# US 2013/0156845 A1 · Lipid formulated single stranded rna

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2013/0156845 A1
- Document ID: US20130156845A1
- Status: Published application
- Kind: A1
- Application number: 13/643,940
- Filed: 2011-04-29
- Published: 2013-06-20
- Earliest claimed: 2010-04-29
- Assignees: Alnylam Pharmaceuticals, Inc.; Isis Pharmaceuticals, Inc.
- Inventors: Muthiah Manoharan; Sayda Elbashir; Kallanthottathil G. Rajeev; Thazha P. Prakash; Walter F. Lima; Eric E. Swayze
- Web page: https://patentgrep.com/patent/US20130156845A1

## CPC

- A61K 9/1272: comprising non-phosphatidyl surfactants as bilayer-forming substances, e.g. cationic lipids or non-phosphatidyl liposomes coated or grafted with polymers (lipids as modifying agents {A61K47/543})
- A61K 9/1275: Lipoproteins or protein-free species thereof, e.g. chylomicrons; Artificial high-density lipoproteins [HDL], low-density lipoproteins [LDL] or very-low-density lipoproteins [VLDL]; Precursors thereof
- A61K 31/7088: Compounds having three or more nucleosides or nucleotides
- C12N 15/111: {General methods applicable to biologically active non-coding nucleic acids}
- C12N 15/88: using microencapsulation, e.g. using {amphiphile} liposome vesicle
- C12N 2310/11: Antisense
- C12N 2320/32: Special delivery means, e.g. tissue-specific
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

The present invention provides compositions comprising a nucleic acid lipid particle and an oligomeric compound and uses thereof. In certain embodiments, such compositions are useful as antisense compounds. Certain such antisense compounds are useful as RNase H antisense compounds or as RNAi compounds.

## Claims

### Claim 1

A composition comprising a nucleic acid lipid particle comprising a single stranded RNA, wherein the nucleic acid lipid particle comprises a lipid formulation comprising 45-65 mol % of a cationic lipid, 5 mol % to about 10 mol %, of a non-cationic lipid, 25-40 mol % of a sterol, and 0.5-5 mol % of a PEG or PEG-modified lipid.

### Claim 2 (depends on 1)

The composition of claim 1, wherein the cationic lipid comprises formula A wherein formula A is
where R100 and R200 are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R300 and R400 are independently lower alkyl or R300 and R400 can be taken together to form an optionally substituted heterocyclic ring.

### Claim 3 (depends on 2)

The composition of claim 2, wherein the cationic lipid comprises 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane.

### Claim 4 (depends on 2)

The composition of claim 2, wherein the cationic lipid comprises 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane, the non-cationic lipid comprises DSPC, the sterol comprises cholesterol and the PEG lipid comprises PEG-DMG.

### Claim 5 (depends on 4)

The composition of claim 4, wherein the cationic lipid comprises 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane and the formulation is selected from the group consisting of:
LNP05
Cationic lipid/DSPC/Cholesterol/PEG-DMG
57.5/7.5/31.5/3.5
lipid:siRNA ~6:1
LNP06
Cationic lipid/DSPC/Cholesterol/PEG-DMG
57.5/7.5/31.5/3.5
lipid:siRNA ~11:1
LNP07
Cationic lipid/DSPC/Cholesterol/PEG-DMG
60/7.5/31/1.5,
lipid:siRNA ~6:1
LNP08
Cationic lipid/DSPC/Cholesterol/PEG-DMG
60/7.5/31/1.5,
lipid:siRNA ~11:1
LNP09
Cationic lipid/DSPC/Cholesterol/PEG-DMG
50/10/38.5/1.5
lipid:siRNA ~10:1

### Claim 6 (depends on 1)

The composition of claim 1, wherein the single stranded RNA comprising a nucleoside having Formula I:
wherein:
Bx is a heterocyclic base moiety;
A is O, S or N(R1);
Z10 is O, S, N(R1), or CH2;
R1 is H, C1-C6 alkyl or substituted C1-C6 alkyl;
T1 is a phosphorus moiety;
T2 is an internucleoside linking group linking the monomer of Formula I to the remainder of the oligomeric compound;
each of Q1 and Q2 is independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl or substituted C2-C6 alkynyl;
G1 is halogen, X1—V, or O—X2;
X1 is O, S or CR2R3;
each R2 and R3 is, independently, H or C1-C6 alkyl;
V is a conjugate group, aryl, (CH2)2[O(CH2)2]tOCH3, where t is from 1-3, (CH2)2F, CH2COOH, CH2CONH2, CH2CONR5R6, CH2COOCH2CH3, CH2CONH(CH2)i—S—R4 where i is from 1 to 10, CH2CONH(CH2)k3NR5R6 where k3 is from 1 to 6, CH2CONH[(CH2)k1—N(H)]k2—(CH2)k1NH2 where each k1 is independently from 2 to 4 and k2 is from 2 to 10;
R4 is H, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl, substituted C2-C6 alkynyl, C6-C14 aryl or a thio protecting group;
R5 and R6 are each, independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl or substituted C2-C6 alkynyl;
X2 is [C(R7)(R8)]n—[(C═O)mX]j—Z;
each R7 and R8 is independently, H, halogen, C1-C6 alkyl or substituted C1-C6 alkyl;
X is O, S or N(E1);
Z is H, halogen, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl, substituted C2-C6 alkynyl or N(E2)(E3);
E1, E2, and E3 are each independently H, C1-C6 alkyl, or substituted C1-C6 alkyl;
n is from 1 to about 6;
m is 0 or 1;
j is 0 or 1;
each substituted group comprises one or more optionally protected substituent groups independently selected from H, halogen, OJ1, N(J1)(J2), ═NJ1; SJ1, N3, CN, OC(=L) J1, OC(=L)N(J1)(J2), C(=L)N(J1)(J2), C(=L)N(H)—(CH2)2N(J1)(J2) or a mono or polycyclic ring system;
L is O, S or NJ3;
each J1, J2 and J3 is, independently, H or C1-C6 alkyl; and
when j is 1, then Z is other than halogen or N(E2)(E3).

