US2023220388A1PendingUtilityA1
Multimeric oligonucleotides with divided strands
Est. expiryApr 30, 2040(~13.8 yrs left)· nominal 20-yr term from priority
Inventors:Jonathan Miles Brown
C12N 15/113C12N 15/1137C12N 2310/14C12N 2310/51C12N 2310/3519C12N 2330/30C12N 15/111A61K 31/713C12N 2310/314C12N 2310/321
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Claims
Abstract
The present disclosure relates to multimeric oligonucleotides comprising subunits, each of the subunits independently comprises a single-stranded or double-stranded oligonucleotide. Each of the subunits is joined to another subunit by a covalent linker, and at least one subunit comprises at least one partial single-stranded oligonucleotide. The present disclosure also relates to methods of synthesizing the multimeric oligonucleotides and the methods of using the multimeric oligonucleotides disclosed herein.
Claims
exact text as granted — not AI-modifiedWhat is claimed is:
1 . A multimeric oligonucleotide comprising subunits, wherein:
each of the subunits independently comprises a single-stranded or double-stranded oligonucleotide; each of the subunits is joined to another subunit by a covalent linker; and at least one subunit comprises at least one partial single-stranded oligonucleotide.
2 . The multimeric oligonucleotide of claim 1 , wherein at least one subunit comprises two partial single-stranded oligonucleotides annealed to a complementary strand to form a double-stranded subunit.
3 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 1:
wherein:
is a single-stranded oligonucleotide;
is a partial single-stranded oligonucleotide; and
● is a covalent linker.
4 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 2:
wherein:
is a single-stranded oligonucleotide;
is a partial single-stranded oligonucleotide; and
● is a covalent linker.
5 . A multimeric oligonucleotide comprising Structure 3:
wherein: each
is independently a partial single-stranded oligonucleotide; and
● is a covalent linker.
6 . The multimeric oligonucleotide of claim 5 , wherein Structure 3 is a homodimer.
7 . The multimeric oligonucleotide of claim 5 , wherein Structure 3 is a heterodimer.
8 . The multimeric oligonucleotide of claim 1 , wherein at least one subunit comprises Structure 4:
wherein:
each is a partial single-stranded oligonucleotide;
• is a covalent linker joined to a partial single-stranded oligonucleotide and an adjoining oligonucleotide subunit; and
is a complementary strand.
9 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 5:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining a single-stranded oligonucleotide to a partial single-stranded oligonucleotide; and
is a complementary strand.
10 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 6:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
● each is a covalent linker joining adjacent oligonucleotides;
each is a complementary strand; and
each of a, h, c, d, e, f, g, h, i, j and k is independently an integer greater than or equal to zero, with the proviso that at least one of c, e, h, and j is greater than or equal to 1.
11 . The multimeric oligonucleotide of claim 10 , wherein each of a, h, c, d, e, f, g, h, i, j and k is independently an integer in the range of 0 to 10, with the proviso that at least one of c, e, h and j is greater than or equal to 1.
12 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 7:
wherein:
are each a single-stranded oligonucleotide;
are each a complementary strand;
are each a partial single-stranded oligonucleotide;
● are each a covalent linker;
m and n are each independently an integer greater than or equal to 1; and
o is an integer greater than or equal to 0.
13 . The multimeric oligonucleotide of claim 12 , wherein m and n are each independently an integer in the range of 1 to 10; and o is an integer in the range of 0 to 10.
14 . The multimeric oligonucleotide of claim 1 , wherein the multimeric, oligonucleotide comprises Structure 8
wherein:
are each a single-stranded oligonucleotide;
are each a complementary strand;
are each a partial single-stranded oligonucleotide;
● are each covalent linkers; and
p and q are each independently an integer greater than or equal to zero.
15 . The multimeric oligonucleotide of claim 14 , wherein p and q are each independently an integer in the range of 0 to 10; or wherein p and q are each independently an integer in the range of 0 to 3.
16 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 9:
wherein:
are each a single-stranded oligonucleotide;
are each a complementary strand;
are each a partial single-stranded oligonucleotide;
● are each a covalent linker;
r is an integer greater than or equal to 1; and
s is an integer greater than or equal to 0.
17 . The multimeric oligonucleotide of claim 16 , wherein r is an integer in the range of 1 to 10 and s is an integer in the range of 0 to 10; or wherein r is an integer in the range of 1 to 3 and s is 0 or 1.
18 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 10:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides; and
each is a complementary strand.
19 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 11:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides;
each is a complementary strand.
