US20240043455A1 - Water soluble fluorscent or colored dyes comprising conjugating groups - Google Patents

Water soluble fluorscent or colored dyes comprising conjugating groups Download PDF

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US20240043455A1
US20240043455A1 US18/481,045 US202318481045A US2024043455A1 US 20240043455 A1 US20240043455 A1 US 20240043455A1 US 202318481045 A US202318481045 A US 202318481045A US 2024043455 A1 US2024043455 A1 US 2024043455A1
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compound
independently
group
occurrence
acid
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C. Frederick Battrell
Kenneth Farber
John C. Kumer
Tracy Matray
Michael VanBrunt
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Sony Group Corp
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Sony Group Corp
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
    • C07F9/02—Phosphorus compounds
    • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
    • C07F9/655—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms
    • C07F9/65515—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms the oxygen atom being part of a five-membered ring
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
    • C07F9/02—Phosphorus compounds
    • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
    • C07F9/553—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having one nitrogen atom as the only ring hetero atom
    • C07F9/572—Five-membered rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/08—Esters of oxyacids of phosphorus
    • C07F9/09—Esters of phosphoric acids
    • C07F9/093—Polyol derivatives esterified at least twice by phosphoric acid groups
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic System
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/08—Esters of oxyacids of phosphorus
    • C07F9/09—Esters of phosphoric acids
    • C07F9/094—Esters of phosphoric acids with arylalkanols
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B57/00—Other synthetic dyes of known constitution
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B57/00—Other synthetic dyes of known constitution
    • C09B57/02—Coumarine dyes
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B69/00—Dyes not provided for by a single group of this subclass
    • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
    • C09B69/101—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B69/00—Dyes not provided for by a single group of this subclass
    • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
    • C09B69/101—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye
    • C09B69/102—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye containing a perylene dye
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B69/00—Dyes not provided for by a single group of this subclass
    • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
    • C09B69/103—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing a diaryl- or triarylmethane dye
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B69/00—Dyes not provided for by a single group of this subclass
    • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
    • C09B69/109—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing other specific dyes

Definitions

  • the present invention is directed to novel fluorescent or colored dyes and methods for their preparation and use in various analytical methods.
  • Fluorescent and/or colored dyes are known to be particularly suitable for applications in which a highly sensitive detection reagent is desirable. Dyes that are able to preferentially label a specific ingredient or component in a sample enable the researcher to determine the presence, quantity and/or location of that specific ingredient or component. In addition, specific systems can be monitored with respect to their spatial and temporal distribution in diverse environments.
  • Fluorescence and colorimetric methods are extremely widespread in chemistry and biology. These methods give useful information on the presence, structure, distance, orientation, complexation and/or location for biomolecules. In addition, time-resolved methods are increasingly used in measurements of dynamics and kinetics. As a result, many strategies for fluorescence or color labeling of biomolecules, such as nucleic acids and protein, have been developed.
  • Perylenes and related dyes have high photochemical persistency (chemical, thermal, and photochemical stability) and high fluorescence quanta yield and are used in a variety of reprographic processes, solar cells, photovoltaic devices, and dye lasers.
  • perylene derivatives have been used primarily as pigments and fluorescent dyes.
  • Perylene dyes of various colors and light-absorbing properties have been reported. For example, Becker S. et al, Chem. Eur. J., 6,213,984, (2000), report the synthesis of thermotropic perylenedicarboximide chromophores that show a color change from blue to orange.
  • Perylene and related chromophores have seen limited use as biomolecular probes, apparently due to the strongly hydrophobic character of these types of molecules and difficulties with regiospecific labeling of biomolecules with the same.
  • the present invention is generally directed to compounds useful as water soluble, fluorescent or colored dyes and probes that enable visual detection of biomolecules and other analytes, as well as reagents for their preparation. Methods for visually detecting a biomolecule and for determining the size of a biomolecule are also described.
  • the water soluble, fluorescent or colored dyes of the invention are intensely colored and/or fluorescent and can be readily observed by visual inspection or other means. In some embodiments the compounds may be observed without prior illumination or chemical or enzymatic activation. By appropriate selection of the dye, as described herein, visually detectable biomolecules of a variety of colors may be obtained.
  • R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , q, w and n are as defined herein.
  • a method for staining a sample comprises adding to said sample a representative compound as described herein in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
  • the present disclosure provides a method for visually detecting a biomolecule, comprising:
  • Other disclosed methods include a method for visually detecting a biomolecule, the method comprising:
  • compositions comprising any one of the disclosed compounds and one or more biomolecules.
  • Use of such composition in analytical methods for detection of the one or more biomolecules is also provided.
  • Alkyl refers to a straight or branched hydrocarbon chain group consisting solely of carbon and hydrogen atoms, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), having from one to twelve carbon atoms (C 1 -C 12 alkyl), preferably one to eight carbon atoms (C 1 -C 8 alkyl) or one to six carbon atoms (C 1 -C 6 alkyl), and which is attached to the rest of the molecule by a single bond, e.g., methyl, ethyl, n-propyl, 1-methylethyl (iso-propyl), n-butyl, n-pentyl, 1,1-dimethylethyl (t-butyl), 3-methylhexyl, 2-methylhexyl, ethenyl, prop-1-enyl, but-1-enyl, pent-1-enyl, penta-1,4-dienyl,
  • Alkylene or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a substituent group, consisting solely of carbon and hydrogen, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), and having from one to twelve carbon atoms, e.g., methylene, ethylene, propylene, n-butylene, ethenylene, propenylene, n-butenylene, propynylene, n-butynylene, and the like.
  • the alkylene chain is attached to the rest of the molecule through a single or double bond and to the substituent group through a single or double bond.
  • the points of attachment of the alkylene chain to the rest of the molecule and to the substituent group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkylene chain may be optionally substituted.
  • aminoalkylene refers to an alkylene, as defined, comprising one or more amino substituents. Unless stated otherwise specifically in the specification, aminoalkylene groups are optionally substituted
  • Alkoxy refers to a group of the formula —OR a where R a is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkoxy group may be optionally substituted.
  • Alkylamino refers to a group of the formula —NHR a or —NR a R a where each R a is, independently, an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkylamino group may be optionally substituted.
  • Alkylether refers to any alkyl group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond.
  • the carbon-oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C—O—C).
  • Alkylethers include at least one carbon oxygen bond, but may include more than one.
  • polyethylene glycol (PEG) is included within the meaning of alkylether.
  • an alkylether group may be optionally substituted. For example, in some embodiments and alkylether is substituted with an alcohol or phosphate.
  • Alkylenether refers to an alkylene group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond.
  • the carbon-oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C—O—C).
  • Alkylenethers include at least one carbon oxygen bond, but may include more than one (i.e., a “polyalkylenether”).
  • PEG linking groups are examples of polyalkylenethers.
  • Hydroxydroxylpolyalkylenether refers to a polyalkylenether comprising at least on hydroxyl substituent.
  • Aminopolyalkylenether refers to a polyalkylenether comprising at least one amino (including alkylamino, arylamino and aralkylamino) substituent. Unless stated otherwise specifically in the specification, alkylenether, polyalkylenether, hydroxylpolyalkylenether and aminopolyalkylenether groups, are optionally substituted.
  • Alkylphospho refers to the —RP( ⁇ O)(R a )R b group, wherein R is an alkylene group, R a is OH, O ⁇ or OR c ; and R b is —Oalkyl or —Oalkylether, wherein R c is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, an alkylphospho group may be optionally substituted.
  • the —Oalkyl or —Oalkylether moiety (R b ) in a alkylphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Oalkylphospho is an alkylphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylphospho group may be optionally substituted.
  • Alkyetherphospho refers to the —RP( ⁇ O)(R a )R b group, wherein R is an alkylenether group, R a is OH, O ⁇ or OR c ; and R b is —Oalkyl or —Oalkylether, wherein Re is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, an alkyletherphopsho group may be optionally substituted.
  • the —Oalkyl or —Oalkylether moiety (R b ) in an alkyletherphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Oalkyletherphospho is an alkyletherphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkyletherphospho group may be optionally substituted.
  • Alkylthiophospho refers to the —P( ⁇ R a )(R b )R c group, wherein R a is O or S, R b is OH, O ⁇ , S ⁇ OR d or SR a ; and R c is —Oalkyl or —Oalkylether, wherein R d is a counter ion (e.g., Na+ and the like) and provided that: R a is S or R b is S ⁇ or SR d ; or provided that R a is S and R b is S ⁇ or SR a . Unless stated otherwise specifically in the specification, a alkylthiophospho group may be optionally substituted.
  • the —Oalkyl or —Oalkylether moiety in a alkythiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Oalkylthiophospho is a alkylthiophospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylthiophospho group may be optionally substituted.
  • Alkyletherthiophospho refers to the —P( ⁇ R a )(R b )R, group, wherein R a is O or S, R b is OH, O, S, OR d or SR a ; and R c is —Oalkyl or —Oalkylether, wherein R d is a counter ion (e.g., Na+ and the like) and provided that: R a is S or R b is S ⁇ or SR d ; or provided that R a is S and R b is S ⁇ or SR a .
  • an alkyletherthiophospho group may be optionally substituted.
  • the —Oalkyl or —Oalkylether moiety in a alkyletherthiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Oalkyletherthiophospho is an alkyletherthiophospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkyletherthiophospho group may be optionally substituted.
  • Amide refers to the —NRaRb radical, wherein R a and R b are independently H, alkyl or aryl. Unless stated otherwise specifically in the specification, an amide group may be optionally substituted.
  • Aryl refers to a carbocyclic ring system group comprising 6 to 18 carbon atoms and at least one carbocyclic aromatic ring.
  • the aryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems.
  • Aryl groups include, but are not limited to, aryl groups derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene.
  • aryl or the prefix “ar-” (such as in “aralkyl”) is meant to include aryl groups that are optionally substituted.
  • Aryloxy refers to a group of the formula —OR a , where R a is an aryl moiety as defined above, for example phenoxy and the like. Unless stated otherwise specifically in the specification, an aryloxy group may be optionally substituted.
  • “Aralkyl” refers to a group of the formula —R b —R, where R b is an alkylene chain as defined above and R, is one or more aryl groups as defined above, for example, benzyl, diphenylmethyl and the like. Unless stated otherwise specifically in the specification, an aralkyl group may be optionally substituted.
  • Oaralkyl is an aralkyl group which is connected to the remainder of the molecule via an oxygen linkage. “ODMT” refers to dimethoxytrityl linked to the rest of the molecule via an O atom. Unless stated otherwise specifically in the specification, an Oaralkyl group may be optionally substituted.
  • Cyanoalkyl refers to an alkyl group comprising at least one cyano substituent.
  • the one or more —CN substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a cyanoalkyl group may be optionally substituted.
  • a “carbocyclic ring” is a ring wherein each ring atom is carbon. Carbocyclic rings may staturated or unsaturated, including aromatic rings. Unless stated otherwise specifically in the specification, a carbocylic group is optionally substituted.
  • Cycloalkyl refers to a stable non-aromatic monocyclic or polycyclic carbocyclic ring, which may include fused or bridged ring systems, having from three to fifteen carbon atoms, preferably having from three to ten carbon atoms, and which is saturated or unsaturated and attached to the rest of the molecule by a single bond.
  • Monocyclic cycloalkyl groups include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
  • Polycyclic cycloalkyl groups include, for example, adamantyl, norbornyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, a cycloalkyl group may be optionally substituted.
  • Cycloalkylalkyl refers to a group of the formula —R b R a where R b is an alkylene chain as defined above and R d is a cycloalkyl group as defined above. Unless stated otherwise specifically in the specification, a cycloalkylalkyl group may be optionally substituted.
  • Multicyclic refers to any molecule having more than one ring.
  • the rings may be either, fused, spirocyclic or separated by one or more atoms (e.g., linked via an acyclic linker).
  • “Spirocyclic” refers to a multicyclic molecule wherein two rings share a single carbon atom.
  • fused refers to any ring structure described herein which is fused to an existing ring structure in the compounds of the invention.
  • the fused ring is a heterocyclyl ring or a heteroaryl ring
  • any carbon atom on the existing ring structure which becomes part of the fused heterocyclyl ring or the fused heteroaryl ring may be replaced with a nitrogen atom.
  • Halo or “halogen” refers to bromo, chloro, fluoro or iodo.
  • Haloalkyl refers to an alkyl group, as defined above, that is substituted by one or more halo groups, as defined above, e.g., trifluoromethyl, difluoromethyl, trichloromethyl, 2,2,2-trifluoroethyl, 1,2-difluoroethyl, 3-bromo-2-fluoropropyl, 1,2-dibromoethyl, and the like. Unless stated otherwise specifically in the specification, a haloalkyl group may be optionally substituted.
  • Heterocyclyl or “heterocyclic ring” refers to a stable 3- to 18-membered aromatic (heteroaryl) or non-aromatic ring group, wherein at least one ring atom is a heteroatom selected from the group consisting of nitrogen, oxygen and sulfur, and the remaining ring atoms are selected from the group consisting of carbon nitrogen, oxygen and sulfur.
  • the heterocyclyl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heterocyclyl group may be optionally oxidized; the nitrogen atom may be optionally quaternized; and the heterocyclyl group may be partially or fully saturated.
  • heterocyclyl groups include, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thiomorph
  • N-heterocyclyl refers to a heterocyclyl group as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl group to the rest of the molecule is through a nitrogen atom in the heterocyclyl group. Unless stated otherwise specifically in the specification, a N-heterocyclyl group may be optionally substituted.
  • Heterocyclylalkyl refers to a group of the formula —R b R c where R b is an alkylene chain as defined above and R c is a heterocyclyl group as defined above, and if the heterocyclyl is a nitrogen-containing heterocyclyl, the heterocyclyl may be attached to the alkyl group at the nitrogen atom. Unless stated otherwise specifically in the specification, a heterocyclylalkyl group may be optionally substituted.
  • Heteroaryl refers to a 5- to 14-membered ring system group comprising one to thirteen carbon atoms, one to six heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur, and at least one aromatic ring.
  • the heteroaryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heteroaryl group may be optionally oxidized; the nitrogen atom may be optionally quaternized.
  • Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzothiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl, benzothiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, 1,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzotriazolyl, benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl, dibenzofuranyl, dibenzothiophenyl, furany
  • N-heteroaryl refers to a heteroaryl group as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl group to the rest of the molecule is through a nitrogen atom in the heteroaryl group. Unless stated otherwise specifically in the specification, an N-heteroaryl group may be optionally substituted.
  • Heteroarylalkyl refers to a group of the formula —R b R f where R b is an alkylene chain as defined above and R f is a heteroaryl group as defined above. Unless stated otherwise specifically in the specification, a heteroarylalkyl group may be optionally substituted.
  • “Hydroxylalkyl” refers to an alkyl group comprising at least one hydroxyl substituent.
  • the one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkyl group may be optionally substituted.
  • “Hydroxylalkylene” refers to an alkylene group comprising at least one hydroxyl substituent.
  • the one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylene group is optionally substituted.
  • “Hydroxylalkylether” refers to an alkylether group comprising at least one hydroxyl substituent.
  • the one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylether group may be optionally substituted.
  • Phosphate refers to the —OP( ⁇ O)(R a )R b group, wherein R a is OH, O ⁇ or OR c ; and R b is OH, O, OR c , a further phosphate group (as in diphosphate and triphosphate) thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, wherein R c is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphate group may be optionally substituted.
  • Phospho refers to the divalent —OP( ⁇ O)(R a )O— group, wherein R a is O ⁇ or OR c ; wherein R c is a counter ion (e.g., H+, Na+ and the like).
  • Phosphoalkyl refers to the —P( ⁇ O)(R a )R b group, wherein R a is OH, O ⁇ or OR c ; and R b is —Oalkyl, wherein R c is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkyl group may be optionally substituted.
  • the —Oalkyl moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Ophosphoalkyl is a phosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkyl group may be optionally substituted.
  • Phosphoalkylene refers to the divalent —OP( ⁇ O)(R a )R b — group, wherein R a is O ⁇ or OR c ; and R b is —Oalkylene, wherein R c is a counter ion (e.g., H+, Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkylene group is optionally substituted.
  • the alkylene moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituent is optionally substituted.
  • Phosphoalkylether refers to the —P( ⁇ O)(R a )R b group, wherein R a is OH, O ⁇ or OR c ; and R b is —Oalkylether, wherein R c is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkylether group may be optionally substituted.
  • the —Oalkylether moiety in a phosphoalkylether group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Ophosphoalkylether is a phosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkylether group may be optionally substituted.
  • “Sulfhydrylalkyl” refers to an alkyl group comprising at least one sulfhydryl substituent.
  • the one or more —SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkyl group may be optionally substituted.
  • “Sulfhydrylalkylether” refers to an alkylether group comprising at least one sulfhydryl substituent.
  • the one or more —SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkylether group may be optionally substituted.
  • “Sulfonate” refers to the —OS(O) 2 R a group, wherein R a is alkyl or aryl. Unless stated otherwise specifically in the specification, a sulfonate group may be optionally substituted.
  • Thioalkyl refers to a group of the formula —SR a where R a is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, a thioalkyl group may be optionally substituted.
  • “Thiophosphate” refers to the —OP( ⁇ R a )(R b )R, group, wherein R a is O or S, R b is OH, O, S, OR d or SR a ; and R c is OH, O, OR a , phosphate group thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, wherein R d is a counter ion (e.g., Na+ and the like) and provided that: R a is S or R b is S ⁇ or SR a ; or provided that R a is S and R b is S ⁇ or SR a . Unless stated otherwise specifically in the specification, a thiophosphate group may be optionally substituted.
  • “Thiophospho” refers to the divalent —R d P( ⁇ R a )(R b )R c — group, wherein R a , R c and R d are each independently O or S; R b is O, S, OR c or SR e ; wherein R c is a counter ion (e.g., H+, Na+ and the like) and provided that: R a is S; or R b is S ⁇ or SR e ; or R c is S; or R d is S, or combinations thereof.
  • R a is S
  • R b is S ⁇ or SR e
  • R c is S
  • R d is S, or combinations thereof.
  • Thiophosphoalkyl refers to the —P( ⁇ R a )(R b )R c group, wherein R a is O or S, R b is OH, O, S, OR d or SR a ; and R c is —Oalkyl, wherein R d is a counter ion (e.g., Na+ and the like) and provided that: R a is S or R b is S ⁇ or SR a ; or provided that R a is S and R b is S ⁇ or SR a . Unless stated otherwise specifically in the specification, a thiophosphoalkyl group may be optionally substituted.
  • the —Oalkyl moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • Othiophosphoalkyl is a thiophosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkyl group may be optionally substituted.
  • Thiophosphoalkylene refers to the divalent —R d P( ⁇ R a )(R b )R c — group, wherein R a and R d are each independently O or S, R b is O, S, OR c or SR e ; and R c is —Oalkylene or —Salkylene, wherein R c is a counter ion (e.g., H+, Na+ and the like) and provided that: R a is S; or R b is S ⁇ or SR e ; or R c is —Salkylene; or R d is S, or combinations thereof.
  • R a is S
  • R b is S ⁇ or SR e
  • R c is —Salkylene
  • R d is S, or combinations thereof.
  • a thiophosphoalkylene group is optionally substituted.
  • the alkylene moiety in a thiophosphoalkylene group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituents are optionally substituted.
  • Thiophosphoalkylether refers to the —P( ⁇ R a )(R b )R c group, wherein R a is O or S, R b is OH, O, S, OR d or SR a ; and R c is —Oalkylether, wherein R d is a counter ion (e.g., Na+ and the like) and provided that: R a is S or R b is S ⁇ or SR a ; or provided that R a is S and R b is S ⁇ or SR a .
  • a thiophosphoalkylether group may be optionally substituted.
  • the —Oalkylether moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Othiophosphoalkylether is a thiophosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkylether group may be optionally substituted.
