Combinatorial library synthesis and pharmaceutically active compounds produced thereby

Abstract

The invention provides new methods for synthesis of nucleotide-based compounds and new libraries of such compounds. Compounds of the invention are useful for a variety of therapeutic applications, including treatment of viral or bacterial infections and associated diseases and disorders.

What is claimed is:  
     
         1 . A compound library comprising two or more compounds of the following  
       
         
           
           
               
               
           
         
       
       Formula I or I′: 
 wherein L is a linking group such as e.g. an amide, ester, diester or the like, or an optionally substituted alkylene (e.g. C 1-20  alkylene), optionally substituted alkenylene (e.g., C 2-20  alkenylene) or alkynylene (e.g., C 2-20  alkynylene) having such groups either as a chain member of pendant to the chain, and which may be optionally substituted with one or more substituents selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or an enzymatically reactive;  
 Q is carbon or a heteroatom such as O, S or N;  
 R is hydrogen or a hydroxyl group or an optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aralkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
 R 1 , R 2 , R 3  and R 4  are each independently selected from a group as defined by R;  
 B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused rings and 1 to 3 N, O or S atoms, or a heterocyclic structure that is covalently linked to the sugar ring;  
 n=1 to 5;  
 and pharmaceutically acceptable salts thereof.  
 
     
     
         2 . The library of  claim 1  wherein at least one compound has a sugar group is in open chain form.  
     
     
         3 . The library of  claim 1  wherein an enantiomerically enriched mixture of a compound is present.  
     
     
         4 . A compound library comprising two or more compounds of the following Formula II or II′:  
       
         
           
           
               
               
           
         
         X and Y are each independently selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or one or both of X and Y are an enzymatically reactive moiety;  
         R is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aralkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
         R 1 , R 2 , and R 3  are each independently selected from a group as defined by R;  
         B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, alkynyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms, or a heterocyclic structure that is covalently linked to the sugar ring;  
         and pharmaceutically acceptable salts thereof.  
       
     
     
         5 . The library of  claim 1  wherein at least one compound is of the following formula IIA or IIA′:  
       
         
           
           
               
               
           
         
         X and Y are each independently selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or one or both of X and Y are an enzymatically reactive moiety;  
         R is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aralkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
         R 1 , R 2  and R 3  are each independently selected from a group as defined by R;  
         B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, alkynyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms, or a heterocyclic structure that is covalently linked to the sugar ring;  
         and pharmaceutically acceptable salts thereof.  
       
     
     
         6 . The library of  claim 1  wherein the library has been constructed using solid-phase synthesis.  
     
     
         7 . The library of  claim 1  wherein the library has been constructed using solution phase synthesis.  
     
     
         8 . Use of the library of  claim 1  to find a specific interacting partner for a nucleic acid.  
     
     
         9 . Use of the library of  claim 1  to find a specific interacting partner for a protein.  
     
     
         10 . The use of  claim 8  wherein the nucleic acid is RNA or DNA.  
     
     
         11 . The use of  claim 9  wherein the protein is an antibody, receptor or ligand.  
     
     
         12 . A compound of the following Formula I or I′:  
       
         
           
           
               
               
           
         
         wherein L is a linking group such as an amide, ester, diester or the like which may be optionally substituted with one or more substituents selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or an enzymatically reactive moiety;  
         Q is carbon or a heteroatom such as O, S or N;  
         R is hydrogen or a hydroxyl group or an optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aralkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
         R 1 , R 2 , R 3  and R 4  are each independently selected from a group as defined by R;  
         B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused rings and 1 to 3 N, O or S atoms, or or B is heteroaromatic or heteroalicyclic group other than an adenine, thymidine, cytosine or guanine;  
         N is an integer of from 1 (where to form a 5-membered ring as depicted or 5-membered acyclic group) to 5;  
         and pharmaceutically acceptable salts thereof.  
       
