WO1998039352A1 - Nouveaux analogues de bicyclonucleoside et d'oligonucleotide - Google Patents

Nouveaux analogues de bicyclonucleoside et d'oligonucleotide Download PDF

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Publication number
WO1998039352A1
WO1998039352A1 PCT/JP1998/000945 JP9800945W WO9839352A1 WO 1998039352 A1 WO1998039352 A1 WO 1998039352A1 JP 9800945 W JP9800945 W JP 9800945W WO 9839352 A1 WO9839352 A1 WO 9839352A1
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group
analog
compound
mmol
solution
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PCT/JP1998/000945
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English (en)
French (fr)
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Takeshi Imanishi
Satoshi Obika
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Takeshi Imanishi
Satoshi Obika
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Application filed by Takeshi Imanishi, Satoshi Obika filed Critical Takeshi Imanishi
Priority to DK98905804.5T priority Critical patent/DK1013661T4/en
Priority to AU61209/98A priority patent/AU720472B2/en
Priority to US13/533,781 priority patent/USRE44779E1/en
Priority to DE98905804T priority patent/DE98905804T1/de
Priority to AT98905804T priority patent/ATE541576T2/de
Priority to ES98905804T priority patent/ES2380354T5/es
Priority to CA002283509A priority patent/CA2283509C/en
Priority to EP98905804.5A priority patent/EP1013661B2/en
Priority to US09/380,638 priority patent/US6268490B1/en
Publication of WO1998039352A1 publication Critical patent/WO1998039352A1/ja

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D493/00—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system
    • C07D493/02—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system in which the condensed system contains two hetero rings
    • C07D493/08—Bridged systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • 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

