Compounds and methods for modulating C90RF72

1. A compound comprising a modified oligonucleotide and a terminal group at the 5′-end of the modified oligonucleotide, wherein

the modified oligonucleotide consists of 21 to 30 linked nucleosides and comprises a nucleobase sequence selected from among: SEQ ID NO: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, and 25;

and wherein the terminal group comprises a phosphorus moiety.

2. The compound of claim 1 , wherein the 5′-terminal nucleoside and terminal group of the compound has Formula I:

wherein:

T 1 is a phosphorus moiety;

A has a formula selected from among:

Q 1 and Q 2 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl, and N(R 3 ) (R 4 );

Q 3 is selected from among: O, S, N(R 5 ), and C(R 6 )(R 7 );

each R 3 , R 4 R 5 , R 6 and R 7 is independently selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, and C 1 -C 6 alkoxy;

M 3 is selected from among: O, S, NR 14 , C(R 15 )(R 16 ), C(R 15 )(R 16 )C(R 17 )(R 18 ), C(R 15 )═C(R 17 ), OC(R 15 )(R 16 ), and OC(R 15 )(Bx 2 );

R 14 is selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

R 15 , R 16 , R 17 and R 18 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

if Bx 2 is present, then Bx 2 is a nucleobase and Bx 1 is selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

if Bx 2 is not present, then Bx 1 is a nucleobase;

either each of J 4 , J 5 , J 6 and J 7 is independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

or J 4 forms a bridge with one of J 5 or J 7 wherein the bridge comprises from 1 to 3 linked biradical groups selected from O, S, NR 19 , C(R 20 )(R 21 ), C(R 20 )═C(R 21 ), C[═C(R 20 )(R 21 )] and C(═O) and the other two of J 5 , J 6 and J 7 are independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

each R 19 , R 20 and R 21 is independently selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, or substituted C 2 -C 6 alkynyl;

one of G 1 and G 2 is selected from among: H, OH, halogen, and O—[C(R 8 )(R 9 )] n —[(C═O) m —X 1 ] j —Z; and the other of G 1 and G 2 is: O-T 2 ;

T 2 is an internucleoside linking group linking the 5′-terminal nucleoside of Formula I to the remainder of the oligonucleotide;

each R 8 and R 9 is independently selected from among: H, halogen, C 1 -C 6 alkyl, and substituted C 1 -C 6 alkyl;

X 1 is O, S or N(E 1 );

Z is selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 - C 6 alkynyl, and N(F 2 )(F 3 );

E 1 , E 2 and E 3 are each independently selected from among: H, C 1 -C 6 alkyl, and substituted C 1 -C 6 alkyl;

n is from 1 to 6;

m is 0 or 1;

j is 0 or 1;

provided that, if j is 1, then Z is other than halogen or N(E 2 )(E 3 );

each substituted group comprises one or more optionally protected substituent groups independently selected from among: a halogen, OJ 1 , N(J 1 )(J 2 ), ═NJ 1 , SJ 1 , N 3 , CN, OC(═X 2 )J 1 , OC(═X 2 )N(J 1 )(J 2 ), and C(═X 2 )N(J 1 )(J 2 );

X 2 is O, S or NJ 3 ; and

each J 1 , J 2 and J 3 is independently selected from among: H and C 1 -C 6 alkyl.

3. The compound of claim 2 , wherein M 3 is selected from among: O, CH═CH, OCH 2 , and OC(H)(Bx 2 ).

4. The compound of claim 2 , wherein each of J 4 , J 5 , J 6 and J 7 is H.

5. The compound of claim 2 , wherein J 4 forms a bridge with either J 5 or J 7 .

6. The compound of claim 2 , wherein A has the formula:

wherein:

Q 1 and Q 2 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, and substituted C 1 -C 6 alkoxy.

7. The compound of claim 6 , wherein each of Q 1 and Q 2 is H.

8. The compound of claim 6 , wherein Q 1 and Q 2 are each independently selected from among: H and a halogen.

9. The compound of claim 6 , wherein one of Q 1 and Q 2 is H and the other of Q 1 and Q 2 is F, CH 3 , or OCH 3 .

10. The compound of claim 2 , wherein T 1 has the formula:

wherein:

R a and R c are each independently selected from among: hydroxyl, protected hydroxyl, thiol, protected thiol, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, amino, protected amino, or substituted amino; and

R b is O or S.

11. The compound of claim 10 , wherein R b is O and R a and R c are each, independently selected from among: OH, OCH 3 , OCH 2 CH 3 , and OCH(CH 3 ) 2 .

