WO2016133913A1 - Fluorescently labeled molecules containing modified tryptophan - Google Patents

Fluorescently labeled molecules containing modified tryptophan Download PDF

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WO2016133913A1
WO2016133913A1 PCT/US2016/018094 US2016018094W WO2016133913A1 WO 2016133913 A1 WO2016133913 A1 WO 2016133913A1 US 2016018094 W US2016018094 W US 2016018094W WO 2016133913 A1 WO2016133913 A1 WO 2016133913A1
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ome
methyl ester
acid methyl
caspase
histidine
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French (fr)
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David Phelps
Gary Johnson
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Seed Research And Development Llc
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/536—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase
    • G01N33/542—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/0019—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules
    • A61K49/0021—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules the fluorescent group being a small organic molecule
    • A61K49/0041—Xanthene dyes, used in vivo, e.g. administered to a mice, e.g. rhodamines, rose Bengal
    • A61K49/0043—Fluorescein, used in vivo
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/005—Fluorescence in vivo characterised by the carrier molecule carrying the fluorescent agent
    • A61K49/0056—Peptides, proteins, polyamino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/08—Tripeptides
    • C07K5/0821—Tripeptides with the first amino acid being heterocyclic, e.g. His, Pro, Trp
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • G01N33/533—Production of labelled immunochemicals with fluorescent label
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/573—Immunoassay; Biospecific binding assay; Materials therefor for enzymes or isoenzymes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/914—Hydrolases (3)
    • G01N2333/948—Hydrolases (3) acting on peptide bonds (3.4)
    • G01N2333/95—Proteinases, i.e. endopeptidases (3.4.21-3.4.99)
    • G01N2333/964—Proteinases, i.e. endopeptidases (3.4.21-3.4.99) derived from animal tissue
    • G01N2333/96425—Proteinases, i.e. endopeptidases (3.4.21-3.4.99) derived from animal tissue from mammals
    • G01N2333/96427—Proteinases, i.e. endopeptidases (3.4.21-3.4.99) derived from animal tissue from mammals in general
    • G01N2333/9643—Proteinases, i.e. endopeptidases (3.4.21-3.4.99) derived from animal tissue from mammals in general with EC number
    • G01N2333/96466—Cysteine endopeptidases (3.4.22)
    • G01N2333/96469—Interleukin 1-beta convertase-like enzymes

Definitions

  • the present disclosure relates to new fluorescent molecules that contain N-alkylated or N-acylated tryptophan and do not substantially quench fluorescent labels attached to the molecules, and the use of such molecules in preparing and studying various compounds, such as substrates and inhibitors for assays of enzymes (e.g., caspases, such as caspase-1 which is an important enzyme in inflammation).
  • enzymes e.g., caspases, such as caspase-1 which is an important enzyme in inflammation.
  • An enzyme substrate or enzyme inhibitor that contains a modified tryptophan and fluorescent label as disclosed herein can be studied without loss of signal by Forster quenching. By reducing or eliminating this quenching, more useful labeled molecules with improved properties for assay development can be prepared.
  • Tryptophan (Tip or W) is one of 20 amino acids naturally occurring in proteins. Only the L-stereoisomer of tryptophan is found in proteins. A distinguishing structural characteristic of tryptophan is its indole ring.
  • Tryptophan occurs at the P4 position in one of the sequences of the interleukin- converting enzyme (ICE; also known as caspase-1) cleavage site. Shen et al., Atherosclerosis, 210(2):422-29 (2010).
  • An amino acid recognition sequence often employed in synthetic inhibitors and synthetic substrates of caspase-1 is WEHD (tryptophan, glutamic acid, histidine, aspartic acid).
  • Tryptophan is a fluorescent amino acid with an emission maximum of -360 nm and a quantum yield ( ⁇ ) of -0.14. Because tryptophan is intrinsically fluorescent, it is subject to and can cause Forster resonance energy transfer, with a Forster radius of 40A.
  • a fluorescent label such as fluorescein (with a Forster radius of 44A) or BODIPY (with a Forster radius of 57A)
  • a molecule containing tryptophan e.g., attached to the N-terminal tryptophan in WEHD
  • the fluorescent label and the tryptophan moieties are well within range to cause Forster resonance energy transfer, which quenches the fluorescence of each moiety.
  • fluorescently labeled caspase-1 probes such as BODIPY-WEHD-fluoromethylketone, relatively useless because the fluorescence of the label is significantly decreased by the tryptophan-induced quenching.
  • the average length of a peptide or amide bond is about 1.33 A (Marsh et al., Adv
  • the molecules disclosed herein can be used in a variety of compounds (e.g., caspase-1 probes, polycaspase probes, probes of other serine proteases, etc.), they provide far-reaching advantages in studying fluorescently labeled molecules containing tryptophan. In other words, there is a need for tryptophan-containing molecules that will not quench the fluorescence of attached fluorescent labels.
  • the present disclosure relates to a fluorescent molecule comprising a sequence of 1-10 natural or synthetic amino acids, wherein at least one amino acid is a modified tryptophan of formula (I)
  • R is selected from -(CH 2 ) n X and -(CO)(CH 2 ) n X, where n is 0-5 and X is H or -CF 3 ;
  • R 2 is selected from OH and the N-terminal group of another of the amino acids; wherein the molecule produces a fluorescent signal that is stronger than a molecule that only differs by R being H.
  • the fluorescent molecule comprises 1-5 natural or synthetic amino acids.
  • R 2 is OH.
  • R is -(CH 2 ) n X, n is 1, and X is H.
  • R is -(CH 2 ) n X, n is 0, and X is - CF 3 .
  • R is - ⁇ CO)(CH 2 ) n X, n is 0, and X is -CF 3 .
  • R is - (CO)(CH 2 ) n X, n is 1, and X is H.
  • the fluorescent label is a dye selected from pyrene dyes, indacene dyes, cyanine dyes, fluorescein dyes, rhodamine dyes, sulforhodamine dyes, and IR dyes.
  • the dye is selected from Cascade Blue, BODIPY, Alexa Fluors, DyLight dyes, FAM, fluorescein isothiocyanate, Cy5, Rhodamine Green, Rhodol Green, Oregon Green dyes, 4,5-dichloro carboxy fluorescein, 5'-hexachloro-fluorescein, carboxytetramethylrhodamine, tetramethylrhodamine, sulforhodamines, 5',6-carboxyl-X- rhodamine, iFluor dyes, and Tide Fluor dyes.
  • the amino acids comprise the following in order: the modified tryptophan of formula (I), glutamic acid, histidine, and aspartic acid.
  • the present disclosure relates to a fluorescent caspase probe of Formula (II):
  • R 3 is selected from 780, ABzC, BODIPY, Cy5, FAM, N-AE, N-AM, and ORGn;
  • Xi is selected from W(N')E(OMe)HD(OMe), 5-F-W(N')E(OMe)HD, 2-CF 3 -W(N')E(OMe)HD, and 6-CF 3 W(N')E(OMe)HD, wherein N' is (NMe), (N-TFM), (N-Ac), or (N-TFA); and R4 is selected from halogen, phenol, and benzoylate.
  • the present disclosure relates to a method of determining in vivo the incidence of inflammation in a living organism, comprising the steps of: (i) administering in vivo a fluorescent caspase probe to a living organism; (ii) subjecting the living organism to a means for in vivo detection of caspase-1 -probe complexes; and (iii) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes.
  • the in vivo detection is performed on at least one portion of the living organism selected from eye, breast, heart, brain and central nervous system, kidney, lung, liver, skin, pancreas, skeletal system, connective tissue, stomach, upper gastrointestinal tract, lower gastrointestinal tract, circulatory system, lymphatic system, sexual organ, prostate, embryologic tissue, muscular system, and gallbladder.
  • the method further comprises the steps of: (a) before administering the probe in step (i), administering in vivo a candidate therapy intended to induce inflammation in the living organism; and (b) after step (iii), determining whether the candidate therapy induces or inhibits inflammation as indicated by the detected presence or absence of caspase-1 -probe complexes, respectively.
  • the present disclosure relates to a method of determining ex vivo the incidence of inflammation in a biological sample extracted from a living organism, comprising the steps of: (i) administering in vivo a fluorescent caspase probe to a portion of a living organism; (ii) extracting a biological sample from the portion of the living organism; (iii) subjecting the biological sample to a means for ex vivo detection of caspase-1 -probe complexes; and (iv) determining the incidence of inflammation as indicated by the presence or absence of caspase- 1 -probe complexes.
  • the present disclosure relates to a method of determining in vitro the incidence of inflammation in a biological sample, comprising the steps of: (i) adding a fluorescent caspase probe to a biological sample; (ii) incubating the sample with the probe under conditions sufficient to form caspase-1 -probe complexes; (iii) subjecting the sample of step (ii) to a means for detecting caspase-1 -probe complexes; and (iv) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes.
  • the method further comprises the step of inducing inflammation in the biological sample before adding the probe in step (i).
  • the biological sample is selected from a blood sample, tissue sample, cell suspension, cellular extract, and tissue homogenate.
  • the present disclosure relates to a composition
  • a composition comprising a fluorescent caspase probe and an excipient.
  • the present disclosure relates to a kit comprising a fluorescent caspase probe, a buffer, and packaging materials.
  • Figure 1 The fluorescent Caspase-1 probe 5-FAM-W(NMe)E(OMe)HD(OMe)- FMK was synthesized at 90% purity per the process described in Prophetic Example 2; it was characterized using HPLC-MS.
  • Figure 1 shows High Performance Liquid Chromatography (HPLC) characterization of the synthesized 5-FAM-W(NMe)E(OMe)HD(OMe)-FMK compound: Wavelength: 215 nm; Flow rate: 1.2 mL/min; Buffer A: 0.1% TF A in water; Buffer B: 0.1%TFA in acetonitrile; Temperature: 45 °C; Column: Discovery, CI 8, 4.6mm x 250 mm, 5 micron, gradient (linear): 30% - 50% buffer B in 20 minutes; Injector volumn: 20 microliters.
  • HPLC High Performance Liquid Chromatography
  • Figure 2 The fluorescent Caspase-1 probe 5-FAM-W(NMe)E(OMe)HD(OMe)- FM was synthesized at 90% purity per the process described in Prophetic Example 2, characterized using HPLC-MS.
  • Figure 2 shows Mass Spectrometry (MS) characterization of the synthesized 5-FAM-W(NMe)E(OMe)HD(OMe)-FMK compound.
  • FIG. 3 Median Fluorescence Intensity (MFI) of PHA-activated THP-1 cells labeled with FAM- WEHD-FMK.
  • THP-1 cells human monocyte cell line
  • PHA phytohemagglutinin
  • Cells were washed with PBS and analyzed using an Attune NxT flow cytometer.
  • the present disclosure relates to fluorescently labeled molecules containing N- alkylated or N-acylated tryptophan that substantially reduces or eliminates loss of signal by Forster quenching, thus providing a molecule that produces a stronger fluorescent signal than a molecule differing only by containing natural, unmodified tryptophan instead of N- alkylated or N-acylated tryptophan.
  • N-alkylated tryptophan includes, but is not limited to, substituting the hydrogen at the 1 -nitrogen position of the indole ring of tryptophan with a group selected from methyl, ethyl, propyl, butyl, pentyl, etc.
  • N-acylated tryptophan includes, but is not limited to, substituting the hydrogen at the 1 -nitrogen position of the indole ring of tryptophan with a group selected from acetyl, ethylacetyl, propylacetyl, butylacetyl, pentylacetyl, etc. Also included are fluorinated derivatives of these alkyl and acyl groups.
  • acylated or refers to a compound to which an acyl group has been attached, wherein the "acyl” group is a carbonyl attached to an alkyl group that is a straight or branched, substituted or unsubstituted, saturated or unsaturated hydrocarbon-based chain having 1-5 carbon atoms.
  • Suitable substituents include but are not limited to halogen, hydroxyl, Ci -3 alkyl, Ci -3 alkoxyl, and carboxyl groups.
  • alkylated refers to a compound to which an alkyl group has been attached, wherein the "alkyl” group is a straight or branched, substituted or unsubstituted, saturated or unsaturated hydrocarbon-based chain having 1 -5 carbon atoms. Suitable substituents include but are not limited to halogen, hydroxyl, alkyl, alkoxyl, carbonyl, and carboxyl groups.
  • biological sample refers to any type of material of biological origin, including but not limited to a blood sample, tissue sample, cell suspension, cellular extract, or tissue homogenate.
  • ex v vo refers to processes or procedures performed on a biological sample (e.g., tissue, cells, blood, etc.) extracted from a living, multicellular organism following the in vivo administration of a caspase probe to the living organism.
  • ex vivo detection includes obtaining a biopsy extracted from a living subject (e.g., a mammal, such as a human) subsequent to in vivo administration of a caspase- 1 probe to that subject, and subjecting the biopsy to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which would be indicative of inflammation in the subject.
  • a biological sample e.g., tissue, cells, blood, etc.
  • ex vivo detection includes obtaining a biopsy extracted from a living subject (e.g., a mammal, such as a human) subsequent to in vivo administration of a caspase- 1 probe to that subject, and subjecting the biopsy to a means for detecting caspase
  • in vitro refers to processes or procedures performed on a biological sample outside a living organism.
  • in vitro administration includes administering (i.e., delivering, applying, etc.) a caspase probe to a biological sample that is outside a living organism; and in vitro detection includes subjecting a biological sample (e.g., cells in a test tube or cultured dish) to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which could reflect whether a candidate therapy present in the sample induces or inhibits inflammation.
  • a biological sample e.g., cells in a test tube or cultured dish
  • caspase- 1 -probe complexes e.g., fluorometry
  • in vivo refers to processes or procedures performed inside a living, multicellular organism.
  • in vivo administration includes administering a caspase probe to a living subject (e.g., a mammal, such as a human); and in vivo detection includes subjecting a living subject to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which would be indicative of inflammation in the subject.
  • incidence refers to the occurrence rate, frequency of an event, or the quantifiable degree to which an event occurs.
  • incubating when used with respect to incubating a sample with a caspase probe, refers to exposure conditions (e.g., time, temperature, pH, etc.) sufficient for the formation of caspase-probe complexes.
  • label refers to a detectable moiety comprising one or more atoms.
  • N-terminal group refers to a moiety attached to the N- terminal position of the recognition sequence of the caspase probes.
  • the N-terminal group can be a detectable or non-detectable group.
  • reactive group refers to a portion of the caspase probe that covalently binds to the active catalytic site of a caspase.
  • recognition sequence refers to a portion of the caspase probes comprising a sequence of 1 to 6 natural amino acids or synthetic analogs thereof, which is selective for one or more caspases.
  • 780 DyLightTM 780 Infrared Dye (infrared specialty dye having a benzopyrillium core and 1-3 sulfonates)
  • ABzC 4-aminobenzyloxycarbonyl coupled to a fluorescent label such as 780, BODIPY, FAM, or ORGn
  • BMK benzoyloxymethyl ketone
  • BODIPY any BODIPY (boron-dipyrromethene) fluorescent dye, such as BODIPY-FL (boron-dipyrromethene fluorescent dye), BODIPY-TMR (boron-dipyrromethene tetramethylrhodamine dye), and BODIPY-TR (boron-dipyrromethene dye); structures shown
  • Cy5 far red excitation dye (structure shown below)
  • DY 750 near-infrared excitation dye (structure shown below)
  • DY 780 near-infrared excitation dye (structure shown below)
  • FAM carboxyfluorescein, including 5-carboxyfluorescein, 6-carboxyfluorescein, or a mixture of 5- and 6-carboxyfluorescein
  • FMOC fluorenylmefhyloxycarbonyl
  • GFP green fluorescent protein
  • N-TFA N-trifluoroacetyl
  • N-TFM N-trifluoromethyl
  • ORGn Oregon Green Dye (fluorinated fluorescein modified with or without pivaloyl groups)
  • TFA trifluoroacetyl, -(CO)CF 3
  • TFM trifluoromethyl, -CF 3
  • VAD L-valyl-L-alanyl-L-aspartic acid
  • the molecules containing modified tryptophan disclosed herein comprise one or more fluorescent labels that allow the probe to be detected by one or more detection techniques - e.g., fiuorometry.
