WO2023176863A1 - RNAi活性を有する化学修飾オリゴヌクレオチド - Google Patents
RNAi活性を有する化学修飾オリゴヌクレオチド Download PDFInfo
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Definitions
- siRNA is useful for identifying gene functions, screening cell lines suitable for producing useful substances, regulating genes involved in diseases, etc.
- it is difficult to maintain its activity in the body because it is easily degraded by RNA degrading enzymes. , has the disadvantage of high synthesis cost. Therefore, various chemical modifications have been attempted to develop oligonucleotides that retain RNAi activity and are highly stable against RNA degrading enzymes and can be produced at low cost.
- Double-stranded oligonucleotides combining DNA, 2'-O-methyl RNA, and 2'-F have been reported, and siRNA in which the 14th position from the 5' end of the antisense strand is 2'-F has been reported. It has been reported (for example, see Patent Documents 1 and 2).
- double-stranded oligonucleotides that combine DNA, 2'-O-methyl RNA, 2'-F RNA, and LNA (2'-O,4'-C-methylene-bridged nuclear acids) have been reported.
- the RNAi activity of siRNA in which the second or 14th position from the 5' end of the antisense strand is 2'-F, DNA, or LNA has been reported (for example, Patent Document 1, Patent Document 3). reference.).
- a 11 -A 12 -A 13 -A 14 -A 15 is any of the following; A11 (2'-OMe RNA) -A12 (2'-OMe RNA) -A13 (ENA) -A14 (RNA) -A15 (2'-OMe RNA), A11 (2'-F RNA) -A12 (2'-OMe RNA) -A13 (ENA) -A14 (RNA) -A15 (2'-OMe RNA), A11 (2'-OMe RNA) -A12 (2'-F RNA) -A13 (ENA) -A14 (RNA) -A15 (2'-OMe RNA), A11 (2'-OMe RNA) -A12 (2'-OMe RNA) -A13 (LNA) -A14 (RNA) -A15 (2'-OMe RNA), A11 (2'-F RNA) -A12 (2'-OMe RNA) -A13 (LNA) -A14 (RNA)
- a 12 is DNA and A 14 is a 2'-O,4'-C-bridged modified nucleoside, or the oligonucleotide according to [6] or a pharmaceutically acceptable oligonucleotide thereof. salt.
- each internucleoside bond in 2 to 5 nucleotides from the 5' end and 3' end of the oligonucleotide is a phosphorothioate bond.
- oligonucleotide or a pharmaceutically acceptable salt thereof [18] The oligonucleotide or a pharmaceutically acceptable salt thereof according to any one of [1] to [17], wherein the number of nucleosides of S O3 , S O5 , A O5 and A O3 is 0 to 2.
- the present invention provides an oligonucleotide with a novel modification pattern that has a sustained RNA interference effect and/or gene expression suppressing effect in an animal body. Similar effects were confirmed when this modification pattern was applied to oligonucleotides for multiple target sequences, making it possible to analyze the functions of various genes using this oligonucleotide. Medicines for diseases are provided.
- FIG. 7 is a diagram showing the hepatic hTfR2 mRNA expression level in hTfR2 Tg mice 7 days after treatment with GalNAc-conjugated TfR2 siRNA.
- FIG. 2 is a diagram showing the base sequence of mRNA of the gene encoding human transferrin receptor 2 (hTfR2) (SEQ ID NO: 1). The underlined sequence (sequences 2847th to 2865th) indicates the target sequence of TfR2-019, and the double underlined sequence (sequence 1536th to 1554th) indicates the target sequence of TfR2-039.
- 14-1 is a diagram showing a continuation of FIG. 14-1.
- the transfectant may be introduced, or it may be exogenous, introduced by a technique such as gene transfer.
- the gene may be a gene existing on a chromosome or an extrachromosomal gene. Exogenous genes include, but are not limited to, those derived from viruses, bacteria, fungi, or protozoa that can infect the recipient. The function of the gene may be known or unknown.
