Carbohydrate or 2′-modified oligonucleotides having alternating internucleoside linkages
View Patent ↗Novel compounds that mimic and/or modulate the activity of wild-type nucleic acids. In general, the compounds are oligonucleotides which contain at least one region of 2′-modified nucleosides connected by alternating phosphodiester and phosphorothioate linkages.
1. A method for reducing the undesired production of a protein in an organism, said method comprising contacting said organism with a compound of formula:
wherein:
each B is a nucleobase;
one of X 1 or X 2 is O, and the other of X 1 or X 2 is S;
each R 1, is, independently, H, hydroxyl, C 1 –C 20 alkyl, C 3 –C 20 alkenyl, C 2 –C 20 alkynyl, halogen, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
or R 1 is a group of formula Z-R 22 —(R 23 ) v ;
Z is O, S, NH, or N—R 22 —(R 23 ) v ;
R 22 is C 1 –C 20 alkyl, C 2 –C 20 alkenyl, or C 2 –C 20 alkynyl;
R 23 is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
v is from 0 to about 10;
or R 1 has the formula:
wherein:
y1 is 0 or 1;
y2 is independently 0 to 10;
y3 is 1 to 10;
E is C 1 –C 10 alkyl, N(Q 1 )(Q 2 ) or N═C(Q 1 )(Q 2 );
each Q 1 and Q 2 is, independently, H, C 1 –C 10 alkyl, substituted alkyl, dialkylaminoalkyl, a nitrogen protecting group, a tethered or untethered conjugate group, a linker to a solid support; or Q 1 and Q 2 , together, are joined in a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;
or R 1 has one of formula I or II:
wherein:
Z 0 is O, S, or NH;
q 1 is from 0 to 10;
q 2 is from 1 to 10;
q 3 is 0 or 1;
q 4 is, 0, 1 or 2;
Z 4 is OM 1 , SM 1 , or N(M 1 ) 2 ;
each M 1 is, independently, H, C 1 –C 8 alkyl, C 1 –C 8 haloalkyl, C(═NH)N(H)M 2 , C(═O)N(H)M 2 or OC(═O)N(H)M 2 ;
M 2 is H or C 1 –C 8 alkyl;
Z 1 , Z 2 and Z 3 comprise a ring system having from about 4 to about 7 carbon atoms, or having from about 3 to about 6 carbon atoms and 1 or 2 hetero atoms wherein said hetero atoms are selected from oxygen, nitrogen and sulfur, and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic; and
Z 5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(Q 1 )(Q 2 ), OQ 1 , halo, SQ 1 or CN;
n is from 2 to 50; and
m is 0 or 1.
2. A method for reducing the undesired production of a protein in an organism, said method comprising contacting said organism with a compound of formula:
wherein:
each B is a nucleobase;
X 1 is S;
X 2 is O;
each R 1 , is, independently, H, hydroxyl, C 1 –C 20 alkyl, C 3 –C 20 alkenyl, C 2 –C 20 alkynyl, halogen, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
or R 1 is a group of formula Z-R 22 —(R 23 ) v ;
Z is O, S, NH, or N—R 22 —(R 23 ) v ;
R 22 is C 1 –C 20 alkyl, C 2 –C 20 alkenyl, or C 2 –C 20 alkynyl;
R 23 is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
v is from 0 to about 10;
or R 1 has the formula:
y1 is 0 or 1;
y2 is independently 0 to 10;
y3 is 1 to 10;
E is C 1 –C 10 alkyl, N(Q 1 )(Q 2 ) or N═C(Q 1 )(Q 2 );
each Q 1 and Q 2 is, independently, H, C 1 –C 10 alkyl, substituted alkyl, dialkylaminoalkyl, a nitrogen protecting group, a tethered or untethered conjugate group, a linker to a solid support; or Q 1 and Q 2 , together, are joined in a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;
or R 1 has one of formula I or II:
wherein:
Z 0 is O, S, or NH;
q 1 is from 0 to 10;
q 2 is from 1 to 10;
q 3 is 0 or 1;
q 4 is, 0, 1 or 2;
Z 4 is OM 1 , SM 1 , or N(M 1 ) 2 ;
each M 1 is, independently, H, C 1 –C 8 alkyl, C 1 –C 8 haloalkyl, C(═NH)N(H)M 2 , C(═O)N(H)M 2 or OC(═O)N(H)M 2 ;
M 2 is H or C 1 –C 8 alkyl;
Z 1 , Z 2 and Z 3 comprise a ring system having from about 4 to about 7 carbon atoms, or having from about 3 to about 6 carbon atoms and 1 or 2 hetero atoms wherein said hetero atoms are selected from oxygen, nitrogen and sulfur, and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic; and
Z 5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(Q 1 )(Q 2 ), OQ 1 , halo, SQ 1 or CN;
n is from 2 to 50; and
m is 0 or 1;
R 2 is H, a hydroxyl protecting group, or an oligonucleotide; and
R 3 is OH, an oligonucleotide, or a linker connected to a solid support.
