Heteroatomic oligonucleoside linkages

• US 6,087,482 A
• Filed: 09/18/1995
• Issued: 07/11/2000
• Est. Priority Date: 07/27/1990
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Sanghvi, Yogesh, Teng, Kelly, Cook, Phillip Dan
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US08/522,374
• Time in Patent Office: 1,758 Days
• Field of Search: 435/6, 536/22.1, 536/23.1, 536/24.5, 536/25.3, 536/24.3, 536/24.31, 536/24.32, 514/44
• US Class Current: 536/22.1
• 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 47/605 the macromolecule containing phosphorus in the main chain, e.g. poly-phosphazene
• 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

Oligonucleotide-mimicking macromolecules that have improved nuclease resistance are provided. Replacement of the normal phosphorodiester inter-sugar linkages found in natural oligonucleotides with four atom linking groups provide unique compounds that are useful in regulating RNA expression and in therapeutics. Methods of synthesis and use also are disclosed.

Claims

1. A compound having structure:

##STR7## wherein;

R_A is CR_3a R_3b, CR_2a R_2b -CR_3a R_3b, CR_2a R_2b -Z₃, Z2-CR_3a R_3b or Z₂ -Z₃ ;

Z₂, Z₃ and Z₄ are, independently, O, S, NR₄, Se, P(=J₁)J₂ or Si(R₆)₂ ;

Z_N is CR_1a R_1b, NR₄, S, Se, P(=J₁)J₂, Si (R₆)₂, or O;

R_1a, R_1b, R_2a, R_2b, R_3a and R_3b are, independently, H, R₅, O-R₅, S-R₅, NR₄ R₅ ;

or, independently, together R_1a and R_1b, or R_2a and R_2b, or R_3a and R_3b are=O;

J₁ is O, S, Se or NR₄ ;

J₂ is OH, OR₅, SH, SR₅, SeH, R₅, BH₃ or NR₄ R₅ ;

R₄, R₅ and R₆ are, independently, H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ substituted or unsubstituted alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

C₆ to C₁₄ aryl;

alicyclic;

heterocyclic;

or a reporter molecule;

R_B is trifluoromethylsulfonyl, methylsulfonyl, halogen O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-toluenesulfonyl, 4-dimethylaminoazobenzene-sulfonyl or 5-dimethylaminonaphthalenesulfonyl;

Y is H, halogen, a labile functional group or a blocking group;

X is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO₂ CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl;

Q is O, CH₂, CHF, CF₂ ; and

B_X is a heterocyclic base.

2. The compound of claim 1 wherein Y is an acid labile functional group.

3. The compound of claim 1 wherein Y is halogen.

4. A compound having structure:

##STR8## wherein;

R_c is OH, SH, NH₂, trifluoromethylsulfonyl, methyl-sulfonyl, halogens, O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-toluenesulfonyl, 4-dimethyl-aminoazobenzenesulfonyl or 5-dimethylaminonaphthalenesulfonyl;

R_D is hydroxyl, Z_T, L₁ -Z_T, L₁ -L₂ -Z_T, L₁ -L₂ -L₃ -Z_T, a nucleoside, a nucleotide, an oligonucleotide or an oligonucleoside;

L₁ is Z₁ or CR_1a R_1b ;

L₂ is Z₂ or CR_2a R_2b ;

L₃ is Z₃ or CR_3a R_3b ;

Z₁, Z₂, Z₃ and Z₄ are, independently, O, NR₄, S, SO, SO₂, Se, P(=J₁) J₂ or Si(R₅)₂ ;

Z_T is NR₄ H, SH, SeH, P(=J₁)J₂ OH, Si(R₆)₂ OH, or OH;

R_1a, R_1b, R_2a, R_2b, R_3a and R₃ b are, independently, H, R₅, O--R₅, S--R₅, NR₄ R₅ ;

or, independently, together R_1a and R_1b, or R_2a and R_2b, or R_3a and R_3b are=O;

J₁ is O, S, Se or NR₄ ;

J₂ is OH, OR₅, SH, SR₅, SeH, R₅, BH₃ or NR₄ R₅ ;

R₄, R₅ and R₆ are, independently, H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ substituted or unsubstituted alkaryl or aralkyl;

a ¹⁴ C containing C7 to C₁₄ alkaryl or aralkyl;

C₆ to C14 aryl;

alicyclic;

heterocyclic;

or a reporter molecule;

X is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO₂ CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl;

Q is O, CH₂, CHF or CF₂ ; and

B_x is a heterocyclic base.

5. The compound of claim 4 wherein said RC has formula OC(O)--R₅ ;

and where R₅ is C₁ -C₁₀ straight chain or branch chain alkyl.