  • the label may be present in one or more parts of the molecule.
  • Suitable fluorescent labels include, but are not limited to, fluorescent proteins, such as green fluorescent protein (GFP) and modifications of GFP that have different absorption/emission properties, phycobiliproteins, complexes of certain rare earth metals (e.g., europium, samarium, terbium, or dysprosium), and fluorescent nanocrystals (quantum dots).
  • fluorescent proteins such as green fluorescent protein (GFP) and modifications of GFP that have different absorption/emission properties
  • phycobiliproteins e.g., complexes of certain rare earth metals (e.g., europium, samarium, terbium, or dysprosium), and fluorescent nanocrystals (quantum dots).
  • fluorescent dyes include, but are not limited to, sulforhodamine 101 (Texas Red), rhodamine dyes (e.g., rhodamine B, rhodamine 6G, rhodamine 19, rhodamine Green, TAMRA (carboxytetramethylrhodamine), TRITC (tetramethylrhodamine isothiocyanate), ROX (5',6-carboxyl-X-rhodamine)), indocyanine green, cyanine dyes (e.g., Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7), Marina Blue, Pacific Blue, Oregon Green dyes (e.g., Oregon Green 88, Oregon Green 514), tetramethylrhodamine, BODIPY dyes, Cascade Blue, fluoresceins (e.g., FAM, JOE (4,5-dichloro carboxy fluorescein), HEX (5'-hexachloro
  • the fluorescent dye has an absorption maximum in the visible (400-800 nm) or near infrared (800-2500 nm) region.
  • the amino acid(s) disclosed herein may be D, L, or D, L mixtures.
  • various suitable synthetic analogs may be used - e.g., other N-alkylated or N- acylated amino acids.
  • molecules containing modified (N-alkylated or N-acylated) tryptophan and containing a fluorescent label that is attached directly to the modified tryptophan or to an amino acid within 1-10 amino acids of the modified tryptophan will produce a fluorescent signal that is substantially stronger (e.g., 2-5 times or 2-10 times stronger) than the fluorescent signal that would be produced if the same molecule were made using natural (not modified) tryptophan.
  • Natural tryptophan can be modified to replace the hydrogen at the 1 -nitrogen position of the indole ring with an alkyl or acyl group to produce a modified tryptophan residue, which may then be used in the preparation of various molecules of the present disclosure using known techniques of chemical synthesis, including known methods of peptide synthesis and fluorescence coupling.
  • modified tryptophan compounds are commercially available or may be prepared as described below:
  • 1 -methyl tryptophan is commercially available (Aldrich Cat. No. 447439). Surprisingly, caspase probes containing methylated tryptophan are synthesized in higher yield than the same caspase probes containing natural tryptophan.
  • 1-trifluoromethyl tryptophan can be synthesized by direct electrophilic trifluoromethylation of the indole nitrogen using a hypervalent iodine reagent. Niedermann et al., Angew Chem Int Ed, 51(26):6511-15 (2012).
  • 1 -acetyl tryptophan can be synthesized according to known methods of chemical synthesis, including acetylation techniques.
  • 1-trifluoroacetyl tryptophan can be synthesized according to known methods of chemical synthesis, including acetylation and fluorination techniques.
  • any of the foregoing compounds can be used as a building block in the same manner as natural tryptophan using known techniques of peptide synthesis to make short or long chain peptides and proteins.
  • fluorescent molecules comprising 1-10 amino acids can be synthesized using liquid phase peptide synthesis (Bodanszky, Principles of Peptide Synthesis (1993)) or solid phase peptide synthesis (Merrifield, J Amer Chem Soc 85(14):2149-54 (1963); Amblard et al., Mol. Biotechnol, 33(3):239-54 (2006)).
  • a suitable liquid phase peptide synthetic pathway is shown below, and generally involves building oligo peptides from the N-terminus of an amino acid by providing a first amino acid (1); protecting or blocking the N-terminus of the amino acid using a protecting or blocking group (e.g., BOC or FMOC); coupling the first amino acid with a C-terminal ester of a second amino acid (2) by reacting the amino acids in the presence of a coupling agent (e.g., dicyclohexyl carbodiimide (DCC), diisopropyl carbodiimide (DIC), usually in the presence of N-hydroxysuccinimide or 1-hydroxybenzotriazole) to form a dipeptide (3); and deprotecting the dipeptide without removing any other protecting groups to yield the free dipeptide acid (4).
  • a coupling agent e.g., dicyclohexyl carbodiimide (DCC), diisopropyl carbodiimide (DIC), usually in the presence of N
  • the dipeptide (4) can be coupled to the suitably derivatized L-aspartic acid ⁇ -methyl ester to yield a desired caspase inhibitor or it can be coupled with a suitably protected amino acid to yield a fully protected tripeptide (5). If desired, by sequential deprotection of the C- terminus of (5) and analogous coupling to another suitably protected amino acid, a fully protected tetrapeptide may be constructed.
  • the molecule is a caspase probe that is prepared by finishing the peptide chain with an aspartic acid portion and adding a fluoromethyl ketone (FMK), benzoyloxymethyl ketone (BMK) or phenoxymethyl ketone (PMK) to the end of the peptide chain as a leaving group that is part of the reactive group and is positioned at the C- terminus of the recognition sequence of the caspase probe.
  • FMK fluoromethyl ketone
  • BMK benzoyloxymethyl ketone
  • PMK phenoxymethyl ketone
  • FMK/BMK/PMK can be attached to the a-carboxylic acid via a methylene group, introduced using diazomethane chemistry.
  • This general synthetic strategy also applies to fluorescent labels that may be attached to one or more amino acids by known peptide coupling techniques.
  • the fluorescent molecule comprises a sequence of 1-10, such as 1-5, natural or synthetic amino acids or combinations thereof, wherein at least one amino acid is a modified tryptophan of Formula (I):
  • R is selected from -(CH 2 ) n X and -(CO)(CH 2 ) n X, where n is 0-5 and X is H or -CF 3 ;
  • R 2 is selected from OH and the N-terminal group of another of the amino acids; and wherein the molecule produces a fluorescent signal that is stronger than a molecule that only differs by R being H.
  • Modified tryptophan molecules of the present disclosure include those containing methylated (including trifluoromethylated) tryptophan and a fluorescent label. Methylation of the indole nitrogen of tryptophan can block the fluorescence quenching due to the tryptophan molecule, allowing the fluorescent label to produce a substantially stronger signal. Examples of such methylated tryptophan molecules include, but are not limited to:
  • Modified tryptophan molecules of the present disclosure include those containing acylated (including trifluoroacylated) tryptophan and a fluorescent label. Acylation of the indole nitrogen of tryptophan can block the fluorescence of the tryptophan molecule, allowing the fluorescent label to produce a substantially stronger signal. Examples of such acylated tryptophan molecules include, but are not limited to:
  • Modified tryptophan molecules of the present disclosure may be incorporated into a wide variety of fluorescently labeled molecules.
  • One class of such molecules are caspase-1 probes.
  • Cellular pathways leading to inflammation involve the activation of members of a protease family of caspases. At least 14 members of the caspase family have been identified in vertebrates. See Saunders, et al., Anal. Biochem., 284, 114-24 (2000).
  • Some caspases e.g., caspase-1, caspase-4, caspase-5, caspase-1 1, caspase- 12 and caspase- 13
  • caspases e.g., caspase-1, caspase-4, caspase-5, caspase-1 1, caspase- 12 and caspase- 13
  • caspase-1 inflammation-related caspase
  • caspase-1 IL-1 converting enzyme
  • ICE-1 IL-1 converting enzyme
  • the detection of active caspases involved in inflammatory pathways indicates an acute or chronic inflammatory response - e.g., inflammation associated with inflammatory diseases such as rheumatoid arthritis or atherosclerosis.
  • One way to detect active caspases involves the use of probes that bind to active caspases and include a detectable group (e.g., a fluorescent label). There is a need to trace and monitor fluorescently labeled caspase probes that are detectable in vitro, in vivo, and ex vivo.
  • a detectable group e.g., a fluorescent label
  • the N-terminal group of a caspase probe may serve to protect the recognition sequence during synthesis of a caspase probe. Additionally, the N-terminal group may include a label. In at least one embodiment, the N-terminal group is absent - e.g., in some instances, an N-terminal protecting group is used during synthesis and may be present in an intermediate precursor of a caspase probe, but is removed to form the final caspase probe. In other words, the caspase probe may be deprotected, yielding a smaller, more cell permeable molecule.
  • an N-terminal protecting group may be present during synthesis in an intermediate precursor of a caspase probe, but may be removed and replaced with an N- terminal labeled moiety - i.e., the N-terminal group of a caspase probe intermediate may be different from the N-terminal group of a final caspase probe.
  • Each caspase probe recognition sequence comprises one or more amino acids and is able to bind to one or more caspases, and may allow the caspase probe to target structurally similar caspases with the same or different affinities and kinetics. For instance, caspase probes containing a recognition sequence comprising WEHD will selectively recognize and allow detection of caspase- 1 over other caspases.
  • Table 1 identifies recognition sequences of caspase probes disclosed herein, all of which are capable of selectively binding to inflammation-related active caspase- 1.
  • caspase probes of the present disclosure have the structure of Formula (II):
  • R 3 is selected from 780, ABzC, BODIPY, Cy5, FAM, N-AE, N-AM, and ORG;
  • X r is selected from W(N')E(OMe)HD(OMe), 5-F-W(N')E(OMe)HD, 2-CF 3 -W(N')E(OMe)HD, and 6-CF 3 W(N')E(OMe)HD, wherein N' is (NMe), (N-TFM), (N-Ac), or (N-TFA); and R4 is selected from halogen, phenol, and benzoylate.
  • halogen is selected from F, CI, and Br.
  • phenol has Formula A: Formula A: Formula A
  • R5, R6, R 7 , R , R 9 is each individually selected from H, F, CI, alkyl, aryl, aralkyl, amino, nitro, or carboxy.
  • at least one of R 5 , R ⁇ , R 7 , R , R 9 is H; and alkyl is C 1-10 alkyl, preferably C 1-6 alkyl.
  • the phenol is phenoxy.
  • benz late has Formula B:
  • R 5 , R ⁇ , R 7 , R 8 , R 9 is each individually selected from H, F, CI, alkyl, aryl, aralkyl, amino, nitro, or carboxy.
  • at least one of R 5 , 3 ⁇ 4, R 7 , Rg, R 9 is H; and alkyl is C 1-10 alkyl, preferably C 1- alkyl.
  • the benzoylate is benzoyloxy.
  • the caspase probes are cell permeant (i.e., exhibit good cell membrane permeability) and can selectively target caspases of interest inside the cells of a living organism.
  • cell permeable fluorescent dyes include, but are not limited to, sulforhodamine 101 (Texas Red), rhodamine dyes (e.g., rhodamine B, rhodamine 6G, rhodamine 19, rhodamine Green, TAMRA (carboxytetramethylrhodamine), TRITC (tetramethylrhodamine isothiocyanate), ROX (5',6-carboxyl-X-rhodamine)), indocyanine green, cyanine dyes (e.g., Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7), Marina Blue, Pacific Blue, Oregon Green dyes (e.g., Oregon Green 88, Oregon Green 514), tetramethylrhodamine
  • the caspase probes do not undergo facile metabolism in vivo, and possess a long half-life (e.g., more than 6 hours) or remain detectable throughout the life of the permeated cell.
  • Examples of compounds of Formula (II) in which X ⁇ is W(NMe)E(OMe)HD(OMe) include:
  • Cy5-W(NMe)E(OMe)HD(OMe)-BMK Cy5-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • BODIPY-W(NMe)E(OMe)HD(OMe)-FMK BODIPY-FL-N-methyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • BODIPY-W(NMe)E(OMe)HD(OMe)-PMK BODIPY-FL-N-methyl-L-tryptophanyl-
  • FAM-W(NMe)E(OMe)HD(OMe)-FMK FAM-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • FAM-W(NMe)E(OMe)HD(OMe)-PMK FAM-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • N-AE-W(NMe)E(OMe)HD(OMe)-BMK 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AE-W(NMe)E(OMe)HD(OMe)-FMK 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AE-W(NMe)E(OMe)HD(OMe)-PMK 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AM-W(NMe)E(OMe)HD(OMe)-BMK 4-aminomethyl-L-N-methyltryptophanyl-
  • N-AM-W(NMe)E(OMe)HD(OMe)-FMK 4-aminomethyl-L-N-methyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • ORGn-W(NMe)E(OMe)HD(OMe)-FMK ORGn-N-methyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • ORGn-W(NMe)E(OMe)HD(OMe)-PMK ORGn-N-methyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • Examples of compounds of Formula (II) in which X ⁇ is W(N-TFM)E(OMe)HD(OMe) include:
  • BODIPY-W( -TFM)E(OMe)HD(OMe)-BMK BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • BODIPY-W(N-TFM)E(OMe)HD(OMe)-FMK BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • BODIPY-W(N-TFM)E(OMe)HD(OMe)-PMK BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • FAM-W(N-TFM)E(OMe)HD(OMe)-FMK FAM-N-trifluoromethyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • N-AE-W(N-TFM)E(OMe)HD(OMe)-BMK 4-aminoethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AE-W(N-TFM)E(OMe)HD(OMe)-FMK 4-aminoethyl-L-N- trifluoromethyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AE-W(N-TFM)E(OMe)HD(OMe)-PM 4-aminoethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AM-W(N-TFM)E(OMe)HD(OMe)-BMK 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AM-W(N-TFM)E(OMe)HD(OMe)-FMK 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-W(N-TFM)E(OMe)HD(OMe)-PMK 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • ORGn- W(N-TFM)E(OMe)HD(OMe)-BMK ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • ORGn-W(N-TFM)E(OMe)HD(OMe)-FMK ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone • ORGn-W(N-TFM)E(OMe)HD(OMe)-PMK: ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • Examples of compounds of Formula (II) in which X ! is W(N-Ac)E(OMe)HD(OMe) include:
  • BODIPY-W(N-Ac)E(OMe)HD(OMe)-BMK BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • BODIPY-W(N-Ac)E(OMe)HD(OMe)-FMK BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • BODIPY-W(N-Ac)E(OMe)HD(OMe)-PMK BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • FAM-W(N-Ac)E(OMe)HD(OMe)-BMK FAM-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • FAM-W(N-Ac)E(OMe)HD(OMe)-FMK FAM-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • ORGn-W(N-Ac)E(OMe)HD(OMe)-BMK ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone • ORGn-W(N-Ac)E(OMe)HD(OMe)-FMK: ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • ORGn-W(N-Ac)E(OMe)HD(OMe)-PMK ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • Examples of compounds of Formula (II) in which Xi is W(N-TFA)E(OMe)HD(OMe) include:
  • BODIPY-W(N-TFA)E(OMe)HD(OMe)-FMK BODIPY-FL-N-trifluoroacetyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • BODIPY-W(N-TFA)E(OMe)HD(OMe)-PMK BODIPY-FL-N-trifluoroacetyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • FAM-W(N-TFA)E(OMe)HD(OMe)-BMK FAM-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • FAM-W(N-TFA)E(OMe)HD(OMe)-FMK FAM-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • ORGn-W(N-TFA)E(OMe)HD(OMe)-BMK ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • ORGn-W(N-TFA)E(OMe)HD(OMe)-FMK ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
  • ORGn-W(N-TFA)E(OMe)HD(OMe)-PMK ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • Examples of compounds of Formula (II) in which X ⁇ is 5-F-W(NMe)E(OMe)HD or 5-F-W(N-TFM)E(OMe)HD include:
  • BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-BMK BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-FMK BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-PMK BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • FAM-5-F-W(NMe)E(OMe)HD(OMe)-BMK FAM-D,L-5-fluoro-N- trif uoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • FAM-5-F-W(NMe)E(OMe)HD(OMe)-FMK FAM-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • FAM-5-F-W(NMe)E(OMe)HD(OMe)-PMK FAM-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AE-5-F-W(NMe)E(OMe)HD(OMe)-BMK N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
  • N-AE-5-F-W(NMe)E(OMe)HD(OMe)-FMK N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AE-5-F-W(NMe)E(OMe)HD(OMe)-PMK N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-BMK 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-FMK 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-PMK 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AM-5-F-W(NMe)E(OMe)HD(OMe)-BMK N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AM-5-F-W(NMe)E(OMe)HD(OMe)-FMK N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-5-F-W(NMe)E(OMe)HD(OMe)-PMK N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-BM 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-FMK 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-PMK 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • ORGn-5-F-W(NMe)E(OMe)HD(OMe)-BMK ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • ORGn-5-F-W(NMe)E(OMe)HD(OMe)-FM ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
  • ORGn-5-F-W(NMe)E(OMe)HD(OMe)-PMK ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
  • Examples of compounds of Formula (II) in which X] is 2-CF 3 -W(NMe)E(OMe)HD or 2-CF 3 -W(N-TFM)E(OMe)HD include:
  • FAM-2-CF 3 W(NMe)E(OMe)HD(OMe)-PMK FAM-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
  • N-AE-2-CF 3 W(N-TFM)E(OMe)HD(OMe)-BM 4-aminoethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AM-2-CF 3 W(N-TFM)E(OMe)HD(OMe)-BM 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AM-2-CF 3 W(N-TFM)E(OMe)HD(OMe)-FM : 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-2-CF 3 W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
  • Examples of compounds of Formula (II) in which X is 6-CF 3 W(NMe)E(OMe)HD or 6-CF 3 W(N-TFM)E(OMe)HD include:
  • BODIPY-6-CF 3 W(NMe)E(OMe)HD(OMe)-BM BODIPY-D,L-6-trifluoromethyl- N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
  • N-AE-6-CF 3 W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminoethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-6-CF 3 W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminomethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
  • N-AM-6-CF 3 W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
  • the caspase probes are used for in vivo detection of caspase-mediated inflammation to assess diseases/conditions associated with inflammation. Inflammation is associated with a wide range of chronic and acute disorders.
