Antisense antibacterial compounds and methods

1. An antisense morpholino oligomer, composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′-cxocyciic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence selected from

a) SEQ ID NO: 11 (ATG TAA ACC TC);

b) SEQ ID NO: 12 (GTT CAT ATG TA);

c) SEQ ID NO: 13 (AAC CCT CTG TT);

d) SEQ ID NO: 14 (TGT TCA TAT GT);

wherein thymine, bases (T) may be uracil bases (U), and where the oligomer is conjugated to a cell-penetrating peptide (CPP).

2. The antisense morpholino oligomer of claim 1 , wherein the antisense morpholino oligomer is of formula (1):

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, steamy', 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 N HC(═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 )5N H—CPP, —C(O)(CH 2 ) 2 N H—CPP, —C(O)(CH 2 ) 2 NHC(O)(CH 2 )5NH—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.

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

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

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

and

R 2 is G.

6. The antisense morpholino oligomer of claim 2 , wherein T is of the formula:

R 6 is of the formula:

and

R 2 is G.

7. The antisense morpholino oligomer of claim 2 , wherein T is of the formula:

and

R 2 is G.

8. The antisense morpholino oligomer of claim 2 , wherein T is of the formula:

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

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

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

wherein R 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. 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 U, acetyl, benzoyl, and stearoyl, R b is selected from H, acetyl, benzoyl, stearoyl, trityl, and 4-methoxytrityl, and X and Nu are as defined in claim 1 .

14. A pharmaceutical composition, comprising a pharmaceutically acceptable carrier and an antisense morpholino oligomer, wherein the antisense morpholino oligomer is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence selected from:

a) SEQ ID NO: 11 (ATG TAA ACC TC);

b) SEQ ID NO: 12 (GTT CAT ATG TA);

C) SEQ ID NO: 13 (AAC CCT CTG TT);

d) SEQ ID NO: 14 (TGT TCA TAT GT);

wherein thymine bases (T) may he uracil bases (U), and where the oligomer is conjugated to a cell-penetrating peptide (CPP).

15. A method of reducing expression and activity of a virulence factor in a bacterium, comprising contacting the bacterium with an antisense morpholino oligomer, wherein the antisense morpholino oligomer is composed of morpholino subunits and phosphorus-containing intersubunit linkages joining a morpholino nitrogen of one subunit to a 5′-exocyclic carbon of an adjacent subunit, and having (a) about 10-40 nucleotide bases, and (b) a targeting sequence selected from:

a) SEQ ID NO: 11 (ATG TAA ACC TC);

b) SEQ ID NO: 12 (GTT CAT ATG TA);

c) SEQ ID NO: 13 (AAC CCT CTG TT);

d) SEQ ID NO: 14 (TGT TCA TAT GT);

wherein thymine bases (T) may be uracil bases (U), and where the oligomer is conjugated to a cell-penetrating peptide (CPP).

16. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 11.

17. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 12.

18. The antisense morpholino oligomer of claim 1 , wherein the targeting sequence is SEQ ID NO: 13.

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