- TTR proprotein convertase subtilisn/kexin type 9
- PCSK9 proprotein convertase subtilisn/kexin type 9
- PKA polo-like kinase
- RRM2 ribonucleotide reductase M2 subunit
- Hsp27 heat shock pro tein 27
- survivin eukaryotic initiation factor-4E (eIF-4E), intercellular adhesion molecule 1 (ICAM-1), alpha subunit of the interleukin 4 receptor (IL-4R-alpha), Factor XI, Factor VII, N-ras, H-ras, K-ras, bcl-2, bcl-xL, Her -1, Her-2, Her-3, Her-4, MDR-1, human ⁇ -catenin gene, DDX3 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked), Myeloid Cell Le ukemia Sequence 1 (MCL1)
- 2'-deoxyadenosine is A(D) or a
- 2'-deoxyguanosine is G(D) or g
- 2'-deoxycytidine is C(D) or c
- thymidine is T(D) or t
- 2'-deoxy-5-methylcytidine may be written as 5C(D) or 5c
- 2'-deoxyuridine may be written as U(D) or u.
- 2'-deoxynucleoside whose base is not specified may be expressed as N(D).
- a phosphodiester bond that may be chemically modified means a phosphodiester bond employed as a natural internucleoside bond or a chemically modified phosphodiester bond.
- a natural internucleoside bond is a phosphodiester bond represented by the following formula (P), and when displaying a base sequence, it is displayed without any letters or symbols between nucleosides.
- chemically modified phosphodiester bond means a bonding mode in which the phosphorus atom contained in the phosphodiester bond is chemically modified.
- Examples of chemically modified phosphodiester bonds include phosphorothioate bonds represented by the following formula (PS), phosphoroamidate bonds that are modified bonds in which a nitrogen atom is added to a phosphorus atom, and alkyl that can be substituted for a phosphorus atom.
- An alkylphosphonate bond is a modified bond with a group added (for example, in the case of a methyl group, it becomes a methylphosphonate bond), and a modified bond is a modified bond with a substitutable alkyl group added to the non-covalently bonded oxygen atom of a phosphate group.
- Examples include phosphotriester bonds. When a phosphorothioate bond is employed, " ⁇ " is displayed between nucleosides in the base sequence display.
- sugar-modified nucleoside refers to a nucleoside in which the sugar moiety of the nucleoside is modified.
- Sugar-modified nucleosides include all modes of sugar modification known in the art to which the present invention pertains. Examples of sugar-modified nucleosides include 2'-modified nucleosides, 3'-modified nucleosides, 4'-thio-modified nucleosides, 4'-thio-2'-modified nucleosides and 2'-O,4'-C-crosslinked nucleosides. Examples include modified nucleosides.
- 2'-O-alkoxyalkylation modifications include 2'-O-methoxyethyl nucleoside ("2'-MOE RNA", “2'-O-methoxyethyl RNA” or "2'-O-methoxyethyl RNA”). It may also be expressed as ⁇ methoxyethoxy RNA.'' The symbol representing the sugar moiety is (m).).
- the 2'-O-methoxyethyl nucleoside corresponding to each base has a structure represented by the following formula, where 2'-O-methoxyethyladenosine is A(m) and 2'-O-methoxyethylguanosine is A(m).
- the 2'-deoxy-2'-fluoronucleoside corresponding to each base has a structure represented by the following formula, and 2'-deoxy-2'-fluoroadenosine is converted into A(F), 2'-deoxy- 2'-fluoroguanosine is G(F), 2'-deoxy-2'-fluorocytidine is C(F), 2'-deoxy-2'-fluoro-5-methylcytidine is 5mC(F), 2'- Deoxy-2'-fluorouridine is sometimes written as U(F), and 2'-deoxy-2'-fluoro-5-methyluridine is sometimes written as T(F). Furthermore, 2'-deoxy-2'-fluoronucleoside whose base is not specified may be expressed as N(F).
- 3'-O-methoxyethylcytidine 3'-O- Methoxyethyl uridine is sometimes written as U (3m), and 3'-O-methoxyethyl-5-methyl uridine is sometimes written as T (3m).
- 3'-O-methoxyethyl nucleoside which does not specify the base, may be expressed as N(3m).
- the manner of linking the sense strand region and the antisense strand region is particularly limited as long as the oligonucleotide of the present invention has an RNA interference effect and/or a gene expression suppressing effect.
- the desired chemical linker or Examples include linking by oligonucleotide linkers.
- Such bases include, for example, chemically modified bases that have base pairing ability equal to or higher than the original base (for example, C and 5C, U and T (5U)), which are the same bases. regarded as.
- sequence identity preferably 80% or more, more preferably 90% or more, even more preferably 91%, 92%, 93%, 94%, 95%, 96%, Refers to sequences having 97%, 98% or 99% identity, or a mismatch of 3 bases, 2 bases or 1 base.
- Nucleotide sequence identity can be calculated using known genetic analysis software such as BLAST (registered trademark).