  • the caspase probes may be used to assess caspase-mediated inflammation associated with a wide range of diseases and conditions, including but not limited to: ulcerative colitis, endotoxic shock, rheumatoid arthritis, juvenile arthritis, osteoarthritis, psoriasis, Crohn's disease, inflammatory bowel disease, multiple sclerosis, insulin dependent diabetes mellitus, gout, psoriatic arthritis, reactive arthritis, viral or post- viral arthritis, and ankylosing spondylarthritis.
  • diseases and conditions including but not limited to: ulcerative colitis, endotoxic shock, rheumatoid arthritis, juvenile arthritis, osteoarthritis, psoriasis, Crohn's disease, inflammatory bowel disease, multiple sclerosis, insulin dependent diabetes mellitus, gout, psoriatic arthritis, reactive arthritis, viral or post- viral arthritis, and ankylosing spondylarthritis.
  • the caspase probes are used for in vitro or in vivo detection of caspase-mediated inflammation to assess the health of a transplant organ or transplanted tissue (pre- and post-transplant), a diseased organ or diseased tissue, or a traumatized organ or traumatized tissue since inflammation can be indicative of impairment.
  • the caspase probes can also be used in drug development.
  • the process of drug development, from start to commercialization is very long and involves numerous steps including identifying in vitro lead drug candidates from a million of compounds, pre-clinical development using in vivo animal models, and finally, clinical trials in humans.
  • High-throughput in vitro screening is a widely used method during the initial stages of drug development, and allows for the simultaneous evaluation of millions of compounds under a given condition. It involves the screening of the candidate therapy compound library against the specific drug target directly or in a more complex assay system.
  • high throughput screen can involve screening a candidate therapy compound library in a cell-based assay, where the activity of the candidate compound is intended to affect the incidence of inflammation. This type of screen can be carried out using cells cultured in multiwell plates with automated operation. Since the ultimate outcome desired by the candidate compound is the effect on inflammation, the caspase probes can be used in cell based screens to quantify the incidence of inflammation in response to tested drug candidates.
  • Caspase probes can also be used for evaluating and/or predicting the efficacy of a particular therapeutic treatment (e.g., an anti-inflammatory), as well as for determining drug- induced impairment or toxicity (e.g., evaluating side effects of a drug treatment by assessing collateral damage to non-target organs).
  • a particular therapeutic treatment e.g., an anti-inflammatory
  • drug- induced impairment or toxicity e.g., evaluating side effects of a drug treatment by assessing collateral damage to non-target organs.
  • the efficacy of an anti-inflammatory could be assessed by administering the anti-inflammatory to a subject, administering in vivo an effective amount of a caspase probe to the subject, and then detecting the degree of inflammation, such that detection of inflammation at or below a predetermined level indicates efficacy of the anti-inflammatory treatment.
  • the subject's naturally occurring level of inflammation could be assessed before the anti- inflammatory treatment as well in order to determine how much inflammation decreases due to administration of the therapy.
  • organs or targets that may be assessed using the caspase probes include, but are not limited to: eye, breast, heart, brain and central nervous system (CNS), kidneys, lungs, liver, skin, pancreas, skeletal system, connective tissue (e.g., joints), stomach, upper gastrointestinal tract, lower gastrointestinal tract, circulatory system (e.g., blood), lymphatic system, sexual organs (male and female), prostate, embryologic tissue, muscular system, and gallbladder.
  • CNS central nervous system
  • the caspase probes may also be used for whole-body imaging to assess inflammation throughout a living organism.
  • the caspase probe is delivered in vitro to a biological sample (e.g., a blood sample, tissue sample, cell suspension, cellular extract, or tissue homogenate) by direct application of the probe to the sample.
  • a biological sample e.g., a blood sample, tissue sample, cell suspension, cellular extract, or tissue homogenate
  • the caspase probes exhibit good cell permeability, there is no need to use additional reagents to facilitate the entry of the probes into cells.
  • the caspase probe is reconstituted in DMSO, further diluted in phosphate buffered saline (PBS) or cell culture media and applied directly to cells in a cell culture dish.
  • PBS phosphate buffered saline
  • caspase-probe complexes After an incubation period under the conditions sufficient for the formation of caspase-probe complexes (1 hour at 37°C), cells are washed with PBS containing 1% of bovine serum albumin (BSA). To determine whether cells exhibit inflammation, the incidence of inflammation can be evaluated by subjecting the biological sample to a means for detecting caspase-1 -probe complexes.
  • BSA bovine serum albumin
  • the caspase probe is administered in vivo to a subject (e.g., animal or human) orally, intravenously, intraperitoneally, intramuscularly, subcutaneously, topically, and/or by direct application to a target organ.
  • the caspase probe is diluted in 10X injection buffer.
  • the injection buffer is PBS.
  • the caspase probes are administered in an effective amount, which is an amount that is sufficient to provide meaningful results with respect to the intended purpose - e.g., diagnostic, drug development, etc.
  • the caspase probe is present in a composition, wherein the composition comprises at least a caspase probe and an excipient.
  • the excipient is a pharmaceutically acceptable excipient.
  • suitable excipients include, but are not limited to, adhesives, binders, bulking agents, carriers, colors, diluents, disintegrating agents, fillers, glidants, granulating agents, lubricating agents, polymers, preservatives, wetting agents, and combinations thereof.
  • one or more excipients is selected from sucrose, lactose, cellulose, gelatin, polyvinylpyrrolidone, and polyethylene glycol.
  • caspase probe to administer depends, in part, on the target for administration. For example, to assess inflammation in the kidney, it is preferable to administer a hydrophilic caspase probe because non-hydrophilic caspase probes are likely to be excreted by the kidney via urinary excretion, and decreases the chance of the administered probes to be detected above background noise in that organ. Put another way, administration of a non-hydrophilic caspase probe increases the possibility of background noise due to unbound caspase probes accumulating in the kidney as unbound probes are eliminated.
  • a non- lipophilic caspase probe e.g., probes containing a trifluoromethyl group
  • administration of a lipophilic probe increases the possibility of background noise from unbound caspase probes as unbound probes are processed through the liver.
  • kits of the present disclosure are used for detecting and quantifying the incidence of inflammation in a biological sample.
  • the kit may comprise one or more caspase probes, one or more buffers (e.g., buffers for delivery of caspase probes to samples), and optionally one or more non-specific fluorescence probes that can be used as a control.
  • Suitable non-specific fluorescence control probes include, but are not limited to DY 680 carboxylic acid, DY 750 carboxylic acid, DY 780 carboxylic acid, BODIPY-FL, BODIPY- TMR, and BODIPY-TR.
  • the choice of control fluorescent dye will match the fluorescent label on the probe.
  • the kit may further include packaging materials with instructions for using the components of the kit, such as how to combine caspase probes with buffers, how to use the caspase probes provided in the kit, storage conditions, etc.
  • Components of the kit may be provided in separate containers (e.g., vials) or combined.
  • the buffer is an injection buffer (e.g., in vivo) or a wash buffer (e.g., in vitro).
  • the buffer may be 10X PBS, which is suitable for use as either an injection buffer or wash buffer.
  • the buffer is provided in an amount of 10-50 niL, more preferably 15-30 mL.
  • the probe is provided in an amount of 25- 500 ⁇ g, more preferably 30-350 ⁇ g.
  • the caspase probe is reconstituted in DMSO, and then optionally diluted in sterile IX PBS.
  • a 1 OX PBS buffer can be diluted to IX PBS using water - e.g., distilled water, water-for-injection, etc.
  • the buffer is supplied at a 2X concentration, and is diluted to IX using an equal amount of water.
  • buffers include, but are not limited to, tris (tris-hydroxymethylamino- methane) buffer (20mM, pH 7.4) and Hanks balanced salt solutions (available from Life Technologies) buffered with 20mM Hepes (4-(2-hydroxyethyl)-l-piperazineethanesulfonic acid).
  • the buffer is a pharmaceutically acceptable buffer.
  • a suitable injection buffer may be prepared according to the following recipe in endotoxin free DI H 2 0: 87.66 g/L of NaCl (1.5 M), 60.53 g/L of Na 2 HP0 4 »12H 2 0+4.84 g/L of NaH 2 P0 4 » 2H 2 0 (0.2 M phosphate), pH 6.9.
  • N-Methyl substitution on fluorescently labeled N-methyl tryptophan prevents tryptophan-induced quenching and maintains caspase- 1 recognition
  • human monocyte cells are cultured in the presence of 10 ⁇ g/mL of phytohemagglutin (PHA; Life Technologies) for 3.5 hours at 37°C.
  • PHA phytohemagglutin
  • Control THP-1 cells are similarly cultured but in the absence of PHA.
  • the cultured cells are plated at a concentration of 10 6 cells per 1 mL of medium.
  • FAM- W(NMe)E(OMe)HD(OMe)-FMK or PROBO Green- W(NMe)E(OMe)HD(OMe)-FMK is added to separately plated cells, and is allowed to incubate for 20 minutes. Subsequent to incubation, cells are washed with PBS, and harvested for flow cytometry analysis.
  • This prophetic example relates to the substantial increase in fluorescence intensity from a fluorescent label attached to a molecule containing modified tryptophan (Compound 1), as compared to the same fluorescently labeled molecule containing natural tryptophan (Comparative Compound 1A).
  • 1-Methyl-L-tryptophan (1-Me-W; Aldrich Cat. No. 447439) is dissolved in the minimum amount of water and carefully treated with one equivalent of IN sodium hydroxide (NaOH) solution. Then 1.5 equivalents of FMOC chloride (Aldrich Cat. No. 23185) and 1.5 equivalents of IN NaOH are added alternately with stirring and cooling (ice-bath) under Schotten-Baumann conditions. After addition of both reagents is complete, the reaction mixture is stirred and allowed to warm slowly to room temperature for one hour. The reaction mixture is carefully acidified to pH about 2 with IN hydrochloric acid (HC1) to yield an off- white solid. This material is collected by vacuum filtration and dried in a vacuum dessicator to yield the desired product, N-FMOC-l-methyl-L-tryptophan. The material is stored at - 20°C until needed.
  • N-FMOC-l-methyl-L-tryptophan from Step (1) is dissolved in dry tetrahydrofuran (THF; Aldrich; Cat. No. 401757) and treated with diisopropylcarbodiimide (DIC; Fluka Cat. No. 38370) dissolved in anhydrous THF. Immediately thereafter, L-glutamic acid 5-methyl ester 2-t-butyl ester in anhydrous THF is added to the stirring suspension.
  • THF dry tetrahydrofuran
  • DIC diisopropylcarbodiimide
  • reaction is allowed to proceed for one hour at room temperature (r.t), filtered to remove solid diisopropylurea, and then the solvent is removed by rotary evaporation to yield N-FMOC- 1- Methyl-L-tryptophanyl-L-glutamic acid ⁇ -methyl ester a-t-butyl ester as a low-melting solid.
  • This material is stored dessicated at -20°C until needed.
  • N-FMOC-l-methyl-L-tryptophanyl-L-glutamic acid ⁇ -methyl ester a-t-butyl ester from Step (2) is dissolved in anhydrous ethyl ether (Aldrich Cat. No. 67381 1) and treated with a stream of hydrogen chloride gas. After 15 minutes, the resulting reaction mixture is rotary evaporated at r.t. to yield the free acid, N-FMOC- L-tryptophanyl-L-glutamic acid ⁇ - methyl ester, which is stored frozen in a vacuum dessicator until needed.
  • N-FMOC- 1-methyl-L-tryptophanyl-L-glutamic acid ⁇ -methyl ester from Step (3) is dissolved in dry tetrahydrofuran (THF; Aldrich; Cat. No. 401757) and then treated with diisopropylcarbodiimide (DIC; Fluka Cat. No. 38370) dissolved in anhydrous THF. Immediately thereafter, L-histidine-Nn-FMOC t-butyl ester in anhydrous THF is added to the stirring suspension.
  • THF dry tetrahydrofuran
  • DIC diisopropylcarbodiimide
  • reaction is allowed to proceed for one hour at room temperature (r.t.), filtered to remove solid diisopropylurea, and then the solvent is removed by rotary evaporation to yield N-FMOC-L-tryptophanyl-L-glutamyl ⁇ -methyl ester-L-histidine- ⁇ - FMOC t-butyl ester.
  • This material is stored frozen in a vacuum dessicator until needed.
