Nucleic acids internally-derivatized with a texaphyrin metal complex and uses thereof

• US 6,022,959 A
• Filed: 11/20/1997
• Issued: 02/08/2000
• Est. Priority Date: 08/20/1996
• Status: Expired due to Fees

• Current Assignee: Pharmacyclics Incorporated (Abbvie Incorporated)
• Original Assignee: Pharmacyclics Incorporated (Abbvie Incorporated)
• Inventors: Crofts, Shaun P., Magda, Darren, Wright, Meredith
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/975,522
• Time in Patent Office: 810 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/25.31, 536/25.34, 536/25.32, 534/11, 534/13, 534/15, 534/16, 540/149, 540/465, 540/472
• 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

Texaphyrin metal complex-oligonucleotide and -oligonucleotide analog conjugates are provided where the texaphyrin is bound to an internal linkage of the oligonucleotide or oligonucleotide analog, the conjugates having catalytic activity for the hydrolysis of ribonucleic acid. Further, conjugates demonstrating catalytic turnover are described, the conjugates being especially effective under conditions where the concentration of RNA target exceeds that of available conjugate.

Claims

1. A conjugate comprising a texaphyrin metal complex bound to an internal linkage of an oligonucleotide or oligonucleotide analog, the conjugate having hydrolytic cleavage activity for ribonucleic acid.

3. The conjugate of claim 1 or 2 wherein the oligonucleotide has an internal ribose moiety, and the texaphyrin metal complex is bound at a 2'"'"' linkage of the ribose moiety.

4. The conjugate of claim 1 or 2 wherein the oligonucleotide analog has an internal branching linker in place of a nucleotide, and the texaphyrin metal complex is covalently bound to the internal branching linker.

5. The conjugate of claim 4 wherein the internal branching linker is a glycerol derivative.

6. The conjugate of claim 4 wherein the internal branching linker is an alkyl amino linker.

7. The conjugate of claim 1 or 2 having catalytic hydrolytic cleavage activity.

8. The conjugate of claim 1 or 2 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide analog, and the oligonucleotide analog contains a derivative selected from the group consisting of methylphosphonate, phosphotriester, phosphorothioate, phosphoramidate, and 2'"'"' O-alkyl ribonucleotide.

9. The conjugate of claim 1 or 2 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide analog, and the oligonucleotide analog contains a 2'"'"'-O-alkyl ribonucleotide.

10. A method of hydrolyzing ribonucleic acid under reaction conditions having excess substrate, the method comprising:

contacting an excess of a ribonucleic acid with a conjugate of claim 1 or 2, said conjugate having at least partial sequence complementarity for said ribonucleic acid; and

incubating said ribonucleic acid and conjugate for a time sufficient to hydrolyze a phosphate ester bond of said ribonucleic acid, allow turnover of the conjugate, and hydrolyze a second phosphate ester bond of said ribonucleic acid.

11. The conjugate of claim 1 wherein the texaphyrin metal complex has the formula:

##STR4## wherein M is a divalent metal cation or a trivalent metal cation having catalytic activity for hydrolysis of ribonucleic acid;

R₁ -R₄, R₇ and R₈ are independently hydrogen, halide, hydroxyl, alkyl, alkenyl, alkynyl, aryl, haloalkyl, nitro, formyl, acyl, hydroxyalkyl, oxyalkyl, oxyhydroxyalkyl, hydroxyalkenyl, hydroxyalkynyl, saccharide, carboxy, carboxyalkyl, carboxyamide, carboxyamidealkyl, amino, aminoalkyl, an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, a sapphyrin molecule, or a couple that is coupled to an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, or a sapphyrin molecule;

R₆ and R₉ are independently selected from the groups of R₁ -R₄, R₇ and R₈, with the proviso that the halide is other than iodide and the haloalkyl is other than iodoalkyl;

R₅ and R₁₀ -R₁₂ are independently hydrogen, alkyl, alkenyl, alkynyl, aryl, hydroxyalkyl, oxyalkyl, oxyhydroxyalkyl, hydroxyalkenyl, hydroxyalkynyl, carboxyalkyl, carboxyamide, carboxyamidealkyl, amino, aminoalkyl, or a couple that is coupled to a saccharide, an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, or a sapphyrin molecule;

at least one of R₁ -R₁₂ is an oligonucleotide, oligonucleotide analog, or a couple that is coupled to an oligonucleotide or an oligonucleotide analog; and

Z is an integer value less than or equal to 5.

12. The conjugate of claim 2 or 11 wherein R₁, R₂, and R₃ are CH₂ CH₃ ;

R₄ is CH₃ ;

R₅, R₆, R₉, R₁₀, R₁₁, and R₁₂ are H;

R₇ is H or OCH₃, and R₈ is a couple that is coupled to an oligonucleotide or is a couple that is coupled to an oligonucleotide analog.

