble organic solvent as described above, and a gradient is applied to gradually increase the concentration thereof.
  • the mobile phase to be used is used.
  • the temperature of the reverse phase column chromatography is usually 20 to 100 ° C, preferably 30 to 80 ° C, and more preferably 40 to 70 ° C.
  • the compositions of the present invention are typically obtained as an eluent fraction for reverse phase column chromatography as described above.
  • composition of the present invention is simply selected from post-treatment steps such as a reprecipitation step, a liquid separation step, an ultrafiltration step, a deprotection step, and a freeze-drying step for isolating the nucleic acid oligomer after the storage step. It may be subjected to one or more steps.
  • the atmosphere in the storage container may be replaced by using an inert gas.
  • the inert gas include nitrogen gas, argon gas, and helium gas.
  • the stabilized solution can be contacted with a poor solvent to precipitate a nucleic acid oligomer and isolate. If necessary, the liquid portion may be removed from the solid-liquid separated state, and then the nucleic acid oligomers precipitated by filtration or the like may be collected and isolated.
  • the poor solvent in the reprecipitation step include organic solvents of C1-C4 having at least one oxygen atom (for example, C1-C4 alcohol, tetrahydrofuran, dioxane). As such a solvent, ethanol or isopropanol is preferable.
  • At least one of acidic aqueous solution such as acetic acid aqueous solution, water, and salt solution is mixed with the stabilized solution, and an organic solvent immiscible with water is added to separate the aqueous layer and the organic layer. It can be liquid to obtain an aqueous layer containing the desired nucleic acid oligomer.
  • the nucleic acid oligomer present in the solution after the storage step can be separated from the low molecular weight components having a desired molecular weight or less by using the ultrafiltration membrane.
  • the acidic aqueous solutions of acetic acid to the solution after storage process or solution mixing of the acidic substance is dissolved in an organic solvent such as acetic acid, By doing so, the protecting group of the nucleic acid oligomer can be deprotected.
  • water can be sublimated by reducing the pressure of the frozen aqueous solution of the nucleic acid oligomer, and the nucleic acid oligomer and water can be separated.
  • nucleic acid extension reaction For the synthesis of nucleic acid oligomers by the phosphoramidite method, a nucleic acid extension reaction can be carried out according to a known method (for example, the method described in Japanese Patent No. 5157168 or Japanese Patent No. 5554881).
  • a nucleic acid extension reaction taking the synthesis of RNA of the scheme shown in FIG. 1 as an example, the method for producing nucleic acid oligomers with reference to the reaction pathways (condensation reaction, oxidation, deprotection) shown below. Will be described.
  • B a is nucleic acid base which may be protected; Tr protecting group; a, X is as defined above, SP is other than nucleoside structure of the inorganic porous support Each part is represented.
  • nucleobases constituting the nucleosides of the inorganic porous carrier (Sp-Nu) having a nucleoside structure and the amidite monomer (Am-1) are the nucleobases as described above or the nucleobases protected by the protective group.
  • a suitable amidite monomer (Am-1) in the compound represented by the following chemical formula (Am-1' ), when R represents a protected hydroxyl group, as a specific protective group, tert- Butyldimethylsilyl (TBDMS) group, bis (2-acetoxy) methyl (ACE) group, (triisopropylsilyloxy) methyl (TOM) group, (2-cyanoethoxy) ethyl (CEE) group, (2-cyanoethoxy) TBDMS RNA Amidites, trade name, ChemGenes Corporation, ACE protected by methyl (CEM) group, para-toluylsulfonylethoxymethyl (TEM) group, (2-cyanoethoxy) methoxymethyl (EMM) group, etc.
  • TDMS tert- Butyldimethylsilyl
  • ACE acetoxy) methyl
  • TOM triisopropylsilyloxy) methyl
  • CEE (2-cyanoeth
  • R represents a group as said, B a represents a nucleic acid base which may be protected.
  • RNA will be described as an example, but it can also be applied to nucleic acid compounds containing nucleotides other than ribonucleotides.
  • the protecting group deprotecting the protecting group of the hydroxyl group of 5 '' of the RNA chain ends which are supported on a solid phase support.
  • a trityl-based protecting group typically, a DMTr group
  • Deprotection can be performed with an acid.
  • the deprotective acid include trifluoroacetic acid, trichloroacetic acid, dichloroacetic acid, trifluoromethanesulfonic acid, methanesulfonic acid, hydrochloric acid, acetic acid, p-toluenesulfonic acid and the like.
  • nucleoside phosphoramidite is bound to the hydroxyl group at the 5-position at the end of the RNA chain deprotected by the deprotection step to produce phosphite.
