Derivatives of 1,2-dihydro-7-hydroxyquinolines containing fused rings
View Patent ↗The present invention describes novel dyes, including coumarins, rhodamines, and rhodols that incorporate additional fused aromatic rings. The dyes of the invention absorb at a longer wavelength than structurally similar dyes that do not possess the fused aromatic rings. Many of the dyes of the invention are useful fluorescent dyes. The invention includes chemically reactive dyes, dye-conjugates, and the use of such dyes in staining samples and detecting ligands or other analytes.
1. A compound of the formula
wherein
R 1 and R 2 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
or R 1 in combination with R 2 forms a fused aromatic or heteroaromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ;
or R 2 in combination with R 3 forms a 5- or 6-membered alicyclic ring;
R 3 and R 4 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, aromatic or heteroaromatic ring, -L-R X and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, hydroxy, or halogen and said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 alkoxy, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 3 in combination with R 4 forms a 5- or 6-membered alicyclic ring;
R 5 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
R 6 is independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
or R 4 in combination with R 5 , or R 5 in combination with R 6 , forms a 5- or 6-membered alicyclic ring;
R 7 is independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, -L-R X and -L-S C ;
one of X and E is O, S, NR 8 , or CR 1′ ═CR 2′ , and the other is absent;
wherein R 8 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, -L-R X and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; and
R 1′ and R 2′ are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
Y is independently selected from the group consisting of H, OH, NH 2 , NO, —(CO)—R 9 , —(CO)—O—R 10 , wherein said R 9 and R 10 are independently H, C 1 –C 6 alkyl, or a substituted or unsubstituted aryl or heteroaryl ring system having 1–2 rings;
Z is independently selected from the group consisting of H, OH, NHR 17 , SH, or C(CR 11 R 12 ) 2 OH; wherein said R 17 is a C 1 –C 6 alkyl that is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said R 11 and R 12 are independently C 1 –C 6 alkyl that are optionally substituted by carboxylic acid, sulfonic acid, or halogen, or R 11 and R 12 taken in combination form a 5- or 6-membered alicyclic ring;
wherein L is a covalent linkage;
R x is a reactive group; and
S C is a conjugated substance;
with the proviso that when R 1 and R 2 from a fused aromatic ring, R 8 is not hydrogen or a C 2 alkyl substituted by carboxylic acid.
2. The compound according to claim 1 , wherein one of X and E is O, or S, and the other is absent.
3. The compound according to claim 2 , wherein said compound is of the formula
wherein X is O or S.
4. The compound according to claim 2 , wherein said compound is of the formula
wherein E is O or S.
5. The compound according to claim 3 , wherein X is S.
6. The compound according to claim 1 , wherein
R 1 is hydrogen or sulfonic acid;
R 3 and R 4 are each methyl;
R 6 and R 7 are each hydrogen or methyl; and
Z is OH.
7. The compound according to claim 1 , wherein Y is H or —(CO)—H or NO.
8. The compound according to claim 1 , wherein said L is independently a single covalent bond or a covalent linkage having 1–20 nonhydrogen atoms selected from the group consisting of C, N, O, P, and S.
9. The compound according to claim 1 , wherein said R X is independently selected from the group consisting of an acrylamide, an activated ester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde, an alkyl halide, an amine, an anhydride, an aniline, an aryl halide, an azide, an aziridine, a boronate, a carboxylic acid, a diazoalkane, a haloacetamide, a halotriazine, a hydrazine, an imido ester, an isocyanate, an isothiocyanate, a maleimide, a phosphoramidite, a reactive platinum complex, a sulfonyl halide, and a thiol group.
10. The compound according to claim 1 , wherein said S C is independently selected from the group consisting of an amino acid, a peptide, a protein, a tyramine, a carbohydrate, a metal chelating moiety, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipid assembly, a polymer, a polymeric microparticle, a biological cell, and a virus.
11. A compound of the formula
wherein R 1 , R 2 , and R 6 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
or R 1 in combination with R 2 forms a fused aromatic or heteroaromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ;
R 3 and R 4 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, an aromatic or heteroaromatic ring, L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, hydroxy, or halogen and said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 alkoxy, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 2 in combination with R 3 , or R 3 in combination with R 4 , forms a 5- or 6-membered alicyclic ring;
R 5 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 4 in combination with R 5 , or R 5 in combination with R 6 , forms a 5- or 6-membered alicyclic ring;
one of X and E is O, S, NR 8 , or CR 1′ ═CR 2′ and the other is absent;
wherein R 8 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, -L-R X and -L-S C, wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; and
R 1′ and R 2′ are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
R 15 and R 16 are independently selected from the group consisting of hydrogen, cyano, nitro, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, an aromatic or heteroaromatic ring system having 1–2 fused rings, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aromatic or heteroaromatic ring system is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
wherein L is a covalent linkage;
R x is a reactive group; and
S C is a conjugated substance.
