U.S. patent application number 13/780338 was filed with the patent office on 2013-09-05 for cyanine compounds.
The applicant listed for this patent is Peter T. Czerney, Surbhi Desai, Boguslawa R. Dworecki, Greg Hermanson, Frank G. Lehmann, Marie Christine Nlend, Matthias S. Wenzel. Invention is credited to Peter T. Czerney, Surbhi Desai, Boguslawa R. Dworecki, Greg Hermanson, Frank G. Lehmann, Marie Christine Nlend, Matthias S. Wenzel.
Application Number | 20130230466 13/780338 |
Document ID | / |
Family ID | 47846213 |
Filed Date | 2013-09-05 |
United States Patent
Application |
20130230466 |
Kind Code |
A1 |
Hermanson; Greg ; et
al. |
September 5, 2013 |
CYANINE COMPOUNDS
Abstract
Compounds used as labels with properties comparable to known
fluorescent compounds. The compounds can be conjugated to proteins
and nucleic acids for biological imaging and analysis. Synthesis of
the compounds, formation and use of the conjugated compounds, and
specific non-limiting examples of each are provided.
Inventors: |
Hermanson; Greg; (Loves
Park, IL) ; Czerney; Peter T.; (Weimar, DE) ;
Desai; Surbhi; (Rockford, IL) ; Wenzel; Matthias
S.; (Jena, DE) ; Dworecki; Boguslawa R.;
(Rockford, IL) ; Lehmann; Frank G.; (Jena, DE)
; Nlend; Marie Christine; (Rockford, IL) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Hermanson; Greg
Czerney; Peter T.
Desai; Surbhi
Wenzel; Matthias S.
Dworecki; Boguslawa R.
Lehmann; Frank G.
Nlend; Marie Christine |
Loves Park
Weimar
Rockford
Jena
Rockford
Jena
Rockford |
IL
IL
IL
IL |
US
DE
US
DE
US
DE
US |
|
|
Family ID: |
47846213 |
Appl. No.: |
13/780338 |
Filed: |
February 28, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61718805 |
Oct 26, 2012 |
|
|
|
61606210 |
Mar 2, 2012 |
|
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|
Current U.S.
Class: |
424/9.6 ;
435/188; 435/7.1; 436/501; 506/9; 530/350; 530/391.3; 536/1.11;
536/23.1; 536/26.6; 548/303.7; 548/455 |
Current CPC
Class: |
C07D 401/14 20130101;
G01N 33/582 20130101; C09B 23/0025 20130101; C07D 403/06 20130101;
C09B 23/0016 20130101; A61K 49/16 20130101; C07K 2317/76 20130101;
A61K 49/143 20130101; C07D 209/18 20130101; C09B 23/06 20130101;
C09B 69/10 20130101; A61K 49/221 20130101; C09B 23/086 20130101;
C09B 23/083 20130101; C09B 23/0066 20130101; C09B 69/00 20130101;
C07K 16/40 20130101; A61K 47/6871 20170801; A61K 49/04 20130101;
A61K 49/12 20130101; C07D 403/08 20130101 |
Class at
Publication: |
424/9.6 ;
548/455; 530/350; 530/391.3; 435/188; 536/26.6; 536/23.1;
548/303.7; 536/1.11; 435/7.1; 436/501; 506/9 |
International
Class: |
C07D 209/18 20060101
C07D209/18 |
Claims
1. A compound of general formula IIa ##STR00295## or general
formula IIb ##STR00296## wherein each of R.sup.1, R.sup.2, R.sup.5,
and R.sup.6 is the same or different and is independently selected
from the group consisting of aliphatic, heteroaliphatic,
sulfoalkyl, heteroaliphatic with terminal SO.sub.3, a PEG group
P-L-Z where P is selected from an ethylene glycol group, a
diethylene glycol group, and a (poly)ethylene glycol group where
the (poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where
s is an integer from 3-6 inclusive, a sulfonamide group
-L-SO.sub.2NH--P-L-Z, and a caboxamide group -L-CONH--P-L-Z; each
of R.sup.7 and R.sup.8 is the same or different and is
independently selected from the group consisting of H, SO.sub.3, a
PEG group P-L-Z where P is selected from an ethylene glycol group,
a diethylene glycol group, and a (poly)ethylene glycol group, where
the (poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where
s is an integer from 3-6 inclusive, a sulfonamide group
--SO.sub.2NH--P-L-Z, and a caboxamide group --CONH--P-L-Z; where L
is selected from the group consisting of a divalent linear
(--(CH.sub.2).sub.o--, o=0 to 15), crossed, or cyclic alkane group
that is optionally substituted by at least one atom selected from
the group consisting of oxygen, substituted nitrogen, and/or
sulfur; where Z is selected from the group consisting of H,
CH.sub.3, alkyl, heteroalkyl, NH.sub.2, --COO.sup.-, --COOH,
--COSH, CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI, --COO-Su
(succinimidyl/sulfosuccinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH.sub.2--I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; and n is an
integer from 1 to 3 inclusive; with the proviso that at least one
of R.sup.1, R.sup.2, R.sup.5, R.sup.6, R.sup.7, and R.sup.8
contains a PEG group.
2. A compound selected from the group consisting of ##STR00297##
##STR00298## wherein each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6
is the same or different and is independently selected from the
group consisting of aliphatic, heteroaliphatic, sulfoalkyl,
heteroaliphatic with terminal SO.sub.3, a PEG group P-L-Z where P
is selected from an ethylene glycol group, a diethylene glycol
group, and a (poly)ethylene glycol group where the (poly)ethylene
glycol group is (CH.sub.2CH.sub.2O).sub.s where s is an integer
from 3-6 inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from H, SO.sub.3, a
PEG group P-L-Z where P is selected from an ethylene glycol group,
a diethylene glycol group, and a (poly)ethylene glycol group where
the (poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where
s is an integer from 3-6 inclusive, a sulfonamide
--SO.sub.2NH--P-L-Z, or a caboxamide --CONH--P-L-Z; where L is
selected from the group consisting of a divalent linear
(--(CH.sub.2).sub.o--, o=0 to 15), crossed, or cyclic alkane group
optionally substituted by at least one atom selected from the group
consisting of oxygen, substituted nitrogen, and/or sulfur; where Z
is selected from the group consisting of H, CH.sub.3, alkyl, a
heteroalkyl group, NH.sub.2, --COO.sup.-, --COOH, --COSH,
CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI, --COO-Su
(succinimidyl/sulfosuccinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic, and heteroaliphatic, and the
biomolecule is a protein, antibody, nucleotide, oligonucleotide,
biotin, or hapten; X is selected from the group consisting of --OH,
--SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl, --Br, I, --NHS
(hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH.sub.2--I, where R is --H, aliphatic, or
heteroaliphatic; Kat is a number of Na.sup.+, K.sup.+, Ca.sup.2+,
ammonia, or other cation(s) needed to compensate the negative
charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; each of R3 and
R4 is the same or different and is independently --H, aliphatic,
heteroaliphatic, or a PEG group P-L-Z where P is selected from an
ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive; or R3 and R4 together form a cyclic structure where R3
and R4 are joined using a divalent structural element selected from
the group consisting of --(CH.sub.2).sub.q--,
--(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of hydrogen, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, a PEG group P-L-Z where P
is selected from an ethylene glycol group, a diethylene glycol
group, and a (poly)ethylene glycol group where the (poly)ethylene
glycol group is (CH.sub.2CH.sub.2O).sub.s where s is an integer
from 3-6 inclusive, and an oxygen-containing group OR.sup.PM where
R.sup.PM is selected from the group consisting of --H, substituted
or unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cyclic alkyl, substituted or
unsubstituted heterocyclic alkyl, substituted or unsubstituted
aryl, and substituted or unsubstituted heteroaryl, where the group
is optionally substituted one or more times with at least one of
hydroxyl, sulfo, carboxy, and/or amino; with the proviso that at
least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6,
R.sup.7, and R.sup.8 contains a PEG group.
3. A compound selected from the group consisting of ##STR00299##
##STR00300## wherein each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6
is the same or different and is independently selected from the
group consisting of aliphatic, heteroaliphatic, sulfoalkyl,
heteroaliphatic with terminal SO.sub.3, a PEG group P-L-Z where P
is selected from an ethylene glycol group, a diethylene glycol
group, and a (poly)ethylene glycol group where the (poly)ethylene
glycol group is (CH.sub.2CH.sub.2O).sub.s where s is an integer
from 3-6 inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from H, SO.sub.3, a
PEG group P-L-Z where P is selected from an ethylene glycol group,
a diethylene glycol group, and a (poly)ethylene glycol group where
the (poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where
s is an integer from 3-6 inclusive, a sulfonamide group
--SO.sub.2NH--P-L-Z, or a caboxamide group --CONH--P-L-Z; where L
is selected from the group consisting of a divalent linear
(--(CH.sub.2).sub.o--, o=0 to 15), crossed, or cyclic alkane group
that can be substituted by at least one atom selected from the
group consisting of oxygen, substituted nitrogen, and/or sulfur;
where Z is selected from the group consisting of H, CH.sub.3,
alkyl, heteroalkyl, NH.sub.2, --COO.sup.-, --COOH, --COSH,
CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI, --COO-Su
(succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COOH, --CONR'-L-COO-Su,
--CONR'-L-COO--STP, --CONR'-L-COO-TFP, --CONR'-L-CONR''.sub.2,
--CONR'-L-CO-biomolecule, --CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of --H, aliphatic group, and heteroaliphatic
group, and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH.sub.2--I, where R is --H, aliphatic, or
heteroaliphatic; Kat is a number of Na.sup.+, K.sup.+, Ca.sup.2+,
ammonia, or other cation(s) needed to compensate the negative
charge brought by the cyanine; m is an integer from 0 to 5
inclusive; p is an integer from 1 to 6 inclusive; each of R3 and R4
is the same or different and is independently hydrogen, an
aliphatic group, a heteroaliphatic group, or a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where s is
an integer from 3-6 inclusive; or R3 and R4 together form a cyclic
structure where R3 and R4 are joined using a divalent structural
element selected from the group consisting of --(CH.sub.2).sub.q--,
--(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of --H, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, a PEG group P-L-Z where P
is selected from an ethylene glycol group, a diethylene glycol
group, and a (poly)ethylene glycol group where the (poly)ethylene
glycol group is (CH.sub.2CH.sub.2O).sub.s where s is an integer
from 3-6 inclusive, and an oxygen-containing group OR.sup.PM where
R.sup.PM is selected from the group consisting of hydrogen,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cyclic alkyl, substituted
or unsubstituted heterocyclic alkyl, substituted or unsubstituted
aryl, and substituted or unsubstituted heteroaryl, where the group
is optionally substituted at least once with at least one of
hydroxyl, sulfo, carboxy, and/or amino; with the proviso that at
least one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6,
R.sup.7, and R.sup.8 contains a PEG group.
4. The compound of claim 3 selected from the group consisting of
##STR00301## ##STR00302## ##STR00303## ##STR00304## ##STR00305##
##STR00306## ##STR00307##
5. A method of labeling at least one biomolecule, the method
comprising providing a composition comprising at least one
excipient and the compound of claim 2 in an effective concentration
to at least one biomolecule under conditions sufficient for
labeling the biomolecule with the compound.
6. The method of claim 5 wherein the biomolecule is selected from
the group consisting of a protein, antibody, enzyme, nucleoside
triphosphate, oligonucleotide, biotin, hapten, cofactor, lectin,
antibody binding protein, carotenoid, carbohydrate, hormone,
neurotransmitter, growth factors, toxin, biological cell, lipid,
receptor binding drug, fluorescent proteins, organic polymer
carrier material, inorganic carrier material, and combinations
thereof.
7. A method of labeling at least one biomolecule, the method
comprising providing a composition comprising at least one
excipient and the compound of claim 3 in an effective concentration
to at least one biomolecule under conditions sufficient for
labeling the biomolecule with the compound.
8. The method of claim 7 wherein the biomolecule is selected from
the group consisting of a protein, antibody, enzyme, nucleoside
triphosphate, oligonucleotide, biotin, hapten, cofactor, lectin,
antibody binding protein, carotenoid, carbohydrate, hormone,
neurotransmitter, growth factors, toxin, biological cell, lipid,
receptor binding drug, fluorescent proteins, organic polymer
carrier material, inorganic carrier material, and combinations
thereof.
9. The method of claim 7 wherein the compound is V19-03005.
10. A method of detecting at least one biomolecule, the method
comprising providing a composition comprising at least one
excipient and the compound of claim 2 in an effective concentration
to at least one biomolecule under conditions sufficient for binding
the compound to the biomolecule, and detecting the
biomolecule-bound compound.
11. The method of claim 10 wherein the biomolecule is selected from
a protein, antibody, enzyme, nucleoside triphosphate,
oligonucleotide, biotin, hapten, cofactor, lectin, antibody binding
protein, carotenoid, carbohydrate, hormone, neurotransmitter,
growth factors, toxin, biological cell, lipid, receptor binding
drug, fluorescent proteins, organic polymer carrier material,
inorganic carrier material, and combinations thereof.
12. The method of claim 10 wherein the at least one biomolecule is
detected in an assay selected from fluorescence microscopy, flow
cytometry, in vivo imaging, immunoassay, hybridization,
chromatographic assay, electrophoretic assay, microwell plate based
assay, fluorescence resonance energy transfer (FRET) system,
bioluminescence resonance energy transfer (BRET) system, high
throughput screening, or microarray.
13. The method of claim 10 wherein the biomolecule is detected by
in vivo imaging comprising providing the biomolecule-bound compound
to at least one of a biological sample, tissue, or organism, and
detecting the biomolecule within the at least one of a biological
sample, tissue, or organism.
14. A method of detecting at least one biomolecule, the method
comprising providing a composition comprising at least one
excipient and the compound of claim 3 in an effective concentration
to at least one biomolecule under conditions sufficient for binding
the compound to the biomolecule, and detecting the
biomolecule-bound compound.
15. The method of claim 14 wherein the biomolecule is selected from
a protein, antibody, enzyme, nucleoside triphosphate,
oligonucleotide, biotin, hapten, cofactor, lectin, antibody binding
protein, carotenoid, carbohydrate, hormone, neurotransmitter,
growth factors, toxin, biological cell, lipid, receptor binding
drug, fluorescent proteins, organic polymer carrier material,
inorganic carrier material, and combinations thereof.
16. The method of claim 14 wherein the at least one biomolecule is
detected in an assay selected from fluorescence microscopy, flow
cytometry, in vivo imaging, immunoassay, hybridization,
chromatographic assay, electrophoretic assay, microwell plate based
assay, fluorescence resonance energy transfer (FRET) system,
bioluminescence resonance energy transfer (BRET) system, high
throughput screening, or microarray.
17. The method of claim 14 wherein the biomolecule is detected by
in vivo imaging comprising providing the biomolecule-bound compound
to at least one of a biological sample, tissue, or organism, and
detecting the biomolecule within the at least one of a biological
sample, tissue, or organism.
18. The method of claim 14 wherein the compound is V19-03005.
19. A kit for labeling and/or detecting at least one biomolecule in
a sample, the kit comprising the compound of claim 2 and at least
one excipient, and instructions for use of the compound to label
and/or detect a biomolecule in a sample.
20. A kit for labeling and/or detecting at least one biomolecule in
a sample, the kit comprising the compound of claim 3 and at least
one excipient, and instructions for use of the compound to label
and/or detect a biomolecule in a sample.
21. The kit of claim 20 wherein the compound is V19-03005.
Description
[0001] This application claims priority to co-pending U.S.
application Ser. Nos. 61/606,210 filed Mar. 2, 2012 and 61/718,805
filed Oct. 26, 2012, each of which is expressly incorporated by
reference herein in its entirety.
[0002] Compounds useful as labels with properties comparable to
known fluorescent compounds are disclosed. The compounds can be
conjugated to proteins and nucleic acids for biological imaging and
analysis. Synthesis of the compounds, formation and use of the
conjugated compounds, and specific non-limiting examples of each
are disclosed.
[0003] Compounds that react with biomolecules (e.g., antigens,
antibodies, DNA-segments with the corresponding complimentary
species for measuring enzyme kinetics, receptor-ligand
interactions, nucleic acid hybridization kinetics in vitro as well
as in vivo, etc.), termed labels or dyes, are useful for, e.g.,
pharmacological characterization of receptors and drugs, binding
data, etc. Compounds such as xanthylium salts (U.S. Pat. No.
5,846,737) and/or cyanines (U.S. Pat. No. 5,627,027) are used for
such applications, but aggregate and form dimers, especially in
aqueous solution, due to planarity of their t-system. Compounds
that have insufficient hydrophilicity undergo non-specific
interactions with various surfaces, resulting in problems when
attempting purify the corresponding conjugate, and an
unsatisfactory signal to noise ratio.
[0004] Efforts are directed to reducing undesirable properties by
introducing substituents that increase the hydrophilicity of the
compounds. For example, sulfonic acid function substituents have
been introduced into the cyanine chromophore. U.S. Pat. No.
6,083,485 (Licha) and U.S. Pat. Nos. 6,977,305 and 6,974,873
(Molecular Probes) disclose cyanine compounds having one of the
common methyl groups in the 3-position of the terminal indole
heterocycle substituted by a .omega.-carboxyalkyl function, and in
which the previously present (e.g. in Cy3 or Cy5) N-alkyl or
N-.omega.-carboxyalkyl functions are replaced by N-.omega.-alkyl
sulfonic acid functions. WO 05/044923 discloses cyanine compounds
having the common methyl substituent in the 3-position of the
terminal indole heterocycle substituted by a N-.omega.-alkyl
sulfonic acid function. In these publications, cyanine compounds
having more than two sulfonic acid function substituents exhibited
higher solubility and correspondingly a lower tendency to dimer
formation, in comparison to cyanine compounds (Cy3, Cy5) described
in U.S. Pat. No. 5,627,027.
[0005] The disclosed cyanine compounds are useful as labels in
optical, especially fluorescence optical, determination and
detection methods. The compounds have high hydrophilicity, high
molar absorbance, high photo-stability, and high storage stability.
These compounds can be excited by monochromatic (e.g., lasers,
laser diodes) or polychromatic (e.g., white light sources) light in
the ultraviolet (UV), visible, and near infrared (NIR) spectral
region to generate emission of fluorescence light.
[0006] Typical application methods are based on the reaction of the
compounds with biomolecules such as proteins (e.g., antigens,
antibodies, etc.), DNA and/or RNA segments, etc. with the
corresponding complimentary species. Thus, among other embodiments,
the compounds are useful to measure enzyme kinetics,
receptor-ligand interactions, and nucleic acid hybridization
kinetics in vitro and/or in vivo. The compounds are useful for the
pharmacological characterization of receptors and/or drugs.
Applications include, but are not limited to, uses in medicine,
pharmacy, biological sciences, materials sciences, environmental
control, detection of organic and inorganic micro samples occurring
in nature, etc.
[0007] The following nomenclature is used to describe embodiments:
550 Compound 1/X, 550 Compound 2/X, 550 Compound 3/X, 550 Compound
4/X, 550 Compound 5/X, 550 Compound 6/X, 650 Compound 1/X, 650
Compound 2/X, 650 Compound 3/X, 650 Compound 4/X, 650 Compound 5/X,
650 Compound 6/X, 755 Compound 1/X, 755 Compound 2/X, 755 Compound
3/X, 755 Compound 4/X, 755 Compound 5/X, 755 Compound 6/X, where
550, 650, and 755 Compounds comprise a polymethine chain of 3
carbon, 5 carbon, and 7 carbon atoms, respectively; the first
number is the length of an ethylene glycol, diethylene glycol, or
(poly)ethylene glycol (collectively referred to herein as PEG) on
an indole N, e.g. 1 is ethylene glycol (PEG.sub.1) on an indole N,
2 is diethylene glycol (PEG.sub.2) on an indole N, 3 is
(poly)ethylene glycol (poly=3, PEG.sub.3) on an indole N, 4 is
(poly)ethylene glycol (poly=4, PEG.sub.4) on an indole N, 5 is
(poly)ethylene glycol (poly=5, PEG.sub.5) on an indole N, and 6 is
(poly)ethylene glycol (poly=6, PEG.sub.6) on an indole N; and X is
the total number of PEG groups on the compound. For example, 650
Compound 4/4 contains PEG.sub.4 on an indole N and a total of four
PEG groups on the compound.
[0008] In one embodiment, the cyanine compounds have, in an
N-position of one heterocycle, ethylene glycol, diethylene glycol,
or an ethylene glycol polymer (i.e., poly(ethylene)glycol,
abbreviated as PEG), and the other heterocycle has, in a
N-position, a function for conjugating the compound to a
biomolecule, and an ethylene glycol, diethylene glycol, or an
ethylene glycol polymer (i.e., poly(ethylene)glycol, abbreviated as
PEG) in another position of the cyanine compound. In one
embodiment, the cyanine compound has, in any position of the
compound, at least one sulfo and/or sulfoalkyl. In one embodiment,
the cyanine compound has, in any position of the compound, a
sulfonamide and/or carboxamide comprising an ethylene glycol group
or an ethylene glycol polymer (i.e., poly(ethylene)glycol,
abbreviated as PEG), either directly or indirectly attached to the
compound. Indirect attachment indicates use of a linker, direct
attachment indicates lack of such a linker. A linker can be any
moiety.