  • examples of the nucleoside phosphoramidite use one hydroxyl group 5 'position is protected with a protecting group (e.g. DMTr group).
  • the condensation step can be carried out by using an activator that activates the nucleoside phosphoramidite.
  • activator include 5-benzylthio-1H-tetrazole (BTT), 1H-tetrazole, 4,5-dicyanoimidazole (DCI), 5-ethylthio-1H-tetrazole (ETT), and N-methylbenzimidazolium.
  • N-MeBIT benzimidazolium triflate
  • BIT N-phenylimidazolium triflate
  • IMT imidazolium triflate
  • NBT 5-nitrobenzimidazolium triflate
  • HOBT 1-hydroxybenzotriazole
  • Activator-42 5- (bis-3,5-trifluoromethylphenyl) -1H-tetrazole
  • condensation step may optionally be capped hydroxyl group at the 5 'position of the unreacted.
  • Capping can be performed using known capping solutions such as acetic anhydride-tetrahydrofuran solution and phenoxyacetic acid anhydride / N-methylimidazole solution.
  • the oxidation step is a step of oxidizing the phosphite formed by the condensation step.
  • the oxidation step can be carried out using an oxidizing agent.
  • the oxidizing agent include iodine, m-chloroperbenzoic acid, tert-butyl hydroperoxide, 2-butanone peroxide, bis (trimethylsilyl) peroxide, 1,1-dihydroperoxycyclododecane, hydrogen peroxide and the like.
  • an "oxidizing agent" for example, sulfur, 3H-1,2-benzodithiol-3-one-1,1-dioxide (Beaucage reagent) ), 3-Amino-1,2,4-dithiazole-5-thione (A DTT), 5-phenyl-3H-1,2,4-dithiazole-3-one (POS), [(N, N-dimethyl) Aminomethylidene) Amino] -3H-1,2,4-dithiazolin-3-thione (DDTT), and phenylacetyldisulfide (PADS) can be used.
  • an "oxidizing agent” for example, sulfur, 3H-1,2-benzodithiol-3-one-1,1-dioxide (Beaucage reagent) ), 3-Amino-1,2,4-dithiazole-5-thione (A DTT), 5-phenyl-3H-1,2,4-dithiazole-3-one (POS), [(N, N-d
  • the oxidizing agent can be used by diluting it with a suitable solvent so as to have a concentration of 0.001 to 2M.
  • the solvent used in the reaction is not particularly limited as long as it is not involved in the reaction, and examples thereof include dichloromethane, acetonitrile, pyridine, and a mixed solvent of any ratio thereof.
  • the oxidation step may be performed after the capping operation, or conversely, the capping operation may be performed after the oxidation step, and the order is not limited.
  • RNA having a desired sequence is synthesized by repeating the above series of condensation reaction, oxidation, and deprotection steps according to the nucleotide sequence of the nucleic acid oligomer to be synthesized. be able to.
  • the RNA chain is cleaved and recovered from the solid phase carrier using ammonia or an amine compound.
  • Examples of the amine compound here include methylamine, ethylamine, isopropylamine, ethylenediamine, diethylamine, triethylamine and the like.
  • Examples of the chain length of the nucleic acid oligomer thus obtained are n ⁇ 60, n ⁇ 80 or n ⁇ 100, and n ⁇ 200.
  • an amine compound is allowed to act to deprotect the protecting group of the phosphoric acid moiety after the synthesis of the nucleic acid having the desired sequence is completed.
  • the amine compound include the described diethylamine and the like.
  • RNA purity measurement method The purity of RNA in the solution after preparative measurement was measured by HPLC. The separated RNA was separated into each component by HPLC (wavelength 260 nm, column DNA PacTM PA200, 4.0 mm ⁇ 250 mm, 8.0 ⁇ m), and the area of the peak of the main product in the total area value of the peaks of the obtained chromatogram. The purity of RNA was calculated from the value.
  • HPLC measurement conditions are shown in Table 1 below.
  • RNA is based on phosphoramidite method, it was synthesized toward 'the side 5' 3 side using nucleic acid synthesis machine (AKTA oligopi lot plus100 GE Healthcare). The synthesis was carried out on a 63 ⁇ mol scale.
  • RNA amidite uridine EMM amidite (described in Example 2 of International Publication No. 2013/027843), citidine EMM amidite (described in Example 3), and adenosine EMM amidite (described in Example 3), respectively.
