Antisense antibacterial compounds and methods

1. An antisense morpholino oligomer of formula (I):

or a pharmaceutically acceptable salt thereof,

where each Nu is a nucleobase which taken together forms a targeting sequence;

X is an integer from 9 to 38;

T is selected from OH and a moiety of the formula:

where each R 4 is independently C 1 -C 6 alkyl, and R 5 is selected from an electron pair and H, and R 6 is selected from OH, —N(R 7 )CH 2 C(O)NH 2 , and a moiety of the formula:

where:

R 7 is selected from H and C 1 -C 6 alkyl, and

R 8 is selected from G, —C(O)—R 9 OH, acyl, trityl, and 4-methoxytrityl, where:

R 9 is of the formula —(O-alkyl) y - wherein y is an integer from 3 to 10 and each of the y alkyl groups is independently selected from C 2 -C 6 alkyl;

each instance of R 1 is —N(R 10 ) 2 R 11 wherein each R 10 is independently C 1 -C 6 alkyl, and

R 11 is selected from an electron pair and H;

R 2 is selected from H, G, acyl, trityl, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:

where L is selected from —C(O)(CH 2 ) 6 C(O)— and —C(O)(CH 2 ) 2 S 2 (CH 2 ) 2 C(O)—, and each R 12 is of the formula —(CH 2 ) 2 OC(O)N(R 14 ) 2 wherein each R 14 is of the formula —(CH 2 ) 6 NHC(═NH)NH 2 ; and

R 3 is selected from an electron pair, H, and C 1 -C 6 alkyl,

wherein G is a cell penetrating peptide (“CPP”) and linker moiety selected from —C(O)(CH 2 ) 5 NH—CPP, —C(O)(CH 2 ) 2 NH—CPP, —C(O)(CH 2 ) 2 NHC(O)(CH 2 ) 5 NH—CPP, and —C(O)CH 2 NH—CPP, or G is of the formula:

wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,

wherein the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a virulence factor, and

wherein the targeting sequence is selected from:

a) SEQ ID NO: 11 (TCA AGT TTT CC);

b) SEQ ID NO: 12 (TCC TTT TAT TC);

c) SEQ ID NO: 13 (CCA TCA AGT TT);

d) SEQ ID NO: 14 (GGC AAT TCC AT);

e) SEQ ID NO: 15 (ATA CTG TCC AA);

wherein X is 9, and thymine bases (T) may be uracil bases(U).

2. The antisense morpholino oligomer of claim 1 , wherein T is selected from:

3. The antisense morpholino oligomer of claim 2 , wherein R 2 is selected from H, G, acyl, trityl, 4-methoxytrityl, benzoyl, and stearoyl.

4. The antisense morpholino oligomer of claim 1 , wherein T is selected from:

and

R 2 is G.

5. The antisense morpholino oligomer of claim 1 , wherein T is of the formula:

R 6 is of the formula:

and R 2 is G.

6. The antisense morpholino oligomer of claim 1 , wherein T is of the formula:

and R 2 is G.

7. The antisense morpholino oligomer of claim 1 , wherein T is of the formula:

8. The antisense morpholino oligomer according to claim 7 , wherein R 2 is selected from H, acyl, trityl, 4-methoxytrityl, benzoyl, and stearoyl.

9. The antisense morpholino oligomer according to claim 8 , wherein at least one instance of R 1 is —N(CH 3 ) 2 .

10. The antisense morpholino oligomer of claim 9 , wherein each R 1 is —N(CH 3 ) 2 .

11. The antisense morpholino oligomer according to claim 1 , wherein the CPP is selected from:

wherein R a is selected from H, acetyl, benzoyl, and stearoyl.

12. The antisense morpholino oligomer according to claim 1 , wherein G is selected from:

wherein R a is selected from H, acetyl, benzoyl, and stearoyl.

