POLYCYCLIC SUGAR SURROGATE-CONTAINING OLIGOMERIC COMPOUNDS AND COMPOSITIONS FOR USE IN GENE MODULATION

• US 20080039618A1
• Filed: 10/12/2007
• Published: 02/14/2008
• Est. Priority Date: 11/05/2002
• Status: Abandoned Application

• Current Assignee: Anne Eldrup, Balkrishen Bhat, Brenda Baker, Charles Allerson, Eric Swayze, Muthiah Manoharan, Richard Griffey
• Original Assignee: Anne Eldrup, Balkrishen Bhat, Brenda Baker, Charles Allerson, Eric Swayze, Muthiah Manoharan, Richard Griffey
• Inventors: Baker, Brenda, Eldrup, Anne, Bhat, Balkrishen, Allerson, Charles, Manoharan, Muthiah, Swayze, Eric, Griffey, Richard
• Application Number:
  US11/871,436
• Publication Number:
  US 20080039618A1
• Time in Patent Office: Days
• US Class Current: 536/24.5
• 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
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/113 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 Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/323 modified ring structure
• CPC Class Codes: C12N 2310/343 having patterns, e.g. ==--==--==--
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3533 Halogen
• CPC Class Codes: C12N 2320/51 modulating the chemical stability, e.g. nuclease-resistance

Abstract

Compositions comprising first and second oligomers are provided wherein at least a portion of the first oligomer is capable of hybridizing with at least a portion of the second oligomer, at least a portion of the first oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and at least one of the first or second oligomers includes a modification comprising a polycyclic sugar surrogate. Oligomer/protein compositions are also provided comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein comprising at least a portion of an RNA-induced silencing complex (RISC), wherein at least one nucleoside of the oligomer has a polycyclic sugar surrogate modification.

Claims

1. A nucleoside comprising a bicyclic sugar moiety having the formula:

wherein

Q is CH₂ or C(═

O);

R is H, a protecting group or C₁-C₁₂ alkyl; and

T₁ and T₂ are each, independently, hydroxyl, a protected hydroxyl, a conjugate group, an activated phosphorus moiety or a covalent attachment to a support medium.

2. The nucleoside of claim 1 wherein Q is CH₂.

3. The nucleoside of claim 1 wherein Q is C(═

O).

4. The nucleoside of claim 1 wherein R is H.

5. The nucleoside of claim 1 wherein R is methyl.

6. The nucleoside of claim 1 having the configuration:

wherein

Bx is a heterocyclic base moiety;

Q is CH₂ or C(═

O);

R is H, a protecting group or C₁-C₁₂ alkyl; and

T₁ and T₂ are each independently, hydroxyl, a protected hydroxyl, a conjugate group, an activated phosphorus moiety or a covalent attachment to a support medium.

7. An oligomeric compound comprising at least one nucleoside comprising a bicyclic sugar moiety having the formula:

wherein

Bx is a heterocyclic base moiety;

Q is CH₂ or C(═

O);

R is H, a protecting group or C₁-C₁₂ alkyl; and

each of T₃ and T₄ is an internucleoside linkage connecting the nucleoside to the oligomeric compound or one of T₃ and T₄ is an internucleoside linkage connecting the nucleoside to the oligomeric compound and the other of the T₃ and T₄ is hydroxyl, a protected hydroxyl, a conjugate group, an activated phosphorus moiety, a covalent attachment to a support medium or an internucleoside linkage attached to a nucleoside, a nucleotide, a nucleoside mimic, an oligonucleoside, an oligonucleotide or an oligonucleotide mimic.

8. The oligomeric compound of claim 7 wherein each nucleoside comprising the bicyclic sugar moiety has the configuration:

wherein

Bx is a heterocyclic base moiety;

Q is CH₂ or C(═

O);

R is H, a protecting group or C₁-C₁₂ alkyl; and

each of T₃ and T₄ is an internucleoside linkage connecting the nucleoside to the oligomeric compound or one of T₃ and T₄ is an internucleoside linkage connecting the nucleoside to the oligomeric compound and the other of the T₃ and T₄ is hydroxyl, a protected hydroxyl, a conjugate group, an activated phosphorus moiety, a covalent attachment to a support medium or an internucleoside linkage attached to a nucleoside, a nucleotide, a nucleoside mimic, an oligonucleoside, an oligonucleotide or an oligonucleotide mimic.

9. The oligomeric compound of claim 7 comprising from about 10 to about 40 nucleosides.

10. The oligomeric compound of claim 7 comprising from about 18 to about 30 nucleosides.

11. The oligomeric compound of claim 7 comprising from about 21 to about 24 nucleosides.

12. The oligomeric compound of claim 7 comprising from about 15 to about 30 nucleosides.

13. The oligomeric compound of claim 7 comprising a plurality of nucleosides linked by internucleoside linking groups wherein each of the internucleoside linking groups is, independently, phosphodiester, phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonate, chiral phosphonate, phosphinate, phosphoramidate, thionophosphoramidate, thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphate, boranophosphate or methylene(methylimino).

14. The oligomeric compound of claim 13 wherein each of the internucleoside linking groups is, independently, phosphodiester or phosphorothioate.