  • guanosine EMM amidite described in Example 5
  • porous glass as a solid phase carrier
  • a toluene dichloroacetate solution as a deblocking solution
  • 5-benzylthio-1H-tetrazole is used, iodine solution is used as an oxidizing agent, 3-amino-1,2,4-dithiazole-5-thione is used as a sulfide agent, and anhydrous phenoxyacetic acid solution is used as a capping solution. This was done using N-methylimidazole solution. After completion of nucleic acid elongation, the cyanoethyl protecting group of the phosphoric acid moiety was selectively deprotected by allowing a diethylamine solution to act on the nucleic acid on the carrier.
  • EMM is an abbreviation for (2-cyanoethoxy) methoxymethyl group.
  • RNA column chromatography purification was performed under the conditions shown in Table 2 below. However, before purification, the mobile phase A was passed through the column at a flow rate of 4.7 mL / min for 12.5 minutes, and then the sample was added. The holding time was 94.2 minutes-95.8 minutes, and the obtained solution was analyzed by HPLC. The purity was calculated by the method described in the measurement method 1. As a result, the purity was 94.2%. The following Examples and Comparative Examples were tested using this preparatively purified RNA solution.
  • Example 1 In Reference Example 1, 99 ⁇ L of the RNA solution preparatively purified by reverse phase column chromatography was placed in a polypropylene vial (Thermofisher) having a capacity of 300 mL, and 1 ⁇ L of an acetonitrile solution of lipoic acid was mixed as an additive solution to obtain a predetermined concentration. Samples were prepared. The vial containing the mixed solution was placed in an incubator (KENIS) whose temperature was adjusted to 60 ° C. and allowed to stand for 8 hours. After standing, the polypropylene vial taken out from the incubator was cooled to room temperature, and the purity was calculated by the method described in the measurement method 1. The results are shown in Table 3.
  • KENIS incubator
  • composition prepared to have a lipoic acid concentration of 3 mM (0.07%) has the following composition according to the calculation. Water: 63.79%, Acetonitrile: 34.89%, Dibutylamine 0.84%, Acetic acid: 0.39%, (1.23% as dibutylammonium acetic acid), Nucleic acid concentration: 0.21 mg / mL (0. 02%).
  • Example 2 In the experiment of Example 1, the experiment was carried out under the same conditions except that the methionine concentration was prepared as a solution of 3 mM (0.05%) by using an aqueous solution of methionine instead of the acetonitrile solution of lipoic acid as the additive solution. was performed, and the purity of RNA after the experiment was measured. The results are shown in Table 3.
  • Example 3 In the experiment of Example 1, an aqueous solution of oxidized glutathione is added as an additive solution instead of the acetonitrile solution of lipoic acid to prepare a solution having a concentration of oxidized glutathione of 0.15 mM (0.01%). The experiment was carried out under the same conditions except for the above, and the purity of RNA after the experiment was measured. The results are shown in Table 3.
  • Example 2 In the experiment of Example 1, as the additive solution, instead of the acetonitrile solution of lipoic acid, a cysteine aqueous solution, an acetonitrile solution of N-acetylcysteine, a reduced glutathione aqueous solution, a dithiotreitol aqueous solution, an L-ascorbic acid aqueous solution, or the following The experiment was carried out under the same conditions except that the aqueous sodium sulfite solution was used at a predetermined concentration. The results are shown in Table 3.
  • Example 4 (Recovery of RNA from a preparatively purified RNA solution)
  • the mixture was mixed so that the concentration of lipoic acid was 3 mM, and the following treatment was carried out using a solution that had been allowed to stand at 60 ° C. for 8 hours.
  • the obtained slurry solution was centrifuged at 3000 g at 25 ° C. for 10 minutes to remove the supernatant.
  • RNA was dissolved in 80 ⁇ L of water and the purity of RNA was calculated by the method described in the measurement method 1, the purity was 85.8%.
  • RNA was dissolved in 80 ⁇ L of water and the purity of RNA in the fraction was calculated by the method described in the measurement method 1, the purity was 70.9%.
  • RNA is based on phosphoramidite method, it was synthesized toward 'the side 5' 3 side using nucleic acid synthesis machine (AKTA oligopi lot plus100 GE Healthcare). The synthesis was carried out on a 53 ⁇ mol scale. Further, in the synthesis, as RNA amidite, uridine EMM amidite (described in Example 2 of International Publication No. 2013/0278 43), citidine EMM amidite (described in Example 3), and adenosine EMM amidite (described in Example 4).