[0009] In one embodiment, the cyanine compounds have, in an
N-position of one heterocycle, an ethylene glycol, diethylene
glycol, or ethylene glycol polymer (i.e., poly(ethylene)glycol,
abbreviated as PEG), and the other heterocycle has, in a
N-position, an ethylene glycol, diethylene glycol, or ethylene
glycol polymer (i.e., poly(ethylene)glycol, abbreviated as PEG) and
a function for conjugating the compound to a biomolecule, and an
ethylene glycol group or an ethylene glycol polymer (i.e.,
poly(ethylene)glycol, abbreviated as PEG) in another position of
the benzocyanine compound. In one embodiment, the cyanine compound
has, in any position of the compound, at least one sulfo and/or
sulfoalkyl. In one embodiment, the cyanine compound has, in any
position of the compound, a sulfonamide and/or carboxamide
comprising an ethylene glycol, diethylene glycol, or ethylene
glycol polymer (i.e., poly(ethylene)glycol, abbreviated as PEG),
either directly or indirectly attached to the compound. Indirect
attachment indicates use of a linker, direct attachment indicates
lack of such a linker. A linker can be any moiety.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIGS. 1A-C show the absorption maxima for compounds and
conjugated compounds.
[0011] FIG. 2 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0012] FIG. 3 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0013] FIG. 4 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0014] FIG. 5 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0015] FIG. 6 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0016] FIG. 7 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0017] FIG. 8 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0018] FIG. 9 shows fluorescence plate functional assay results
with inventive compounds and commercial dyes in one embodiment.
[0019] FIGS. 10A-B show the average total unbound fluorescence
intensity with inventive compounds and commercial dyes in one
embodiment.
[0020] FIGS. 11A-B show the average total unbound fluorescence
intensity with inventive compounds and commercial dyes in one
embodiment.
[0021] FIGS. 12A-B show the average total unbound fluorescence
intensity with inventive compounds and commercial dyes in one
embodiment.
[0022] FIGS. 13A-B show the average total unbound fluorescence
intensity with inventive compounds and commercial dyes in one
embodiment.
[0023] FIGS. 14A-E show immunofluorescence assay results with
inventive compounds and commercial dyes in one embodiment.
[0024] FIG. 15 shows the immunofluorescence assay results of FIG.
14 expressed as fluorescence intensity.
[0025] FIG. 16 shows the immunofluorescence assay results of FIG.
14 expressed as signal-to-background ratio.
[0026] FIGS. 17A-D show immunofluorescence assay results with
inventive compounds and commercial dyes in one embodiment.
[0027] FIG. 18 shows the immunofluorescence assay results of FIG.
17 expressed as fluorescence intensity.
[0028] FIG. 19 shows the immunofluorescence assay results of FIG.
17 expressed as signal-to-background ratio.
[0029] FIGS. 20A-D show immunofluorescence assay results with
inventive compounds and commercial dyes in one embodiment.
[0030] FIG. 21 shows the immunofluorescence assay results of FIG.
20 expressed as fluorescence intensity.
[0031] FIG. 22 shows the immunofluorescence assay results of FIG.
20 expressed as signal-to-background ratio.
[0032] Unless otherwise noted, reference to general formulas (e.g.,
I, II, III, IV, V, and VI, each subsequently described),
encompasses their respective a, b, c, etc. structures.
[0033] In one embodiment, the compound is a compound according to
general formula Ia with "a" indicating the chain from the right
indole N terminates in COX:
##STR00001##
or general formula Ib with "b" indicating the chain from the right
indole N terminates in OH:
##STR00002##
where each of R.sup.1 and R.sup.2 is the same or different and is
independently selected from the group consisting of an aliphatic,
heteroaliphatic, sulfoalkyl, heteroaliphatic with terminal
SO.sub.3, a PEG group P-L-Z where P is selected from an ethylene
glycol group, a diethylene glycol group, and a (poly)ethylene
glycol group where the (poly)ethylene glycol group is
(CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6 inclusive,
a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a caboxamide group
-L-CONH--P-L-Z; where L is selected from the group consisting of a
divalent linear (--(CH.sub.2).sub.o--, o=0 to 15), crossed, or
cyclic alkane group that can be substituted by at least one atom
selected from the group consisting of oxygen, substituted nitrogen,
and/or sulfur; where Z is selected from the group consisting of H,
CH.sub.3, alkyl, heteroalkyl, NH.sub.2, --COO.sup.-, --COOH,
--COSH, CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI, --COO-Su
(succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; and n is an
integer from 1 to 3 inclusive; with the proviso that at least one
of R.sup.1 and R.sup.2 contains a PEG group.
[0034] In one embodiment, the PEG group is selected from
--C--C--O--C (ethylene glycol with terminal methyl),
--C--C--O--C--C--O--C (diethylene glycol with terminal methyl),
--C--C--O--C--C--O--C--C--O--C--C--O--C ((poly)ethylene glycol (3)
with terminal methyl), --C--C--O--C--C--O--C--C--O--C--C--O--C
((poly)ethylene glycol (4) with terminal methyl),
--C--C--O--C--C--O--C--C--O--C--C--O--C--C--O--C ((poly)ethylene
glycol (5) with terminal methyl), or
C--C--O--C--C--O--C--C--O--C--C--O--C--C--C--O--C--C--O--C
((poly)ethylene glycol (6) with terminal methyl). In one
embodiment, the PEG group P may be either uncapped, e.g., lack a
terminal methyl, or may be capped with an atom or group other than
a methyl. In one embodiment, the PEG group P terminates with a Z
group, where Z is selected from H, CH.sub.3, a CH.sub.3 group,
alkyl, or a heteroalkyl group.
[0035] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R.sup.2 is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 1. In one
embodiment the compound is general formula I where R1 is sulfoalkyl
and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 1; o is 3; and n is 1. In one embodiment,
the compound is general formula I where R1 is sulfoalkyl and R2 is
a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is
2; o is 3; and n is 1. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 1. In
one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 4; o is 3; and n is 1. In one embodiment the
compound is general formula I, where R1 is sulfoalkyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5;
o is 3; and n is 1.
[0036] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 2. In one embodiment the
compound is general formula I where R1 is sulfoalkyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 2. In one embodiment the compound is general
formula I, where R1 is sulfoalkyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 2. In
one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 2. In one embodiment the
compound is general formula I where R1 is sulfoalkyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 2. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
2.
[0037] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 3. In one embodiment the
compound is general formula I where R1 is sulfoalkyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 3. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 3. In
one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 3. In one embodiment,
the compound is general formula I, where R1 is sulfoalkyl and R2 is
a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is
4; o is 3; and n is 3. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
3.
[0038] In one embodiment the compound is general formula I where R1
is methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 1. In one embodiment the
compound is general formula I where R1 is methyl and R2 is a PEG
group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is
3; and n is 1. In one embodiment the compound is general formula I
where R1 is methyl and R2 is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 1. In one
embodiment the compound is general formula I where R1 is methyl and
R2 is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide;
m is 3; o is 3; and n is 1. In one embodiment, the compound is
general formula I, where R1 is methyl and R2 is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is
1. In one embodiment the compound is general formula I where R1 is
methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 5; o is 3; and n is 1.
[0039] In one embodiment the compound is general formula I where R1
is methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 2. In one embodiment the
compound is general formula I where R1 is methyl and R2 is a PEG
group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is
3; and n is 2. In one embodiment the compound is general formula I
where R1 is methyl and R2 is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 2. In one
embodiment the compound is general formula I where R1 is methyl and
R2 is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide;
m is 3; o is 3; and n is 2. In one embodiment the compound is
general formula I where R1 is methyl and R2 is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is
2. In one embodiment the compound is general formula I where R1 is
methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 5; o is 3; and n is 2.
[0040] In one embodiment, the compound is general formula I where
R1 is methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 3. In one embodiment,
the compound is general formula I where R1 is methyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 3. In one embodiment the compound is general
formula I where R1 is methyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 3. In
one embodiment, the compound is general formula I where R1 is
methyl and R2 is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 3. In one embodiment,
the compound is general formula I where R1 is methyl and R2 is a
PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 3. In one embodiment, the compound is general
formula I where R1 is methyl and R2 is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; n is 3.
[0041] In one embodiment the compound is general formula I where R1
and R2 are PEG groups; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 1. In one embodiment the
compound is general formula I where R1 and R2 are PEG groups; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is
1. In one embodiment the compound is general formula I where R1 and
R2 are PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide;
m is 2; o is 3; and n is 1. In one embodiment the compound is
general formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 1. In one
embodiment, the compound is general formula I, where R1 and R2 are
PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 1. In one embodiment the compound is general
formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is 1.
[0042] In one embodiment the compound is general formula I where R1
and R2 are PEG groups; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 2. In one embodiment the
compound is general formula I where R1 and R2 are PEG groups; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is
2. In one embodiment the compound is general formula I where R1 and
R2 are PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide;
m is 2; o is 3; and n is 2. In one embodiment the compound is
general formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 2. In one
embodiment the compound is general formula I where R1 and R2 are
PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 2. In one embodiment the compound is general
formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is 2.
[0043] In one embodiment the compound is general formula I where R1
and R2 are PEG groups; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 0; o is 3; and n is 3. In one embodiment the
compound is general formula I where R1 and R2 are PEG groups; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is
3. In one embodiment the compound is general formula I where R1 and
R2 are PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide;
m is 2; o is 3; and n is 3. In one embodiment the compound is
general formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 3. In one
embodiment, the compound is general formula I, where R1 and R2 are
PEG groups; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 3. In one embodiment the compound is general
formula I where R1 and R2 are PEG groups; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is 3.
[0044] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where
P is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 0; o is 3; and n is 1. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a sulfonamide group
-L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 1; o is 3; and n is 1. In one embodiment
the compound is general formula I where R1 is sulfoalkyl and R2 is
a sulfonamide group -L-SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is
1. In one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where P
is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 3; o is 3; and n is 1. In one embodiment, the compound is
general formula I, where R1 is sulfoalkyl and R2 is a sulfonamide
group -L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 1. In one
embodiment the compound is general formula I where R1 is sulfoalkyl
and R2 is a sulfonamide group -L-SO.sub.2NH--P where P is a PEG
group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is
3; and n is 1.
[0045] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where
P is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 0; o is 3; and n is 2. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a sulfonamide group
-L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 1; o is 3; and n is 2. In one embodiment
the compound is general formula I where R1 is sulfoalkyl and R2 is
a sulfonamide group -L-SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is
2. In one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where P
is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 3; o is 3; and n is 2. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a sulfonamide group
-L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 4; o is 3; and n is 2. In one embodiment
the compound is general formula I where R1 is sulfoalkyl and R2 is
a sulfonamide group -L-SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
2.
[0046] In one embodiment the compound is general formula I where R1
is sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where
P is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 0; o is 3; and n is 3. In one embodiment the compound is general
formula I where R1 is sulfoalkyl and R2 is a sulfonamide group
-L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 1; o is 3; and n is 3. In one embodiment
the compound is general formula I where R1 is sulfoalkyl and R2 is
a sulfonamide group -L-SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is
3. In one embodiment the compound is general formula I where R1 is
sulfoalkyl and R2 is a sulfonamide group -L-SO.sub.2NH--P where P
is a PEG group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 3; o is 3; and n is 3. In one embodiment, the compound is
general formula I, where R1 is sulfoalkyl and R2 is a sulfonamide
group -L-SO.sub.2NH--P where P is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 3. In one
embodiment the compound is general formula I where R1 is sulfoalkyl
and R2 is a sulfonamide group -L-SO.sub.2NH--P where P is a PEG
group; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is
3; and n is 3.
[0047] In one embodiment, an isolated enantiomeric mixture selected
from diastereomer Ia of general formula Ia shown below:
##STR00003##
diastereomer Ib of general formula Ia shown below:
##STR00004##
diastereomer Ic of general formula Ib shown below:
##STR00005##
or diastereomer Id of general formula Ib shown below:
##STR00006##
is provided, where each of R.sup.1 and R.sup.2 is the same or
different and is independently selected from the group consisting
of aliphatic, heteroaliphatic, sulfoalkyl, heteroaliphatic with
terminal SO.sub.3, a PEG group P-L-Z where P is selected from an
ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; where L is selected from the group
consisting of a divalent linear (--(CH.sub.2).sub.o--, o=0 to 15),
crossed, or cyclic alkane group that can be substituted by at least
one atom selected from the group consisting of oxygen, substituted
nitrogen, and/or sulfur; where Z is selected from the group
consisting of H, CH.sub.3, alkyl, heteroalkyl, NH.sub.2,
--COO.sup.-, --COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl,
--COBr, --COI, --COO-Su (succinimidyl/sulfosuccinimidyl),
--COO--STP (4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COOH, --CONR'-L-COO-Su,
--CONR'-L-COO--STP, --CONR'-L-COO-TFP, --CONR'-L-CONR''.sub.2,
--CONR'-L-CO-biomolecule, --CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of --H, aliphatic, and heteroaliphatic, and the
biomolecule is a protein, antibody, nucleotide, oligonucleotide,
biotin, or hapten; X is selected from the group consisting of --OH,
--SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl, --Br, I, --NHS
(hydroxysuccinimidyl/sulfo-succinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; and n is an
integer from 1 to 3 inclusive; with the proviso that at least one
of R.sup.1 and R.sup.2 contains a PEG group.
[0048] In one embodiment, the compound has general formula IIa with
"a" indicating the chain from the right indole N terminates in
COX:
##STR00007##
or general formula IIb with "b" indicating the chain from the right
indole N terminates in COH:
##STR00008##
where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6 is the same or
different and is independently selected from the group consisting
of aliphatic, heteroaliphatic, sulfoalkyl, heteroaliphatic with
terminal SO.sub.3, a PEG group P-L-Z where P is selected from an
ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from the group
consisting of H, SO.sub.3, a PEG group P-L-Z where P is selected
from an ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group --SO.sub.2NH--P-L-Z, and a
caboxamide group --CONH--P-L-Z; where L is selected from the group
consisting of a divalent linear (--(CH.sub.2).sub.o--, o=0 to 15),
crossed, or cyclic alkane group that can be substituted by at least
one atom selected from the group consisting of oxygen, substituted
nitrogen, and/or sulfur; where Z is selected from the group
consisting of H, CH.sub.3, alkyl, heteroalkyl, NH.sub.2,
--COO.sup.-, --COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl,
--COBr, --COI, --COO-Su (succinimidyl/sulfosuccinimidyl),
--COO--STP (4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfo-succinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH.sub.2--I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; and n is an
integer from 1 to 3 inclusive; with the proviso that at least one
of R.sup.1, R.sup.2, R.sup.5, R.sup.6, R.sup.7, and R.sup.8
contains a PEG group.
[0049] In one embodiment the compound is general formula II where
R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 1. In one embodiment the compound is general formula II
where R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 1. In one embodiment the compound is general
formula II where R1, R5, and R6 are methyl and R2 is a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; o is 3; and n is 1. In one embodiment the
compound is general formula II where R1, R5, and R6 are methyl and
R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 3; o is 3; and n is 1. In one embodiment
the compound is general formula II where R1, R5, and R6 are methyl
and R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 1. In one
embodiment the compound is general formula II where R1, R5, and R6
are methyl and R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
1.
[0050] In one embodiment the compound is general formula II where
R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 2. In one embodiment the compound is general formula II
where R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 2. In one embodiment the compound is general
formula II where R1, R5, and R6 are methyl and R2 is a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; o is 3; and n is 2. In one embodiment the
compound is general formula II where R1, R5, and R6 are methyl and
R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 3; o is 3; and n is 2. In one embodiment
the compound is general formula II where R1, R5, and R6 are methyl
and R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 2. In one
embodiment the compound is general formula II where R1, R5, and R6
are methyl and R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
2.
[0051] In one embodiment the compound is general formula II where
R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 3. In one embodiment the compound is general formula II
where R1, R5, and R6 are methyl and R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
o is 3; and n is 3. In one embodiment the compound is general
formula II where R1, R5, and R6 are methyl and R2 is a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; o is 3; and n is 3. In one embodiment the
compound is general formula II where R1, R5, and R6 are methyl and
R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 3; o is 3; and n is 3. In one embodiment
the compound is general formula II where R1, R5, and R6 are methyl
and R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 3. In one
embodiment the compound is general formula II where R1, R5, and R6
are methyl and R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
3.
[0052] In one embodiment the compound is general formula II where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 1. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is
3; and n is 1. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is
3; and n is 1. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is
3; and n is 1. In one embodiment, the compound is general formula
II, where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 1. In one embodiment the compound is general
formula II where R5 and R6 are methyl; R1 and R2 are PEG groups; R7
and R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 5; o is 3; and n is 1.
[0053] In one embodiment the compound is general formula II where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 2. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is
3; and n is 2. In one embodiment the compound is general formula
II, where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2;
o is 3; and n is 2. In one embodiment, the compound is general
formula II, where R5 and R6 are methyl; R1 and R2 are PEG groups;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 2. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 2. In one
embodiment, the compound is general formula II, where R5 and R6 are
methyl; R1 and R2 are PEG groups; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
2.
[0054] In one embodiment the compound is general formula II where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is
3; and n is 3. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is
3; and n is 3. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is
3; and n is 3. In one embodiment the compound is general formula II
where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is
3; and n is 3. In one embodiment, the compound is general formula
II, where R5 and R6 are methyl; R1 and R2 are PEG groups; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4;
o is 3; and n is 3. In one embodiment the compound is general
formula II where R5 and R6 are methyl; R1 and R2 are PEG groups; R7
and R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 5; o is 3; and n is 3.
[0055] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
1.
[0056] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 2. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 2. In
one embodiment, the compound is general formula H, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 2. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 2. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 2. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
2.
[0057] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
sulfonamide -L-SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; o is 3; and n is
3.
[0058] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
a caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; o is 3; and n is 1. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is caboxamide
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 4; o is 3; and n is 1. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is a caboxamide group
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 5; o is 3; and n is 1.
[0059] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
a caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 2. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is a
caboxamide --CONH--P where P is a PEG group; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 2. In one
embodiment, the compound is general formula II, where R5 and R6 are
methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is caboxamide
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; o is 3; and n is 2. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is caboxamide --CONH--P
where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 2. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is caboxamide --CONH--P
where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 4; o is 3; and n is 2. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is a caboxamide group
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 5; o is 3; and n is 2.
[0060] In one embodiment, the compound is general formula II, where
R5 and R6 are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is
a caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 0; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; o is 3; and n is 3. In
one embodiment, the compound is general formula II, where R5 and R6
are methyl; R1 and R2 are PEG groups; R7 is sulfo; R8 is caboxamide
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; o is 3; and n is 3. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is carboxamide --CONH--P
where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; o is 3; and n is 3. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is caboxamide --CONH--P
where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 4; o is 3; and n is 3. In one embodiment,
the compound is general formula II, where R5 and R6 are methyl; R1
and R2 are PEG groups; R7 is sulfo; R8 is a caboxamide group
--CONH--P where P is a PEG group; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 5; o is 3; and n is 3.
[0061] In one embodiment, the compound has general formula IIIa
with "a" indicating the chain from the right indole N terminates in
COX:
##STR00009##
or general formula IIIb with "b" indicating the chain from the
right indole N terminates in COH:
##STR00010##
where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6 is the same or
different and is independently selected from the group consisting
of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic
with terminal SO.sub.3, a PEG group P-L-Z where P is selected from
an ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from the group
consisting of H, SO.sub.3, a PEG group P-L-Z where P is selected
from an ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group --SO.sub.2NH--P-L-Z, and a
caboxamide group --CONH--P-L-Z; where L is selected from the group
consisting of a divalent linear (--(CH.sub.2).sub.o--, o=0 to 15),
crossed, or cyclic alkane group that can be substituted by at least
one atom selected from the group consisting of oxygen, substituted
nitrogen, and/or sulfur; where Z is selected from the group
consisting of H, CH.sub.3, alkyl, heteroalkyl, NH.sub.2,
--COO.sup.-, --COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl,
--COBr, --COI, --COO-Su (succinimidyl/sulfosuccinimidyl),
--COO--STP (4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfo-succinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, NH.sub.2, --NR-L-CO.sub.2H, --NR-L-CO--NHS,
--NR-L-CO-STP, --NR-L-CO-TFP, --NR-L-CO-benzotriazole, --NR-L-CHO,
--NR-L-maleimide, and --NR-L-NH--CO--CH2-I, where R is --H or an
aliphatic or heteroaliphatic group; Kat is a number of Na.sup.+,
K.sup.+, Ca.sup.2+, ammonia, or other cation(s) needed to
compensate the negative charge brought by the cyanine; m is an
integer from 0 to 5 inclusive; p is an integer from 1 to 6
inclusive; and n is an integer from 1 to 3 inclusive; and at least
one of R.sup.1, R.sup.2, R.sup.5, R.sup.6, R.sup.7, and R.sup.8
contains a PEG group.
[0062] In one embodiment, the compound is general formula III,
where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is
1; and n is 1. In one embodiment, the compound is general formula
III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
p is 2; and n is 1. In one embodiment, the compound is general
formula III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7
and R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 2; p is 3; and n is 1. In one embodiment, the compound is
general formula III, where R1, R5, and R6 are methyl; R2 is a PEG
group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; p is 4; and n is 1. In one embodiment,
the compound is general formula III, where R1, R5, and R6 are
methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 1. In one
embodiment, the compound is general formula III, where R1, R5, and
R6 are methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
1.
