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 the group consisting:

SEQ ID NO: 26 (CATTACCCCTC);

SEQ ID NO: 27 (CCATTACCCCT);

SEQ ID NO: 28 (TCCATTACCCC);

SEQ ID NO: 29 (TGTCCATTACC);

SEQ ID NO: 30 (TTGTCCATTAC);

SEQ ID NO: 31 (GTTGTCCATTA);

SEQ ID NO: 32 (TGTTGTCCATT);

SEQ ID NO: 33 (ATGTTGTCCAT);

SEQ ID NO: 34 (TTTACAAGTGC);

SEQ ID NO: 35 (CCTCCGAGGGA);

SEQ ID NO: 36 (ACACGTTGTTC); and

SEQ ID NO: 37 (AGTTCAGCGAC),

or a variant having at least 80% sequence identity to SEQ ID NOS: 26-37,

wherein thymine bases (T) are optionally 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:

and R 2 is G.

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

7. The antisense morpholino oligomer according to claim 6 , wherein R 2 is selected from H, acyl, trityl, 4-methoxytrityl, benzoyl, and stearoyl.

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

9. The antisense morpholino oligomer of claim 8 , wherein each R 1 is —N(CH 3 ) 2 .

10. The antisense morpholino oligomer according to any one of claim 1 , wherein the CPP is selected from:

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

11. The antisense morpholino oligomer of claim 1 , wherein G is selected from:

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

12. The antisense morpholino oligomer of claim 1 , wherein the antisense oligomer is of the formula (VII) selected from:

or a pharmaceutically acceptable salt of any of the foregoing,

wherein R a is selected from H, acetyl, benzoyl, and stearoyl, R b is selected from H, acetyl, benzoyl, stearoyl, trityl, and 4-methoxytrityl, and X and Nu.

13. The antisense morpholino oligomer of claim 12 , wherein R a is acetyl and R b is H.

14. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 26.

15. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 27.

16. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 28.

17. A pharmaceutical composition, comprising a pharmaceutically acceptable carrier and an antisense morpholino oligomer of claim 1 .

18. A method of reducing expression and activity of a virulence factor in a bacterium, comprising contacting the bacterium with an antisense morpholino oligomer of claim 1 .

19. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 29.

20. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 30.

21. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 31.

22. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 32.

23. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 33.

24. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 34.

25. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 35.

26. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 36.

27. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 37.