4'-desmethyl nucleoside analogs, and oligomers thereof

• US 5,998,603 A
• Filed: 05/20/1997
• Issued: 12/07/1999
• Est. Priority Date: 09/29/1994
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Teng, Kelly, Cook, Phillip Dan
• Primary Examiner(s): Degen, Nancy
• Assistant Examiner(s): LARSON, THOMAS GEORGE
• Application Number:
  US08/809,239
• Time in Patent Office: 931 Days
• Field of Search: 536/22.1, 536/23.1, 536/24.3, 536/24.5, 536/25.3, 536/25.32, 536/26.6, 536/27.1, 536/27.21, 536/27.6, 536/27.81, 536/28.1, 536/28.4, 536/28.5 , 536/28.53, 536/28.54, 435/6, 435/375, 514/44
• US Class Current: 536/25.3
• CPC Class Codes: A61K 31/70 Carbohydrates; Sugars; Derivatives thereof sorbitol A61K31/047
• CPC Class Codes: A61K 47/59 obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
• CPC Class Codes: A61K 47/60 the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
• CPC Class Codes: A61K 49/0006 Skin tests, e.g. intradermal testing, test strips, delayed hypersensitivity
• CPC Class Codes: C07D 405/04 directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 405/14 containing three or more hetero rings
• CPC Class Codes: C07F 7/1804 Compounds having Si-O-C linkages Si-O-acyl linkages C07F7/1896
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/16 Purine radicals
• 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

Tetrahydrofuranyl compounds are provided that are functionalized to include pendant conjugate groups, and which are useful in diagnostic assays and as research reagents. Novel intermediates for the synthesis of the compounds are also provided.

Claims

1. A compound of structure:

##STR13## wherein;

R_L is azido or a group of formula;

space="preserve" listing-type="equation">R.sub.C --[Y].sub.e --Z--

wherein;

Z is O, S or HN;

Y is a bivalent linker;

e is 0 or 1;

R_C is alkyl, alkenyl, alkynyl, aryl, alkaryl, aralkyl, phosphinyl, a polyglycol, a polyamine, a polyether, a polythioether, an aromatic or nonaromatic ring system, a steroid molecule, a reporter molecule, an aromatic lipophilic molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, a carbohydrate, a terpene molecule, a phospholipid, an intercalator, a cell receptor binding molecule, a crosslinking agent, or a porphyrin;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoxylalkyl, O-alkylamino, or F;

Q is O, S, CH₂, CHF or CF₂ ; and

R_D is H, hydroxyl, an activated phosphorous group, a nucleoside, an activated nucleotide, a nucleotide, an oligonucleotide, an oligonucleoside or a protected derivative thereof.

2. A compound having structure:

##STR14## wherein;

L is a group of formula;

space="preserve" listing-type="equation">R.sub.7 --[W].sub.a --[S--(CH.sub.2).sub.q ].sub.u --[HN--(CH.sub.2).sub.n ].sub.t --[O--(CH.sub.2).sub.m ].sub.v --Z--

wherein;

t, u and v are each independently integers from 0 to 200;

m, n and q are each independently integers from 1 to 4;

Z is S, O or HN;

R₇ is R_C, H, or a protecting group;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoylalkyl, O-alkylamino, or F;

Q is O;

R_D is H, hydroxyl, an activated phosphorous group, a nucleoside, an activated nucleotide, a nucleotide, an oligonucleotide, an oligonucleoside or a protected derivative thereof;

W is the residue of a linking moiety, said linking moiety being selected from the group consisitng of acid chlorides, anhydrides, cyclic anhydrides, alkyl halides, organometallics, chloroformates, isocynates, hydrazines, acids, hydroxylamines, semicarbazides, thiosemicarbazides, hydrazones, hydrazides, trityl thio, oximes, hydrazide-hydrazones, semicarbazomes and semithiocarbazones;

a is 0 or 1;

R_C is alkyl, alkenyl, alkynyl, aryl, Alkaryl, aralkyl, phosphinyl, a polyglycol, a polyamine, a polyether, a polythioether, an aromatic or nonaromatic ring system, a steroid molecule, a reporter molecule, an aromatic lipophilic molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, a carbohydrate, a terpene molecule, a phospholipid, an intercalator, a cell receptor binding molecule, a crosslinking agent, or a porphyrin; and

provided that t, u and v are not all simultaneously 0.

3. A compound of claim 2 wherein t and u are 0.

4. A compound of claim 2 wherein t and u are 0, and m is 2.

5. A comound of claim 2 wherein u and v are 0.

6. A compound of claim 2 wherein u and v are 0 and n is 2.

7. A compound of claim 2 wherein X is H or OH.

8. A compound of claim 2 wherein R_D is H or OH.

9. A compound of claim 2 wherein R_D is an activated phosphorous group.

10. A compound of claim 2 wherein R_D is an oligonucleotide.

11. A comound of claim 2 wherein t and v are 0.

12. A compound of claim 2 wherein t and v are 0 and q is 2.

13. A compound of claim 2 wherein Z is O or N.

14. A compound of claim 2 wherein R_C is a steroid molecule.

15. A compound of claim 14 wherein the steroid molecule is cholic acid, deoxycholic acid, dehydrocholic acid, cortisone, digoxigenin, testosterone, cholesterol or 3-trimethylaminomethylhydrazido cortisone.

16. A compound of claim 2 wherein R_C is a water soluble vitamin.

17. A compound of claim 16 wherein the water soluble vitamin is thiamine, riboflavin, nicotinic acid, pyridoxal phosphate, pyridoxine, pyridoxamine, deoxypyridoxine, pantothenic acid, biotin, folic acid, 5'"'"'-deoxyadenosylcobalamin, inositol, choline or ascorbic acid.