3. A method for reducing the undesired production of a protein in an organism, said method comprising contacting said organism with a compound of formula:
(5′) W 1 -W 2 -W 3 (3′)
wherein:
W 1 has the Formula:
wherein:
each B is a nucleobase;
one of X 1 or X 2 is O, and the other of X 1 or X 2 is S;
each R 1 , is, independently, H, hydroxyl, C 1 –C 20 alkyl, C 3 –C 20 alkenyl, C 2 -C 20 alkynyl, halogen, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
or R 1 is a group of formula Z-R 22 —(R 23 ) v ;
Z is O, S, NH, or N—R 22 —(R 23 ) v ;
R 22 is C 1 –C 20 alkyl, C 2 –C 20 alkenyl, or C 2 –C 20 alkynyl;
R 23 is hydrogen, amino, halogen, hydroxyl, thiol, keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, O-alkyl, S-alkyl, NH-alkyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, amino, N-phthalimido, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, aryl, heterocycle, carbocycle, intercalator, reporter molecule, conjugate, polyamine, polyamide, polyalkylene glycol, or polyether;
v is from 0 to about 10;
or R 1 has the formula:
y1 is 0 or 1;
y2 is independently 0 to 10;
y3 is 1 to 10;
E is C 1 –C 10 alkyl, N(Q 1 )(Q 2 ) or N═C(Q 1 )(Q 2 );
each Q 1 and Q 2 is, independently, H, C 1 –C 10 alkyl, substituted alkyl, dialkylaminoalkyl, a nitrogen protecting group, a tethered or untethered conjugate group, a linker to a solid support; or Q 1 and Q 2 , together, are joined in a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O;
or R 1 has one of formula I or II:
wherein:
Z 0 is O, S, or NH;
q 1 is from 0 to 10;
q 2 is from 1 to 10;
q 3 is 0 or 1;
q 4 is, 0, 1 or 2;
Z 4 is OM 1 , SM 1 , or N(M 1 ) 2 ;
each M 1 is, independently, H, C 1 –C 8 alkyl, C 1 –C 8 haloalkyl, C(═NH)N(H)M 2 , C(═O)N(H)M 2 or OC(═O)N(H)M 2 ;
M 2 is H or C 1 –C 8 alkyl;
Z 1 , Z 2 and Z 3 comprise a ring system having from about 4 to about 7 carbon atoms, or having from about 3 to about 6 carbon atoms and 1 or 2 hetero atoms wherein said hetero atoms are selected from oxygen, nitrogen and sulfur, and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic; and
Z 5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(Q 1 )(Q 2 ), OQ 1 , halo, SQ 1 or CN;
n is from 2 to 50; and
m is 0 or 1;
R 2 is H, a hydroxyl protecting group, or an oligonucleotide;
W 3 has the Formula:
wherein R 3 is OH, an oligonucleotide, or a linker connected to a solid support; and
W 2 is a plurality of covalently bound nucleosides linked by phosphodiester or phosphorothioate linkages.
4. The method of claim 1 wherein R 1 is —O—CH 2 —CH 2 —O—CH 3 .
5. The method of claim 1 wherein n is about 5 to about 50.
6. The method of claim 1 wherein n is about 8 to about 30.
7. The method of claim 1 wherein n is about 4 to about 15.
8. The method of claim 1 wherein n is 2 to about 10.
9. The method of claim 2 wherein R 1 is —O—CH 2 —CH 2 —O—CH 3 .
10. The method of claim 2 wherein R 2 is H, and R 3 is OH.
11. The method of claim 2 wherein R 2 is a phosphodiester-linked oligonucleotide or a phosphorothioate linked oligonucleotide.
12. The method of claim 2 wherein R 3 is a phosphodiester-linked oligonucleotide or a phosphorothioate linked oligonucleotide.
13. The method of claim 2 wherein R 2 and R 3 are each a phosphodiester-linked oligonucleotide or a phosphorothioate linked oligonucleotide.
14. The method of claim 3 wherein R 1 is —O—CH 2 —CH 2 —O—CH 3 .
15. The method of claim 3 wherein R 2 is H, and R 3 is OH.
16. The method of claim 3 wherein n is about 5 to about 50.
17. The method of claim 3 wherein n is about 8 to about 30.
18. The method of claim 3 wherein n is about 4 to about 15.
19. The method of claim 3 wherein n is 2 to about 10.
20. The method of claim 3 wherein W 2 is a plurality of covalently bound nucleosides linked by phosphodiester linkages.
21. The method of claim 3 wherein W 2 is a plurality of covalently bound nucleosides linked by phosphorothioate linkages.