  • substituted means any of the above groups (i.e., alkyl, alkylene, aminoalkylene, alkoxy, alkylamino, alkylether, alkylenether, polyalkylenether, hydroxylpolyalkylenether, aminopolyalkylenether, alkylphospho, alkyletherphospho, alkylthiophospho, alkyletherthiophospho, amide, thioalkyl, aryl, aryloxy, aralkyl, Oaralkyl, cyanoalkyl, carbocyclic ring, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl, heteroarylalkyl, hydroxylalkyl, a hydroxylalkylene, aminoalkyl, hydroxylalkylether, phosphoalkyl
  • “Substituted” also means any of the above groups in which one or more hydrogen atoms are replaced by a higher-order bond (e.g., a double- or triple-bond) to a heteroatom such as oxygen in oxo, carbonyl, carboxyl, and ester groups; and nitrogen in groups such as imines, oximes, hydrazones, and nitriles.
  • a higher-order bond e.g., a double- or triple-bond
  • nitrogen in groups such as imines, oximes, hydrazones, and nitriles.
  • substituted includes any of the above groups in which one or more hydrogen atoms are replaced with —NR g R h , —NR g C( ⁇ O)R h , —NR g C( ⁇ O)NR g R h , —NRgC( ⁇ O)OR h , —NRgSO 2 R h , —OC( ⁇ O)NR g R h , —OR g , —SR g , —SOR g , —SO 2 R g , —OSO 2 R g , —SO 2 OR g , ⁇ NSO 2 R g , and —SO 2 NR g R h .
  • “Substituted also means any of the above groups in which one or more hydrogen atoms are replaced with —C( ⁇ O)R g , —C( ⁇ O)OR g , —C( ⁇ O)NR g R h , —CH 2 SO 2 R g , —CH 2 SO 2 NR g R h .
  • R g and R h are the same or different and independently hydrogen, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl.
  • “Substituted” further means any of the above groups in which one or more hydrogen atoms are replaced by a bond to an amino, cyano, hydroxyl, imino, nitro, oxo, thioxo, halo, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl group.
  • each of the foregoing substituents may also be optionally substituted with one or more of the above substituents.
  • Conjugation refers to the overlap of one p-orbital with another p-orbital across an intervening sigma bond. Conjugation may occur in cyclic or acyclic compounds.
  • a “degree of conjugation” refers to the overlap of at least one p-orbital with another p-orbital across an intervening double bond. For example, 1, 3-butadine has one degree of conjugation, while benzene and other aromatic compounds typically have multiple degrees of conjugation. Fluorescent and colored compounds typically comprise at least one degree of conjugation.
  • Fluorescent refers to a molecule which is capable of absorbing light of a particular frequency and emitting light of a different frequency. Fluorescence is well-known to those of ordinary skill in the art.
  • Cold refers to a molecule which absorbs light within the colored spectrum (i.e., red, yellow, blue and the like).
  • a “linker” refers to a contiguous chain of at least one atom, such as carbon, oxygen, nitrogen, sulfur, phosphorous and combinations thereof, which connects a portion of a molecule to another portion of the same molecule or to a different molecule, moiety or solid support (e.g., microparticle). Linkers may connect the molecule via a covalent bond or other means, such as ionic or hydrogen bond interactions.
  • biomolecule refers to any of a variety of biological materials, including nucleic acids, carbohydrates, amino acids, polypeptides, glycoproteins, hormones, aptamers and mixtures thereof. More specifically, the term is intended to include, without limitation, RNA, DNA, oligonucleotides, modified or derivatized nucleotides, enzymes, receptors, prions, receptor ligands (including hormones), antibodies, antigens, and toxins, as well as bacteria, viruses, blood cells, and tissue cells.
  • the visually detectable biomolecules of the invention i.e., compounds of structure (I) having a biomolecule linked thereto
  • a biomolecule i.e., compounds of structure (I) having a biomolecule linked thereto
  • visible and “visually detectable” are used herein to refer to substances that are observable by visual inspection, without prior illumination, or chemical or enzymatic activation. Such visually detectable substances absorb and emit light in a region of the spectrum ranging from about 300 to about 900 nm. Preferably, such substances are intensely colored, preferably having a molar extinction coefficient of at least about 40,000, more preferably at least about 50,000, still more preferably at least about 60,000, yet still more preferably at least about 70,000, and most preferably at least about 80,000 M ⁇ 1 cm ⁇ 1 .
  • the biomolecules of the invention may be detected by observation with the naked eye, or with the aid of a optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners.
  • Visually detectable substances are not limited to those which emit and/or absorb light in the visible spectrum. Substances which emit and/or absorb light in the ultraviolet (UV) region (about 10 nm to about 400 nm), infrared (IR) region (about 700 nm to about 1 mm), and substances emitting and/or absorbing in other regions of the electromagnetic spectrum are also included with the scope of “visually detectable” substances.
  • UV ultraviolet
  • IR infrared
  • the term “photostable visible dye” refers to a chemical moiety that is visually detectable, as defined hereinabove, and is not significantly altered or decomposed upon exposure to light.
  • the photostable visible dye does not exhibit significant bleaching or decomposition after being exposed to light for at least one hour. More preferably, the visible dye is stable after exposure to light for at least 12 hours, still more preferably at least 24 hours, still yet more preferably at least one week, and most preferably at least one month.
  • Nonlimiting examples of photostable visible dyes suitable for use in the compounds and methods of the invention include azo dyes, thioindigo dyes, quinacridone pigments, dioxazine, phthalocyanine, perinone, diketopyrrolopyrrole, quinophthalone, and truarycarbonium.
  • perylene derivative is intended to include any substituted perylene that is visually detectable. However, the term is not intended to include perylene itself.
  • anthracene derivative e.g., perylene, pyrene, anthracene or naphthalene derivative
  • a derivative is an imide, bisimide or hydrazamimide derivative of perylene, anthracene, naphthalene, or pyrene.
  • the visually detectable biomolecules of the invention are useful for a wide variety of biochemical and biomedical applications in which there is a need to determine the presence, location, or quantity of a particular biomolecule.
  • the invention provides a method for visually detecting a biomolecule, comprising: (a) providing a biological system with a visually detectable biomolecule comprising the compound of structure (I) linked to a biomolecule; and (b) detecting the biomolecule by its visible properties.
  • the phrase “detecting the biomolecule by its visible properties” means that the biomolecule, without illumination or chemical or enzymatic activation, is observed with the naked eye, or with the aid of a optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners.
  • a densitometer may be used to quantify the amount of visually detectable biomolecule present.
  • the relative quantity of the biomolecule in two samples can be determined by measuring relative optical density. If the stoichiometry of dye molecules per biomolecule is known, and the extinction coefficient of the dye molecule is known, then the absolute concentration of the biomolecule can also be determined from a measurement of optical density.
  • biological system is used to refer to any solution or mixture comprising one or more biomolecules in addition to the visually detectable biomolecule.
  • biological systems include cells, cell extracts, tissue samples, electrophoretic gels, assay mixtures, and hybridization reaction mixtures.
  • Microparticle is a type of solid support and refers to any of a number of small particles useful for attachment to compounds of the invention, including, but not limited to, glass beads, magnetic beads, polymeric beads, nonpolymeric beads, and the like.
  • a microparticle comprises polystyrene beads.
  • Base pairing moiety refers to a heterocyclic moiety capable of hybridizing with a complementary heterocyclic moiety via hydrogen bonds (e.g., Watson-Crick base pairing).
  • Base pairing moieties include natural and unnatural bases.
  • Non-limiting examples of base pairing moieties are RNA and DNA bases such adenosine, guanosine, thymidine, cytosine and uridine and analogues thereof.
  • the invention disclosed herein is also meant to encompass all compounds of structure (I) being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number.
  • isotopes that can be incorporated into the disclosed compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2H, 3 H, 11 C, 13 C, 14 C, 13 N, 15 N, 15 O, 17 O, 18 O, 31 P, 32 P, 35 S, 18 F, 36 Cl, 123 I and 125 I respectively.
  • Isotopically-labeled compounds of structure (I) can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described below and in the following Examples using an appropriate isotopically-labeled reagent in place of the non-labeled reagent previously employed.
  • Solid compound and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
  • “Optional” or “optionally” means that the subsequently described event or circumstances may or may not occur, and that the description includes instances where said event or circumstance occurs and instances in which it does not.
  • “optionally substituted alkyl” means that the alkyl group may or may not be substituted and that the description includes both substituted alkyl groups and alkyl groups having no substitution.
  • Salt includes both acid and base addition salts.
  • Acid addition salt refers to those salts which are formed with inorganic acids such as, but not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4-acetamidobenzoic acid, camphoric acid, camphor-10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane-1,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, formic acid, fumaric acid, galactaric acid, gentisic acid, glucoheptonic
  • Base addition salt refers to those salts which are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like.
  • Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like.
  • Particularly preferred organic bases are isoprop
  • solvate refers to an aggregate that comprises one or more molecules of a compound of the invention with one or more molecules of solvent.
  • the solvent may be water, in which case the solvate may be a hydrate.
  • the solvent may be an organic solvent.
  • the compounds of the present invention may exist as a hydrate, including a monohydrate, dihydrate, hemihydrate, sesquihydrate, trihydrate, tetrahydrate and the like, as well as the corresponding solvated forms.
  • the compounds of the invention may be true solvates, while in other cases the compounds of the invention may merely retain adventitious water or another solvent or be a mixture of water plus some adventitious solvent.
  • the compounds of the invention may contain one or more asymmetric centers and may thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids.
  • the present invention is meant to include all such possible isomers, as well as their racemic and optically pure forms.
  • Optically active (+) and ( ⁇ ), (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques, for example, chromatography and fractional crystallization.
  • Conventional techniques for the preparation/isolation of individual enantiomers include chiral synthesis from a suitable optically pure precursor or resolution of the racemate (or the racemate of a salt or derivative) using, for example, chiral high pressure liquid chromatography (HPLC).
  • HPLC high pressure liquid chromatography
  • stereoisomer refers to a compound made up of the same atoms bonded by the same bonds but having different three-dimensional structures, which are not interchangeable.
  • the present invention contemplates various stereoisomers and mixtures thereof and includes “enantiomers”, which refers to two stereoisomers whose molecules are nonsuperimposeable mirror images of one another.