  • each formula of uridine 2 'OMe amidites, cytidine 2' below OMe amidites adenosine 2 'OMe amidites, and guanosine 2' to OMe amidite as described), and guanosine EMM amidite (the example 5 , Porous glass is used as the solid phase carrier, dichloroacetate toluene solution is used as the deblocking solution, 5-benzylthio-1H-tetrazole is used as the condensing agent, iodine solution is used as the oxidizing agent, and the sulfurizing agent is used.
  • 3-Amino-1,2,4-dithiazole-5-thione was used, and an anhydrous phenoxyacetic acid solution and an N-methylimidazole solution were used as capping solutions.
  • the cyanoethyl protecting group of the phosphoric acid moiety was selectively deprotected by allowing a diethylamine solution to act on the nucleic acid on the carrier.
  • EMM is an abbreviation for (2-cyanoethoxy) methoxymethyl group.
  • RNA column chromatography purification was performed under the conditions shown in Table 4 below. However, before purification, the mobile phase A was passed through the column at a flow rate of 4.7 mL / min for 12.5 minutes, and then the sample was added. The holding time was 66.7 minutes-70.9 minutes, and the obtained solution was analyzed by HPLC. The purity was calculated by the method described in the measurement method 1. As a result, the purity was 94.2%. The following Examples and Comparative Examples were tested using this preparatively purified RNA solution.
  • Example 5 In Reference Example 2, 99 ⁇ L of the RNA solution preparatively purified by reverse phase column chromatography was placed in a polypropylene vial (Thermofisher) having a capacity of 300 mL, and 1 ⁇ L of an aqueous solution of L-methionine was mixed as an additive solution to form L-methionine. A sample having a concentration of 1.5 mM was prepared. The vial containing the mixed solution was placed in an incubator (KENIS) whose temperature was adjusted to 60 ° C. and allowed to stand for 8 hours. After standing, the polypropylene vial taken out from the incubator was cooled to room temperature, and the purity was calculated by the method described in the measurement method 1. The results are shown in Table 5.
  • KENIS incubator
  • the composition prepared to have a concentration of L-methionine of 1.5 mM (0.02%) has the following composition according to the calculation. Water: 62.95%, Acetonitrile: 32.21%, Methanol: 3.59%, Dibutylamine 0.82%, Acetic acid: 0.38%, (1.20% as dibutylammonium acetic acid), Nucleic acid concentration: 0 .31 mg / mL (0.03%).
  • Example 6 In the experiment of Example 5, the concentration of N-formyl-L-methionine was 3 mM (0.06) using a methanol solution of N-formyl-L-methionine instead of the aqueous solution of L-methionine as the additive solution. The experiment was carried out under the same conditions except that it was prepared as a solution of%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 7 In the experiment of Example 5, the concentration of N-acetyl-DL-methionine was 3 mM (0.06) using a methanol solution of N-acetyl-DL-methionine instead of the aqueous solution of L-methionine as the additive solution. The experiment was carried out under the same conditions except that it was prepared as a solution of%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 8 In the experiment of Example 5, the concentration of N-benzoyl-DL-methionine was 3 mM (0.08) using a methanol solution of N-benzoyl-DL-methionine instead of the aqueous solution of L-methionine as the additive solution. The experiment was carried out under the same conditions except that it was prepared as a solution of%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 9 In the experiment of Example 5, a methanol solution of N-carbobenzoxi-DL-methionine was used as the additive solution instead of the aqueous solution of L-methionine, and the concentration of N-carbobenzoxi-DL-methionine was 3 mM. The experiment was carried out under the same conditions except that it was prepared as a solution of (0.12%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 10 In the experiment of Example 5, as an additive solution, N-Fmoc-L-methionine was dissolved in a mixed solvent of methanol and acetonitrile (mixing ratio 50:50 (v / v)) instead of the aqueous solution of L-methionine. The experiment was carried out under the same conditions except that the solution was used to prepare the concentration of N-Fmoc-L-methionine as a solution of 3 mM (0.10%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 11 In the experiment of Example 5, an aqueous solution of L-methionine methyl hydrochloride was used as the additive solution instead of the aqueous solution of L-methionine, and the concentration of L-methionine methyl hydrochloride was 3 mM (0.07%). The experiment was carried out under the same conditions except that it was prepared as a solution, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 12 The same applies to the experiment of Example 5 except that the dibutyl sulfide concentration is prepared as a solution of 3 mM (0.05%) by using an acetonitrile solution of dibutyl sulfide instead of the aqueous solution of L-methionine as the additive solution.
  • the experiment was carried out under the conditions of the above, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 13 The same applies to the experiment of Example 5 except that the dibutyl sulfide concentration is prepared as a solution of 3 mM (0.07%) by using an acetonitrile solution of dihexyl sulfide instead of the aqueous solution of L-methionine as the additive solution.