- S 1 to S 19 each represent one nucleoside, and S a is 0 to 5, preferably 0 to 4, more preferably 0 to 3, 0 to 2, or 0 to 1. Represents a nucleoside. Furthermore, regarding the overhang structure of the sense strand region, the one added to the 5' end is indicated as SO5 , and the one added to the 3' end is indicated as S O3 , and each has 0 to 5, preferably 0 to 4, or more. Preferably, it represents 0 to 3, 0 to 2, or 0 to 1 nucleosides.
- the S3M-oligonucleotide is characterized in that the nucleoside located at the 3' end of the complementary region in the sense strand region (ie, S 1 in formula (I) above) is a 3'-modified nucleoside.
- Such 3'-modified nucleosides are not particularly limited as long as the S3M-oligonucleotide has an RNA interference effect and/or a gene expression suppressing effect, but preferably 3'-deoxy-3'-fluoroRNA (3' -F RNA), 3'-OMe RNA, or 3'-MOE RNA, more preferably 3'-OMe RNA.
- One embodiment of the complementary region in the sense strand region of the S3M-oligonucleotide is the 11th, 12th, 13th, and 15th nucleoside from the 3' end (i.e., S 11 , S 12 , S 13 and S in formula (I) above). At least one of 15 ) is 2'-F RNA, and the other nucleosides are 2'-OMe RNA, 2'-F RNA, DNA, or a combination thereof.
- S 11 , S 12 , S 13 and S 15 are all 2'-F RNA.
- the antisense strand region of the S3M-oligonucleotide refers to the region represented by the above formula (II), ie, A O5 to A O3 .
- the complementary regions in the antisense strand region of the S3M-oligonucleotide are indicated as A 1 to A 19 numbered from the 5'-terminal nucleoside, and A a located on the 3' side of the complementary region. That is, the complementary region of the antisense strand is the region A 1 to A a in the above formula (II).
- a 12 is DNA.
- the modification pattern of A 11 -A 12 -A 13 -A 14 -A 15 in the antisense strand complementary region is preferably one of the following formulas (IIIi) to (IIIl). .
- 2'-O-methoxyethylguanosine, 2'-O-methoxyethyladenosine, 2'-O-methoxyethyl-5-methylcytidine, 2'-O-methoxyethyl-5-methyluridine can synthesize the corresponding phosphoramidite reagent according to the patent (US6261840) or the literature (Martin, P. Helv. Chim. Acta. (1995) 78, 486-504.), using commercially available phosphoramidite reagents. You can also do that.
- thioating oligonucleotide analogs in addition to sulfur, tetraethylthiuram disulfide (TETD, Applied Biosystems), Beaucage reagent, phenylacetyl disulfide/pyridine-acetonitrile (1:1 v/v) solution (Ravikumar, Using reagents such as V.T. et al. Bioorg. Med. Chem. . Chem. The thioate derivative can be obtained according to the method described in Soc., 112, 1253 (1990).
- the oligonucleotide of the present invention includes an oligonucleotide bound to a transport unit for transporting the oligonucleotide to a target tissue or target cell.
- a transport unit for transporting the oligonucleotide to a target tissue or target cell.
- a unit having an aminoalkyl phosphate group for example, the alkyl has 3 to 9 carbon atoms
- an oligonucleotide to which such a transport unit is bound for example, a unit having an aminoalkyl phosphate group (for example, the alkyl has 3 to 9 carbon atoms) introduced into the desired chemical structure can be used as an oligonucleotide.
- oligonucleotides in which an aptamer, which is a nucleic acid molecule that binds to a protein, is attached to the end of the oligonucleotide.
- metal salts such as iron salts, zinc salts, copper salts, nickel salts, cobalt salts; inorganic salts such as ammonium salts, t-octylamine salts, dibenzylamine salts, morpholine salts, glucosamine salts, phenylglycine alkyl ester salts , ethylenediamine salt, N-methylglucamine salt, guanidine salt, diethylamine salt, triethylamine salt, dicyclohexylamine salt, N,N'-dibenzylethylenediamine salt, chloroprocaine salt, procaine salt, diethanolamine salt, N-benzyl-phenethylamine salt , amine salts such as organic salts such as piperazine salts, tetramethylammonium salts, tris(hydroxymethyl)aminomethane salts; such as hydrofluoride, hydrochloride, hydrobromide, hydroiodide.
- colloidal dispersion systems are expected to have the effect of increasing the stability of compounds in vivo, and the effect of efficiently transporting compounds to specific organs, tissues, or cells.
