Heteroarylcyanine dyes

Abstract

The present invention provides heteroaryl functionalized cyanine dyes including a reactive functional moiety, or which are conjugated to a carrier molecule.

1 . A fluorescent compound having the formula:
   A-Q-B   
       wherein
 Q has a formula which is a member selected from: 
 
       
         
           
           
               
               
           
         
       
       wherein
 D is a member selected from H, halogen, OR a , SR a , NR a R b , CR a R b R c , 
 
       
         
           
           
               
               
           
         
         wherein
 R a , R b , R c  and R d  are members independently selected from H, R 8 , R 8 Z o , R 8 CO 2 H, R 8 SO 3 H, 
 
       
       
         
           
           
               
               
           
         
         wherein
 Z o  and R q  are independently selected from OH, O—, a reactive functional group, a component of a reactive functional group and a linkage fragment covalently binding said compound to a carrier molecule; 
 v is 0, 1, 2, 3, 4, or 5 and, when v is equal to or greater than 2, each R d  moiety is independently selected; 
 e is 0, 1, 2, 3, 4, or 5 and, when e is equal to or greater than 2, each R d  or R q  is independently selected; 
 R e  is selected from H, R 18 , R 18 Z 1 , SO 3 H, CO 2 H, R 18 SO 3 H, CONH 18 SO 3 H, CONHR 18 C(O)Z 1 , 
 wherein
 R 8  and R 18  are independently selected from a bond, substituted or unsubstituted substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; 
 Z 1  is selected from OH, O—, a reactive functional group, a component of a reactive functional group and a linkage fragment covalently binding said compound to a carrier molecule; 
 
 
         n is 1, 2 or 3; 
         p is 0, 1 or 2; and 
         R m  is a member selected from: 
       
       
         
           
           
               
               
           
         
         wherein
 w is an integer from 1 to 10; 
 u is 0, 1, 2, 3, 4, or 5 and, when u is two or greater, each R o  is independently selected; 
 R o  is a member selected from OH, O—, a reactive functional group, a component of a reactive functional group and a linkage fragment binding the compound to a carrier molecule; 
 
         B is a moiety which is a member selected from Formulae I, II and III; 
       
       
         
           
           
               
               
           
         
         wherein
 X 1  is a member selected from CR 1 R 2 , O, S and NR 1 , 
 wherein
 R 1 , R 2  and R 3  are independently CH 2 R 7 ; 
 
 X 2  and X 3  are members independently selected from O, S, N, NH, CR 22 , and CR 22 R 23 , wherein
 R 4 , R 5 , R 6 , R 22  and R 23  are members independently selected from H, R 28 ,
 R 28 Z 2 , SO 3 H, CO 2 H, R 28 SO 3 H, C(O)NHR 28 SO 3 H, CONHR 28 C(O)Z 2 , 
 
 
 
       
       
         
           
           
               
               
           
         
         
           
             wherein
 R p  and Z 2  are independently selected from OH, O—, a reactive functional group, a component of a reactive functional group and a linkage fragment covalently binding said compound to a carrier molecule; 
 g is an integer selected from 0, 1, 2, 3, and 4, and when g is greater than or equal to 2, each R g  or R p  is independently selected; 
 R g  is a member selected from H, R 38 , R 38 Z 3 , SO 3 H, CO 2 H, R 38 SO 3 H, CONHR 38 SO 3 H, CONHR 38 C(O)Z 2 , 
 wherein 
  R 28  and R 38  are independently selected from a bond substituted or unsubstituted substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; 
  Z 3  is a reactive functional group or is a linkage fragment covalently binding said compound to a carrier molecule; 
 
           
         
         A is a moiety selected from substituted or unsubstituted indole, substituted or unsubstituted imidazole, substituted or unsubstituted thiazole, and substituted or unsubstituted oxazole, 
         at least one of R a , R b , R c , R d , R 1 , R 2 , R 3 , R 4 , R 5  and R 6  is a reactive functional group, a component of a reactive functional group or is a linkage fragment covalently binding said compound to a carrier molecule; and 
         said compound comprises at least three SO 3 H moieties. 
       