6. The compound of claim 4 wherein said RC is OC(O) CH₃.

7. A method for forming a covalent linkage having structure:

##STR9## comprising the steps of;

a) providing a first compound having structure;

##STR10## wherein;

L₁ -L₂ -L₃ -L₄ is CR_1a R_1b -CR_2a -R_2b -CR_3a -R_3b -Z₄, CR_1a R_1b -CR_2a -R_2b -Z₃ -Z₄, CR_1a R_1b -Z₂ -CR_2a R_2b -₄, Z₁ -CR_1a R_1b -CR_2a R_2b Z₄, CR_1a R_1b -Z₂ -Z₃ -Z₄, Z₁ -CR_2a R_2b -Z₃ -Z₄ or Z₁ -Z₂ -CR_3a R_3b -Z₄ ;

R_E is Y-Z_N -R_A -Z₄ ;

Z₂, Z₃ and Z₄ are, independently, O, S, NR₄, Se, P(=j₁)J₂ or Si(R₆)₂ ;

R_A is CR_3a R_3b, CR_2a R_2b -CR_3a R_3b, CR_2a R_2b -Z₃, Z₂ -CR_3a R_3b or Z₂ -Z₃ ;

Z_N is CR_1a R_1b, NR₄, S, Se, P(=J₁)J₂, Si(R₆)₂, or O;

Y is a labile functional group;

R_1a, R_1b, R_2a, R_2b, R_3a and R_3b are, independently, H, R₅, O-R₅, S-R₅, NR₄ R₅ ;

or, independently, together R_1a and R_1b, or R_2a and R_2b, or R_3a and R_3b are=O;

J₁ is O, S, Se or NR₄ ;

J₂ is OH, OR₅, SH, SR₅, SeH, R₅, BH₃ or NR₄ R₅ ;

R₄, R₅ and R₆ are, independently, H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ substituted or unsubstituted alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

C₆ to C₁₄ aryl;

alicyclic;

heterocyclic;

or a reporter molecule;

X is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl;

Q is O or CH₂ ;

Bx is a heterocyclic base;

b) removing said Y group in a manner generating an anion at Z_N ; and

c) reacting said first compound having said anion thereon with a second compound of the structure;

##STR11## wherein;

R_B is trifluoromethylsulfonyl, methylsulfonyl, halogen, O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-toluenesulfonyl, 4-dimethylaminoazobenzene-sulfonyl or 5-dimethylaminonaphthalenesulfonyl.

9. The method of claim 7 including repeating said steps b) and c) multiple times.

8. A method for forming a covalent linkage having structure:

##STR12## comprising the steps of;

providing a first compound having structure;

##STR13## contacting said first compound with a second compound having structure;

##STR14## said contacting being for a time and under reaction conditions effective to form said linkage;

wherein;

(3'"'"')-L₁ -L₂ -L₃ -L₄ -(5'"'"') is CR_1a R_1b -CR_2a R_2b -CR_3a R_3b -Z₄, CR_1a R_1b -CR_2a R_2b -Z₃ -Z₄, CR_1a R_1b -Z₂ -CR_2a R_2b -Z₄, Z₁ -CR_1a R_1b -CR_2a R_2b -Z₄, CR_1a R_1b -Z₂ -Z₃ -Z₄, Z₁ -CR_2a R_2b -Z₃ -Z₄ or Z₁ -Z₂ -CR_3a R_3b -Z₄ ;

R_c is trifluoromethylsulfonyl, methylsulfonyl, halogen, O-trichloroacetimidate, acyloxy, dialkyl phosphite, 2,4,6-trichlorophenyl, p-toluenesulfonyl, 4-dimethylaminoazobenzene-sulfonyl or 5-dimethylaminonaphthalenesulfonyl;

R_F is CR_1a R_1b -CR_2a R_2b -CR_3a R_3b -Z₄, CR_1a R_1b -CR_2a R_2b -Z₃ -Z₄, CR_1a R_1b -Z₂ -CR_2a R_2b -Z₄, Z₁ -CR_1a R_1b -CR_2a R_2b -Z₄, CR_1a R_1b -Z₂ -Z₃ -Z₄, Z-₁ -CR_2a R_2b -Z₃ -Z₄ or Z₁ -Z₂ -CR_3a R_3b Z₄ ;

R_E is R_C, a nucleoside, a nucleotide, an oligonucleotide, an oligonucleoside or hydroxymethyl;

R_D is R_F, hydroxyl, a nucleoside, a nucleotide, an oligonucleotide or an oligonucleoside;

Z₁, Z₂, Z₃ and Z4 are, independently, O, S, NR₄, Se, P(=J₁)J₂ or Si(R₆)₂ ;

R_1a, R_1b, R_2a, R_2b, R_3a and R_3b are, independently, H, R₅, O-R₅, S-R₅, NR₄ R₅ ;

or, independently, together R_1a and R_1b, or R_2a and R_2b, or R_3a and R_3b are=O;

J₁ is O, S, Se or NR₄ ;

J₂ is OH, OR₅, SH, SR₅, SeH, R₅ , BH₃ or NR₄ R₅ ;

R₄, R₅ and R₆ are, independently, H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ substituted or unsubstituted alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

C₆ to C₁₄ aryl;

alicyclic;

heterocyclic;

a reporter molecule;

X is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO₂ CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl;

Q is O or CH₂ ; and

Bx is a heterocyclic base.