Definitions

  • the present invention relates to novel nucleoside and nucleotide analogs, and more particularly to nucleotide analogs suitable for antisense molecules.
  • Antisense oligonucleotides are one of the most promising fields in recent years as pharmaceuticals, as they specifically regulate the expression of unwanted genes.
  • the antisense method is based on the concept of controlling the flow of so-called centralola dogma using DNA ⁇ RNA ⁇ protein using an antisense oligonucleotide.
  • nucleic acid derivatives and analogs have been synthesized and studied. For example, phosphorothioate in which the oxygen atom on the phosphorus atom has been replaced by an ⁇ atom, methylphosphonate in which the methyl group has been replaced by a methyl group, and more recently, those in which the phosphorus atom has been replaced by a carbon atom, and also the structure of the sugar moiety Some have been synthesized, and others have been modified with modified nucleobases. In any case, derivatives and analogs that are sufficiently satisfactory in terms of stability in vivo, ease of synthesis, and sequence specificity (selective control of specific gene expression only) Is currently not available.
  • the inventors of the present invention designed a nucleic acid analog having a sugar moiety conformation immobilized thereon, which is considered to be useful in the antisense method, and designed a nucleoside analog having a unit structure thereof. The synthesis was performed, and it was confirmed that the oligonucleotide analogs prepared using this were extremely useful as antisense molecules.
  • FIG. 1 is a chart showing a time-dependent change in ultraviolet absorption (260 nm) when a natural oligonucleotide is decomposed with exonuclease.
  • FIG. 2 is a chart showing the change over time in the ultraviolet absorption (260 nm) when the oligonucleotide (X 2) of the present invention is decomposed with exonuclease.
  • nucleoside analog of the present invention can be represented by the following general formula (I)
  • B is pyrimidine or purine nucleobase or an analog thereof, and X and Y are the same or different and are hydrogen, an alkyl group, an alkenyl group, an alkynyl group, a cycloalkyl group, an aralkyl group, an aryl group, or an acyl group. Or a silyl group], or an amidite derivative thereof.
  • the alkyl group refers to a linear or branched alkyl group having 1 to 20 carbon atoms, such as a methyl group, an ethyl group, an n-propyl group, an i-propyl group, an n-butyl group, and a t-alkyl group. Butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl and the like.
  • the alkenyl group refers to a linear or branched alkenyl group having 2 to 20 carbon atoms, and examples thereof include a vinyl group, an aryl group, a butenyl group, a pentenyl group, a geranyl group, and a farnesyl group. .
  • the alkynyl group refers to a linear or branched alkynyl group having 2 to 20 carbon atoms, and includes, for example, an ethynyl group, a propynyl group, a butynyl group and the like.
  • the cycloalkyl group refers to a cycloalkyl group having 3 to 8 carbon atoms, and examples thereof include a cyclopropyl group, a cyclobutyl group, a cyclopentyl group, a cyclohexyl group, a cyclohexyl group, and a cyclooctyl group.
  • Heterocyclic groups in which one or more arbitrary methylene on the ring of the cycloalkyl group is substituted with an oxygen atom, a sulfur atom, or a nitrogen atom substituted with an alkyl group are also included, and examples include a tetrahydroviranyl group.
  • the aryl group means a monovalent substituent obtained by removing one hydrogen atom from an aromatic heterocyclic group or an aromatic hydrocarbon group, and preferably, by removing one hydrogen atom from an aromatic hydrocarbon group.
  • a monovalent substituent means, for example, a phenyl group, a tolyl group, a xylyl group, a biphenyl group, a naphthyl group, an anthryl group, a phananthryl group and the like.
  • the carbon atom on the ring of the aryl group may be substituted by one or more groups such as a halogen atom, a lower alkyl group, a hydroxyl group, an alkoxy group, an amino group, a nitro group and a trifluoromethyl group.
  • substituents include a halogen atom, a hydroxyl group, an amino group, an alkoxy group, an aryloxy group and the like.
  • An aralkyl group is a group in which an alkyl group is bonded to an aralkyl group, and the aralkyl group may be substituted.
  • An aralkyl group which may be substituted is a group in which an aralkyl group is bonded to an aralkyl group, wherein at least one hydrogen atom of an aryl group and an alkyl group is substituted with the following substituent. Means a good group.
  • substituent include an acyl group, an amino group, an aryl group, an alkyl group, a cycloalkyl group, an alkoxy group, a hydroxyl group, a nitro group, and a halogen atom.
  • the amino group may or may not be substituted.
  • the substituted amino group include an alkylamino group, an arylamino group, and an acylamino group.
  • alkoxy groups include methoxy, ethoxy, n-propoxy, i-pro Examples include a oxy group, an n-butoxy group, an i-butoxy group, an s-butoxy group, a t-butoxy group, a pentyloxy group, a hexyloxy group, and a phenoxy group.
