JPWO2020154342A5

JPWO2020154342A5 -

Info

Publication number: JPWO2020154342A5
Application number: JP2021541718A
Authority: JP
Publication date: 2023-01-26

Claims

An oligonucleotide having the structure:
[A _m ]-X ¹ -X ² -X ³ -[B _n ]
wherein each of A and B is a nucleotide;
m and n are each independently an integer from 1 to 50;
X ¹ , X ² , and X ³ are each independently a nucleotide, and at least one of X ¹ , X ² , or X ³ is represented by Formulas IV:

having any one structure of
wherein N ¹ is hydrogen or a nucleobase;
R ¹ is hydroxy, halogen, or C ₁ -C ₆ alkoxy;
R ² is hydrogen, hydroxy, halogen, or C ₁ -C ₆ alkoxy;
R ³ is hydrogen, hydroxy, halogen, or C ₁ -C ₆ alkoxy;
R ⁴ is hydrogen, hydroxy, halogen, or C ₁ -C ₆ alkoxy;
Said oligonucleotide, wherein R ⁵ is hydrogen, hydroxy, halogen, or C ₁ -C ₆ alkoxy.

Claim ¹ wherein ^R4 is hydrogen and R5 is not hydrogen or hydroxy, ^R5 is hydrogen and ^R4 is not hydrogen, or ^R5 is hydroxy and ^R4 is not hydrogen Oligonucleotides according to.

3. The oligonucleotide of claim 1 or claim 2, wherein at least 80% of said nucleotides of [ _Am ] and/or [ _Bn ] comprise nucleobases, sugars and internucleoside linkages.

The oligonucleotide of any one of claims _1-3 , wherein ^R1 is hydroxy, halogen, or OCH3.

The oligonucleotide of any one of claims 1-4, wherein ^R2 is hydrogen.

At least one of X ¹ , X ² , or X ³ has the structure of Formula I, Formula II, or Formula V above, and any of X ¹ , X ² , or X ³ is The oligonucleotide according to any one of claims 1 to 5, which does not have the structure of

At least one of X ¹ , X ² , or X ³ has the structure of Formula I or Formula II above, and any of X ¹ , X ² , or X ³ has the structure of Formula III, Formula IV, or Formula V above. The oligonucleotide according to any one of claims 1 to 6, which does not have the structure of

The oligonucleotide of any one of claims 1-7, wherein said halogen is fluoro.

9. Any one of claims 1-8, wherein at least one of X ¹ , X ² and X ³ has the structure of Formula I above, wherein R ¹ is fluoro and N ¹ is a nucleobase. The oligonucleotide according to paragraph.

10. The oligonucleotide of claim 9, wherein X1 has the structure of Formula ^I above, wherein ^R1 is fluoro and N1 is ^a nucleobase.

11. ^The oligonucleotide of claim 9 or 10, wherein X2 has the structure of Formula I above, wherein ^R1 is fluoro and N1 is ^a nucleobase.

The oligonucleotide of any one of claims 9-11, wherein X ³ has the structure of formula I above, wherein R ¹ is fluoro and N ¹ is a nucleobase.

9. Any one of claims 1-8, wherein at least one of X ¹ , X ² , and X ³ has the structure of Formula I above, wherein R ¹ is hydroxy and N ¹ is a nucleobase. The oligonucleotide according to paragraph.

14. The oligonucleotide of claim 13, wherein X1 has the structure of Formula ^I above, wherein ^R1 is hydroxy and N1 is ^a nucleobase.

15. ^The oligonucleotide of claim 13 or 14, wherein X2 has the structure of Formula I above, wherein ^R1 is hydroxy and N1 is ^a nucleobase.

The oligonucleotide of any one of claims 13-15, wherein X ³ has the structure of formula I above, wherein R ¹ is hydroxy and N ¹ is a nucleobase.

9. Any one of claims 1-8, wherein at least one of X ¹ , X ² , and X ³ has the structure of Formula I above, wherein R ¹ is methoxy and N ¹ is a nucleobase. The oligonucleotide according to paragraph.