- Colloidal dispersions include, but are not limited to, commonly used lipid-based polymer complexes, nanocapsules, microspheres, beads, and oil-in-water emulsifiers, micelles, mixed micelles, and liposomes.
- Representative phospholipids include phosphatidylcholine, dipalmitoylphosphatidylcholine, and distearoylphosphatidylcholine.
- active targeting includes, for example, viral protein coat (Morishita et al., Proc. Natl. Acad. Sci. (U.S.A.), 1993, 90, p. 8474-), monoclonal antibodies, (or suitable binding moieties thereof), sugars, glycolipids or proteins (or suitable oligopeptide fragments thereof) to liposomes, or organs and cells other than their naturally occurring localized sites.
- viral protein coat Menishita et al., Proc. Natl. Acad. Sci. (U.S.A.), 1993, 90, p. 8474-
- monoclonal antibodies or suitable binding moieties thereof
- sugars or glycolipids or proteins (or suitable oligopeptide fragments thereof)
- liposomes or organs and cells other than their naturally occurring localized sites.
- examples include techniques for modifying liposomes by changing their composition in order to achieve distribution in different types.
- compositions and formulations for topical administration include transdermal patches, ointments, lotions, creams, gels, lozenges, suppositories, sprays, liquids, and powders.
- Examples 1 to 52 and Reference Examples 1 to 3 This compound was synthesized using the phosphoramidite method (Nucleic Acids Research, 12, 4539 (1984), Nature Communications 6, Article number: 6317 (2015)). Specific sequences and structures are listed in Tables 1-1 to 1-10.
- the compounds of Examples 1 to 17, Examples 48 to 52, Reference Example 2, and Reference Example 3 are siRNAs that target mRNA for the gene encoding human transferrin receptor 2 (TfR2). It is. Furthermore, the compounds of Examples 1 to 4 and Reference Example 2 are located at positions 1536 to 1554 in the base sequence of human TfR2 (hTfR2) mRNA shown in SEQ ID NO: 1, and the compounds of Examples 5 to 17 and Reference Example 3 are located at positions 2847 to 2865.
- Example 48 TfR2-019.94DUG.s1 and Example 49 (TfR2-019.94DUG.s2) have the 3' end of the antisense strand region in the compound of Example 16 (TfR2-019.94DUG). siRNA in which each overhang structure is one nucleotide or is absent.
- the compounds of Example 50 TfR2-019.94DUG.e1) and Example 51 (TfR2-019.94DUG.e2) have the target sequence of the compound of Example 16 (TfR2-019.94DUG) on the 5' end side.
- Sequences each having a length of 1 or 2 nucleotides were used as target sequences, and the lengths of the complementary regions were 20 bp and 21 bp, respectively. It is a certain siRNA.
- the compound of Example 52 (TfR2-019.94DUG.e3) has the overhang structure of the 3' end of the antisense strand region in the compound of Example 16 (TfR2-019.94DUG) as G(M)U(M). This is siRNA.
- the "2'-O-methyl nucleoside” portion was synthesized using the phosphoramidite described in Nucleic Acids Research 17, 3373 (1989).
- the "DNA” portion was synthesized using the phosphoramidite described in Nucleic Acids Research 11, 4539 (1984).
- the 5'-position of the 5'-terminal nucleotide and the 3'-position of the 3'-terminal nucleotide of each oligonucleotide are hydrogen atoms, as shown in the structural diagram of each nucleoside described above. It is a hydroxyl group bonded to the oxygen atom inside. However, if "GN" is the terminal, no hydrogen atom bond is required.
- Test Example 1 Screening of TfR2 siRNA on HepG2 cells by reverse transfection method siRNA was screened as follows by reverse transfection method. On the day of transfection, 2 wells of siRNA samples per type, 2 wells of negative control (NT) using distilled water instead of siRNA, and siRNA against hTfR2, which is the compound of Reference Example 2 or 3, as a positive control. A chemically modified compound (TfR2-039.23DUG or TfR2-019.22DUG) was prepared in two wells.
- HepG2 cells (2 x 10 ⁇ 4 cells/mL) prepared using DMEM containing 10% FBS pre-warmed to 37°C were seeded at 80 ⁇ L per well.
- the final concentration of siRNA was adjusted to a 10-fold or 50-fold common ratio from 10 nM.
- cDNA was synthesized by performing RNA extraction and reverse transcription reaction according to the protocol of the kit. Using the obtained cDNA, the amount of endogenous hTfR2 mRNA expression was measured by quantitative PCR. As a housekeeping gene, the mRNA expression level of h18S was measured.