  • a “tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule.
  • the present invention includes tautomers of any said compounds.
  • Various tautomeric forms of the compounds are easily derivable by those of ordinary skill in the art.
  • Bonding refers to the process by which one molecule or atom associates with another atom or molecule. Bonding includes, ionic bonding, covalent bonding, chelation, association complexes, hydrogen bonding and the like.
  • a moiety capable of bonding with an analyte molecule or solid support is moiety capable of associating with the analyte molecule or solid support by any of the above means. In one embodiments, the moiety binds with the analyte molecule or solid support by covalent bonding (i.e., the moiety is capable of forming a covalent bond with the analyte molecule or solid support).
  • the compound has the following structure (I):
  • R 2 or R 3 is -L 9 -L 10 ) z -L 11 -Q. In other embodiments, at least one of R 2 or R 3 is -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I).
  • q is 1 and w is 0 for each integral value of n.
  • the compound has the following structure (Ia):
  • the compound has the following structure (Ib):
  • the compound has one of the following structures (Ic), (Id), (Ie) or (If):
  • w is 1 for at least one integral value of n.
  • the compound has the following structure (Ig):
  • R 5 is oxo and R 4 is O ⁇ or OZ.
  • R 2 is H or an electron pair
  • R 3 is -L 9 -(L 10 ) z -L 11 -Q.
  • R 2 is hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl or sulfhydrylalkylether, and R 3 is -L 9 -(L 10 ) z -L 11 -Q.
  • R 2 has one of the following structures:
  • R 3 is -L 9 -L 10 ) z -L 11 -Q
  • R 2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2 is optionally substituted with a substituent selected from —OH, —NH 2 and —SH.
  • R 2 has one of the following structures:
  • R 2 is -L 9 -L 10 ) z -L 11 -Q
  • R 3 is OH or phosphate
  • R 2 is -L 9 -L 10 ) z -L 11 -Q
  • R 3 is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH 2 and —SH.
  • R 3 has one of the following structures:
  • R 2 is -L 9 -L 10 ) z -L 11 -Q
  • R 3 is OH or phosphate
  • R 4a and R 4b are each O ⁇ and R 5a and R 5b are each oxo. In some other embodiments, R 4a and R 4b are each O ⁇ and R 5a and R 5b are each thioxo. In some different embodiments, R 4a and R 4b are each S ⁇ and R 5a and R 5b are each thioxo. In more different embodiments, R 4a and R 4b are each S ⁇ and R 5a and R 5b are each oxo.
  • At least one of a, b or c is 2.
  • each of a, b and c is 2.
  • At least one of a, b or c is 6.
  • each of a, b and c is 6.
  • n is an integer from 1 to 5. In some embodiments, n is an integer from 2 to 15. In some different embodiments, n is an integer from 2 to 10. In some other embodiments, n is an integer from 2 to 5.
  • Still other embodiments provide a compound having the following structure (II):
  • At least one of R 2 or R 3 is -L 9 -L 10 ) z -L-Q. In different embodiments, at least one of R 2 or R 3 is-L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I).
  • R 3 is -L 9 -(L 10 ) z -L 11 -Q
  • R 2 is an electron pair or H.
  • R 3 is -L 9 -L 10 ) z -L 11 -Q
  • R 2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2 is optionally substituted with a substituent selected from —OH, —NH 2 and —SH.
  • R 2 has one of the following structures:
  • R 2 is -L 9 -L 10 ) z -L 11 -Q
  • R 3 is OH or phosphate.
  • R 2 is -L 9 -L 10 ) z -L 11 -Q
  • R 3 is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH 2 , and —SH.
  • R 3 has one of the following structures:
  • R 4 is O and R 5 is oxo at each occurrence.
  • L 1 , L 3 and L 7 are each alkylene linkers.
  • L 1 and L 3 are each alkylene linkers and L 7 is absent.
  • alkylene is methylene.
  • At least one of R 2 or R 3 is -L 9 -L 10 ) z -L 11 -Q. In different embodiments, at least one of R 2 or R 3 is -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I).
  • x, y and z are each 1.
  • x is 0 and y and z are each 1.
  • M 1 is generally a visually detectable moiety or substance.
  • M 1 may be visually detectable in the UV, visible or IR spectrum.
  • M 1 is, at each occurrence, independently fluorescent or colored.
  • M 1 is fluorescent.
  • M 1 is not a purine or pyrimidine base, such as, but not limited to guanine, cytosine, thymidine and adenine. In other embodiments, M 1 is not a porphyrin. In other embodiments, M 1 is not one of the following:
  • M 1 comprises three or more aryl or heteroaryl rings, or combinations thereof, for example four or more aryl or heteroaryl rings, or combinations thereof, or even five or more aryl or heteroaryl rings, or combinations thereof.
  • M 1 comprises six aryl or heteroaryl rings, or combinations thereof.
  • the rings are fused.
  • M 1 comprises three or more fused rings, four or more fused rings, five or more fused rings, or even six or more fused rings.
  • M 1 is cyclic.
  • M 1 is carbocyclic.
  • M 1 is heterocyclic.
  • M 1 at each occurrence, independently comprises an aryl moiety.
  • the aryl moiety is multicyclic.
  • the aryl moiety is a fused-multicyclic aryl moiety, for example which may comprise at least 3, at least 4, or even more than 4 aryl rings.
  • M 1 at each occurrence, independently comprises at least one heteroatom.
  • the heteroatom is nitrogen, oxygen or sulfur.
  • M 1 at each occurrence, independently comprises at least one substituent.
  • the substituent is a fluoro, chloro, bromo, iodo, amino, alkylamino, arylamino, hydroxy, sulfhydryl, alkoxy, aryloxy, phenyl, aryl, methyl, ethyl, propyl, butyl, isopropyl, t-butyl, carboxy, sulfonate, amide, or formyl group.
  • M 1 at each occurrence, independently is a dimethylaminostilbene, quinacridone, fluorophenyl-dimethyl-BODIPY, his-fluorophenyl-BODIPY, acridine, terrylene, sexiphenyl, porphyrin, benzopyrene, (fluorophenyl-dimethyl-difluorobora-diaza-indacene)phenyl, (bis-fluorophenyl-difluorobora-diaza-indacene)phenyl, quaterphenyl, bi-benzothiazole, ter-benzothiazole, bi-naphthyl, bi-anthracyl, squaraine, squarylium, 9, 10-ethynylanthracene or ter-naphthyl moiety.
  • M 1 is, at each occurrence, independently p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, or perylene amide or a derivative thereof.
  • M 1 is, at each occurrence, independently a coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-1,8-naphthalimide dye.
  • M 1 at each occurrence is the same. In other embodiments, each M 1 is different. In still more embodiments, one or more M 1 is the same and one or more M 1 is different.
  • M 1 is pyrene, perylene, perylene monoimide or 6-FAM or derivative thereof. In some other embodiments, M 1 has one of the following structures:
  • M 2 is selected from any one of the above described M 1 moieties. In some embodiments, M 1 and M 2 are the same. In other embodiments, M 1 and M 2 are different.
  • At least one occurrence of M 2 is a base pairing moiety.
  • each occurrence of M 2 is a base pairing moiety.
  • the base pairing moiety is a purine, a pyrimidine, a dihydropyrimidine or a derivative thereof.
  • the base pairing moiety has one of the following structures:
  • n is an integer from 1 to 5.
  • n is an integer from 2 to 10, or 2 to 5, such as 3.
  • n is 1.
  • n is 2.
  • n is 3.
  • n is 4.
  • n is 5.
  • n is 6.
  • n is 7.
  • n is 8.
  • n is 9.
  • n is 10.
  • methylene spacer units i.e., x, y and z
  • x is 0. In other embodiments x is 1. In more embodiments, x is 2. In some embodiments x is 3. In other embodiments x is 4. In more embodiments, x is 5.
  • y is 0. In other embodiments y is 1. In more embodiments, y is 2. In some embodiments y is 3. In other embodiments y is 4. In more embodiments, y is 5.
  • z is 1-5. In some embodiments z is 0. In other embodiments z is 1. In more embodiments, z is 2. In some embodiments z is 3. In other embodiments z is 4. In more embodiments, z is 5.
  • x is 1, y is 0 and z is 1. In other embodiments, x is 0, y is 1 and z is 1.
  • L 9 is present.
  • L 9 is C 1 -C 6 alkylene.
  • L 10 is selected from the group consisting of polyalkylenether, phospho and phosphoalkylene.
  • L 10 is selected from the group consisting of
  • a is an integer from 1 to 6 and b is an integer from 2 to 10.
  • (L 10 ) z has one of the following structures:
  • b is an integer from 2-10, for example 5.
  • L 9 and L 11 are each independently a C 1 -C 6 alkylene linker. In some embodiments, L 9 is a C 2 alkylene linker. In other embodiments, L 11 is a C 6 alkylene linker.
  • Q is a moiety capable of bonding with an analyte molecule or a solid support.
  • Q provides a means of connecting the compound of structure (I) to an analyte molecule or a solid support (e.g., by a covalent bond).
  • Q is a reactive group capable of forming a covalent bond with an analyte molecule or a solid support.
  • the type of Q group and connectivity of the Q group to the remainder of the compound of structure (I) is not limited.
  • the Q is a moiety which is not susceptible to hydrolysis under aqueous conditions, but is sufficiently reactive to form a bond with a corresponding group on an analyte molecule or solid support (e.g., an amine).
  • Q is a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group.
  • Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, ⁇ -haloamide, biotin, amino or a maleimide.
  • the activated ester is an N-succinimide ester, imidoester or polyflourophenyl ester.
  • the alkyne is an alkyl azide or acyl azide.
  • —SH can be readily conjugated to many analyte molecules, bifinctiponal linker groups and/or solid supports (e.g., by formation of a disulfide bond with a free sulfhydryl on the analyte molecule or solid support).
  • At least one of R 2 or R 3 is -L 9 -L 10 ) z -L 11 -Q or -L 9 -(L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 -I, where I represents, independently, a further compound of structure (I).
  • “Compound of structure (I)” refers to any of the compounds described herein, which are encompassed by structure (I).
