Synthesis and uses of nucleic acid compounds with conformationally restricted monomers
View Patent ↗Processes for synthesis of conformationally restricted nucleomonomers (CRN) by ozonolysis or oxidation of a 2′-vinyl substituted nucleoside precursor with protected 3′-hydroxyl, 4′-hydroxymethyl and 5′-hydroxyl positions. The CRN nucleomonomers can be used to prepare nucleic acid compounds. CRN nucleomonomers for nucleic acid compounds can be prepared in high yields and in multi-gram scale. The nucleic acid compounds can be of various regulatory classes such as antisense RNA for therapeutic modalities useful for treating or preventing diseases or disorders by up- or down-regulating the expression of genes and other nucleic acid based regulatory systems in a cell.
1. A method for making a compound having Formula V
wherein R 1 is a substituent protecting group, R 2 is a substituent protecting group, one or both of R 1 and R 2 are bulky substituent protecting groups, R 1 and R 2 are optionally linked, R 3 is a protecting group, and B is a nucleobase or nucleobase analog, the method comprising providing a compound having Formula II,
transforming the compound having Formula II by ozonolysis or oxidation, followed by contacting with a reducing agent, and isolating the compound having Formula V, wherein the bulky substituent protecting groups are selected from trimethylsilyl (TMS), tert-butyldimethylsilyl (TBDMS), tri-iso-propylsilyloxymethyl (TOM) and dimethoxytrityl (DMT).
2. The method of claim 1 , wherein B is 1-uracilyl or 5-methyl-1-uracilyl.
3. The method of claim 1 , wherein R 1 and R 2 , optionally linked, is a 1,1,3,3-tetraalkyldisiloxane-1,3-diyl group.
4. The method of claim 1 , wherein R 1 and R 2 , optionally linked, is a 1,1,3,3-tetraisopropyldisiloxane-1,3-diyl group.
5. The method of claim 1 , wherein R 3 is benzyl.
6. The method of claim 1 , wherein the yield of the compound having Formula V by ozonolysis is at least 50% at a scale of at least 5 grams of the compound having Formula V.
7. The method of claim 1 , wherein the yield of the compound having Formula V by ozonolysis is at least 50% at a scale of at least 10 grams of the compound having Formula V.
8. The method of claim 1 , wherein the yield of the compound having Formula V ozonolysis is at least 70% at a scale of at least 10 grams of the compound having Formula V.
9. The method of claim 1 , wherein the yield of the compound having Formula V ozonolysis is at least 80% at a scale of at least 10 grams of the compound having Formula V.
10. The method of claim 1 , further comprising transforming the compound having Formula V to a conformationally restricted nucleomonomer CRN having Formula VI,
by the steps of:
deprotecting the 4′-hydroxymethyl groups of Formula V; and
forming a 2′-4′ —CH 2 OCH 2 — bridge.
11. The method of claim 10 , wherein the conformationally restricted nucleomonomer is a pyrimidine CRN.
12. A compound having the structure
wherein R is methyl, R 1 is independently H, alkyl, or a protecting group, and R 2 is independently H, alkyl, a protecting group, or a phosphoramidityl group.
13. A nucleic acid compound comprising a residue of the compound of claim 12 .
14. The nucleic acid compound of claim 13 , wherein the nucleic acid compound is a single stranded oligonucleotide or a double-stranded oligonucleotide.
15. The nucleic acid compound of claim 13 , wherein the nucleic acid compound is a microRNA, an antimir, an antagomir, a microRNA mimetic, a microRNA precursor, an RNA, a short interfering RNA or siRNA, a DNA, an RNA and DNA, a meroduplex RNA or mdRNA, a short hairpin RNA or shRNA, or an antisense oligonucleotide.
16. A compound having the structure
17. A nucleic acid compound comprising a residue of the compound of claim 16 .
18. The nucleic acid compound of claim 17 , wherein the nucleic acid compound is a single stranded oligonucleotide or a double-stranded oligonucleotide.
19. The nucleic acid compound of claim 17 , wherein the nucleic acid compound is a microRNA, an antimir, an antagomir, a microRNA mimetic, a microRNA precursor, an RNA, a short interfering RNA or siRNA, a DNA, an RNA and DNA, a meroduplex RNA or mdRNA, a short hairpin RNA or shRNA, or an antisense oligonucleotide.