20 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 12:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides; and
each is a complementary strand.
21 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 13:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides; and
each is a complementary strand.
22 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 14:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides; and
each is a complementary strand.
23 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 15:
wherein:
each is a single-stranded oligonucleotide;
each is a partial single-stranded oligonucleotide;
each ● is a covalent linker joining adjacent oligonucleotides; and
each is a complementary strand.
24 . The multimeric oligonucleotide of claim 1 , wherein the multimeric oligonucleotide comprises Structure 16:
wherein each
is a single-stranded oligonucleotide;
is a complementary strand;
is a partial single-stranded oligonucleotide;
● is a covalent linker; and
t and u are each independently an integer greater than or equal to 0 with the proviso that at least one of t and u are an integer greater than or equal to 1.
25 . The multimeric oligonucleotide of claim 24 , wherein t and u are each independently an integer in the range of 0 to 10 with the proviso that at least one of t and u are an integer greater than or equal to 1; or wherein t and u are each independently an integer in the range of 0 to 3 with the proviso that at least one oft and u are an integer greater than or equal to 1.
26 . The multimeric oligonucleotide of any of claims 1 - 25 , wherein each partial single-stranded oligonucleotide is 5-14 nucleotides in length.
27 . The multimeric oligonucleotide of any of claims 1 - 26 , wherein at least two subunits are active against different cellular targets.
28 . The multimeric oligonucleotide of claim 27 , wherein all of the subunits are active against different cellular targets.
29 . The multimeric oligonucleotide of any of claims 1 - 26 , wherein at least two subunits are active against the same cellular target.
30 . The multimeric oligonucleotide of claim 29 , wherein all of the subunits are active against different cellular targets.
31 . The multimeric oligonucleotide of any of claims 1 - 30 , wherein the multimeric oligonucleotide comprises four or more subunits.
32 . The multimeric oligonucleotide of claim 31 , wherein the multimeric oligonucleotide comprises four, five, six, seven, eight, nine, or ten subunits.
33 . The multimeric oligonucleotide of any of claims 1 - 32 , wherein each nucleic acid in the multimeric oligonucleotide is RNA, DNA, or an artificial or non-natural nucleic acid analog.
34 . The multimeric oligonucleotide of any of claims 1 - 33 , wherein at least one subunit is siRNA, saRNA, or miRNA.
35 . The multimeric oligonucleotide of claim 34 , wherein all of the subunits are siRNA.
36 . The multimeric oligonucleotide of claim 34 , wherein all of the subunits are saRNA.
37 . The multimeric oligonucleotide of claim 34 , wherein all of the subunits are miRNA.
38 . The multimeric oligonucleotide of any of claims 1 - 33 , wherein at least one subunit is a single-stranded subunit.
39 . The multimeric oligonucleotide of claim 38 , wherein the at least one single-stranded subunit is an antisense oligonucleotide.
40 . The multimeric oligonucleotide of any one of claims 1 - 39 , wherein at least one covalent linker ● is a cleavable covalent linker.
41 . The multimeric oligonucleotide of claim 40 , wherein the cleavable covalent linker comprises an acid cleavable bond, a reductant cleavable bond, a bio-cleavable bond, or an enzyme cleavable bond.
42 . The multimeric oligonucleotide of claim 40 or 41 , wherein the cleavable covalent linker is cleavable under intracellular conditions.
43 . The multimeric oligonucleotide of any of claims 1 - 42 , wherein each covalent linker is, independently, a disulfide bond or a compound of Structure 25:
wherein:
S is attached by a covalent bond or by a linker to an oligonucleotide subunit;
each R 1 is independently a C 2 -C 10 alkyl, C 2 -C 10 alkoxy, or C 1 -C 10 aryl group;
R 2 is a thiopropionate or disulfide group; and
each X is independently selected from:
44 . The multimeric oligonucleotide of claim 43 , wherein the compound of Structure 25 is
wherein each terminal S is attached by a covalent bond or by a linker to an oligonucleotide subunit.
45 . The multimeric oligonucleotide of claim 43 , wherein the compound of Structure 25 is a compound according to Structure 26:
wherein each terminal S is attached by a covalent bond or by a linker to an oligonucleotide subunit.
46 . The multimeric oligonucleotide of claim 43 , wherein the compound of Structure 25 is a compound according to Structure 27:
wherein each terminal S is attached by a covalent bond or by a linker to an oligonucleotide subunit.
47 . The multimeric oligonucleotide of claim 43 , wherein the compound of Structure 25 is a compound according to Structure 28:
wherein each terminal S is attached by a covalent bond or by a linker to an oligonucleotide subunit.