[0063] In one embodiment, the compound is general formula III,
where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is
1; and n is 2. In one embodiment, the compound is general formula
III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
p is 2; and n is 2. In one embodiment, the compound is general
formula III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7
and R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 2; p is 3; and n is 2. In one embodiment, the compound is
general formula III, where R1, R5, and R6 are methyl; R2 is a PEG
group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; p is 4; and n is 2. In one embodiment,
the compound is general formula III, where R1, R5, and R6 are
methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 2. In one
embodiment, the compound is general formula III, where R1, R5, and
R6 are methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
2.
[0064] In one embodiment, the compound is general formula III,
where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is
1; and n is 3. In one embodiment, the compound is general formula
III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 1;
p is 2; and n is 3. In one embodiment, the compound is general
formula III, where R1, R5, and R6 are methyl; R2 is a PEG group; R7
and R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m
is 2; p is 3; and n is 3. In one embodiment, the compound is
general formula III, where R1, R5, and R6 are methyl; R2 is a PEG
group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 3; p is 4; and n is 3. In one embodiment,
the compound is general formula III, where R1, R5, and R6 are
methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 3. In one
embodiment, the compound is general formula III, where R1, R5, and
R6 are methyl; R2 is a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
3.
[0065] In one embodiment the compound is general formula III where
R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and R8 are
sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is
1; and n is 1. In one embodiment the compound is general formula
III where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and
R8 are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is
1; p is 2; and n is 1. In one embodiment the compound is general
formula III where R5 and R6 are methyl; R1 and R2 are a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 2; p is 3; and n is 1. In one embodiment the
compound is general formula III where R5 and R6 are methyl; R1 and
R2 are a PEG group; R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP,
or --NR-L-maleimide; m is 3; p is 4; and n is 1. In one embodiment
the compound is general formula III where R5 and R6 are methyl; R1
and R2 are a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 4; p is 5; n is 1. In one
embodiment the compound is general formula III where R5 and R6 are
methyl; R1 and R2 are a PEG group; R7 and R8 are sulfo; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; n is 1.
[0066] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0;
p is 1; and n is 2. In one embodiment, the compound is general
formula III, where R5 and R6 are methyl; R1 and R2 are a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 1; p is 2; and n is 2. In one embodiment,
the compound is general formula III, where R5 and R6 are methyl; R1
and R2 are a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 2. In one
embodiment, the compound is general formula III, where R5 and R6
are methyl; R1 and R2 are a PEG group; R7 and R8 are sulfo; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is
2. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 and R8 are sulfo;
X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and
n is 2. In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5;
p is 6; and n is 2.
[0067] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0;
p is 1; and n is 3. In one embodiment, the compound is general
formula III, where R5 and R6 are methyl; R1 and R2 are a PEG group;
R7 and R8 are sulfo; X is --OH, --NHS, --O-TFP, or
--NR-L-maleimide; m is 1; p is 2; and n is 3. In one embodiment,
the compound is general formula III, where R5 and R6 are methyl; R1
and R2 are a PEG group; R7 and R8 are sulfo; X is --OH, --NHS,
--O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 3. In one
embodiment, the compound is general formula III, where R5 and R6
are methyl; R1 and R2 are a PEG group; R7 and R8 are sulfo; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is
3. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 and R8 are sulfo;
X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and
n is 3. In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 and R8
are sulfo; X is --OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 5;
p is 6; and n is 3.
[0068] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is sulfonamide --SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
1. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
1.
[0069] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is sulfonamide --SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
2. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
2.
[0070] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is sulfonamide --SO.sub.2NH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
3. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is
sulfonamide --SO.sub.2NH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
3.
[0071] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is a caboxamide group --CONH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
1. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 1. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
1.
[0072] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is a caboxamide group --CONH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
2. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 2. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
2.
[0073] In one embodiment, the compound is general formula III,
where R5 and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo;
R8 is a caboxamide group --CONH--P where P is a PEG group; X is
--OH, --NHS, --O-TFP, or --NR-L-maleimide; m is 0; p is 1; and n is
3. In one embodiment, the compound is general formula III, where R5
and R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 1; p is 2; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 2; p is 3; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 3; p is 4; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 4; p is 5; and n is 3. In
one embodiment, the compound is general formula III, where R5 and
R6 are methyl; R1 and R2 are a PEG group; R7 is sulfo; R8 is a
caboxamide group --CONH--P where P is a PEG group; X is --OH,
--NHS, --O-TFP, or --NR-L-maleimide; m is 5; p is 6; and n is
3.
[0074] In one embodiment, the compound is 550 Compound 1/2
##STR00011##
[0075] 550 Compound 1/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-2-((1E,3E)-3-(1-(2-methoxyethyl)--
3-methyl-5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)prop-1-enyl)-3-
-methyl-3H-indolium-5-sulfonate) contains an ethylene glycol on the
indole N of the left heterocycle, i.e., a methylated ethylene
glycol, as shown in the structure above, and the ethylene glycol
can be represented in abbreviated format as --[C--C--O].sub.1--,
which is used throughout. The methyl group on the ethylene glycol
prevents the terminal --OH from oxidation. Oxidation is known to
occur, over time, on an unprotected terminus of an ethylene glycol
group, diethylene glycol group, or (poly)ethylene glycol group,
collectively referred to herein as an unprotected PEG terminus.
Adding a methyl ether provides this protection, and prevents
reaction with electrophilic reactive groups.
[0076] In embodiments, e.g., for functional assays, the inventive
compounds are activated. Activation of the compound adds a chemical
moiety such that the compound is in a form that can be conjugated
to a biological moiety. Examples of chemical moieties for
activation are described below with reference to activation of 550
Compound 1, but one skilled in the art appreciates that activation
is not limited to these examples. One non-limiting example of an
activated compound is the NHS-ester of 550 Compound 1/2, shown
below:
##STR00012##
[0077] In one embodiment, the compound is a NHS-ester of 550
Compound 1/2 where, according to general formula I, o is 1, shown
below:
##STR00013##
[0078] In one embodiment, the compound is an NHS-ester of 550
Compound 1/2 where, according to general formula I, o is 5, shown
below:
##STR00014##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=1, is shown
below:
##STR00015##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=2, is shown
below:
##STR00016##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=3, is shown
below:
##STR00017##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=4, is shown
below:
##STR00018##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=5, is shown
below:
##STR00019##
One non-limiting example of a NHS-ester of 550 Compound 1/3,
according to general formula III, where m=1 and p=6, is shown
below:
##STR00020##
One non-limiting example of a NHS-ester of 550 Compound 2/3,
according to general formula III, where m=2 and p=1, is shown
below:
##STR00021##
One non-limiting example of a NHS-ester of 550 Compound 2/3,
according to general formula III, where m=2 and p=2, is shown
below:
##STR00022##
One non-limiting example of a NHS-ester of 550 Compound 2/3,
according to general formula III, where m=2 and p=3, is shown
below:
##STR00023##
One non-limiting example of a NHS-ester of 550 Compound 3/3,
according to general formula III, where m=3 and p=1, is shown
below:
##STR00024##
One non-limiting example of a NHS-ester of 550 Compound 3/3,
according to general formula III, where m=3 and p=2, is shown
below:
##STR00025##
One non-limiting example of a NHS-ester of 550 Compound 3/3,
according to general formula III, where m=3 and p=3, is shown
below:
##STR00026##
One non-limiting example of a NHS-ester of 550 Compound 4/3,
according to general formula III, where m=4 and p=1, is shown
below:
##STR00027##
One non-limiting example of a NHS-ester of 550 Compound 5/3,
according to general formula III, where m=5 and p=1, is shown
below:
##STR00028##
One non-limiting example of a NHS-ester of 550 Compound 6/3,
according to general formula III, where m=6 and p=1, is shown
below:
##STR00029##
One non-limiting example of an activated 550 Compound 1/2 is a
tetrafluorophenyl (TFP)-ester form of 550 Compound 1, shown
below:
##STR00030##
One non-limiting example of an activated 550 Compound 1/2 is a
sulfotetrafluorophenyl (STP)-ester form of 550 Compound 1, shown
below:
##STR00031##
One non-limiting example of an activated 550 Compound 1/2 is a
hydrazide form of 550 Compound 1, shown below:
##STR00032##
One non-limiting example of an activated 550 Compound 1/2 is a
maleimide form of 550 Compound 1, shown below:
##STR00033##
[0079] In one embodiment, the compound is 550 Compound 2/2
##STR00034##
[0080] 550 Compound 2/2
(1-(5-carboxypentyl)-2-((1E,3E)-3-(1-(2-(2-methoxyethoxy)ethyl)-3-methyl--
5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)prop-1-enyl)-3-(2-metho-
xyethyl)-3-methyl-3H-indolium-5-sulfonate) contains a diethylene
glycol on the indole N of the left heterocycle. 550 Compound 2/2,
with the diethylene glycol shown in abbreviated notation used
throughout, represents the following structure.
##STR00035##
The methyl group on the ethylene glycol prevents the terminal --OH
from oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 550 Compound 2/2 is activated as
described above, one non-limiting example of which is the NHS-ester
form of 550 Compound 2/2, shown below.
##STR00036##
In one embodiment, the compound is 550 Compound 3/2
##STR00037##
[0081] 550 Compound 3/2
(1-(5-carboxypentyl)-2-((1E,3E)-3-(1-(2-(2-(2-methoxyethoxy)ethoxy)ethyl)-
-3-methyl-5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)prop-1-enyl)--
3-(2-methoxyethyl)-3-methyl-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. 550
Compound 3/2, with the (poly)ethylene glycol shown in abbreviated
notation used throughout, represents the following structure.
##STR00038##
The methyl group on the ethylene glycol prevents the terminal --OH
from oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 550 Compound 3/2 is activated as
described above.
[0082] In one embodiment, the compound is 550 Compound 4/2
##STR00039##
[0083] 550 Compound 4/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-2-((1E,3E)-3-(3-methyl-5-
-sulfonato-3-(3-sulfonatopropyl)-1-(2,5,8,11-tetraoxamidecan-13-yl)indolin-
-2-ylidene)prop-1-enyl)-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. 550
Compound 4/2, with the (poly)ethylene glycol shown in abbreviated
notation used throughout, represents the following structure.
##STR00040##
The methyl group on the ethylene glycol prevents the terminal --OH
from oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 550 Compound 4/2 is activated as
described above.
[0084] In one embodiment, the compound is 550 Compound 5/2
##STR00041##
[0085] 550 Compound 5/2
(2-((1E,3E)-3-(1-(2,5,8,11,14-pentaoxahexadecan-16-yl)-3-methyl-5-sulfona-
to-3-(3-sulfonatopropyl)indolin-2-ylidene)prop-1-enyl)-1-(5-carboxypentyl)-
-3-(2-methoxyethyl)-3-methyl-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. 550
Compound 5/2, with the (poly)ethylene glycol shown in abbreviated
notation used throughout, represents the following structure.
##STR00042##
The methyl group on the ethylene glycol prevents the terminal --OH
from oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 550 Compound 5/2 is activated as
described above.
[0086] In one embodiment, the compound is 550 Compound 6/2
##STR00043##
[0087] 550 Compound 6/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-2-((1E,3E)-3-(3-methyl-1-
-(2,5,8,11,14,17-hexaoxanonadecan-19-yl)-5-sulfonato-3-(3-sulfonatopropyl)-
indolin-2-ylidene)prop-1-enyl)-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. 550
Compound 6/2, with the (poly)ethylene glycol shown in abbreviated
notation used throughout, represents the following structure.
##STR00044##
The methyl group on the ethylene glycol prevents the terminal --OH
from oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 550 Compound 6/2 is activated as
described above.
[0088] In embodiments, the degree of sulfonation is varied to,
e.g., vary the compound's degree of hydrophilicity or
hydrophobicity. One non-limiting example is a monosulfonate form of
550 Compound 1/2, shown below, but it is understood that the single
sulfo group can be at any of the described positions:
##STR00045##
[0089] One non-limiting example is a disulfonate form of 550
Compound 1/2, shown below, but it is understood that each of the
two sulfo groups can be at any of the described positions:
##STR00046##
[0090] One non-limiting example is a trisulfonate form of 550
Compound 1/2, shown below, but it is understood that each of the
three sulfo groups can be at any of the described positions:
##STR00047##
[0091] One non-limiting example is a tetrasulfonate form of 550
Compound 1/2, shown below, but it is understood that each of the
four sulfo groups can be at any of the described positions:
##STR00048##
[0092] In embodiments, the compound contains one or more
substitutions of the polymethine linker. In one embodiment, the
compound has general formula IVa with "a" indicating an ethylene
glycol, diethylene glycol, or (poly)ethylene glycol group on the
left indole N, and the chain on the right indole N terminating in
COX:
##STR00049##
general formula IVb with "b" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left
indole N, and the chain on the right indole N terminating in
COH:
##STR00050##
general formula IVc with "c" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left and
right indole N, and the chain on the right indole N terminating in
COX:
##STR00051##
or general formula IVd with "d" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left
indole N, and the chain on the right indole N terminating in
COH:
##STR00052##
where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6 is the same or
different and is independently selected from the group consisting
of an aliphatic, heteroaliphatic, sulfoalkyl, heteroaliphatic with
terminal SO.sub.3, a PEG group P-L-Z where P is selected from an
ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from either H,
SO.sub.3, a PEG group P-L-Z where P is selected from an ethylene
glycol group, a diethylene glycol group, and a (poly)ethylene
glycol group, where the (poly)ethylene glycol group is
(CH.sub.2CH.sub.2O).sub.s, where s is an integer from 3-6
inclusive, a sulfonamide group --SO.sub.2NH--P-L-Z, or a caboxamide
group --CONH--P-L-Z; where L is selected from the group consisting
of a divalent linear (--(CH.sub.2).sub.o--, o=0 to 15), crossed, or
cyclic alkane group that can be substituted by at least one atom
selected from the group consisting of oxygen, substituted nitrogen,
and/or sulfur; where Z is selected from the group consisting of H,
CH.sub.3, alkyl, a heteroalkyl group, NH.sub.2, --COO.sup.-,
--COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI,
--COO-Su (succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-.beta.-phosphoramidite, --CONR'-L-CHO,
--CONR'-L-maleimide, and --CONR'-L-NH--CO--CH.sub.2--I; R' and R''
is selected from the group consisting of H, aliphatic group, and
heteroaliphatic group, and the biomolecule is a protein, antibody,
nucleotide, oligonucleotide, biotin, or hapten; X is selected from
the group consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2,
--F, --Cl, --Br, I, --NHS hydroxysuccinimidyl/sulfosuccinimidyl),
--O-TFP (2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; p is an integer from 1 to 6 inclusive; each of R3 and R4
is the same or different and is independently hydrogen, an
aliphatic group, a heteroaliphatic group, or a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where s is
an integer from 3-6 inclusive; or R3 and R4 together form a cyclic
structure where R3 and R4 are joined using a divalent structural
element selected from the group consisting of --(CH.sub.2).sub.q--,
--(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of hydrogen, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, a substituted or
unsubstituted aryl-, phenoxy- or phenylmercapto function; and Y is
selected from the group consisting of hydrogen, alkyl, sulfoalkyl,
fluorine, chlorine, bromine, and a PEG group P-L-Z where P is
selected from an ethylene glycol group, a diethylene glycol group,
and a (poly)ethylene glycol group where the (poly)ethylene glycol
group is (CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6
inclusive; with the proviso that at least one of R.sup.1, R.sup.2,
R.sup.3, R.sup.4, R.sup.5, R.sup.6, R.sup.7, and R.sup.8 contains a
PEG group.
[0093] In one embodiment, the compound of general formula IV
wherein each of R3 and R4 is the same or different and is
independently hydrogen, an aliphatic group, or a heteroaliphatic
group, or R3 and R4 together form a cyclic structure where R3 and
R4 are directly joined or joined using a divalent structural
element selected from the group consisting of --(CH.sub.2).sub.q--
and CH.dbd.CH, where q is an integer from 1 to 2 inclusive, to
result in a 3-, 4-, or 5-membered ring.
[0094] One non-limiting example is a substituted polymethine form
of 550 Compound 1/2, shown below:
##STR00053##
[0095] One non-limiting example is a substituted polymethine form
of 550 Compound 2/2, shown below:
##STR00054##
[0096] One non-limiting example is a substituted polymethine form
of 550 Compound 3/2, shown below:
##STR00055##
[0097] One non-limiting example is a substituted polymethine form
of 550 Compound 4/2, shown below:
##STR00056##
[0098] One non-limiting example is a substituted polymethine form
of 550 Compound 5/2, shown below:
##STR00057##
[0099] One non-limiting example is a substituted polymethine form
of 550 Compound 6/2, shown below:
##STR00058##
[0100] One non-limiting example is a substituted polymethine form
of 550 having an ethylene glycol, diethylene glycol, or
(poly)ethylene glycol as described for general formula IV, such as
the compound shown below:
##STR00059##
[0101] In embodiments, an ethylene glycol group, diethylene glycol
group, and/or a (poly)ethylene glycol group, which will
collectively be referred to as a PEG group, unless specifically
defined, may be present at position(s) in addition to such groups
being present on the indole N atom(s).
[0102] One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00060##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00061##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00062##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00063##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00064##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00065##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00066##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R1 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00067##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00068##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00069##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00070##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00071##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00072##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00073##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00074##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R2 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00075##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00076##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are a diethylene glycol group terminating with
a methyl group, shown below:
##STR00077##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (3) group
terminating with a methyl group, shown below:
##STR00078##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, shown below:
##STR00079##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 4/4 according to general formula III
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are sulfo, shown
below:
##STR00080##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 4/4 according to general formula III
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are H, shown
below:
##STR00081##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (5) group
terminating with a methyl group, shown below:
##STR00082##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (6) group
terminating with a methyl group, shown below:
##STR00083##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R8 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00084##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R8 is sulfonamide --SO.sub.2NH--P--Z where Z is a methyl
group, shown below:
##STR00085##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R8 is carboxamide --CONH--P--Z where Z is a methyl group,
shown below:
##STR00086##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R7 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00087##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R7 is a sulfonamide group --SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00088##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/2 according to general formula II
where R7 is a carboxamide group --CONH--P--Z where Z is a methyl
group, shown below:
##STR00089##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R7 and R8 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00090##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R7 and R8 are a sulfonamide group --SO.sub.2NH--P--Z
where Z is a methyl group, shown below:
##STR00091##
One non-limiting example of an additionally PEG-substituted
compound is a 550 Compound 1/3 according to general formula II
where both R7 and R8 are a carboxamide group --CONH--P--Z where Z
is a methyl group, shown below:
##STR00092##
[0103] In one embodiment, the compound is 650 Compound 1/2
##STR00093##
[0104] 650 Compound 1/2
((2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulf-
onatoindolin-2-ylidene)penta-1,3-dienyl)-1-(2-methoxyethyl)-3-methyl-3-(3--
sulfonatopropyl)-3H-indolium-5-sulfonate tri sodium salt) contains
an ethylene glycol on the indole N of the left heterocycle, i.e., a
methylated ethylene glycol. The methyl group on the ethylene glycol
prevents the terminal --OH from oxidation. Oxidation is known to
occur, over time, on an unprotected PEG terminus (i.e., an
unprotected ethylene glycol group, diethylene glycol group, or
(poly)ethylene glycol group). Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups.
[0105] In embodiments, e.g., for functional assays, the inventive
compounds are activated. Activation of the compound adds a chemical
moiety such that the compound is in a form that can be conjugated
to a biological moiety. Examples of chemical moieties for
activation are described below with reference to activation of 650
Compound 1, but one skilled in the art appreciates that activation
is not limited to these examples. One non-limiting example of an
activated compound is the NHS-ester of 650 Compound 1/2, shown
below:
##STR00094##
In one embodiment, the compound is a NHS-ester of 650 Compound 1/2
where, according to general formula I, o is 1, shown below:
##STR00095##
[0106] In one embodiment, the compound is an NHS-ester of 650
Compound 1/2 where, according to general formula I, o is 5, shown
below:
##STR00096##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to formula III, where m=1 and p=1, is shown below:
##STR00097##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to general formula III, where m=1 and p=2, is shown
below:
##STR00098##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to general formula III, where m=1 and p=3, is shown
below:
##STR00099##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to general formula III, where m=1 and p=4, is shown
below:
##STR00100##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to general formula III, where m=1 and p=5, is shown
below:
##STR00101##
One non-limiting example of a NHS-ester of 650 Compound 1/3,
according to general formula III, where m=1 and p=6, is shown
below:
##STR00102##
One non-limiting example of a NHS-ester of 650 Compound 2/3,
according to general formula III, where m=2 and p=1, is shown
below:
##STR00103##
One non-limiting example of a NHS-ester of 650 Compound 2/3,
according to general formula III, where m=2 and p=2, is shown
below:
##STR00104##
One non-limiting example of a NHS-ester of 650 Compound 2/3,
according to general formula III, where m=2 and p=3, is shown
below:
##STR00105##
One non-limiting example of a NHS-ester of 650 Compound 3/3,
according to general formula III, where m=3 and p=1, is shown
below:
##STR00106##
One non-limiting example of a NHS-ester of 650 Compound 3/3,
according to general formula III, where m=3 and p=2, is shown
below:
##STR00107##
One non-limiting example of a NHS-ester of 650 Compound 3/3,
according to general formula III, where m=3 and p=3, is shown
below:
##STR00108##
One non-limiting example of a NHS-ester of 650 Compound 4/3,
according to general formula III, where m=4 and p=1, is shown
below:
##STR00109##
One non-limiting example of a NHS-ester of 650 Compound 5/3,
according to general formula III, where m=5 and p=1, is shown
below:
##STR00110##
One non-limiting example of a NHS-ester of 650 Compound 6/3,
according to general formula III, where m=6 and p=1, is shown
below:
##STR00111##
One non-limiting example of an activated 650 Compound 1/2 is the
tetrafluorophenyl (TFP)-ester of 650 Compound 1/2, shown below:
##STR00112##
One non-limiting example of an activated 650 Compound 1/2 is the
sulfotetrafluorophenyl (STP)-ester of 650 Compound 1/2, shown
below:
##STR00113##
One non-limiting example of an activated 650 Compound 1/2 is the
hydrazide of 650 Compound 1, shown below:
##STR00114##
One non-limiting example of an activated 650 Compound 1/2 is the
maleimide of 650 Compound 1, shown below:
##STR00115##
In one embodiment, the compound is 650 Compound 2/2
##STR00116##
[0107] 650 Compound 2/2
(2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulfo-
natoindolin-2-ylidene)penta-1,3-dienyl)-1-(2-(2-methoxyethoxy)ethyl)-3-met-
hyl-3-(3-sulfonatopropyl)-3H-indolium-5-sulfonate tri sodium salt.)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 650 Compound 2/2 is
activated as described above, one non-limiting example of which is
the NHS-ester form of 650 Compound 2/2, shown below.