12. The compound of claim 2 , wherein one of G 1 and G 2 is selected from among: a halogen, OCH 3 , OCH 2 F, OCHF 2 , OCF 3 , OCH 2 CH 3 , O(CH 2 ) 2 F, OCH 2 CHF 2 , OCH 2 CF 3 , OCH 2 —CH═CH 2 , O(CH 2 ) 2 —OCH 3 , O(CH 2 ) 2 —SCH 3 , O(CH 2 ) 2 —OCF 3 , O(CH 2 ) 3 —N(R 10 )(R 11 ), O(CH 2 ) 2 —ON(R 10 )(R 11 ), O(CH 2 ) 2 —O(CH 2 ) 2 —N(R 10 )(R 11 ), OCH 2 C(═O)—N(R 10 )(R 11 ), OCH 2 C(═O)—N(R 12 )—(CH 2 ) 2 —N(R 10 )(R 11 ), and O(CH 2 ) 2 —N(R 12 )—C(═NR 13 )[N(R 10 )(R 11 )]; wherein R 10 , R 11 , R 12 and R 13 are each, independently, H or C 1 -C 6 alkyl.

13. The compound of claim 2 , wherein one of G 1 and G 2 is selected from among: a halogen, OCH 3 , OCF 3 , OCH 2 CH 3 , OCH 2 CF 3 , OCH 2 —CH═CH 2 , O(CH 2 ) 2 —OCH 3 , O(CH 2 ) 2 —O(CH 2 ) 2 —N(CH 3 ) 2 , OCH 2 C(═O)—N(H)CH 3 , OCH 2 C(═O)—N(H)—(CH 2 ) 2 —N(CH 3 ) 2 , and OCH 2 —N(H)—C(═NH)NH 2 .

14. The compound of claim 2 , wherein one of G 1 and G 2 is selected from among: F, OCH 3 , and O(CH 2 ) 2 —OCH 3 .

15. The compound of claim 14 , wherein one of G 1 and G 2 is O(CH 2 ) 2 —OCH 3 .

16. The compound of claim 2 , wherein the 5′-terminal nucleoside and terminal group of the compound has Formula III:

17. The compound of claim 16 , wherein A has the formula:

wherein Q 1 and Q 2 are each independently selected from among: H, a halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, and substituted C 1 -C 6 alkoxy.

18. The compound of claim 17 , wherein Q 1 and Q 2 are each independently selected from among: H, F, CH 3 , and OCH 3 .

19. The compound of claim 2 , wherein the 5′-terminal nucleoside and the terminal group has Formula V:

wherein:

Bx is selected from among: uracil, thymine, cytosine, 5-methyl cytosine, adenine, and guanine;

one of G 1 and G 2 is selected from among: a halogen, OCH 3 , OCF 3 , OCH 2 CH 3 , OCH 2 CF 3 , OCH 2 —CH═CH 2 , O(CH 2 ) 2 —OCH 3 , O(CH 2 ) 2 —O(CH 2 ) 2 —N(CH 3 ) 2 , OCH 2 C(═O)—N(H)CH 3 , OCH 2 C(═O)—N(H)—(CH 2 ) 2 —N(CH 3 ) 2 , and OCH 2 —N(H)—C(═NH)NH 2 ;

and the other of G 1 and G 2 is O—T 2 , wherein T 2 is a phosphorothioate internucleoside linking group linking the compound of Formula V to the remainder of the oligonucleotide.

20. The compound of claim 1 , wherein the modified oligonucleotide comprises at least two modified sugar moieties.

21. The compound of claim 20 , wherein the modified oligonucleotide is fully modified.

22. The compound of claim 20 , wherein each modified sugar moiety is independently selected from among: 2′-F, 2′-MOE, 2′-OMe, LNA, F-HNA, and cEt.

23. The compound of claim 1 , wherein the modified oligonucleotide comprises at least one region having sugar motif:

-[(A) x -(B) y -(A) z ] q

wherein

A is a modified nucleoside of a first type,

B is a modified nucleoside of a second type;

each x and each y is independently 1 or 2;

z is 0 or 1; and

q is 3-15.

24. The compound of claim 1 , wherein the modified oligonucleotide comprises 1-4 3′-terminal nucleosides, each comprising the same modified sugar moiety, wherein the modified sugar moiety of the 1-4 3′-terminal nucleosides is different from the modified sugar moiety of the immediately adjacent nucleoside.

25. The compound of claim 24 , wherein the 3′-terminal nucleosides are each 2′-MOE nucleosides.

26. The compound of claim 24 , comprising two 3′-terminal nucleosides.

27. The compound of claim 1 , wherein the modified oligonucleotide comprises at least one modified internucleoside linkage.

28. The compound of claim 27 , wherein each internucleoside linkage of the modified oligonucleotide is selected from a phosphorothioate internucleoside linkage and an unmodified, phosphate internucleoside linkage.

29. The compound of claim 1 , wherein the compound comprises a second modified oligonucleotide comprising a nucleobase sequence selected from among: SEQ ID NO: 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, and 49, such that the modified oligonucleotide and the second modified oligonucleotide form a duplex oligonucleotide.

30. The compound of claim 1 , wherein the phosphorus moiety is an unmodified phosphate.

31. The compound of claim 1 , wherein the phosphorus moiety is a 5′-(E)-vinylphosphonate group having the formula:

32. The compound of claim 1 , wherein the compound is an oligomeric compound.

33. The compound of claim 32 , wherein the oligomeric compound is paired with a second oligomeric compound to form a duplex.

34. The compound of claim 1 , wherein the compound is single-stranded.

35. A method of reducing C9orf72 foci comprising contacting a cell with the compound of claim 1 .