48 . The multimeric oligonucleotide any of claims 43 - 47 , wherein the covalent linker of Structure 25 is formed from a covalent linker precursor according to Structure 29:
wherein each R is independently a C 2 -C 10 alkyl, C 2 -C 10 alkoxy, or C 1 -C 10 aryl group; and
R 2 is a thiopropionate or disulfide group.
49 . The multimeric oligonucleotide of any of claims 1 - 48 , wherein at least one covalent linker is attached to the 3′ or 5′ terminus of an oligonucleotide subunit.
50 . The multimeric oligonucleotide of claim 49 , wherein all covalent linkers are attached to the 3′ or 5′ terminus of an oligonucleotide subunit.
51 . The multimeric oligonucleotide of any of claims 1 - 49 , wherein at least one covalent linker is attached to an internal nucleotide of an oligonucleotide subunit.
52 . The multimeric oligonucleotide of any of claims 1 - 51 , wherein at least one covalent linker e comprises a nucleotide linker.
53 . The multimeric oligonucleotide of claim 52 , wherein the nucleotide linker is between 2-6 nucleotides in length.
54 . The multimeric oligonucleotide of any of claims 1 - 53 , wherein each covalent linker is the same.
55 . The multimeric oligonucleotide of any of claims 1 - 53 wherein at least one covalent linker ● is different from the other covalent linkers.
56 . The multimeric oligonucleotide of any of claims 1 - 55 , at least two subunits are joined by a covalent linker ● between the 3′ end of a first subunit and the 3′ of a second subunit.
57 . The multimeric oligonucleotide of any of claims 1 - 56 , wherein at least two subunits are joined by a covalent linker ● between the 5′ end of a first subunit and the 3′ of a second subunit.
58 . The multimeric oligonucleotide as in any of claims 1 - 57 , wherein at least two subunits are joined by a covalent linker ● between the 5′ end of a first subunit and the 5′ of a second subunit.
59 . The multimeric oligonucleotide of any of claims 1 - 58 , further comprising a chemical or biological moiety that is not an oligonucleotide.
60 . The multimeric oligonucleotide as in any of claims 1 - 59 , wherein the multimeric oligonucleotide is at least 75, 80, 85, 90, 95, 96, 97, 98, 99, or 100% pure.
61 . A method of synthesizing a multimeric oligonucleotide comprising Structure 16:
wherein each is an single-stranded oligonucleotide, each is a partial single-stranded oligonucleotide, each is a complementary strand; each ● is a covalent linker joining adjacent oligonucleotides, and t and u are each independently an integer greater than or equal to 1;
the method comprising annealing Structure 17
and Structure 18
with complementary strands , thereby forming Structure 16.
62 . A method of synthesizing a multimeric oligonucleotide comprising Structure 8:
wherein each is a single-stranded oligonucleotide, each is a partial single-stranded oligonucleotide, each is a complementary strand; each ● is a covalent linker joining adjacent oligonucleotides, and p and q are each independently an integer greater than or equal to 1;
the method comprising annealing Structure 19,
Structure 20,
and one or more of Structure 21,
with complementary strands , thereby forming Structure 8.
63 . A method of synthesizing a multimeric oligonucleotide comprising Structure 9A:
wherein each is a single-stranded oligonucleotide, each is a partial single-stranded oligonucleotide, each is a complementary strand; each ● is a covalent linker joining adjacent oligonucleotides; and r and s are each independently an integer greater than or equal to the method comprising annealing Structure 22
and Structure 23
and one or more of Structure 24
with complementary strands , thereby forming Structure 9A.
64 . A method of synthesizing a multimeric oligonucleotide comprising Structure 9B:
wherein each is a single-stranded oligonucleotide; each is a partial single-stranded oligonucleotide; each is a complementary strand; each • is a covalent linker joining adjacent oligonucleotides; and r is an integer greater than or equal to 1;
the method comprising annealing Structure 22,
and one or more of Structure 24
and a partial single-stranded oligonucleotide with complementary strands , thereby forming Structure 9B.
65 . A composition comprising the multimeric oligonucleotide of any of claims 1 - 60 and a pharmaceutically acceptable excipient.
66 . A composition comprising the multimeric oligonucleotide of any of claims 1 - 60 for use in the manufacture of a medicament.
67 . A method for treating a subject comprising administering to the subject an effective amount of the multimeric oligonucleotide of any of claims 1 - 60 .Cited by (0)
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