##STR00117##
[0108] In one embodiment, the compound is 650 Compound 3/2
##STR00118##
[0109] 650 Compound 3/2
(2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulfo-
natoindolin-2-ylidene)penta-1,3-dienyl)-1-(2-(2-(2-methoxyethoxy)ethoxy)et-
hyl)-3-methyl-3-(3-sulfonatopropyl)-3H-indolium-5-sulfonate tri
sodium salt) contains a (poly)ethylene glycol on the indole N of
the left heterocycle. The methyl group on the ethylene glycol
prevents the terminal --OH from oxidation. Oxidation is known to
occur, over time, on an unprotected PEG terminus. Adding a methyl
ether provides this protection, and prevents reaction with
electrophilic reactive groups. For functional assays, 650 Compound
3/2 is activated as described above, one non-limiting example of
which is the NHS-ester form of 650 Compound 3/2, shown below.
##STR00119##
[0110] In one embodiment, the compound is 650 Compound 4/2
##STR00120##
[0111] 650 Compound 4/2
(2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulfo-
natoindolin-2-ylidene)penta-1,3-dienyl)-3-methyl-3-(3-sulfonatopropyl)-1-(-
2,5,8,11-tetraoxamidecan-13-yl)-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. The
methyl group on the ethylene glycol prevents the terminal --OH from
oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 650 Compound 4/2 is activated as
described above.
[0112] In one embodiment, the compound is 650 Compound 5/2
##STR00121##
[0113] 650 Compound 5/2
(2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulfo-
natoindolin-2-ylidene)penta-1,3-dienyl)-1-(2,5,8,11,14-pentaoxahexadecan-1-
6-yl)-3-methyl-3-(3-sulfonatopropyl)-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 650 Compound 5/2 is
activated as described above.
[0114] In one embodiment, the compound is 650 Compound 6/2
##STR00122##
[0115] 650 Compound 6/2
(2-((1E,3E,5E)-5-(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-5-sulfo-
natoindolin-2-ylidene)penta-1,3-dienyl)-3-methyl-1-(2,5,8,11,14,17-hexaoxa-
nonadecan-19-yl)-3-(3-sulfonatopropyl)-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 650 Compound 6/2 is
activated as described above.
[0116] In embodiments, the compound contains one or more
substitutions of the polymethine linker. In one embodiment, the
compound has general formula Va
##STR00123##
general formula Vb
##STR00124##
general formula Vc
##STR00125##
or general formula Vd
##STR00126##
where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6 is the same or
different and is independently selected from the group consisting
of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic
with terminal SO.sub.3, a PEG group P-L-Z where P is selected from
an ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group, where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s, where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from either H,
SO.sub.3, a PEG group P-L-Z where P is selected from an ethylene
glycol group, a diethylene glycol group, and a (poly)ethylene
glycol group where the (poly)ethylene glycol group is
(CH.sub.2CH.sub.2O).sub.s where s is an integer from 3-6 inclusive,
a sulfonamide group --SO.sub.2NH--P-L-Z, or a caboxamide group
--CONH--P-L-Z; where L is selected from the group consisting of a
divalent linear (--(CH.sub.2).sub.o--, o=0 to 15), crossed, or
cyclic alkane group that can be substituted by at least one atom
selected from the group consisting of oxygen, substituted nitrogen,
and/or sulfur; where Z is selected from the group consisting of H,
CH.sub.3, alkyl, a heteroalkyl group, NH.sub.2, --COO.sup.-,
--COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI,
--COO-Su (succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-.beta.-phosphoramidite, --CONR'-L-CHO,
--CONR'-L-maleimide, and --CONR'-L-NH--CO--CH.sub.2--I; R' and R''
is selected from the group consisting of H, aliphatic group, and
heteroaliphatic group, and the biomolecule is a protein, antibody,
nucleotide, oligonucleotide, biotin, or hapten; X is selected from
the group consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2,
--F, --Cl, --Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl),
--O-TFP (2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; p is an integer from 1 to 6 inclusive; each of R3 and R4
is the same or different and is independently hydrogen, an
aliphatic group, a heteroaliphatic group, or a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where s
is an integer from 3-6 inclusive; or R3 and R4 together form a
cyclic structure where R3 and R4 are joined using a divalent
structural element selected from the group consisting of
--(CH.sub.2).sub.q--, --(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of hydrogen, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, and a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where s
is an integer from 3-6 inclusive; with the proviso that at least
one of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6,
R.sup.7, and R.sup.8 contains a PEG group.
[0117] In one embodiment, the compound of general formula V wherein
each of R3 and R4 is the same or different and is independently
hydrogen, an aliphatic group, or a heteroaliphatic group, or R3 and
R4 together form a cyclic structure where R3 and R4 are directly
joined or joined using a divalent structural element selected from
the group consisting of --(CH.sub.2).sub.q-- and CH.dbd.CH, where q
is an integer from 1 to 2 inclusive, to result in a 3-, 4-, or
5-membered ring.
[0118] In one embodiment, an isolated enantiomeric mixture selected
from diastereomer Ia of general formula Va
##STR00127##
diastereomer Ib of general formula Va
##STR00128##
diastereomer Ic of general formula Vb
##STR00129##
or diastereomer of general formula Vb
##STR00130##
is provided, where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6
is the same or different and is independently selected from the
group consisting of an aliphatic, heteroaliphatic, sulfoalkyl
group, heteroaliphatic with terminal SO.sub.3, a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where s is
an integer from 3-6 inclusive, a sulfonamide group
-L-SO.sub.2NH--P-L-Z, and a caboxamide group -L-CONH--P-L-Z; each
of R.sup.7 and R.sup.8 is the same or different and is
independently selected from either H, SO.sub.3, a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s where s is
an integer from 3-6 inclusive, a sulfonamide group
--SO.sub.2NH--P-L-Z, or a caboxamide group --CONH--P-L-Z; where L
is selected from the group consisting of a divalent linear
(--(CH.sub.2).sub.o--, o=0 to 15), crossed, or cyclic alkane group
that can be substituted by at least one atom selected from the
group consisting of oxygen, substituted nitrogen, and/or sulfur;
where Z is selected from the group consisting of H, CH.sub.3,
alkyl, a heteroalkyl group, NH.sub.2, --COO.sup.-, --COOH, --COSH,
CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI, --COO-Su
(succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; o is an integer from 0 to 12 inclusive; each of R3 and
R4 is the same or different and is independently hydrogen, an
aliphatic group, a heteroaliphatic group, or a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where s
is an integer from 3-6 inclusive; or R3 and R4 together form a
cyclic structure where R3 and R4 are joined using a divalent
structural element selected from the group consisting of
--(CH.sub.2).sub.q--, --(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of hydrogen, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, and a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where s
is an integer from 3-6 inclusive; with the proviso that at least
one of R.sup.1, R.sup.2, R.sup.3, and R.sup.4 contains a PEG
group.
[0119] In one embodiment, the compound of general formula V wherein
each of R3 and R4 is the same or different and is independently
hydrogen, an aliphatic group, or a heteroaliphatic group, or R3 and
R4 together form a cyclic structure where R3 and R4 are directly
joined or joined using a divalent structural element selected from
the group consisting of --(CH.sub.2).sub.q-- and CH.dbd.CH, where q
is an integer from 1 to 2 inclusive, to result in a 3-, 4-, or
5-membered ring.
[0120] One non-limiting example is a substituted polymethine form
of 650 Compound 1/2, shown below:
##STR00131##
[0121] One non-limiting example is a substituted polymethine form
of 650 Compound 2/2, shown below:
##STR00132##
[0122] One non-limiting example is a substituted polymethine form
of 650 Compound 3/2, shown below:
##STR00133##
[0123] One non-limiting example is a substituted polymethine form
of 650 Compound 4/2, shown below:
##STR00134##
[0124] One non-limiting example is a substituted polymethine form
of 650 Compound 5/2, shown below:
##STR00135##
[0125] One non-limiting example is a substituted polymethine form
of 650 Compound 6/2, shown below:
##STR00136##
[0126] One non-limiting example is a substituted polymethine form
of 650 Compound 1/3 having an ethylene glycol, diethylene glycol,
or (poly)ethylene glycol as described for general formula V, such
as the compound shown below:
##STR00137##
[0127] One non-limiting example is a substituted polymethine form
of 650 Compound 1/2, shown below:
##STR00138##
[0128] One non-limiting example is a substituted polymethine form
of 650 Compound 2/2, shown below:
##STR00139##
[0129] One non-limiting example is a substituted polymethine form
of 650 Compound 3/2, shown below:
##STR00140##
[0130] One non-limiting example is a substituted polymethine form
of 650 Compound 4/2, shown below:
##STR00141##
[0131] One non-limiting example is a substituted polymethine form
of 650 Compound 5/2, shown below:
##STR00142##
[0132] One non-limiting example is a substituted polymethine form
of 650 Compound 6/2, shown below:
##STR00143##
[0133] One non-limiting example is a substituted polymethine form
of 650 Compound 1/3 having an ethylene glycol, diethylene glycol,
or (poly)ethylene glycol as described for general formula V, such
as the compound shown below:
##STR00144##
[0134] In embodiments, the degree of sulfonation is varied to,
e.g., vary the compound's degree of hydrophilicity or
hydrophobicity. One non-limiting example is a monosulfonate form of
650 Compound 1/2, shown below, but it is understood that the single
sulfo group can be at any of the described positions:
##STR00145##
[0135] One non-limiting example is a disulfonate form of 650
Compound 1/2, shown below, but it is understood that each of the
two sulfo groups can be at any of the described positions:
##STR00146##
[0136] One non-limiting example is a trisulfonate form of 650
Compound 1/2, shown below, but it is understood that each of the
three sulfo groups can be at any of the described positions:
##STR00147##
[0137] One non-limiting example is a tetrasulfonate form of 650
Compound 1/2, shown below, but it is understood that each of the
four sulfo groups can be at any of the described positions:
##STR00148##
[0138] In various embodiments, an ethylene glycol group, diethylene
glycol group, and/or a (poly)ethylene glycol group, which will
collectively be referred to as a PEG group, unless specifically
defined, may be present at position(s) in addition to such groups
being present on the N atom(s) of the indole structure.
[0139] One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00149##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00150##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00151##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00152##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00153##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00154##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00155##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R1 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00156##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00157##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00158##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00159##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00160##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00161##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00162##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00163##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R2 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00164##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00165##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a diethylene glycol group terminating with
a methyl group, shown below:
##STR00166##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (3) group
terminating with a methyl group, shown below:
##STR00167##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, shown below:
##STR00168##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 4/4 according to general formula III
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are sulfo, shown
below:
##STR00169##
[0140] One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 4/4 according to general formula III
(V19-03005) where both R1 and R2 are a (poly)ethylene glycol (4)
group terminating with a methyl group, and R7 and R8 are sulfo,
shown below:
##STR00170##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 4/4 according to general formula III
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are H, shown
below:
##STR00171##
[0141] One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 4/4 according to general formula III
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are H, shown
below:
##STR00172##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (5) group
terminating with a methyl group, shown below:
##STR00173##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (6) group
terminating with a methyl group, shown below:
##STR00174##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a sulfonamide group -L-SO.sub.2NH--P--Z
where Z is a methyl group, shown below:
##STR00175##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R1 and R2 are a carboxamide -L-CONH--P--Z where Z is a
methyl group, shown below:
##STR00176##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R8 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00177##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R8 is sulfonamide --SO.sub.2NH--P--Z where Z is a methyl
group, shown below:
##STR00178##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R8 is carboxamide --CONH--P--Z where Z is a methyl group,
shown below:
##STR00179##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R7 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00180##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R7 is a sulfonamide group --SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00181##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/2 according to general formula II
where R7 is a carboxamide group --CONH--P--Z where Z is a methyl
group, shown below:
##STR00182##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R7 and R8 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00183##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R7 and R8 are a sulfonamide group --SO.sub.2NH--P--Z
where Z is a methyl group, shown below:
##STR00184##
One non-limiting example of an additionally PEG-substituted
compound is a 650 Compound 1/3 according to general formula II
where both R7 and R8 are a carboxamide group --CONH--P--Z where Z
is a methyl group, shown below:
##STR00185##
[0142] In one embodiment, the compound is 755 Compound 1/2
##STR00186##
[0143] 755 Compound 1/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-2-((1E,3E,5E,7E)-7-(1-(2-methoxye-
thyl)-3-methyl-5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)hepta-1,-
3,5-trienyl)-3-methyl-3H-indolium-5-sulfonate tri sodium salt)
contains an ethylene glycol on the indole N of the left
heterocycle, i.e., a methylated ethylene glycol. The methyl group
on the ethylene glycol prevents the terminal --OH from oxidation.
Oxidation is known to occur, over time, on an unprotected PEG
terminus (i.e., an unprotected terminus of an ethylene glycol
group, diethylene glycol group, or (poly)ethylene glycol group).
Adding a methyl ether provides this protection, and prevents
reaction with electrophilic reactive groups.
[0144] In embodiments, e.g., for functional assays, the inventive
compounds are activated. Activation of the compound adds a chemical
moiety such that the compound is in a form that can be conjugated
to a biological moiety. Examples of chemical moieties for
activation are described below with reference to activation of 755
Compound 1/2, but one skilled in the art appreciates that
activation is not limited to these examples. One non-limiting
example of an activated compound is the NHS-ester of 755 Compound
1/2, shown below:
##STR00187##
[0145] In one embodiment, the compound is an NHS-ester of 755
Compound 1/2 where, according to general formula I, o is 1, shown
below:
##STR00188##
[0146] In one embodiment, the compound is an NHS-ester of 755
Compound 1/2 where, according to general formula I, o is 5, shown
below:
##STR00189##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=1, is shown
below:
##STR00190##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=2, is shown
below:
##STR00191##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=3, is shown
below:
##STR00192##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=4, is shown
below:
##STR00193##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=5, is shown
below:
##STR00194##
One non-limiting example of a NHS-ester of 755 Compound 1/3,
according to general formula III, where m=1 and p=6, is shown
below:
##STR00195##
One non-limiting example of a NHS-ester of 755 Compound 2/3,
according to general formula III, where m=2 and p=1, is shown
below:
##STR00196##
One non-limiting example of a NHS-ester of 755 Compound 2/3,
according to general formula III, where m=2 and p=2, is shown
below:
##STR00197##
One non-limiting example of a NHS-ester of 755 Compound 2/3,
according to general formula III, where m=2 and p=3, is shown
below:
##STR00198##
One non-limiting example of a NHS-ester of 755 Compound 3/3,
according to general formula III, where m=3 and p=1, is shown
below:
##STR00199##
One non-limiting example of a NHS-ester of 755 Compound 3/3,
according to general formula III, where m=3 and p=2, is shown
below:
##STR00200##
One non-limiting example of a NHS-ester of 755 Compound 3/3,
according to general formula III, where m=3 and p=3, is shown
below:
##STR00201##
One non-limiting example of a NHS-ester of 755 Compound 4/3,
according to general formula III, where m=4 and p=1, is shown
below:
##STR00202##
One non-limiting example of a NHS-ester of 755 Compound 5/3,
according to general formula III, where m=5 and p=1, is shown
below:
##STR00203##
One non-limiting example of a NHS-ester of 755 Compound 6/3,
according to general formula III, where m=6 and p=1, is shown
below:
##STR00204##
One non-limiting example of an activated 755 Compound 1/2 is a
tetrafluorophenyl (TFP)-ester form of 755 Compound 1/2, shown
below:
##STR00205##
One non-limiting example of an activated 755 Compound 1/2 is a
sulfotetrafluorophenyl (STP)-ester form of 755 Compound 1/2, shown
below:
##STR00206##
One non-limiting example of an activated 755 Compound 1/2 is a
hydrazide form of 755 Compound 1/2, shown below:
##STR00207##
One non-limiting example of an activated 755 Compound 1/2 is a
maleimide form of 755 Compound 1/2, shown below:
##STR00208##
[0147] In one embodiment, the compound is 755 Compound 2/2
##STR00209##
[0148] 755 Compound 2/2
(1-(5-carboxypentyl)-2-((1E,3E,5E,7E)-7-(1-(2-(2-methoxyethoxy)ethyl)-3-m-
ethyl-5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)hepta-1,3,5-trien-
yl)-3-(2-methoxyethyl)-3-methyl-3H-indolium-5-sulfonate) contains a
(poly)ethylene glycol on the indole N of the left heterocycle. The
methyl group on the ethylene glycol prevents the terminal --OH from
oxidation. Oxidation is known to occur, over time, on an
unprotected PEG terminus. Adding a methyl ether provides this
protection, and prevents reaction with electrophilic reactive
groups. For functional assays, 755 Compound 2/2 is activated as
described above, one non-limiting example of which is the NHS-ester
form of 755 Compound 2/2, shown below.
##STR00210##
[0149] In one embodiment, the compound is 755 Compound 3/2
##STR00211##
[0150] 755 Compound 3/2
(1-(5-carboxypentyl)-2-((1E,3E,5E,7E)-7-(1-(2-(2-(2-methoxyethoxy)ethoxy)-
ethyl)-3-methyl-5-sulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)hepta-1-
,3,5-trienyl)-3-(2-methoxyethyl)-3-methyl-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 755 Compound 3/2 is
activated as described above, one non-limiting example of which is
the NHS-ester form of 755 Compound 3/2, shown below.
##STR00212##
[0151] In one embodiment, the compound is 755 Compound 4/2
##STR00213##
[0152] 755 Compound 4/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-2-((1E,3E,5E,7E)-7-(3-me-
thyl-5-sulfonato-3-(3-sulfonatopropyl)-1-(2,5,8,11-tetraoxamidecan-13-yl)i-
ndolin-2-ylidene)hepta-1,3,5-trienyl)-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 755 Compound 4/2 is
activated as described above.
[0153] In one embodiment, the compound is 755 Compound 5/2
##STR00214##
[0154] 755 Compound 5/2
(2-((1E,3E,5E,7E)-7-(1-(2,5,8,11,14-pentaoxahexadecan-16-yl)-3-methyl-5-s-
ulfonato-3-(3-sulfonatopropyl)indolin-2-ylidene)hepta-1,3,5-trienyl)-1-(5--
carboxypentyl)-3-(2-methoxyethyl)-3-methyl-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 755 Compound 5/2 is
activated as described above.
[0155] In one embodiment, the compound is 755 Compound 6/2
##STR00215##
[0156] 755 Compound 6/2
(1-(5-carboxypentyl)-3-(2-methoxyethyl)-3-methyl-2-((1E,3E,5E,7E)-7-(3-me-
thyl-1-(2,5,8,11,14,17-hexaoxanonadecan-19-yl)-5-sulfonato-3-(3-sulfonatop-
ropyl)indolin-2-ylidene)hepta-1,3,5-trienyl)-3H-indolium-5-sulfonate)
contains a (poly)ethylene glycol on the indole N of the left
heterocycle. The methyl group on the ethylene glycol prevents the
terminal --OH from oxidation. Oxidation is known to occur, over
time, on an unprotected PEG terminus. Adding a methyl ether
provides this protection, and prevents reaction with electrophilic
reactive groups. For functional assays, 755 Compound 6/2 is
activated as described above.
