Compositions for enhancing transport of molecules into cells

• US 20040265879A1
• Filed: 04/29/2004
• Published: 12/30/2004
• Est. Priority Date: 04/29/2003
• Status: Active Grant

• Current Assignee: Sarepta Therapeutics, Inc.
• Original Assignee: Avi Biopharma, Inc.
• Inventors: Iversen, Patrick L., Moulton, Hong M., Stein, David A., Nelson, Michelle H., Kroeker, Andrew D.
• Granted Patent: US 7,468,418 B2
• Time in Patent Office: Days
• US Class Current: 435/6.16
• CPC Class Codes: A61K 47/64 Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent peptidic linkers A61K47/65
• CPC Class Codes: A61K 49/0043 Fluorescein, used in vivo
• CPC Class Codes: A61K 49/0054 Macromolecular compounds, i.e. oligomers, polymers, dendrimers
• CPC Class Codes: A61K 49/0056 Peptides, proteins, polyamino acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/87 Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/314 Phosphoramidates
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring
• CPC Class Codes: C12N 2310/3513 Protein; Peptide
• CPC Class Codes: C12N 2320/32 Special delivery means, e.g. tissue-specific

Abstract

Compositions and methods for enhancing delivery of molecules, e.g. biological agents, into cells are described. The composition is a conjugate of the biological agent, preferably a nucleic acid analog having a substantially uncharged backbone, covalently linked to a peptide transporter moiety as described. Conjugation of the peptide transporter to a substantially uncharged nucleic acid analog, such as a morpholino oligomer, is also shown to enhance binding of the oligomer to its target sequence and enhance antisense activity.

Claims

1. A method for enhancing the ability of an nucleic acid analog having a substantially uncharged backbone and a targeting base sequence to bind to a target sequence in a nucleic acid, the method comprising

conjugating to the nucleic acid analog a peptide consisting of 8 to 16 subunits selected from X subunits, Y subunits, and optional Z subunits, including at least six X subunits, at least two Y subunits, and at most three Z subunits, where >

50% of said subunits are X subunits, and where

(a) each X subunit independently represents arginine or an arginine analog, said analog being a cationic α

-amino acid comprising a side chain of the structure R¹ N═

C(NH₂)R², where R¹ is H or R;

R² is R, NH₂, NHR, or NR₂, where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;

R¹ and R² may together form a ring; and

the side chain is linked to said amino acid via R¹ or R²;

(b) each Y subunit independently represents a neutral amino acid —

C(O)—

(CHR)_n—

NH—

, where (i) n is 2 to 7 and each R is independently H or methyl, or (ii) n is 1 and R is a neutral side chain selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said neutral side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every four carbon atoms; and

(c) each Z subunit independently represents an amino acid selected from alanine, asparagine, cysteine, glutamine, glycine, histidine, lysine, methionine, serine, and threonine.

3. The method of claim 1, wherein said nucleic acid analog is conjugated to said peptide via a Y subunit, a cysteine subunit, or an uncharged, non-amino acid linker moiety.

4. The method of claim 1, wherein said neutral amino acid subunit —

C(O)—

(CHR)_n—

NH—

, where n is 2 to 7 and each R is independently H or methyl, is of the form —

C(O)—

(CH₂)_n-1(CHR)—

NH—

.

5. The method of claim 1, wherein the peptide includes at least eight X subunits.

6. The method of claim 1, wherein said at least two Y subunits include

(i) two neutral, hydrophobic α

-amino acid subunits having side chains independently selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every six carbon atoms, and wherein said subunits are contiguous or are flanking a linker moiety, or

(ii) two neutral, hydrophobic amino acid subunits —

C(O)—

(CH₂)_n-1(CHR)—

NH—

, where n is 2 to 7 and R is H or methyl.

7. The method of claim 6, wherein each X is an arginine subunit.

8. The method of claim 1, wherein the peptide has exactly two Y subunits of type (i) which are contiguous or are flanking a cysteine subunit.

9. The method of claim 8, wherein each Y represents a hydrophobic ac-amino acid subunit having an aryl or aralkyl side chain.

10. The method of claim 9, wherein each Y is independently selected from the group consisting of phenylalanine, tyrosine, tryptophan, leucine, isoleucine, and valine.