13. An antisense morpholino oligomer of formula (VII) selected from:

or a pharmaceutically acceptable salt of any of the foregoing,

wherein R a is H or acetyl,

each Nu is a nucleobase which taken together forms a targeting sequence, and the targeting sequence is selected from:

f) SEQ ID NO: 11 (TCA AGT TTT CC);

g) SEQ ID NO: 12 (TCC TTT TAT TC);

h) SEQ ID NO: 13 (CCA TCA AGT TT);

i) SEQ ID NO: 14 (GGC AAT TCC AT);

j) SEQ ID NO: 15 (ATA CTG TCC AA);

wherein X is 9, and thymine bases (T) may be uracil bases(U).

14. A pharmaceutical composition, comprising a pharmaceutically acceptable carrier and an antisense morpholino oligomer of formula (I):

or a pharmaceutically acceptable salt thereof,

where each Nu is a nucleobase which taken together forms a targeting sequence;

X is an integer from 9 to 38;

T is selected from OH and a moiety of the formula:

where each R 4 is independently C 1 -C 6 alkyl, and R 5 is selected from an electron pair and H, and R 6 is selected from OH, —N(R 7 )CH 2 C(O)NH 2 , and a moiety of the formula:

where:

R 7 is selected from H and C 1 -C 6 alkyl, and

R 8 is selected from G, —C(O)—R 9 OH, acyl, trityl, and 4-methoxytrityl, where:

R 9 is of the formula —(O-alkyl) y - wherein y is an integer from 3 to 10 and each of the y alkyl groups is independently selected from C 2 -C 6 alkyl;

each instance of R 1 is —N(R 10 ) 2 R 11 wherein each R 10 is independently C 1 -C 6 alkyl, and R 11 is

selected from an electron pair and H;

R 2 is selected from H, G, acyl, trityl, 4-methoxytrityl, benzoyl, stearoyl, and a moiety of the formula:

where L is selected from —C(O)(CH 2 ) 6 C(O)— and —C(O)(CH 2 ) 2 S 2 (CH 2 ) 2 C(O)—, and each R 12 is of the formula —(CH 2 ) 2 OC(O)N(R 14 ) 2 wherein each R 14 is of the formula —(CH 2 ) 6 NHC(═NH)NH 2 ; and

R 3 is selected from an electron pair, H, and C 1 -C 6 alkyl,

wherein G is a cell penetrating peptide (“CPP”) and linker moiety selected from

—C(O)(CH 2 ) 5 NH—CPP, —C(O)(CH 2 ) 2 NH—CPP, —C(O)(CH 2 ) 2 NHC(O)(CH 2 ) 5 NH—CPP,

and —C(O)CH 2 NH—CPP, or G is of the formula:

wherein the CPP is attached to the linker moiety by an amide bond at the CPP carboxy terminus, with the proviso that only one instance of G is present,

wherein the targeting sequence specifically hybridizes to a bacterial mRNA target sequence that encodes a virulence factor, and

wherein the targeting sequence is selected from:

k) SEQ ID NO: 11 (TCA AGT TTT CC);

l) SEQ ID NO: 12 (TCC TTT TAT TC);

m) SEQ ID NO: 13 (CCA TCA AGT TT);

n) SEQ ID NO: 14 (GGC AAT TCC AT);

o) SEQ ID NO: 15 (ATA CTG TCC AA);

wherein X is 9, and thymine bases (T) may be uracil bases(U).

15. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

16. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

17. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

18. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.

19. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

20. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

21. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

22. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.

23. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

24. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

25. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

26. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.

27. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

28. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

29. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

30. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein W is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.

31. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

32. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

33. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

34. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.

35. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 11 (TCA AGT TTT CC) wherein X is 9.

36. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 12 (TCC TTT TAT TC) wherein X is 9.

37. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 13 (CCA TCA AGT TT) wherein X is 9.

38. The antisense oligomer of claim 13 , wherein the antisense oligomer is:

or a pharmaceutically acceptable salt thereof, wherein R a is H or acetyl, and the targeting sequence consists of SEQ ID NO: 14 (GGC AAT TCC AT) wherein X is 9.