[0157] In embodiments, the compound contains one or more
substitutions of the polymethine linker. In one embodiment, the
compound has general formula VIa with "a" indicating an ethylene
glycol, diethylene glycol, or (poly)ethylene glycol group on the
left indole N, and the chain on the right indole N terminating in
COX:
##STR00216##
general formula VIb with "b" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left
indole N, and the chain on the right indole N terminating in
COH:
##STR00217##
general formula VIc with "c" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left and
right indole N, and the chain on the right indole N terminating in
COX:
##STR00218##
or general formula VId with "d" indicating an ethylene glycol,
diethylene glycol, or (poly)ethylene glycol group on the left and
right indole N, and the chain on the right indole N terminating in
COH:
##STR00219##
where each of R.sup.1, R.sup.2, R.sup.5, and R.sup.6 is the same or
different and is independently selected from the group consisting
of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic
with terminal SO.sub.3, a PEG group P-L-Z where P is selected from
an ethylene glycol group, a diethylene glycol group, and a
(poly)ethylene glycol group, where the (poly)ethylene glycol group
is (CH.sub.2CH.sub.2O).sub.s, where s is an integer from 3-6
inclusive, a sulfonamide group -L-SO.sub.2NH--P-L-Z, and a
caboxamide group -L-CONH--P-L-Z; each of R.sup.7 and R.sup.8 is the
same or different and is independently selected from either H,
SO.sub.3, a PEG group P-L-Z where P is selected from an ethylene
glycol group, a diethylene glycol group, and a (poly)ethylene
glycol group, where the (poly)ethylene glycol group is
(CH.sub.2CH.sub.2O).sub.s, where s is an integer from 3-6
inclusive, a sulfonamide group --SO.sub.2NH--P-L-Z, or a caboxamide
group --CONH--P-L-Z; where L is selected from the group consisting
of a divalent linear (--(CH.sub.2).sub.o--, o=0 to 15), crossed, or
cyclic alkane group that can be substituted by at least one atom
selected from the group consisting of oxygen, substituted nitrogen,
and/or sulfur; where Z is selected from the group consisting of H,
CH.sub.3, alkyl, a heteroalkyl group, NH.sub.2, --COO.sup.-,
--COOH, --COSH, CO--NH--NH.sub.2, --COF, --COCl, --COBr, --COI,
--COO-Su (succinimidyl/sulfo-succinimidyl), --COO--STP
(4-sulfo-2,3,5,6-tetrafluorophenyl), --COO-TFP
(2,3,5,6-tetrafluorophenyl), --COO-benzotriazole,
--CO-benzotriazole, --CONR'--CO--CH.sub.2--I, --CONR'R'',
--CONR'-biomolecule, --CONR'-L-COO.sup.-, --CONR'-L-COOH,
--CONR'-L-COO-Su, --CONR'-L-COO--STP, --CONR'-L-COO-TFP,
--CONR'-L-CONR''.sub.2, --CONR'-L-CO-biomolecule,
--CONR'-L-CO--NH--NH.sub.2, --CONR'-L-OH,
--CONR'-L-O-phosphoramidite, --CONR'-L-CHO, --CONR'-L-maleimide,
and --CONR'-L-NH--CO--CH.sub.2--I; R' and R'' is selected from the
group consisting of H, aliphatic group, and heteroaliphatic group,
and the biomolecule is a protein, antibody, nucleotide,
oligonucleotide, biotin, or hapten; X is selected from the group
consisting of --OH, --SH, --NH.sub.2, --NH--NH.sub.2, --F, --Cl,
--Br, I, --NHS (hydroxysuccinimidyl/sulfosuccinimidyl), --O-TFP
(2,3,5,6-tetrafluorophenoxy), --O-STP
(4-sulfo-2,3,5,6-tetrafluorophenoxy), --O-benzotriazole,
-benzotriazole, --NR-L-OH, --NR-L-O-phosphoramidite, --NR-L-SH,
--NR-L-NH.sub.2, --NR-L-NH--NH.sub.2, --NR-L-CO.sub.2H,
--NR-L-CO--NHS, --NR-L-CO-STP, --NR-L-CO-TFP,
--NR-L-CO-benzotriazole, --NR-L-CHO, --NR-L-maleimide, and
--NR-L-NH--CO--CH2-I, where R is --H or an aliphatic or
heteroaliphatic group; Kat is a number of Na.sup.+, K.sup.+,
Ca.sup.2+, ammonia, or other cation(s) needed to compensate the
negative charge brought by the cyanine; m is an integer from 0 to 5
inclusive; p is an integer from 1 to 6 inclusive; each of R3 and R4
is the same or different and is independently hydrogen, an
aliphatic group, a heteroaliphatic group, or a PEG group P-L-Z
where P is selected from an ethylene glycol group, a diethylene
glycol group, and a (poly)ethylene glycol group, where the
(poly)ethylene glycol group is (CH.sub.2CH.sub.2O).sub.s, where s
is an integer from 3-6 inclusive; or R3 and R4 together form a
cyclic structure where R3 and R4 are joined using a divalent
structural element selected from the group consisting of
--(CH.sub.2).sub.q--, --(CH.sub.2).sub.qO(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qS(CH.sub.2).sub.q'--,
--(CH.sub.2).sub.qCH.dbd.CH--, --OCH.dbd.CH-- where each of q and
q' is the same or different and is a integer from 2 to 6 inclusive;
and Y is selected from the group consisting of hydrogen, alkyl,
sulfoalkyl, fluorine, chlorine, bromine, a PEG group P-L-Z where P
is selected from an ethylene glycol group, a diethylene glycol
group, and a (poly)ethylene glycol group, where the (poly)ethylene
glycol group is (CH.sub.2CH.sub.2O).sub.s, where s is an integer
from 3-6 inclusive, and an oxygen-containing group OR.sup.PM where
R.sup.PM is selected from the group consisting of hydrogen,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cyclic alkyl, substituted
or unsubstituted heterocyclic alkyl, substituted or unsubstituted
aryl, and substituted or unsubstituted heteroaryl, where the group
can be substituted with at least one of hydroxyl, sulfo, carboxy,
and/or amino; with the proviso that at least one of R.sup.1,
R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, R.sup.7, and R.sup.8
contains a PEG group.
[0158] In one embodiment, the compound of general formula VI where
each of R3 and R4 is the same or different and is independently
hydrogen, an aliphatic group, or a heteroaliphatic group, or R3 and
R4 together form a cyclic structure where R3 and R4 are directly
joined or joined using a divalent structural element selected from
the group consisting of --(CH.sub.2).sub.q-- and CH.dbd.CH, where q
is an integer from 1 to 2 inclusive, to result in a 3-, 4-, or
5-membered ring.
[0159] In one embodiment, the compound of general formula VI
wherein R3 and R4 together form a cyclic structure where R3 and R4
are joined using a divalent structural element of
--(CH.sub.2).sub.q--, where q is 3, to result in a 6-membered ring,
and Y is OR.sup.PM where R.sup.PM is a substituted 6-membered aryl
group, where the substituted group is sulfo.
[0160] One non-limiting example is a substituted polymethine form
of 755 Compound 1/2, shown below:
##STR00220##
[0161] One non-limiting example is a substituted polymethine form
of 755 Compound 2/2, shown below:
##STR00221##
[0162] One non-limiting example is a substituted polymethine form
of 755 Compound 3/2, shown below:
##STR00222##
[0163] One non-limiting example is a substituted polymethine form
of 755 Compound 4/2, shown below:
##STR00223##
[0164] One non-limiting example is a substituted polymethine form
of 755 Compound 5/2, shown below:
##STR00224##
[0165] One non-limiting example is a substituted polymethine form
of 755 Compound 6/2, shown below:
##STR00225##
[0166] One non-limiting example is a substituted polymethine form
of 755 Compound 1/3 having an ethylene glycol, diethylene glycol,
or (poly)ethylene glycol as described for general formula VI, such
as the compound shown below:
##STR00226##
[0167] One non-limiting example is a substituted polymethine form
of 755 Compound 4/4 having an ethylene glycol, diethylene glycol,
or (poly)ethylene glycol as described for general formula VI, such
as the compound shown below:
##STR00227##
[0168] In embodiments, the degree of sulfonation is varied to,
e.g., vary the compound's degree of hydrophilicity or
hydrophobicity. One non-limiting example is a monosulfonate form of
755 Compound 1/2, shown below, but it is understood that the single
sulfo group can be at any of the described positions:
##STR00228##
[0169] One non-limiting example is a disulfonate form of 755
Compound 1/2, shown below, but it is understood that the each of
the two sulfo groups can be at any of the described positions:
##STR00229##
[0170] One non-limiting example is a trisulfonate form of 755
Compound 1/2, shown below, but it is understood that the each of
the three sulfo groups can be at any of the described
positions:
##STR00230##
[0171] One non-limiting example is a tetrasulfonate form of 755
Compound 1, shown below, but it is understood that the each of the
four sulfo groups can be at any of the described positions:
##STR00231##
[0172] In embodiments, an ethylene glycol group, diethylene glycol
group, and/or a (poly)ethylene glycol group, which will
collectively be referred to as a PEG group unless specifically
defined, may be present at position(s) in addition to such groups
being present on the N atom(s) of the indole structure. One
non-limiting example of an additionally PEG-substituted compound is
a 755 Compound 1/2 according to general formula II where R1 is an
ethylene glycol group terminating with a methyl group, shown
below:
##STR00232##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00233##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00234##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00235##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00236##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00237##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00238##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R1 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00239##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00240##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a diethylene glycol group terminating with a methyl
group, shown below:
##STR00241##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (3) group terminating with a
methyl group, shown below:
##STR00242##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (4) group terminating with a
methyl group, shown below:
##STR00243##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (5) group terminating with a
methyl group, shown below:
##STR00244##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a (poly)ethylene glycol (6) group terminating with a
methyl group, shown below:
##STR00245##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a sulfonamide group -L-SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00246##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R2 is a carboxamide -L-CONH--P--Z where Z is a methyl group,
shown below:
##STR00247##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00248##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a diethylene glycol group terminating with
a methyl group, shown below:
##STR00249##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (3) group
terminating with a methyl group, shown below:
##STR00250##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, shown below:
##STR00251##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 4/4 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are sulfo, shown
below:
##STR00252##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 4/4 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (4) group
terminating with a methyl group, and R7 and R8 are H, shown
below:
##STR00253##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (5) group
terminating with a methyl group, shown below:
##STR00254##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a (poly)ethylene glycol (6) group
terminating with a methyl group, shown below:
##STR00255##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a sulfonamide group -L-SO.sub.2NH--P--Z
where Z is a methyl group, shown below:
##STR00256##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R1 and R2 are a carboxamide -L-CONH--P--Z where Z is a
methyl group, shown below:
##STR00257##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R8 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00258##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R8 is sulfonamide --SO.sub.2NH--P--Z where Z is a methyl
group, shown below:
##STR00259##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R8 is carboxamide --CONH--P--Z where Z is a methyl group,
shown below:
##STR00260##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R7 is an ethylene glycol group terminating with a methyl
group, shown below:
##STR00261##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R7 is a sulfonamide group --SO.sub.2NH--P--Z where Z is a
methyl group, shown below:
##STR00262##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/2 according to general formula II
where R7 is a carboxamide group --CONH--P--Z where Z is a methyl
group, shown below:
##STR00263##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R7 and R8 are an ethylene glycol group terminating with
a methyl group, shown below:
##STR00264##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R7 and R8 are a sulfonamide group --SO.sub.2NH--P--Z
where Z is a methyl group, shown below:
##STR00265##
One non-limiting example of an additionally PEG-substituted
compound is a 755 Compound 1/3 according to general formula II
where both R7 and R8 are a carboxamide group --CONH--P--Z where Z
is a methyl group, shown below:
##STR00266##
[0173] The disclosed compounds are used and are useful as
chromophores and/or fluorophores. For example, they can be used for
optical labelling and, therefore, for the qualitative and/or
quantitative detection of proteins, nucleic acids, oligomers, DNA,
RNA, biological cells, lipids, mono-, oligo- and polysaccharides,
ligands, receptors, polymers, drugs, polymeric beads, etc.
[0174] The inventive compounds, containing the disclosed
functionality or functionalities, may be synthesized using methods
known in the art, e.g., as described as follows with all references
expressly incorporated by reference herein in their entirety. The
hydrophilicity or hydrophobicity of the inventive compounds is
modified by the number and location of hydrophilic groups, such as
sulfo, carboxy, hydroxy, etc., groups. In embodiments, the number
and location of hydrophilic groups is symmetrical, such that the
number and location of hydrophilic group(s) on one of the indoles
of the inventive cyanine compound is also found on the other
indole. In various embodiments, at least one hydrophilic group is
found on each of the indoles of the inventive cyanine compound.
Similarly, solubility, lack of aggregation, reactivity, lack of
cross-reactivity, etc., are effected by the number and location of
the disclosed functionality or functionalities on the compound.
[0175] In one embodiment, short PEG groups are added on opposite
sides and opposite ends of indole cyanine compounds to effectively
surround the hydrophobic core structure of the molecule. In another
embodiment, sulfonate groups are added to the outer phenyl rings of
indole cyanine dyes along with the symmetrical placement of short
PEG chains on opposite sides and opposite ends.
[0176] Adding PEG 1-6, if at the appropriate positions to
strategically surround the core dye structure, have significant
beneficial effects on the hydrophilicity and performance of these
dyes in biological applications. Previous attempts to make dyes
more hydrophilic and less "sticky" toward biomolecules included the
addition of multiple sulfonates or much longer PEG chains to some
locations on dye molecules. However, the addition of too many
sulfonates, while having the effect of increasing the relative
water solubility of dyes, can create undesirable nonspecific
binding character due to negative charge interactions with
positively charged biomolecules, particularly proteins. In
addition, previous attempts to make dyes more water soluble by
adding longer PEG chains to one or two sites on a dye has the
detrimental effect of dramatically increasing the molecular weight
of the dye, possibly preventing efficient access of dye-labeled
antibodies and other dye-labeled targeting molecules to bind with
inner cellular targets, while also not fully surrounding and
masking the hydrophobic dye core structure. The inventors have
discovered that by using short PEG chain modifications at critical
sites on a dye structure that the total molecular size of labeled
molecules can be limited, while nonspecificity is dramatically
reduced by masking the hydrophobic dye core.
[0177] In one embodiment, PEG 1-6 group(s) are added on opposite
sides and opposite ends of indole cyanine compounds to effectively
surround the hydrophobic core structure of the molecule. In another
embodiment, sulfonate groups are added to the outer phenyl rings of
indole cyanine dyes along with the symmetrical placement of short
PEG chains on opposite sides and opposite ends.
[0178] The core indocyanine structure without additional
functionalities, along with its synthesis, was described by Konig
in U.S. Pat. No. 1,524,791 and BP 434875, and included 3-, 5-, and
7-membered polymethine chains.
##STR00267##
Synthesis of numerous modifications of the core indocyanine
structure have been described. Such modifications provided various
functionalities, e.g., synthesis of N-isothiocyanato-alkyl- and
aromatic-carboxyalkyl-functionalized indocyanines were described in
U.S. Pat. Nos. 5,627,027; 6,048,982; 4,981,977; U.S. Publication
No. 2006/0199949; Southwick, Anal. Chem. 67 (1995) 1742-48).
##STR00268##
Synthesis of indocyanines with one or two N-carboxyalkyl
functionalities were described in U.S. Pat. Nos. 5,268,486;
5,486,616; 5,569,587; 5,569,766; JP 03217837.
##STR00269##
Synthesis of indocyanines containing C-carboxyalkyl groups were
described in JP 05-313304; U.S. Publication Nos. 2006/0099638,
2006/0004188; 2002/0077487; 2002/0064794; U.S. Pat. Nos. 6,977,305
and 6,974,873.
##STR00270##
Synthesis of indocyanines with N- and C-sulfoalkyl groups were
described in JP 05-313304; WO 2005/044923; U.S. Publication No.
2007/0203343.
##STR00271## ##STR00272##
Synthesis of indocyanines with mixed C-carboxyalkyl and
C-sulfoalkyl were described in EP 1792949 and U.S. Pat. No.
7,745,640.
##STR00273##
Synthesis of indocyanaines having a PEG-containing, N-carboxyalkyl
spacer were described in U.S. Pat. No. 6,939,532.
##STR00274##
Functionalization of the N-carboxyalkyl with an
amino-functionalized PEG-alkyl chain, and N- and C-substituted
PEG-alkyl chains, were described in U.S. Publication No.
2009/0305410.
##STR00275## ##STR00276##
Synthesis of various polymethine bridge substitutions, and other
functionalizations of indocyanines, were described in Strekowski,
Heterocyclic Polymethine Dyes: Synthesis, Properties and
Applications, (2008) Springer-Verlag, Berlin Heidelberg; Gragg,
"Synthesis of Near-Infrared Heptamethine Cyanine Dyes" (2010).
Chemistry Theses. Paper 28.
http://digitalarchive.gsu.edu/chemistry_theses/28; Patonay et al.
(2004) Noncovalent Labeling of Biomolecules with Red and
Near-Infrared Dyes, Molecules 9 (2004) 40-49; and U.S. Pat. No.
7,172,907.
[0179] In one embodiment, the compound is synthesized by a
condensation reaction, known to one skilled in the art of the two
differently substituted indole heterocycles separated by a
(poly)methine linker or bridge, e.g., C1, C3, or C5. Other
synthesis methods are possible. As only one example, one of the
indole heterocycles is first reacted with the C1, C3, or C5 linker.
The 1:1 condensation product is isolated, and then condensed with
the second indole heterocycle to result in the cyanine compound.
The sequence of reacting the indole heterocycles is irrelevant.
Thus, a plurality of differently functionalized, strongly
hydrophilic, diastereomeric compounds that differ in total charge
and specificity/reactivity of the active groups used for their
immobilization, were prepared.
[0180] Conjugates of the compounds were prepared by covalently
coupling the compounds to a biomolecule using the functional
substituent on the N-position of the indole ring. This functional
substituent was activated by routine protein chemistry reaction
methods known to one skilled in the art. The activated compound may
be converted to, e.g, and without limitation, a
N-hydroxysuccinimide (NHS)-ester, an acid fluoride, a
tetrafluorophenyl (TFP)- or sulfotetrafluorophenyl (STP)-ester, an
iodoacetyl group, a maleimide, a hydrazide, a sulfonyl chloride, or
a phenylazide. Methods for preparing such compounds are known to
one skilled in the art. In one embodiment, the activated
substituent was then reacted with an amino group on the biomolecule
under conditions to conjugate the desired biomolecule.
[0181] In one embodiment, a non-activated carboxyl group on the
N-position of the indole in the compound was coupled to an amine
using a carbodimide.
[0182] In one embodiment, a N-hydroxysuccinimidyl ester
(X.dbd.--NHS) of a compound was formed as follows: 20 .mu.mol dye
with X.dbd.OH (carboxyalkyl group), 8 mg (40 .mu.mol)
dicyclohexylcarbodiimide, and 5 mg (40 .mu.mol)
N-hydroxysuccinimide were dissolved in 2 ml DMF and 100 .mu.l
water. Six .mu.l (40 .mu.mol) triethylamine was added. The reaction
mixture was stirred at room temperature (about 20.degree. C. to
about 22.degree. C.) for 24 hours and then filtered. The solvent
was removed and the residue was washed with diethylether. The
reaction proceeded quantitatively.
[0183] In one embodiment, a male imide
(X.dbd.--NH--CH.sub.2CH.sub.2-maleimide) of a compound is formed as
follows: 20 .mu.mol dye with X.dbd.--NHS
(N-hydroxysuccinimid-ester) was dissolved in 2 ml DMF and 100 .mu.l
water and mixed with 7.6 mg (30 .mu.mol)
2-maleimidoethylamine-trifluoracetate and 5 .mu.l (30 .mu.mol)
N-ethyldiisopropyl-amine. The reaction mixture is stirred for 3 h
at room temperature (about 20.degree. C. to about 22.degree. C.).
The solvent was evaporated under reduced pressure. The residue is
washed with diethylether and acetone and dried in vacuum. The
reaction proceeds quantitatively.
[0184] In one embodiment, a iodoacetamide
(X.dbd.--NH--CH.sub.2CH.sub.2--NH--CO--CH.sub.2--I) of a compound
is formed as follows: 20 .mu.mol dye with X.dbd.--NHS
(N-hydroxysuccinimid-ester) was dissolved in 2 ml DMF and 100 .mu.l
water, followed by addition of 40 mg (300 .mu.mol)
ethylendiamindihydrochloride and 26 .mu.l (150 .mu.mol)
N-ethyldiisopropyl-amine. The reaction mixture is stirred for 3 h
at room temperature (about 20.degree. C. to about 22.degree. C.).
The solvent is then evaporated under reduced pressure, the residue
was dissolved in methanol, and the ethylendiamindihydrochlorid was
removed by filtration. The methanol is evaporated under reduced
pressure. The residue is dissolved in 2 ml dry DMF, followed by
addition of 7 mg (25 .mu.mol) N-succinimidyl iodoacetate and 4
.mu.l (25 .mu.mol) N-ethyldiisopropylamine. The reaction mixture is
stirred for 3 h at room temperature. The solvent was evaporated
under reduced pressure and the residue was purified by reverse
phase HPLC.
[0185] In one embodiment, a hydroxyl group, such as a terminal
hydroxyl group, can be subsequently activated to a reactive
derivative able to link with, for example, proteins and other
molecules. Examples of activating groups include tosyl chloride
(TsCl), tresyl chloride (TrCl), disuccinimidyl carbonate (DSC),
divinyl sulfone, bis-epoxy compounds, carbonyl diimidazole (CDI),
2-fluoro-1-methylpyridinium (FMP), and trichloro-s-triazine (TsT).
In one embodiment, the hydroxyl group is activated to a
succinimidyl carbonate, which is reactive with amines.
[0186] Coupling between the compound and the biomolecule may be
performed as follows. The compound was reacted with the biomolecule
in an organic or aqueous solution at pH between pH 5-pH 12
inclusive. The compound need not be dissolved in an organic
solvent, such as dimethyl formamide (DMF) or dimethyl sulfoxide
(DMSO) prior to adding the biomolecule. In one embodiment, coupling
reaction may be performed in a 100% aqueous solution. In one
embodiment, the coupling reaction occurs at room temperature (about
20.degree. C. to about 22.degree. C.).
[0187] To form a composition (dye), at least one biocompatible
excipient was added to the compound(s), as known to one of ordinary
skill in the art. Excipients include, but are not limited to,
buffers, solubility enhancing agents, stabilizing agents, etc.