  • Halogen atoms include fluorine, chlorine, bromine and iodine.
  • aralkyl group examples include, for example, a trityl group, a benzyl group, a phenethyl group, a tritylmethyl group, a diphenylmethyl group, a naphthylmethyl group, and a 4,4′-dimethoxytrityl (DMTr) group. Is the DMT r group.
  • acetyl group examples include an acetyl group, a formyl group, a propionyl group, a benzoyl group, and a benzyloxycarbonyl group.
  • silyl group examples include a trialkylsilyl group, and preferably a trimethylsilyl group, a triethylsilyl group, a triisopropylsilyl group, a t-butyldimethylsilyl group, a t-butyldiphenylsilyl group, and the like. Preferably it is a trimethylsilyl group.
  • the nucleotide analog of the present invention has the general formula (la)
  • ⁇ is a pyrimidine or purine nucleobase or an analog thereof
  • BB are the same or different and is a pyrimidine or purine nucleic acid base or their analogues
  • R represents hydrogen, hydroxyl, Ri halogen or alkoxy groups der
  • WW 2 are the same or different and are hydrogen, an alkyl group , An alkenyl group, an alkynyl group, a cycloalkyl group, an aralkyl group, an aryl group, an acyl group, a silyl group or a natural nucleoside via a phosphoric acid residue or a phosphoric diester bond, a synthetic nucleoside, or an oligo containing these nucleosides a nucleotide or Helsingborg nucleotide
  • n 1 or n 2 are the same or different, is an integer of 0-5 0
  • N 3 is an integer of 1 to 5 0, where, n When 1 and / or n 2 is 2 or more, B 1 and B may not be the same, and R may not be the same.
  • the pyrimidine or purine nucleobase is thymine, peracyl, cytosine, adenine, guanine and derivatives thereof.
  • nucleond analog and nucleotide analog of the present invention can be synthesized as follows ( (1) Synthesis of nucleoside analog) O— 98/39352
  • the second method is based on D-ribose [3] AGM Barrett et al., J. Org. Chem., 55, 3853 (1990); 4) GH Jones et al., Ibid., 44, 1309 (1979) )], Via compound 13. That is, compound 13 is converted into compound 16 in three steps, and the ring-closing reaction under basic conditions yields the target methylglycol. The sil compound 17 was obtained. Substitution of the OMe group at position 1 of this compound with various natural nucleobases or non-natural nucleobase analogs is possible by various methods already developed. For example, methods such as the following compounds 17 to 20 can be used.
  • a third method is to use diacetone D-glucose, which is obtained from D-glucose in one step and is commercially available, as a starting material.
  • Reference 5 Compound 31 is prepared according to RD Youssefyeh, JPH Verheyden and JG Moffatt., J. Org. Chem., 44, 1301-1309 (1979). Then, as shown in the following formula, compound 31 was stepwise protected with two kinds of primary hydroxyl groups with t-butyldiphenylsilyl group and P-toluenesulfonyl group, and acetylated to give compound 34.
  • Compound 8 is reacted with 2-cyanoethyl-N, N, ⁇ ', N * -tetraisopropylphosphoramidite to obtain an amide 21 and then combined with a natural nucleoside amidite to form an automatic DNA synthesizer. Is used to synthesize various oligonucleotide analogs.
  • the synthesized crude product is purified using Oligopak and reversed-phase chromatography columns, and the purity of the purified product is confirmed by HPLC analysis.
  • One or more monomer units of compound 8 can be present in the oligonucleotide analog. In addition, it may be present at two or more positions in the oligonucleotide analog in an isolated state via one or more natural nucleotides. According to the present invention, it is possible to synthesize an antisense molecule in which the nucleotide analog (nucleoside analog) of the present invention is introduced at a required position in a required number (length). The total length of the oligonucleotide analog is 2 to 50, preferably 10 to 30, nucleoside units.
  • oligonucleotide analogs are not easily degraded by various nucleases, and can exist in the living body for a long time after administration to the living body. For example, they form stable duplexes with messenger RNA to inhibit the biosynthesis of pathogenic proteins, or form triplexes with double-stranded DNA in the genome to form messenger RNAs. Inhibits transcription to It will also be able to control the growth of infected viruses. From these facts, the oligonucleotide analogs (antisense molecules) using the nucleoside analogs of the present invention can be used as pharmaceuticals for treating diseases by inhibiting the function of specific genes, such as antitumor agents and antiviral agents. Is expected to be useful.
  • the antisense molecule using the nucleotide (nucleotide) analog of the present invention may be formulated into a parenteral administration preparation by combining conventional auxiliaries such as a buffer and / or a stabilizer, or a ribosome preparation. Can be.
  • a common pharmaceutical carrier can be compounded to prepare an ointment, cream, solution, salve or the like.
  • Compound 3 White powder rap 119-120 ° C.
  • Methyl 5-0-(t-butyldiphenylsilyl) synthesis of 1-3-0,4-C-methylene-1 / 3-D-ribofuranoside (18)