  • N-FMOC- 1 -methyl-L-tryptophanyl-L-glutamyl ⁇ -methyl ester- L-histidine-N7r-FMOC t-butyl ester from Step (4) is dissolved in anhydrous ethyl ether (Aldrich Cat. No. 67381 1) and treated with a stream of hydrogen chloride gas. After 15 minutes, the resulting reaction mixture is rotary evaporated at r.t. to yield the free acid N-FMOC-L-tryptophanyl-L-glutamyl ⁇ -methyl ester-L-histidine-N7c-FMOC. This material is stored frozen in a vacuum dessicator until needed.
  • N-FMOC- 1 -methyl-L-tryptophanyl-L-glutamyl ⁇ -methyl ester-L-histidyl-N -FMOC from Step 5 is dissolved in a mixture of piperidine (Aldrich Cat. No. 104094) and dimethylformamide (AlfaAesar Cat. No. A13547) at r.t. for 10 minutes. The solvent is removed at r.t. by rotary evaporation and is air dried in a vacuum dessicator.
  • 1-Methyl-L- tryptophanyl-L-glutamyl ⁇ -methyl ester-L-histidine is stored at -20°C and protected from light and moisture until needed.
  • 5-FAM-N-hydroxysuccinimido ester (AnaSpec Cat. No. AS-81007) is dissolved in acetonitrile (Fisher Cat. No. 01034) in a round-bottomed flask covered with foil to exclude light, and treated with 1-methyl-L-tryptophanyl-L-glutan yl ⁇ -methyl ester-L-histidine from Step 6 and 1 equivalent of triethylamine (Aldrich Cat. No. T0886) dissolved in acetonitrile (Aldrich Cat. No. 271004). The reaction is monitored by tic until complete (about 2 hours).
  • reaction mixture is quickly filtered in the dark and the solvent is removed by rotary evaporation using a dark round-bottomed flask to yield 5-Carboxyfluoresceinyl-l-methyl-L- tryptophanyl-L-glutamyl ⁇ -methyl ester-L-histidine as a colored solid.
  • This material is stored frozen, and protected from light and moisture until needed.
  • 5-Carboxyfluoresceinyl- 1 -methyl-L-tryptophanyl-L-glutamyl ⁇ -methyl ester-L- histidine from Step 7 is dissolved in methylene chloride (Fisher Cat. No. D150) and treated with stirring while cooling in an ice bath with an equimolar amount of L-aspartic acid ⁇ - methyl ester fluoromethyl ketone hydrochloride (American Peptide Corporation) and an equimolar amount of diisopropylethylamine (DIEA; Aldrich Cat. No. D125806).
  • DIEA diisopropylethylamine
  • Comparative Compound 1 A is synthesized in the same manner as Compound 1 except that L-tryptophan is used in place of 1-Methyl-L-tryptophan as a starting material. Following the synthesis of Compound 1 and Comparative Compound 1A, excitation and emission spectra are obtained for the fluorescently labeled tryptophans on each compound, and quantum yields are also determined. The spectral data are compiled using a Molecular Devices SpectraMax M2 Plate Reader.
  • a molecule containing modified tryptophan produces a fluorescent signal that is substantially stronger (e.g., 2-5 times or 2-10 times stronger) than the fluorescent signal produced by a molecule that differs only in that it contains natural (not modified) tryptophan.
  • THP-1 cells human monocyte cell line

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Abstract

The present disclosure relates to new fluorescent molecules that contain N-alkylated or N-acylated tryptophan and do not substantially quench fluorescent labels attached to the molecules, and the use of such molecules in preparing and studying various compounds, such as substrates and inhibitors for assays of enzymes (e.g., caspases, such as caspase-1 which is an important enzyme in inflammation). An enzyme substrate or enzyme inhibitor that contains a modified tryptophan and fluorescent label as disclosed herein can be studied without loss of signal by Förster quenching. By reducing or eliminating this quenching, more useful labeled molecules with improved properties for assay development can be prepared.

Description

FLUORESCENTLY LABELED MOLECULES CONTAINING
MODIFIED TRYPTOPHAN
PRIORITY
This application claims priority to United States Provisional Application Number 62/116,815, filed 16 February 2015. The entire content is hereby incorporated herein by reference.
FIELD
The present disclosure relates to new fluorescent molecules that contain N-alkylated or N-acylated tryptophan and do not substantially quench fluorescent labels attached to the molecules, and the use of such molecules in preparing and studying various compounds, such as substrates and inhibitors for assays of enzymes (e.g., caspases, such as caspase-1 which is an important enzyme in inflammation). An enzyme substrate or enzyme inhibitor that contains a modified tryptophan and fluorescent label as disclosed herein can be studied without loss of signal by Forster quenching. By reducing or eliminating this quenching, more useful labeled molecules with improved properties for assay development can be prepared.
BACKGROUND
Tryptophan (Tip or W) is one of 20 amino acids naturally occurring in proteins. Only the L-stereoisomer of tryptophan is found in proteins. A distinguishing structural characteristic of tryptophan is its indole ring.
Figure imgf000002_0001
Tryptophan
Tryptophan occurs at the P4 position in one of the sequences of the interleukin- converting enzyme (ICE; also known as caspase-1) cleavage site. Shen et al., Atherosclerosis, 210(2):422-29 (2010). An amino acid recognition sequence often employed in synthetic inhibitors and synthetic substrates of caspase-1 is WEHD (tryptophan, glutamic acid, histidine, aspartic acid). Tryptophan is a fluorescent amino acid with an emission maximum of -360 nm and a quantum yield (□) of -0.14. Because tryptophan is intrinsically fluorescent, it is subject to and can cause Forster resonance energy transfer, with a Forster radius of 40A. When a fluorescent label such as fluorescein (with a Forster radius of 44A) or BODIPY (with a Forster radius of 57A) is attached to a molecule containing tryptophan (e.g., attached to the N-terminal tryptophan in WEHD) the fluorescent label and the tryptophan moieties are well within range to cause Forster resonance energy transfer, which quenches the fluorescence of each moiety. This appears to render fluorescently labeled caspase-1 probes, such as BODIPY-WEHD-fluoromethylketone, relatively useless because the fluorescence of the label is significantly decreased by the tryptophan-induced quenching.
The average length of a peptide or amide bond is about 1.33 A (Marsh et al., Adv
Protein Chem, 22:249 (1967)). Because Forster resonance energy transfer depends on the 6th power of distance, the energy transfer greatly depends on the distance of the label from the indole ring of tryptophan.
Steady-state and time-resolved fluorescence measurements have been reported to exhibit pronounced quenching efficiency of a number of dyes by tryptophan. In particular, red-absorbing dyes ATTO 655 and ATTO 680 are strongly quenched almost exclusively by tryptophan due to the formation of weak or non-fluorescent ground-state complexes. Rhodamine, fluorescein, and bora-diaza-indacene derivatives that absorb at shorter wavelengths are also substantially quenched. Labeling of dyes on tryptophan, tryptophan- containing peptides and proteins has demonstrated that these fluorescence quenching processes make it difficult to develop fluorescence-based diagnostic assays with tryptophan- containing peptides. (Marme et al., Bioconjugate Chem, 14:1 133-39 (2003)).
Even if a standard linker is inserted between tryptophan and the fluorescent label, the flexibility of the linker can still allow for the relatively flat fluorescent dye molecule to come into proximity with the relatively flat indole ring of tryptophan and lead to a type of stacking in which charge transfer processes quench the fluorescent signal. (Gudgin et al., Mol Immunol, 22:45-55 (1985)).
As a result of these natural phenomena, researchers have used non-tryptophan- containing sequences, such as YVAD, to study inhibition of caspase-1 with fluorescently labeled probes. However, it has been shown (Garcia-Calvo et al., J Biol Chem, 273:32608-13 (1998)) that YVAD is about 13.5 times less selective for caspase-1 than is WEHD. Thus, a molecule that looks and acts like WEHD and which does not quench fluorescence would be very important for mechanistic studies and assays involving caspase-1 and caspase-mediated inflammation. Direct study of caspase-1 using the most selective recognition sequences and the brightest probes will be a great help to researchers and clinicians who study or monitor inflammation, which will in turn make it easier to discover drugs that can be used in the treatment of inflammation.
Since the molecules disclosed herein can be used in a variety of compounds (e.g., caspase-1 probes, polycaspase probes, probes of other serine proteases, etc.), they provide far-reaching advantages in studying fluorescently labeled molecules containing tryptophan. In other words, there is a need for tryptophan-containing molecules that will not quench the fluorescence of attached fluorescent labels.
SUMMARY
In one aspect, the present disclosure relates to a fluorescent molecule comprising a sequence of 1-10 natural or synthetic amino acids, wherein at least one amino acid is a modified tryptophan of formula (I)
Figure imgf000004_0001
wherein R is selected from -(CH2)nX and -(CO)(CH2)nX, where n is 0-5 and X is H or -CF3; Ri is selected from Y and LY, where Y is a fluorescent label, and L is selected from -CH2-NH-, -(CH2)2-NH-, -C(=0)-CH2-NH-, -C(=0)-0-CH2-C6H6-NH-, and -C(=0)-0- CH2-C6H6-CH2-NH-; and R2 is selected from OH and the N-terminal group of another of the amino acids; wherein the molecule produces a fluorescent signal that is stronger than a molecule that only differs by R being H. In another aspect, the fluorescent molecule comprises 1-5 natural or synthetic amino acids. In another aspect, R2 is OH. In another aspect, R is -(CH2)nX, n is 1, and X is H. In another aspect, R is -(CH2)nX, n is 0, and X is - CF3. In another aspect, R is -{CO)(CH2)nX, n is 0, and X is -CF3. In another aspect, R is - (CO)(CH2)nX, n is 1, and X is H.
In another aspect, the fluorescent label is a dye selected from pyrene dyes, indacene dyes, cyanine dyes, fluorescein dyes, rhodamine dyes, sulforhodamine dyes, and IR dyes. Preferably, the dye is selected from Cascade Blue, BODIPY, Alexa Fluors, DyLight dyes, FAM, fluorescein isothiocyanate, Cy5, Rhodamine Green, Rhodol Green, Oregon Green dyes, 4,5-dichloro carboxy fluorescein, 5'-hexachloro-fluorescein, carboxytetramethylrhodamine, tetramethylrhodamine, sulforhodamines, 5',6-carboxyl-X- rhodamine, iFluor dyes, and Tide Fluor dyes. In another aspect, the amino acids comprise the following in order: the modified tryptophan of formula (I), glutamic acid, histidine, and aspartic acid.
In another aspect, the present disclosure relates to a fluorescent caspase probe of Formula (II):
R3 Xi R4 (n)
wherein R3 is selected from 780, ABzC, BODIPY, Cy5, FAM, N-AE, N-AM, and ORGn; Xi is selected from W(N')E(OMe)HD(OMe), 5-F-W(N')E(OMe)HD, 2-CF3-W(N')E(OMe)HD, and 6-CF3W(N')E(OMe)HD, wherein N' is (NMe), (N-TFM), (N-Ac), or (N-TFA); and R4 is selected from halogen, phenol, and benzoylate.
In another aspect, the present disclosure relates to a method of determining in vivo the incidence of inflammation in a living organism, comprising the steps of: (i) administering in vivo a fluorescent caspase probe to a living organism; (ii) subjecting the living organism to a means for in vivo detection of caspase-1 -probe complexes; and (iii) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes. In another aspect, the in vivo detection is performed on at least one portion of the living organism selected from eye, breast, heart, brain and central nervous system, kidney, lung, liver, skin, pancreas, skeletal system, connective tissue, stomach, upper gastrointestinal tract, lower gastrointestinal tract, circulatory system, lymphatic system, sexual organ, prostate, embryologic tissue, muscular system, and gallbladder. In another aspect, the method further comprises the steps of: (a) before administering the probe in step (i), administering in vivo a candidate therapy intended to induce inflammation in the living organism; and (b) after step (iii), determining whether the candidate therapy induces or inhibits inflammation as indicated by the detected presence or absence of caspase-1 -probe complexes, respectively.
In another aspect, the present disclosure relates to a method of determining ex vivo the incidence of inflammation in a biological sample extracted from a living organism, comprising the steps of: (i) administering in vivo a fluorescent caspase probe to a portion of a living organism; (ii) extracting a biological sample from the portion of the living organism; (iii) subjecting the biological sample to a means for ex vivo detection of caspase-1 -probe complexes; and (iv) determining the incidence of inflammation as indicated by the presence or absence of caspase- 1 -probe complexes.
In another aspect, the present disclosure relates to a method of determining in vitro the incidence of inflammation in a biological sample, comprising the steps of: (i) adding a fluorescent caspase probe to a biological sample; (ii) incubating the sample with the probe under conditions sufficient to form caspase-1 -probe complexes; (iii) subjecting the sample of step (ii) to a means for detecting caspase-1 -probe complexes; and (iv) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes. In another aspect, the method further comprises the step of inducing inflammation in the biological sample before adding the probe in step (i). In another aspect, the biological sample is selected from a blood sample, tissue sample, cell suspension, cellular extract, and tissue homogenate.
In another aspect, the present disclosure relates to a composition comprising a fluorescent caspase probe and an excipient.
In another aspect, the present disclosure relates to a kit comprising a fluorescent caspase probe, a buffer, and packaging materials.
BRIEF DESCRIPTION OF FIGURES
Figure 1: The fluorescent Caspase-1 probe 5-FAM-W(NMe)E(OMe)HD(OMe)- FMK was synthesized at 90% purity per the process described in Prophetic Example 2; it was characterized using HPLC-MS. Figure 1 shows High Performance Liquid Chromatography (HPLC) characterization of the synthesized 5-FAM-W(NMe)E(OMe)HD(OMe)-FMK compound: Wavelength: 215 nm; Flow rate: 1.2 mL/min; Buffer A: 0.1% TF A in water; Buffer B: 0.1%TFA in acetonitrile; Temperature: 45 °C; Column: Discovery, CI 8, 4.6mm x 250 mm, 5 micron, gradient (linear): 30% - 50% buffer B in 20 minutes; Injector volumn: 20 microliters.
Figure 2: The fluorescent Caspase-1 probe 5-FAM-W(NMe)E(OMe)HD(OMe)- FM was synthesized at 90% purity per the process described in Prophetic Example 2, characterized using HPLC-MS. Figure 2 shows Mass Spectrometry (MS) characterization of the synthesized 5-FAM-W(NMe)E(OMe)HD(OMe)-FMK compound.
Figure 3: Median Fluorescence Intensity (MFI) of PHA-activated THP-1 cells labeled with FAM- WEHD-FMK. THP-1 cells (human monocyte cell line) were activated with 10 μg/ml PHA (phytohemagglutinin) for 3.5 hours at 37°C followed by labeling with 5- F AM- W(NMe)E(OMe)HD(OMe)-FMK_(0.75 μΜ) for 20 minutes at 37°C. Cells were washed with PBS and analyzed using an Attune NxT flow cytometer. Activated and non- activated cells were gated by forward and side scatter properties and median fluorescence intensities of the each population was determined (non-activated = 554, activated = 2352). DETAILED DESCRIPTION
The present disclosure relates to fluorescently labeled molecules containing N- alkylated or N-acylated tryptophan that substantially reduces or eliminates loss of signal by Forster quenching, thus providing a molecule that produces a stronger fluorescent signal than a molecule differing only by containing natural, unmodified tryptophan instead of N- alkylated or N-acylated tryptophan. N-alkylated tryptophan includes, but is not limited to, substituting the hydrogen at the 1 -nitrogen position of the indole ring of tryptophan with a group selected from methyl, ethyl, propyl, butyl, pentyl, etc. N-acylated tryptophan includes, but is not limited to, substituting the hydrogen at the 1 -nitrogen position of the indole ring of tryptophan with a group selected from acetyl, ethylacetyl, propylacetyl, butylacetyl, pentylacetyl, etc. Also included are fluorinated derivatives of these alkyl and acyl groups.
