Modified oligonucleotides for use in treatment of tauopathies
Oligonucleotides comprising modifications at the 2′ and/or 3′ positions(s) along with methods of making and use against Alzheimer disease and other tauopathies are disclosed.
1. A chimeric oligonucleotide complementary to at least a portion of the MAPT gene represented by Formula (VI):
5′X-Y-Z3′ (VI),
wherein
X-Y-Z is a chimeric oligonucleotide comprising a sequence of 18 to 22 nucleosides, and is optionally conjugated at the 5′ and/or 3′ end to a ligand targeting group;
X is a domain comprising a sequence of modified nucleosides that is 3-10 nucleosides in length;
Z is a domain comprising a sequence of modified nucleosides that is 3-10 nucleosides in length; and
Y is a domain comprising a sequence of 2 to 10 2′-deoxy-nucleosides linked through thiophosphate intersubunit linkages, and
wherein the oligonucleotide shows affinity to at least one of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:5 or SEQ ID NO:6,
wherein the X and/or Z domain comprises one or more oligonucleotide where the modification is 2′-O-methoxyethoxy-N3′→P5′.
2. The chimeric oligonucleotide of claim 1 , wherein the Y domain is 6 to 10 nucleosides in length.
3. The chimeric oligonucleotide of claim 1 , wherein the X and/or Z domains comprise a sequence of modified nucleosides linked through N3′→P5′ phosphoramidate or N3′→P5′ thiophosphoramidate intersubunit linkages.
4. The chimeric oligonucleotide of claim 1 , wherein the Y domain comprises at least one phosphodiester intersubunit linkage.
5. The chimeric oligonucleotide of claim 1 , wherein the Y domain consists of 2′-deoxy-nucleosides linked through thiophosphate intersubunit linkages, and optionally one or two phosphodiester intersubunit linkage.
6. The chimeric oligonucleotide of claim 1 , wherein the X domain comprises modified nucleosides where the modification is independently selected from the group consisting of 2′-F, 2′-F—N3′→P5′, 2′-OMe, 2′-OMe-N3′→P5′, 2′-O-methoxyethoxy, 2′-O-methoxyethoxy-N3′→P5′, conformationally restricted nucleosides, 2′-OH—N3′→P5′ thiophosphoramidate and 2′-OH—N3′→P5′ phosphoramidate.
7. The chimeric oligonucleotide of claim 1 , wherein the functional domain of Z comprises modified nucleosides where the modification is selected from the group consisting of 2′-F, 2′-F—N3′→P5′, 2′-OMe, 2′-OMe-N3′→P5′, 2′-O-methoxyethoxy, 2′-O-methoxyethoxy-N3′→P5′, conformationally restricted nucleosides, 2′-OH—N3′→P5′ thiophosphoramidate and 2′-OH—N3′→P5′ phosphoramidate.
8. The chimeric oligonucleotide of claim 1 , wherein the X and/or Z domains comprise one or more 2′-deoxy-nucleosides linked through a N3′→P5′ phosphoramidate intersubunit linkage.
9. The chimeric oligonucleotide of claim 1 , wherein the X and Z domains comprise one or more 2′-arabino-F and/or 2′-ribo-F modified nucleoside, wherein each said nucleoside is independently linked through at least one of an N3′→P5′ phosphoramidate or N3′→P5′ thiophosphoramidate intersubunit linkage.
10. The chimeric oligonucleotide of claim 1 , wherein the X and Z domains comprise one or more 2′-OMe modified nucleosides, wherein each said nucleoside is independently linked through at least one of N3′→P5′ phosphoramidate, N3′→P5′ thiophosphoramidate, or thiophosphate intersubunit linkages.
11. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides in each of the X and Z domains are 2′-OMe modified nucleosides linked through thiophosphate intersubunit linkages, and wherein the modified nucleosides include 5-methylcytosine nucleobases.
12. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides include 2,6-diaminopurine nucleobases.
13. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides include 5-methyluracil nucleobases.
14. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides include 2,6-diaminopurine nucleobases, but not adenine and 5-methyluracil nucleobases.
15. The chimeric oligonucleotide of claim 1 , wherein the Y domain comprises 6-8 2′-deoxy-nucleosides.
16. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides in each of the X and Z domains comprise 2′-OMe modified nucleosides and conformationally restricted nucleosides optionally linked through thiophosphate intersubunit linkages, and wherein the 2′-OMe modified nucleosides include 5-methylcytosine nucleobases.
17. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides in each of the X and Z domains comprise 2′-OMe and conformationally restricted nucleosides.
18. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides in each of the X and Z domains comprise conformationally restricted nucleosides and, wherein at least one modified nucleoside includes a N3′→P5′ phosphoramidate or a N3′→P5′ thiophosphoramidate intersubunit linkage.
19. The chimeric oligonucleotide of claim 1 , wherein the Y domain comprises 7-8 2′-deoxy-nucleosides.
20. The chimeric oligonucleotide of claim 1 , wherein the modified nucleosides include 2′-OMe modified nucleosides, and the 2′-OMe modified nucleosides include 5-methyluracil nucleobases.
21. The chimeric oligonucleotide of claim 1 , wherein the Y domain comprises 9-10 2′-deoxy-nucleosides.
22. The chimeric oligonucleotide of claim 1 , wherein the X and Z domains comprise nucleotides represented by the Formula (A1):
wherein
A is independently in each instance NH or O;
B is independently in each instance an unmodified or modified nucleobase;
W is independently in each instance OR or SR, where R is H or a positively charged counter ion;
R′ and R″ are each independently in each instance selected from the group consisting of H, F, Cl, OH, OMe, Me, and O-methoxyethoxy;
R′″ is H, or R′ and R′″ together form —O—CH 2 — or —O—(CH 2 ) 2 —, and
a is an integer of 3 to 9,
wherein when R′, R″ and R′″ are each H, then A is NH, and optionally when A is O, then W is SR.
23. The chimeric oligonucleotide of claim 1 , wherein the X domain comprises one or more oligonucleotide where the modification is 2′-O-methoxyethoxy-N3′→P5′.
24. The chimeric oligonucleotide of claim 1 , wherein the Z domain comprises one or more oligonucleotide where the modification is 2′-O-methoxyethoxy-N3′→P5′.
25. The chimeric oligonucleotide of claim 1 , wherein the nucleobase sequence of the oligonucleotide corresponds to SEQ ID NO: 1, SEQ ID NO: 40, SEQ ID NO: 41 or SEQ ID NO: 42.
26. A pharmaceutical composition comprising an oligonucleotide of claim 1 and a pharmaceutically acceptable excipient.
27. The pharmaceutical composition of claim 26 , wherein the composition is suitable for intrathecal or intracerebroventricular delivery.
28. A method of inhibiting MAPT gene expression in a CNS cell comprising contacting the cell with an oligonucleotide of claim 1 .
29. A method of inhibiting transcription of MAPT mRNA in a CNS cell comprising contacting the cell with an oligonucleotide of claim 1 .
30. The oligonucleotide of claim 1 , wherein said oligonucleotide complexed with an MAPT gene has a melting temperature (Tm) of >37° C.
31. A method of inhibiting expression of a MAPT mRNA in a CNS cell comprising contacting the cell with an oligonucleotide or composition comprising an oligonucleotide of claim 1 , wherein the oligonucleotide contains a nucleobase sequence that is complementary or hybridizes to at least a portion of the MAPT mRNA.
32. A method of modulating expression of a MAPT gene by contacting a target nucleic acid with an antisense compound comprising an oligonucleotide of claim 1 , wherein the oligonucleotide contains a nucleobase sequence that is complementary or hybridizes to at least a portion of the MAPT gene.