Peptide oligonucleotide conjugates
Oligonucleotide analogues conjugated to carrier peptides are provided. The disclosed compounds are useful for the treatment of various diseases, for example diseases where inhibition of protein expression or correction of aberrant mRNA splice products produces beneficial therapeutic effects.
1. A conjugate comprising:
(a) a carrier peptide comprising amino acid subunits, the carrier peptide comprising a proline (P) amino acid subunit at the carboxy terminus of the carrier peptide;
(b) a nucleic acid analogue comprising a substantially uncharged backbone and a targeting base sequence for sequence-specific binding to a target nucleic acid, wherein the nucleic acid analog is 8 to 40 bases in length; and
(c) a covalent attachment between the nucleic acid analog and the carrier peptide, the covalent attachment comprising the carboxy-terminal proline and an optional linker group;
wherein:
two or more of the amino acid subunits are positively charged amino acids, no more than seven contiguous amino acid subunits are arginine, and the covalent attachment between the nucleic acid analog and the carrier peptide is not 6-aminohexanoic acid or β-alanine.
2. The conjugate of claim 1 , wherein the nucleic acid analog is 8 to 20 bases in length.
3. The conjugate of claim 1 , wherein the nucleic acid analog is 8 to 16 bases in length.
4. The conjugate of claim 1 , wherein the nucleic acid analog is 10 to 30 bases in length.
5. The conjugate of claim 1 , wherein the nucleic acid analog is 12 to 25 bases in length.
6. The conjugate of claim 1 , wherein the nucleic acid analog is 8 to 12 bases in length.
7. The conjugate of claim 1 , wherein the carrier peptide is selected from SEQ ID NOS: 60, 69, 70, 89-121, 125, 130-160, 162-257, 276, 277, 281-288, 293-297, 300, 302-412, 419-552, and 554-566.
8. The conjugate of claim 1 , wherein the carrier peptide is selected from SEQ ID NOS: 130, 157-160, 251, 256, 386-388, and 540.
9. The conjugate of claim 1 , wherein the carrier peptide is SEQ ID NO: 159.
10. The conjugate of claim 1 , wherein the carrier peptide is of a formula selected from:
wherein:
Y is an integer from 4 to 7; and
R is selected from H, acetyl, benzoyl, and stearoyl.
11. The conjugate of claim 10 , wherein the carrier peptide is of the formula:
and Y is 6.
12. The conjugate of claim 1 , wherein the conjugate is selected from:
or a pharmaceutically acceptable salt of either of the foregoing, wherein:
X is an integer from 0 to 38;
R is selected from H, acetyl, benzoyl, and stearoyl;
R 1 is selected from H, acetyl, benzoyl, and stearoyl;
R 2 is selected from H, acetyl, benzoyl, stearoyl, trityl, and 4-methoxytrityl; and
each Pi is a purine or pyrimidine base-pairing moiety which taken together form a targeting base sequence,
wherein Xaa is the carboxy-terminal proline.
13. The conjugate of claim 12 , wherein X is 6 to 18.
14. The conjugate of claim 12 , wherein X is 6 to 14.
15. The conjugate of claim 12 , wherein X is 8 to 28.
16. The conjugate of claim 12 , wherein X is 10 to 23.
17. The conjugate of claim 12 , wherein X is 6 to 10.
18. The conjugate of claim 12 , wherein the carrier peptide is selected from SEQ ID NOS: 130, 157-160, 251, 256, 386-388, and 540.
19. The conjugate of claim 12 , wherein the carrier is SEQ ID NO: 159.
20. The conjugate of claim 12 , wherein each Pi is independently selected from adenine, cytosine, guanine, uracil, thymine, and inosine.
21. A compound selected from:
or a pharmaceutically acceptable salt of any of the foregoing, wherein:
X is an integer from 0 to 38;
Y is an integer from 4 to 9;
Z is 6 or 9;
R is selected from H, acetyl, benzoyl, and stearoyl;
R 1 is selected from H, acetyl, benzoyl, and stearoyl;
R 2 is selected from H, acetyl, benzoyl, stearoyl, trityl, and 4-methoxytrityl; and
each Pi is a purine or pyrimidine base-pairing moiety which taken together form a targeting base sequence.
22. The conjugate of claim 21 , wherein X is 6 to 18.
23. The conjugate of claim 21 , wherein X is 6 to 14.
24. The conjugate of claim 21 , wherein X is 8 to 28.
25. The conjugate of claim 21 , wherein X is 10 to 23.
26. The conjugate of claim 21 , wherein X is 6 to 10.
27. The compound of claim 21 , wherein each Pi is independently selected from adenine, cytosine, guanine, uracil, thymine, and inosine.
28. The compound of claim 21 , wherein the compound is:
or a pharmaceutically acceptable salt thereof.
29. The compound of claim 28 , wherein R is H.
30. The compound of claim 28 , wherein R is acetyl.
31. The conjugate of claim 28 , wherein X is 6 to 18.
32. The conjugate of claim 28 , wherein X is 6 to 14.
33. The conjugate of claim 28 , wherein X is 8 to 28.
34. The conjugate of claim 28 , wherein X is 10 to 23.
35. The conjugate of claim 28 , wherein X is 6 to 10.
36. The compound of claim 28 , wherein each Pi is independently selected from adenine, cytosine, guanine, uracil, thymine, and inosine.
37. The conjugate of claim 1 , wherein the conjugate is selected from:
or a pharmaceutically acceptable salt of either of the foregoing, wherein:
Z is an integer from 0 to 38;
R is selected from H, acetyl, benzoyl, and stearoyl;
R 1 is selected from H, acetyl, benzoyl, and stearoyl;
R 2 is selected from H, acetyl, benzoyl, stearoyl, trityl, and 4-methoxytrityl;
X, at each occurrence, is independently selected from:
wherein R 3 is selected
from H, methyl, and an electron pair; and
each Pi is a purine or pyrimidine base-pairing moiety which taken together form a targeting base sequence,
wherein Xaa is the carboxy-terminal proline.