IP Library › Granted Patent US 12,247,203
Granted Patent B2
US 12,247,203 · App. 17/055,710 · Granted Mar 11, 2025

Modified RNA agents with reduced off-target effect

Inventors: Shigeo Matsuda (Cambridge, MA); Mark K. Schlegel (Cambridge, MA); Maja Janas (Cambridge, MA); Vasant R. Jadhav (Cambridge, MA); Martin Maier (Cambridge, MA); Klaus Charisse (Cambridge, MA); Muthiah Manoharan (Cambridge, MA); Kallanthottathil Rajeev (Cambridge, MA); Jayaprakash K. Nair (Cambridge, MA)
C12N15/113C12N2310/14C12N2310/318C12N2310/323C12N2310/33C12N2310/344C12N2310/53
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Quick Facts
Patent No.
US 12,247,203
App. No.
17/055,710
Granted
Mar 11, 2025
Kind
B2
Abstract

One aspect of the present invention relates to double-stranded RNA (dsRNA) agent capable of inhibiting the expression of a target gene. The antisense strand of the dsRNA molecule comprises at least one thermally destabilizing nucleotide occurring at a seed region; the dsRNA comprises at least four 2′-fluoro modifications, and the sense strand of the dsRNA molecule comprises ligand, wherein the ligand is an ASGPR ligand. Other aspects of the invention relate to pharmaceutical compositions comprising these dsRNA molecules suitable for therapeutic use, and methods of inhibiting the expression of a target gene by administering these dsRNA molecules, e.g., for the treatment of various disease conditions.

Claims (96)

1. A double-stranded RNA (dsRNA) molecule capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 40 nucleotides, wherein the antisense strand has sufficient complementarity to the target sequence to mediate RNA interference, wherein said antisense strand comprises one thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5′ region, counting from the 5′-end of the antisense strand, wherein the destabilizing modification is a Modified Unlocked Nucleic Acid (mUNA), and wherein (i) said sense strand comprises an ASGPR ligand; or (ii) the dsRNA has a melting temperature of from about 40° C. to about 80° C.

2. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

3. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

4. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OMe; F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; or 7-deazapurines; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

5. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), 0-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

6. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

7. The dsRNA molecule according to claim 1 , wherein the destabilizing modification mUNA is selected from the group consisting of

wherein:

R is H, OMe; F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; or 7-deazapurines; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers.

8. The dsRNA molecule according to claim 1 , wherein the thermally destabilizing modification of the duplex is selected from the group consisting of

wherein Base is nucleobase and * represents either R, S or racemic.

9. The dsRNA molecule according to claim 1 , wherein the dsRNA comprises at least four 2′-fluoro.

10. The dsRNA molecule according to claim 9 , wherein there are no 2′-fluoro modifications at nucleotide positions 3-9 of the antisense strand, counting from the 5′-end of the antisense strand.

11. The dsRNA molecule according to claim 1 , having the following characteristics:

a) the thermally destabilizing modification of the duplex is located in position 4-8 of the 5′ region of the antisense strand, counting from the 5′-end of the antisense strand;

b) and each of the sense and antisense strands comprise at least two 2′-fluoro modifications; and

c) an ASGPR ligand attached to either end of the sense strand.

12. The dsRNA molecule according to claim 1 , wherein the antisense strand has at least two of the following characteristics:

a) the thermally destabilizing modification of the duplex modification is located in position 4 to 8 of the antisense strand, counting from the 5′-end of the antisense strand;

b) at least two 2′-fluoro modifications;

c) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2 (counting from the 5′ end);

d) it has a length of 18 to 35 nucleotides.

13. The dsRNA molecule according to claim 12 , wherein there are no 2′-fluoro modifications at nucleotide positions 3-9 of the antisense strand, counting from the 5′-end of the antisense strand.

14. The dsRNA molecule according to claim 1 , wherein the sense strand has at least one of the following characteristics:

a) the ASGPR ligand attached to either end of the sense strand;

b) at least two 2′-fluoro modifications;

c) the sense strand and the antisense strand show sufficient complementarity to form a double stranded region spanning at least 19 nucleotide positions and wherein the thermally destabilizing modification of the duplex is located within said double-stranded region.

15. The dsRNA molecule according to claim 14 , wherein there are no 2′-fluoro modifications at nucleotide positions 3-9 of the antisense strand, counting from the 5′-end of the antisense strand.

16. The dsRNA molecule of claim 1 further comprising at least one thermally destabilizing modification selected from the group consisting of

wherein B is nucleobase.

17. The dsRNA molecule according to claim 1 , wherein the thermally destabilizing modification is located in position 7 of the antisense strand.

18. A method for silencing a target gene in a cell, the method comprising a step of introducing the dsRNA molecule of claim 1 into the cell.

19. A compound selected:

(i) from the group consisting of:

wherein:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H, or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(ii) from the group consisting of:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H or Me;

B=A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(iii) from the group consisting of:

R is H, OMe; F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; O-nPr; O-alkyl; or O-alkylamino;

R′ is H or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; or 7-deazapurines; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(iv) from the group consisting of:

R=H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; O-alkylamino;

R′=H, Me;

B=A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(v) from the group consisting of:

R is H, OH; OMe; Cl, F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; CCH (alkyne), O-nPr; O-alkyl; or O-alkylamino;

R′ is H or Me;

B is A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; 7-deazapurines, phenoxazine; G-clamp; non-canonical mono, or bi and tricyclic heterocycles; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(vi) from the group consisting of:

wherein:

R is H, OMe; F; OH; O—(CH 2 ) 2 OMe; SMe, NMe 2 ; NH 2 ; Me; O-nPr; O-alkyl; or O-alkylamino;

R′ is H or Me;

B=A; C; 5-Me-C; G; I; U; T; Y; 2-thiouridine; 4-thiouridine; C5-modified pyrimidines; C2-modified purines; N8-modified purines; phenoxazine; G-clamp; non-canonical mono, bi and tricyclic heterocycles; pseudouracil; isoC; isoG; 2,6-diaminopurine; pseudocytosine; 2-aminopurine; xanthosine; N6-alkyl-A; O6-alkyl-G; or 7-deazapurines; and

Stereochemistry is R or S and combination of R and S for the unspecified chiral centers; or

(vii) from the group consisting of:

wherein Base is nucleobase and * represents either R, S or racemic.

20. A nucleic acid comprising a compound of claim 19 .

Assignments (2)
SECURITY INTEREST Recorded Oct 1, 2025
From: ALNYLAM PHARMACEUTICALS, INC.; SIRNA THERAPEUTICS, INC.
To: BANK OF AMERICA, N.A.
Reel/Frame 072996/0337 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 10, 2024
From: MATSUDA, SHIGEO; SCHLEGEL, MARK K.; JANAS, MAJA; JADHAV, VASANT R.; MAIER, MARTIN; CHARISSE, KLAUS; MANOHARAN, MUTHIAH; RAJEEV, KALLANTHOTTATHIL; NAIR, JAYAPRAKASH K.
To: ALNYLAM PHARMACEUTICALS, INC.
Reel/Frame 068545/0715 →
Continuity (3)
Provisional Application 62719291 · Aug 17, 2018
Provisional Application 62672405 · May 16, 2018
Related Publication 20210238595A1 · Aug 5, 2021
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