Polyamide nucleic acid derivatives, and agents, and processes for preparing them

Abstract

The present invention relates to PNA derivatives which carry, at the C terminus, or at both the C and N termini of the PNA backbone, one or more phosphoryl radicals. The phosphoryl radicals carry, where appropriate, one or more labeling groups, groups for crosslinking, groups which promote intracellular uptake, or groups which increase the binding affinity of the PNA derivative for nucleic acids. The invention furthermore relates to a process for preparing the above-mentioned PNA derivatives and to their use as pharmaceuticals or diagnostic agents.

1 - 25 . Canceled.  
     
     
         26 . A method for detecting a nucleic acid of interest, said method comprising 
 providing a PNA derivative which carries one or more phosphoryl radicals at the C terminus or at the C and N termini of the PNA backbone, wherein the phosphoryl radicals comprise oxo-, thio- and imino-phosphoryl radicals, and wherein at least one of the phosphoryl radicals carries one or more deprotonatable groups, and wherein the phosphoryl radicals are linked to the PNA backbone by way of an oxygen-phosphorus bond, a sulfur-phosphorus bond or a nitrogen-phosphorus bond, either directly or by way of a spacer,    labeling the PNA derivative with a detectable label, wherein the PNA derivative comprises a base sequence that hybridizes with at least one sequence present in the nucleic acid of interest under selected conditions,    combining said labeled PNA derivative with a sample suspected of containing the nucleic acid of interest, and    detecting specific binding of said labeled PNA derivative to said nucleic acid of interest,    wherein specific binding indicates the presence of the nucleic acid of interest in the sample.    
     
     
         27 . The method of claim  25 , wherein the method further comprises quantifying the detected nucleic acids.  
     
     
         28 . The method of claim  25 , wherein the nucleic acid of interest is a nucleic acid of a microorganism or a virus.  
     
     
         29 . The method of claim  25 , wherein the method is fluorescence in-situ hybridization (FISH).  
     
     
         30 - 32 . Canceled.  
     
     
         33 . A process for preparing a PNA derivative of Formula I  
       
         
           
           
               
               
           
         
       
       wherein 
 q is 0;  
 D′ is, independently of each other, hydroxyl, mercapto, amino, alkylamino, or acylamino;  
 V is oxygen, sulfur, or NR 1 ;  
 V′ is, independently of any other V′, oxygen, sulfur, NR 1 , U—(CR 3 R 4 ) u′ —C(O)—NH, or U—(CH 2 CH 2 O) u′ —CH 2 —C(O)—NH;  
 U is, independently of any other U, oxygen, sulfur, or NH;  
 u′ is, independently of any other u′, from 1 to 10;  
 W and W′ are, independently of each other, oxygen, sulfur, or NR 1 ;  
 Y and Y′ are, independently of each other, hydroxyl, mercapto, oxyanion, thioate, or NR 1 R 2 ;  
 X and X′ are, independently of each other, 
 U—(C 2 -C 22 -alkanediyl)—U,  
 U—(CH 2 CH 2 —O) u′ ,  
 a labeling group,  
 a group for crosslinking,  
 a group which promotes intracellular uptake, or  
 a group which increases the binding affinity of the PNA derivative for nucleic acids;  
 
 Z and Z′ are, independently of each other, 
 hydroxyl,  
 mercapto,  
 oxyanion,  
 thioate,  
 NR 1 R 2 ,  
 C 1 -C 22 -alkyl,  
 C 1 -C 8 -arylalkyl.  
 C 1 -C 22 -alkyl-U.  
 C 1 -C 18 -arylalkyl-U,  
 hydroxy-C 1 -C 18 —U,  
 aminoalkyl-U,  
 mercaptoalkyl-U,  
 a group of the formula R 7 (CH 2 CH 2 —O) m′ , wherein R 7  is hydroxyl, amino, or C 1 -C 22 -alkoxy, and m′ is from 1 to 100,  
 a labeling group,  
 a crosslinking group,  
 a group which promotes intracellular uptake, or  
 a group which increases the binding affinity of the PNA derivative for nucleic acids;  
 