18. The oligo of claim 17, wherein X1 has the structure of Formula ^I above, wherein ^R1 is methoxy, N1 is ^a nucleobase ^, and ^each of X2 and X3 is a ribonucleotide. nucleotide.

19. ^The oligonucleotide of claim 17 or 18, wherein X2 has the structure of formula I above, wherein ^R1 is methoxy and N1 is ^a nucleobase.

The oligonucleotide of any one of claims 17-19, wherein X ³ has the structure of Formula I above, wherein R ¹ is methoxy and N ¹ is a nucleobase.

9. Any one of claims 1-8, wherein at least one of X ¹ , X ² and X ³ has the structure of Formula II above, wherein R ² is hydrogen and N ¹ is a nucleobase. The oligonucleotide according to paragraph.

22. The oligonucleotide of claim 21, wherein X2 has the structure of Formula ^II above, wherein ^R2 is hydrogen and N1 is ^a nucleobase.

The oligonucleotide of any one of claims 1-6, wherein at least one of X ¹ and X ² has the structure of formula V above.

24. ^The oligonucleotide of claim 23, wherein X2 has the structure of Formula ^V above, wherein ^R4 is hydrogen and R5 is hydrogen.

24. ^The oligonucleotide of claim 23, wherein X2 has the structure of Formula ^V above, wherein ^R4 is hydrogen and R5 is hydroxy.

24. ^The oligonucleotide of claim 23, wherein X1 has the structure of Formula ^V above, wherein ^R4 is hydrogen and R5 is hydrogen.

24. ^The oligonucleotide of claim 23, wherein X1 has the structure of Formula ^V above, wherein ^R4 is hydrogen and R5 is hydroxy.

24. ^The oligonucleotide of claim 23, wherein X2 has the structure of Formula ^V above, wherein ^R4 is hydrogen and R5 is methoxy.

When X ¹ has the structure of any one of Formulas IV above, each of X ² and X ³ is independently a ribonucleotide, 2′-O—C ₁ -C ₆ alkyl nucleotide, 2′- an amino nucleotide, an arabinonucleic acid nucleotide, a bicyclic nucleotide, a 2′-F-nucleotide, a 2′-O-methoxyethyl nucleotide, a constrained ethyl nucleotide, an LNA nucleotide, or a DNA nucleotide, and X ² is each of X ¹ and X ³ is independently a ribonucleotide, 2′-O—C ₁ -C ₆ alkyl nucleotide, 2′-aminonucleotide, arabinonucleotide nucleotide, bicyclic of the formula nucleotide, 2′-F-nucleotide, 2′-O-methoxyethyl nucleotide, constrained ethyl nucleotide, LNA nucleotide, or DNA nucleotide, where X ³ has the structure of any one of formulas IV above , X ¹ and X ² are independently ribonucleotides, 2′-O—C ₁ -C ₆ alkyl nucleotides, 2′-amino nucleotides, arabinonucleotide nucleotides, bicyclic nucleotides, 2′-F-nucleotides , 2′-O-methoxyethyl nucleotides, constrained ethyl nucleotides, LNA nucleotides, or DNA nucleotides, and each of X ¹ and X ² has the structure of any one of Formulas IV above, then X ³ is , ribonucleotides, 2′-O—C ₁ -C ₆ alkyl nucleotides, 2′-aminonucleotides, arabinonucleotides, bicyclic nucleotides, 2′-F-nucleotides, 2′-O-methoxyethyl nucleotides, constrained ethyl When X 1 and X 3 are nucleotides, LNA nucleotides, or DNA nucleotides and each of X ¹ and X ³ has the structure of any one of Formulas IV above, X ² is a ribonucleotide, 2′-O—C ₁ to C ₆ alkyl nucleotide, 2′-amino nucleotide, arabinonucleic acid nucleotide, bicyclic nucleotide, 2′-F-nucleotide, 2′-O-methoxyethyl nucleotide, constrained ethyl nucleotide, LNA nucleotide, or DNA nucleotide, and X ² and X ³ each have the structure of any one of formulas IV above, X ¹ is a ribonucleotide, 2′-O—C ₁ -C ₆ alkyl nucleotide, 2′-amino nucleotide, arabino nucleic acid 29. The oligonucleotide of any one of claims 1-28, which is a nucleotide, a bicyclic nucleotide, a 2'-F-nucleotide, a 2'-O-methoxyethyl nucleotide, a constrained ethyl nucleotide, an LNA nucleotide, or a DNA nucleotide. nucleotide.

