Oligonucleotide phosphate esters

• US 6,015,886 A
• Filed: 02/05/1997
• Issued: 01/18/2000
• Est. Priority Date: 05/24/1993
• Status: Expired due to Term

• Current Assignee: Chemgenes Corporation, Lakewood Amedex Inc.
• Original Assignee: Chemgenes Corporation, Oligos Etc., Inc.
• Inventors: Srivastava, Suresh C., Arrow, Amy, Raza, Syed K., Dale, Roderic M. K.
• Primary Examiner(s): CRANE, LAWRENCE E
• Application Number:
  US08/795,926
• Time in Patent Office: 1,077 Days
• Field of Search: 536/23.1, 536/25.1, 536/24.3, 536/24.5, 514/44, 435/6
• US Class Current: 536/23.1
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

Abstract

This invention relates to synthetic oligonucleotides that are useful for antisense based therapeutic applications. The synthetic oligonucleotides of this invention have modifications in the sugar phosphate backbone for improved antisense properties.

Claims

1. A compound represented by the formula:

##STR11## wherein O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester internucleosidyl group, and said R'"'"' is selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs to C-15; and

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorocytosinyl), 1-(5-chlorouracilyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

13. A composition comprising an oligonucleotide sequence and an acceptable carrier, wherein said oligonucleotide sequence contains one of the oligonucleotide structures of any of claims 1-12.

14. The composition of claim 13 wherein said pharmaceutically acceptable carrier is a lipofectin.

2. A compound represented by the formula:

##STR12## wherein n is 1-60;

O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triesters located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is selected from the group of alkyl radicals consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-15;

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅, S^- and NR"'"'"'R"" wherein N is nitrogen, R"'"'"' is a second alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons, and R"" is a third alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons; and

B, B'"'"' and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-chlorocytosinyl), 1-(5-chlorouracilyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

3. A compound represented by the formula:

##STR13## wherein O is oxygen;

C is carbon, and H is hydrogen;

X is selected from the group consisting of ethyl, propyl, alkyl homologs up to 16 carbons and allyl;

R'"'"' is part of an alkyl phosphate triester group located at the internucleosidyl position, and said R'"'"' is an alkyl selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher homologs up to C-15; and

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

4. A compound represented by the formula:

##STR14## wherein O is oxygen;

C is carbon, and H is hydrogen;

X is an alkyl group selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to C-15;

R'"'"' is part of an alkyl phosphate triesters located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is an alkyl selected from the group consisting of methyl, ethyl, isopropyl, propyl, and higher alkyl homologs up to C-15;

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

5. A compound represented by the formula:

##STR15## wherein n is 1-60;

O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester group located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is an alkyl group selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-15;

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅, OC₃ H₇, O-iso C₃ H₇, S^-, and NR"'"'"'R"" wherein N is nitrogen, R"'"'"' is a second alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons, and R"" is a third alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons;

X is selected from the group consisting of methyl, ethyl, propyl, isopropyl and higher alkyl homologs to C-15; and

B, B'"'"' and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

6. A compound represented by the formula:

##STR16## wherein n is 1-60;

wherein O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester groups, and said R'"'"' is selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-15;

X is selected from the group consisting of methyl, ethyl, propyl, and isopropyl and higher alkyl homologs to C-15;

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅, OC₃ H₇, O-iso C₃ H₇, S^-, and NR"'"'"'R"" wherein N is nitrogen, R"'"'"' is a second alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons, and R"" is a third alkyl radical selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to 16 carbons; and

B, B'"'"', B" and B"" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

7. A compound represented by the formula:

##STR17## wherein O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester internucleosidyl group, and said R'"'"' is selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs to C-5; and

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl),1-(5-chlorocytosinyl), 1-(5-chlorouracilyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

8. A compound represented by the formula:

##STR18## wherein n is 1-60;

O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triesters located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is selected from the group of alkyl radicals consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-5; and

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅,, and S^- ;

B, B'"'"' and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorocytosinyl), 1-(5-chlorouracilyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

9. A compound represented by the formula:

##STR19## wherein O is oxygen;

C is carbon, and H is hydrogen;

X is selected from the group consisting of ethyl, propyl, alkyl homologs up to 5 carbons and allyl;

R'"'"' is part of an alkyl phosphate triester group located at the internucleosidyl position, and said R'"'"' is an alkyl selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher homologs up to C-5; and

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bronmocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

10. A compound represented by the formula:

##STR20## wherein O is oxygen;

C is carbon, and H is hydrogen;

X is an alkyl group selected from the group consisting of methyl, ethyl, propyl, isopropyl and alkyl homologs up to C-5;

R'"'"' is part of an alkyl phosphate triesters located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is an alkyl selected from the group consisting of methyl, ethyl, isopropyl, propyl, and higher alkyl homologs up to C-5; and

B and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

11. A compound represented by the formula:

##STR21## wherein n is 1-60;

O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester group located at the terminal 3'"'"' internucleosidyl position, and said R'"'"' is an alkyl group selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-5;

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅, OC₃ H₇, O-iso C₃ H₇, and S^-,

X is selected from the group consisting of methyl, ethyl, propyl, isopropyl and higher alkyl homologs to C-5; and

B, B'"'"' and B" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).

12. A compound represented by the formula:

##STR22## wherein n is 1-60;

wherein O is oxygen;

C is carbon, and H is hydrogen;

R'"'"' is part of an alkyl phosphate triester groups, and said R'"'"' is selected from the group consisting of methyl, ethyl, isopropyl, propyl and higher alkyl homologs up to C-5;

X is selected from the group consisting of methyl, ethyl, propyl, and isopropyl and higher alkyl homologs to C-5;

R" is selected from the group consisting of OH, OCH₃, OC₂ H₅, OC₃ H₇, O-iso C₃ H₇, and S^- ; and

B, B'"'"', B" and B"" are natural and modified nucleobase radicals selected from the group consisting of 9-adeninyl, 1-thyminyl, 1-cytosinyl, 9-guaninyl, 9-hypoxanthinyl, 1-(5-methylcytosinyl), 1-(5-azacytosinyl), 1-(5-bromouracilyl), 1-(5-bromocytosinyl), 1-(5-fluorouracilyl), 1-(5-fluorocytosinyl), 1-(5-chlorouracilyl), 1-(5-chlorocytosinyl), 1-(5-iodouracilyl), 1-(5-iodocytosinyl), 1-(5-propynyluracilyl) and 1-(5-propynylcytosinyl).