  • the dimer may be formed between any one of R 2 or R 3 and another one of R 2 or R 3 .
  • an exemplary dimer, wherein the dimer is formed between two R 2 groups is illustrated below (Ia′):
  • R 1 , R 3 , R 4 , R 5 , L 1 , L 3 , L 7 , L 9 , L 10 , L 11 and z are each independently as defined for any of the foregoing embodiments.
  • the dimers are also illustrated as follows (Ia′):
  • the disulfide linker between the two compounds of structure (I), i.e., -L 9 (L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 - can have various structures.
  • -L 9 (L 10 ) z -L 11 -S—S-L 11 -(L 10 ) z -L 9 - has one of the following structures:
  • Q is an analyte molecule or solid support.
  • the analyte molecule is a biomolecule.
  • the biomolecule is a nucleic acid, amino acid or a polymer thereof.
  • the biomolecule is a nucleic acid, peptide, carbohydrate, lipid, enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer, antigen or prion.
  • the analyte molecule is a drug, vitamin or small molecule.
  • R 7 , R 8 , R 9 , R 10 , R 11 and R 12 when present, are each H.
  • x 1 , y 1 and z 1 are each 1.
  • each x 1 is 0 and each y 1 and z 1 are 1.
  • each x 2 is 1 and each y 2 and z 2 are 0.
  • M 1 is as defined in any one of the foregoing embodiments.
  • M 1 is perylene.
  • Q is as defined in any one of the foregoing embodiments.
  • Q is —SH.
  • each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • R 20 is phosphate, —CH 2 OPO 3 2 — or CH 2 OH.
  • the compound has the following structure:
  • M 1 is as defined in any one of the foregoing embodiments.
  • M 1 is perylene.
  • each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • R 20 is phosphate, CH 2 OPO 3 2 — or CH 2 OH.
  • the disulfide dimer has the following structure:
  • M 1 has the following structure:
  • M 1 is as defined in any one of the foregoing embodiments.
  • M 1 is perylene.
  • Q is as defined in any one of the foregoing embodiments.
  • Q is —SH.
  • each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • R 20 is phosphate, CH 2 OPO 3 2 — or CH 2 OH.
  • the compound has the following structure:
  • M 1 has the following structure:
  • M 1 is as defined in any one of the foregoing embodiments.
  • M 1 is perylene.
  • each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • R 20 is phosphate, CH 2 OPO 3 2 — or CH 2 OH.
  • the disulfide dimer has the following structure:
  • M 1 has the following structure:
  • compositions comprising any of the foregoing compounds and one or more biomolecules are provided in various other embodiments. In some embodiments, use of such compositions in analytical methods for detection of the one or more biomolecules are also provided.
  • the compounds are useful in various analytical methods.
  • the disclosure provides a method of staining a sample, the method comprising adding to said sample a compound of structure (I), wherein R 2 is -L 9 -L 10 ) z -L 11 -Q, Q is a moiety capable of bonding with an analyte molecule and R 3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
  • R 2 is a linker comprising a covalent linkage to a biomolecule.
  • a biomolecule for example, a nucleic acid, amino acid or a polymer thereof (e.g., polynucleotide or polypeptide).
  • the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
  • R 2 comprises a linker comprising a covalent linkage to a microparticle.
  • the microparticle is a polymeric bead or nonpolymeric bead.
  • said optical response is a fluorescent response.
  • said sample comprises cells, and some embodiments further comprise observing said cells by flow cytometry.
  • the method further comprises distinguishing the fluorescence response from that of a second fluorophore having detectably different optical properties.
  • the disclosure provides a method for visually detecting a biomolecule, comprising:
  • a nucleic acid, amino acid or a polymer thereof e.g., polynucleotide or polypeptide
  • the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
  • a method for visually detecting a biomolecule comprising:
  • any embodiment of the compounds of structure (I), as set forth above, and any specific choice set forth herein for a R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , q, w and n variable in the compounds of structure (I), as set forth above, may be independently combined with other embodiments and/or variables of the compounds of structure (I) to form embodiments of the inventions not specifically set forth above.
  • Suitable protecting groups include hydroxy, amino, mercapto and carboxylic acid.
  • Suitable protecting groups for hydroxy include trialkylsilyl or diarylalkylsilyl (for example, t-butyldimethylsilyl, t-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl, benzyl, and the like.
  • Suitable protecting groups for amino, amidino and guanidino include t-butoxycarbonyl, benzyloxycarbonyl, and the like.
  • Suitable protecting groups for mercapto include —C(O)—R 11 (where R 11 is alkyl, aryl or arylalkyl), p-methoxybenzyl, trityl and the like.
  • Suitable protecting groups for carboxylic acid include alkyl, aryl or arylalkyl esters.
  • Protecting groups may be added or removed in accordance with standard techniques, which are known to one skilled in the art and as described herein. The use of protecting groups is described in detail in Green, T. W. and P. G. M. Wutz, Protective Groups in Organic Synthesis (1999), 3rd Ed., Wiley.
  • the protecting group may also be a polymer resin such as a Wang resin, Rink resin or a 2-chlorotrityl-chloride resin.
  • Reaction Scheme I illustrates and exemplary method for preparing compounds of structure I.
  • R 2′ and R 3′ represent R 2 and R 3 moieties as defined herein, or precursors to R 2 and R 3 moieties or protected derivatives thereof which can be converted to the desired R 2 and R 3 moieties using techniques known in the art and provided in the examples below.
  • compounds of structure a can be purchased or prepared by methods well-known to those of ordinary skill in the art.
  • Reaction of a with M 1 -X, where x is a halogen such as bromo under Suzuki coupling conditions known in the art results in compounds of structure b.
  • Compounds of structure b can be modified to obtain number of other compounds of structure I.
  • compounds of structure b can be oligomerized to obtain other compounds of structure I (i.e., where n is greater than 1, such as 2-10).
  • exemplary methods for oligomerization include methods analogous to phosphoramadite-based solid-phase oligonucleotide synthesis, which is well known in the art.
  • Reaction Scheme II illustrates an alternative method for preparation of compounds of structure I.
  • R 2′ and R 3′ represent R 2 and R 3 moieties as defined herein, or precursors to R 2 and R 3 moieties or protected derivatives thereof which can be converted to the desired R 2 and R 3 moieties using techniques known in the art and provided in the examples below.
  • a compound of structure c which can be purchased or prepared by well-known techniques, is reacted with M 1 -Z to yield compounds of structure d.
  • Y and Z represent function groups having complementary reactivity (i.e., functional groups which react to form a covalent bond).
  • Z may be pendant to M 1 or a part of the structural backbone of M, for example a cyclic anhydride.
  • Y may be any number of functional groups, such as amino.
  • the compounds of structure I are oligomers comprising from 2-10 repeating units.
  • Such oligomers can be prepared using methods analogous to well-known automated DNA synthesis methods. DNA synthesis methods are well-known in the art. Briefly, two alcohol groups are functionalized with a dimethoxytrityl (DMT) group and a 2-cyanoethyl-N,N-diisopropylamino phosphoramidite group, respectively. The phosphoramidite group is coupled to an alcohol group, typically in the presence of an activator such as tetrazole, followed by oxidation of the phosphorous atom with iodine.
  • DMT dimethoxytrityl
  • 2-cyanoethyl-N,N-diisopropylamino phosphoramidite group respectively.
  • the phosphoramidite group is coupled to an alcohol group, typically in the presence of an activator such as tetrazole, followed by oxidation of the phosphorous atom with i
  • the dimethoxytrityl group can be removed with acid (e.g., chloroacetic acid) to expose the free alcohol, which can be reacted with a phosphoramidite group.
  • acid e.g., chloroacetic acid
  • the 2-cyanoethyl group can be removed after oligomerization by treatment with aqueous ammonia.
  • Preparation of the phosphoramidites used in the oligomerization methods is also well-known in the art.
  • a primary alcohol e.g., R 3
  • a secondary alcohol e.g., R 2
  • R 3 a primary alcohol
  • R 2 a secondary alcohol
  • R 2 is then functionalized as a phosphoramidite by reaction with an appropriate reagent such as 2-cyanoethyl N,N-dissopropylchlorophosphoramidite.
  • Phosphoramidites and precursor molecules were analyzed using an Agilent Infinity 1260 UHPLC system with a diode array detector and High Performance Autosampler using an Aapptec® SpiritTM Peptide C 18 column (4.6 mm ⁇ 100 mm, 5 ⁇ m particle size). Excitation and emission profiles experiments were recorded on a Cary Eclipse spectra photometer.
  • oligomer dyes were synthesized on an ABI 394 DNA synthesizer using standard protocols for the phosphoramidite-based coupling approach.
  • the chain assembly cycle for the synthesis of oligomers was the following: (i) detritylation, 3% trichloroacetic acid in dichloromethane, 1 min; (ii) coupling, 0.1 M phosphoramidite and 0.45 M tetrazole in acetonitrile, 10 min; (iii) capping, 0.5 M acetic anhydride in THF/lutidine, 1/1, v/v 15 s; (iv) oxidation, 0.1 M iodine in THF/pyridine/water, 10/10/1, v/v/v, 30 s.
  • Example 1 exemplifies a water soluble dye substance, modified to contain an activated ester group (2 and 3), which can be conjugated to macromolecules having primary amine functional groups.
  • a dye sequence (1) containing a disulfide linker is reduced with tris(2-carboxyethyl)phosphine (TCEP) to release two smaller dye sequences, each with a Fluor and a free thiol terminus.
  • TCEP tris(2-carboxyethyl)phosphine
  • Equation 3 was used to calculate the moles of TCEP required to achieve a 11.3:1 molar ratio of TCEP to COMPOUND 1.
  • Equation 4 was used to calculate the volume of TCEP to add to COMPOUND 1:
  • the HCl salt of TCEP is acidic and reduction of the COMPOUND 1 needs to occur at slightly acidic to neutral pH (e.g. pH 6-7).
  • the NaPO 4 buffer should be in approximately 5-fold or higher molar excess maintain a pH of 6.5. Since the molarity of 0.6 M NaPO 4 stock solution is 5.45-fold higher than the 0.111 M TCEP stock solution, an equal volume of the stock added to TCEP is sufficient to buffer the reaction.