When X ¹ has the structure of any one of Formulas IV above, each of X ² and X ³ is independently a ribonucleotide, a 2′-F-nucleotide, a 2′-O-methoxyethyl nucleotide, or a DNA nucleotide, and X ² has the structure of any one of Formulas IV above, each of X ¹ and X ³ is independently a ribonucleotide, 2′-F-nucleotide, 2′- O-methoxyethyl nucleotides, or DNA nucleotides, and when X ³ has the structure of any one of Formulas IV above, each of X ¹ and X ² is independently a ribonucleotide, 2′-F -nucleotide, 2'-O-methoxyethyl nucleotide, or DNA nucleotide, and each of X ¹ and X ² has the structure of any one of Formulas IV above, X ³ is a ribonucleotide, 2 is a '-F-nucleotide, a 2'-O-methoxyethyl nucleotide, or a DNA nucleotide, and each of X ¹ and X ³ has the structure of any one of Formulas IV above, X ² is a ribonucleotide; X 1 when it is a nucleotide, 2′-F-nucleotide, 2′-O-methoxyethyl nucleotide, or DNA nucleotide, and each of X ² and X ³ has the structure of any ^one of Formulas IV above is a ribonucleotide, a 2'-F-nucleotide, a 2'-O-methoxyethyl nucleotide, or a DNA nucleotide.

when X ¹ has the structure of any one of formulas IV above, when each of X ² and X ³ is a ribonucleotide, and when X ² has the structure of any one of formulas IV above , each of X ¹ and X ³ is a ribonucleotide, and X ³ has the structure of any one of Formulas IV above, each of X ¹ and X ² is a ribonucleotide, and X ¹ and X ² has the structure of any one of Formulas IV above, X ³ is a ribonucleotide, and each of X ¹ and X ³ has the structure of any one of Formulas IV above. 31. The oligonucleotide of claim 30, wherein X ² is a ribonucleotide, and X ¹ is a ribonucleotide when each of X ² and X ³ has the structure of any one of Formulas IV above. .

32. Any one of claims 1-21 and 23-31, wherein none of X ¹ , X ² and X ³ have the structure of Formula II above, wherein N ¹ is a nucleobase of oligonucleotides.

33. The oligonucleotide of claim 32, wherein ^none of X1 ^, X2, and X3 have the structure of Formula ^II above, wherein N1 is ^a cytosine nucleobase.

The oligonucleotide of any one of claims 1-25 and 28-33, wherein X ¹ comprises a uracil or thymine nucleobase.

35. The oligonucleotide of claim 34, wherein X1 comprises ^a uracil nucleobase.

The oligonucleotide of any one of claims 1-25 and 28-33, wherein X ¹ comprises a hypoxanthine nucleobase.

The oligonucleotide of any one of claims 1-25 and 28-33, wherein X ¹ comprises a cytosine nucleobase.

38. The oligonucleotide of any one of claims 1-37 ^, comprising an X3 guanine nucleobase.

38. The oligonucleotide of any one of claims 1-37 ^, wherein X3 comprises a hypoxanthine nucleobase.

38. The oligonucleotide of any one of claims 1-37 ^, wherein X3 comprises an adenine nucleobase.

41. The oligonucleotide of any one of claims 1-23, 27, 28, and ^29-40 , wherein X2 comprises a cytosine or 5-methylcytosine nucleobase.

42. ^The oligonucleotide of claim 41, wherein X2 comprises a cytosine nucleobase.

6. ^The oligonucleotide of any one of claims 1-5, wherein X2 has the structure of any one of formulas IV above.

44. ^The oligonucleotide of any one of claims 1-43, wherein X2 is not a 2'-O-methyl nucleotide.

