Nucleic acid compounds with conformationally restricted monomers and uses thereof

Abstract

This disclosure provides single-stranded and multi-stranded nucleic acid compounds having one or more double-stranded regions that regulate the function or expression of nucleic acid molecules expressed in a cell or a cell regulatory system dependent upon a nucleic acid. The disclosure provides a range of nucleic acid compounds having one or more conformationally restricted nucleomonomers (CRN). Certain nucleic acid compounds may have one or more conformationally restricted nucleomonomers and one or more hydroxymethyl substituted nucleomonomers (UNA). The nucleic acid compounds are useful in various therapeutic modalities.

1 . A nucleic acid compound comprising a first strand having from 10 to 60 nucleomonomers, wherein from 1 to 45 of the nucleomonomers of the first strand are the same or different conformationally restricted nucleomonomers each independently selected from
 Monomer R having the formula:   
       
         
           
           
               
               
           
         
         
           wherein X is independently for each occurrence selected from O, S, CH 2 , C═O, C═S, C═CH 2 , CHF or CF 2 ; 
           R 2  and R 3  are phosphodiester linkages of the nucleic acid compound; and 
           B is a nucleobase or nucleobase analog; and 
         
         Monomer Q having the formula: 
       
       
         
           
           
               
               
           
         
         
           wherein X and Y are independently for each occurrence selected from O, S, CH 2 , C═O, C═S, C═CH 2 , CHF, CF 2 ; 
           Z is independently for each occurrence selected from N or CH; 
           R 2  is independently for each occurrence selected from hydrogen, —F, —OH, —OCH 3 , —OCH 3 OCH 3 , —OCH 2 CH 3 OCH 3 , —CH 2 CH 3 OCH 3 , —CH(OCH 3 )CH 3 , allyl; 
           R 1  and R 3  are phosphodiester linkages of the nucleic acid compound; and 
           B is a nucleobase or nucleobase analog; 
         
       
       wherein each nucleobase or nucleobase analog in the strand is independently selected from adenine, cytosine, guanine, uracil, hypoxanthine, thymine, 7-deazaadenine, inosine, C-phenyl, C-naphthyl, inosine, an azole carboxamide, nebularine, a nitropyrrole, a nitroindole, 2-aminopurine, 2,6-diaminopurine, hypoxanthine, pseudouridine, 5-methyluridine, 5-propynylcytidine, isocytidine, isoguanine, 7-deazaguanine, 2-thiopyrimidine, 6-thioguanine, 4-thiothymine, 4-thiouracil, O 6 -methylguanine, N 6 -methyladenine, O 4 -methylthymine, 5,6-dihydrothymine, 2-thioribothymidine, 5,6-dihydrouracil, 4-methylindole, ethenoadenine, deoxyuridine, and any existing deoxy analogs of the foregoing. 
     
     
         2 . The compound of  claim 1 , wherein the compound contains two or more of the same or different Monomer R. 
     
     
         3 . The compound of  claim 1 , wherein the compound contains two or more of the same or different Monomer Q. 
     
     
         4 . The compound of  claim 1 , wherein the first strand has from 19 to 27 nucleomonomers. 
     
     
         5 . The compound of  claim 1 , wherein the nucleic acid is RNA. 
     
     
         6 . The compound of  claim 1 , wherein the nucleic acid is RNA and DNA. 
     
     
         7 . The compound of  claim 1 , further comprising one or more hydroxymethyl substituted nucleomonomers. 
     
     
         8 . The compound of  claim 1 , further comprising one or two additional strands each having from 7 to 60 nucleomonomers, wherein at least a portion of each of the additional strands is complementary to a portion of the first strand, wherein the first strand and the one or two additional complementary strands can anneal to form one or more duplex portions having a total of from 8 to 60 base pairs in the duplex portions, and wherein one or more of the nucleomonomers of the one or two additional strands is a conformationally restricted nucleomonomer. 
     
     
         9 . The compound of  claim 8 , wherein any one or more of the strands includes a sequence for PLK1 selected from SEQ ID NOs:161-220. 
     
     
         10 . The compound of  claim 8 , wherein any one or more of the strands includes a sequence for Survivin BIRC5 selected from SEQ ID NOs:1-160. 
     
     
         11 . The compound of  claim 8 , wherein any one or more of the strands includes a sequence for Factor VII selected from SEQ ID NOs:474-495. 
     
     
         12 . The compound of  claim 8 , wherein any one or more of the strands includes a sequence for ApoB selected from SEQ ID NOs:496-507. 
     
     
         13 . The compound of  claim 8 , wherein any one or more of the strands includes a sequence selected from SEQ ID NOs:221-230, 231-245, 246-255, 256-265, 266-275, 276-285, 286-295, 296-305, 306-315, 316-325, 326-335, 336-345, 346-355, 356-365, 366-375, 376-385, 386-395, 396-405, 406-415, 416-425, 426-435, 436-445, 446-455, 456-465, 508-517, and 518-527. 
     
     
         14 . The compound of  claim 8 , wherein the conformationally restricted nucleomonomers are only present in either of the one or more additional strands, and the first strand does not contain any conformationally restricted nucleomonomers. 
     
     
         15 . The compound of  claim 8 , wherein the melting temperature of the compound is increased by at least 1° C. over the same compound that does not contain any conformationally restricted nucleomonomers. 
     
     
         16 . The compound of  claim 8 , wherein the compound is an siRNA. 
     
     
         17 . The compound of  claim 8 , wherein the compound is an mdRNA. 
     
     
         18 . The compound of  claim 8 , wherein the compound is RNA and DNA. 
     
     
         19 . The compound of  claim 8 , wherein one of the additional strands has one or more nicks. 
     
     
         20 . The compound of  claim 8 , wherein the compound has one or more duplex gaps that are each independently from 1 to 10 unpaired nucleomonomers in length. 
     
     
         21 . The compound of  claim 8 , wherein the compound has a blunt end. 
     
     
         22 . The compound of  claim 8 , wherein the compound has a 3′-end overhang. 
     
     
         23 . The compound of  claim 8 , further comprising one or more hydroxymethyl substituted nucleomonomers. 
     
     
         24 . The compound according to  claim 1  for use in delivering an RNA agent into a cell or an organism. 
     
     
         25 . The compound according to  claim 1  for use in mediating nucleic acid modification of a target nucleic acid in a cell or an organism. 
     
     
         26 . The compound according to  claim 1  for use in decreasing expression levels of a target mRNA in a cell or an organism. 
     
     
         27 . The compound according to  claim 1  for use in inhibiting an endogenous nucleic acid-based regulatory system in a cell or an organism. 
     
     
         28 . The compound according to  claim 1  for use in gene regulation, gene analysis, or RNA interference. 
     
     
         29 . The compound according to  claim 1  for use in the manufacture of a medicament for a therapeutic target, including targets for cancers, metabolic diseases, inflammatory diseases, and viral infections. 
     
     
         30 . The compound according to  claim 1  for use in treating a disease, condition or disorder, including cancers, metabolic diseases, inflammatory diseases, and viral infections. 
     
     
         31 . A method for treating a disease, condition or disorder in a subject including cancers, metabolic diseases, inflammatory diseases, and viral infections, the method comprising administering to the subject a compound according to  claim 1 .