  • COMPOUND 1 products There are two reduced COMPOUND 1 products: the 5′-ECC-SH species which has an expected mass of 785 Daltons and the HS-CCE-3′ species which has an expected mass of 865 Daltons.
  • HPLC-MS analysis showed HNSA activated dye sequences were somewhat subject to degradation via either buffer-related methanol addition or hydration at the HNSA ester position of the molecule, but also showed that intact COMPOUND 1-HNSA reacted predictably with TRIS. Only the results for the 5′-ECC—S-HNSA product are shown.
  • a water soluble dye with a functional maleimide group was synthesized by reacting a water soluble dye containing a terminal primary amine (compound 4) with the N-Hydroxysuccinimidyl group of Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (Sulfo-SMCC).
  • Sulfo-SMCC is acidic and addition of the compound 4 should occur at slightly basic to neutral pH (e.g. pH 7.5-8.5).
  • the pH of the reaction was approximately 7.5 using litmus paper. Incubate the reaction overnight at lab room temperature (approximately 23° C.). Calculate the final concentrations of the reactants for the reaction. Measure the pH of the reaction using litmus paper that spans a pH range of 7-14. Remove a sample for HPLC/MS analysis before reaction and once the reaction is complete. M.S. analysis of compound 4 before reaction: Calculated MW is 888.4. MW found is 887.2. M.S. analysis of compound 5 before reaction: Calculated MW is 1107.2. MW found is 1106.4.
  • Compound 5 was purified to an overall purity of 78% from the crude reaction mixture as follows:

Abstract

Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I):or a stereoisomer, tautomer or salt thereof, wherein R1, R2, R3, R4, R5, L1, L3, L4, L6, L7, L8, M1, M2, q, w and n are as defined herein. Methods associated with preparation and use of such compounds are also provided.

Description

    BACKGROUND OF THE INVENTION Field
  • The present invention is directed to novel fluorescent or colored dyes and methods for their preparation and use in various analytical methods.
    • Description of the Related Art
  • Fluorescent and/or colored dyes are known to be particularly suitable for applications in which a highly sensitive detection reagent is desirable. Dyes that are able to preferentially label a specific ingredient or component in a sample enable the researcher to determine the presence, quantity and/or location of that specific ingredient or component. In addition, specific systems can be monitored with respect to their spatial and temporal distribution in diverse environments.
  • Fluorescence and colorimetric methods are extremely widespread in chemistry and biology. These methods give useful information on the presence, structure, distance, orientation, complexation and/or location for biomolecules. In addition, time-resolved methods are increasingly used in measurements of dynamics and kinetics. As a result, many strategies for fluorescence or color labeling of biomolecules, such as nucleic acids and protein, have been developed.
  • Perylenes and related dyes have high photochemical persistency (chemical, thermal, and photochemical stability) and high fluorescence quanta yield and are used in a variety of reprographic processes, solar cells, photovoltaic devices, and dye lasers. However, perylene derivatives have been used primarily as pigments and fluorescent dyes. Perylene dyes of various colors and light-absorbing properties have been reported. For example, Becker S. et al, Chem. Eur. J., 6,213,984, (2000), report the synthesis of thermotropic perylenedicarboximide chromophores that show a color change from blue to orange. Perylene and related chromophores have seen limited use as biomolecular probes, apparently due to the strongly hydrophobic character of these types of molecules and difficulties with regiospecific labeling of biomolecules with the same.
  • There is thus a need in the art for water soluble dyes and biomarkers that permit visual or fluorescent detection of biomolecules without prior illumination or chemical or enzymatic activation. Ideally, such dyes and biomarkers should be intensely colored or fluorescent and should be available in a variety of colors and fluorescent wavelengths. The present invention fulfills this need and provides further related advantages.
    • BRIEF SUMMARY
  • In brief, the present invention is generally directed to compounds useful as water soluble, fluorescent or colored dyes and probes that enable visual detection of biomolecules and other analytes, as well as reagents for their preparation. Methods for visually detecting a biomolecule and for determining the size of a biomolecule are also described. The water soluble, fluorescent or colored dyes of the invention are intensely colored and/or fluorescent and can be readily observed by visual inspection or other means. In some embodiments the compounds may be observed without prior illumination or chemical or enzymatic activation. By appropriate selection of the dye, as described herein, visually detectable biomolecules of a variety of colors may be obtained.
  • In one embodiment, compounds having the following structure (I) are provided:
  • Figure US20240043455A1-20240208-C00002
  • or a stereoisomer, tautomer or salt thereof, wherein R1, R2, R3, R4, R5, L1, L3, L4, L6, L7, L8, M1, M2, q, w and n are as defined herein.
  • In another embodiment, a method for staining a sample is provided, the method comprises adding to said sample a representative compound as described herein in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
  • In still other embodiments, the present disclosure provides a method for visually detecting a biomolecule, comprising:
      • (a) providing a representative compound described herein; and
      • (b) detecting the compound by its visible properties.
  • Other disclosed methods include a method for visually detecting a biomolecule, the method comprising:
      • (a) admixing any of the disclosed compounds with one or more biomolecules; and
      • (b) detecting the compound by its visible properties.
  • Other embodiments are directed to a composition comprising any one of the disclosed compounds and one or more biomolecules. Use of such composition in analytical methods for detection of the one or more biomolecules is also provided.
  • These and other aspects of the invention will be apparent upon reference to the following detailed description.
    • DETAILED DESCRIPTION OF THE INVENTION
  • In the following description, certain specific details are set forth in order to provide a thorough understanding of various embodiments of the invention. However, one skilled in the art will understand that the invention may be practiced without these details.
  • Unless the context requires otherwise, throughout the present specification and claims, the word “comprise” and variations thereof, such as, “comprises” and “comprising” are to be construed in an open, inclusive sense, that is, as “including, but not limited to”.
  • Reference throughout this specification to “one embodiment” or “an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, the appearances of the phrases “in one embodiment” or “in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in one or more embodiments.
      • “Amino” refers to the —NH2 group.
      • “Carboxy” refers to the —CO2H group.
      • “Cyano” refers to the —CN group.
      • “Formyl” refers to the —C(═O)H group.
      • “Hydroxy” or “hydroxyl” refers to the —OH group.
      • “Imino” refers to the ═NH group.
      • “Nitro” refers to the —NO2 group.
      • “Oxo” refers to the ═O substituent group.
      • “Sulfhydryl” refers to the —SH group.
      • “Thioxo” refers to the ═S group.
  • “Alkyl” refers to a straight or branched hydrocarbon chain group consisting solely of carbon and hydrogen atoms, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), having from one to twelve carbon atoms (C1-C12 alkyl), preferably one to eight carbon atoms (C1-C8 alkyl) or one to six carbon atoms (C1-C6 alkyl), and which is attached to the rest of the molecule by a single bond, e.g., methyl, ethyl, n-propyl, 1-methylethyl (iso-propyl), n-butyl, n-pentyl, 1,1-dimethylethyl (t-butyl), 3-methylhexyl, 2-methylhexyl, ethenyl, prop-1-enyl, but-1-enyl, pent-1-enyl, penta-1,4-dienyl, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like. Unless stated otherwise specifically in the specification, an alkyl group may be optionally substituted.
  • “Alkylene” or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a substituent group, consisting solely of carbon and hydrogen, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), and having from one to twelve carbon atoms, e.g., methylene, ethylene, propylene, n-butylene, ethenylene, propenylene, n-butenylene, propynylene, n-butynylene, and the like. The alkylene chain is attached to the rest of the molecule through a single or double bond and to the substituent group through a single or double bond. The points of attachment of the alkylene chain to the rest of the molecule and to the substituent group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkylene chain may be optionally substituted.
  • “Aminoalkylene” refers to an alkylene, as defined, comprising one or more amino substituents. Unless stated otherwise specifically in the specification, aminoalkylene groups are optionally substituted
  • “Alkoxy” refers to a group of the formula —ORa where Ra is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkoxy group may be optionally substituted.
  • “Alkylamino” refers to a group of the formula —NHRa or —NRaRa where each Ra is, independently, an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkylamino group may be optionally substituted.
  • “Alkylether” refers to any alkyl group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond. The carbon-oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C—O—C). Alkylethers include at least one carbon oxygen bond, but may include more than one. For example, polyethylene glycol (PEG) is included within the meaning of alkylether. Unless stated otherwise specifically in the specification, an alkylether group may be optionally substituted. For example, in some embodiments and alkylether is substituted with an alcohol or phosphate.
  • “Alkylenether” refers to an alkylene group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond. The carbon-oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C—O—C). Alkylenethers include at least one carbon oxygen bond, but may include more than one (i.e., a “polyalkylenether”). PEG linking groups are examples of polyalkylenethers. “Hydroxylpolyalkylenether” refers to a polyalkylenether comprising at least on hydroxyl substituent.
  • “Aminopolyalkylenether” refers to a polyalkylenether comprising at least one amino (including alkylamino, arylamino and aralkylamino) substituent. Unless stated otherwise specifically in the specification, alkylenether, polyalkylenether, hydroxylpolyalkylenether and aminopolyalkylenether groups, are optionally substituted.
  • “Alkylphospho” refers to the —RP(═O)(Ra)Rb group, wherein R is an alkylene group, Ra is OH, O− or ORc; and Rb is —Oalkyl or —Oalkylether, wherein Rc is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, an alkylphospho group may be optionally substituted. For example, in certain embodiments, the —Oalkyl or —Oalkylether moiety (Rb) in a alkylphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Oalkylphospho is an alkylphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylphospho group may be optionally substituted.
  • “Alkyetherphospho” refers to the —RP(═O)(Ra)Rb group, wherein R is an alkylenether group, Ra is OH, O− or ORc; and Rb is —Oalkyl or —Oalkylether, wherein Re is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, an alkyletherphopsho group may be optionally substituted. For example, in certain embodiments, the —Oalkyl or —Oalkylether moiety (Rb) in an alkyletherphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Oalkyletherphospho is an alkyletherphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkyletherphospho group may be optionally substituted.