Definitions
As used herein, the term "acylated" or refers to a compound to which an acyl group has been attached, wherein the "acyl" group is a carbonyl attached to an alkyl group that is a straight or branched, substituted or unsubstituted, saturated or unsaturated hydrocarbon-based chain having 1-5 carbon atoms. Suitable substituents include but are not limited to halogen, hydroxyl, Ci-3 alkyl, Ci-3 alkoxyl, and carboxyl groups.
As used herein, the term "alkylated" refers to a compound to which an alkyl group has been attached, wherein the "alkyl" group is a straight or branched, substituted or unsubstituted, saturated or unsaturated hydrocarbon-based chain having 1 -5 carbon atoms. Suitable substituents include but are not limited to halogen, hydroxyl, alkyl, alkoxyl, carbonyl, and carboxyl groups.
As used herein, the term "biological sample" refers to any type of material of biological origin, including but not limited to a blood sample, tissue sample, cell suspension, cellular extract, or tissue homogenate.
As used herein, the term "ex v vo" refers to processes or procedures performed on a biological sample (e.g., tissue, cells, blood, etc.) extracted from a living, multicellular organism following the in vivo administration of a caspase probe to the living organism. For example, ex vivo detection includes obtaining a biopsy extracted from a living subject (e.g., a mammal, such as a human) subsequent to in vivo administration of a caspase- 1 probe to that subject, and subjecting the biopsy to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which would be indicative of inflammation in the subject.
As used herein, the term "in vitro " refers to processes or procedures performed on a biological sample outside a living organism. For example, in vitro administration includes administering (i.e., delivering, applying, etc.) a caspase probe to a biological sample that is outside a living organism; and in vitro detection includes subjecting a biological sample (e.g., cells in a test tube or cultured dish) to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which could reflect whether a candidate therapy present in the sample induces or inhibits inflammation.
As used herein, the term "in vivo" refers to processes or procedures performed inside a living, multicellular organism. For example, in vivo administration includes administering a caspase probe to a living subject (e.g., a mammal, such as a human); and in vivo detection includes subjecting a living subject to a means for detecting caspase- 1 -probe complexes (e.g., fluorometry), which would be indicative of inflammation in the subject.
As used herein, the term "incidence" refers to the occurrence rate, frequency of an event, or the quantifiable degree to which an event occurs.
As used herein, the term "incubating", when used with respect to incubating a sample with a caspase probe, refers to exposure conditions (e.g., time, temperature, pH, etc.) sufficient for the formation of caspase-probe complexes.
As used herein, the term "label" (including "labeled," "labeled with," etc.) refers to a detectable moiety comprising one or more atoms.
As used herein, the term "N-terminal group" refers to a moiety attached to the N- terminal position of the recognition sequence of the caspase probes. The N-terminal group can be a detectable or non-detectable group.
As used herein, the term "reactive group" refers to a portion of the caspase probe that covalently binds to the active catalytic site of a caspase.
As used herein, the term "recognition sequence" refers to a portion of the caspase probes comprising a sequence of 1 to 6 natural amino acids or synthetic analogs thereof, which is selective for one or more caspases.
The following abbreviations, among others, may appear throughout this application: 780 = DyLight™ 780 Infrared Dye (infrared specialty dye having a benzopyrillium core and 1-3 sulfonates)
ABzC = 4-aminobenzyloxycarbonyl coupled to a fluorescent label such as 780, BODIPY, FAM, or ORGn
BOC = tert-butyloxycarbonyl
BMK = benzoyloxymethyl ketone
BODIPY = any BODIPY (boron-dipyrromethene) fluorescent dye, such as BODIPY-FL (boron-dipyrromethene fluorescent dye), BODIPY-TMR (boron-dipyrromethene tetramethylrhodamine dye), and BODIPY-TR (boron-dipyrromethene dye); structures shown
Figure imgf000009_0001
BODIPY-FL BODIPY-TMR BODIPY-TR
CF3 = trifluoromethyl
Cy5 = far red excitation dye (structure shown below)
DY 680 = far red excitation dye (structure shown below)
DY 750 = near-infrared excitation dye (structure shown below)
DY 780 = near-infrared excitation dye (structure shown below)
Figure imgf000009_0002
DY 680 DY 750
Figure imgf000010_0001
FAM = carboxyfluorescein, including 5-carboxyfluorescein, 6-carboxyfluorescein, or a mixture of 5- and 6-carboxyfluorescein
FMK = fluoromethyl ketone
FMOC = fluorenylmefhyloxycarbonyl
5-F-W = 5-fluorotryptophan
GFP = green fluorescent protein
HD = L-histidyl-L-aspartic acid
N-Ac= N-acylated
N-AE = N-aminoethyl coupled to a fluorescent label such as 780, BODIPY, FAM, or ORGn N-AM = N-aminomethyl coupled to a fluorescent label such as 780, BODIPY, FAM, or ORGn
NMe = N-methyl
N-TFA= N-trifluoroacetyl
N-TFM= N-trifluoromethyl
OMe = methyl ester, -C02CH3
ORGn = Oregon Green Dye (fluorinated fluorescein modified with or without pivaloyl groups)
PMK = phenoxymethyl ketone
TFA = trifluoroacetyl, -(CO)CF3
TFM = trifluoromethyl, -CF3
TMR = tetramethylrhodamine
VAD = L-valyl-L-alanyl-L-aspartic acid
WE = L-tryptophanyl-L-glutamic acid Label
The molecules containing modified tryptophan disclosed herein comprise one or more fluorescent labels that allow the probe to be detected by one or more detection techniques - e.g., fiuorometry. The label may be present in one or more parts of the molecule.
Suitable fluorescent labels include, but are not limited to, fluorescent proteins, such as green fluorescent protein (GFP) and modifications of GFP that have different absorption/emission properties, phycobiliproteins, complexes of certain rare earth metals (e.g., europium, samarium, terbium, or dysprosium), and fluorescent nanocrystals (quantum dots). Other suitable fluorescent dyes include, but are not limited to, sulforhodamine 101 (Texas Red), rhodamine dyes (e.g., rhodamine B, rhodamine 6G, rhodamine 19, rhodamine Green, TAMRA (carboxytetramethylrhodamine), TRITC (tetramethylrhodamine isothiocyanate), ROX (5',6-carboxyl-X-rhodamine)), indocyanine green, cyanine dyes (e.g., Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7), Marina Blue, Pacific Blue, Oregon Green dyes (e.g., Oregon Green 88, Oregon Green 514), tetramethylrhodamine, BODIPY dyes, Cascade Blue, fluoresceins (e.g., FAM, JOE (4,5-dichloro carboxy fluorescein), HEX (5'-hexachloro- fluorescein), FITC (fluorescein isothiocyanate)), Alexa Fluor dyes (e.g., Alexa Fluor 350, Alexa Fluor 430, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700, Alexa Fluor 750), DyLight dyes (e.g.,. DyLight780, DyLight 800CW), Rhodol Green, sulforhodamines, iFluor dyes, and Tide Fluor dyes. Preferably, the fluorescent dye has an absorption maximum in the visible (400-800 nm) or near infrared (800-2500 nm) region.
Use of Modified Tryptophan in Amino Acid Sequences
In general, the amino acid(s) disclosed herein may be D, L, or D, L mixtures. Additionally, various suitable synthetic analogs may be used - e.g., other N-alkylated or N- acylated amino acids. In accordance with the present disclosure, molecules containing modified (N-alkylated or N-acylated) tryptophan and containing a fluorescent label that is attached directly to the modified tryptophan or to an amino acid within 1-10 amino acids of the modified tryptophan will produce a fluorescent signal that is substantially stronger (e.g., 2-5 times or 2-10 times stronger) than the fluorescent signal that would be produced if the same molecule were made using natural (not modified) tryptophan. Synthesis of Modified Tryptophan
Natural tryptophan can be modified to replace the hydrogen at the 1 -nitrogen position of the indole ring with an alkyl or acyl group to produce a modified tryptophan residue, which may then be used in the preparation of various molecules of the present disclosure using known techniques of chemical synthesis, including known methods of peptide synthesis and fluorescence coupling. For example, the following modified tryptophan compounds are commercially available or may be prepared as described below:
(1) Synthesis of 1 -methyl tryptophan: 1 -methyl tryptophan is commercially available (Aldrich Cat. No. 447439). Surprisingly, caspase probes containing methylated tryptophan are synthesized in higher yield than the same caspase probes containing natural tryptophan.
(2) Synthesis of 1-trifluoromethyl tryptophan: 1-trifluoromethyl tryptophan can be synthesized by direct electrophilic trifluoromethylation of the indole nitrogen using a hypervalent iodine reagent. Niedermann et al., Angew Chem Int Ed, 51(26):6511-15 (2012).
(3) Synthesis of 1 -acetyl tryptophan: 1 -acetyl tryptophan can be synthesized according to known methods of chemical synthesis, including acetylation techniques.
(4) Synthesis of 1-trifluoroacetyl tryptophan: 1-trifluoroacetyl tryptophan can be synthesized according to known methods of chemical synthesis, including acetylation and fluorination techniques.
Given that the free amino and free acid groups of natural tryptophan are not changed during modification, commonly employed methods of synthesizing peptides in the C-terminal or N-terminal direction will be unaffected. Thus, any of the foregoing compounds can be used as a building block in the same manner as natural tryptophan using known techniques of peptide synthesis to make short or long chain peptides and proteins.
Synthesis of Molecules Containing Modified Tryptophan and Fluorescent Label(s)
According to at least one embodiment, fluorescent molecules comprising 1-10 amino acids can be synthesized using liquid phase peptide synthesis (Bodanszky, Principles of Peptide Synthesis (1993)) or solid phase peptide synthesis (Merrifield, J Amer Chem Soc 85(14):2149-54 (1963); Amblard et al., Mol. Biotechnol, 33(3):239-54 (2006)). An example of a suitable liquid phase peptide synthetic pathway is shown below, and generally involves building oligo peptides from the N-terminus of an amino acid by providing a first amino acid (1); protecting or blocking the N-terminus of the amino acid using a protecting or blocking group (e.g., BOC or FMOC); coupling the first amino acid with a C-terminal ester of a second amino acid (2) by reacting the amino acids in the presence of a coupling agent (e.g., dicyclohexyl carbodiimide (DCC), diisopropyl carbodiimide (DIC), usually in the presence of N-hydroxysuccinimide or 1-hydroxybenzotriazole) to form a dipeptide (3); and deprotecting the dipeptide without removing any other protecting groups to yield the free dipeptide acid (4). The dipeptide (4) can be coupled to the suitably derivatized L-aspartic acid β-methyl ester to yield a desired caspase inhibitor or it can be coupled with a suitably protected amino acid to yield a fully protected tripeptide (5). If desired, by sequential deprotection of the C- terminus of (5) and analogous coupling to another suitably protected amino acid, a fully protected tetrapeptide may be constructed.
Figure imgf000013_0001
In at least one embodiment, the molecule is a caspase probe that is prepared by finishing the peptide chain with an aspartic acid portion and adding a fluoromethyl ketone (FMK), benzoyloxymethyl ketone (BMK) or phenoxymethyl ketone (PMK) to the end of the peptide chain as a leaving group that is part of the reactive group and is positioned at the C- terminus of the recognition sequence of the caspase probe. Thus, relatively large quantities of BOC-L-aspartic acid β-methyl ester should be made. Alternatively, using a different protection strategy, FMOC-L-aspartic acid β-methyl ester may be made. From these molecules, FMK/BMK/PMK can be attached to the a-carboxylic acid via a methylene group, introduced using diazomethane chemistry. This general synthetic strategy also applies to fluorescent labels that may be attached to one or more amino acids by known peptide coupling techniques. General Structure of Fluorescently Labeled Molecules Containing Methylated or Acylated Tryptophan
In at least one embodiment, the fluorescent molecule comprises a sequence of 1-10, such as 1-5, natural or synthetic amino acids or combinations thereof, wherein at least one amino acid is a modified tryptophan of Formula (I):
Figure imgf000014_0001
wherein R is selected from -(CH2)nX and -(CO)(CH2)nX, where n is 0-5 and X is H or -CF3; R\ is selected from Y and LY, where Y is a fluorescent label, and L is a linker selected from -CH2-NH-, -(CH2)2-NH- -C(=0)-C¾-NH- -C(=0)-0-CH2-C6H6-NH- and -C(=0)-0- CH2-C6H6-CH2-NH-; R2 is selected from OH and the N-terminal group of another of the amino acids; and wherein the molecule produces a fluorescent signal that is stronger than a molecule that only differs by R being H.
Methylated Tryptophan in Fluorescently Labeled Tryptophan Derivatives
Modified tryptophan molecules of the present disclosure include those containing methylated (including trifluoromethylated) tryptophan and a fluorescent label. Methylation of the indole nitrogen of tryptophan can block the fluorescence quenching due to the tryptophan molecule, allowing the fluorescent label to produce a substantially stronger signal. Examples of such methylated tryptophan molecules include, but are not limited to:
• BOC- 1 -Me-W: N-BOC- 1 -methyl-L-tryptophan
· FMOC- 1 -Me- W: N-FMOC-l -methyl-L-tryptophan
• BOC- 1 -TFM-W: N-BOC- 1 -Trifluoromethyl-L-tryptophan
• FMOC- 1 -TFM-W : N-FMOC- 1 -Trifluoromethyl-L-tryptophan
Acylated Tryptophan in Fluorescently Labeled Tryptophan Derivatives
Modified tryptophan molecules of the present disclosure include those containing acylated (including trifluoroacylated) tryptophan and a fluorescent label. Acylation of the indole nitrogen of tryptophan can block the fluorescence of the tryptophan molecule, allowing the fluorescent label to produce a substantially stronger signal. Examples of such acylated tryptophan molecules include, but are not limited to:
• BOC-l-Ac-W: N-BOC- 1 -acetyl-L-tryptophan • FMOC-l-Ac-W: N-FMOC-l-acetyl-L-tryptophan
• BOC- 1 -TFA-W: N-BOC- 1 -trifluoroacetyl-L-tryptophan
• FMOC- 1 -TFA-W: N-FMOC- 1 -trifluoroacetyl-L-tryptophan Modified Tryptophan in Fluorescently Labeled Caspase-1 Probes
Modified tryptophan molecules of the present disclosure may be incorporated into a wide variety of fluorescently labeled molecules. One class of such molecules are caspase-1 probes. Cellular pathways leading to inflammation involve the activation of members of a protease family of caspases. At least 14 members of the caspase family have been identified in vertebrates. See Saunders, et al., Anal. Biochem., 284, 114-24 (2000). Some caspases (e.g., caspase-1, caspase-4, caspase-5, caspase-1 1, caspase- 12 and caspase- 13) are involved in inflammatory pathways. One such inflammation-related caspase (i.e., caspase-1) was first identified as an IL-1 converting enzyme (ICE-1) required for activation of the IL-1 beta and IL-18 cytokines in inflammatory responses. The detection of active caspases involved in inflammatory pathways indicates an acute or chronic inflammatory response - e.g., inflammation associated with inflammatory diseases such as rheumatoid arthritis or atherosclerosis.
During inflammation, high levels of active caspases are expressed. One way to detect active caspases involves the use of probes that bind to active caspases and include a detectable group (e.g., a fluorescent label). There is a need to trace and monitor fluorescently labeled caspase probes that are detectable in vitro, in vivo, and ex vivo.
