Cytidine-5-carboxamide modified nucleotide compositions and methods related thereto

Patent metadata

Field	Value
Publication number	US-9938314-B2
Application number	US-201414917056-A
Country	US
Kind code	B2
Filing date	Nov 19, 2014
Priority date	Nov 21, 2013
Publication date	Apr 10, 2018
Grant date	Apr 10, 2018

Abstract

Described herein are 5-position modified cytosine nucleotides and nucleosides as well as phosphoramidites and triphosphates derivatives thereof. Further provided are methods of making and using the same, and compositions and uses of the modified nucleosides as part of a nucleic acid molecule (e.g., aptamer).

First claim

The invention claimed is:

1. A compound comprising the structure shown in Formula I:

wherein
R is independently a —(CH 2 ) n —, wherein n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10;
R X1 comprises

* denotes the point of attachment of the R X1 group to the —(CH 2 ) n — group; and
R X4 is independently selected from the group consisting of a branched or linear lower alkyl (C1-C20); a hydroxyl group; a halogen (F, Cl, Br, I); nitrile (CN); boronic acid (BO 2 H 2 ); carboxylic acid (COOH); carboxylic acid ester (COOR X2 ); primary amide (CONH 2 ); secondary amide (CONHR X2 ); tertiary amide (CONR X2 R X3 ); sulfonamide (SO 2 NH 2 ); N-alkylsulfonamide (SONHR x2 );
R X2 and R X3 are independently, for each occurrence, selected from the group consisting of a branched or linear lower alkyl (C1-C20); phenyl (C 6 H 5 ); an R X4 substituted phenyl ring (R X4 C 6 H 4 ), wherein R X4 is defined above; a carboxylic acid (COOH); a carboxylic acid ester (COOR X5 ), wherein R X5 is a branched or linear lower alkyl (C1-C20); and cycloalkyl, wherein R X2 =R X3 =(CH 2 ) n ;
X is independently selected from the group consisting of —H, —OH, —OMe, —O-allyl, —F, —OEt, —OPr, —OCH 2 CH 2 OCH 3 and -azido;
R′ is independently selected from the group consisting of a —H, —OAc; —OBz; —P(NiPr 2 )(OCH 2 CH 2 CN); and —OSiMe 2 tBu;
R″ is independently selected from the group consisting of a hydrogen, 4,4′-dimethoxytrityl (DMT) and triphosphate (—P(O)(OH)—O—P(O)(OH)—O—P(O)(OH) 2 ) or a salt thereof;

and salts thereof.

2. The compound of claim 1 , wherein R X4 is independently selected from the group consisting of a branched or linear lower alkyl (C1-C6); a —OH; a —F and carboxylic acid (COOH).

3. The compound of claim 1 , wherein X is independently selected from the group consisting of —H, —OH, —OMe and —F.

4. The compound of claim 1 , wherein R′ is selected from the group consisting of a —H, —OAc and —P(NiPr 2 )(OCH 2 CH 2 CN).

5. The compound of claim 1 , R″ is a triphosphate (—P(O)(OH)—O—P(O)(OH)—O—P(O)(OH) 2 ).

6. The compound of claim 1 , wherein n is 0, 1, 2 or 3.

7. A nucleic acid molecule comprising the compound of claim 1 .

8. A method for making a compound having Formula I:

wherein
R is independently a —(CH 2 ) n —, wherein n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10;
R X1 comprises

* denotes the point of attachment of the R X1 group to the —(CH 2 ) n — group;
R X4 is independently selected from the group consisting of a branched or linear lower alkyl (C1-C20); a hydroxyl group; halogen (F, Cl, Br, I); nitrile (CN); boronic acid (BO 2 H 2 ); carboxylic acid (COOH); carboxylic acid ester (COOR X2 ); primary amide (CONH 2 ); secondary amide (CONHR X2 ); tertiary amide (CONR X2 R X3 ); sulfonamide (SO 2 NH 2 ); N-alkylsulfonamide (SONHR X2 );
R X2 and R X3 are independently, for each occurrence, selected from the group consisting of a branched or linear lower alkyl (C1-C20); phenyl (C 6 H 5 ); an R X4 substituted phenyl ring (R X4 C 6 H 4 ), wherein R X4 is defined above; a carboxylic acid (COOH); a carboxylic acid ester (COOR X5 ), wherein R X5 is a branched or linear lower alkyl (C1-C20); and cycloalkyl, wherein R X2 =R X3 =(CH 2 ) n ;
X is independently selected from the group consisting of —H, —OH, —OMe, —O-allyl, —F, —OEt, —OPr, —OCH 2 CH 2 OCH 3 and -azido;
R′ is independently selected from the group consisting of a —H, —OAc; —OBz; —P(NiPr 2 )(OCH 2 CH 2 CN); and —OSiMe 2 tBu;
R″ is independently selected from the group consisting of an hydrogen, 4,4′-dimethoxytrityl (DMT) and triphosphate (—P(O)(OH)—O—P(O)(OH)—O—P(O)(OH) 2 ) or a salt thereof;
the method comprising providing a compound having Formula IX

wherein,
R X6 is an iodine or bromine group;
R X7 and R X8 are independently, for each occurrence, a hydrogen or protecting group;
X is independently selected from the group consisting of —H, —OH, —OMe, —O-allyl, —F, —OEt, —OPr, —OCH 2 CH 2 OCH 3 and -azido; and
transforming the compound having Formula IX by a palladium(0) catalyzed reaction in the presence of R X1 —R—NH 2 , carbon monoxide and a solvent; and
isolating the compound having Formula I.

9. The method of claim 8 , wherein R X4 is independently selected from the group consisting of a branched or linear lower alkyl (C1-C6); a —OH; a —F and carboxylic acid (COOH).

10. The method of claim 8 , wherein R′ is selected from the group consisting of a —H, —OAc and —P(NiPr 2 )(OCH 2 CH 2 CN).

11. The method of claim 8 , R″ is a hydrogen or triphosphate (—P(O)(OH)—O—P(O)(OH)—O—P(O)(OH) 2 ); or salt thereof.

12. The method of claim 8 , wherein n is 1, 2 or 3.

13. The method of claim 8 , wherein the protecting group is selected from the group consisting of triphenylmethyl, p-anisyldiphenylmethyl, di-p-anisyldiphenylmethyl, p-dimethoxy trityltrityl, formyl, t-butyloxycarbonyl, benzyloxycarbonyl, 2-chlorobenzyloxycarbonyl, 4-chlorobenzoyloxycarbonyl, 2,4-dichlorobenzyloxycarbonyl, furfurylcarbonyl, t-amyloxycarbonyl, adamantyloxycarbonyl, 2-phenylpropyl-(2)-oxycarbonyl, 2-(4-biphenyl)propyl-(2)-oxycarbonyl, 2-nitrophenylsulfenyl and diphenylphosphinyl.

Assignees

• Somalogic Inc

Inventors

• ROHLOFF John
• Janjic Nebojsa
• Gawande Bharat Nathu

Classifications

• C07H19/073

  with 2-deoxyribosyl as the saccharide radical · CPC title

• C07H19/10

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

• C07H1/00

  Processes for the preparation of sugar derivatives · CPC title

• C07H19/06 Primary

  Pyrimidine radicals · CPC title

• C07H21/00

  Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids · CPC title