# US 11,110,174 B2 · Carbohydrate conjugates as delivery agents for oligonucleotides

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- Number: US 11,110,174 B2
- Document ID: US11110174B2
- Status: Granted
- Kind: B2
- Application number: 16/861,494
- Filed: 2020-04-29
- Published: 2020-09-24
- Granted: 2021-09-07
- Earliest claimed: 2007-12-04
- Assignees: Alnylam Pharmaceuticals, Inc.
- Applicants: Alnylam Pharmaceuticals, Inc.
- Inventors: Muthiah Manoharan; Kallanthottathil G. Rajeev; Jayaprakash Nair; Martin Maier
- Web page: https://patentgrep.com/patent/US11110174B2

## CPC

- A61K 47/28: Steroids, e.g. cholesterol, bile acids or glycyrrhetinic acid
- A61K 47/554: {the modifying agent being a steroid plant sterol, glycyrrhetic acid, enoxolone or bile acid}
- A61K 31/70: Carbohydrates; Sugars; Derivatives thereof (sorbitol A61K31/047)
- A61K 31/7004: Monosaccharides having only carbon, hydrogen and oxygen atoms
- A61K 31/7052: having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
- A61K 31/7088: Compounds having three or more nucleosides or nucleotides
- A61K 31/713: Double-stranded nucleic acids or oligonucleotides
- A61K 47/16: containing nitrogen, {e.g. nitro-, nitroso-, azo-compounds, nitriles, cyanates}
- A61K 47/22: Heterocyclic compounds, e.g. ascorbic acid, tocopherol or pyrrolidones
- A61K 47/543: {Lipids, e.g. triglycerides; Polyamines, e.g. spermine or spermidine}
- A61K 47/549: {Sugars, nucleosides, nucleotides or nucleic acids}
- A61K 47/56: the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
- A61K 47/60: the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
- A61P 3/06: Antihyperlipidemics
- A61P 3/10: for hyperglycaemia, e.g. antidiabetics
- A61P 25/00: Drugs for disorders of the nervous system
- A61P 35/00: Antineoplastic agents
- A61P 37/02: Immunomodulators
- C07H 21/02: with ribosyl as saccharide radical
- A61K 48/00: Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
- Y02A 50/30: Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
- Y02P 20/55: Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
- 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)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02P: CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS

## Abstract

The present invention provides a phosphorothioate-modified oligonucleotide comprising a structure shown below: The present invention also provides a phosphorothioate-modified oligonucleotide comprising a structure having formula (CIII):

## Claims

### Claim 1

A ligand-containing conjugate having the structure shown in formula (I):
wherein:
A and B are each independently for each occurrence O, N(RN), or S;
one of X and Y is a solid support, optionally linked via a linker group, or a phosphoramidite, and the other of X and Y is a protecting group;
R is L1 or has the structure shown in formula (II)-(V)
q2A, q2B, q3A, q3B, q4A, q4B, q5A, q5B and q5C represent independently for each occurrence 0-20 and wherein the repeating unit can be the same or different;
Q is absent, -(P7-Q7-R7)p-T7- , or -T7-Q7-TT-B′-T8′-Q8-T8-;
P2A, P2B, P3A, P3B, P4A, P4B, P5A, P5B, P5C, P7, T2A, T2B, T3A, T3B, T4A, T4B, T5A, T5B, T5C, T7, T7′, T8 and T8′ are each independently for each occurrence absent, CO, NH, O, S, OC(O), C(O)O, NHC(O), C(O)NH, CH2, CH2NH, NHCH2, OCH2 or CH2O;
B′ is —CH2—N(BL)—CH2—;
BL is -TB-QB-TB′-Rx;
Q2A, Q2B, Q3A, Q3B, Q4A, Q4B, Q5A, Q5B, Q5C, Q7, Q8 and QB are independently for each occurrence absent, alkylene, substituted alkylene and wherein one or more methylenes can be interrupted or terminated by one or more of O, S, S(O), SO2, N(RN), C(R′)═C(R′), C≡C or C(O);
TB and TB′ are each independently for each occurrence absent, CO, NH, O, S, OC(O), C(O)O, NHC(O), C(O)NH, NHC(O)NH, NHC(O)O, OC(O)NH, CH2, CH2NH, NHCH2, OCH2, or CH2O;
Rx is a lipophile, or a cationic lipid;
R2A, R2B, R3A, R3B, R4A, R4B, R5A, R5B, R5c, and R7 are each independently for each occurrence absent, NH, O, S, CH2, C(O)O, OC(O), C(O)NH, NHC(O), NHCH(Ra)C(O), C(O)—CH(Ra)—NH, CO, CH═N—O
or heterocyclyl;
L1, L2A, L2B, L3A, L3B, L4A, L4B, L5A, L5B and L5C are each independently for each occurrence a carbohydrate or a derivative thereof having hydroxyl protecting group(s);
R′ and R″ are each independently H, C1-C6 alkyl, OH, SH, or N(RN)2;
RN is independently for each occurrence methyl, ethyl, propyl, isopropyl, butyl or benzyl;
Ra is H or amino acid side chain; and
p represents independently for each occurrence 0-20.