Caspase Probe N-Terminal Group (Protecting Group)
The N-terminal group of a caspase probe may serve to protect the recognition sequence during synthesis of a caspase probe. Additionally, the N-terminal group may include a label. In at least one embodiment, the N-terminal group is absent - e.g., in some instances, an N-terminal protecting group is used during synthesis and may be present in an intermediate precursor of a caspase probe, but is removed to form the final caspase probe. In other words, the caspase probe may be deprotected, yielding a smaller, more cell permeable molecule. Alternatively, an N-terminal protecting group may be present during synthesis in an intermediate precursor of a caspase probe, but may be removed and replaced with an N- terminal labeled moiety - i.e., the N-terminal group of a caspase probe intermediate may be different from the N-terminal group of a final caspase probe. Caspase Probe Recognition Sequence
Each caspase probe recognition sequence comprises one or more amino acids and is able to bind to one or more caspases, and may allow the caspase probe to target structurally similar caspases with the same or different affinities and kinetics. For instance, caspase probes containing a recognition sequence comprising WEHD will selectively recognize and allow detection of caspase- 1 over other caspases.
Table 1 identifies recognition sequences of caspase probes disclosed herein, all of which are capable of selectively binding to inflammation-related active caspase- 1.
Table 1
Figure imgf000016_0001
According to at least one embodiment, caspase probes of the present disclosure have the structure of Formula (II):
R3 Xi R4 (Π)
wherein R3 is selected from 780, ABzC, BODIPY, Cy5, FAM, N-AE, N-AM, and ORG; Xr is selected from W(N')E(OMe)HD(OMe), 5-F-W(N')E(OMe)HD, 2-CF3-W(N')E(OMe)HD, and 6-CF3W(N')E(OMe)HD, wherein N' is (NMe), (N-TFM), (N-Ac), or (N-TFA); and R4 is selected from halogen, phenol, and benzoylate. In at least one embodiment, halogen is selected from F, CI, and Br. In at least one embodiment, phenol has Formula A: Formula A
Figure imgf000017_0001
wherein R5, R6, R7, R , R9 is each individually selected from H, F, CI, alkyl, aryl, aralkyl, amino, nitro, or carboxy. In a preferred embodiment, at least one of R5, R^, R7, R , R9 is H; and alkyl is C1-10 alkyl, preferably C1-6 alkyl. Preferably, the phenol is phenoxy. In at least one embodiment, benz late has Formula B:
Formula B
Figure imgf000017_0002
wherein R5, R^, R7, R8, R9 is each individually selected from H, F, CI, alkyl, aryl, aralkyl, amino, nitro, or carboxy. In a preferred embodiment, at least one of R5, ¾, R7, Rg, R9 is H; and alkyl is C1-10 alkyl, preferably C1- alkyl. Preferably, the benzoylate is benzoyloxy.
one embodiment, the caspase probes are cell permeant (i.e., exhibit good cell membrane permeability) and can selectively target caspases of interest inside the cells of a living organism. Preferably, cell permeable fluorescent dyes include, but are not limited to, sulforhodamine 101 (Texas Red), rhodamine dyes (e.g., rhodamine B, rhodamine 6G, rhodamine 19, rhodamine Green, TAMRA (carboxytetramethylrhodamine), TRITC (tetramethylrhodamine isothiocyanate), ROX (5',6-carboxyl-X-rhodamine)), indocyanine green, cyanine dyes (e.g., Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7), Marina Blue, Pacific Blue, Oregon Green dyes (e.g., Oregon Green 88, Oregon Green 514), tetramethylrhodamine, BODIPY dyes, Cascade Blue, fluoresceins (e.g., FAM, JOE (4,5-dichloro carboxy fluorescein), HEX (5'-hexachloro-fluorescein), FITC (fluorescein isothiocyanate)), Alexa Fluor dyes (e.g., Alexa Fluor 350, Alexa Fluor 430, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700, Alexa Fluor 750), DyLight dyes (e.g.,. DyLight780, DyLight 800CW), Rhodol Green, sulforhodamines, iFluor dyes, and Tide Fluor dyes. In at least one embodiment, the caspase probes do not undergo facile metabolism in vivo, and possess a long half-life (e.g., more than 6 hours) or remain detectable throughout the life of the permeated cell. Examples of compounds of Formula (II) in which X{ is W(NMe)E(OMe)HD(OMe) include:
• 780-W(NMe)E(OMe)HD(OMe)-BMK: 780-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• 780-W(NMe)E(OMe)HD(OMe)-FMK: 780-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• 780-W(NMe)E(OMe)HD(OMe)-PMK: 780-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
· Cy5-W(NMe)E(OMe)HD(OMe)-BMK: Cy5-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• Cy5-W(NMe)E(OMe)HD(OMe)-FMK: Cy5-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• Cy5-W(NMe)E(OMe)HD(OMe)-PMK: Cy5-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• ABzC-W(NMe)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-L-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ABzC-W(NMe)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-L-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ABzC-W(NMe)E(OMe)HD(OMe)-PM : 4-aminobenzyloxycarbonyl-L-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
· BODIPY-W(NMe)E(OMe)HD(OMe)-BMK: BODIPY-FL-N-methyl-L-tryptophanyl-
L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• BODIPY-W(NMe)E(OMe)HD(OMe)-FMK: BODIPY-FL-N-methyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone · BODIPY-W(NMe)E(OMe)HD(OMe)-PMK: BODIPY-FL-N-methyl-L-tryptophanyl-
L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• FAM-W(NMe)E(OMe)HD(OMe)-FMK: FAM-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone • FAM-W(NMe)E(OMe)HD(OMe)-PMK: FAM-N-methyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• N-AE-W(NMe)E(OMe)HD(OMe)-BMK: 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AE-W(NMe)E(OMe)HD(OMe)-FMK: 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AE-W(NMe)E(OMe)HD(OMe)-PMK: 4-aminoethyl-L-N-methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
· N-AM-W(NMe)E(OMe)HD(OMe)-BMK: 4-aminomethyl-L-N-methyltryptophanyl-
L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AM-W(NMe)E(OMe)HD(OMe)-FMK: 4-aminomethyl-L-N-methyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
· N-AM-W(NMe)E(OMe)HD(OMe)-PMK: 4-aminomethyl-L-N-methyltryptophanyl-
L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• O Gn-W(NMe)E(OMe)HD(OMe)-BMK: ORGn-N-methyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• ORGn-W(NMe)E(OMe)HD(OMe)-FMK: ORGn-N-methyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• ORGn-W(NMe)E(OMe)HD(OMe)-PMK: ORGn-N-methyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
For convenience, structures of representative compounds of several of the foregoing formula are shown below.
780-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000020_0001
FAM-ABzC-W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000020_0002
Figure imgf000020_0003
FAM-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000021_0001
FAM-N-AE-W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000021_0002
FAM-N-AM-W(NMe)E(OMe)HD(OMe)-PMK
Figure imgf000021_0003
ORGn-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000022_0001
Examples of compounds of Formula (II) in which X\ is W(N-TFM)E(OMe)HD(OMe) include:
• 780-W(N-TFM)E(OMe)HD(OMe)-BMK: 780-N-trifluoromethyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• 780-W(N-TFM)E(OMe)HD(OMe)-FMK: 780-N-trifluoromethyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• 780-W(N-TFM)E(OMe)HD(OMe)-PMK: 780-N-trifluoromethyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• ABzC-W(N-TFM)E(OMe)HD(OMe)-BM : 4-aminobenzyloxycarbonyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ABzC-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ABzC-W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• BODIPY-W( -TFM)E(OMe)HD(OMe)-BMK: BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• BODIPY-W(N-TFM)E(OMe)HD(OMe)-FMK: BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone • BODIPY-W(N-TFM)E(OMe)HD(OMe)-PMK: BODIPY-FL-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• FAM-W(N-TFM)E(OMe)HD(OMe)-FMK: FAM-N-trifluoromethyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• F AM- W(N-TFM)E(OMe)HD(OMe)-PMK : FAM-N-trifluoromethyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• N-AE-W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminoethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AE-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminoethyl-L-N- trifluoromethyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AE-W(N-TFM)E(OMe)HD(OMe)-PM : 4-aminoethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• N-AM-W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
· N-AM-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AM-W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-L-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ORGn- W(N-TFM)E(OMe)HD(OMe)-BMK : ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• ORGn-W(N-TFM)E(OMe)HD(OMe)-FMK: ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone • ORGn-W(N-TFM)E(OMe)HD(OMe)-PMK: ORGn-N-trifluoromethyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
For convenience, structures of representative compounds of the foregoing formula shown below.
780-W(N-TFM)E(OMe)HD(OMe)-BMK
Figure imgf000024_0001
FAM-ABzC-W(N-TFM)E(OMe)HD(OMe)-FMK
Figure imgf000024_0002
BODIPY-W(N-TFM)E(OMe)HD(OMe)-PM
Figure imgf000025_0001
Examples of compounds of Formula (II) in which X! is W(N-Ac)E(OMe)HD(OMe) include:
· 780-W(N-Ac)E(OMe)HD(OMe)-BMK: 780-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• 780-W(N-Ac)E(OMe)HD(OMe)-FMK: 780-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• 780-W(N-Ac)E(OMe)HD(OMe)-PMK: 780-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• BODIPY-W(N-Ac)E(OMe)HD(OMe)-BMK: BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• BODIPY-W(N-Ac)E(OMe)HD(OMe)-FMK: BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• BODIPY-W(N-Ac)E(OMe)HD(OMe)-PMK: BODIPY-FL-N-acetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• FAM-W(N-Ac)E(OMe)HD(OMe)-BMK: FAM-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
· FAM-W(N-Ac)E(OMe)HD(OMe)-FMK: FAM-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• FAM-W(N-Ac)E(OMe)HD(OMe)-PMK: FAM-N-acetyl-L-tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• ORGn-W(N-Ac)E(OMe)HD(OMe)-BMK: ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone • ORGn-W(N-Ac)E(OMe)HD(OMe)-FMK: ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• ORGn-W(N-Ac)E(OMe)HD(OMe)-PMK: ORGn-N-acetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone For convenience, structures of representative compounds of the foregoing formula are shown below.
780-W(N-Ac)E(OMe)HD(OMe)-BMK
Figure imgf000026_0001
BODIPY-W(N-Ac E(OMe)HD(OMe)-FMK
Figure imgf000026_0002
Examples of compounds of Formula (II) in which Xi is W(N-TFA)E(OMe)HD(OMe) include:
· 780-W(N-TFA)E(OMe)HD(OMe)-BM : 780-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone • 780-W(N-TFA)E(OMe)HD(OMe)-FMK: 780-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• 780-W(N-TFA)E(OMe)HD(OMe)-PMK: 780-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone · BODIPY-W(N-TFA)E(OMe)HD(OMe)-BMK: BODIPY-FL-N-trifluoroacetyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• BODIPY-W(N-TFA)E(OMe)HD(OMe)-FMK: BODIPY-FL-N-trifluoroacetyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• BODIPY-W(N-TFA)E(OMe)HD(OMe)-PMK: BODIPY-FL-N-trifluoroacetyl-L- tryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• FAM-W(N-TFA)E(OMe)HD(OMe)-BMK: FAM-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• FAM-W(N-TFA)E(OMe)HD(OMe)-FMK: FAM-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• FAM-W(N-TFA)E(OMe)HD(OMe)-PMK: FAM-N-trifluoroacetyl-L-tryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• ORGn-W(N-TFA)E(OMe)HD(OMe)-BMK: ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone
• ORGn-W(N-TFA)E(OMe)HD(OMe)-FMK: ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone
• ORGn-W(N-TFA)E(OMe)HD(OMe)-PMK: ORGn-N-trifluoroacetyl-L-tryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
For convenience, structures of representative compounds of the foregoing formula are shown below. FAM-W N-TFA)E(OMe)HD(OMe)-PMK
Figure imgf000028_0001
ORGn- W( -TF A)E(OMe)HD OMe)-BMK
Figure imgf000028_0002
Examples of compounds of Formula (II) in which X\ is 5-F-W(NMe)E(OMe)HD or 5-F-W(N-TFM)E(OMe)HD include:
• 780-5-F-W(NMe)E(OMe)HD(OMe)-BMK: 780-D,L-5-fluoro-N-methyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• 780-5-F-W(NMe)E(OMe)HD(OMe)-FMK: 780-D,L-5-fluoro-N-methyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• 780-5-F-W(NMe)E(OMe)HD(OMe)-PMK: 780-D,L-5-fluoro-N-methyltryptophanyl- L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ABzC-5-F-W(NMe)E(OMe)HD(OMe)-BMK: 4-Aminobenzyloxycarbonyl-D,L-5- fluoro-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ABzC-5-F-W(NMe)E(OMe)HD(OMe)-FMK: 4-Aminobenzyloxycarbonyl-D,L-5- fluoro-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone; • ABzC-5-F-W(NMe)E(OMe)HD(OMe)-PMK: 4-Aminobenzyloxycarbonyl-D,L-5- fluoro-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ABzC-5-F-W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-D,L-5- fluoro-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ABzC-5-F-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-D,L-5- fluoro-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
· ABzC-5-F-W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-D,L-5- fluoro-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-BMK: BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-FMK: BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-PMK: BODIPY-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• FAM-5-F-W(NMe)E(OMe)HD(OMe)-BMK: FAM-D,L-5-fluoro-N- trif uoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
· FAM-5-F-W(NMe)E(OMe)HD(OMe)-FMK: FAM-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• FAM-5-F-W(NMe)E(OMe)HD(OMe)-PMK: FAM-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• N-AE-5-F-W(NMe)E(OMe)HD(OMe)-BMK: N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; • N-AE-5-F-W(NMe)E(OMe)HD(OMe)-FMK: N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AE-5-F-W(NMe)E(OMe)HD(OMe)-PMK: N-aminoethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
· N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AE-5-F-W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminoethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• N-AM-5-F-W(NMe)E(OMe)HD(OMe)-BMK: N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AM-5-F-W(NMe)E(OMe)HD(OMe)-FMK: N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AM-5-F-W(NMe)E(OMe)HD(OMe)-PMK: N-aminomethyl-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
· N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-BM : 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-D,L-5-fluoro-N- trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone; • ORGn-5-F-W(NMe)E(OMe)HD(OMe)-BMK: ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ORGn-5-F-W(NMe)E(OMe)HD(OMe)-FM : ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ORGn-5-F-W(NMe)E(OMe)HD(OMe)-PMK: ORGn-D,L-5-fluoro-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
For convenience, structures of representative compounds of the foregoing formula are shown below.
