5′ phosphate mimics

Patent metadata

Field	Value
Publication number	US-10131908-B2
Application number	US-201414551714-A
Country	US
Kind code	B2
Filing date	Nov 24, 2014
Priority date	Jul 7, 2009
Publication date	Nov 20, 2018
Grant date	Nov 20, 2018

Abstract

The present invention provides nucleosides and oligonucleotides comprising a 5′ phosphate mimics of formula (IVc) or (Vc),

One aspect of the present invention relates to modified nucleosides and oligonucleotides comprising such dinucleotide of formula (Ia). Another aspect of the invention relates to a method of inhibiting the expression of a gene in call, the method comprising (a) contacting an oligonucleotide of the invention with the cell; and (b) maintaining the cell from step (a) for a time sufficient to obtain degradation of the mRNA of the target gene.

First claim

We claim:

1. A nucleoside represented by formula (IV):

or isomers thereof, wherein:
D 1 is H, a hydroxyl protecting group, a solid support, or a reactive phosphorus group;
K is O, S, NR′, or optionally substituted alkyl;
B is selected from the group consisting of hydrogen, unsubstituted or substituted aliphatic, a natural nucleobase, a modified nucleobase, and a universal nucleobase;
R is H, OH, SH, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, or optionally substituted dialkylamino;
L and J are independently absent or selected from the group consisting of S, O, NR′, alkylene, alkenylene, and alkynylene;
R′ is hydrogen, acyl, aliphatic or substituted aliphatic; and
W 1 and V 1 are each independently selected from the group consisting of a boronic group B(OH) 2 , and

or alternatively, W 1 and V 1 , taken together with the atoms to which they are bonded, form a phosphorous-atom-containing heterocyclic ring;
Z is O, S or NR′;
Z 1 is O or S,
X and Y are each independently selected from the group consisting of H, O − , OH, SH, SM, OM, borane (BH 3 ), optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, and optionally substituted dialkylamino; or X and Y, taken together with the atoms to which they are bonded, form

wherein

is an optionally substituted C 2 -C 8 alkylene;
M is a metal counter ion with an overall charge of +1; and
m and n are independently 1-10.

2. The nucleoside of claim 1 , wherein V 1 and W 1 are taken together with the atom to which they are bonded to form a nucleoside represented by formula (V):

or isomers thereof, wherein:
D 1 is H, a hydroxyl protecting group, a solid support, or a reactive phosphorus group;
K is O, S, NR′, or an optionally substituted alkyl;
B is selected from the group consisting of hydrogen, unsubstituted or substituted aliphatic, a natural nucleobase, a modified nucleobase, and a universal nucleobase;
X is H, OH, OM, SH, SM, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, or optionally substituted dialkylamino, where M is a metal counter ion;
Z is O, S, or NR′;
R is H, OH, SH, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, or optionally substituted dialkylamino;
R′ is hydrogen, acyl, or unsubstituted or substituted aliphatic;
L and J are each independently absent or selected from the group consisting of S, O, NR′, alkylene, alkenylene, and alkynylene; and
m and n are each independently 1-10.

3. An oligonucleotide comprising a nucleoside represented by formula (IVa):

or isomers thereof, wherein:
R is H, OH, SH, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, optionally substituted dialkylamino, or an internucleoside linking group attaching the nucleoside to the oligonucleotide;
T 1 is hydroxyl, a protected hydroxyl, a linked conjugate group or an internucleoside linking group attaching the nucleoside to the oligonucleotide, wherein at least one of T 1 and R is an internucleoside linking group attaching the nucleoside to the oligonucleotide;
K is independently for each occurrence O, S, NR′, or optionally substituted alkyl;
each B is selected from the group consisting of hydrogen, unsubstituted or substituted aliphatic, a natural nucleobase, a modified nucleobase, and a universal nucleobase;
L and J are each independently absent or selected from the group consisting of S, O, NR′, alkylene, alkenylene, and alkynylene;
W 1 and V 1 are independently selected from the group consisting of a boronic group (B(OH) 2 ), and

or alternatively, W 1 and V 1 , taken together with the atoms to which they are bonded, form a phosphorous-atom-containing heterocyclic ring;
Z is O, S, or NR′;
Z 1 is O or S;
R′ is hydrogen, acyl, or unsubstituted or substituted aliphatic;
X and Y are each independently selected from the group consisting of H, O − , OH, SH, SM, OM, borane (BH 3 ), optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkylthip, optionally substituted alkylamino, and optionally substituted dialkylamino; or X and Y, taken together with the atoms to which they are bonded, form

where

is an optionally substituted C 2 -C 8 alkylene;
M is a metal counter ion; and
m and n are each independently 1-10.

4. The oligonucleotide of claim 3 , wherein the nucleoside is represented by formula (Va):

or isomers thereof, wherein:
R is H, OH, SH, halogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, optionally substituted dialkylamino, or an internucleoside linking group attaching the nucleoside to the oligonucleotide;
T 1 is hydroxyl, a protected hydroxyl, a linked conjugate group or an internucleoside linking group attaching the nucleoside to the oligonucleotide, wherein at least one of Ti and R is an internucleoside linking group attaching the nucleoside to the oligonucleotide;
K is independently for each occurrence O, S, NR′, or optionally substituted alkyl;
each B is selected from the group consisting of hydrogen, unsubstituted or substituted aliphatic, a natural nucleobase, a modified nucleobase, and a universal nucleobase;
X is H, OH, OM, SH, SM, optionally substituted alkyl, optionally substituted alkoxy, optionally substituted alkylthio, optionally substituted alkylamino, or optionally substituted dialkylamino, where M is a metal counter ion;
Z is O, S, or NR′;
R′ is hydrogen, acyl, or unsubstituted or substituted aliphatic;
L and J are each independently absent or selected from the group consisting of S, O, NR′, alkylene, alkenylene, and alkynylene; and
m and n are each independently 1-10.

5. The oligonucleotide of claim 3 , wherein said oligonucleotide comprises at least one non-phosphodiester backbone linkage.

6. The oligonucleotide of claim 5 , wherein the non-phosphodiester of at least one of said non-phosphodiester backbone linkages is selected from a group consisting of phosphorothioate, phosphorodithioate, alkyl-phosphonate, and phosphoramidate.

7. The oligonucleotide of claim 5 , wher

Assignees

• Alnylam Pharmaceuticals Inc

Inventors

• Manoharan Muthiah
• Rajeev Kallanthottathil G
• Prhavc Marija
• Zlatev Ivan

Classifications

• C07H19/11

  containing cyclic phosphate · CPC title

• C12N15/113 Primary

  Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)} · CPC title

• C07H19/20

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title

• C07H19/213 Primary

  containing cyclic phosphate · CPC title

• C07H19/10

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title