### Claim 7 (depends on 1)

The composition of claim 1, wherein the single stranded RNA comprising a nucleoside having Formula II:
wherein:
Bx is a heterocyclic base moiety;
T3 is a phosphorus moiety;
Z10 is O, S, N(R1), or CH2;
T4 is an internucleoside linking group linking the monomer of Formula II to the remainder of the oligomeric compound;
Q1, Q2, Q3 and Q4 are each, independently, H, halogen, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl or substituted C2-C6 alkynyl, hydroxyl, substituted oxy, O—C1-C6 alkyl, substituted O—C1-C6 alkyl, S—C1-C6 alkyl, substituted S—C1-C6 alkyl, N(R1)—C1-C6 alkyl or substituted N(R1)—C1-C6 alkyl;
R1 is H, C1-C6 alkyl or substituted C1-C6 alkyl;
G2 is H, OH, halogen, O-aryl or O—[C(R4)(R5)]n—[(C═O)mX]j—Z;
each R4 and R5 is, independently, H, halogen, C1-C6 alkyl or substituted C1-C6 alkyl;
X is O, S or N(E1);
Z is H, halogen, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl, substituted C2-C6 alkynyl or N(E2)(E3);
E1, E2, and E3 are each independently H, C1-C6 alkyl, or substituted C1-C6 alkyl;
n is from 1 to about 6;
m is 0 or 1;
j is 0 or 1;
each substituted group comprises one or more optionally protected substituent groups independently selected from H, halogen, OJ1, N(J1)(J2), ═NJ1, SJ1, N3, CN, OC(=L)J1, OC(=L)N(J1)(J2), C(=L)N(J1)(J2), C(=L)N(H)—(CH2)2N(J1)(J2), a mono or poly cyclic ring system, a phosphate group or a phosphorus moiety;
L is O, S or NJ3;
each J1, J2 and J3 is, independently, H or C1-C6 alkyl;
when j is 1 then Z is other than halogen or N(E2)(E3); and
when Q1, Q2, Q3 and Q4 are each H, or when Q1 and Q2 are H and Q3 and Q4 are each F, or when Q1 and Q2 are each H and one of Q3 and Q4 is H and the other of Q3 and Q4 is R9, then G2 is other than H, hydroxyl, OR9, halogen, CF3, CCl3, CHCl2 or CH2OH, wherein R9 is alkyl, alkenyl, alkynyl, aryl or alkaryl.