[0188] In one embodiment, a kit for performing an assay method
comprises a disclosed compound, and instructions for performing the
method using the compound.
[0189] The disclosed activated compounds (i.e., the compound
modified with a reactive group) are useful to label macromolecules
(e.g., antibodies, streptavidin, etc) using methods known to one
skilled in the art, e.g., Hermanson, Bioconjugate Techniques, 2nd
Ed., London, Elsevier Inc. 2008. The reaction was carried out for
1-2 h at room temperature (about 20.degree. C. to about 22.degree.
C.), and then desalted by dialyzing against several changes of
phosphate buffered saline (pH 7.2) or purified by gel filtration to
remove the unreacted fluorescent dye. The resulting
compound-biomolecule conjugate was used to detect, e.g., specific
proteins in immunoassays, sugars in glycoproteins with lectins,
protein-protein interactions, oligonucleotides in nucleic acid,
hybridization, and in electrophoretic mobility shift assays
(EMSA).
[0190] The resulting compound-biomolecule conjugates exhibited
fluorescent properties. In this embodiment, they were used in
optical methods including fluorescence optical qualitative and
quantitative determination methods. Examples of such methods
include, but are not limited to, microscopy, immunoassays,
hybridization methods, chromatographic and electrophoretic methods,
fluorescence resonance energy transfer (FRET) systems,
bioluminescence resonance energy transfer (BRET), high throughput
screenings, analysis of receptor-ligand interactions on a
microarray, etc.
[0191] Compounds in any embodiment were used as dyes for optical
labelling of organic or inorganic biomolecules, referred to as
recognition units. Recognition units are molecules having
specificity and/or affinity for a specific group of molecules.
Examples include, but are not limited to, antibodies that have
affinity for antigens, enzymes that bind and/or react with a
specific bond or bonds within a sequence of amino acids in a
peptide or react with a substrate, cofactors such as metals that
enhance or inhibit specific interactions, lectins that bind
specific sugars or sugar sequences (e.g., oligosaccharides,
polysaccharides, dextrans, etc.), biotin binding proteins such as
avidin and streptavidin that bind biotin and biotinylated
molecules, antibody binding proteins such as Protein A, Protein G,
Protein A/G and Protein L, sequences of amino acids or metals that
have affinity for each other (e.g., histidine sequences that bind
nickel or copper, phosphate containing proteins that bind gallium,
aluminium, etc.), specific sequences of nucleic acids such as DNA
and/or RNA oligonucleotides that have affinity for proteins,
specific sequences of amino acids that have affinity for DNA and/or
RNA, haptens, carotenoids, hormones (e.g., neurohormones),
neurotransmitters, growth factors, toxins, biological cells,
lipids, receptor binding drugs or organic or inorganic polymeric
carrier materials, fluorescent proteins such as phycobilliproteins
(e.g., phycoethrin, allophycocyanin), etc. Ionic interactions
between recognition units and the disclosed compounds results in
labeling of the recognition units. The recognition unit and
compound can be covalently bound. The result is a conjugate for
qualitative or quantitative determination of various biomaterials
or other organic or inorganic materials using optical methods.
[0192] The inventive compounds and/or conjugates are used in
optical, including fluorescence optical, qualitative and/or
quantitative determination methods to diagnose properties of cells
(molecular imaging), in biosensors (point of care measurements),
for investigation of the genome, and in miniaturizing technologies.
Microscopy, cytometry, cell sorting, fluorescence correlation
spectroscopy (FCS), ultra high throughput screening (uHTS),
multicolor fluorescence in situ hybridisation (mc-FISH),
FRET-systems, BRET-systems, and microarrays (DNA- and
protein-chips) are exemplary application fields. As known to one
skilled in the art, a microarray is a grid-like arrangement where
more than two different molecules are immobilized in a known
predefined region on at least one surface, and is useful to
evaluate receptor ligand interactions. As known to one skilled in
the art, a receptor is a naturally occurring or synthetic molecule
that exhibits an affinity to a given ligand. Receptors can be used
in a pure form or bound to another specie. Receptors can be coupled
covalently or noncovalently to a binding partner either directly or
indirectly (e.g., through a coupling mediator). Receptor examples
include, but are not limited to, agonists and antagonists for cell
membrane receptors, toxins and other poisons, viral epitopes,
hormones (e.g., opiates, steroids), hormone receptors, peptides,
enzymes, enzyme substrates, drugs acting as cofactors, lectins,
sugars, oligonucleotides, nucleic acids, oligosaccharides, cells,
cell fragments, tissue fragments, proteins, antibodies, etc. As
known to one skilled in the art, a ligand is a molecule that is
recognized by a certain receptor. Ligand examples include, but are
not limited to, agonists and antagonists for cell membrane
receptors, toxins and other poisons, viral epitopes, hormones
(e.g., opiates, steroids), hormone receptors, peptides, enzymes,
enzyme substrates, drugs acting as cofactors, lectins, sugars,
oligonucleotides, nucleic acids, oligosaccharides, proteins,
antibodies, etc.
[0193] The following non-limiting examples further describe the
compounds, methods, compositions, uses, and embodiments.
EXAMPLE 1
Synthesis of 4-methyl-5-oxohexane sulfonic acid used to synthesize
Example 2 compound
2,3-dimethyl-3-(3-sulfopropyl)-3H-indole-5-sulfonic acid
di-potassium salt and Example 8 compound
1,2-dimethyl-1-(3-sulfopropyl)-1H-benzo[e]indole-6,8-disulfonic
acid tripotassium salt
##STR00277##
[0195] Sodium hydride (2.1 g, 80 wt %=69 mmol) was slurried in 10
ml of dry THF. The suspension was cooled to 0.degree. C. and a
solution of ethyl-2-methylacetoacetate (10 g, 69 mmol) in 10 ml of
dry THF was added dropwise. The solution was stirred at room
temperature for 1 h. A solution of 1,3-propanesultone (8.42 g, 69
mmol) in 10 ml of dry THF was added dropwise. Once the addition was
complete, the solution was stirred for 2 h at 40.degree. C. The
solution was evaporated to dryness. The residue was dissolved in
100 ml water. The aqueous solution was extracted twice with
ethylacetate, then 100 ml concentrated HCl was added and the
solution was refluxed for 2 h. The solvent was evaporated in
vacuum. The residue was purified by column chromatography (silica,
methanol/dichloromethane) to give 4-methyl-5-oxohexane sulfonic
acid. Yield 10 g; MS (ESI-): 193.2 [M].sup.-
EXAMPLE 2
Synthesis of 2,3-dimethyl-3-(3-sulfopropyl)-3H-indole-5-sulfonic
acid di-potassium salt used to synthesize Example 3 compound
1-(2-methoxy-ethyl)-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-indolium
and Example 4 compound
1-[2-(2-methoxy-ethoxy)-ethyl]-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-
-indolium and Example 5 compound
1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-2,3-dimethyl-5-sulfo-3-(3-sulfo-
-propyl)-3H-indolium and Example 6 compound
1-(5-carboxypentyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
##STR00278##
[0197] Ten g (51 mmol) 4-hydrazino-benzene sulfonic acid and 9.85 g
(51 mmol) 4-methyl-5-oxohexane sulfonic acid were dissolved in 50
ml acetic acid. The solution was heated at 140.degree. C. for 4 h.
The solvent was evaporated in vacuum. The oily residue was
dissolved in 20 ml methanol, then 50 ml of a saturated solution of
KOH in 2-propanol was added to yield a yellow precipitate. The
solid was filtered off and dried in vacuum. Yield 11 g, MS (ESI-):
172.5 [M].sup.2-
EXAMPLE 3
Synthesis of
1-(2-methoxy-ethyl)-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-indolium
used to synthesize 550, 650, 755 Compound 1
##STR00279##
[0199] A mixture of 5 g (12.4 mmol)
2,3-dimethyl-3-(3-sulfopropyl)-3H-indole-5-sulfonic acid
dipotassium salt and 5.89 g (25.6 mmol) 2-methoxyethyl-p-toluene
sulfonate was heated under argon for 24 h. The residue was purified
by column chromatography (reversed phase silica, methanol/water,
TFA).
[0200] Yield 2.3 g, MS (ESI-): 404.1 [M-H].sup.-
EXAMPLE 4
Synthesis of
1-[2-(2-methoxy-ethoxy)-ethyl]-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-
-indolium used to synthesize 550, 650, 755 Compound 2
##STR00280##
[0202] A mixture of 5 g (12.4 mmol)
2,3-dimethyl-3-(3-sulfopropyl)-3H-indole-5-sulfonic acid
dipotassium salt and 7.1 g (25.6 mmol)
[2-(2-methoxyethoxy)ethoxy]-p-toluene sulfonate was heated under
argon for 24 h. The residue was purified by column chromatography
(reversed phase silica, methanol/water, TFA).
[0203] Yield 2.0 g. MS (ESI-): 448.2 [M-H].sup.-
EXAMPLE 5
Synthesis of
1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-2,3-dimethyl-5-sulfo-3-(3-sulfo-
-propyl)-3H-indolium used to synthesize 550, 650, 755 Compound
3
##STR00281##
[0205] A mixture of 5 g (12.8 mmol)
2,3-dimethyl-3-(3-sulfopropyl)-3H-indole-5-sulfonic acid
dipotassium salt and 8.14 g (25.6 mmol)
[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]p-toluene sulfonate was heated
under argon for 24 h. The residue was purified by column
chromatography (reversed phase silica, methanol/water, TFA). Yield
1.9 g, MS (ESI-): 492.1 [M-H].sup.-
EXAMPLE 6
Synthesis of
1-(5-carboxypentyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
used to synthesize Example 7 compound
1-(5-carboxypentyl)-3-methyl-2-((E)-2-phenylamino-vinyl)-5-sulfo-3-(3-sul-
fo-propyl)-3H-indolium and Example 8 compound
1-(5-carboxypentyl)-3-methyl-2-((1E,3E)-4-phenylamino-buta-1,3-dienyl)-5--
sulfo-3-(3-sulfopropyl)-3H-indolium and Example 9 compound
1-(5-carboxypentyl)-3-methyl-2-((1E,3E,5E)-6-phenylamino-hexa-1,3,5-trien-
yl)-5-sulfo-3-(3-sulfopropyl)-3H-indolium
##STR00282##
[0207] Both 5 g (15.7 mmol) 6-hydrazino-naphthalene-1,3-disulfonic
acid and 4.93 g (25 mmol) 4-methyl-5-oxohexane sulfonic acid were
dissolved in 50 ml acetic acid. The solution was heated at
140.degree. C. for 4 h. The solvent was evaporated in a vacuum. The
oily residue was dissolved in 20 ml methanol, then 50 ml of a
saturated solution of KOH in 2-propanol was added to yield a yellow
precipitate. The solid was filtered off and dried in vacuum. Yield
4.1 g, MS (ESI-): 158.2 [M].sup.3-
EXAMPLE 7
Synthesis of
1-(5-carboxypentyl)-3-methyl-2-((E)-2-phenylamino-vinyl)-5-sulfo-3-(3-sul-
fo-propyl)-3H-indolium used to synthesize 550 Compounds
##STR00283##
[0209] A combination of 0.92 g (2 mmol)
1-(5-carboxypentyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
and 0.43 g (2.2 mmol) N,N'-diphenylformamidine was dissolved in 20
ml methanol and stirred for 4 h under reflux. The solvent was
removed under vacuum. The residue was washed carefully with ethyl
acetate. A dark yellow solid was obtained which was processed
without further purification. MS (ESI-): 563.1 [M-H].sup.-
EXAMPLE 8
Synthesis of
1-(5-carboxypentyl)-3-methyl-2-((1E,3E)-4-phenylamino-buta-1,3-dienyl)-5--
sulfo-3-(3-sulfopropyl)-3H-indolium used to synthesize 650
Compounds
##STR00284##
[0211] A combination of 0.92 g (2 mmol)
1-(5-carboxypentyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
and 0.57 g (2.2 mmol) malonaldehyde-bisphenylimine-hydrochloride
were dissolved in 10 ml acetic acid and 10 ml acetic anhydride and
stirred for 4 h at 120.degree. C. The solvent was removed under
vacuum. The residue was washed carefully with ethyl acetate. A dark
brown solid was obtained which was processed without further
purification. MS (ESI-): 589.2 [M-H].sup.-
EXAMPLE 9
Synthesis of
1-(5-carboxypentyl)-3-methyl-2-((1E,3E,5E)-6-phenylamino-hexa-1,3,5-trien-
yl)-5-sulfo-3-(3-sulfopropyl)-3H-indolium used to synthesize 755
Compounds
##STR00285##
[0213] A combination of 0.92 g (2 mmol)
1-(5-carboxypentyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
and 0.63 g (2.2 mmol) glutacondianil-hydrochloride were dissolved
in 10 ml acetic acid and 10 ml acetic anhydride and stirred for 4 h
at 120.degree. C. The solvent was removed under vacuum. The residue
was washed carefully with ethyl acetate. A dark solid was obtained
which was processed without further purification. MS (ESI-): 615.2
[M-H].sup.-
EXAMPLE 10
Synthesis of 550 Compound 1
2-{(E)-3-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3-dihyd-
ro-indol-(2E)-ylidene]-propenyl}-1-(2-methoxy-ethyl)-3-methyl-5-sulfo-3-(3-
-sulfo-propyl)-3H-indolium tri sodium salt
##STR00286##
[0215] Five hundred sixty-four mg (1 mmol)
1-(5-carboxypentyl)-3-methyl-2-((E)-2-phenylamino-vinyl)-5-sulfo-3-(3-sul-
fopropyl)-3H-indolium and 404 mg (1 mmol)
1-(2-methoxy-ethyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
were dissolved in 20 ml of acetic acid/acetic anhydride (1/1),
followed by 200 mg sodium acetate. The solution was stirred under
reflux for 15 min. After cooling to room temperature, 20 ml
diethylether was added. The resulting precipitate (mixture of the
diastereomers 550 Compound 1 (isomer 1) and 550 Compound 1 (isomer
2)) was extracted by suction, washed with ether, and dried.
[0216] The residue was purified by column chromatography (RP-18,
acetonitrile/water and concentrated HCl) to separate the
diastereomers from each other. The diastereomer that first eluted
from the column was termed diastereomer 1 (550 Compound 1 (isomer
1)). The diastereomer that eluted second from the column was termed
diastereomer 2 (550 Compound 1 (isomer 2)). The diastereomers were
separated, followed by neutralization and evaporation. Purification
of the single diastereomeric compound was completed on a RP-18
column, acetonitrile/water. The corresponding fractions were pooled
and the solvent was removed by distillation. The two products
(diastereomers 550 Compound 1 (isomer 1) and 550 Compound 1 (isomer
2)) were dried in high vacuum.
[0217] 550 Compound 1 (isomer 1):
[0218] yield: 12%
[0219] UV-vis (PBS): .lamda.max=557 nm, .lamda.em=572 nm
[0220] MS (ESI-) [M/z]: 291.2 [M].sup.3-; 448.3 [M+Na].sup.2-
[0221] 550 Compound 1 (isomer 2):
[0222] yield: 23%
[0223] UV-vis (PBS): .lamda.max=557 nm, .lamda.em=572 nm
[0224] MS (ESI-) [M/z]: 291.1 [M].sup.3-; 448.2 [M+Na].sup.2-
EXAMPLE 11
Synthesis of 550 Compound 2
2-{(E)-3-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3-dihyd-
ro-indol-(2E)-ylidene]-propenyl}-1-[2-(2-methoxy-ethoxy)-ethyl]-3-methyl-5-
-sulfo-3-(3-sulfo-propyl)-3H-indolium tri sodium salt
##STR00287##
[0226] Both 1 mmol
1-(5-carboxypentyl)-3-methyl-2-((E)-2-phenylamino-vinyl)-5-sulfo-3-(3-sul-
fopropyl)-3H-indolium and 1 mmol
1-[2-(2-methoxy-ethoxy)-ethyl]-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-
-indolium were dissolved in 20 ml acetic acid/acetic anhydride
(1/1) followed by the addition of 200 mg sodium acetate. The
solution was stirred under reflux for 15 min. After cooling to room
temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 550-1 compound 2 and
550-2 compound 2) was extracted by suction, washed with ether and
dried.
[0227] The residue was purified by column chromatography (RP-18,
acetonitrile/water and concentrated HCl), thereby separating the
diastereomers from each other, as described in Example 10.
EXAMPLE 12
Synthesis of 550 Compound 3
2-{(E)-3-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3-dihyd-
ro-indol-(2E)-ylidene]-propenyl}-1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-
-3-methyl-5-sulfo-3-(3-sulfo-propyl)-3H-indolium tri sodium
salt
##STR00288##
[0229] One mmol
1-(5-carboxypentyl)-3-methyl-2-((E)-2-phenylamino-vinyl)-5-sulfo-3-(3-sul-
fopropyl)-3H-indolium and 1 mmol
1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-2,3-dimethyl-5-sulfo-3-(3-sulfo-
-propyl)-3H-indolium were dissolved in 20 ml acetic acid/acetic
anhydride (1/1) followed by the addition of 200 mg sodium acetate.
The solution was stirred under reflux for 15 min. After cooling to
room temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 550-1 compound 2 and
550-2 compound 2) was extracted by suction, washed with ether and
dried.
[0230] The residue was purified by column chromatography (RP-18,
acetonitrile/water and concentrated HCl), thereby separating the
diastereomers from each other, as described in Example 10.
EXAMPLE 13
650 Compound 1
Synthesis of
2-{(1E,3E)-5-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3--
dihydro-indol-(2E)-ylidene]-penta-1,3-dienyl}-1-(2-methoxy-ethyl)-3-methyl-
-5-sulfo-3-(3-sulfopropyl)-3H-indolium tri sodium salt
##STR00289##
[0232] Both 90 mg (1 mmol)
1-(5-carboxypentyl)-3-methyl-2-((1E,3E)-4-phenylamino-buta-1,3-dienyl)-5--
sulfo-3-(3-sulfopropyl)-3H-indolium and 404 mg (1 mmol)
1-(2-methoxy-ethyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
were dissolved in 20 ml of acetic acid/acetic anhydride (1/1)
followed by the addition of 200 mg of sodium acetate. The solution
was stirred under reflux for 15 min. After cooling to room
temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 650 Compound 1 (isomer 1)
and 650 Compound 1 (isomer 2)) was extracted by suction, washed
with ether, and dried.
[0233] The residue was purified by column chromatography (RP-18,
acetonitrile/water and concentrated HCl) to separate the
diastereomers from each other. The diastereomer that first eluted
from the column was termed diastereomer 1 (650 Compound 1 (isomer
1)). The diastereomer that eluted second from the column was termed
diastereomer 2 (650 Compound 1 (isomer 2)). The diastereomers were
separated, followed by neutralization and evaporation. Purification
of the single diastereomeric compound was completed on a RP-18
column, acetonitrile/water. The corresponding fractions were pooled
and the solvent was removed by distillation. The two products
(diastereomers 650 Compound 1 (isomer 1) and 650 Compound 1 (isomer
2)) were dried in high vacuum.
[0234] 650 Compound 1 (isomer 1):
[0235] yield: 11%
[0236] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0237] MS (ESI-) [M/z]: 299.7 [M].sup.3-; 461.0 [M+Na].sup.2-
[0238] 650 Compound 1 (isomer 2):
[0239] yield: 24%
[0240] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0241] MS (ESI-) [M/z]: 299.6 [M].sup.3-; 461.1 [M+Na].sup.2-
EXAMPLE 14
650 Compound 2
Synthesis of
2-{(1E,3E)-5-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3--
dihydro-indol-(2E)-ylidene]-penta-1,3-dienyl}-1-[2-(2-methoxy-ethoxy)-ethy-
l]-3-methyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium tri sodium
salt
##STR00290##
[0243] Both 564 mg (1 mmol)
1-(5-carboxypentyl)-3-methyl-2-((1E,3E)-4-phenylamino-buta-1,3-dienyl)-5--
sulfo-3-(3-sulfopropyl)-3H-indolium and 449 mg (1 mmol)
1-[2-(2-methoxy-ethoxy)-ethyl]-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H--
indolium were dissolved in 20 ml of acetic acid/acetic anhydride
(1/1) followed by the addition of 200 mg of sodium acetate. The
synthesis and work-up were carried out according to Example 13.
[0244] 650-1 compound 2:
[0245] yield: 11%
[0246] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0247] MS (ESI-) [M/z]: 314.4 [M].sup.3-; 483.0 [M+Na].sup.2-
[0248] 650-2 compound 2:
[0249] yield: 16%
[0250] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0251] MS (ESI-) [M/z]: 314.5 [M].sup.3-; 483.1 [M+Na].sup.2-
EXAMPLE 15
650 Compound 3
Synthesis of
2-{(1E,3E)-5-[1-(5-carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,3--
dihydro-indol-(2E)-ylidene]-penta-1,3-dienyl}-1-{2-[2-(2-methoxy-ethoxy)-e-
thoxy]-ethyl}-3-methyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium tri
sodium salt--650 compound 3
##STR00291##
[0253] Both 564 mg (1 mmol)
1-(5-carboxypentyl)-3-methyl-2-((1E,3E)-4-phenylamino-buta-1,3-dienyl)-5--
sulfo-3-(3-sulfopropyl)-3H-indolium and 493 mg (1 mmol)
1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-2,3-dimethyl-5-sulfo-3-(3-sulfo-
propyl)-3H-indolium were dissolved in 20 ml acetic acid/acetic
anhydride (1/1) followed by the addition of 200 mg sodium acetate.