 R 1  and R 2  are, independently of each other, a radical consisting of hydrogen or C 1 -C 6 -alkyl, preferably hydrogen.  
 R 3  and R 4  are, independently of each other, a radical consisting of hydrogen or C 1 -C 6 -alkyl, or the radical of an amino acid side chain, wherein adjacent radicals R 3  and R 4  in V′ can also form a C 5 -C 8 -cycloalkyl ring  
 n is from 0 to 10;  
 m is from 0 to 10;  
 and wherein {POLY} is described by Formula II  
                     
 wherein {BLOCK} is, independently of any other {BLOCK}, a group selected from Formula IIIA,  
                     
 and Formulae IV A to IV G,  
                     
 wherein each {BLOCK} building block can be different,  
 and wherein  
 z″ is from 0 to 100;  
 G is (CR 5 R 6 ) u′ , C(O)NH—(CR 1 R 2 ) t′ , or C(O)NH—(CH 2 CH 2 ) u′ —CH 2 CH 2 , wherein t′ is from 2 to 10;  
 A is, independently of any other A, a group (CR 1 R 2 ) s , wherein s is from 1 to 3;  
 B is, independently of any other B, either 
 an aromatic radical, a heteroaromatic radical, hydrogen, hydroxyl, or C 1 -C 18 -alkyl, or  
 a nucleobase which occurs naturally, and is customary in nucleotide chemistry, or which does not occur naturally, or its prodrug form;  
 
 D is, independently of any other D, a group (CR 3 R 4 ) t , wherein t is from 2 to 10;  
 E is, independently of any other E, a group (CR 5 R 6 ) u′ ,  
 R 5  and R 6  are, independently of each other, a radical consisting of hydrogen, C 1 -C 6 -alkyl, or the radical of an amino acid side chain, 
 wherein adjacent R 5  and R 6  radicals can form a C 5 -C 8 -cycloalkyl ring or a spiro compound;  
 
 wherein R 1 , R 2 , R 3 , R 4 , and u′ are as defined above  
 and physiologically tolerated salts of the PNA derivative of Formula 1,  
 with the provisos that at least one Y, Y′, Z, or Z′ radical is hydroxyl, mercapto, oxyanion, or thioate, and that at least one B radical is a nucleobase;  
 said process comprising 
 a) linking the C-terminus of an amidonucleic acid, which is optionally N-terminally protected, to a solid phase-bound phosphorylating reagent, or binding an amidonucleic acid which is phosphorylated C-terminally to a solid support,  
 b) optionally, extending the backbone of the PNA oligomer by sequentially coupling with amidonucleic acid monomers, and  
 c) optionally, deprotecting the N-terminus of the PNA oligomer.  
 
 
     
     
         34 . The process as claimed in  claim 33 , wherein the PNA is prepared using t-butyloxycarbonyl (BOC), 9-fluorenylmethoxycarbonyl (Fmoc), or monomethoxytrityl (Mmt) protecting groups.  
     
     
         35 . The process as claimed in  claim 33 , wherein the PNA is prepared using solid supports.  
     
     
         36 . The process as claimed in  claim 35 , wherein CPG, tentagel, or aminomethylpolystyrene is used as the solid support.  
     
     
         37 . The process for preparing a PNA derivative of the Formula I as claimed in  claim 33 , further comprising purifying the PNA derivative using chromatography or electrophoresis.  
     
     
         38 . The process as claimed in  claim 37 , wherein the PNA derivative is purified using chromatography using a basic stationary phase and a gradient of an acid or salt-containing eluent.  
     
     
         39 . The process as claimed in  claim 38 , wherein the stationary phase is an anion exchanger or a mixed-mode phase.  
     
     
         40 - 80 . Canceled.  
     
     
         81 . A process for preparing a PNA derivative of Formula I  
       
         
           
           
               
               
           
         
       
       wherein 
 q is 1;  
 D′ is, independently of each other, hydroxyl, mercapto, amino, alkylamino, or acylamino;  
 V is oxygen, sulfur, or NR 1 ;  
 V′ is, independently of any other V′, oxygen, sulfur, NR 1 , U—(CR 3 R 4 ) u′ —C(O)—NH, or U—(CH 2 CH 2 O) u′ —CH 2 —C(O)—NH;  
 U is, independently of any other U, oxygen, sulfur, or NH;  
 u′ is, independently of any other u′, from 1 to 10;  
 W and W′ are, independently of each other, oxygen, sulfur, or NR 1 ;  
 Y and Y′ are, independently of each other, hydroxyl, mercapto, oxyanion, thioate, or NR 1 R 2 ;  
 X and X′ are, independently of each other, 
 U—(C 2 -C 22 -alkanediyl)—U,  
 U—(CH 2 CH 2 —O) u′ ,  
 a labeling group,  
 a group for crosslinking,  
 a group which promotes intracellular uptake, or  
 a group which increases the binding affinity of the PNA derivative for nucleic acids;  
 