12. The compound according to claim 11 , wherein said one of X and E is O or S.
13. The compound according to claim 12 , wherein
R 6 and R 7 are hydrogen;
R 3 and R 4 are each methyl;
R 1 is hydrogen or sulfonic acid;
one of R 15 and R 16 is -L-R x or -L-S C , and the other is hydrogen, C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl; or cyano;
wherein L is a single covalent bond, or L is a covalent linkage having 1–20 nonhydrogen atoms selected from the group consisting of C, N, O, P, and S, and
wherein R X , is independently selected from the group consisting of an acrylamide, an activated ester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde, an alkyl halide, an amine, an anhydride, an aniline, an aryl halide, an azide, an aziridine, a boronate, a carboxylic acid, a diazoalkane, a haloacetamide, a halotriazine, a hydrazine, an imido ester, an isocyanate, an isothiocyanate, a maleimide, a phosphoramidite, a reactive platinum complex, a sulfonyl halide, and a thiol group; and
wherein S C is independently selected from the group consisting of an amino acid, a peptide, a protein, a tyramine, a carbohydrate, a metal chelating moiety, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipid assembly, a polymer, a polymeric microparticle, a biological cell, and a virus.
14. The compound according to claim 11 , wherein one of said R 15 or R 16 is an aromatic or heteroaromatic ring system having 1–2 fused rings that is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl.
15. A compound of the formula:
wherein R 1 , R 2 , and R 6 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
or R 1 in combination with R 2 forms a fused aromatic or heteroaromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ;
R 3 and R 4 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, an aromatic or heteroaromatic ring, L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, hydroxy, or halogen and said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 alkoxy, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 2 in combination with R 3 , or R 3 in combination with R 4 , forms a 5- or 6-membered alicyclic ring;
R 5 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 4 in combination with R 5 , or R 5 in combination with R 6 , forms a 5- or 6-membered alicyclic ring;
one of X and E is O, S, NR 8 , or CR 1′ ═CR 2′ , and the other is absent;
wherein R 8 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, -L-R X and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; and
R 1′ and R 2′ are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
R 20 and R 21 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 , alkoxy, aromatic or heteroaromatic ring, -L-R x and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
J is O or NR 37 R 38 ;
wherein R 37 and R 38 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; or R 37 in combination with R 38 forms a saturated 5- or 6-membered heterocycle that is a piperidine, a morpholine, a pyrrolidine or a piperazine, wherein said heterocycle is optionally substituted by methyl, carboxylic acid, or a carboxylic acid ester of a C 1 –C 6 alkyl;
or R 37 in combination with R 20 , or R 38 in combination with R 21 , or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more sulfonic acids, or C 1 –C 6 alkyl that is optionally substituted by sulfonic acid;
Q is N or CR 28 , wherein R 28 is independently selected from the group consisting of hydrogen, F, CN, carboxylic acid, a carboxylic acid ester of a C 1 –C 6 alcohol, a C 1 –C 6 alkyl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; or R 28 is of the formula
wherein R 30 , R 31 , R 32 , R 33 and R 34 are independently selected from the group consisting of hydrogen, F, Cl, Br, I, sulfonic acid, carboxylic acid, CN, nitro, hydroxy, azido, amino, hydrazino, C 1 –C 18 alkyl, C 1 –C 18 alkoxy, C 1 –C 18 alkylthio, C 1 –C 18 alkanoylamino, C 1 –C 18 alkylaminocarbonyl, C 2 –C 36 dialkylaminocarbonyl, C 1 –C 18 alkyloxycarbonyl, C 7 –C 18 arylcarboxamido, -L-R x and -L-S C , wherein said alkyl or aryl portions of said R 30 , R 31 , R 32 , R 33 and R 34 are optionally substituted one or more times by substituents selected from the group consisting of F, Cl, Br, I, hydroxy, carboxylic acid, a carboxylic acid ester of a C 1 –C 6 alcohol, sulfonic acid, amino, C 1 –C 6 alkylamino, C 2 –C 6 dialkylamino and C 1 –C 6 alkoxy; or a pair of adjacent R 30 , R 31 , R 32 , R 33 and R 34 substituents when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid; and
wherein L is a covalent linkage;
R x is a reactive group; and
S C is a conjugated substance.
