Chiral library screen
The invention relates to a method of identifying stereodefined phosphorothioate oligonucleotide variants with reduced toxicity by creating and screening libraries of stereodefined chiral phosphorothioate variants for compounds with reduced toxicity, either in vitro or in vivo.
1. A method of reducing the toxicity of an LNA antisense oligonucleotide (parent oligonucleotide), wherein the antisense oligonucleotide is 10-20 nucleotides in length, comprising the steps of;
a) creating a library of stereodefined oligonucleotide variants (child oligonucleotides) each retaining a nucleobase sequence of at least 10 contiguous nucleotides of the parent oligonucleotide, wherein each child oligonucleotide has a pattern of chiral phosphorothioate linkages that differs from the parent and other child oligonucleotides,
b) screening the library created in step a) for their in vitro hepatotoxicity in a cell, and
c) identifying one or more child oligonucleotides present in the library which has a reduced hepatotoxicity in the cell as compared to the parent oligonucleotide.
2. The method according to claim 1 , wherein the parent oligonucleotide is an antisense gapmer oligonucleotide.
3. The method according to claim 2 , wherein each member of the library of stereodefined oligonucleotide variants comprises at least one stereodefined phosphorothioate internucleoside linkage in the gap-region of the gapmer.
4. The method according to claim 2 , wherein each member of the library of stereodefined oligonucleotide variants comprises at least one stereodefined phosphorothioate internucleoside linkage in one or both wing-regions of the gapmer.
5. The method according to claim 1 wherein each member of the library of stereodefined defined oligonucleotide variants comprises at least 2 stereodefined phosphorothioate linkages, wherein the remaining phosphorothioate linkages may optionally be non-stereodefined defined phosphorothioate linkages.
6. The method according to claim 1 , wherein all phosphorothioate linkages present in each member of the library of stereodefined defined oligonucleotide variants are stereodefined phosphorothioate linkages.
7. The method according to claim 2 , wherein all internucleoside linkages present in each member of the library of stereodefined defined oligonucleotide variants are stereodefined phosphorothioate linkages.
8. The method according to claim 1 , wherein each member of the library of stereodefined oligonucleotide variants retains the pattern of modified and unmodified nucleosides present in the parent oligonucleotide.
9. The method according to claim 2 , wherein the parent gapmer oligonucleotide is a LNA gapmer.
10. The method according to claim 1 , wherein the method further comprises the step of determining the IC50 of the one or more of the child oligonucleotides identified in step c).
11. The method according to claim 10 , wherein the child oligonucleotides identified in step c. retain at least 25% of the IC50 of the parent.
12. The method according to claim 10 , wherein the stereodefined oligonucleotide variant(s) identified in step c. retain an EC50 value of not larger than 3 to 10 times that of the parent compound.
13. The method according to claim 1 , wherein the parent oligonucleotide and the members of the library of stereodefined oligonucleotide variants comprise at least one LNA nucleoside selected from the group consisting of beta-D-oxy-LNA, 6′-methyl beta-D-oxy LNA nucleosides and S(cET).
14. The method according to claim 1 , wherein the library screen performed in step b) comprises screening for hepatotoxicity in vitro in primary hepatocytes.