Carboxy X rhodamine analogs
View Patent ↗The present invention provides novel fluorescent dyes and kits containing the same, which are useful for labeling a wide variety of biomolecules, cells and microorganisms. The present invention also provides various methods of using the fluorescent dyes for research and development, forensic identification, environmental studies, diagnosis, prognosis and/or treatment of disease conditions.
1. A compound according to formula (IIIa), (IIIb) or (IIIc):
wherein
R 11 is independently H or C 1-4 alkyl, L-R or L-C S ;
L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;
R is a reactive group;
C S is a conjugated substance selected from the group consisting of solid supports, resin particles, beads, assay plates, proteins, nucleotides, polynucleotides, enzyme substrates, antibodies, nanobodies, polypeptides, polypeptide-based toxins, amino acids, lipids, carbohydrates, haptens, drugs, ion-complexing agents, microparticles, polymers, cells, viruses, fluorophores, chloroalkanes, and cyanobenzothiazoles;
R 2 and R 16 can be independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;
R 3 and R 4 are H, alkyl, L-R, L-C S , L-CO 2 H, L-SO 3 H or together form a carbocyclic, aryl, heteroaryl, or heterocyclic ring;
alternatively, R 2 and R 3 and independently R 4 and R 16 together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;
R 5 , R 12 , R 13 , R 14 and R 15 are independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;
R 20 , R 21 , R 22 and R 23 are independently H or C 1-6 alkyl or one or more of R 20 and R 21 , R 21 and R 22 , R 22 and R 23 , together form an aryl, heteroaryl, carbocyclic or heterocyclic ring;
R 11 and R 12 may together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;
R 6-10 are independently H, F, Cl, Br, I, OH, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;
X is CHR 23 , O, S or NR 30 ; and
R 30 is H, C 1-4 alkyl or —C(O)C 1-4 alkyl.
2. A compound according to claim 1 , wherein the compound is a compound of formula (Ia) or (Ib):
wherein
R 1 and R 11 are independently H or C 1-4 alkyl, L-R or L-C S ;
L is a covalent linkage that is linear or branched, cyclic or heterocyclic saturated or unsaturated, having 1-16 non hydrogen atoms such that the linkage contains any combination of ester, acid, amine, amide, alcohol, ether, thioether or halide groups or single, double, triple or aromatic carbon-carbon bond;
R is a reactive group;
C S is a conjugated substance selected from the group consisting of solid supports, resin particles, beads, assay plates, proteins, nucleotides, polynucleotides, enzyme substrates, antibodies, nanobodies, polypeptides, polypeptide-based toxins, amino acids, lipids, carbohydrates, haptens, drugs, ion-complexing agents, microparticles, polymers, cells, viruses, fluorophores, chloroalkanes, and cyanobenzothiazoles;
R 2 , R 5 , R 12 and R 15 are independently H, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;
R 20 , R 21 , R 22 , R 23 , R 24 , R 25 , and R 26 are independently H or C 1-6 alkyl or one or more of R 20 and R 21 , R 21 and R 22 , R 22 and R 23 , R 24 and R 25 , R 25 and R 26 , and R 26 and R 23 together form an aryl, heteroaryl, carbocyclic or heterocyclic ring;
R 1 and R 2 and/or R 11 and R 12 may together form a carbocyclic, heterocyclic, aryl or heteroaryl ring;
R 5-10 are independently H, halo, OH, alkyl, aryl, heteroaryl, CO 2 H, SO 3 H, L-CO 2 H, L-SO 3 H, L-R or L-C S ;
each X is independently CHR 23 , O, S or NR 30 ; and
R 30 is H, C 1-4 alkyl or —C(O)C 1-4 alkyl.
3. A compound according to claim 1 wherein at least one of R 24 , R 25 or R 26 is H.
4. A compound according to claim 1 wherein X is CH 2 .
5. A compound according to claim 1 wherein R 1 and R 2 form a 5-7 membered carbocyclic ring.
6. A compound according to claim 1 wherein R 12 is H, Cl or OMe.
7. A compound according to claim 1 wherein R 11 and R 12 form a 5-7 membered carbocyclic ring.
8. A compound according to claim 1 wherein at least one of R 20 , R 21 , R 22 and R 23 is H.
9. A compound according to claim 1 wherein R 2 is H, Cl or OMe.
10. A compound according to claim 1 wherein R 3 is C 1-4 alkyl.
11. A compound according to claim 10 wherein R 3 is methyl or ethyl.
12. A compound according to claim 1 wherein R 4 is C 1-4 alkyl.
13. A compound according to claim 12 wherein R 4 is methyl or ethyl.
14. A compound according to claim 1 wherein R 3 is part of a heterocycle.
15. A compound according to claim 1 wherein R 4 is part of a heterocycle.
16. A compound according to claim 1 wherein R 5 is H.
17. A compound according to claim 1 wherein R 15 is H.
18. A compound according to claim 1 wherein R 6 is H or halogen.
19. A compound according to claim 1 wherein R 9 is H or halogen.
20. A compound according to claim 1 wherein R w is H, F, Cl CO 2 H or SO 3 H.
21. A compound according to claim 1 wherein one of R 7 and R 8 is -L-R, -L-CO 2 H or -L-C S and the other is H, Cl, or F.
22. A compound according to claim 1 wherein L is —CO—, —SCH 2 CO—, or —SO 2 —.
23. A compound according to claim 1 wherein L is a self-immolative linker selected from the group consisting of
24. A compound according to claim 1 wherein R is
25. A compound according to claim 1 wherein C S is NHCH 2 CH 2 (OCH 2 CH 2 ) m (CH 2 ) 6 Cl, wherein n is 2-6.
26. A compound according to claim 1 wherein C S comprises a nucleoside.
27. A compound according to claim 1 wherein C S comprises an oligonucleotide.
28. A compound selected from the group consisting of: