Novel sirna structures

Abstract

The invention relates to siRNA compounds possessing novel sequences and structural motifs which down-regulate the expression of specific human genes. The invention also relates to pharmaceutical compositions comprising such compounds and a pharmaceutically acceptable carrier. The present invention also provides a method of treating and/or preventing the incidence or severity of various diseases or conditions associated with the genes and/or symptoms associated with such diseases or conditions comprising administering to a subject in need of treatment for such disease or condition and/or symptom the compound or the pharmaceutical composition in a therapeutically effective dose so as to thereby treat the subject.

1 . A double-stranded nucleic acid compound having structure (IX) set forth below: 
       
         
           
                 
                 
                 
               
                   (IX) 
                   5′ (N)x -Z 3′ 
                   (antisense strand) 
                 
                     
                 
                     
                   3′ Z′-(N′)y-z″ 5′ 
                   (sense strand) 
                 
             
                
                
                
               
            
           
         
         wherein each of N and N′ is a ribonucleotide which may be unmodified or modified, or an unconventional moiety; 
         wherein each of (N)x and (N′)y is an oligonucleotide in which each consecutive N or N′ is joined to the next N or N′ by a covalent bond; 
         wherein Z and Z′ may be present or absent, but if present is independently 1-5 consecutive nucleotides covalently attached at the 3′ terminus of the strand in which it is present; 
         wherein z″ may be present or absent, but if present is a capping moiety covalently attached at the 5′ terminus of (N′)y; 
         wherein x=18 to 27; 
         wherein y=18 to 27; 
         wherein (N)x comprises modified and unmodified ribonucleotides, each modified ribonucleotide having a 2′-O-methyl on its sugar, wherein N at the 3′ terminus of (N)x is a modified ribonucleotide, (N)x comprises at least five alternating modified ribonucleotides beginning at the 3′ end and at least nine modified ribonucleotides in total and each remaining N is an unmodified ribonucleotide; 
         wherein in (N′)y at least one unconventional moiety is present, which unconventional moiety may be an abasic ribose moiety, an abasic deoxyribose moiety, a modified or unmodified deoxyribonucleotide, a mirror nucleotide, and a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond; and 
         wherein the sequence of (N)x is substantially or fully complementary to the sequence of (N′)y; and the sequence of (N′)y is substantially or fully identical to the sequence of an mRNA encoded by a target gene. 
       
     
     
         2 . The compound according to  claim 1 , wherein x=y=19. 
     
     
         3 . (canceled) 
     
     
         4 . (canceled) 
     
     
         5 . The compound according to  claim 2 , wherein the at least one unconventional moiety is a mirror nucleotide. 
     
     
         6 . The compound according to  claim 5 , wherein the mirror nucleotide is present at position 17, position 18 or positions 17 and 18. 
     
     
         7 .- 8 . (canceled) 
     
     
         9 . The compound according to  claim 40 , wherein (N)x comprises nine alternating modified ribonucleotides. 
     
     
         10 . The compound according to  claim 40 , wherein z″ is present. 
     
     
         11 . (canceled) 
     
     
         12 . A double-stranded nucleic acid compound having structure (X) set forth below: 
       
         
           
                 
                 
                 
                 
               
                     
                   (X) 
                   5′ (N)x - Z 3′ 
                   (antisense strand) 
                 
                     
                     
                 
                     
                     
                   3′ Z′-(N′)y-z″ 5′ 
                   (sense strand) 
                 
             
                
                
                
               
            
