Multimeric oligonucleotide compounds

Abstract

The disclosure provides multimeric oligonucleotide compounds, comprising two or more target-specific oligonucleotides (e.g., antisense oligonucleotides (ASOs)), each being resistant to cleavage, and linked together by a cleavable linker. In particular, two or more linked target-specific oligonucleotides, each to a different target, allows concomitant inhibition of multiple genes' expression levels, while exhibiting favorable pharmacokinetic and pharmacodynamic properties. Methods of making and uses of the described compounds are also provided

1 . A compound comprising the general formula: X-L-[X-L] i -X,
 wherein i is an integer from 0 to 9, the value of which indicates the number of units of [X-L] i  present in the compound,   wherein each X is independently a targeting oligonucleotide of 8 to 50 nucleotides in length having a region of complementarity comprising at least 7 contiguous nucleotides complementary to a target region of a genomic target sequence, and each L is a linker that links at least two Xs and that is more susceptible to cleavage in a mammalian extract than each X,   wherein when i=0, and wherein the general formula is 5′X3′-L-5′X3′ and when the target regions complementary to the first X and second X do not overlap in the genomic target sequence, the 5′-end of the target region complementary to the first X and the 3′-end of the target region complementary to the second X are not within a distance of 0 to 4 nucleotides in the genomic target sequence,   wherein at least one L does not comprise an oligonucleotide having a self-complementary nucleotide sequence, and wherein at least one L does not comprise an oligonucleotide having a nucleotide sequence that is complementary to a region of the genomic target sequence that is contiguous with the target regions complementary to two immediately flanking Xs, and wherein at least one L does not comprise an oligonucleotide and at least one L does not comprise a disulfide bond.   
     
     
         2 . (canceled) 
     
     
         3 . The compound of  claim 1 , wherein for at least one L the linker comprises an oligonucleotide that is more susceptible to cleavage by an endonuclease in the mammalian extract than the targeting oligonucleotides. 
     
     
         4 . The compound of  claim 1 , wherein at least one L is a linker having a nucleotide sequence comprising from 1 to 10 thymidines or uridines. 
     
     
         5 . The compound of  claim 1 , wherein at least one L is a linker having a nucleotide sequence comprising deoxyribonucleotides linked through phosphodiester internucleotide linkages. 
     
     
         6 . The compound of  claim 1 , wherein at least one L is a linker having a nucleotide sequence comprising from 1 to 10 thymidines linked through phosphodiester internucleotide linkages. 
     
     
         7 . (canceled) 
     
     
         8 . The compound of  claim 1 , wherein at least one L is a linker having the formula: 
       
         
           
           
               
               
           
         
       
       wherein Z is an oligonucleotide. 
     
     
         9 . The compound of  claim 8 , wherein Z has a nucleotide sequence comprising from 1 to 10 thymidines or uridines. 
     
     
         10 - 16 . (canceled) 
     
     
         17 . The compound of  claim 1 , wherein at least one L is a linker comprising the formula —(CH 2 ) n S—S(CH 2 ) m —, wherein n and m are independently integers from 0 to 10. 
     
     
         18 - 29 . (canceled) 
     
     
         30 . A compound comprising at least two targeting oligonucleotides of 8 to 50 nucleotides in length linked through a linker that is at least 2-fold more sensitive to enzymatic cleavage in the presence of a mammalian extract than the at least two targeting oligonucleotides, wherein each targeting oligonucleotide has a region of complementarity comprising at least 7 contiguous nucleotides complementary to a target region of a genomic target sequence, and wherein at least one L does not comprise an oligonucleotide and at least one L does not comprise a disulfide bond. 
     
     
         31 . (canceled) 
     
     
         32 . The compound of  claim 30 , wherein the linker is an oligonucleotide. 
     
     
         33 - 64 . (canceled) 
     
     
         65 . A composition comprising a compound of  claim 1  and a carrier. 
     
     
         66 - 67 . (canceled) 
     
     
         68 . A pharmaceutical composition comprising a compound of  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         69 . A kit comprising a container housing the composition of  claim 65 . 
     
     
         70 . A method of increasing expression of a target gene in a cell, the method comprising: contacting the cell with the compound of  claim 1 , and maintaining the cell under conditions in which the compound enters into the cell, wherein the genomic target sequence of at least one targeting oligonucleotide of the compound is present in the sense strand of an lncRNA gene, the product of which inhibits expression of the target gene. 
     
     
         71 . (canceled) 
     
     
         72 . A method of increasing levels of a target gene in a subject, the method comprising administering the compound of  claim 1  to the subject, wherein the genomic target sequence of at least one targeting oligonucleotide of the compound is present in the sense strand of an lncRNA gene, the product of which inhibits expression of the target gene. 
     
     
         73 . A method of treating a condition associated with decreased levels of a target gene in a subject, the method comprising administering the compound of  claim 1  to the subject, wherein the genomic target sequence of at least one targeting oligonucleotide of the compound is present in the sense strand of an lncRNA gene, the product of which inhibits expression of the target gene. 
     
     
         74 . A method of modulating activity of a target gene in a cell, the method comprising: contacting the cell with the compound of  claim 1 , and maintaining the cell under conditions in which the compound enters into the cell, wherein the genomic target sequence of at least one targeting oligonucleotide is present in the sense strand of the target gene. 
     
     
         75 . (canceled) 
     
     
         76 . A method of modulating levels of a target gene in a subject, the method comprising administering the compound of  claim 1  to the subject, wherein the genomic target sequence of at least one targeting oligonucleotide is present in the sense strand of the target gene. 
     
     
         77 . (canceled)