     
     
         2 . The compound according to  claim 1 , wherein A is a substituted or unsubstituted indolinium moiety. 
     
     
         3 . The compound according to  claim 1 , wherein A has a formula which is a member selected from: 
       
         
           
           
               
               
           
         
         wherein
 X 1′  is a member selected from CR 1′ R 2′ , O, S and NR 1′ , 
 wherein
 R 1′ , R 2′  and R 3′  are independently CH 2 R 7′ ; 
 
 X 2′  and X 3′  are members independently selected from O, S, N, NH, CR 22′ , and CR 22′ R 23′ , 
 wherein
 R 4′ , R 5′ , R 6′ , R 7′ , R 22′  and R 23′  are members independently selected from H,
 R 28′ , R 28′ Z 2′ , SO 3 H, CO 2 H, R 28′ SO 3 H, CONHR 28′ SO 3 H, CONHR 28′ C(O)Z 2′ , 
 
 
 
       
       
         
           
           
               
               
           
         
         
           
             wherein
 Z 2′  is a reactive functional group or is a linkage fragment covalently binding said compound to a carrier molecule; 
 g′ is selected from 0, 1, 2, 3, 4 and 5, and when it is greater than or equal to 2, each R g′  is independently selected; 
 R g′  is a member selected from H, R 38′ , R 38′ , Z 3′ , SO 3 H, CO 2 H, 
  R 38′ SO 3 H, CONHR 38′ SO 3 H, CONHR 38′ (O)Z 3′ , 
 wherein 
  R 28′  and R 38′  is a bond or is a member selected from substituted or unsubstituted substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; and 
  Z 3′  is a member selected from a reactive functional group, a component of a reactive functional group and a linkage fragment covalently binding said compound to a carrier molecule. 
 
           
         
       
     
     
         4 . The compound according to  claim 1 , wherein at least one of X 3  and X 3′  is S. 
     
     
         5 . The compound according to  claim 1 , wherein at least one of X 2  and X 2′  is CH. 
     
     
         6 . The compound according to  claim 1 , wherein at least one of R 6  and R 6′  is SO 3   − . 
     
     
         7 . The compound according to  claim 1 , wherein R a , R b , R c  and R d  are members independently selected from H, and substituted or unsubstituted alkyl having from 1 to 20 carbon atoms. 
     
     
         8 . The compound according to  claim 1 , wherein X 2 , X 2′ , X 3  and X 3′  are members independently selected from O, S, N, NH, CH, CH 2  and C(CH 3 ) 2 . 
     
     
         9 . The compound according to  claim 1 , wherein at least one member selected from X 2 , X 2′ , X 3  and X 3′  is selected from NH, O and S. 
     
     
         10 . The compound according to  claim 1 , wherein not more than one member selected from X 2 , X 2′ , X 3  and X 3′  is O. 
     
     
         11 . The compound according to  claim 1 , wherein none of X 2 , X 2′ , X 3  and X 3′  is O. 
     
     
         12 . The compound according to  claim 1 , having a formula which is a member selected from: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         13 . The compound according to  claim 1 , having a formula selected from: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
       
     
     
         14 . The compound according to  claim 1 , having a formula which is a member selected from: 
       
         
           
           
               
               
           
         
       
     
     
         15 . The compound according to  claim 1 , having the formula: 
       
         
           
           
               
               
           
         
       
       wherein
 R 61 , R 61′ , R 62  and R 62′  are members independently selected from H, CH 3 , COOH, NH(CH 2 ) 2 SO 3 H; 
 Z and Z′ are members independently selected from N and CH; and 
 n is 1, 2 or 3. 
 
     
     
         16 . The compound according to  claim 1 , having a formula selected from: 
       
         
           
           
               
               
           
         
       
       wherein
 Z and Z′ are members independently selected from N and CH; 
 n is 1, 2 or 3; and 
 R 65 , R 65′ , R 66  and R 66′  are independently members selected from substituted or unsubstituted alkyl having from 2 to 6 carbon atoms. 
 
     
     
         17 . The compound according to  claim 16 , wherein Z 8  and Z 8′  are members independently selected from N(R 75 )R 76 C(O)Z 12 , in which
 R 75  is a member selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; 
 R 76  is a member selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; and 
 Z 12  is selected from OH, O—, a reactive functional group, a component of a reactive functional group and a linkage fragment covalently binding the compound to a carrier molecule. 
 
