Oligonucleotide compositions and methods of use thereof
Among other things, the present disclosure provides RHO oligonucleotides, compositions, and methods. In some embodiments, provided oligonucleotides comprise nucleobase modifications, sugar modifications, internucleotidic linkage modifications and/or patterns thereof, and have improved properties, activities and/or selectivities. In some embodiments, the present disclosure provides RHO oligonucleotides, compositions and methods for preventing and/or treating RHO-related conditions, disorders or diseases, such as retinopathy (e.g, retinal degeneration, retinal degenerative disease, retinal degenerative disorder, inherited retinal degenerative disorder, retinitis pigmentosa, autosomal dominant retinitis pigmentosa, etc.).
1 . An oligonucleotide, wherein the oligonucleotide comprises a plurality of chiral internucleotidic linkages each of which independently comprises a stereodefined linkage phosphorus, wherein the pattern of backbone chiral centers of the oligonucleotide comprises [(Rp/Op)n(Sp)m]y, wherein:
n is 1-10;
m is 1-50;
y is 2-10;
Op indicates a linkage phosphorus being achiral;
Rp indicates a linkage phosphorus having R configuration;
Sp indicates a linkage phosphorus having S configuration;
at least one [(Rp/Op)n(Sp)m] comprises RpSpSp; and
wherein:
the oligonucleotide comprises a natural phosphate linkage;
the oligonucleotide comprises one or more modified internucleotidic linkages and each modified internucleotidic linkage is independently a phosphorothioate internucleotidic linkage; and
the base sequence of the oligonucleotide is or comprises a sequence that is at least 75% identical or complementary to a target sequence in a RHO gene or a transcript thereof and the base sequence of the oligonucleotide is complementary to a RHO sequence at a SNP, wherein the SNP is rs104893768.
2 . The oligonucleotide of claim 1 , wherein the base sequence of the oligonucleotide comprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more contiguous nucleobases of a base sequence that is identical to or complementary to a base sequence of a RHO gene or a transcript thereof.
3 . The oligonucleotide of claim 1 , wherein the pattern of backbone chiral centers comprises (Sp)t[(Rp(Sp)m]y, wherein t is 1-50 and each m is independently 2-50.
4 . The oligonucleotide of claim 3 , wherein the oligonucleotide comprises or consists of a wing-core-wing structure, wherein each sugar in a wing independently comprises 2′-OR, wherein R is substituted or unsubstituted C 1-6 alkyl.
5 . The oligonucleotide of claim 4 , wherein the core comprises no sugar modification that is 2′-OR, wherein R is substituted or unsubstituted C 1-6 alkyl.
6 . The oligonucleotide of claim 5 , wherein each wing independently comprises 2 nucleobases.
7 . The oligonucleotide of claim 6 , wherein the core comprises 10 nucleobases.
8 . The oligonucleotide of claim 7 , wherein each wing independently comprises one or more phosphorothioate internucleotidic linkages and optionally one or more natural phosphate linkages.
9 . The oligonucleotide of claim 8 , wherein the pattern of backbone chiral centers of the core comprises (Sp)t[(Rp)n(Sp)m]y, wherein:
t is 1-50;
n is 1;
m is 2-50;
y is 1-10;
Rp indicates a linkage phosphorus having R configuration; and
Sp indicates a linkage phosphorus having S configuration.
10 . The oligonucleotide of claim 9 , wherein the base sequence of the core comprises a nucleobase which is or is complementary to a nucleobase that can differentiate one Rho allele from the other allele(s), wherein an Rp internucleotidic linkage of RpSpSp or SpRpSpSp is at −3, −2,−1, +1, +2, or +3 position relative to the nucleobase, wherein “−” is counting toward the 5′-end, “+” is counting toward the 3′-end, and an internucleotidic linkage is at −1 position if it bonds to the 5′ of the nucleoside comprising the nucleobase, at +1 position if it bonds to the 3′ of the nucleoside comprising the nucleobase.
11 . The oligonucleotide of claim 1 , wherein the oligonucleotide is conjugated with a lipid moiety, a carbohydrate moiety, or a targeting moiety.
12 . The oligonucleotide of claim 1 , wherein the oligonucleotide is in a form of a pharmaceutically acceptable salt.
13 . The oligonucleotide of claim 1 , wherein each phosphorothioate internucleotidic linkage in the oligonucleotide independently has a diastereomeric purity of at least 90%.
14 . A chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides, wherein the oligonucleotides share:
1) a common constitution, and
2) the same linkage phosphorus stereochemistry at one or more chiral internucleotidic linkages (chirally controlled internucleotidic linkages),
wherein about 1-100% of all oligonucleotides within the composition that share the common constitution are the oligonucleotides of the plurality, and
each oligonucleotide of the plurality is independently an oligonucleotide of claim 1 .
15 . The composition of claim 14 , wherein each phosphorothioate internucleotidic linkage is independently chirally controlled.
16 . A pharmaceutical composition comprising an oligonucleotide of claim 1 and a pharmaceutically acceptable carrier.
17 . A method for preventing, treating or ameliorating a RHO-related condition, disorder or disease in a subject susceptible thereto or suffering therefrom, comprising administering to the subject a therapeutically effective amount of an oligonucleotide of claim 1 .
18 . The method of claim 17 , wherein the RHO-related condition, disorder or disease is retinopathy or retinitis pigmentosa.
19 . A method for decreasing the activity, expression and/or level of a RHO target gene or its gene product in a cell, comprising contacting the cell with an oligonucleotide of claim 1 .
20 . The oligonucleotide of claim 1 , wherein the oligonucleotide is:
Geo*SGeoTeoAeom5Ceo*RT*Sm5C*SG*SA*SA*SG*ST*SG*RG Sm5C*STeoGeom5CeoGeo*STeo (SEQ ID NO: 311), or
Geo*SGeoTeoAeom5Ceo*RT*Sm5C*SG*SA*SA*SG*ST*SG*RG* Sm5C*SmU*SmG*Sm5mC*SmG*SmU (SEQ ID NO: 148),
or a pharmaceutically acceptable salt form thereof, wherein:
f represents a 2′-F modified nucleoside;
m represents a 2′-OMe modified nucleoside;
eo represents a 2′-OCH 2 CH 2 OCH 3 modified nucleoside;
m5 represents a nucleobase of 5-methylcytosine;
m5Ceo represents 5-methyl 2′-O-methoxyethyl C;
*S represents a phosphorothioate internucleotidic linkage in the Sp configuration; and
*R represents a phosphorothioate internucleotidic linkage in the Rp configuration.