### Claim 2 (depends on 1)

The ligand-containing conjugate of claim 1, wherein:
A and B are each O;
one of X and Y is a solid support, a solid support linked via a —C(O)CH2CH2C(O)—group, or a phosphoramidite, and the other of X and Y is a hydroxyl protecting group;
R has the structure shown in formula (V);
Q is P7-Q7-T7;
Q7 is alkene; and
L5A, L5B, and L5C are each independently for each occurrence a derivative of a carbohydrate, having hydroxyl protecting group(s).

### Claim 3 (depends on 2)

The ligand-containing conjugate of claim 2, wherein the carbohydrate is selected from the group consisting of galactose, galactosamine, N-acetylgalactosamine (GalNAc), D-galactosaminitol, mannose, mannosamine, mannose-6-phosphate, glucose, glucosamine, N-acetyl-glucosamine (GluNAc), glucose-6- phosphate, glucosaminitol, glucose glyceraldehyde, fucose, fucosamine, fuculose, lactose, allose, altrose, arabinose, cladinose, erythrose, erythrulose, fructose, D-fucitol, L-fucitol, L-glycero-D-mannos-heptose, glycerol, glycerone, gulose, idose, lyxose, psicose, quinovose, quinovosamine, rhamnose, rhamnitol, rhamnosamine, ribose, ribulose, sedoheptulose, sorbose, tagatose, talose, tartaric acid, threose, xylose, and xylulose.

### Claim 4 (depends on 3)

The ligand-containing conjugate of claim 3, wherein the carbohydrate is N-acetylgalactosamine (GalNAc).

### Claim 5 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is selected from the group consisting of:
wherein:
each of m, n, p, q, s, and t is independently an interger of 1 to 17, and
each of R′ and R″ is independently H or alkyl.

### Claim 6 (depends on 2)

The ligand-containing conjugate of claim 2, wherein the ligand-containing conjugate has the structure of
wherein n is an interger of 1 to 17, X is a solid support or a solid support linked via a —C(O)CH2CH2C(O)—group, and Y is a hydroxyl protecting group.

### Claim 7 (depends on 2)

The ligand-containing conjugate of claim 2, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 8 (depends on 2)

The ligand-containing conjugate of claim 2, wherein the ligand-containing conjugate is
wherein
wherein is a solid support.

### Claim 9 (depends on 2)

The ligand-containing conjugate of claim 2, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 10 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 11 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 12 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 13 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 14 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 15 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is

### Claim 16 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 17 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is
wherein
is a solid support.

### Claim 18 (depends on 1)

The ligand-containing conjugate of claim 1, wherein the ligand-containing conjugate is

### Claim 19 (depends on 2)

A method of synthesizing a ligand-conjugated oligonucleotide, comprising:
providing a ligand-containing conjugate of claim 2, and
conjugating the ligand-containing conjugate to an oligonucleotide.

### Claim 20 (depends on 19)

The method of claim 19, wherein conjugating the ligand-containing conjugate is carried out by growing the oligonucleotide to the ligand-containing conjugate.