     
     
         18 . The compound according to  claim 1 , wherein R 4 , R 5 , R 6 , R 7 , R 22  and R 23  are independently selected from: 
       
         
           
           
               
               
           
         
       
       wherein
 R g  is a member selected from H, R 38 , R 38 Z 3 , SO 3 H, CO 2 H, R 38 SO 3 H, CONHR 38 SO 3 H, CONHR 38 CO 2 H; 
 R 38  is a bond or is a member selected from substituted or unsubstituted substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; and 
 Z 3  is selected from OH, O—, a reactive functional group, a component of a reactive functional group or is a linkage fragment covalently binding the compound to a carrier molecule. 
 
     
     
         19 . The compound according to  claim 1 , wherein R 4′ , R 5′ , R 6′ , R 7′ , R 22′  and R 23′  are members independently selected from: 
       
         
           
           
               
               
           
         
       
       wherein
 R g′  is a member selected from H, R 38′ , R 3′8 Z′ 3 , SO 3 H, CO 2 H, R 3′8 SO 3 H, CONHR 38′ SO 3 H, CONHR 38′ CO 2 H; 
 R 38′  is a bond or is a member selected from substituted or unsubstituted substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl; and 
 Z 3′  is selected from OH, O—, a reactive functional group, a component of a reactive functional group or is a linkage fragment covalently binding the compound to a carrier molecule. 
 
     
     
         20 . (canceled) 
     
     
         21 . The compound according to  claim 1 , wherein said reactive functional group is a member selected from an amine, a hydroxy, an aldehyde, a ketone, a hydroxylamine, a sulfhydryl, an isocyanate, an isothiocyanate, a haloacetamide, a hydrazine, an ester, an anhydride, an acyl azide, an acyl halide, a sulfonyl halide, a maleimide, a carbodiimide, a phosphoramidite, and an imidazole. 
     
     
         22 . The compound according to  claim 1 , wherein said reactive functional group is a member selected from: 
       
         
           
           
               
               
           
         
         
           
           
               
               
           
         
         wherein
 each r is independently selected from the integers from 1 to 10; 
 G is a halogen; and 
 R 30  and R 31  are members independently selected from H and halogen and at least one of R 30  and R 31  is halogen. 
 
       
     
     
         23 . The compound according to  claim 1 , wherein said linkage fragment has a formula which is a member selected from:
 —(CH 2 ) t S(CH 2 ) z —, —(CH 2 ) x SC(O)NR(CH 2 ) z —, —(CH 2 ) x SC(O)O(CH 2 ) z —, —(CH 2 ) x NR(CH 2 ) z —, —(CH 2 ) x NRC(O)(CH 2 ) z —, —(CH 2 ) x NRC(O)O(CH 2 ) z —, —(CH 2 ) x O(CH 2 ) z —, —(CH 2 ) 0 T-PEG-, —(CH 2 ) x C(O)(CH 2 ) z S—, —S-maleimide-N—, —RNC(O)NR—, —RNS(O)NR—, —S(O) 2 NR— wherein
 T is a member selected from S, NH, NHC(O), C(O)NH, NHC(O)O, OC(O)NH, and 0; 
   o is an integer from 1 to 50; and   t, x and z are independently selected from the integers from 0 to 10.   
     
     
         24 . The compound according to  claim 1 , wherein said carrier molecule comprises the structure: 
       
         
           
           
               
               
           
         
         wherein
 u is selected from the integers from 1 to 8; 
 J is a member selected from H, OH, and OMe; and 
 Y is a nucleobase. 
 
       
     
     
         25 . The compound according to  claim 1  wherein the linkage fragment binding the fluorescent compound to said carrier molecule has the formula: 
       
         
           
           
               
               
           
         
       
       wherein L D  is a member selected from: 
       
         
           
           
               
               
           
         
       
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . (canceled) 
     
     
         30 . (canceled) 
     
     
         31 . (canceled) 
     
     
         32 . (canceled) 
     
     
         33 . (canceled)