Multiple oligonucleotide moieties on peptide carrier

Patent metadata

Field	Value
Publication number	US-11103587-B2
Application number	US-201916265883-A
Country	US
Kind code	B2
Filing date	Feb 1, 2019
Priority date	May 23, 2014
Publication date	Aug 31, 2021
Grant date	Aug 31, 2021

Abstract

The present disclosure relates to antisense oligonucleotides (AONs), such as phosphorodiamidate morpholino oligonucleotides (PMOs). The present disclosure further relates to the conjugation of multiple PMOs to cationic cell penetrating peptides (CPPs) to enhance the uptake of PMOs into skeletal and cardiac muscle cells.

First claim

What is claimed is:

1. A peptide-antisense oligonucleotide (peptide-AON) conjugate comprising a polycationic peptide covalently conjugated to at least two antisense oligonucleotides (AONs),
wherein each AON comprises:
(a) 15 to 30 subunits of a phosphorodiamidate morpholino (PMO),
wherein each subunit comprises a naturally occurring purine or pyrimidine nucleotide base selected from the group consisting of C, G, A, and T;

(b) a nucleotide base sequence that is complementary to at least 8 contiguous bases of a target pre-mRNA, mRNA, microRNA, or long non-coding RNA of a gene;
(c) from 0 to 3 repeating subunits where the naturally occurring purine nucleotide base is G;
(d) less than 60% of said subunits where the naturally occurring purine or pyrimidine nucleotide base is C or G; and
(e) a non-self-complimentary sequence;
wherein the polycationic peptide is a cationic cell penetrating peptide (CPP), and wherein the peptide-AON conjugate comprises a cleavable linker containing a cleavage motif.

2. The peptide-AON conjugate of claim 1 , wherein the cleavable linker comprises FK or FX at the P1/P1′ position, where X is any naturally occurring amino acid.

3. The peptide-AON conjugate of claim 1 , wherein the cleavage motif is a hydrolytic enzyme cleavage motif.

4. The peptide-AON conjugate of claim 1 , wherein the CPP comprises:
(a) RXRRXRRXRRXRXB (SEQ ID NO: 43),
where R is D-arginine, X is 6-aminohexanoic acid, and B is β-alanine; or

(b) RXRRBRRXRRBRXB (SEQ ID NO: 44),
wherein R is D-arginine, X is 6-aminohexanoic acid, and B is β-alanine.

5. The peptide-AON conjugate of claim 1 , wherein the CPP comprises the formula: variable sequence-spacer-linker,
wherein the variable sequence is Ac—R(O)nR, wherein n≥7; wherein O is a sequence of residues selected from R, X, and Z; wherein R is L-arginine, X is 3-cis-aminocyclohexane, and Z is cis-2-aminocyclopentane-1-carbonyl, and
wherein the variable sequence:
(i) comprises an α-, β-, γ-, or δ-amino acid, or a cycloalkane structure;
(ii) causes the compound to be targeted to the nucleus;
(iii) causes the compound to be targeted to the cytosol; or
(iv) causes the compound to be targeted to the mitochondria.

6. The peptide-AON conjugate of claim 1 , wherein the polycationic peptide comprises the formula: variable sequence-spacer-linker,
wherein the variable sequence is Ac—R(O)nR, wherein n≥7; wherein O is a sequence of residues selected from R, X, and Z; wherein R is L-arginine, X is 3-cis-aminocyclohexane, and Z is cis-2-aminocyclopentane-1-carbonyl, and
wherein the spacer:
(i) comprises an aminohexanoic acid (Ahx); or

(ii) comprises (Ahx)B, wherein B is selected from β-alanine or β-glycine.

7. The peptide-AON conjugate of claim 1 , wherein the polycationic peptide comprises the formula variable sequence-spacer-linker,
wherein the variable sequence is Ac—R(O)nR, wherein n≥7; wherein O is a sequence of residues selected from R, X, and Z; wherein R is L-arginine, X is 3-cis-aminocyclohexane, and Z is cis-2-aminocyclopentane-1-carbonyl, and
wherein the linker:
(i) comprises the sequence FS;
(ii) comprises the sequence FSQ;
(iii) comprises the sequence FSQK; or
(iv) comprises the sequence FxyB, wherein F is phenylalanine, x is any amino acid and y is selected from glutamic acid (E), aspartic acid (D), lysine (K), serine (S), and threonine (T) or a non-natural analog of E, D, K, S or T, and B is β-alanine.

8. The peptide-AON conjugate of claim 1 , wherein the CPP comprises the formula: variable sequence-spacer-linker,
wherein the variable sequence is Ac—R(O)nR, wherein n≥7; wherein O is a sequence of residues selected from R, X, and Z; wherein R is L-arginine, X is 3-cis-aminocyclohexane, and Z is cis-2-aminocyclopentane-1-carbonyl,
wherein the spacer comprises an aminohexanoic acid (Ahx) and
wherein the linker comprises FSQG-OH.

9. The peptide-AON conjugate of claim 1 , wherein the CPP comprises the formula: variable sequence-spacer-linker,
wherein the variable sequence is Ac—R(O)nR, wherein n≥7; wherein O is a sequence of residues selected from R, X, and Z; wherein R is L-arginine, X is 3-cis-aminocyclohexane, and Z is cis-2-aminocyclopentane-1-carbonyl,
wherein the linker comprises the sequence FxyB, wherein F is phenylalanine, x is any amino acid and y is selected from glutamic acid (E), aspartic acid (D), lysine (K), serine (S), and threonine (T), and B is β-alanine; and wherein y is a non-natural analog of threonine; and wherein n is 7, and
wherein the spacer is (Ahx).

10. The peptide-AON conjugate of claim 1 , wherein the CPP comprises a sequence selected from the group consisting of: SEQ ID NOs. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11.

11. The peptide-AON conjugate of claim 1 , wherein the CPP is selected from the group consisting of:

(i) No. 1216:

(SEQ ID NO.: 56)

Ac-(RXRRBR) 2 XFD(d-Glu)EG-OH;

(ii) No. 1218:

(SEQ ID NO.: 58)

Ac-E(RXRRBR) 2 XFKG-OH;

(iii) No. 1219:

(SEQ ID NO.: 59)

Ac-E(RXRRBR) 2 XFKEG-OH;

(iv) No. 1220:

(SEQ ID NO.: 60)

Ac-E(RXRRBR) 2 XFK(d-Glu)EG-OH;

(v) No. 1221:

(SEQ ID NO.: 61)

Ac-(d-Glu)E(RXRRBR) 2 XFKG-amide

(vi) No. 1222:

(SEQ ID NO.: 62)

Ac-(dGlu)E(RXRRBR) 2 XFKG-OH;

(vii) No. 1223:

(SEQ ID NO.: 63)

Ac-(d-Glu)E(RXRRBR) 2 XFKEG-OH;

or

(viii) No. 1224:

(SEQ ID NO.: 64)

Ac-(d-Glu)E(RXRRBR) 2 XFK((d-Glu)EG-OH,

Assignees

• Genzyme Corp

Inventors

• Weeden Timothy E
• Nelson Carol A
• Wentworth Bruce M
• Clayton Nicholas P
• Leger Andrew

Classifications

• C12N2320/32

  Special delivery means, e.g. tissue-specific · CPC title

• A61K47/549 Primary

  Sugars, nucleosides, nucleotides or nucleic acids · CPC title

• C12N2310/3145

  with the nitrogen in 3' or 5'-position · CPC title

• C12N2310/3233

  Morpholino-type ring · CPC title

• C12N15/111 Primary

  General methods applicable to biologically active non-coding nucleic acids · CPC title