  • the experiment was carried out under the conditions of the above, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 14 In the experiment of Example 5, an aqueous solution of thiazolidine-2-carboxylic acid was used as the additive solution instead of the aqueous solution of L-methionine, and the concentration of thiazolidine-2-carboxylic acid was 3 mM (0.04%). The experiment was carried out under the same conditions except for the preparation as, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 15 In the experiment of Example 5, 2-isobutyl-4 was used as an additive solution using an acetonitrile solution of 2-isobutyl-4,5-dimethyl-3-thiazolin (isomer mixture) instead of the aqueous solution of L-methionine. The experiment was carried out under the same conditions except that the concentration of 5-dimethyl-3-thiazolin (isomer mixture) was prepared as a solution of 3 mM (0.06%), and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 16 Except for preparing the 4-oxotian concentration as a 3 mM (0.04%) solution in the experiment of Example 5 by using an acetonitrile solution of 4-oxotian instead of the aqueous solution of L-methionine as the additive solution. The experiment was carried out under the same conditions, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • Example 17 In the experiment of Example 5, as an additive solution, an acetonitrile solution of 1,4-thioxane was used instead of the aqueous solution of L-methionine, and the concentration of 1,4-thioxane was set to 3 mM (0.03%). The experiment was carried out under the same conditions except for the preparation, and the purity of RNA after the experiment was measured. The results are shown in Table 5.
  • RNA whose hydroxyl groups were deprotected using the tetrabutylammonium fluoride obtained in Reference Example 2 was purified by column chromatography under the conditions shown in Table 6 below. However, before purification, the mobile phase A was passed through the column at a flow rate of 4.7 mL / min for 12.5 minutes, and then the sample was added. The holding time was 91.7 minutes-94.2 minutes, and the obtained solution was analyzed by HPLC. The purity was calculated by the method described in the measurement method 1. As a result, the purity was 95.1%. The following Examples and Comparative Examples were tested using this preparatively purified RNA solution.
  • Example 18 In Reference Example 3, 99 ⁇ L of the RNA solution preparatively purified by reverse phase column chromatography was placed in a polypropylene vial (Thermofisher) having a capacity of 300 mL, and 1 ⁇ L of an acetonitrile solution of ⁇ -lipoic acid was mixed as an additive solution, and ⁇ -A sample having a lipoic acid concentration of 3 mM was prepared.
  • the vial containing the mixed solution was placed in an incubator (KENIS) whose temperature was adjusted to 60 ° C. and allowed to stand for 14 hours. After standing, the polypropylene vial taken out from the incubator was cooled to room temperature, and the purity was calculated by the method described in the measurement method 1. The results are shown in Table 7.
  • composition prepared to have an ⁇ -lipoic acid concentration of 3.0 mM (0.07%) has the following composition according to the calculation. Water: 59.69%, Acetonitrile: 35.38%, Methanol: 3.84%, Hexylamine 0.61%, Acetic acid: 0.36% (0.97% as hexylammonium acetic acid), Nucleic acid concentration: 0 .35 mg / mL (0.04%).
  • Example 19 In the experiment of Example 18, an aqueous solution of L-methionine is used as the additive solution instead of the acetonitrile solution of ⁇ -lipoic acid, and the concentration of L-methionine is prepared as a solution of 3 mM (0.05%). The experiment was carried out under the same conditions except for the above, and the purity of RNA after the experiment was measured. The results are shown in Table 7.
  • Example 20 In the experiment of Example 18, the DL-methionine concentration is prepared as a solution of 3 mM (0.05%) by using an aqueous solution of DL-methionine instead of the acetonitrile solution of ⁇ -lipoic acid as an additive solution. The experiment was carried out under the same conditions except for the above, and the purity of RNA after the experiment was measured. The results are shown in Table 7.
  • Example 21 In the experiment of Example 18, an aqueous solution of oxidized glutathione is used as an additive solution instead of an acetonitrile solution of ⁇ -lipoic acid, and the concentration of oxidized glutathione is prepared as a solution of 3 mM (0.01%). The experiment was carried out under the same conditions except for the above, and the purity of RNA after the experiment was measured. The results are shown in Table 7.
  • the present invention it is possible to obtain a composition in which a nucleic acid oligomer having a phosphorothioate bond is stabilized, and thus the composition can be efficiently produced.
  • SEQ ID NOs: 1 and 2 in the sequence listing represent the base sequences of oligonucleotides produced according to the production method of the present invention.

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JPWO2021210409A1 (https=) 2021-10-21
CN115397831A (zh) 2022-11-25

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