     
     
         13 . A compound of the following Formula II or II′:  
       
         
           
           
               
               
           
         
         X and Y are each independently selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or one or both of X and Y are an enymatically reactive moiety;  
         R is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aralkyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
         R 1 , R 2  and R 3  are each independently selected from a group as defined by R;  
         B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms, or a heterocyclic structure that is covalently linked to the sugar ring;  
         and pharmaceutically acceptable salts thereof.  
       
     
     
         14 . A compound of  claim 12  wherein the sugar group is in open chain form.  
     
     
         15 . A compound of  claim 12  wherein an enantiomerically enriched mixture of a compound is present.  
     
     
         16 . A compound of the following Formula IIA or IIA′:  
       
         
           
           
               
               
           
         
         X and Y are each independently selected from a group consisting of O, S, Se, NR 1 NR 2 , CR 1 CR 2 , OR, SR and SeR, or one or both of X and Y are an enzymatically reactive moiety;  
         R is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted arakyl, optionally substituted cycloalkyl, optionally substituted cycloalkenyl, optionally substituted carbocyclic aryl, an optionally substituted mononucleotide, an optionally substituted polynucleotide, or an optionally substituted heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms;  
         R 1 , R 2  and R 3  are each independently selected from a group as defined by R;  
         B is optionally substituted adenine, optionally substituted thymidine, optionally substituted cytosine or an optionally substituted guanine, preferably where the optional substituents are alkyl, carbocyclic aryl, or heteroaromatic or heteroalicyclic group preferably having from 1 to 3 separate or fused ring and 1 to 3 N, O or S atoms, or a heterocyclic structure that is covalently linked to the sugar ring;  
         and pharmaceutically acceptable salts thereof.  
       
     
     
         17 . A method for treating virally infected cells comprising administering to the cells an anti-viral effective amount of a compound of  claim 12 .  
     
     
         18 . The method of  claim 17  wherein the cells are infected with a herpes virus.  
     
     
         19 . The method of  claim 17  wherein the cells are infected with a cytomegalovirus.  
     
     
         20 . The method of  claim 17  wherein the cells are infected with a hepatitis B virus.  
     
     
         21 . A method for treating bacterially infected cells comprising administering to the cells an anti-bacterial effective amount of a compound of  claim 12 .  
     
     
         22 . The method of  claim 21  wherein the mammal is suffering from a mycobacterium infection.  
     
     
         23 . A method for treating a mammal suffering from or susceptible to a viral infection, comprising administering to the mammal an anti-viral effective amount of a compound of  claim 12 .  
     
     
         24 . The method of  claim 23  wherein the mammal is suffering from a herpes infection.  
     
     
         25 . The method of  claim 23  wherein the mammal is suffering from a cytomegalovirus infection.  
     
     
         26 . The method of  claim 23  wherein the mammal is suffering from a hepatitis B virus infection.  
     
     
         27 . A method for treating a mammal suffering from or susceptible to a bacterial infection, comprising administering to the mammal an anti-bacterial effective amount of a compound of  claim 12 .  
     
     
         28 . A pharmaceutical composition comprising a compound of any one of  claim 12  and a pharmaceutically acceptable carrier.  
     
     
         29 . A method for synthesis of a compound library, comprising: 
 adding one or more reagents to a reaction vessel capable of agitation and containing a resin reaction support material;    agitating the reaction vessel during reaction of the reagents; and    centrifuging the reaction vessel and removing desired reaction materials therefrom.    
     
     
         30 . The library of  claim 1  wherein the library comprises phosphorothioate compounds.  
     
     
         31 . The library of  claim 1  wherein the library comprises thiophosphoramidate compounds.  
     
     
         32 . The library of  claim 1  wherein the library comprises phosphoramidothionate compounds.  
     
     
         33 . The library of  claim 1  wherein the library comprises carbamate compounds.  
     
     
         34 . The compound of  claim 12  wherein the compound is a phosphorothioate compound.  
     
     
         35 . The compound of  claim 12  wherein the compound is a thiophosphoramidate compound.  
     
     
         36 . The compound of  claim 12  wherein the compound is a phosphoramidothionate compound.  
     
     
         37 . The compound of  claim 12  wherein the compound is a carbamate compound.