11. The method of claim 9, wherein each Y is independently selected from phenylalanine and tyrosine.

12. The method of claim 11, wherein the peptide has the formula Arg₉Phe₂.

13. The method of claim 1, wherein each Y is a neutral, hydrophobic amino acid subunit —

CO—

(CH₂)_n-1CHR—

NH—

, where n is 2 to 7 and R is H.

14. The method of claim 13, wherein n is 5, such that Y is a 6-aminohexanoic acid subunit.

15. The method of claim 14, wherein each X is an arginine subunit.

16. The method of claim 14, wherein said peptide comprises arginine dimers alternating with single Y subunits.

17. The method of claim 16, wherein the peptide has the formula (RYR)₄.

18. The method of claim 16, wherein the peptide has the formula (RRY)₄, and the nucleic acid analog is linked to a terminal Y subunit.

19. The method of claim 1, wherein the nucleic acid analog is a morpholino oligomer, comprising morpholino subunits linked by phosphorus-containing linkages between the morpholino nitrogen of one subunit and an exocyclic carbon at the morpholino 3-position of an adjacent subunit.

20. The method of claim 19, wherein said morpholino subunits are joined by uncharged phosphorodiamidate linkages, in accordance with the structure:

21. The method of claim 1, wherein said conjugating forms a peptide-oligomer conjugate which is effective to:

(a) inhibit expression of targeted mRNA in a protein expression system;

(b) inhibit splicing of targeted pre-mRNA;

or

(c) inhibit replication of a virus, by targeting cis-acting elements which control nucleic acid replication or mRNA transcription of the virus;

to a greater degree than said oligomer in unconjugated form.

65. A composition for intracellular delivery of a substantially uncharged nucleic acid analog in vivo, comprising a conjugate as provided in claim 1 and a suspension of insoluble gas-containing microbubbles in an aqueous vehicle comprising at least one filmogenic compound selected from a protein, surfactant, lipid, polysaccharide, and combinations thereof

66. The composition of claim 65, wherein the microbubbles are suspended in an aqueous vehicle comprising albumin, and the insoluble gas is selected from the group consisting of perfluoromethane, perfluoroethane, perfluoropropane, perfluorobutane, and perfluoropentane.

2. The method of claim 2, wherein said peptide, when conjugated to an antisense oligomer having said substantially uncharged backbone, is effective to enhance the binding of the antisense oligomer to its target sequence, relative to the antisense oligomer in unconjugated form, as evidenced by:

(i) a decrease in expression of an encoded protein, when binding of the antisense oligomer to its target sequence is effective to block a translation start codon for the encoded protein, or

(ii) an increase in expression of an encoded protein, when binding of the antisense oligomer to its target sequence is effective to block an aberrant splice site in a pre-mRNA which encodes said protein when correctly spliced.

22. A peptide-nucleic acid analog conjugate, comprising

a nucleic acid analog having a substantially uncharged backbone and a targeting base sequence, and

covalently linked to the nucleic acid analog, a peptide consisting of 8 to 16 subunits selected from X subunits, Y subunits, and optional Z subunits, including at least eight X subunits, at least two Y subunits, and at most three Z subunits, wherein >

50% of said subunits are X subunits, and where

(a) each X subunit independently represents arginine or an arginine analog, said analog being a cationic α

-amino acid subunit comprising a side chain of the structure R¹N═

C(NH₂)R², where R¹ is H or R;

R² is R, NH₂, NHR, or NR₂, where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;

R¹ and R² may together form a ring; and

the side chain is linked to said amino acid subunit via R¹ or R²;

(b) said at least two Y subunits include

(i) two neutral α

-amino acid subunits having side chains independently selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every four carbon atoms, and wherein said subunits are contiguous or are flanking a linker moiety, or

(ii) two neutral, hydrophobic amino acid subunits —

C(O)—

(CH₂)_n-1(CHR)—

NH—

, where n is 2 to 7 and R is H or methyl; and

(c) Z represents an amino acid subunit selected from alanine, asparagine, cysteine, glutamine, glycine, histidine, lysine, methionine, serine, and threonine.

23. The conjugate of claim 22, wherein said peptide, when conjugated to an antisense oligomer having said substantially uncharged backbone, is effective to enhance the binding of the antisense oligomer to its target sequence, relative to the antisense oligomer in unconjugated form, as evidenced by:

(i) a decrease in expression of an encoded protein, when binding of the antisense oligomer to its target sequence is effective to block a translation start codon for the encoded protein, or

(ii) an increase in expression of an encoded protein, when binding of the antisense oligomer to its target sequence is effective to block an aberrant splice site in a pre-mRNA which encodes said protein when correctly spliced.