  • Triethylamine (3.71 ml, 26.6 mraol) and t-butyl were added to a methylene chloride solution (50 ml) of compound 31 (2.50 g, 8.08 mmol) prepared according to the above reference 5) under a nitrogen stream and ice cooling.
  • Diphenylsilyl chloride (6.94 ml, 26.7 mmol) was added, and the mixture was stirred at room temperature for 10.5 hours. After adding a saturated aqueous solution of sodium bicarbonate to the reaction solution, the mixture was extracted with ethyl acetate. The organic layer was washed with a saturated saline solution and dried over sodium sulfate.
  • triethylamine (395 ⁇ , 2.83 mmol) and p-toluenesulfonyl chloride (139.2) were added to a solution of 32 (250 mg, 0.456 mmol) in methylene chloride. mg, 0.730 mmol) and 4-dimethylaminopyridine (8.92 mg, 0.0730 mmol), and the mixture was stirred at room temperature for 15.5 hours. After adding a saturated aqueous solution of sodium bicarbonate to the reaction solution, the mixture was extracted with ethyl acetate. The organic layer was washed with brine and dried over sodium sulfate.
  • acetic anhydride (6.0 ml, 63.6 mmol) and concentrated sulfuric acid (56 jul, 1.10 mol) were added to an acetic acid solution (56 ml) of 34 (3.70 g, 5.27 mmol), and the mixture was stirred at room temperature for 2 hours. did. After the reaction solution was poured into ice water (300 ml) and stirred for 30 minutes, saturated saline was added, and the mixture was extracted with ethyl acetate. The organic layer was dried over magnesium sulfate.
  • tetrabutylammonium fluoride (1.0 M in THF, 379 ⁇ , 0.379 raol) was added to a solution of 37 (188.7 mg, 0.316 mmol) in tetrahydrofuran (1 ml), and the mixture was stirred at room temperature for 2.5 hours. did.
  • the reaction solution was evaporated under reduced pressure, and the crude product obtained was purified by silica gel column chromatography (AcOEt-hexane, 1: 1 ⁇ 1: 0) to give a white powder (38) (94.6 mg, 0.262 mg). Ol, 83%).
  • the oligomer was cleaved from the support by treatment with concentrated aqueous ammonia according to a conventional method, the cyanoethyl group on the phosphorus atom was removed, and the protecting groups of adenine, guanine and cytosine were removed.
  • the resulting 5 '— 0— DMT r-oligonucleotide analog was purified on reverse phase column chromatography (Millipore, Oligo-Pak TM SP) by removing the DMT r group with 5 ml of trifluoroacetic acid.
  • the target oligonucleotide analog was obtained.
  • the various oligonucleotide analogs synthesized in Example 2 were used as antisense strands, and the melting temperature (Tm value) of annealed natural strands of DNA or RNA was measured to determine the melting temperature (Tm value) of the present invention.
  • Tm value melting temperature
  • the final concentrations were NaC 110 Om.
  • a nitrogen stream was passed through the cell chamber of the spectrophotometer (Shimadzu UV-2100PC) to prevent dew condensation, the sample solution was gradually cooled to 5 ° C, and kept at 5 ° C for another 20 minutes before measuring. It has started.
  • the sample temperature was increased by 0.2 ° C per minute to 90 ° C, and ultraviolet absorption at 260 nm was measured at 0.1 ° C intervals.
  • the cell was used with a lid, and the measurement was performed with one drop of mineral oil added to the surface of the sample solution.
  • oligomers in which one or two units (X) of the nucleoside analog (general formula (la)) of the present invention were introduced into a natural DNA chain, hybridized with a complementary DNA oligomer. 2 to 7 degrees (approximately 2 times per modified residue) as compared to the natural chain as assessed by Tm value, and as high as 11 degrees for all T substituted with X (X6) did.
  • the increase in the Tm value of the oligomer introduced with one or two oligomers was 410 to 10 degrees (4 to 6 degrees per modified residue) compared to the natural chain.
  • a buffer solution of snake venom phosphodiesterase (0.003 U / ml, 400 1) was mixed with the buffer solution of the oligonucleotide kept at C (10 M, 400 H). The mixed solution was placed in a quartz cell (800 il) maintained at 37 ° C, and the increase in ultraviolet absorption (260 nm) due to the decomposition of the oligonucleotide was measured over time using SHIMADZU UV-2100PC.
  • the buffer composition used was 0.1 mM Tris-HCl (pH 8.6), 0.1 mM NaCl, and 14 mM MgCl 2, and was sufficiently degassed before measurement.
  • FIG. 1 naturally chain
  • FIG. 2 X 2
  • the UV absorption value of the natural chain became constant at about 30 minutes after the start of the oxygen reaction, and became constant at about 90 minutes for X2.
  • this analog provides an oligonucleotide analog antisense molecule that is not easily hydrolyzed by an enzyme in a living body, has high binding ability to a sense strand, and is easy to synthesize.
  • Sequence type nucleotide, nucleotide analog
  • Sequence type nucleotide, nucleotide analog Number of strands: single strand
  • Sequence type nucleotide, nucleotide analog Number of strands: single strand
  • Sequence type nucleotide, nucleotide analog Number of strands: single strand
  • Sequence type nucleotide, nucleotide analog
  • Sequence type nucleotide, nucleotide analog
  • Sequence type nucleotide, nucleotide analog
  • Sequence type nucleotide, nucleotide analog Number of strands: single strand

