Oligonucleotide
An oligonucleotide having improved affinity for AGO2 is disclosed. The oligonucleotide has a nucleotide residue or a nucleoside residue represented by formula (I) wherein X 1 is an oxygen atom or the like, R 1 is formula (IIA), wherein R 5A is halogen or the like, and R 6A is a hydrogen atom or the like, or formula (IVA) wherein Y 3A is a nitrogen atom or the like, and Y 4A is CH or the like, or the like, R 2 is a hydrogen atom, hydroxy, halogen, or optionally substituted lower alkoxy, and R 3 is a hydrogen atom or the like at the 5′ end thereof, and the nucleotide residue or the nucleoside residue binds to an adjacent nucleotide residue through the oxygen atom at position 3. A method for improving the knockdown activity of an oligonucleotide wherein the oligonucleotide has a knockdown activity against an mRNA encoding a protein involved in a disease.
1. An oligonucleotide, comprising a nucleotide residue or a nucleoside residue represented by formula (I) at the 5' end thereof, wherein the nucleotide residue or the nucleoside residue binds to an adjacent nucleotide residue through the oxygen atom at position 3 :
wherein X 1 is an oxygen atom or a sulfur atom,
R 1 is formula (II):
wherein Y 1 is a nitrogen atom,
R 5 is a hydrogen atom, halogen, cyano, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, unsubstituted or substituted lower alkynyl, unsubstituted or substituted lower alkoxy, unsubstituted or substituted lower alkylthio, unsubstituted or substituted aryl, an unsubstituted or substituted aromatic heterocyclic group, or —NR 10a R 10b wherein R 10a and R 10b may be the same or different, and each is a hydrogen atom or unsubstituted or substituted lower alkyl,
R 6 is a hydrogen atom, halogen, cyano, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, unsubstituted or substituted lower alkynyl, unsubstituted or substituted lower alkoxy, unsubstituted or substituted lower alkylthio, unsubstituted or substituted lower alkanoyl, unsubstituted or substituted aryl, unsubstituted or substituted aralkyl, unsubstituted or substituted aryloxy, unsubstituted or substituted arylthio, unsubstituted or substituted aroyl, an unsubstituted or substituted aromatic heterocyclic group, unsubstituted or substituted aromatic heterocyclic alkyl, unsubstituted or substituted aromatic heterocyclicoxy, unsubstituted or substituted aromatic heterocyclicthio, unsubstituted or substituted aromatic heterocyclic carbonyl, or —NR 11a R 11b wherein R 11a and R 11b may be the same or different, and each is a hydrogen atom, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, unsubstituted or substituted lower alkynyl, unsubstituted or substituted aryl, unsubstituted or substituted aralkyl, unsubstituted or substituted aromatic heterocyclic alkyl, unsubstituted or substituted lower alkanoyl, unsubstituted or substituted lower alkylsulfonyl, unsubstituted or substituted aroyl, unsubstituted or substituted arylsulfonyl, an unsubstituted or substituted aromatic heterocyclic group, unsubstituted or substituted aromatic heterocyclic carbonyl, or unsubstituted or substituted aromatic heterocyclic sulfonyl,
R 7 is a hydrogen atom, or
R 1 is formula (III):
wherein Y 2 is a nitrogen atom, R 6a is an amino group and R 7a is a hydrogen atom, or
R 1 is formula (IV):
wherein R 12 is a hydrogen atom,
is a double bond,
Y 3 is CR 14e wherein R 14e is a hydrogen atom, cyano, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, or unsubstituted or substituted lower alkynyl and
Y 4 is CR 14f wherein R 14f is a hydrogen atom, halogen, cyano, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, unsubstituted or substituted lower alkynyl, unsubstituted or substituted aryl, unsubstituted or substituted aralkyl, an unsubstituted or substituted aromatic heterocyclic group, or unsubstituted or substituted aromatic heterocyclic alkyl, or
R 1 is formula (V):
wherein R 12a is a hydrogen atom, ring A is an aromatic ring or a heteroaromatic ring, n 1 is an integer of 0 to 4, R 16 is halogen, hydroxy, sulfanyl, nitro, cyano, unsubstituted or substituted lower alkyl, unsubstituted or substituted lower alkenyl, unsubstituted or substituted lower alkynyl, unsubstituted or substituted lower alkoxy, unsubstituted or substituted lower alkylamino, unsubstituted or substituted di-lower alkylamino, provided that when n 1 is an integer of 2 to 4, the respective R 16 's may be the same or different, with the proviso that when ring A is a benzene ring and n 1 is 2, R 16 's are not lower alkoxy,
R 2 is a hydrogen atom, hydroxy, halogen, or unsubstituted or substituted lower alkoxy, and
R 3 is a hydrogen atom or
wherein n2 is 1.
2. The oligonucleotide according to claim 1 , wherein X 1 is an oxygen atom.
3. The oligonucleotide according to claim 1 , wherein R 1 is formula (II).
4. The oligonucleotide according to claim 1 , wherein R 1 is formula (III).
5. The oligonucleotide according to claim 1 , wherein R 1 is formula (IV).
6. The oligonucleotide according to claim 1 , wherein R 1 is formula (V).
7. The oligonucleotide according to claim 6 , wherein ring A is formula (A1):
provided that the case where ring A is represented by formula (A1'):
is excluded, formula (A2):
wherein n 1 is an integer of 0 to 2, and X 2 is NH, an oxygen atom, or a sulfur atom, or formula (A3):
wherein n 1 is an integer of 0 to 2.
8. The oligonucleotide according to claim 1 , wherein R 3 is.
9. The oligonucleotide according to claim 1 , wherein R 2 is a hydrogen atom, hydroxy, a fluorine atom, or methoxy.
10. The oligonucleotide according to claim 1 , wherein the oligonucleotide has a length of 10 to 80 bases.