  • “Alkylthiophospho” refers to the —P(═Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O−, S− ORd or SRa; and Rc is —Oalkyl or —Oalkylether, wherein Rd is a counter ion (e.g., Na+ and the like) and provided that: Ra is S or Rb is S− or SRd; or provided that Ra is S and Rb is S− or SRa. Unless stated otherwise specifically in the specification, a alkylthiophospho group may be optionally substituted. For example, in certain embodiments, the —Oalkyl or —Oalkylether moiety in a alkythiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Oalkylthiophospho is a alkylthiophospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylthiophospho group may be optionally substituted.
  • “Alkyletherthiophospho” refers to the —P(═Ra)(Rb)R, group, wherein Ra is O or S, Rb is OH, O, S, ORd or SRa; and Rc is —Oalkyl or —Oalkylether, wherein Rd is a counter ion (e.g., Na+ and the like) and provided that: Ra is S or Rb is S− or SRd; or provided that Ra is S and Rb is S− or SRa. Unless stated otherwise specifically in the specification, an alkyletherthiophospho group may be optionally substituted. For example, in certain embodiments, the —Oalkyl or —Oalkylether moiety in a alkyletherthiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Oalkyletherthiophospho is an alkyletherthiophospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkyletherthiophospho group may be optionally substituted.
  • “Amide” refers to the —NRaRb radical, wherein Ra and Rb are independently H, alkyl or aryl. Unless stated otherwise specifically in the specification, an amide group may be optionally substituted.
  • “Aryl” refers to a carbocyclic ring system group comprising 6 to 18 carbon atoms and at least one carbocyclic aromatic ring. For purposes of this invention, the aryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems. Aryl groups include, but are not limited to, aryl groups derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene. Unless stated otherwise specifically in the specification, the term “aryl” or the prefix “ar-” (such as in “aralkyl”) is meant to include aryl groups that are optionally substituted.
  • “Aryloxy” refers to a group of the formula —ORa, where Ra is an aryl moiety as defined above, for example phenoxy and the like. Unless stated otherwise specifically in the specification, an aryloxy group may be optionally substituted.
  • “Aralkyl” refers to a group of the formula —Rb—R, where Rb is an alkylene chain as defined above and R, is one or more aryl groups as defined above, for example, benzyl, diphenylmethyl and the like. Unless stated otherwise specifically in the specification, an aralkyl group may be optionally substituted.
  • “Oaralkyl” is an aralkyl group which is connected to the remainder of the molecule via an oxygen linkage. “ODMT” refers to dimethoxytrityl linked to the rest of the molecule via an O atom. Unless stated otherwise specifically in the specification, an Oaralkyl group may be optionally substituted.
  • “Cyanoalkyl” refers to an alkyl group comprising at least one cyano substituent. The one or more —CN substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a cyanoalkyl group may be optionally substituted.
  • A “carbocyclic ring” is a ring wherein each ring atom is carbon. Carbocyclic rings may staturated or unsaturated, including aromatic rings. Unless stated otherwise specifically in the specification, a carbocylic group is optionally substituted.
  • Cycloalkyl” refers to a stable non-aromatic monocyclic or polycyclic carbocyclic ring, which may include fused or bridged ring systems, having from three to fifteen carbon atoms, preferably having from three to ten carbon atoms, and which is saturated or unsaturated and attached to the rest of the molecule by a single bond. Monocyclic cycloalkyl groups include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Polycyclic cycloalkyl groups include, for example, adamantyl, norbornyl, decalinyl, 7,7-dimethyl-bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, a cycloalkyl group may be optionally substituted.
  • “Cycloalkylalkyl” refers to a group of the formula —RbRa where Rb is an alkylene chain as defined above and Rd is a cycloalkyl group as defined above. Unless stated otherwise specifically in the specification, a cycloalkylalkyl group may be optionally substituted.
  • “Multicyclic” refers to any molecule having more than one ring. The rings may be either, fused, spirocyclic or separated by one or more atoms (e.g., linked via an acyclic linker).
  • “Spirocyclic” refers to a multicyclic molecule wherein two rings share a single carbon atom.
  • “Fused” refers to any ring structure described herein which is fused to an existing ring structure in the compounds of the invention. When the fused ring is a heterocyclyl ring or a heteroaryl ring, any carbon atom on the existing ring structure which becomes part of the fused heterocyclyl ring or the fused heteroaryl ring may be replaced with a nitrogen atom.
  • “Halo” or “halogen” refers to bromo, chloro, fluoro or iodo.
  • “Haloalkyl” refers to an alkyl group, as defined above, that is substituted by one or more halo groups, as defined above, e.g., trifluoromethyl, difluoromethyl, trichloromethyl, 2,2,2-trifluoroethyl, 1,2-difluoroethyl, 3-bromo-2-fluoropropyl, 1,2-dibromoethyl, and the like. Unless stated otherwise specifically in the specification, a haloalkyl group may be optionally substituted.
  • “Heterocyclyl” or “heterocyclic ring” refers to a stable 3- to 18-membered aromatic (heteroaryl) or non-aromatic ring group, wherein at least one ring atom is a heteroatom selected from the group consisting of nitrogen, oxygen and sulfur, and the remaining ring atoms are selected from the group consisting of carbon nitrogen, oxygen and sulfur. Unless stated otherwise specifically in the specification, the heterocyclyl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heterocyclyl group may be optionally oxidized; the nitrogen atom may be optionally quaternized; and the heterocyclyl group may be partially or fully saturated. Examples of such heterocyclyl groups include, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thiomorpholinyl, and 1,1-dioxo-thiomorpholinyl. Unless stated otherwise specifically in the specification, Unless stated otherwise specifically in the specification, a heterocyclyl group may be optionally substituted.
  • “N-heterocyclyl” refers to a heterocyclyl group as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl group to the rest of the molecule is through a nitrogen atom in the heterocyclyl group. Unless stated otherwise specifically in the specification, a N-heterocyclyl group may be optionally substituted.
  • “Heterocyclylalkyl” refers to a group of the formula —RbRc where Rb is an alkylene chain as defined above and Rc is a heterocyclyl group as defined above, and if the heterocyclyl is a nitrogen-containing heterocyclyl, the heterocyclyl may be attached to the alkyl group at the nitrogen atom. Unless stated otherwise specifically in the specification, a heterocyclylalkyl group may be optionally substituted.
  • “Heteroaryl” refers to a 5- to 14-membered ring system group comprising one to thirteen carbon atoms, one to six heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur, and at least one aromatic ring. For purposes of this invention, the heteroaryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heteroaryl group may be optionally oxidized; the nitrogen atom may be optionally quaternized. Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzothiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl, benzothiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, 1,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzotriazolyl, benzo[4,6]imidazo[1,2-a]pyridinyl, carbazolyl, cinnolinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, naphthyridinyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl, 1-oxidopyridinyl, 1-oxidopyrimidinyl, 1-oxidopyrazinyl, 1-oxidopyridazinyl, 1-phenyl-1H-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, pyridazinyl, quinazolinyl, quinoxalinyl, quinolinyl, quinuclidinyl, isoquinolinyl, tetrahydroquinolinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, and thiophenyl (i.e., thienyl). Unless stated otherwise specifically in the specification, a heteroaryl group may be optionally substituted.
  • “N-heteroaryl” refers to a heteroaryl group as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl group to the rest of the molecule is through a nitrogen atom in the heteroaryl group. Unless stated otherwise specifically in the specification, an N-heteroaryl group may be optionally substituted.
  • “Heteroarylalkyl” refers to a group of the formula —RbRf where Rb is an alkylene chain as defined above and Rf is a heteroaryl group as defined above. Unless stated otherwise specifically in the specification, a heteroarylalkyl group may be optionally substituted.
  • “Hydroxylalkyl” refers to an alkyl group comprising at least one hydroxyl substituent. The one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkyl group may be optionally substituted.
  • “Hydroxylalkylene” refers to an alkylene group comprising at least one hydroxyl substituent. The one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylene group is optionally substituted.
  • “Hydroxylalkylether” refers to an alkylether group comprising at least one hydroxyl substituent. The one or more —OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylether group may be optionally substituted.
  • “Phosphate” refers to the —OP(═O)(Ra)Rb group, wherein Ra is OH, O− or ORc; and Rb is OH, O, ORc, a further phosphate group (as in diphosphate and triphosphate) thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, wherein Rc is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphate group may be optionally substituted.
  • “Phospho” refers to the divalent —OP(═O)(Ra)O— group, wherein Ra is O− or ORc; wherein Rc is a counter ion (e.g., H+, Na+ and the like).
  • “Phosphoalkyl” refers to the —P(═O)(Ra)Rb group, wherein Ra is OH, O− or ORc; and Rb is —Oalkyl, wherein Rc is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkyl group may be optionally substituted. For example, in certain embodiments, the —Oalkyl moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Ophosphoalkyl is a phosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkyl group may be optionally substituted.
  • “Phosphoalkylene” refers to the divalent —OP(═O)(Ra)Rb— group, wherein Ra is O− or ORc; and Rb is —Oalkylene, wherein Rc is a counter ion (e.g., H+, Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkylene group is optionally substituted. For example, in certain embodiments, the alkylene moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituent is optionally substituted.
  • “Phosphoalkylether” refers to the —P(═O)(Ra)Rb group, wherein Ra is OH, O− or ORc; and Rb is —Oalkylether, wherein Rc is a counter ion (e.g., Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkylether group may be optionally substituted. For example, in certain embodiments, the —Oalkylether moiety in a phosphoalkylether group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Ophosphoalkylether is a phosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkylether group may be optionally substituted.
  • “Sulfhydrylalkyl” refers to an alkyl group comprising at least one sulfhydryl substituent. The one or more —SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkyl group may be optionally substituted.
  • “Sulfhydrylalkylether” refers to an alkylether group comprising at least one sulfhydryl substituent. The one or more —SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkylether group may be optionally substituted.
  • “Sulfonate” refers to the —OS(O)2Ra group, wherein Ra is alkyl or aryl. Unless stated otherwise specifically in the specification, a sulfonate group may be optionally substituted.
  • “Thioalkyl” refers to a group of the formula —SRa where Ra is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, a thioalkyl group may be optionally substituted.