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PCT/JP1998/000945 1997-03-07 1998-03-09 Nouveaux analogues de bicyclonucleoside et d'oligonucleotide WO1998039352A1 (fr)

Priority Applications (9)

Application Number Priority Date Filing Date Title
DK98905804.5T DK1013661T4 (en) 1997-03-07 1998-03-09 2'-O, 4'-C-methylene bicyclonucleosides
AU61209/98A AU720472B2 (en) 1997-03-07 1998-03-09 Novel bicyclonucleoside and oligonucleotide analogue
US13/533,781 USRE44779E1 (en) 1997-03-07 1998-03-09 Bicyclonucleoside and oligonucleotide analogues
DE98905804T DE98905804T1 (de) 1997-03-07 1998-03-09 Bicyclonukleosid- und oligonukleotid-analoga
AT98905804T ATE541576T2 (de) 1997-03-07 1998-03-09 2'-o,4'-c-methylen bicyclonukleoside
ES98905804T ES2380354T5 (es) 1997-03-07 1998-03-09 2'-O,4'-C-metilen biciclonucleósidos
CA002283509A CA2283509C (en) 1997-03-07 1998-03-09 Novel bicyclonucleoside and oligonucleotide analogue
EP98905804.5A EP1013661B2 (en) 1997-03-07 1998-03-09 2'-O,4'-C-methylene bicyclonucleosides
US09/380,638 US6268490B1 (en) 1997-03-07 1998-03-09 Bicyclonucleoside and oligonucleotide analogues

Applications Claiming Priority (2)

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JP9/53409 1997-03-07
JP5340997 1997-03-07

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US09/380,638 A-371-Of-International US6268490B1 (en) 1997-03-07 1998-03-09 Bicyclonucleoside and oligonucleotide analogues
US90456701A Continuation 1997-03-07 2001-07-16

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Cited By (569)

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WO2000047599A1 (fr) * 1999-02-12 2000-08-17 Sankyo Company, Limited Nouveaux analogues de nucleosides et d'oligonucleotides
WO2000056748A1 (en) * 1999-03-18 2000-09-28 Exiqon A/S Xylo-lna analogues
WO2000066604A2 (en) * 1999-05-04 2000-11-09 Exiqon A/S L-ribo-lna analogues
WO2001007455A1 (fr) * 1999-07-22 2001-02-01 Sankyo Company, Limited Analogues de bicyclonucléosides
WO2001048190A2 (en) * 1999-12-23 2001-07-05 Exiqon A/S Therapeutic uses of lna-modified oligonucleotides
US6303315B1 (en) 1999-03-18 2001-10-16 Exiqon A/S One step sample preparation and detection of nucleic acids in complex biological samples
US6316198B1 (en) 1999-03-18 2001-11-13 Exiqon A/S Detection of mutations in genes by specific LNA primers
WO2002018388A1 (fr) * 2000-08-29 2002-03-07 Takeshi Imanishi Analogues de nucleosides et derives d'oligonucleotides renfermant ces analogues
WO2003033696A1 (fr) * 2001-10-18 2003-04-24 Sankyo Company, Limited Compose antisens vegf
US6639059B1 (en) 1999-03-24 2003-10-28 Exiqon A/S Synthesis of [2.2.1]bicyclo nucleosides
US6670461B1 (en) 1997-09-12 2003-12-30 Exiqon A/S Oligonucleotide analogues
US6734291B2 (en) 1999-03-24 2004-05-11 Exiqon A/S Synthesis of [2.2.1]bicyclo nucleosides
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WO2004072284A1 (en) 2003-02-11 2004-08-26 Antisense Therapeutics Ltd Modulation of insulin like growth factor i receptor expression
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US7229767B2 (en) 2001-03-27 2007-06-12 University Of Delaware Genomics applications for modified OLIGO nucleotides
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EP1959012A2 (en) 2004-12-29 2008-08-20 Exiqon A/S Novel oligonucleotide compositions and probe sequences useful for detection and analysis of microRNAs and their target mRNAs
EP1992643A2 (en) 2001-06-20 2008-11-19 Genentech, Inc. Compositions and methods for the diagnosis and treatment of tumor
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