15. The oligomeric compound of claim 7 further comprising at least one nucleoside having formula I:

wherein

Bx is a heterocyclic base moiety;

J is H, hydroxyl, protected hydroxyl or a sugar substituent group; and

each of T₅ and T₆ is an internucleoside linkage connecting the nucleoside to the oligomeric compound or one of T₅ and T₆ is an internucleoside linkage connecting the nucleoside to the oligomeric compound and the other of the T₅ and T₆ is hydroxyl, a protected hydroxyl, a conjugate group, an activated phosphorus moiety, a covalent attachment to a support medium or an internucleoside linkage attached to a nucleoside, a nucleotide, a nucleoside mimic, an oligonucleoside, an oligonucleotide or an oligonucleotide mimic.

16. The oligomeric compound of claim 15 comprising a plurality of nucleosides having formula I wherein each J is, independently, H, hydroxyl, protected hydroxyl or a sugar substituent group.

17. The oligomeric compound of claim 15 wherein each sugar substituent group is, independently, alkyl, alkenyl, alkynyl, O-, S- or N-alkyl;

O-, S- or N-alkenyl;

O-, S,- or N-alkynyl;

O-alkyl-O-alkyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O[(CH₂)_nO]_mCH₃, OCH₂C(═

O)N(H)(CH₃), O(CH₂)_nOCH₃, O(CH₂)_nNH₂, O(CH₂)_nCH₃, O(CH₂)_nONH₂, O(CH₂)_nON[(CH₂)_nCH₃]₂, SH, SCH₃, OCN, F, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group or a reporter group;

wherein alkyl groups are C₁ to C₁₀ and are substituted or unsubstituted, alkenyl groups are C₂ to C₁₀ and are substituted or unsubstituted, and alkynyl groups are C₂ to C₁₀ and are substituted or unsubstituted and where n and m are each independently from 1 to about 10.

18. The oligomeric compound of claim 17 wherein each of the sugar substituents groups is, independently, OCH₂C(═

O)N(H)(CH₃), O—

CH₂CH₂OCH₃, O(CH₂)₂ON(CH₃)₂, O—

(CH₂)₂—

O—

(CH₂)₂—

N(CH₃)₂, O—

CH₃, OCH₂CH₂CH₂NH₂, CH₂—

CH═

CH₂, O—

CH₂—

CH═

CH₂ or F.

19. The oligomeric compound of claim 15 wherein each of the sugar substituent groups independently, comprises formula II:

wherein;

R_d is a single bond, O, S or C(═

O);

R_e is C₁-C₁₀ alkyl, N(R_k)(R_m), N(R_k)(R_n), N═

C(R_p)(R_q), N═

C(R_p)(R_r) or has formula IIIa;

R_p and R_q, are each independently hydrogen or C₁-C₁₀ alkyl;

R_r is —

R_x—

R_y;

each R_s, R_t, R_u, and R_v is, independently, hydrogen, C(O)R_w, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl, alkylsulfonyl, arylsulfonyl, a chemical functional group or a conjugate group, wherein the substituent groups are selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl, and alkynyl;

or optionally, R_u and R_v, together form a phthalimido moiety with the nitrogen atom to which they are attached;

each R_w is, independently, substituted or unsubstituted C₁-C₁₀ alkyl, trifluoromethyl, cyanoethyloxy, methoxy, ethoxy, t-butoxy, allyloxy, 9-fluorenylmethoxy, 2-(trimethylsilyl)-ethoxy, 2,2,2-trichloroethoxy, benzyloxy, butyryl, iso-butyryl, phenyl or aryl;

R_k is hydrogen, a nitrogen protecting group or —

R_x—

R_y;

R_x is a bond or a linking moiety;

R_y is a chemical functional group, a conjugate group or a solid support medium;

each R_m and R_n is, independently, H, a nitrogen protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl, wherein the substituent groups are selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl, alkynyl;

or R_m and R_n, together, are a nitrogen protecting group, are joined in a ring structure that optionally includes an additional heteroatom selected from N and O or are a chemical, functional group;

m_a is 1 to about 10;

each mb is, independently, 0 or 1;

mc is 0 or an integer from 1 to 10;

md is an integer from 1 to 10; and

provided that when mc is 0, md is greater than 1.

20. A composition comprising a first oligomeric compound and a second oligomeric compound;

the first oligomeric compound is complementary to and capable of hybridizing with the second oligomeric compound;

the first oligomeric compound is complementary to and capable of hybridizing to a selected target nucleic acid,

wherein at least one of the first and the second oligomeric compounds comprises at least one nucleoside of claim 1;

and

wherein the composition further comprises one or more optional overhangs, phosphate moieties, conjugate groups or oligomer terminal groups.

21. The composition of claim 20 wherein the first and the second oligomeric compounds are a complementary pair of siRNA oligomeric compounds.

22. The composition of claim 20 wherein the first and the second oligomeric compounds are an antisense/sense pair of oligomeric compounds.

23. The composition of claim 20 wherein each of the first and the second oligomeric compounds has from about 10 to about 40 nucleosides.

24. The composition of claim 20 wherein each of the first and the second oligomeric compounds has from about 18 to about 30 nucleosides.

25. The composition of claim 20 wherein each of the first and the second oligomeric compounds has from about 21 to about 24 nucle