Modifications of antimetabolite gemcitabine for incorporation in CpG oligonucleotides

Abstract

This Divisional application of patent application Ser. No. 10/768,996, entitled “Novel Oligonucleotides And Related Compounds” discloses a class of chemical compounds which have been demonstrated to possess cancer fighting properties. The parent application disclosed oligonucleotides for selectively killing cancerous cells over noncancerous cells by incorporating and covalently linking antimetabolite prodrugs via CpG moieties, for the anitmetabolite Gemcitabine and other compounds with known cancer fighting properties. This application discloses modifications of Gemcitabine for incorporation into CpG oligonucleotides for improved biochemical and biological properties.

1 . A compound having purity in excess of 97% by HPLC, having the formula: 
       
         
           
           
               
               
           
         
         wherein R is selected from the group consisting of H, a C1-C6 alkyl, a halogen, a C2-C6 alkenyl, and a C2-C6 alkynyl; 
         x is an exocyclic amine-protecting group that is a member of the group ((C1-C6) alkanoyl group containing a straight or a branched chain alkyl group, an aryl or substituted aryl having a C1-C6 alkyl or halogen as a substituent on the aryl ring, phenoxy acetyl or appropriately protected phenoxy acetyl, trifluroacetyl, FMOC group, imine derivative, formamidine, dimethylformamidine, and dialkylformamidine); and
 y, and z are each selected from the group (H, a hydroxyl-protecting group that is stable during oligonucleotide synthesis, phosphoramidite, and a group that can be attached to a solid support). 
 
       
     
     
         2 . A compound having purity in excess of 97% by HPLC, having the formula: 
       
         
           
           
               
               
           
         
       
       wherein R is selected from the group consisting of (H, C1-C6 alkyl, halogen, C2-C6 alkenyl, and C2-C6 alkynyl);
 x is an exocyclic amine-protecting group that is a member of the group ((C1-C6) alkanoyl group containing a straight or a branched chain alkyl group, an aryl or substituted aryl having a C1-C6 alkyl or halogen as a substituent on the aryl ring, phenoxy acetyl or appropriately protected phenoxy acetyl, trifluroacetyl, FMOC group, imine derivative, formamidine, dimethylformamidine, and dialkylformamidine); and 
 y, and z are each selected from the group (H, a hydroxyl-protecting group that is stable during oligonucleotide synthesis, phosphoramidite, an active ester, and a group that can be attached to a solid support). 
 
     
     
         3 . The compound of  claim 1  or  2  having purity in excess of 98% by HPLC. 
     
     
         4 . The compound of  claim 1 , wherein z is C(O)-M-C(O)—NH, where NH is attached to a solid support, where M is selected from the group consisting of (succinyl, oxalyl, hydroquinolynyl, C1-C20 alkyl, ethyloxyglycol, and a combination of alkyl and ethyleneglycoxy). 
     
     
         5 . The compound of  claim 2 , wherein z is C(O)-M-C(O)—NH, where NH is attached to a solid support, M is selected from the group consisting of (succinyl, oxalyl, hydroquinolynyl, C1-C20 alkyl, ethyloxyglycol, and a combination of alkyl and ethyleneglycoxy). 
     
     
         6 . The compound of  claim 1 , where said active ester z has the structure: 
       
         
           
           
               
               
           
         
       
       wherein M is selected from the group consisting of (succinyl, oxalyl, hydroquinolynyl, C1-C20 alkyl, ethyloxyglycol, and a combination of alkyl and ethyleneglycoxy). 
     
     
         7 . A compound of  claim 2 , where said active ester z has the formula: 
       
         
           
           
               
               
           
         
       
       wherein M is selected from the group consisting of (succinyl, oxalyl, hydroquinolynyl, C1-C20 alkyl, ethyloxyglycol, and a combination of alkyl and ethyleneglycoxy). 
     
     
         8 . The compound of  claim 2  where said phosphoramidite z has the formula: 
       
         
           
           
               
               
           
         
       
       and R′ and R″ are independently selected from the group consisting of a C1-C6 alkyl and a C2-C6 cycloalkyl. 
     
     
         9 . A compound of  claim 1 , where said phosphoramidite z has the formula: 
       
         
           
           
               
               
           
         
         and R′ and R″ are independently selected from the group consisting of a C1-C6 alkyl and a C2-C6 cycloalkyl. 
       
     
     
         10 . The compound of  claim 8  or  9  having purity in excess of 98% by HPLC.