Design of oligonucleotide analogs as therapeutic agents

Abstract

The invention relates to design of short oligonucleotides and analogs thereof (such as, di-, and trinucleotide compounds) useful for various therapeutic applications. It is believed that the compounds of the invention can be used as antiviral agents, anticancer agents and so on. In certain embodiments, the compounds of the invention can modulate immune-stimulatory pathways and non-TLR pathways. The invention also relates to design modified oligonucleotides for therapeutic applications, by excluding nucleotide segments having off-target effects from the modified oligonucleotides. In another aspect, the invention provides pharmaceutical compositions including one or more compounds of the invention. It is believed that the compounds and compositions as described herein have therapeutic utility against a variety of diseases, including viral diseases, autoimmune diseases (such as, allergy, asthma, and inflammatory disorders) and cancer.

1 - 25 . (canceled) 
     
     
         26 . A method of modulating the immune-mediated effects of a single-stranded or double-stranded RNA in a subject, the method comprising administering to the subject an effective amount of a chemically modified siRNA in which the nucleotide sequence of a compound of formula (I): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof is incorporated into one or both strands of the siRNA, wherein
 R 1  and R 2 , each independently, are hydrogen, OH, O-alkyl, alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-aryl, or O-heteroarylaryl; 
 R 3  is selected from hydrogen, alkyl, substituted alkyl, C(O)-alkyl, C(O)O-alkyl, C(O)-aryl, C(O)O-aryl, C(O)NH-alkyl, and C(O)NH-aryl; 
 Y and Z, each independently, are O or S; 
 B 1  and B 2 , on each occurrence, independently are adeninyl, guaninyl, thyminyl, cytosinyl, uracilyl, or a modified nucleoside moiety; 
 R 4  is hydrogen or a monophosphate, diphosphate, or triphosphate group; and 
 m is 1, 2, 3, 4, 5, or 6. 
 
     
     
         27 . The method of  claim 26 , wherein each of R 1  and R 2  is independently hydrogen, OH, or O-alkyl. 
     
     
         28 . The method of  claim 26 , wherein Z is O and Y is S. 
     
     
         29 . The method of  claim 26 , wherein R 3  is hydrogen or alkyl. 
     
     
         30 . The method of  claim 26 , wherein m is 1, 2, or 3. 
     
     
         31 . The method of  claim 26 , wherein the compound of formula (I) is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof. 
     
     
         32 . The method of  claim 31 , wherein the compound of formula (I) is incorporated into one strand of the chemically modified siRNA. 
     
     
         33 . The method of  claim 31 , wherein the compound of formula (I) is incorporated into both strands of the chemically modified siRNA. 
     
     
         34 . A method of modulating the immune-mediated effects of a single-stranded or double-stranded RNA in a subject, the method comprising administering to the subject an effective amount of a chemically modified siRNA comprising nucleotide overhangs in which the nucleotide sequence of a compound of formula (I): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof is incorporated into the nucleotide overhangs of the siRNA, wherein
 R 1  and R 2 , each independently, are hydrogen, OH, O-alkyl, alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-aryl, or O-heteroarylaryl; 
 R 3  is selected from hydrogen, alkyl, substituted alkyl, C(O)-alkyl, C(O)O-alkyl, C(O)-aryl, C(O)O-aryl, C(O)NH-alkyl, and C(O)NH-aryl; 
 Y and Z, each independently, are O or S; 
 B 1  and B 2 , on each occurrence, independently are adeninyl, guaninyl, thyminyl, cytosinyl, uracilyl, or a modified nucleoside moiety; 
 R 4  is hydrogen or a monophosphate, diphosphate, or triphosphate group; and 
 m is 1, 2, 3, 4, 5, or 6. 
 
     
     
         35 . The method of  claim 34 , wherein each of R 1  and R 2  is independently hydrogen, OH, or O-alkyl. 
     
     
         36 . The method of  claim 34 , wherein Z is O and Y is S. 
     
     
         37 . The method of  claim 34 , wherein R 3  is hydrogen or alkyl. 
     
     
         38 . The method of  claim 34 , wherein m is 1, 2, or 3. 
     
     
         39 . The method of  claim 34 , wherein the compound of formula (I) is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof. 
     
     
         40 . The method of  claim 39 , wherein the compound of formula (I) is incorporated into one strand of the chemically modified siRNA. 
     
     
         41 . The method of  claim 39 , wherein the compound of formula (I) is incorporated into both strands of the chemically modified siRNA. 
     