45. The oligonucleotide of claim 44, wherein X ¹ , X ² and X ³ are not 2'-O-methyl nucleotides.

46. The oligonucleotide of any one of claims 1-45, wherein [A _m ] comprises at least one nuclease-resistant nucleotide.

[A _m ] is at least one 2′-O—C ₁ -C ₆ alkyl nucleotide, at least one 2′-amino nucleotide, at least one arabinonucleic acid nucleotide, at least one bicyclic nucleotide; at least one 2'-F-nucleotide, at least one 2'-O-methoxyethyl nucleotide, at least one constrained ethyl (cEt) nucleotide, at least one LNA nucleotide, and/or at least one DNA 47. The oligonucleotide of any one of claims 1-46, comprising nucleotides.

[A _m ] is at least one 2′-O-methyl nucleotide, at least one 2′-F-nucleotide, at least one 2′-O-methoxyethyl nucleotide, at least one cEt nucleotide, at least 48. Oligonucleotide according to claim 47, comprising one LNA nucleotide and/or at least one DNA nucleotide.

The oligonucleotide of any one of claims 1-48, wherein [A _m ] comprises at least five terminal 2'-O-methyl nucleotides.

The oligonucleotide of any one of claims 1-49, wherein [A _m ] comprises at least one phosphorothioate linkage.

51. The oligonucleotide of any one of claims 1-50, wherein [A _m ] comprises at least four terminal phosphorothioate linkages.

52. The oligonucleotide of claim 50 or claim 51, wherein at least one phosphorothioate linkage is sterically pure.

53. The oligonucleotide of any one of claims 1-52, wherein [B _n ] comprises at least one nuclease-resistant nucleotide.

[B _n ] is at least one 2′-O—C ₁ -C ₆ alkyl nucleotide, at least one 2′-amino nucleotide, at least one arabinonucleic acid nucleotide, at least one bicyclic nucleotide; at least one 2'-F-nucleotide, at least one 2'-O-methoxyethyl nucleotide, at least one cEt nucleotide, at least one LNA nucleotide, and/or at least one DNA nucleotide; An oligonucleotide according to any one of claims 1-53.

[B _n ] is at least one 2′-O-methyl nucleotide, at least one 2′-F-nucleotide, at least one 2′-O-methoxyethyl nucleotide, at least one cEt nucleotide, at least 55. Oligonucleotide according to claim 54, comprising one LNA nucleotide and/or at least one DNA nucleotide.

56. The oligonucleotide of any one of claims 1-55, wherein [B _n ] comprises at least 5 terminal 2'-O-methyl nucleotides.

57. The oligonucleotide of any one of claims 1-56, wherein [B _n ] comprises at least one phosphorothioate linkage.

58. The oligonucleotide of any one of claims 1-57, wherein [B _n ] comprises at least four terminal phosphorothioate linkages.

59. The oligonucleotide of claim 57 or claim 58, wherein at least one phosphorothioate linkage is sterically pure.

57. The oligonucleotide of any one of claims 1-56, wherein at least 20% of said nucleotides combined of all [A _m ] and [B _n ] are 2'-O-methyl nucleotides.

The oligonucleotide of any one of claims 1-60, wherein said oligonucleotide further comprises a 5' cap structure.

The oligonucleotide of any one of claims 1-61, wherein said oligonucleotide comprises at least one alternative nucleobase.

63. The oligonucleotide of any one of claims 1-62, wherein the 5 ' terminal nucleotide is a 2'-aminonucleotide.

64. The oligonucleotide of any one of claims 1-63, wherein A and B taken together consist of 18-80 nucleotides.

65. The oligonucleotide of any one of claims 1-64, wherein m is 5-40.

66. The oligonucleotide of any one of claims 1-65, wherein n is 5-40.

m and n are each independently an integer from 5 to 40, and at least one of X ¹ , X ² and X ³ has the structure of Formula I above, wherein R ¹ is fluoro, hydroxy or methoxy, N ¹ is a nucleobase, or has the structure of Formula V above, wherein R ⁴ is hydrogen, R ⁵ is hydrogen, and the structure of Formula I or Formula V above is ^a ribonucleotide ^, and [A _m ] and [B _n ] each have at least 5 terminal 2′ ^- O-methyl nucleotides and at least 4 terminal 2. The oligonucleotide of claim 1, comprising phosphorothioate linkages, wherein at least 20% of said nucleotides combined of all [A _m ] and [B _n ] are 2′-O-methyl nucleotides.