16. The compound according to claim 15 , wherein said Q is N.
17. The compound according to claim 15 , wherein said J is O and said Q is CR 28 .
18. The compound according to claim 17 , wherein one of said R 5 , R 21 , R 30 , R 31 , R 32 , R 33 , and R 34 is -L-R x or -L-S C .
19. The compound according to claim 15 , wherein
said R 3 and R 4 are each methyl;
R 1 is H or a sulfonic acid;
R 6 is H; and
J is NR 37 R 38 .
20. The compound according to claim 19 , wherein Q is CR 28 and R 28 is of the formula
wherein one of R 30 , R 31 , R 32 , R 33 , and R 34 is -L-R x or -L-S C ; and
wherein L is a single covalent bond, or L is a covalent linkage having 1–20 nonhydrogen atoms selected from the group consisting of C, N, O, P, and S, and
wherein R X , is independently selected from the group consisting of an acrylamide, an activated ester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde, an alkyl halide, an amine, an anhydride, an aniline, an aryl halide, an azide, an aziridine, a boronate, a carboxylic acid, a diazoalkane, a haloacetamide, a halotriazine, a hydrazine, an imido ester, an isocyanate, an isothiocyanate, a maleimide, a phosphoramidite, a reactive platinum complex, a sulfonyl halide, and a thiol group; and
wherein S C is independently selected from the group consisting of an amino acid, a peptide, a protein, a tyramine, a carbohydrate, a metal chelating moiety, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipid assembly, a polymer, a polymeric microparticle, a biological cell, and a virus.
21. A compound of the formula
wherein R 1 , R 2 , and R 6 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
or R 1 in combination with R 2 forms a fused aromatic or heteroaromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ;
R 3 and R 4 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, an aromatic or heteroaromatic ring, L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, hydroxy, or halogen and said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 alkoxy, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 2 in combination with R 3 , or R 3 in combination with R 4 , forms a 5- or 6-membered alicyclic ring;
R 5 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 4 in combination with R 5 , or R 5 in combination with R 6 , forms a 5- or 6-membered alicyclic ring;
one of E and X is O, S, NR 8 , or CR 1′ ═CR 2′ , and the other is absent;
wherein R 8 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, -L-R X and -L-S C, wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; and
R 1′ and R 2′ are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, C 1 –C 6 alkoxy, aryl, heteroaryl, -L-R X and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or halomethyl;
R 21 , R 23 , R 24 , and R 25 are independently selected from the group consisting of hydrogen, cyano, nitro, halogen, carboxylic acid, sulfonic acid, C 1 –C 6 alkyl, aromatic or heteroaromatic ring, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, or halogen said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
Q is N or CR 28 , wherein R 28 is independently selected from the group consisting of hydrogen, F, CN, carboxylic acid, a carboxylic acid ester of a C 1 –C 6 alcohol, a C 1 –C 6 alkyl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; or R 28 is of the formula
wherein R 30 , R 31 , R 32 , R 33 and R 34 are independently selected from the group consisting of hydrogen, F, Cl, Br, I, sulfonic acid, carboxylic acid, CN, nitro, hydroxy, azido, amino, hydrazino, C 1 –C 18 alkyl, C 1 –C 18 alkoxy, C 1 –C 18 alkylthio, C 1 –C 18 alkanoylamino, C 1 –C 18 alkylaminocarbonyl, C 2 –C 36 dialkylaminocarbonyl, C 1 –C 18 alkyloxycarbonyl, C 7 –C 18 arylcarboxamido, -L-R x and -L-S C , wherein said alkyl or aryl portions of said R 30 , R 31 , R 32 , R 33 and R 34 are optionally substituted one or more times by substituents selected from the group consisting of F, Cl, Br, I, hydroxy, carboxylic acid, a carboxylic acid ester of a C 1 –C 6 alcohol, sulfonic acid, amino, C 1 –C 6 alkylamino, C 2 –C 6 dialkylamino and C 1 –C 6 alkoxy; or a pair of adjacent R 30 , R 31 , R 32 , R 33 and R 34 substituents when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid; and
wherein L is a covalent linkage;
R x is a reactive group; and
S C is a conjugated substance.