     
         42 . A method of modulating the immune-mediated effects of a double-stranded or single-stranded RNA in a subject, the method comprising administering to the subject an effective amount of a chemically modified siRNA in which the nucleotide sequence of a compound of formula (II): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof is incorporated into one or both strands of the siRNA, wherein
 X is absent, O, NH, NR, or S; 
 X 1  is absent, O, or NH; 
 A is absent, aryl, or aralkyl; 
 R is alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-alkyl, O-heteroaryl, or steroidal; 
 R 1  and R 2 , each independently, are hydrogen, OH, O-alkyl, alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-aryl, or O-heteroarylaryl; 
 R 3  is hydrogen, alkyl, substituted alkyl, C(O)-alkyl, C(O)O-alkyl, C(O)-aryl, C(O)O-aryl, C(O)NH-alkyl, or C(O)NH-aryl; 
 Y and Z, each independently, are O or S; 
 B 1  and B 2 , on each occurrence, independently are adeninyl, guaninyl, thyminyl, cytosinyl, uracilyl, or a modified nucleoside moiety; 
 R 4  is hydrogen or a monophosphate, diphosphate, or triphosphate group; and 
 m is 1, 2, 3, 4, 5, or 6; and 
 n is 0, 1, 2, 3, 4, or 5. 
 
     
     
         43 . The method of  claim 42 , wherein each of X and X 1  is independently O. 
     
     
         44 . The method of  claim 42 , wherein A is absent and n is 1. 
     
     
         45 . The method of  claim 42 , wherein Z is O and Y is S. 
     
     
         46 . The method of  claim 42 , wherein each of R 1  and R 2  is independently hydrogen, OH, or O-alkyl. 
     
     
         47 . The method of  claim 42 , wherein R 3  is hydrogen or alkyl. 
     
     
         48 . The method of  claim 42 , wherein m is 1, 2, or 3. 
     
     
         49 . The method of  claim 42 , wherein the compound of formula (II) is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof. 
     
     
         50 . The method of  claim 49 , wherein the compound of formula (II) is incorporated into one strand of the chemically modified siRNA. 
     
     
         51 . The method of  claim 49 , wherein the compound of formula (II) is incorporated into both strands of the chemically modified siRNA. 
     
     
         52 . A method of modulating the immune-mediated effects of a single-stranded or double-stranded RNA in a subject, the method comprising administering to the subject an effective amount of a chemically modified siRNA comprising nucleotide overhangs in which the nucleotide sequence of a compound of formula (II): 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof is incorporated into the nucleotide overhangs of the siRNA, wherein
 X is absent, O, NH, NR, or S; 
 X 1  is absent, O, or NH; 
 A is absent, aryl, or aralkyl; 
 R is alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-alkyl, O-heteroaryl, or steroidal; 
 R 1  and R 2 , each independently, are hydrogen, OH, O-alkyl, alkyl, substituted alkyl, cycloalkyl, aryl, substituted aryl, aralkyl, heterocyclyl, O-aryl, or O-heteroarylaryl; 
 R 3  is hydrogen, alkyl, substituted alkyl, C(O)-alkyl, C(O)O-alkyl, C(O)-aryl, C(O)O-aryl, C(O)NH-alkyl, or C(O)NH-aryl; 
 Y and Z, each independently, are O or S; 
 B 1  and B 2 , on each occurrence, independently are adeninyl, guaninyl, thyminyl, cytosinyl, uracilyl, or a modified nucleoside moiety; 
 R 4  is hydrogen or a monophosphate, diphosphate, or triphosphate group; and 
 m is 1, 2, 3, 4, 5, or 6; and 
 n is 0, 1, 2, 3, 4, or 5. 
 
     
     
         53 . The method of  claim 52 , wherein each of X and X 1  is independently O. 
     
     
         54 . The method of  claim 52 , wherein A is absent and n is 1. 
     
     
         55 . The method of  claim 52 , wherein Z is O and Y is S. 
     
     
         56 . The method of  claim 52 , wherein each of R 1  and R 2  is independently hydrogen, OH, or O-alkyl. 
     
     
         57 . The method of  claim 52 , wherein R 3  is hydrogen or alkyl. 
     
     
         58 . The method of  claim 52 , wherein m is 1, 2, or 3. 
     
     
         59 . The method of  claim 52 , wherein the compound of formula (II) is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
       or a pharmaceutically acceptable salt thereof. 
     
     
         60 . The method of  claim 59 , wherein the compound of formula (II) is incorporated into one strand of the chemically modified siRNA. 
     
     
         61 . The method of  claim 59 , wherein the compound of formula (II) is incorporated into both strands of the chemically modified siRNA.