24. The conjugate of claim 22, wherein said peptide, when conjugated to an antisense oligomer having said substantially uncharged backbone, is effective to enhance the binding of the antisense oligomer to its target sequence, relative to the antisense oligomer in unconjugated form, as evidenced by:

(i) a decrease in expression of an encoded protein in a cell free translation system, when binding of the antisense oligomer to its target sequence is effective to block a translation start codon for the encoded protein, or

(ii) an increase in expression of an encoded protein in a cell free translation system, when binding of the antisense oligomer to its target sequence is effective to block an aberrant splice site in a pre-mRNA which encodes said protein when correctly spliced.

25. The conjugate of claim 22, wherein said peptide is effective to enhance the transport of the nucleic acid analog into a cell, relative to the analog in unconjugated form.

26. The conjugate of claim 22, wherein said nucleic acid analog is conjugated to said peptide via a linker moiety selected from a Y subunit, a cysteine subunit, and an uncharged, non-amino acid linker moiety.

27. The conjugate of claim 22, wherein for each X, the side chain moiety is guanidyl.

28. The conjugate of claim 27, wherein each X is an arginine subunit.

29. The conjugate of claim 22, wherein the peptide has exactly two Y subunits of type (i) which are contiguous or are flanking a cysteine subunit.

30. The conjugate of claim 29, wherein each Y represents a hydrophobic α

-amino acid subunit having an aryl or aralkyl side chain.

31. The conjugate of claim 30, wherein each Y is independently selected from the group consisting of phenylalanine, tyrosine, tryptophan, leucine, isoleucine, and valine.

32. The conjugate of claim 31, wherein each Y is independently selected from phenylalanine and tyrosine.

33. The conjugate of claim 32, consisting of arginine subunits, phenylalanine subunits, a linker moiety, and the nucleic acid analog.

34. The conjugate of claim 33, wherein the peptide has the formula Arg₉Phe₂.

35. The conjugate of claim 22, wherein each Y is —

C(O)—

(CH₂)_n-1(CHR)—

NH—

, where n is 2 to 7 and R is H.

36. The conjugate of claim 35, wherein n is 5, such that Y is a 6-aminohexanoic acid subunit.

37. The conjugate of claim 36, wherein each X is an arginine subunit.

38. The conjugate of claim 36, wherein the peptide comprises arginine dimers alternating with single Y subunits.

39. The conjugate of claim 38, wherein the peptide has the formula (RYR)₄.

40. The conjugate of claim 38, wherein the peptide has the formula (RRY)₄, and the nucleic acid analog is linked to a terminal Y subunit.

41. The conjugate of claim 22, wherein the nucleic acid analog is a morpholino oligomer, comprising morpholino subunits linked by phosphorus-containing linkages between the morpholino nitrogen of one subunit and an exocyclic carbon at the morpholino 3-position of an adjacent subunit.

42. The conjugate of claim 41, wherein said morpholino subunits are joined by uncharged phosphorodiamidate linkages, in accordance with the structure:

43. The conjugate of claim 29, wherein said conjugate is effective to:

(a) inhibit expression of targeted mRNA in a protein expression system;

(b) inhibit splicing of targeted pre-mRNA;

or

(c) inhibit replication of a virus, by targeting cis-acting elements which control nucleic acid replication or mRNA transcription of the virus;

to a greater degree than said oligomer in unconjugated form.

44. The conjugate of claim 43, wherein said inhibition is in a cell free system.

45. A method for enhancing cell uptake of a pharmacological agent, the method comprising

conjugating to the agent a peptide consisting of 8 to 16 subunits selected from X subunits, Y subunits, and optional Z subunits, including at least six X subunits, at least two Y subunits, and at most three Z subunits, wherein >

50% of said subunits are X subunits, and where

(a) each X subunit independently represents arginine or an arginine analog, said analog being a cationic α

-amino acid comprising a side chain of the structure R¹N═

C(NH₂)R², where R¹ is H or R;

R² is R, NH₂, NHR, or NR₂, where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;

R¹ and R² may together form a ring; and

the side chain is linked to said amino acid via R¹ or R²;

(b) each Y subunit independently represents a neutral amino acid —

C(O)—

(CHR)—

NH—

, where R is a neutral side chain selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said neutral side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every four carbon atoms; and

(c) each Z subunit independently represents an amino acid selected from alanine, asparagine, cysteine, glutamine, glycine, histidine, lysine, methionine, serine, and threonine.