### Claim 8 (depends on 1)

The composition of claim 1, wherein the single stranded RNA comprising a nucleoside having Formula III:
wherein:
each Bx is independently a heterocyclic base moiety;
T4 is an internucleoside linking group attaching the nucleoside of Formula III to the remainder of the oligonucleotide;
each of q1 and q2 is, independently selected from H, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl and substituted C2-C6 alkynyl;
X1 is S, NR16, or CR10R11 wherein each R10 and R11 is, independently, H, F, C1-C6 haloalkyl, or C1-C6 alkyl; and
R1 is selected from a halogen, X2—V, and O—X4;
Or
each of q1 and q2 is, independently, selected from H, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl and substituted C2-C6 alkynyl;
X1 is O, S, NR16R17, or CR10R11 wherein each R10 and R11 is, independently, H, F, C1-C6 haloalkyl, or C1-C6 alkyl; and
R1 is X2—V;
Or
each of q1 and q2 is, independently, selected from C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C1-C6 alkenyl and substituted C2-C6 alkynyl;
X1 is O, S, NR16R17, or CR10R11 wherein each R10 and R11 is, independently, H, F, C1-C6 haloalkyl, or C1-C6 alkyl; and
R1 is selected from a halogen, X2—V, and O—X4;
X2 is O, S or CR7R8 wherein each R7 and R8 is, independently, H or C1-C6 alkyl;
V is selected from cholesterol, (CH2)2[O(CH2)2]tOCH3, where t is from 1-3, (CH2)2F, CH2COOH, CH2CONH2, CH2CONR5R6, CH2COOCH2CH3, CH2CONH(CH2)i—S—R4 where i is from 1 to 10, CH2CONH(CH2)JNR5R6 where j is from 1 to 6, and CH2CONH[(CH2)k1—N(H)]k—(CH2)k1NH2 where each k1 is independently from 2 to 4 and k2 is from 2 to 10;
R4 is selected from H, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, substituted C2-C6 alkenyl, substituted C2-C6 alkynyl, C6-C14 aryl or a thio protecting group;
R5 and R6 are each, independently, selected from H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl or substituted C2-C6 alkynyl;
R16 is selected from H, C1-C6 alkyl, or substituted C1-C6 alkyl;
X4 is [C(Ra)(Rb)]n—[(C═O)mXc]k—Rd wherein
each Ra and Rb is independently H or halogen;
Xc is O, S or N(E1);
Rd is H, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, substituted C1-C6 alkyl, s substituted C2-C6 alkenyl, substituted C2-C6 alkynyl or NE2E3;
each E1, E2, and E3 is independently H, C1-C6 alkyl, or substituted C1-C6 alkyl;
n is 1 to 6;
m is 0 or 1; and
k is 0 or 1;
X3 is OH or SH;
Ya is O or S;
each Yb and Yc is, independently, selected from OH, SH, alkyl, alkoxy, substituted C1-C6 alkyl and substituted C1-C6 alkoxy; and
R9 is selected from a halogen, X2—V, and O—X4;
wherein each substituted group is, independently, mono or poly substituted with optionally protected substituent groups independently selected from halogen, oxo, OJ1, NJ1J2, SJ1, N3, OC(═O)J1 and CN, wherein each J1 and J2 is, independently, H or C1-C6 alkyl; and J4 is hydrogen, or a protecting group.

### Claim 9 (depends on 8)

The composition of claim 8 wherein R1 is selected from halogen, O-alkyl, O-haloalkyl, O-alkoxy.

### Claim 10 (depends on 8)

The composition of claim 8 wherein R1 is F.

### Claim 11 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is O—C2-C4 alkyl or haloalkyl.

### Claim 12 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is OCH3.

### Claim 13 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is O(CH2)2OCH3.

### Claim 14 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is FCH2CH4.

### Claim 15 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is (CH2)2[O(CH2)2]tOCH3, where t is from 1-3.

### Claim 16 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is selected from, trifluoroalkoxy, azido, aminooxy, S-alkyl, N(J4)-alkyl, O-alkenyl, S-alkenyl, N(J4)-alkenyl, O-alkynyl, S-alkynyl, N(J4)-alkynyl, and X2—V.

### Claim 17 (depends on 8)

The oligomeric compound of claim 8 wherein R1 is X2—V.

### Claim 18 (depends on 17)

The oligomeric compound of claim 17 wherein V is (CH2)2F.

### Claim 19 (depends on 17)

The oligomeric compound of claim 17 wherein V is CH2CONH(CH2)i—S—R4

### Claim 20 (depends on 17)

The oligomeric compound of claim 17 wherein V is CH2CONH[(CH2)k1—N(H)]k2—(CH2)k1NH2.

### Claim 21 (depends on 17)

The oligomeric compound of claim 17 wherein V is CH2CONH—(CH2)3—N(H)—(CH2)4—N(H)—(CH2)3NH2.

### Claim 22 (depends on 17)

The oligomeric compound of claim 17 wherein V is CH2CONH(CH2)JNR5R6.

### Claim 23 (depends on 22)

The oligomeric compound of claim 22 wherein R5 is methyl and R6 is methyl.

### Claim 24 (depends on 8)

The oligomeric compound of claim 8, wherein X2 is O.

### Claim 25 (depends on 8)

The oligomeric compound of claim 8, wherein X2 is S.

### Claim 26 (depends on 8)

The oligomeric compound of claim 8, wherein X2 is CR7R8.

### Claim 27 (depends on 8)

The oligomeric compound of claim 8, wherein at least one of q1 and q2 is C1-C6 alkyl or substituted C1-C6 alkyl.

### Claim 28 (depends on 27)

The oligomeric compound of claim 27 wherein at least one of q1 and q2 is C1-C6 alkyl.

### Claim 29 (depends on 6)

The oligomeric compound of claim 6, wherein the phosphorus moiety is P(Ya)(Yb)(Yc), where Ya is O or S, and each Yb and Yc is, independently, selected from OH, SH, alkyl, alkoxy, substituted C1-C6 alkyl and substituted C1-C6 alkoxy.

### Claim 30 (depends on 29)

The oligomeric compound of claim 29 wherein Ya is O and Yb and Yc are each OH.

### Claim 31 (depends on 1)

The composition of claim 1, further comprising a lipoprotein.

### Claim 32 (depends on 1)

The composition of claim 1, further comprising apolipoprotein E (ApoE).