13. The conjugate of claim 12 wherein the couple is O(CH₂)₃ PO₄ or O(CH₂)₆ PO₄.

14. The conjugate of claim 2 or 11 wherein R₁ is (CH₂)₂ CH₂ OH;

R₂ and R₃ are CH₂ CH₃ ;

R₄ is CH_3;

R₅, R₆, R₉, R₁₀, R₁₁, and R₁₂ are H;

R₇ is OCH₃, and R₈ is a couple that is coupled to an oligonucleotide or is a couple that is coupled to an oligonucleotide analog.

15. The conjugate of claim 14 wherein the couple is O(CH₂)₃ PO₄ or O(CH₂)₆ PO₄.

16. The conjugate of claim 2 or 11 wherein the trivalent metal cation is Eu(III), Gd(III), Tb(III), or Dy(III).

17. The conjugate of claim 1 or 2 wherein the oligonucleotide or oligonucleotide analog forms a region of local melting with the ribonucleic acid at or near a site of texaphyrin metal complex attachment.

18. A method for synthesizing the texaphyrin metal complex-oligonucleotide conjugate of claim 3, comprising:

coupling a 2'"'"' hydroxyl of a ribonucleotide residue internal to the oligonucleotide to an amidite derivative of a texaphyrin metal complex.

19. A method for synthesizing the texaphyrin metal complex-oligonucleotide analog conjugate of claim 4, comprising:

coupling the internal branching linker to an amidite derivative of a texaphyrin metal complex.

20. A method of hydrolyzing ribonucleic acid under reaction conditions having excess conjugate, the method comprising:

contacting the ribonucleic acid with a conjugate of claim 1 or 2; and

incubating the ribonucleic acid and the conjugate under reaction conditions having excess conjugate and for a time sufficient to hydrolyze a phosphate ester bond of the ribonucleic acid.

21. The method of claim 10 wherein the ribonucleic acid is messenger RNA or viral RNA.

22. The method of claim 20 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide, the oligonucleotide has an internal ribose moiety, and the texaphyrin metal complex is bound at a 2'"'"' linkage of the ribose moiety.

23. The method of claim 10 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide, the oligonucleotide has an internal ribose moiety, and the texaphyrin metal complex is bound at a 2'"'"' linkage of the ribose moiety.

24. The method of claim 20 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide analog, the oligonucleotide analog has an internal branching linker in place of a nucleotide, and the texaphyrin metal complex is covalently bound to the internal branching linker.

25. The method of claim 10 wherein the texaphyrin metal complex is bound to an internal linkage of an oligonucleotide analog, the oligonucleotide analog has an internal branching linker in place of a nucleotide, and the texaphyrin metal complex is covalently bound to the internal branching linker.

2. A conjugate comprising a texaphyrin metal complex bound to an internal linkage of an oligonucleotide or oligonucleotide analog, the conjugate having hydrolytic cleavage activity for ribonucleic acid wherein the texaphyrin metal complex has the formula:

##STR3## wherein M is a divalent metal cation or a trivalent metal cation having catalytic activity for hydrolysis of ribonucleic acid;

R₁ -R₄, R₇ and R₈ are independently hydrogen, halide, hydroxyl, alkyl, alkenyl, alkynyl, aryl, haloalkyl, nitro, formyl, acyl, hydroxyalkyl, oxyalkyl, oxyhydroxyalkyl, hydroxyalkenyl, hydroxyalkynyl, saccharide, carboxy, carboxyalkyl, carboxyamide, carboxyamidealkyl, amino, aminoalkyl, an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, a sapphyrin molecule, or a couple that is coupled to an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, or a sapphyrin molecule;

R₆ and R₉ are independently selected from the groups of R₁ -R₄, R₇ and R₈, with the proviso that the halide is other than iodide and the haloalkyl is other than iodoalkyl;

R₅ and R₁₀ -R₁₂ are independently hydrogen, alkyl, alkenyl, alkynyl, aryl, hydroxyalkyl, oxyalkyl, oxyhydroxyalkyl, hydroxyalkenyl, hydroxyalkynyl, carboxyalkyl, carboxyamide, carboxyamidealkyl, amino, aminoalkyl, or a couple that is coupled to a saccharide, an oligonucleotide, an oligonucleotide analog, a catalytic group, an antibody, a steroid, a hormone, a peptide having affinity for a biological receptor, or a sapphyrin molecule;

at least one of R₁ -R₁₂ is an oligonucleotide, oligonucleotide analog, or a couple that is coupled to an oligonucleotide or an oligonucleotide analog; and

Z is an integer value less than or equal to 5.