68. The oligonucleotide of any one of claims 1-67, wherein said oligonucleotide further comprises one or more RNA-acting adenosine deaminase (ADAR) recruitment domains.

A conjugate comprising the oligonucleotide of any one of claims 1-68 conjugated to a targeting moiety.

70. The conjugate of claim 69, wherein said targeting moiety is a lipid, sterol, carbohydrate and/or peptide.

a compound,
The oligonucleotide according to any one of claims 1 to 68 or the complex according to claim 69 or 70,
mRNA and
Said oligonucleotide or said complex and said mRNA are hybridized to each other, said composite comprising a first mismatch at an adenosine of said mRNA.

72. The composite of Claim 71, wherein said composite comprises a second mismatch that is 4 nucleotides 5' to said first mismatch.

73. The composite of claims 71 or 72, wherein the composite contains 1, 2, 3, 4, 5, 6, 7, or 8 mismatches.

The conjugate of any one of claims 71-73, wherein said mRNA comprises adenosine, which may be deaminated to provide therapeutic results.

74. The composite of any one of claims 71-73, wherein said mRNA comprises a guanosine to adenosine mutation compared to the corresponding native mRNA.

76. The compound of claim 75, wherein said guanosine to adenosine mutation is a missense or nonsense mutation.

The compound of any one of claims 71-76, wherein said first mismatch is at an adenosine in the start codon of said mRNA.

The compound of any one of claims 71-76, wherein said first mismatch is at an adenosine in the stop codon of said mRNA.

79. The compound of claim 78, wherein said stop codon is a premature stop codon.

A method for producing a conjugate according to any one of claims 71 to 79, wherein the cell is an oligonucleotide according to any one of claims 1 to 68 or a conjugate according to claim 69 or The method, comprising contacting with

A method for deamination of adenosine in mRNA comprising contacting a cell with an oligonucleotide according to any one of claims 1-68 or a conjugate according to claims 69 or 70. .

A medicament for treating a disorder in a subject in need thereof, comprising an effective amount of an oligonucleotide according to any one of claims 1 to 68 or a conjugate according to claim 69 or 70 Including , medicine .

The disorder is cystic fibrosis, albinism, alpha-1-antitrypsin deficiency, Alzheimer's disease, amyotrophic lateral sclerosis, asthma, thalassemia 11, Cadasil syndrome, Charcot-Marie-Tooth disease, chronic obstruction pulmonary disease, distal spinal muscular atrophy, Duchenne/Becker muscular dystrophy, dystrophic epidermolysis bullosa, epidermolysis bullosa, Fabry disease, factor V Leiden-related disorders, familial adenomatous polyposis, galactosemia , Gaucher disease, glucose-6-phosphate dehydrogenase deficiency, hemophilia, hereditary hemochromatosis, Hunter's syndrome, Huntington's disease, Hurler's syndrome, inflammatory bowel disease, hereditary polyagglutination syndrome, Leber congenital amaurosis, Lesch・Nyhan syndrome, Lynch syndrome, Marfan syndrome, mucopolysaccharidosis, muscular dystrophy, myotonic dystrophy type I and II, neurofibroma, Niemann-Pick disease type A, B and C, NY-ESO-1 related Cancer, Parkinson's disease, Peutz-Jeghers syndrome, phenylketonuria, Pompe disease, primary ciliary disease, prothrombin mutation-related disorder, pulmonary hypertension, retinitis pigmentosa, Sandhoff disease, severe combined immunodeficiency syndrome, sickle 83. The medicament of claim 82, which is erythrocytic anemia, spinal muscular atrophy, Stargardt disease, Tay-Sachs disease, Usher syndrome, X-linked immunodeficiency, Sturge-Weber syndrome, Rett syndrome, or cancer.