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US 2024/0309372 A1Published application
Stabilization of oligonucleotide and oligonucleotide-protein complex using alkylated phosphate
AssigneeUniversity of Massachusetts
InventorsKen Yamada, Anastasia Khvorova
Life of this patent
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Abstract
Provided herein are stable, modified oligonucleotides comprising a 5′-alkyl phosphate or derivatives thereof and methods for preparing the same.
Claims20
A modified oligonucleotide or a pharmaceutically acceptable salt thereof comprising a 5′ end, a 3′ end, and at least one modified intersubunit linkage of Formula I:
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, or SH;
- Z is O or O(CH2)n, wherein n is 1 to 10;
- R1 is C1-C30 alkyl, C2-C30 alkenyl, C2-C30 alkynyl, (C1-C6 alkyl-O—C1-C6 alkyl)1-10, C1-C30 heteroalkyl, C3-C12 cycloalkyl, C3-C12 heterocycloalkyl, C6-C12 aryl, C5-C12 heteroaryl, C1-C60 alkylaryl, C1-C60 alkylheteroaryl, or C1-C6 alkyamine, any of which is optionally substituted with one, two, or three substituents selected from R4;
- R2 is OH, SH, NH2, or is a linker attached to a solid support;
- R3 is alkyl, allyl, or aryl;
- and
- each R4 is independently OH, OPO4, C(O)C1-C6 alkyl, C(O)C3-C6 heterocycloalkyl, C5-C12 heteroaryl, C6-C12 aryl, halo, C2-C6 alkenyl, or C2-C6 alkynyl, wherein C1-C6 alkyl is optionally substituted with one, two, or three substituents selected from NH2, OH, phenyl, phenyl-OH, and C5-C12 heteroaryl;
- alternatively, R1 is selected from:
- wherein:
- m is 2, 3, 4, 5, or 6;
- n is an integer between 1 and 20;
- V is absent or CH2;
- R5 is an amino acid side chain;
- and
- R6 is absent, acetyl, or benzoyl.
16 more elements
A method of synthesizing a modified oligonucleotide or a pharmaceutically acceptable salt thereof comprising a 5′ end, a 3′ end, and at least one modified intersubunit linkage of Formula I:
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, or SH;
- Z is O or O(CH2)n, wherein n is 1 to 10;
- R1 is C1-C30 alkyl, C2-C30 alkenyl, C2-C30 alkynyl, (C1-C6 alkyl-O—C1-C6 alkyl)1-10, C1-C30 heteroalkyl, C3-C12 cycloalkyl, C3-C12 heterocycloalkyl, C6-C12 aryl, C5-C12 heteroaryl, C1-C60 alkylaryl, C1-C60 alkylheteroaryl, or C1-C6 alkyamine, any of which is optionally substituted with one, two, or three substituents selected from R4;
- R2 is OH, SH, NH2, or is attached to a solid support;
- R3 is alkyl, allyl, or aryl;
- and
- each R4 is independently OH, OPO4, C(O)C1-C6 alkyl, C(O)C3-C6 heterocycloalkyl, C5-C12 heteroaryl, C6-C12 aryl, halo, C2-C6 alkenyl, or C2-C6 alkynyl, wherein C1-C6 alkyl is optionally substituted with one, two, or three substituents selected from NH2, OH, phenyl, phenyl-OH, and C5-C12 heteroaryl;
- alternatively, R1 is selected from:
- wherein:
- m is 2, 3, 4, 5, or 6;
- n is an integer between 1 and 20;
- V is absent or CH2;
- R5 is an amino acid side chain;
- and
- R6 is absent, acetyl, or benzoyl,
- the method comprising:
- (a) contacting a compound of Formula (II);
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, or SH;
- Z is O or O(CH2)n, wherein n is 1 to 10;
- R2 is OH, SH, NH2, or is attached to a solid support;
- R3 is alkyl, allyl, or aryl;
- R7 is a protecting group;
- and
- Q is OH or (CH2)nOH, wherein n is 1 to 10;
- with a chlorophosphoramidite of Formula (III)
- to form the compound of Formula (IV):
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, and SH;
- Z is O or O(CH2)n wherein n is 1 to 10;
- R2 is OH, SH, NH2, or is attached to a solid support;
- and
- R7 is a protecting group;
- (b) contacting the compound of Formula (IV) with an alcohol to form a compound of Formula (V):
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, and SH;
- Z is O or O(CH2)n, wherein n is 1 to 10;
- R2 is OH, SH, NH2, or is attached to a solid support;
- R7 is a protecting group;
- and
- R1 is defined supra;
- (c) contacting the compound of Formula (V) with an oxidizing agent to form a compound of Formula (VI):
- wherein:
- B is a base pairing moiety;
- W is O, CH2, or O(CH2)n, wherein n is 1 to 10;
- X is H, OH, OR3, halogen, SH, SR3, NR32, or C1-6-alkoxy;
- Y is O−, OH, OR3, NH−, NH2, NR32, BH3, S−, R3, or SH;
- Z is O or O(CH2)n, wherein n is 1 to 10;
- R2 is OH, SH, NH2, or is attached to a solid support;
- R7 is a protecting group;
- and
- R1 is defined supra;
- (d) contacting the compound of Formula (VI) with a deprotecting agent to form a compound of Formula (I).
63 more elements
Dependencies are inferred from the claim text.