780-5-F-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000031_0001
FAM-ABzC-5-F-W(NMe)E OMe)HD(OMe)-FMK
Figure imgf000031_0002
BODIPY-5-F-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000032_0001
FAM-5-F-W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000032_0002
FAM-N-AE-5-F-W(NMe)E(OMe)HD(OMe)-PMK
Figure imgf000032_0003
BODIPY-N-AM-5-F-W(N-TFM)E(OMe)HD(OMe)-PM
Figure imgf000033_0001
ORGn-5-F-W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000033_0002
Examples of compounds of Formula (II) in which X] is 2-CF3-W(NMe)E(OMe)HD or 2-CF3-W(N-TFM)E(OMe)HD include:
• 780-2-CF3W(NMe)E(OMe)HD(OMe)-BMK: 780-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• 780-2-CF3W(NMe)E(OMe)HD(OMe)-FMK: 780-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fiuoromethyl ketone;
• 780-2-CF3W(NMe)E(OMe)HD(OMe)-PMK: 780-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ABzC-2-CF3W(NMe)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-D,L-2- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; • ABzC-2-CF3W(NMe)E(OMe)HD(OMe)-FM : 4-aminobenzyloxycarbonyl-D,L-2- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ABzC-2-CF3W(NMe)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-D,L-2- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ABzC-2-CF3W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-D,L- 2-trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
· ABzC-2-CF3W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• ABzC-2-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
• BODIPY-2-CF3W(NMe)E(OMe)HD(OMe)-BMK: BODIPY-D,L-2-trifluoromethyl- N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• BODIPY-2-CF3W(NMe)E(OMe)HD(OMe)-FMK: BODIPY-,L-2-trifluorornethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• BODIPY-2-CF3W(NMe)E(OMe)HD(OMe)-PMK: BODIPY-D,L-2-trifluoromethyl- N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
· FAM-2-CF3W(NMe)E(OMe)HD(OMe)-BMK: FAM-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• FAM-2-CF3W(NMe)E(OMe)HD(OMe)-FMK: FAM-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• FAM-2-CF3W(NMe)E(OMe)HD(OMe)-PMK: FAM-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone; • N-AE-2-CF3W(N-TFM)E(OMe)HD(OMe)-BM : 4-aminoethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AE-2-CF3W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminoethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• N-AE-2-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminoethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
• N-AM-2-CF3W(N-TFM)E(OMe)HD(OMe)-BM : 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AM-2-CF3W(N-TFM)E(OMe)HD(OMe)-FM : 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• N-AM-2-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-D,L-2- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
• ORGn-2-CF3W(NMe)E(OMe)HD(OMe)-BMK: ORGn-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ORGn-2-CF3W(NMe)E(OMe)HD(OMe)-FMK: ORGn-D,L-2-trifluorornethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ORGn-2-CF3W(NMe)E(OMe)HD(OMe)-PMK: ORGn-D,L-2-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
For convenience, structures of representative compounds of the foregoing formula are shown below. 780-2-CF3W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000036_0001
BODIPY-2-CF3W(NMe E(OMe)HD(OMe)-BMK
Figure imgf000036_0002
FAM-2-CFW(NMeE(OMe)HD(OMe)-FMK
Figure imgf000037_0001
BODIPY-N-AM-2-CF3W(N-TFM)E(OMe)HD(OMe)-BMK
Figure imgf000037_0002
ORGn-2-CF3W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000038_0001
Examples of compounds of Formula (II) in which X is 6-CF3W(NMe)E(OMe)HD or 6-CF3W(N-TFM)E(OMe)HD include:
· 780-6-CF3W(NMe)E(OMe)HD(OMe)-BMK: 780-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; and
• 780-6-CF3W(NMe)E(OMe)HD(OMe)-FMK: 780-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• 780-6-CF3W(NMe)E(OMe)HD(OMe)-PM : 780-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone.
• ABzC-6-CF3W(NMe)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-D,L-6- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone;
• ABzC-6-CF3W(NMe)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-D,L-6- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
· ABzC-6-CF3W(NMe)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-D,L-6- trifluoromethyl-N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone;
• ABzC-6-CF3W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminobenzyloxycarbonyl-D,L- 6-trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone; • ABzC-6-CF3W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminobenzyloxycarbonyl-D,L-6- trifluorornethyl-N-trifluoromethyltryptophanyl-L-glutarnic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• ABzC-6-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminobenzyloxycarbonyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
• BODIPY-6-CF3W(NMe)E(OMe)HD(OMe)-BM : BODIPY-D,L-6-trifluoromethyl- N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; and
· BODIPY-6-CF3W(NMe)E(OMe)HD(OMe)-FMK: BODIPY-D,L-6-trifluoromethyl-
N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• BODIPY-6-CF3W(NMe)E(OMe)HD(OMe)-PMK: BODIPY-D,L-6-trifluoromethyl- N-methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
• FAM-6-CF3W(NMe)E(OMe)HD(OMe)-BMK: FAM-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; and
• FAM-6-CF3W(NMe)E(OMe)HD(OMe)-FMK: FAM-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• FAM-6-CF3W(NMe)E(OMe)HD(OMe)-PMK: FAM-D,L-6-trifluoromethyl-N- methyltryptophanyl-L- glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone
· N-AE-6-CF3W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminoethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AE-6-CF3W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminoethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• N-AE-6-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminoethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone; • N-AM-6-CF3W(N-TFM)E(OMe)HD(OMe)-BMK: 4-aminomethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester benzoyloxymethyl ketone;
• N-AM-6-CF3W(N-TFM)E(OMe)HD(OMe)-FMK: 4-aminomethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester fluoromethyl ketone;
• N-AM-6-CF3W(N-TFM)E(OMe)HD(OMe)-PMK: 4-aminomethyl-D,L-6- trifluoromethyl-N-trifluoromethyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L- aspartic acid methyl ester phenoxymethyl ketone;
· ORGn-6-CF3W(NMe)E(OMe)HD(OMe)-BMK: ORGn-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester benzoyloxymethyl ketone; and
• ORGn-6-CF3W(NMe)E(OMe)HD(OMe)-FMK: ORGn-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester fluoromethyl ketone;
• ORGn-6-CF3W(NMe)E(OMe)HD(OMe)-PMK: ORGn-D,L-6-trifluoromethyl-N- methyltryptophanyl-L-glutamic acid methyl ester-L-histidine-L-aspartic acid methyl ester phenoxymethyl ketone.
For convenience, structures of representative compounds of the foregoing formula are shown below.
780-6-CF3W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000040_0001
ORGn-ABzC-6-CF3W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000041_0001
BODIPY-6-CF3W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000041_0002
FAM-6-CF3W(N-Me)E(OMe)HD(OMe)-BMK
Figure imgf000041_0003
ORGn-N-AE-6-CF3W(NMe)E(OMe)HD(OMe)-FMK
Figure imgf000042_0001
n-6-CF3W(NMe)E(OMe)HD(OMe)-BMK
Figure imgf000042_0002
Diagnostic Uses of Fluorescent Caspase-1 Probes
Assessing Diseases/Conditions Associated With Caspase-Mediated Inflammation In at least one embodiment, the caspase probes are used for in vivo detection of caspase-mediated inflammation to assess diseases/conditions associated with inflammation. Inflammation is associated with a wide range of chronic and acute disorders. Consequently, the caspase probes may be used to assess caspase-mediated inflammation associated with a wide range of diseases and conditions, including but not limited to: ulcerative colitis, endotoxic shock, rheumatoid arthritis, juvenile arthritis, osteoarthritis, psoriasis, Crohn's disease, inflammatory bowel disease, multiple sclerosis, insulin dependent diabetes mellitus, gout, psoriatic arthritis, reactive arthritis, viral or post- viral arthritis, and ankylosing spondylarthritis.
Assessing Organ and Tissue Health
In at least one embodiment, the caspase probes are used for in vitro or in vivo detection of caspase-mediated inflammation to assess the health of a transplant organ or transplanted tissue (pre- and post-transplant), a diseased organ or diseased tissue, or a traumatized organ or traumatized tissue since inflammation can be indicative of impairment.
Drug Development With Caspase-1 Probes
In addition to research purposes, the caspase probes can also be used in drug development. The process of drug development, from start to commercialization is very long and involves numerous steps including identifying in vitro lead drug candidates from a million of compounds, pre-clinical development using in vivo animal models, and finally, clinical trials in humans. High-throughput in vitro screening is a widely used method during the initial stages of drug development, and allows for the simultaneous evaluation of millions of compounds under a given condition. It involves the screening of the candidate therapy compound library against the specific drug target directly or in a more complex assay system. For example, high throughput screen can involve screening a candidate therapy compound library in a cell-based assay, where the activity of the candidate compound is intended to affect the incidence of inflammation. This type of screen can be carried out using cells cultured in multiwell plates with automated operation. Since the ultimate outcome desired by the candidate compound is the effect on inflammation, the caspase probes can be used in cell based screens to quantify the incidence of inflammation in response to tested drug candidates.
Caspase probes can also be used for evaluating and/or predicting the efficacy of a particular therapeutic treatment (e.g., an anti-inflammatory), as well as for determining drug- induced impairment or toxicity (e.g., evaluating side effects of a drug treatment by assessing collateral damage to non-target organs). For instance, the efficacy of an anti-inflammatory could be assessed by administering the anti-inflammatory to a subject, administering in vivo an effective amount of a caspase probe to the subject, and then detecting the degree of inflammation, such that detection of inflammation at or below a predetermined level indicates efficacy of the anti-inflammatory treatment. The subject's naturally occurring level of inflammation could be assessed before the anti- inflammatory treatment as well in order to determine how much inflammation decreases due to administration of the therapy.
Administration or Delivery of Caspase-1 Probes
Examples of organs or targets that may be assessed using the caspase probes include, but are not limited to: eye, breast, heart, brain and central nervous system (CNS), kidneys, lungs, liver, skin, pancreas, skeletal system, connective tissue (e.g., joints), stomach, upper gastrointestinal tract, lower gastrointestinal tract, circulatory system (e.g., blood), lymphatic system, sexual organs (male and female), prostate, embryologic tissue, muscular system, and gallbladder. The caspase probes may also be used for whole-body imaging to assess inflammation throughout a living organism.
In at least one embodiment, the caspase probe is delivered in vitro to a biological sample (e.g., a blood sample, tissue sample, cell suspension, cellular extract, or tissue homogenate) by direct application of the probe to the sample. Given that the caspase probes exhibit good cell permeability, there is no need to use additional reagents to facilitate the entry of the probes into cells. In one instance, the caspase probe is reconstituted in DMSO, further diluted in phosphate buffered saline (PBS) or cell culture media and applied directly to cells in a cell culture dish. After an incubation period under the conditions sufficient for the formation of caspase-probe complexes (1 hour at 37°C), cells are washed with PBS containing 1% of bovine serum albumin (BSA). To determine whether cells exhibit inflammation, the incidence of inflammation can be evaluated by subjecting the biological sample to a means for detecting caspase-1 -probe complexes.
In at least one other embodiment, the caspase probe is administered in vivo to a subject (e.g., animal or human) orally, intravenously, intraperitoneally, intramuscularly, subcutaneously, topically, and/or by direct application to a target organ. The caspase probe is diluted in 10X injection buffer. Preferably, the injection buffer is PBS. The caspase probes are administered in an effective amount, which is an amount that is sufficient to provide meaningful results with respect to the intended purpose - e.g., diagnostic, drug development, etc. In at least one embodiment, the caspase probe is present in a composition, wherein the composition comprises at least a caspase probe and an excipient. Preferably, the excipient is a pharmaceutically acceptable excipient. Suitable excipients include, but are not limited to, adhesives, binders, bulking agents, carriers, colors, diluents, disintegrating agents, fillers, glidants, granulating agents, lubricating agents, polymers, preservatives, wetting agents, and combinations thereof. Preferably, one or more excipients is selected from sucrose, lactose, cellulose, gelatin, polyvinylpyrrolidone, and polyethylene glycol.
The choice of which caspase probe to administer depends, in part, on the target for administration. For example, to assess inflammation in the kidney, it is preferable to administer a hydrophilic caspase probe because non-hydrophilic caspase probes are likely to be excreted by the kidney via urinary excretion, and decreases the chance of the administered probes to be detected above background noise in that organ. Put another way, administration of a non-hydrophilic caspase probe increases the possibility of background noise due to unbound caspase probes accumulating in the kidney as unbound probes are eliminated. Alternatively, to assess inflammation in the liver, it is preferable to administer a non- lipophilic caspase probe (e.g., probes containing a trifluoromethyl group) because lipophilic caspase probes are likely to be metabolized in the liver, again decreasing the chances of the administered probes to be detected above background noise in that organ - i.e., administration of a lipophilic probe increases the possibility of background noise from unbound caspase probes as unbound probes are processed through the liver.
Kits Containing Caspase-1 Probes
In general, the kits of the present disclosure are used for detecting and quantifying the incidence of inflammation in a biological sample. The kit may comprise one or more caspase probes, one or more buffers (e.g., buffers for delivery of caspase probes to samples), and optionally one or more non-specific fluorescence probes that can be used as a control. Suitable non-specific fluorescence control probes include, but are not limited to DY 680 carboxylic acid, DY 750 carboxylic acid, DY 780 carboxylic acid, BODIPY-FL, BODIPY- TMR, and BODIPY-TR. In general, the choice of control fluorescent dye will match the fluorescent label on the probe. The kit may further include packaging materials with instructions for using the components of the kit, such as how to combine caspase probes with buffers, how to use the caspase probes provided in the kit, storage conditions, etc. Components of the kit may be provided in separate containers (e.g., vials) or combined.
In at least one embodiment, the buffer is an injection buffer (e.g., in vivo) or a wash buffer (e.g., in vitro). For example, the buffer may be 10X PBS, which is suitable for use as either an injection buffer or wash buffer. Preferably, the buffer is provided in an amount of 10-50 niL, more preferably 15-30 mL. Preferably, the probe is provided in an amount of 25- 500 μg, more preferably 30-350 μg. In at least one embodiment, the caspase probe is reconstituted in DMSO, and then optionally diluted in sterile IX PBS. A 1 OX PBS buffer can be diluted to IX PBS using water - e.g., distilled water, water-for-injection, etc. In at least one embodiment, the buffer is supplied at a 2X concentration, and is diluted to IX using an equal amount of water.
Other suitable buffers include, but are not limited to, tris (tris-hydroxymethylamino- methane) buffer (20mM, pH 7.4) and Hanks balanced salt solutions (available from Life Technologies) buffered with 20mM Hepes (4-(2-hydroxyethyl)-l-piperazineethanesulfonic acid). In at least one embodiment, the buffer is a pharmaceutically acceptable buffer. For example, a suitable injection buffer may be prepared according to the following recipe in endotoxin free DI H20: 87.66 g/L of NaCl (1.5 M), 60.53 g/L of Na2HP04»12H20+4.84 g/L of NaH2P04 »2H20 (0.2 M phosphate), pH 6.9.
PROPHETIC EXAMPLES
The present invention is next described by means of the following prophetic examples. The use of these or other examples anywhere in the specification is illustrative only, and in no way limits the scope and meaning of the invention or of any exemplified form. Likewise, the invention is not limited to any particular preferred embodiments described herein. Indeed, modifications and variations of the invention may be apparent to those skilled in the art upon reading this specification, and can be made without departing from its spirit and scope. The invention is therefore to be limited only by the terms of the claims, along with the full scope of equivalents to which the claims are entitled. EXAMPLE IP
N-Methyl substitution on fluorescently labeled N-methyl tryptophan prevents tryptophan-induced quenching and maintains caspase- 1 recognition
To induce inflammation, human monocyte cells (THP-1) are cultured in the presence of 10 μg/mL of phytohemagglutin (PHA; Life Technologies) for 3.5 hours at 37°C. Control THP-1 cells are similarly cultured but in the absence of PHA. The cultured cells are plated at a concentration of 106 cells per 1 mL of medium. Following incubation, FAM- W(NMe)E(OMe)HD(OMe)-FMK or PROBO Green- W(NMe)E(OMe)HD(OMe)-FMK is added to separately plated cells, and is allowed to incubate for 20 minutes. Subsequent to incubation, cells are washed with PBS, and harvested for flow cytometry analysis. Flow cytometry analysis of cells pre-treated with PHA and incubated with FAM- W(NMe)E(OMe)HD(OMe)-FMK or PROBO Green- W(NMe)E(OMe)HD(OMe)-FMK shows a strong bright fluorescent signal. In contrast, cells cultured in the absence of PHA and incubated with FAM-W(NMe)E(OMe)HD(OMe)-FMK or PROBO Green- W(NMe)E(OMe)HD(OMe)-FMK show a weaker fluorescent signal. Thus, the presence of a fluorescent signal in cells pre-treated with PHA is indicative of inflammation and the presence of caspase-1. Furthermore, these results demonstrate that tryptophan N-methyl substitution enables N-terminal substitution by different fluorophores to provide readily observable fluorescence, and the indole substitution does not prohibit the modified inhibitor from binding irreversibly to caspase- 1.