- Quantitative PCR was performed as follows using IDT Prime Time Gene Expression Master Mix (manufactured by Integrated DNA Technologies). The obtained cDNA was used as a stock solution. Per well of a 384-well PCR plate (manufactured by Applied Biosystems), 5 ⁇ L of IDT Prime Time Gene Expression Master Mix, 0.25 ⁇ L of hTfR2 primer (Hs.PT.58.20599 434, Integrated DNA Technologies) or 0. Mix 25 ⁇ L of h18S primer (Hs.PT.39a.22214856.g, Integrated DNA Technologies), 2.75 ⁇ L of distilled water, and 2 ⁇ L of cDNA (10 ⁇ L in total), and add 2 wells for each cDNA.
- Test Example 1-1 hTfR2 knockdown activity using HepG2 cells Evaluation of hTfR2 mRNA expression level 2 days after introducing siRNA into HepG2 cells using the reverse transfection method in the same manner as Test Example 1 I did it.
- TfR2-019 and TfR2-019.94DUG were used as siRNA.
- TfR2-019 is a double-stranded oligonucleotide consisting of a sense strand region and an antisense strand region, each of which is an independent oligonucleotide, and the complementary regions of the sense strand region and antisense strand region are all naturally occurring oligonucleotides.
- the relative hTfR2 mRNA expression level of the specimen treated with each siRNA was calculated and expressed as a relative value when the hTfR2 mRNA expression level in the negative control (NT) was set as 1.0. The results are shown in FIG.
- the mRNA expression levels of mTfR2 and h18S were measured as the average value between 2 wells.
- the mRNA expression level of mTfR2 was normalized with the mRNA expression level of h18S, a housekeeping gene.
- the relative mTfR2 mRNA expression levels of the samples treated with each siRNA were calculated as relative values when the mTfR2 mRNA expression level in the negative control was set to 1.0, and are shown in Tables 5 to 8, respectively.
- Test Example 3 Pharmaceutical efficacy evaluation test of GalNAc-conjugated TfR2 siRNA in normal mice TfR2 siRNA conjugated with GalNAc is known to increase plasma iron concentration in normal mice (WO2012/177921), and therefore, this document The compound of Reference Example 1 (AD47882.23DUG) and the compounds of Examples 18 to 25 (AD47882 The following tests were conducted using .41DUG to 48DUG).
- mouse ⁇ -actin (mActb) primer (Mm.PT.39a.22214843.g, manufactured by Integrated DNA Technologies) was used, mixed in the proportions described above, and Two wells were prepared and quantitative PCR was performed.
- the mRNA amounts of mTfR2 and mActb were measured as the average value between two wells.
- the mRNA expression level of mTfR2 was normalized with the mRNA expression level of mActb, a housekeeping gene.
- the relative mRNA amount in the siRNA treatment group was calculated and expressed as a relative value when the mRNA amount in the vehicle group was set to 1.0 (mean value ⁇ standard error).
- the results of the mTfR2 mRNA expression level are shown in FIG. 9F.
- Test Example 9 Drug efficacy evaluation test of GalNAc conjugate TfR2 siRNA in human TfR2-expressing mice Using male or female TfR2 humanized mice having the human TfR2 gene locus, which were created at Special Immunology Research Institute Co., Ltd., In order to verify the effect of GalNAc-conjugated TfR2 siRNA, the following experiment was performed. As TfR2 siRNA conjugated with GalNAc, TfR2-019.88DUG (Example 9), TfR2-019.92DUG (Example 14), TfR2-019.93DUG (Example 15), TfR2-019.94DUG (Example 16) was used.
- mice Seven days after the start of drug treatment, the mice were euthanized by exsanguination under isoflurane anesthesia, the livers were collected, and the amount of hTfR2 mRNA expression was measured. RNA extraction and quantitative PCR were performed as described in Test Example 5. The mRNA expression level of hTfR2 was normalized with the mRNA expression level of mActb, a housekeeping gene. The primers for hTfR2 described in Test Examples 1 and 2 were used. The results of hTfR2 mRNA expression level are shown in FIG. 13. Relative mRNA amounts in other groups were calculated and expressed as relative values when the mRNA amount in the vehicle group was set to 1.0 (mean value ⁇ standard error).
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| WO2026069321A1 (en) * | 2024-09-27 | 2026-04-02 | Dexcel Pharma Technologies Ltd | Nucleic acids for inhibiting expression of transferrin receptor 2 |
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