22. A compound of the formula:
wherein E and E′ are each S; X is absent; R 1 in combination with R 2 forms an aromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ; and R 41 in combination with R 42 forms an aromatic ring that is optionally sulfonated one or more times, or said ring is substituted by -L-R X or -L-S C ;
R 6 and R 46 are independently selected from the group consisting of hydrogen, cyano, halogen, carboxylic acid, sulfonic acid C 1 –C 6 alkyl, C 1 –C 8 alkoxy, aryl, heteroaryl, -L-R x and -L-S C , wherein said alkyl or alkoxy is optionally substituted by carboxylic acid, sulfonic acid, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 perfluoroalkyl, cyano, halogen, azido, carboxylic acid, sulfonic acid, or hakomethyl;
R 3 , R 4 , R 43 , and R 44 are independently selected from the group consisting of hydrogen, C 1 –C 6 alkyl, an aromatic or heteroaromatic ring, L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, hydroxy, or halogen and said aromatic or heteroaromatic ring is optionally substituted one or more times by C 1 –C 6 alkyl, C 1 –C 6 alkoxy, C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 3 in combination with R 4 , or R 43 in combination with R 44 , or any combination thereof, forms a 5- or 6-membered alicyclic ring;
R 5 and R 45 are independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, aryl, heteroaryl, -L-R x and -L-S C wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen and said aryl or heteroaryl is optionally substituted one or more times by C 1 –C 6 perfluoroalkyl, cyano, halogen, carboxylic acid, sulfonic acid, or halomethyl;
or R 4 in combination with R 5 , or R 5 in combination with R 6 , or R 44 in combination with R 45 , or R 45 in combination with R 46 , or any combination thereof, forms a 5- or 6-membered alicyclic ring;
wherein R 8 is independently selected from the group consisting of hydrogen, methyl, carboxymethyl, C 2 –C 6 alkyl, -L-R x and -L-S C wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; and
Q is N or CR 28 , wherein R 28 is independently selected from the group consisting of hydrogen, F, CN, carboxylic acid, a carboxylic acid ester of a C 1 –C 6 alcohol, a C 1 –C 6 alkyl, -L-R x and -L-S C , wherein said alkyl is optionally substituted by carboxylic acid, sulfonic acid, amino, or halogen; or R 28 is of the formula
wherein R 30 , R 31 , R 32 , R 33 , and R 34 are independently selected from the group consisting of hydrogen, F, Cl, Br, I, sulfonic acid, carboxylic acid, CN, nitro, hydroxy, azido, amino, hydrazino, C 1 –C 18 alkyl, C 1 –C 18 alkoxy, C 1 –C 18 alkylthio, C 1 –C 18 alkanoyiamino, C 1 –C 18 alkylaminocarbonyl, C 2 –C 36 dialkylaminocarbonyl, C 1 –C 18 alkyloxycarbonyl, C 2 –C 18 arylcarboxamido, -L-R x and -L-S C , wherein said alkyl or aryl portions of said R 30 , R 31 , R 32 , R 33 and R 34 are optionally substituted one or more times by substituents selected from the group consisting of F, Cl, Br, I, hydroxy, carboxylic acid, a carboxylic acid ester of a C 6 –C 6 alcohol, sulfonic acid, amino, C 1 –C 6 alkylamino, C 2 –C 6 dialkylamino and C 1 –C 6 alkoxy; or a pair of adjacent R 30 , R 31 , R 32 , R 33 , and R 34 substituents when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid; and
wherein L is a covalent linkage;
R x is a reactive group; and
S C is conjugated substance;
with the proviso that at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 8 , R 28 , R 30 , R 31 , R 32 , R 33 , R 34 , R 41 , R 42 , R 43 , R 44 , R 45 is a conjugated substance.
23. The compound according to claim 22 , wherein said conjugated substance is independently selected from the group consisting of an amino acid, a peptide, a protein, a tyramine, a carbohydrate, a metal chelating moiety, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipid assembly, a polymer, a polymeric microparticle, a biological cell, and a virus.
24. The compound according to claim 23 , wherein said conjugated substance is a metal chelating moiety wherein said metal chelating moiety is optionally substituted by a reactive group.
25. The compound according to claim 24 , wherein said metal chelating moiety is BAPTA.
26. The compound according to claim 25 , wherein said R 28 is said BAPTA.
27. The compound according to claim 26 , wherein said reactive group is selected from the group consisting of a carboxylic acid, a succinimidyl ester of a carboxylic acid, a maleimide, a cadaverine, a benzophenone, an aryl azide and a diazirine.
28. The compound according to claim 26 , wherein said compound is according to formula
29. The compound according to claim 27 , wherein said compound is according to formula