EXAMPLE 2P
This prophetic example relates to the substantial increase in fluorescence intensity from a fluorescent label attached to a molecule containing modified tryptophan (Compound 1), as compared to the same fluorescently labeled molecule containing natural tryptophan (Comparative Compound 1A).
Synthesis of 5-FAM-W(NMe E(OMe)HD(OMe)-FMK (Compound 1)
(1) FMOC-W(NMe) (N-FMOC-l-Methyl-L-tryptophan)
1-Methyl-L-tryptophan (1-Me-W; Aldrich Cat. No. 447439) is dissolved in the minimum amount of water and carefully treated with one equivalent of IN sodium hydroxide (NaOH) solution. Then 1.5 equivalents of FMOC chloride (Aldrich Cat. No. 23185) and 1.5 equivalents of IN NaOH are added alternately with stirring and cooling (ice-bath) under Schotten-Baumann conditions. After addition of both reagents is complete, the reaction mixture is stirred and allowed to warm slowly to room temperature for one hour. The reaction mixture is carefully acidified to pH about 2 with IN hydrochloric acid (HC1) to yield an off- white solid. This material is collected by vacuum filtration and dried in a vacuum dessicator to yield the desired product, N-FMOC-l-methyl-L-tryptophan. The material is stored at - 20°C until needed.
(2) FMOC-W(NMe)E(OMe) O-t-Bu (N-FMOC-l-methyl-L-tryptophanyl-L-glutamic acid y-methyl ester a-t-butyl ester)
N-FMOC-l-methyl-L-tryptophan from Step (1) is dissolved in dry tetrahydrofuran (THF; Aldrich; Cat. No. 401757) and treated with diisopropylcarbodiimide (DIC; Fluka Cat. No. 38370) dissolved in anhydrous THF. Immediately thereafter, L-glutamic acid 5-methyl ester 2-t-butyl ester in anhydrous THF is added to the stirring suspension. The reaction is allowed to proceed for one hour at room temperature (r.t), filtered to remove solid diisopropylurea, and then the solvent is removed by rotary evaporation to yield N-FMOC- 1- Methyl-L-tryptophanyl-L-glutamic acid γ-methyl ester a-t-butyl ester as a low-melting solid. This material is stored dessicated at -20°C until needed.
(3) FMOC-W(NMe)E(OMe) (N-FMOC-l-methyl-L-tryptophanyl-L-glutamic acid y- methyl ester)
N-FMOC-l-methyl-L-tryptophanyl-L-glutamic acid γ-methyl ester a-t-butyl ester from Step (2) is dissolved in anhydrous ethyl ether (Aldrich Cat. No. 67381 1) and treated with a stream of hydrogen chloride gas. After 15 minutes, the resulting reaction mixture is rotary evaporated at r.t. to yield the free acid, N-FMOC- L-tryptophanyl-L-glutamic acid γ- methyl ester, which is stored frozen in a vacuum dessicator until needed.
(4) FMOC-W(NMe)E(OMe)H(FMOC) O-t-Bu (N-FMOC- 1-methyl-L-tryptophanyl-L- glutamyl y-methyl ester-L-histidine-Nn-FMOC t-butyl ester)
N-FMOC- 1-methyl-L-tryptophanyl-L-glutamic acid γ-methyl ester from Step (3) is dissolved in dry tetrahydrofuran (THF; Aldrich; Cat. No. 401757) and then treated with diisopropylcarbodiimide (DIC; Fluka Cat. No. 38370) dissolved in anhydrous THF. Immediately thereafter, L-histidine-Nn-FMOC t-butyl ester in anhydrous THF is added to the stirring suspension. The reaction is allowed to proceed for one hour at room temperature (r.t.), filtered to remove solid diisopropylurea, and then the solvent is removed by rotary evaporation to yield N-FMOC-L-tryptophanyl-L-glutamyl γ-methyl ester-L-histidine-Νπ- FMOC t-butyl ester. This material is stored frozen in a vacuum dessicator until needed.
(5) FMOC-W(NMe)E(OMe)H(FMOC) (N-FMOC-L-tryptophanyl-L-glutamyl y- methyl ester-L-histidine-Nn-FMOC)
N-FMOC- 1 -methyl-L-tryptophanyl-L-glutamyl γ-methyl ester- L-histidine-N7r-FMOC t-butyl ester from Step (4) is dissolved in anhydrous ethyl ether (Aldrich Cat. No. 67381 1) and treated with a stream of hydrogen chloride gas. After 15 minutes, the resulting reaction mixture is rotary evaporated at r.t. to yield the free acid N-FMOC-L-tryptophanyl-L-glutamyl γ-methyl ester-L-histidine-N7c-FMOC. This material is stored frozen in a vacuum dessicator until needed.
(6) W(NMe)E(OMe)H (1-methyl-L-tryptophanyl-L-glutamyl y-methyl ester-L- histidine)
N-FMOC- 1 -methyl-L-tryptophanyl-L-glutamyl γ-methyl ester-L-histidyl-N -FMOC from Step 5 is dissolved in a mixture of piperidine (Aldrich Cat. No. 104094) and dimethylformamide (AlfaAesar Cat. No. A13547) at r.t. for 10 minutes. The solvent is removed at r.t. by rotary evaporation and is air dried in a vacuum dessicator. 1-Methyl-L- tryptophanyl-L-glutamyl γ-methyl ester-L-histidine is stored at -20°C and protected from light and moisture until needed.
(7) 5-FAM- W(NMe)E(OMe)H (5-Carboxyfluoresceinyl-l-methyl-L-tryptophanyl-L- glutamyl y-methyl ester-L-histidine)
5-FAM-N-hydroxysuccinimido ester (AnaSpec Cat. No. AS-81007) is dissolved in acetonitrile (Fisher Cat. No. 01034) in a round-bottomed flask covered with foil to exclude light, and treated with 1-methyl-L-tryptophanyl-L-glutan yl γ-methyl ester-L-histidine from Step 6 and 1 equivalent of triethylamine (Aldrich Cat. No. T0886) dissolved in acetonitrile (Aldrich Cat. No. 271004). The reaction is monitored by tic until complete (about 2 hours). The reaction mixture is quickly filtered in the dark and the solvent is removed by rotary evaporation using a dark round-bottomed flask to yield 5-Carboxyfluoresceinyl-l-methyl-L- tryptophanyl-L-glutamyl γ-methyl ester-L-histidine as a colored solid. This material is stored frozen, and protected from light and moisture until needed.
(8) 5-FAM- W(NMe )E( OMe )HD( OMe ) -FMK (5-Carboxyfluoresceinyl-l-Methyl-L- tryptophanyl-L-glutamyl y-methyl ester -L-histidyl-L-aspartic acid β-methyl ester fluoromethyl ketone)
5-Carboxyfluoresceinyl- 1 -methyl-L-tryptophanyl-L-glutamyl γ-methyl ester-L- histidine from Step 7 is dissolved in methylene chloride (Fisher Cat. No. D150) and treated with stirring while cooling in an ice bath with an equimolar amount of L-aspartic acid β- methyl ester fluoromethyl ketone hydrochloride (American Peptide Corporation) and an equimolar amount of diisopropylethylamine (DIEA; Aldrich Cat. No. D125806). An equimolar amount of diisopropylcarbodiimide (DIC; Fluka Cat. No. 38370) dissolved in methylene chloride is added and the reaction mixture is stirred for one hour, filtered by suction and the resulting 5-FAM-l-methyl-L-tryptophanyl-L-glutamyl γ-methyl ester-L- histidyl-L-aspartic acid β-methyl ester fluoromethyl ketone is air dried in a vacuum dessicator. This product is stored at -20°C and protected from light and moisture until needed. Synthesis of 5-FAM- WE(OMe)HD(OMe)-FMK (Comparative Compound 1 A)
Comparative Compound 1 A is synthesized in the same manner as Compound 1 except that L-tryptophan is used in place of 1-Methyl-L-tryptophan as a starting material. Following the synthesis of Compound 1 and Comparative Compound 1A, excitation and emission spectra are obtained for the fluorescently labeled tryptophans on each compound, and quantum yields are also determined. The spectral data are compiled using a Molecular Devices SpectraMax M2 Plate Reader.
Results:
Figure imgf000050_0001
Given the foregoing, it can be concluded that a molecule containing modified tryptophan produces a fluorescent signal that is substantially stronger (e.g., 2-5 times or 2-10 times stronger) than the fluorescent signal produced by a molecule that differs only in that it contains natural (not modified) tryptophan.
WORKING EXAMPLES
The present invention is next described by means of the following non-limiting working examples.
EXAMPLE 1W
Representative compound 5-FAM-W(NMe)E(OMe)HD(OMe)-FMK was prepared using liquid phase peptide synthesis, following the process described in Example 2P (refer to "Compound 1" synthesis scheme). HPLC analysis of the resulting product, under the conditions listed below, provided the HPLC Chromatogram shown in Figure 1. Mass Spectral analysis of the product, under the conditions listed below, is shown in Figure 2.
EXAMPLE 2W
5-FAM-W(NMe)E( OMe)HD(OMe)-FMK Labeling of Caspase 1 in PHA Activated THP-1 Cells
THP-1 cells (human monocyte cell line) were activated with 10 μg/ml PHA
(phytohemagglutinin) for 3.5 hours at 37°C followed by labeling with 5-FAM- W(NMe)E(OMe)HD(OMe)-FMK (0.75 μΜ) for 20 minutes at 37°C. Cells were washed with PBS and analyzed using an Attune NxT flow cytometer. Activated and non-activated cells were gated by forward and side scatter properties and median fluorescence intensities of the each population was determined (non-activated = 554, activated = 2352). Data for 5- FAM-W(NMe)E(OMe)HD(OMe)-FMK for the above assay is shown in Figure 3. All references cited and/or discussed in this specification are incorporated herein by reference in their entireties and to the same extent as if each reference was individually incorporated by reference.

Claims

We claim:
1. A fluorescent molecule comprising a sequence of 1-10 natural or synthetic amino acids, wherein at least one amino acid is a modified tryptophan of formula (I)
Figure imgf000052_0001
wherein R is selected from -(CH2)nX and -(CO)(CH2)nX, where n is 0-5 and X is H or - CF3;
Ri is selected from Y and LY, where Y is a fluorescent label, and L is selected from - CH2-NH-, -(CH2)2-NH-, -C(=0)-CH2-NH-, -C(=0)-0-CH2-C6H6-NH-, and -C(=0)-0-CH2- C6H6-CH2-NH-; and
R2 is selected from OH and the N-terminal group of another of the amino acids;
wherein the molecule produces a fluorescent signal that is stronger than a molecule that only differs by R being H.
2. The fluorescent molecule of claim 1, comprising 1-5 natural or synthetic amino acids.
3. The fluorescent molecule of claim 1, wherein R2 is OH.
4. The fluorescent molecule of claim 1, wherein R is -(CH2)nX, n is 1, and X is H.
5. The fluorescent molecule of claim 1, wherein R is -(CH2)nX, n is 0, and X is -CF3.
6. The fluorescent molecule of claim 1 , wherein R is -(CO)(CH2)nX, n is 0, and X is - CF3.
7. The fluorescent molecule of claim 1, wherein R is -(CO)(CH2)nX, n is 1, and X is H.
8. The fluorescent molecule of claim 1 , wherein the fluorescent label is a dye selected from pyrene dyes, indacene dyes, cyanine dyes, fluorescein dyes, rhodamine dyes, sulforhodamine dyes, and IR dyes.
9. The fluorescent molecule of claim 8, wherein the dye is selected from Cascade Blue, BODIPY, Cy Dyes, Alexa Fluors, DyLight dyes, FAM, fluorescein isothiocyanate,
Rhodamine Green, Rhodol Green, Oregon Green dyes, 4,5-dichloro carboxy fluorescein, 5'- hexachloro-fluorescein, carboxytetramethylrhodamine, tetramethylrhodamine,
sulforhodamines, 5',6-carboxyl-X-rhodamine, iFluor dyes, and Tide Fluor dyes.
10. The fluorescent molecule of claim 1, wherein the amino acids comprise the following in order: the modified tryptophan of formula (I), glutamic acid, histidine, and aspartic acid.
11. A fluorescent caspase probe of Formula (II) : 3 Xi R4 (Π)
wherein R3 is selected from 780, ABzC, BODIPY, FAM, Cy5, N-AE, N-AM, and ORGn; X! is selected from W(N')E(OMe)HD(OMe), 5-F-W(N')E(OMe)HD, 2-CF3- W(N')E(OMe)HD, and 6-CF3W(N')E(OMe)HD, wherein N' is (NMe), (N-TFM), (N-Ac), or (N-TFA); and R4 is selected from halogen, phenol, and benzoylate.
12. A method of determining in vivo the incidence of inflammation in a living organism, comprising the steps of:
(i) administering in vivo a fluorescent caspase probe of claim 11 to a living organism; (ii) subjecting the living organism to a means for in vivo detection of caspase- 1 -probe complexes; and
(iii) determining the incidence of inflammation as indicated by the presence or absence of caspase- 1 -probe complexes.
13. The method of claim 12, wherein the in vivo detection is performed on at least one portion of the living organism selected from eye, breast, heart, brain and central nervous system, kidney, lung, liver, skin, pancreas, skeletal system, connective tissue, stomach, upper gastrointestinal tract, lower gastrointestinal tract, circulatory system, lymphatic system, sexual organ, prostate, embryologic tissue, muscular system, and gallbladder.
14. The method of claim 12, further comprising the steps of:
(a) before administering the probe in step (i), administering in vivo a candidate therapy intended to induce inflammation in the living organism; and (b) after step (iii), determining whether the candidate therapy induces or inhibits inflammation as indicated by the detected presence or absence of caspase-1 -probe complexes, respectively.
15. A method of determining ex vivo the incidence of inflammation in a biological sample extracted from a living organism, comprising the steps of:
(i) administering in vivo a fluorescent caspase probe of claim 11 to a portion of a living organism;
(ii) extracting a biological sample from the portion of the living organism;
(iii) subjecting the biological sample to a means for ex vivo detection of caspase-1 -probe complexes; and
(iv) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes.
16. A method of determining in vitro the incidence of inflammation in a biological sample, comprising the steps of:
(i) adding a fluorescent caspase probe of claim 11 to a biological sample;
(ii) incubating the sample with the probe under conditions sufficient to form caspase- 1- probe complexes;
(iii) subjecting the sample of step (ii) to a means for detecting caspase-1 -probe complexes; and
(iv) determining the incidence of inflammation as indicated by the presence or absence of caspase-1 -probe complexes.
17. The method of claim 16, further comprising the step of inducing inflammation in the biological sample before adding the probe in step (i).
18. The method of claim 16, wherein the biological sample is selected from a blood sample, tissue sample, cell suspension, cellular extract, and tissue homogenate.
19. A composition comprising a fluorescent caspase probe of claim 11 and an excipient.
20. A kit comprising a fluorescent caspase probe of claim 1 1, a buffer, and packaging materials.
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