46. The method of claim 45, wherein said agent is conjugated to said peptide via a Y subunit, a cysteine subunit, or an uncharged, non-amino acid linker moiety.

47. The method of claim 45, wherein said at least two Y subunits include two neutral, hydrophobic α

-amino acid subunits having side chains independently selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every six carbon atoms, and wherein said subunits are contiguous or are flanking a linker moiety.

48. The method of claim 47, wherein each X is an arginine subunit.

49. The method of claim 45, wherein the peptide has exactly two Y subunits which are contiguous or are flanking a cysteine subunit.

50. The method of claim 49, wherein each Y represents a hydrophobic α

-amino acid subunit having an aryl or aralkyl side chain.

51. The method of claim 50, wherein each Y is independently selected from the group consisting of phenylalanine, tyrosine, tryptophan, leucine, isoleucine, and valine.

52. The method of claim 51, wherein the peptide has the formula Arg₉Phe₂.

53. A conjugate comprising a pharmacological agent covalently linked to a peptide, wherein the peptide consists of 8 to 16 subunits selected from X subunits, Y subunits, and optional Z subunits, including at least six X subunits, at least two Y subunits, and at most three Z subunits, wherein >

50% of said subunits are X subunits, and where

(a) each X subunit independently represents arginine or an arginine analog, said analog being a cationic α

-amino acid comprising a side chain of the structure R¹ N═

C(NH₂)R², where R¹ is H or R;

R² is R, NH₂, NHR, or NR₂, where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;

R¹ and R² may together form a ring; and

the side chain is linked to said amino acid via R¹ or R²;

(b) each Y subunit independently represents a neutral amino acid —

C(O)—

(CHR)—

NH—

, where R is a neutral side chain selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said neutral side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every *four carbon atoms; and

(c) each Z subunit independently represents an amino acid selected from alanine, asparagine, cysteine, glutamine, glycine, histidine, lysine, methionine, serine, and threonine.

54. The conjugate of claim 53, wherein said peptide is effective to enhance the transport of the agent into a cell, relative to the agent in unconjugated form.

55. The conjugate of claim 53, wherein said agent is conjugated to said peptide via a Y subunit, a cysteine subunit, or an uncharged, non-amino acid linker moiety.

56. The conjugate of claim 53, wherein the peptide includes at least eight X subunits.

57. The conjugate of claim 53, wherein said at least two Y subunits include two neutral, hydrophobic α

-amino acid subunits having side chains independently selected from substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, and aralkyl, wherein said side chain, when selected from substituted alkyl, alkenyl, and alkynyl, includes at most one heteroatom for every six carbon atoms, and wherein said subunits are contiguous or are flanking a linker moiety.

58. The conjugate of claim 53, wherein for each X, the side chain moiety is guanidyl.

59. The conjugate of claim 58, wherein each X is an arginine subunit.

60. The conjugate of claim 53, wherein the peptide has exactly two Y subunits which are contiguous or are flanking a cysteine subunit.

61. The conjugate of claim 60, wherein each Y represents a hydrophobic α

-amino acid subunit having an aryl or aralkyl side chain.

62. The conjugate of claim 61, wherein each Y is independently selected from the group consisting of phenylalanine, tyrosine, tryptophan, leucine, isoleucine, and valine.

63. The conjugate of claim 61, wherein each Y is independently selected from phenylalanine and tyrosine.

64. The conjugate of claim 63, wherein the peptide has the formula Arg₉Phe₂.

67. An antisense composition having

(i) a plurality of subunits connected by intersubunit linkages, and supporting a sequence of bases effective to hybridize to a complementary-sequence target polynucleotide, to form a target/antisense duplex;

and

(ii) carried on at least six contiguous intersubunit linkages, a charged moiety of the structure R¹N═

C(NH₂)R², where R¹ is H or R;

R² is R, NH₂, NHR, or NR₂, where R is lower alkyl or lower alkenyl and may further include oxygen or nitrogen;

R¹ and R² may together form a ring; and

the side chain moiety is linked to said amino acid subunit via R¹ or R².

68. The composition of claim 67, wherein the subunits are morpholino subunits, and the linkages are phosphorodiamidate linkages.