The synthesis and work-up were carried out according to Example
13.
[0254] 650-1 compound 3:
[0255] yield: 10%
[0256] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0257] MS (ESI-) [M/z]: 329.2 [M].sup.3-; 505.0 [M+Na].sup.2-
[0258] 650-2 compound 3:
[0259] yield: 23%
[0260] UV-vis (PBS): .lamda.max=654 nm, .lamda.em=672 nm
[0261] MS (ESI-) [M/z]: 329.1 [M].sup.3-; 505.1 [M+Na].sup.2-
EXAMPLE 16
Synthesis of 755 Compound 1
2-{(1E,3E,5E)-7-[1-(5-Carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,-
3-dihydro-indol-(2E)-ylidene]-hepta-1,3,5-trienyl}-1-(2-methoxy-ethyl)-3-m-
ethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium tri sodium salt
##STR00292##
[0262] Six hundred and sixteen mg (1 mmol)
1-(5-Carboxypentyl)-3-methyl-2-((1E,3E,5E)-6-phenylamino-hexa-1,3,5-trien-
yl)-5-sulfo-3-(3-sulfopropyl)-3H-indolium and 404 mg (1 mmol)
1-(2-methoxy-ethyl)-2,3-dimethyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
were dissolved in 20 ml of acetic acid/acetic anhydride (1/1)
followed by the addition of 200 mg of sodium acetate. The solution
was stirred under reflux for 15 min. After cooling to room
temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 755 Compound 1 (isomer 1)
and 755 Compound 1 (isomer 2)) was extracted by suction, washed
with ether, and dried.
[0263] The residue was purified by column chromatography (RP-18,
acetonitrile/water and concentrated HCl) to separate the
diastereomers from each other. The diastereomer that first eluted
from the column was termed diastereomer 1 (755 Compound 1 (isomer
1)). The diastereomer that eluted second from the column was termed
diastereomer 2 (755 Compound 1 (isomer 2)). The diastereomers were
separated, followed by neutralization and evaporation. Purification
of the single diastereomeric compound was completed on a RP-18
column, acetonitrile/water. The corresponding fractions were pooled
and the solvent was removed by distillation. The two products
(diastereomers 755 Compound 1 (isomer 1) and 755 Compound 1 (isomer
2)) were dried in high vacuum.
[0264] 755 Compound 1 (isomer 1):
[0265] yield: 8%
[0266] UV-vis (PBS): .lamda..sub.max=752 nm; .lamda..sub.em=778
nm
[0267] MS (ESI-) [M/z]: 308.4 [M].sup.3-; 474.2 [M+Na].sup.2-
[0268] 755 Compound 1 (isomer 2):
[0269] yield: 16%
[0270] UV-vis (PBS): .lamda..sub.max=752 nm; .lamda..sub.em=778
nm
[0271] MS (ESI-) [M/z]: 308.4 [M].sup.3-; 474.2 [M+Na].sup.2-.
EXAMPLE 17
Synthesis of 755 Compound 2
2-{(1E,3E,5E)-7-[1-(5-Carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,-
3-dihydro-indol-(2E)-ylidene]-hepta-1,3,5-trienyl}-1-(2-methoxy-ethoxy)-3--
methyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
##STR00293##
[0272] Both 1 mmol
1-(5-Carboxypentyl)-3-methyl-2-((1E,3E,5E)-6-phenylamino-hexa-1,3,5-trien-
yl)-5-sulfo-3-(3-sulfopropyl)-3H-indolium and 1 mmol
1-[2-(2-methoxy-ethoxy)-ethyl]-2,3-dimethyl-5-sulfo-3-(3-sulfo-propyl)-3H-
-indolium were dissolved in 20 ml acetic acid/acetic anhydride
(1/1) followed by the addition of 200 mg sodium acetate. The
solution was stirred under reflux for 15 min. After cooling to room
temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 755 compound 2 (isomer 1)
and 755 compound 2 (isomer 2)) was extracted by suction, washed
with ether and dried. The residue is purified by column
chromatography (RP-18, acetonitrile/water and concentrated HCl),
thereby separating the diastereomers from each other, as described
in Example 16.
EXAMPLE 18
Synthesis of 755 Compound 3
2-{(1E,3E,5E)-7-[1-(5-Carboxypentyl)-3-methyl-5-sulfo-3-(3-sulfopropyl)-1,-
3-dihydro-indol-(2E)-ylidene]-hepta-1,3,5-trienyl}-1-{2-[2-(2-methoxy-etho-
xy)-ethoxy]-ethyl}-3-methyl-5-sulfo-3-(3-sulfopropyl)-3H-indolium
##STR00294##
[0273] Both 1 mmol
1-(5-carboxypentyl)-3-methyl-2-((1E,3E,5E)-6-phenylamino-hexa-1,3,5-trien-
yl)-5-sulfo-3-(3-sulfopropyl)-3H-indolium and 1 mmol
1-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethyl}-2,3-dimethyl-5-sulfo-3-(3-sulfo-
-propyl)-3H-indolium were dissolved in 20 ml acetic acid/acetic
anhydride (1/1) followed by the addition of 200 mg sodium acetate.
The solution was stirred under reflux for 15 min. After cooling to
room temperature, 20 ml diethylether was added. The resulting
precipitate (mixture of the diastereomers 755 compound 3 (isomer 1)
and 755 compound 3 (isomer 2)) was extracted by suction, washed
with ether and dried. The residue is purified by column
chromatography (RP-18, acetonitrile/water and concentrated HCl),
thereby separating the diastereomers from each other, as described
in Example 16.
EXAMPLE 19
[0274] Properties of 650 Compounds as NHS esters were compared with
commercially available dyes, as shown below.
TABLE-US-00001 650 1/1-NHS 650 1/1-NHS Alexa Fluor
(tetrasulfonated) 650 4/4-NHS (disulfonated) 647-NHS CF 647-NHS MW
(g/mol) 1066 1424.63 789.91 ~1150 3241 Ex (nm) 652 658 651 650 650
Em (nm) 672 681 665 665 665 .epsilon. (M.sup.-1 cm.sup.-1) 250,000
250,000 250,000 239,000 240,000 (theoretical) PEG 1/1 4/4 1/1 N/A
unknown (length/# of chain) Sulfonate 4 2 2 unknown
[0275] Properties of 755 Compounds as NHS esters were compared with
commercially available dyes as shown below:
TABLE-US-00002 DyLight 800-NHS 755 Compound 4/4-NHS MW (g/mol) 1050
1684.9 Ex (nm) 777 783 Em (nm) 794 797 .epsilon. (M.sup.-1
cm.sup.-1) 270,000 270,000 (theoretical) PEG N/A 4/4 (length/number
of PEG groups on compound Sulfonates 3 3
[0276] Excitation/emission spectra of 755 Compound 4/4-NHS was
within +/-10 nm compared to DyLight 800-NHS.
EXAMPLE 20
[0277] DyLight 650 1/1 and DyLight 650 4/4 were dissolved in
dimethylformamide (DMF) at 10 mg/ml, mixed on a vortex mixer for 15
seconds, and observed to determine if the dyes went into solution.
The dyes were then allowed to incubate for five minutes and again
mixed on a vortex mixer for 30 seconds. DyLight 650 (4/4) dissolved
immediately and DyLight 650 (1/1) did not go into solution until it
was incubated for five minutes and mixed again.
EXAMPLE 21
[0278] Inventive and commercial compounds, each as the NHS ester,
were conjugated to goat anti-mouse (GAM) and goat anti-rabbit (GAR)
antibodies. GAM and GAR at 10 mg/ml in phosphate buffered saline
(PBS), were dialyzed against 50 mM borate buffer, pH 8.5. The
compounds were reconstituted in DMF, and CF 647 was reconstituted
in dimethylsulfoxide (DMSO), at 10 mg/ml and combined at
2.5.times., 5.times., 10.times., or 15.times. molar excess with GAM
or GAR for about two hours at room temperature to label the
antibodies.
[0279] Labeled compounds, also termed dyes or labels, were
subjected to PDDR to remove the unlabeled (free) compound; 100-200
.mu.l of the packed resin was used per mg of protein purified. The
purified antibody-labeled dyes were then diluted 1:50 in PBS and
scanned for absorbance from 700 nm to 230 nm on a UV Cary
spectrophotometer to determine the protein concentration, and to
determine the mole dye to mole protein ratio. Each conjugate was
diluted 1:10 in 50% glycerol and heated in the presence of 10 mM
dithiothreitol (DTT) for 5 min at 95.degree. C., then separated by
electrophoresis on polyacrylamide gels in the presence of sodium
dodecyl sulfate (SDS-PAGE). The gels were scanned using the Typhoon
9400 Imager to verify removal of the unconjugated compound.
Labeling efficiency was compared, with results showing degree of
labeling below, where 650 Compound 1/1 (4S) denotes four sulfo
groups on the compound and 650 Compound 1/1 (2S) denotes two sulfo
groups on the compound.
TABLE-US-00003 GAM 2.5X 5X 10X 15X 650 Compound 4/4-NHS 2.4 4.7 9.6
14.2 650 Compound 1/1 (4S)-NHS 2.6 4.4 7.9 10.0 CF 647-NHS 1.7 2.9
4.3 5.1 Alexa Fluor 647-NHS 2.4 4.0 6.5 8.2
TABLE-US-00004 GAR 2.5X 5X 10X 15X 650 Compound 4/4-NHS 2.3 4.6 8.5
13.4 650 Compound 1/1 (4S)-NHS 2.8 4.1 7.6 10.0 CF 647-NHS 1.7 2.6
4.2 4.9 Alexa Fluor 647-NHS 2.3 3.6 6.1 7.7
Labeling efficiency was the highest for all 650 Compound 4/4
conjugates, followed by 650 Compound 1/1, compared to the other
dyes at each molar excess. 650 Compound 1/1 and CF 647 required
extra time for complete solubility.
[0280] 755 Compound 4/4 and DyLight 800, each as the NHS ester,
were conjugated to goat anti-mouse (GAM) and goat anti-rabbit (GAR)
antibodies as described above. Briefly, 755 Compound 4/4-NHS and
DyLight 800-NHS were reconstituted at 10 mg/ml in DMF. Each
compound showed good solubility. One mg in 100 .mu.l of GAM or GAR
was prepared at 10.0 mg/ml in borate buffer pH 8.5. Ten mg in 1000
.mu.l of GAM was prepared at 10.0 mg/ml in borate buffer pH 8.5.
Ten mg in 1000 .mu.l of GAM was prepared at 10.0 mg/ml in PBS pH
7.4. GAM and GAR were labeled with each compound at 2.5.times.,
5.times., 7.times. (10 mg) and 9.times. molar excesses. Ten mg GAM
was labeled with each compound at 5.times. and 7.times. molar
excesses in borate buffer. Ten mg GAM was labeled with each
compound at 5.times. and 7.times. molar excesses in PBS buffer, and
incubated for greater than 60 min. Conjugates were purified on
Pierce Dye Removal Resin in Harvard columns with 100-200 .mu.l
resin per mg of each conjugate. All the conjugates were diluted
1:50 and scanned on UV Cary Spectrophotometer. Absorption maxima
for free compounds is shown in FIG. 1A, where free dye 755 Compound
4/4-NHS showed a single absorption peak at 783 nm and free Dye
DyLight 800-NHS showed a single absorption peak at 770 nm.
Absorption maxima of GAM conjugates with 755 Compound 4/4 (D/P of
2.2) and DyLight 800 (D/P of 1.4), are shown in FIG. 1B, with
baseline 100% transmission shown. 755 Compound 4/4-GAM conjugates
showed a single absorption peak at 783 nm and DyLight 800-GAM
conjugates showed 2 peaks: major at 775 nm and minor at 706 nm.
Absorption maxima of GAR conjugates with 755 Compound 4/4 (D/P of
2.2), DyLight 800 (D/P of 1.4), and IR800-GAR (D/P of 2.6;
conjugate made using LI-COR IR800 Dye) are shown in FIG. 1C, with
baseline 100% transmission shown. 755 Compound 4/4-GAR conjugates
showed a single absorption peak at 783 nm, DyLight 800-GAR
conjugates showed 2 absorption peaks: major at 774 nm and minor at
705 nm, and IR800-GAR showed a main peak at 779 nm and a minor peak
at 709 nm. The secondary peak observed with DyLuight 800 at 706 nm
is approximately 60% of the main peak at 775 nm, and this secondary
peak can affect the readout depending on the instrumentation
used.
[0281] Labeling efficiency was compared, with results showing
degree of labeling (D/P) below.
TABLE-US-00005 2.5X 5X 7X 9X GAM borate buffer 755 Compound 4/4-NHS
0.97 1.72 2.24 2.94 DyLight 800-NHS 0.74 1.12 1.41 1.91 GAR borate
buffer 755 Compound 4/4-NHS 0.84 1.64 2.22 2.91 DyLight 800-NHS
0.71 1.17 1.39 1.88 GAM borate buffer 755 Compound 4/4-NHS 1.75
2.32 DyLight 800-NHS 1.20 1.55 GAM PBS buffer 755 Compound 4/4-NHS
0.74 1.16 DyLight 800-NHS 0.89 1.15
[0282] Conjugation of 755 Compound 4/4 in borate buffer resulted in
about 50% higher labeling efficiency than DyLight 800 at similar
molar excess. For both dyes, conjugations performed in PBS buffer
pH 7.2 showed about two times less labeling efficiency compared to
conjugations in borate buffer pH 8.5. DyLight 800 conjugates at
7.times. molar excess in borate buffer precipitated within three
days and 755 Compound 4/4 conjugates had no visible precipitation
after three weeks. Use of 755 Compound 4/4 at 5.times. molar excess
avoids dye aggregation and yields a similar D/P as DyLight 800 at
7.times. molar excess.
EXAMPLE 22
[0283] Performance of the dye-GAM conjugates and dye-GAR conjugates
was evaluated in a functional assay. Wells of a 96 white opaque
plate were coated with target proteins mouse IgG immunoglobulin or
rabbit IgG immunoglobulin. One hundred .mu.l mouse or rabbit IgG at
a concentration of 10 .mu.g/ml was applied to the corresponding
wells in columns 1 and 2. The target proteins were serially diluted
1:1 from the wells in columns 2 to 11 using 100 .mu.l PBS. One
hundred .mu.l of the samples from the wells in column 11 were
discarded. One hundred .mu.l PBS was added to the wells in column
12. The plates were incubated overnight at 4.degree. C. and then
blocked 2.times.200 .mu.l with Thermo Scientific SuperBlock.RTM.
Blocking Buffer. The coated plates were washed 2.times.200 .mu.l
with PBS-Tween and 1.times.200 .mu.l with PBS. Based on the
calculated concentrations, GAM and GAR conjugates were diluted
1:250 (of 1 mg/ml) in PBS buffer. Conjugates diluted in PBS to 4
.mu.g/ml were added to the corresponding plates (100 .mu.l/well)
and then incubated for 1 h in the dark. The plates were washed with
2.times.200 .mu.l with PBS-Tween and 1.times.200 .mu.l with PBS and
filled with PBS buffer (100 .mu.l/well) prior to scanning on Tecan
Safire to detect fluorescence intensity.
[0284] As shown in FIGS. 2-9, the relative fluorescence units (RFU)
or signal-to-background ratio (S/B) of the dyes were compared at
various concentrations, using the indicated conjugation
conditions.
[0285] FIG. 2 shows results of a functional assay using GAR
conjugated with either 650 Compound 4/4 (diamonds), 650 Compound
1/1 (circles), CF 647 (triangles), or Alexa Fluor 647 (squares) at
a 2.5.times. molar excess of the dyes, showing relative
fluorescence units (RFU) versus amount of target antibody per well
(ng/well). FIG. 3 shows the signal-to-background ratio (SB) of the
functional assay of FIG. 2, showing either 650 Compound 4/4
(diamonds), 650 Compound 1/1 (circles), CF 647 (triangles), or
Alexa Fluor 647 (squares) at a 2.5.times. molar excess of the dyes.
FIG. 4 shows results of a functional assay using GAR conjugated
with either 650 Compound 4/4 (diamonds), 650 Compound 1/1
(circles), CF 647 (triangles), or Alexa Fluor 647 (squares) at a
5.times. molar excess of the dyes, showing relative fluorescence
units (RFU) versus amount of target anibody per well (ng/well).
FIG. 5 shows the signal-to-background ratio (SB) of the functional
assay of FIG. 4, showing either 650 Compound 4/4 (diamonds), 650
Compound 1/1 (circles), CF 647 (triangles), or Alexa Fluor 647
(squares) at a 5.times. molar excess of the dyes. 650 Compound
1/1-GAR was the best performing conjugate at all molar excesses. Up
to 125 ng/well of rabbit IgG, the 650 Compound 4/4-GAR showed
similar binding fluorescence as Alexa Fluor 647-GAR but better than
CF 647-GAR. CF 647 showed significantly lower performance of all
the conjugates.
[0286] FIG. 6 shows results of a functional assay using GAM
conjugated with either 650 Compound 4/4 (diamonds), 650 Compound
1/1 (circles), CF 647 (triangles), or Alexa Fluor 647 (squares) at
a 2.5.times. molar excess of the dyes, showing relative
fluorescence units (RFU) versus amount of target antibody per well
(ng/well). FIG. 7 shows the signal-to-background ratio (SB) of the
functional assay of FIG. 6, showing either 650 Compound 4/4
(diamonds), 650 Compound 1/1 (circles), CF 647 (triangles), or
Alexa Fluor 647 (squares) at a 2.5.times. molar excess of the dyes.
FIG. 8 shows results of a functional assay using GAM conjugated
with either 650 Compound 4/4 (diamonds), 650 Compound 1/1
(circles), CF 647 (triangles), or Alexa Fluor 647 (squares) at a
5.times. molar excess of the dyes, showing relative fluorescence
units (RFU) versus amount of target antibody per well (ng/well).
FIG. 9 shows the signal-to-background ratio (SB) of the functional
assay of FIG. 8, showing either 650 Compound 4/4 (diamonds), 650
Compound 1/1 (circles), CF 647 (triangles), or Alexa Fluor 647
(squares) at a 5.times. molar excess of the dyes. 650 Compound
1/1-GAM was the best performing conjugate at all molar excesses. Up
to 125 ng/well of mouse IgG, 650 Compound 4/4-GAM showed similar
binding fluorescence as Alexa Fluor 647-GAM but better than CF
647-GAM. CF-647 showed significantly lower performance of all the
conjugates.
[0287] Performance of the dye-GAM conjugates and dye-GAR conjugates
was evaluated in a functional fluorescence plate assay, as
described above. After incubation, the plates were scanned on LiCor
Odyssey at 800 channel (unbound). Plates were washed 2.times.200
.mu.l with PBS-Tween20 and 1.times.200 .mu.l with PBS and filled
with PBS buffer (100 .mu.l/well) prior to scanning on LiCor Odyssey
at 800 channel (bound). Average total unbound fluorescence
intensity is shown in FIG. 10A, and the corresponding plate image
in FIG. 10B, showing 1 (755 Compound 4/4-GAR; 2.5.times. molar
excess; D/P 0.84), 2 (755 Compound 4/4-GAR; 5.times. molar excess;
D/P 1.64), 3 (755 Compound 4/4-GAR; 7.times. molar excess; D/P
2.22), 4 (755 Compound 4/4-GAR; 9.times. molar excess; D/P 2.91), 5
(DyLight 800-GAR; 2.5.times. molar excess; D/P 0.71), 6 (DyLight
800-GAR; 5.times. molar excess; D/P 1.17), 7 (DyLight 800-GAR;
7.times. molar excess; D/P 1.39), and 8 (DyLight 800-GAR; 9.times.
molar excess; D/P 1.88). Average total bound fluorescence intensity
is shown in FIG. 11A, with 755 Compound 4/4-GAR (solid lines) and
DyLight 800-GAR (dotted lines) at either 2.5.times. molar excess
(triangles), 5.times. molar excess (diamonds), 7.times. molar
excess (circles), or 9.times. molar excess (squares). FIG. 11B
shows the plate image of FIG. 11A, showing 1 (755 Compound 4/4-GAR;
2.5.times. molar excess), 2 (755 Compound 4/4-GAR; 5.times. molar
excess), 3 (755 Compound 4/4-GAR; 7.times. molar excess), 4 (755
Compound 4/4-GAR; 9.times. molar excess), 5 (DyLight 800-GAR;
2.5.times. molar excess), 6 (DyLight 800-GAR; 5.times. molar
excess), 7 (DyLight 800-GAR; 7.times. molar excess), and 8 (DyLight
800-GAR; 9.times. molar excess). In the above functional
fluorescence plate assays, 755 Compound 4/4-GAR showed
significantly higher binding fluorescence intensity compared to
DyLight 800-GAR conjugates in borate buffer.