           
         
         wherein each of N and N′ is a ribonucleotide which may be unmodified or modified, or an unconventional moiety; 
         wherein each of (N)x and (N′)y is an oligonucleotide in which each consecutive N or N′ is joined to the next N or N′ by a covalent bond; 
         wherein Z and Z′ may be present or absent, but if present is independently 1-5 consecutive nucleotides covalently attached at the 3′ terminus of the strand in which it is present; 
         wherein z″ may be present or absent but if present is a capping moiety covalently attached at the 5′ terminus of (N′)y; 
         wherein x=18 to 27; 
         wherein y=18 to 27; 
         wherein (N)x comprises modified or unmodified ribonucleotides, and optionally at least one unconventional moiety; 
         wherein in (N′)y at least one unconventional moiety is present, which unconventional moiety may be an abasic ribose moiety, an abasic deoxyribose moiety, a modified or unmodified deoxyribonucleotide, a mirror nucleotide, a non-base pairing nucleotide analog or a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond; and 
         wherein the sequence of (N)x is substantially or fully complementary to the sequence of (N′)y; and the sequence of (N′)y is substantially or fully identical to the sequence of an mRNA encoded by a target gene. 
       
     
     
         13 . The compound according to  claim 12 , wherein x=y=19. 
     
     
         14 - 34 . (canceled) 
     
     
         35 . The compound according  claim 47 , wherein the oligonucleotide sequences of (N)x and (N′)y comprise any one of the sequence pairs set forth in SEQ ID NOS: 229 and 230; 231-232; 233-234; 235-236; 237-238; 239-240; 241-242; 243-244; 245-246; 247-248; 249-250; 251-252; 253-254; or 255-256. 
     
     
         36 . A pharmaceutical composition comprising the compound according to  claim 38 ; and a pharmaceutically acceptable carrier. 
     
     
         37 . A method for treating or preventing the incidence or severity of a disease or condition in a subject in need thereof wherein the disease or condition and/or symptoms associated therewith is selected from the group consisting of, glaucoma, ocular ischemic conditions including anterior ischemic optic neuropathy, cord injury, and ION, comprising administering to the subject a pharmaceutical composition according to  claim 36  in an amount effective to prevent or treat the disease or condition. 
     
     
         38 . The compound according to  claim 2 , wherein the target gene encodes a human RhoA mRNA (SEQ ID NO:46). 
     
     
         39 . The compound according to  claim 38 , wherein in (N′)y the unconventional moiety is a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond. 
     
     
         40 . The compound according to  claim 39 , wherein the nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond is present at positions 17 and 18; or at positions 17, 18 and 19. 
     
     
         41 . The compound according to  claim 10 , wherein z″ is a capping moiety selected from the group consisting of an abasic ribose moiety, an abasic deoxyribose moiety, and inverted abasic ribose moiety, an inverted abasic deoxyribose moiety, C6-amino-Pi, and a mirror nucleotide, covalently attached at the 5′ terminus of (N′)y. 
     
     
         42 . The compound according to  claim 9 , wherein (N)x comprises 2′-O-methyl sugar modified ribonucleotides at positions 1, 3, 5, 7, 9, 11, 13, 15, 17 and 19. 
     
     
         43 . The compound according to  claim 9 , wherein (N)x comprises 2′-O-methyl sugar modified ribonucleotides at positions 2, 4, 6, 8, 11, 13, 15, 17 and 19. 
     
     
         44 . The compound according to  claim 38 , wherein z″ is absent. 
     
     
         45 . The compound according to  claim 38 , wherein at least one of Z or Z′ is present. 
     
     
         46 . The compound according to  claim 38 , wherein both Z and Z′ are absent. 
     
     
         47 . The compound according to  claim 38 , wherein (N)x is fully complementary to the sequence of (N′)y; and the sequence of (N′)y is substantially identical or fully identical to the sequence of the RhoA mRNA. 
     
     
         48 . The compound according  claim 47 , wherein the oligonucleotide sequences of (N)x and (N′)y comprise any one of the sequence pairs set forth in SEQ ID NOS:87121-87122; 87123-87124; 87125-87126; 87127-87128; 87129-87130; 87131-87132; 87133-87134; 87135-87136; 87137-87138; 87139-87140; 87141-87142; 87143-87144; 87145-87146; 87147-87148; 87149-87150; or 87151-87152.