18. A compound of claim 2 wherein R_C is a lipid soluble vitamin.

19. A compound of claim 18 wherein the lipid soluble vitamin is a retinal, a retinol, retinoic acid, β

-carotene, vitamin D, cholecalciferol, a tocopherol, or a phytol.

20. A compound of claim 2 wherein R_C is a protein.

21. A compound of claim 20 wherein the protein is a phosphodiesterase, a peroxidase, a phosphatase or a nuclease.

22. A compound of claim 2 wherein R_C is a reporter molecule.

23. A compound of claim 22 wherein the reporter molecule is a chromaphore, a fluorophore or a radiolabel-containing moiety.

24. A compound of claim 23 wherein the fluorophore is fluorescein, chrysine, anthracene, perylene, pyrene, rhodamine.

25. A compound of claim 2 wherein X is F, O-alkyl having from one to six carbons, O-alkoxyalkyl having from 2 to 6 carbons, or O-alkylamino having from one to six carbons.

26. A compound of claim 2 wherein R_D is H or OH.

27. A compound having structure:

##STR15## wherein;

R_C is O-alkyl, O-alkenyl, O-alkynyl, O-aryl, O-alkaryl, O-aralkyl, a polyglycol, an aromatic or nonaromatic ring system, a polyamine, a polyether, a steroid molecule, a reporter molecule, an aromatic lipophilic molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, a carbohydrate, a terpene molecule, a phospholipid, an intercalator, a cell receptor binding molecule, a crosslinking agent, or a porphyrin;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoxylalkyl, O-alkylamino, or F;

Q is O, S, CH₂, CHF or CF₂ ; and

R_D is H, hydroxyl, an activated phosphorous group, a nucleoside, an activated nucleotide, a nucleotide, an oligonucleotide, an oligonucleoside or a protected protected derivative thereof.

28. A compound of claim 27 wherein R_C is a polyether, a polyamine or a non-aromatic lipophilic molecule.

29. A compound of structure:

##STR16## wherein;

J is a leaving group;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoxylalkyl, O-alkylamino, or F;

Q is O, S, CH₂, CHF or CF₂ ; and

R_D is H, hydroxyl, an activated phosphorous group, a nucleoside, an activated nucleotide, a nucleotide, an oligonucleotide, an oligonucleoside or a protected derivative thereof.

30. A compound of claim 29 wherein J is OH, SH, NH₂, trifluoromethylsulfonyl, methylsulfonyl, halogen, O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-toluenesulfonyl, 4-dimethylaminoazobenzenesulfonyl or 5-dimethylaminonaphthalenesulfonyl.

31. A method for forming a 4'"'"'-desmethyl conjugate oligomer having structure:

##STR17## comprising the steps of;

(a) providing a first synthon having structure;

##STR18## and (b) contacting the first synthon with a second synthon having structure;

##STR19## the contacting being for a time and under reaction conditions sufficient to form the conjugated oligomer;

wherein;

R_L is azido or a group of formula;

space="preserve" listing-type="equation">R.sub.C --[Y].sub.e --Z--

Z is O, S or HN;

Y is a bivalent linker;

e is 0 or 1;

R_C is alkyl, alkenyl, alkynyl, aryl, alkaryl, aralkyl, phosphinyl, a polyglycol, a polyamine, a polyether, a polythioether, an aromatic or nonaromatic ring system, a steroid molecule, a reporter molecule, an aromatic lipophilic molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, a carbohydrate, a terpene molecule, a phospholipid, an intercalator, a cell receptor binding molecule, a crosslinking agent, or a porphyrin;

E is a phosphodiester, phosphorothioate, phosphorodithioate, phosphoramidate, alkyl phosphonate or phosphotriester phosphorous linking group;

R_E is an activated phosphorous group;

W is H, a hydroxyl protecting group or a solid state support;

k is an integer from 0 to 50;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoxylalkyl, O-alkylamino, or F; and

Q is O, S, CH₂, CHF or CF₂.

32. A method for forming a 4'"'"'-desmethyl conjugated monomer having structure:

##STR20## comprising the steps of;

(a) providing a synthon having structure;

##STR21## and (b) contacting this synthon with an activated conjugating group;

the contacting being for a time and under reaction conditions sufficient to form the conjugated monomer;

wherein;

R_L is a group of formula;

space="preserve" listing-type="equation">R.sub.C --[Y].sub.e --Z--

Z is O, S or HN;

Y is a bivalent linker;

e is 0 or 1;

R_C is alkyl, alkenyl, alkynyl, aryl, alkaryl, aralkyl, phosphinyl, a polyglycol, a polyamine, a polyether, a polythioether, an aromatic or nonaromatic ring system, a steroid molecule, a reporter molecule, an aromatic lipophilic molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, a carbohydrate, a terpene molecule, a phospholipid, an intercalator, a cell receptor binding molecule, a crosslinking agent, or a porphyrin;

J is a leaving group;

B_X is a nucleobase;

X is H, OH, O-alkyl, O-alkoxylalkyl, O-alkylamino, or F;

Q is O, S, CH₂, CHF or CF₂ ; and

R_D is H, hydroxyl, an activated phosphorous group, a nucleoside, an activated nucleotide, a nucleotide, an oligonucleotide, an oligonucleoside or a protected derivative thereof.

33. The method of claim 32 wherein J is OH, SH, NH₂, trifluoromethylsulfonyl, methylsulfonyl, halogen, O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-tolueresulfonyl, 4-dimethylaminoazobenzenesulfonyl or 5-dimethylaminonaphthalenesulfonyl.

34. The method of claim 32 wherein J is trifluoromethylsulfonyl, methylsulfonyl, halogen or acyloxy.