[0288] Average total unbound fluorescence intensity is shown in
FIG. 12A, and corresponding plate image in FIG. 12B, showing 1 (755
Compound 4/4-GAR; 7.times. molar excess; D/P 2.22), 2 (DyLight
800-GAR; 7.times. molar excess; D/P 1.39), 3 (IR800-GAR (Rockland);
D/P 2.6), and 4 (DyLight 800-GAR (Rockland); D/P 2.1). Average
total bound fluorescence intensity is shown in FIG. 13A, with 755
Compound 4/4-GAR (diamonds; 7.times. molar excess; D/P 2.24),
DyLight 800-GAR (circles; 7.times. molar excess; D/P 1.39),
IR800-GAR (Rockland) (triangles; D/P 2.6), and DyLight 800-GAR
(Rockland) (squares; D/P 2.1). FIG. 13B shows the plate image of
FIG. 13A, showing 1 (755 Compound 4/4-GAR; 7.times. molar excess),
2 (DyLight 800-GAR; 7.times. molar excess), 3 (IR800-GAR
(Rockland)), and 4 (DyLight 800-GAR (Rockland)). In the above
functional fluorescence plate assays, 755 Compound 4/4-GAR showed
significantly higher binding fluorescence intensity compared to
DyLight 800-GAR conjugates in borate buffer. At similar D/P of
about 2, 755 Compound 4/4-GAR performed better than IR800-GAR
(conjugate made by Rockland using IR800 Dye from LiCOR; sold in
lyophilized form) and DyLight 800-GAR (conjugate made by Rockland
using DyLight 800; sold in lyophilized form). No quenching at high
dye molar excesses was observed with 755 Compound 4/4.
EXAMPLE 23
[0289] The inventive compounds and commercial dye were evaluated
for immunofluorescence in cell based assays using the following
protocol. Plates containing U2OS cells (human osteosarcoma cell
line) were fixed in 4% paraformaldehyde in PBS/0.1% Triton X-100
for 15 min at room temperature. The cells were then permeabilized
with 2% BSA in PBS/0.1% Triton X-100 for 15 min at room
temperature. Negative controls contain only 2% BSA/PBS-0.1%
Triton-X100 blocker. Diluted primary antibodies, mouse-anti-protein
disulphide isomerase (PDI) or rabbit-anti-HDAC2, diluted in 2%
BSA/PBS-0.1% Triton-X100 were added to the plates and incubated for
one hour at room temperature. Negative controls contain only 2%
BSA/PBS-0.1% Triton-X100 blocker. The plates were washed
3.times.100 .mu.l with PBS. Based on the calculated protein
concentrations, the conjugates made in Example 22 were diluted to 4
.mu.g/ml in PBS/0.1% Triton X-100 and added to the plates (50
.mu.l/well) and incubated one hour in the dark at room temperature.
After incubation, the primary antibody solution was removed from
the plates, and the plates were washed 3.times.100 .mu.l with PBS.
One hundred .mu.l of 0.1 .mu.g/ml Hoechst dye in PBS was added per
well. The plates were then scanned on an ArrayScan.RTM. Plate
Reader for imaging and quantitation.
[0290] FIGS. 14A-E shows results of an immunofluorescence assay
using rabbit-anti-HDAC2 as a primary antibody, and either 650
Compound 4/4-GAR (FIG. 14A; column A), 650 Compound 1/1 (4S)-GAR
(FIG. 14B; column A), CF 647-GAR (FIG. 14C; column A), Alexa Fluor
647-GAR (FIG. 14D; column A), or 650 Compound 1/1 (2S)-GAR (FIG.
14E; column A) as secondary antibody, with negative controls shown
in column B, where the compound was conjugated to GAR (secondary
antibody) at 2.5.times. molar excess (row 1), 5.times. molar excess
(row 2), 10.times. molar excess (row 3), or 15.times. molar excess
(row 4). Non-specific binding was observed with all the conjugates
at high dye molar excesses. 650 Compound 4/4-GAR was not as bright
as 650 Compound 1/1-GAR at the lower molar excesses 2.5.times. and
5.times.. However, 650 Compound 4/4-GAR did not appear to quench,
which was observed with 650 Compound 1/1-GAR. CF 647-GAR and Alexa
Fluor 647-GAR conjugates showed lower intensity at all molar
excesses.
[0291] Quantitative analysis of the data of FIGS. 14A-E, expressed
as Mean Total Intensity, which is the average total intensity of
all pixels within a defined area or defined primary object such as
a nucleus, is shown in FIG. 15, and signal to background ratio
(S/B) is shown in FIG. 16, at molar excesses of 2.5.times. (open
bars), 5.times. (upward diagonal lined bars), 10.times. (downward
diagonal lined bars), and 15.times. (vertical lined bars). 650
Compound 1/1-GAR and 650 Compound 4/4-GAR showed the highest
fluorescence intensity. While 650 Compound 4/4-GAR does not appear
to quench, 650 Compound 1/1, CF 647, and Alexa Fluor 647 conjugates
showed significant quenching at high molar excesses. CF 647-GAR and
Alexa 647-GAR conjugates showed lower intensity at all molar
excesses.
[0292] FIGS. 17A-D show immunofluorescence assay results using
mouse-anti-PDI as a primary antibody, and either 650 Compound
4/4-GAR (FIG. 17A; column A), 650 Compound 1/1 (4S)-GAR (FIG. 17B;
column A), CF 647-GAR (FIG. 17C; column A), or Alexa Fluor 647-GAR
(FIG. 17D; column A) as secondary antibody, with negative controls
shown in column B, where the compound was conjugated to GAM
(secondary antibody) at 2.5.times. molar excess (row 1), 5.times.
molar excess (row 2), 10.times. molar excess (row 3), or 15.times.
molar excess (row 4). No non-specific binding was observed with any
the dyes (purified with 200 .mu.l of resin/mg of protein). 650
Compound 4/4-GAM was the brightest at all molar excesses. 650
Compound 1/1, CF 647, and Alexa Fluor 647 conjugates showed
significant quenching above 2.5.times. molar excess. CF 647-GAM and
Alexa 647-GAM conjugates showed lower intensity at all molar
excesses.
[0293] Quantitative analysis of the data of FIGS. 17A-D, expressed
as Mean Total Intensity, which is the average total intensity of
all pixels within a defined area or defined primary object such as
a nucleus, is shown in FIG. 18 and signal to background ratio (S/B)
is shown in FIG. 19, at molar excesses of 2.5.times. (open bars),
5.times. (upward diagonal lined bars), 10.times. (downward diagonal
lined bars), and 15.times. (vertical lined bars). 650 Compound 1/1,
CF 647, and Alexa Fluor 647 conjugates showing their highest
binding intensity at 2.5.times. dye molar excess. 650 Compound
4/4-GAM was the brightest at all molar excesses. 650 Compound
4/4-GAM showed quenching above 5.times. molar excess, while 650
Compound 1/1, CF 647, and Alexa Fluor 647 conjugates showed
significant quenching above 2.5.times. molar excess. CF 647-GAM and
Alexa 647-GAM conjugates showed lower intensity at all molar
excesses.
[0294] FIGS. 20A-D shows results of an immunofluorescence assay
using rabbit-anti-HDAC2 as a primary antibody, and either 650
Compound 4/4-GAR (FIG. 20A; column A), 650 Compound 1/1 (4S)-GAR
(FIG. 20B; column A), CF 647-GAR (FIG. 20C; column A), or Alexa
Fluor 647-GAR (FIG. 20D; column A) as secondary antibody, with
negative controls shown in column B, where the compound was
conjugated to GAR (secondary antibody) at 2.5.times. molar excess
(row 1), 5.times. molar excess (row 2), 10.times. molar excess (row
3), or 15.times. molar excess (row 4). No non-specific binding was
observed with any of the conjugates (purified with 200 .mu.l of
resin/mg of protein). 650 Compound 4/4-GAR was the brightest at all
molar excesses. 650 Compound 1/1, CF 647, and Alexa Fluor 647
conjugates showed significant quenching above 2.5.times. molar
excess. CF 647-GAR and Alexa 647-GAR conjugates showed lower
intensity at all molar excesses.
[0295] Quantitative analysis of the data of FIGS. 20A-D, expressed
as Mean Total Intensity, which is the average total intensity of
all pixels within a defined area or defined primary object such as
a nucleus, is shown in FIG. 21 and signal to background ratio (S/B)
is shown in FIG. 22, at molar excesses of 2.5.times. (open bars),
5.times. (upward diagonal lined bars), 10.times. (downward diagonal
lined bars), and 15.times. (vertical lined bars). 650 Compound 1/1,
CF 647, and Alexa Fluor 647 conjugates showed the highest binding
intensity at 2.5.times. dye molar excess, however 650 Compound 4/4
was the brightest at all molar excesses. While 650 Compound 4/4-GAR
did not appear to quench, 650 Compound 1/1, CF 647, and Alexa Fluor
647 conjugates showed significant quenching above 2.5.times. molar
excess. CF 647-GAR and Alexa 647-GAR conjugates showed lower
intensity at all molar excesses.
[0296] The data indicated that excitation/emission spectra of 650
Compound 4/4-NHS was within +/-10 nm compared to 650 Compound
1/1-NHS, Alexa Fluor 647-NHS, and CF 647-NHS ester. Labeling
efficiency of 650 Compound 4/4 was the highest, followed by 650
Compound 1/1, compared to the other dyes at each molar excess. 650
Compound 1/1 and CF 647 required extra time for complete
solubility. 650 Compound 1/1-GAM/R was the best performing
conjugate at all molar excesses. Up to 125 ng/well of mouse/rabbit
IgG, 650 Compound 4/4-GAM showed similar binding fluorescence as
650 Compound 1/1-GAM and Alexa Fluor 647-GAM, but better than CF
647-GAM. CF 647 showed significantly lower performance of all dyes.
When purified with 200 .mu.l of resin/mg of protein, the conjugates
did not show any non-specific binding. Conjugates made with 650
Compound 4/4 (GAM/R) were the brightest and showed the highest
signal to background ratios. 650 Compound 1/1, CF 647, and Alexa
Fluor 647 conjugates showed significant quenching above 2.5.times.
molar excess. CF 647 and Alexa Flour 647 conjugates showed lower
intensity at all molar excesses.
EXAMPLE 24
[0297] The inventive compounds are evaluated for stability. All
compounds are packed under argon in plastic vials. The vials are
sealed with a drying pad in an aluminium coated pouch, and then
stored at 50.degree. C. for seven days.
EXAMPLE 25
[0298] The inventive compounds are evaluated in direct fluorescence
labeling of cell surface proteins using methods known in the art.
For example, suitable cell plates, such as IMR90 cells (human lung
embryonic fibroblast), are washed and then incubated with the
conjugates. The cell plates are then washed and imaged using an
appropriate instrument, such as a Thermo Scientific ArrayScan VTI
HCS Reader.
EXAMPLE 26
[0299] The inventive compounds are used for in vivo imaging to
obtain information about biological tissues that are not readily
accessible. The compounds are responsive to light in the near
infrared (NIR) region of the spectrum, which is a part of the
spectrum that has minimal interference from the absorbance of
biological materials. In one embodiment, the compounds are used for
fluorescent imaging of targets within animals. For example, in vivo
imaging information can be obtained using methods such as X-ray,
magnetic resonance imaging, positron emission tomography,
ultrasound imaging and probing, and other non-invasive methods used
for diagnosing and treating disease. Light in the NIR region, from
about 650 nm to about 1000 nm wavelength, can permeate through
several centimeters of tissue and therefore, can be used for in
vivo imaging. Fluorescent dyes, such as the inventive compounds
that are responsive to light in these longer wavelengths, can be
used as conjugates with targeting molecules such as antibodies to
bind and accumulate in, e.g., diseased tissue such as tumors, and
may be used to distinguish healthy from diseased tissue. In some
methods, the inventive compound may be attached to a biomolecule,
such as a protein, peptide, or a drug, which is localized or
retained in the desired tissue environment. Fluorescent in vivo
imaging using NIR dyes such as the inventive compounds are
diagnostic agents to discretely target disease tissue directly
within animals or humans.
[0300] For in vivo imaging, the compound or a conjugate of the
compound with a targeting agent, is administered to a tissue (e.g.,
intravenously), permitted to accumulate with excess compound
removed by the circulatory system, then the tissue is irradiated
with light at an appropriate wavelength. NIR fluorescent light is
recorded and/or an image is generated from the data obtained to
specifically detect and visualize the targeted cells or tissues.
The dose of compound administered can differ depending upon the
specific tissue, application, etc., as long as the method achieves
a detectable concentration of the compound in the tissue to be
assessed.
EXAMPLE 27
[0301] The inventive dyes were evaluated in biodistribution and
bioclearance studies. One mg NHS-DyLight 650 4/4 and NHS-DyLight
650 1/1 are reconstituted to 10 mg/ml and diluted to 1 mg/ml in
PBS. The dyes are incubated for 30 minutes and then quenched by
adding one-tenth volume of 3M N-ethanolamine. One hundred .mu.L of
1 mg/mL of each hydrolyzed dye solution is intravenously injected
via the retro orbital plexus of non-tumored nude mice. One mouse is
injected for each dye. The animals are imaged on a Carestream MSFX
at 0 h, 3 h, 6 h, 12 h, and 24 h post injection. After the final
time point, animals are sacrificed and tissues collected for ex
vivo imaging. The heart, liver, spleen, lungs, and kidneys are
gathered from one mouse from each cohort, and fixed and stained
using hematoxalin and eosin. Colorimetric images are acquired at
20.times. on a Nikon 90i microscope. The results show that the
hydrolyzed NHS-DyLight 650 4/4 is removed from the circulatory
system, whereas hydrolyzed NHS-DyLight 650 1/1 NHS-Alexa 647
accumulate in the liver.
EXAMPLE 28
In vivo imaging using 650 Compound 4/4 conjugated to anti-HER2
antibody
[0302] 650 Compound 4/4-NHS is conjugated to a rabbit anti-HER2
antibody (Genscript USA, Piscataway N.J.) by reconstituting the
compound in dimethylformamide (DMF) at 10 mg/ml, then incubated at
10.times. molar excess with rabbit anti-HER2 antibody (0.1 mg) for
1 h at room temperature to result in a 650 Compound 4/4-anti-HER2
conjugate. The sample is then subjected to PDDR to remove unlabeled
(free) 650 Compound 4/4. Ten microgram of the conjugate is injected
intravenously (IV) to athymic mice bearing BT474 tumors. The
animals are imaged over time at 1, 24, 48, 72, 96, and 120 hours
post-injection using Pearl Impulse Imager from LI-COR Biosciences
(LI-COR Instruments, Lincoln Nebr.).
[0303] Upon whole body imaging, fluorescence intensity is observed
to be distributed over the whole animal during the first hour
imagining and diminishes significantly at 72 hours. After 96 hours,
the signal is localized and specific to the tumor.
EXAMPLE 29
In vivo imaging using either monosulfonated or disulfonated 650
Compound 4/4
[0304] The compound may be rendered less hydrophilic, i.e., more
hydrophobic or less negatively charged, by altering the number of
sulfonate groups. Fewer sulfonates render the compound more
hydrophobic and less negatively charged. In this embodiment, the
compound may be more readily retained in a desired tissue or
location if the appropriate number of sulfonates is determined. For
example, compound penetration into cells is more efficient if fewer
sulfonates are on the compound. The compound may contain one, two,
three, or four sulfonate groups. Hydrophobic compounds are also
known to more efficiently cross the cell membrane, and therefore
are more desirable when the target of interest is located within
the cell.
[0305] Alendronate, a compound that binds to, and is retained in,
LNCap prostate cancer cells, is conjugated with disulfonated or
monosulfonated 650 Compound 4/4 by incubating a solution containing
1 mM disulfonated or monosulfonated 650 Compound 4/4-NHS in 1 ml of
PBS and 0.5 ml tetrahydrofuran (THF) with 0.1 mM alendronate and
0.2 mM diisopropylethylamine at room temperature overnight. The
conjugate is purified using reverse phase HPLC with 0-50% methanol
against a 0.1 M ammonium acetate buffer, and is then
lyophilized.
[0306] LNCap cells are grown orthotopically in nude mice. 650
Compound 1 (isomer 1)-alendronate (5 nmole) is injected into the
tumor. Control mice are injected with free 650 Compound 4/4
containing a carboxylic acid residue instead of the reactive NHS
ester. X-ray and near infra-red fluorescence images are
captured.
[0307] Upon imaging the whole mouse, both the monosulfonated and
disulfonated 650 Compound 4/4-alendroneate conjugate is retained in
mouse tissue but the free dyes are not retained; the conjugate is
retained in the LNCap cell-induced tumor for at least 18 hrs.
EXAMPLE 30
In vivo imaging using either monosulfonated or disulfonated 650
Compound 4/4
[0308] A drug delivery nanoparticle system conjugated with
disulfonated and monosulfonated 650 Compound 4/4 is prepared as
follows. A solution containing 1 mM disulfonated or monosulfonated
650 Compound 4/4-NHS in 1 ml of PBS is incubated overnight at room
temperature with 0.1 mM of an anti-cancer drug conjugated with
transferrin in the form of a nanoparticle. The resulting 650
Compound 4/4-nanoparticle conjugates are purified by
centrifugation, and then lyophilized.
[0309] The 650 Compound 4/4-nanoparticle conjugates (1 nmole) are
injected intravenously into the tail vein of different mice.
Control mice are injected with non-reactive 650 Compound 4/4 dye
containing a carboxylic acid residue instead of a reactive NHS
ester. X-ray and near infra-red fluorescence images of mouse brain
are captured.
[0310] Both 650 Compound 4/4-nanoparticle conjugates are found to
localize in the mouse brain for greater than about 24 hours after
injection. Tumor size progressively decreases after injection of
650 Compound 4/4-nanoparticle conjugate, compared to 650 Compound
4/4-nanoparticle without the anti-cancer drug.
EXAMPLE 31
[0311] The mono-sulfonated derivative could be on any one of six
possible positions on the 650 compound, accounting for the
stereochemistry around the carbon positions on the rings as well as
the non-symmetrical nature of the two ends of each dye. Similarly,
the di- and tri-substituted sulfonates could be on multiple
possible positions on the inventive compounds.
EXAMPLE 32
[0312] Log P (partition coefficient) and log D (distribution
coefficient) of inventive and commercial compounds were determined
to assess compound hydrophilicity. The log P value of a compound is
the logarithm of a compound's partition coefficient between
n-octanol and water log(C.sub.octanol/C.sub.water), and is a well
established measure of a compound's hydrophilicity. Log P is a
constant for the molecule under its neutral form. Low
hydrophilicity, and thus high log P, causes poor absorption or
permeation. For compounds to have a reasonable probability of being
well absorbed, their log P is generally <5.0. Lipophilicity is
not determined by the partitioning of the neutral species in
octanol/water, but by the distribution of both the neutral and
positively charged forms of the molecule. Log D is related to
hydrophilicity of a compound. The distribution coefficient, given
by log D, takes into account all neutral and charged forms of the
molecule. Because the charged forms generally do not enter the
octanol phase, this distribution varies with pH. In the pH range
where the molecule is mostly un-ionized, log D=log P. In the pH
range where a significant fraction is ionized, log D becomes a
function of log P, pH, and pKa. If one assumes that charged
molecules do not enter the octanol at all, log D can be expressed
as log D=log P-log(1+10**(pH-pKa)).
[0313] The following table provides theoretical calculated log D
and log P values for 755 Compound 4/4 and DyLight 800 measured by
the ChemAxon program.
TABLE-US-00006 755 Compound 4/4 pH LogD 1.50 -1.43 5.00 -1.77 6.50
-1.77 7.40 -1.77 LogP ionic species = -1.8 LogP nonionic species =
1.0 (3.2 considering tautomerization/resonance) LogD at pI = 0.2
(2.4 considering tautomerization/resonance)
TABLE-US-00007 DyLight 800 pH LogD 1.50 1.44 (1.42 considering
tautomerization/resonance) 5.00 -0.31 6.50 -0.32 7.40 -0.32 LogP
ionic species = -0.3 LogP nonionic species = 2.4 (4.7 considering
tautomerization/resonance) LogD at pI = 2.8 (5.1 considering
tautomerization/resonance)
[0314] The log P and log D calculations comparing 755 Compound 4/4
with four PEG.sub.4 chains and the DyLight 800 dye from Thermo
Fisher with no PEG modifications illustrates the unexpected
benefits that even short PEG.sub.4 chains have on the
hydrophilicity of cyanine-type dyes. Although the literature
teaches the hydrophilicity benefits of longer PEG polymer
modifications on small dye molecules, it does not suggest that such
benefits occur with short PEG chains. The DyLight 800 dye
calculation of log D indicated that the three sulfonates on the
molecule resulted in a mildly hydrophilicity index of -0.32 around
neutral pH. By contrast, 755 Compound 4/4 displayed much better
hydrophilicity with a log D determination of -1.77 at the same
neutral pH values. This calculated difference in the hydrophilicity
corresponded to observed results that the PEGylated dye goes into
aqueous solution much more readily that the more hydrophobic
DyLight 800 dye. Increased solubility of the PEGylated dye was also
seen when dissolving the dyes in a water-miscible organic solvent
such as DMF or DMSO. Conjugates of 755 Compound 4/4 with antibody
molecules were much more stable in solution at all levels of
dye-to-protein ratios than the DyLight 800 conjugates. In fact,
DyLight 800-antibody conjugates tended to precipitate out of
solution during the conjugation reaction and had stability issues
upon storage, whereas 755 Compound 4/4-antibody conjugates did not
precipitate during conjugation and did not have storage stability
issues. These observations emphasized the unexpected benefits the
invention provided for cyanine dye compounds modified with the
relatively short PEG chains described herein.
[0315] The embodiments shown and described in the specification are
only specific embodiments of inventors who are skilled in the art
and are not limiting in any way. Therefore, various changes,
modifications, or alterations to those embodiments may be made
without departing from the spirit of the invention in the scope of
the following claims. The references cited are expressly
incorporated by reference herein in their entirety.
* * * * *
References