 Z and Z′ are, independently of each other, 
 hydroxyl,  
 mercapto,  
 oxyanion,  
 thioate,  
 NR 1 R 2 .  
 C 1 -C 22 -alkyl,  
 C 1 -C 8 -arylalkyl,  
 C 1 -C 22 -alkyl-U,  
 C 1 -C 8 -arylalkyl-U,  
 hydroxy-C 1 -C 18 —U  
 aminoalkyl-U,  
 mercaptoalkyl-U,  
 a group of the formula R 7 (CH 2 CH 2 —O) m′ , wherein R 7  is hydroxyl, amino, or C 1 -C 22 -alkoxy, and m′ is from 1 to 100,  
 a labeling group,  
 a crosslinking group,  
 a group which promotes intracellular uptake, or  
 a group which increases the binding affinity of the PNA derivative for nucleic acids;  
 
 R 1  and R 2  are, independently of each other, a radical consisting of hydrogen or C 1 -C 6 -alkyl, preferably hydrogen,  
 R 3  and R 4  are, independently of each other, a radical consisting of hydrogen or C 1 -C 6 -alkyl, or the radical of an amino acid side chain, wherein adjacent radicals R 3  and R 4  in V′can also form a C 5-1 -C 8 -cycloalkyl ring;  
 n is from 0 to 10;  
 m is from 0 to 10;  
 and wherein {POLY} is described by Formula II  
                     
 wherein {BLOCK} is, independently of any other {BLOCK}, a group selected from Formula IIIA,  
                     
 and Formulae IV A to IV G,  
                     
 wherein each {BLOCK} building block can be different,  
 and wherein  
 z″ is from 0 to 100;  
 G is (CR 5 R 6 ) u′ , C(O)NH—(CR 1 R 2 ) t′ , or C(O)NH—(CH 2 CH 2 O) u′ —CH 2 CH 2 , wherein t′ is from 2 to 10;  
 A is, independently of any other A, a group (CR 1 R 2 ) s , wherein s is from 1 to 3;  
 B is, independently of any other B, either 
 an aromatic radical, a heteroaromatic radical, hydrogen, hydroxyl, or C 1 -C 18 -alkyl, or  
 a nucleobase which occurs naturally, and is customary in nucleotide chemistry, or which does not occur naturally, or its prodrug form;  
 
 D is, independently of any other D, a group (CR 3 R 4 ) t , wherein t is from 2 to 10;  
 E is, independently of any other E, a group (CR 5 R 6 ) u′ ,  
 R 5  and R 6  are, independently of each other, a radical consisting of hydrogen, C 1 -C 6 -alkyl, or the radical of an amino acid side chain, 
 wherein adjacent R 5  and R 6  radicals can form a C 5 -C 8 -cycloalkyl ring or a spiro compound;  
 
 wherein R 1 , R 2 , R 3 , R 4 , and u′are as defined above;  
 and physiologically tolerated salts of the PNA derivative of Formula I,  
 with the provisos that at least one Y, Y′, Z, or Z′ radical is hydroxyl, mercapto, oxyanion, or thioate, and that at least one B radical is a nucleobase;  
 said process comprising 
 a) linking the C-terminus of an amidonucleic acid, which is optionally N-terminally protected, to a solid phase-bound phosphorylating reagent, or binding an amidonucleic acid which is phosphorylated C-terminally to a solid support,  
 b) optionally, extending the backbone of the PNA oligomer by sequentially coupling with amidonucleic acid monomers,  
 c) optionally, deprotecting the N-terminally protected PNA backbone,  
 d) coupling a phosphorus (III) or a phosphorus (IV) group to the N-terminus of the PNA backbone using activated phosphorylating reagents optionally containing a spacer,  
 e) optionally, repeating step d), and  
 f) optionally, oxidizing the phosphorus (III) group to a phosphorus (V) group.