  • “Thiophosphate” refers to the —OP(═Ra)(Rb)R, group, wherein Ra is O or S, Rb is OH, O, S, ORd or SRa; and Rc is OH, O, ORa, phosphate group thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, wherein Rd is a counter ion (e.g., Na+ and the like) and provided that: Ra is S or Rb is S− or SRa; or provided that Ra is S and Rb is S− or SRa. Unless stated otherwise specifically in the specification, a thiophosphate group may be optionally substituted.
  • “Thiophospho” refers to the divalent —RdP(═Ra)(Rb)Rc— group, wherein Ra, Rc and Rd are each independently O or S; Rb is O, S, ORc or SRe; wherein Rc is a counter ion (e.g., H+, Na+ and the like) and provided that: Ra is S; or Rb is S− or SRe; or Rc is S; or Rd is S, or combinations thereof.
  • “Thiophosphoalkyl” refers to the —P(═Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O, S, ORd or SRa; and Rc is —Oalkyl, wherein Rd is a counter ion (e.g., Na+ and the like) and provided that: Ra is S or Rb is S− or SRa; or provided that Ra is S and Rb is S− or SRa. Unless stated otherwise specifically in the specification, a thiophosphoalkyl group may be optionally substituted. For example, in certain embodiments, the —Oalkyl moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
  • “Othiophosphoalkyl is a thiophosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkyl group may be optionally substituted.
  • “Thiophosphoalkylene” refers to the divalent —RdP(═Ra)(Rb)Rc— group, wherein Ra and Rd are each independently O or S, Rb is O, S, ORc or SRe; and Rc is —Oalkylene or —Salkylene, wherein Rc is a counter ion (e.g., H+, Na+ and the like) and provided that: Ra is S; or Rb is S− or SRe; or Rc is —Salkylene; or Rd is S, or combinations thereof. Unless stated otherwise specifically in the specification, a thiophosphoalkylene group is optionally substituted. For example, in certain embodiments, the alkylene moiety in a thiophosphoalkylene group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituents are optionally substituted.
  • “Thiophosphoalkylether” refers to the —P(═Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O, S, ORd or SRa; and Rc is —Oalkylether, wherein Rd is a counter ion (e.g., Na+ and the like) and provided that: Ra is S or Rb is S− or SRa; or provided that Ra is S and Rb is S− or SRa. Unless stated otherwise specifically in the specification, a thiophosphoalkylether group may be optionally substituted. For example, in certain embodiments, the —Oalkylether moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether. “Othiophosphoalkylether is a thiophosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkylether group may be optionally substituted.
  • The term “substituted” used herein means any of the above groups (i.e., alkyl, alkylene, aminoalkylene, alkoxy, alkylamino, alkylether, alkylenether, polyalkylenether, hydroxylpolyalkylenether, aminopolyalkylenether, alkylphospho, alkyletherphospho, alkylthiophospho, alkyletherthiophospho, amide, thioalkyl, aryl, aryloxy, aralkyl, Oaralkyl, cyanoalkyl, carbocyclic ring, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl, heteroarylalkyl, hydroxylalkyl, a hydroxylalkylene, aminoalkyl, hydroxylalkylether, phosphoalkyl, phosphoalkylene, phosphoalkylether, sulfhydrylalkyl, sulfhydrylalkylether, sulfonate, thiophosphoalkyl, thiophosphoalkylene, and/or thiophosphoalkylether) wherein at least one hydrogen atom is replaced by a bond to a non-hydrogen atoms such as, but not limited to: a halogen atom such as F, Cl, Br, and I; an oxygen atom in groups such as hydroxyl groups, alkoxy groups, and ester groups; a sulfur atom in groups such as thiol groups, thioalkyl groups, sulfone groups, sulfonyl groups, and sulfoxide groups; a nitrogen atom in groups such as amines, amides, alkylamines, dialkylamines, arylamines, alkylarylamines, diarylamines, N-oxides, imides, and enamines; a silicon atom in groups such as trialkylsilyl groups, dialkylarylsilyl groups, alkyldiarylsilyl groups, and triarylsilyl groups; and other heteroatoms in various other groups. “Substituted” also means any of the above groups in which one or more hydrogen atoms are replaced by a higher-order bond (e.g., a double- or triple-bond) to a heteroatom such as oxygen in oxo, carbonyl, carboxyl, and ester groups; and nitrogen in groups such as imines, oximes, hydrazones, and nitriles. For example, “substituted” includes any of the above groups in which one or more hydrogen atoms are replaced with —NRgRh, —NRgC(═O)Rh, —NRgC(═O)NRgRh, —NRgC(═O)ORh, —NRgSO2Rh, —OC(═O)NRgRh, —ORg, —SRg, —SORg, —SO2Rg, —OSO2Rg, —SO2ORg, ═NSO2Rg, and —SO2NRgRh. “Substituted also means any of the above groups in which one or more hydrogen atoms are replaced with —C(═O)Rg, —C(═O)ORg, —C(═O)NRgRh, —CH2SO2Rg, —CH2SO2NRgRh. In the foregoing, Rg and Rh are the same or different and independently hydrogen, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl.
  • “Substituted” further means any of the above groups in which one or more hydrogen atoms are replaced by a bond to an amino, cyano, hydroxyl, imino, nitro, oxo, thioxo, halo, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl group. In addition, each of the foregoing substituents may also be optionally substituted with one or more of the above substituents.
  • “Conjugation,” with respect to the “M” moiety, refers to the overlap of one p-orbital with another p-orbital across an intervening sigma bond. Conjugation may occur in cyclic or acyclic compounds. A “degree of conjugation” refers to the overlap of at least one p-orbital with another p-orbital across an intervening double bond. For example, 1, 3-butadine has one degree of conjugation, while benzene and other aromatic compounds typically have multiple degrees of conjugation. Fluorescent and colored compounds typically comprise at least one degree of conjugation.
  • “Fluorescent” refers to a molecule which is capable of absorbing light of a particular frequency and emitting light of a different frequency. Fluorescence is well-known to those of ordinary skill in the art.
  • “Colored” refers to a molecule which absorbs light within the colored spectrum (i.e., red, yellow, blue and the like).
  • A “linker” refers to a contiguous chain of at least one atom, such as carbon, oxygen, nitrogen, sulfur, phosphorous and combinations thereof, which connects a portion of a molecule to another portion of the same molecule or to a different molecule, moiety or solid support (e.g., microparticle). Linkers may connect the molecule via a covalent bond or other means, such as ionic or hydrogen bond interactions.
  • For purposes of the present invention, the term “biomolecule” refers to any of a variety of biological materials, including nucleic acids, carbohydrates, amino acids, polypeptides, glycoproteins, hormones, aptamers and mixtures thereof. More specifically, the term is intended to include, without limitation, RNA, DNA, oligonucleotides, modified or derivatized nucleotides, enzymes, receptors, prions, receptor ligands (including hormones), antibodies, antigens, and toxins, as well as bacteria, viruses, blood cells, and tissue cells. The visually detectable biomolecules of the invention (i.e., compounds of structure (I) having a biomolecule linked thereto) are prepared, as further described herein, by contacting a biomolecule with a compound having a reactive group that enables attachment of the biomolecule to the compound via any available atom or functional group, such as an amino, hydroxy, carboxyl, or sulfhydryl group on the biomolecule.
  • The terms “visible” and “visually detectable” are used herein to refer to substances that are observable by visual inspection, without prior illumination, or chemical or enzymatic activation. Such visually detectable substances absorb and emit light in a region of the spectrum ranging from about 300 to about 900 nm. Preferably, such substances are intensely colored, preferably having a molar extinction coefficient of at least about 40,000, more preferably at least about 50,000, still more preferably at least about 60,000, yet still more preferably at least about 70,000, and most preferably at least about 80,000 M−1 cm−1. The biomolecules of the invention may be detected by observation with the naked eye, or with the aid of a optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners. Visually detectable substances are not limited to those which emit and/or absorb light in the visible spectrum. Substances which emit and/or absorb light in the ultraviolet (UV) region (about 10 nm to about 400 nm), infrared (IR) region (about 700 nm to about 1 mm), and substances emitting and/or absorbing in other regions of the electromagnetic spectrum are also included with the scope of “visually detectable” substances.
  • For purposes of the invention, the term “photostable visible dye” refers to a chemical moiety that is visually detectable, as defined hereinabove, and is not significantly altered or decomposed upon exposure to light. Preferably, the photostable visible dye does not exhibit significant bleaching or decomposition after being exposed to light for at least one hour. More preferably, the visible dye is stable after exposure to light for at least 12 hours, still more preferably at least 24 hours, still yet more preferably at least one week, and most preferably at least one month. Nonlimiting examples of photostable visible dyes suitable for use in the compounds and methods of the invention include azo dyes, thioindigo dyes, quinacridone pigments, dioxazine, phthalocyanine, perinone, diketopyrrolopyrrole, quinophthalone, and truarycarbonium.
  • As used herein, the term “perylene derivative” is intended to include any substituted perylene that is visually detectable. However, the term is not intended to include perylene itself. The terms “anthracene derivative”, “naphthalene derivative”, and “pyrene derivative” are used analogously. In some preferred embodiments, a derivative (e.g., perylene, pyrene, anthracene or naphthalene derivative) is an imide, bisimide or hydrazamimide derivative of perylene, anthracene, naphthalene, or pyrene.
  • The visually detectable biomolecules of the invention are useful for a wide variety of biochemical and biomedical applications in which there is a need to determine the presence, location, or quantity of a particular biomolecule. In another aspect, therefore, the invention provides a method for visually detecting a biomolecule, comprising: (a) providing a biological system with a visually detectable biomolecule comprising the compound of structure (I) linked to a biomolecule; and (b) detecting the biomolecule by its visible properties. For purposes of the invention, the phrase “detecting the biomolecule by its visible properties” means that the biomolecule, without illumination or chemical or enzymatic activation, is observed with the naked eye, or with the aid of a optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners. A densitometer may be used to quantify the amount of visually detectable biomolecule present. For example, the relative quantity of the biomolecule in two samples can be determined by measuring relative optical density. If the stoichiometry of dye molecules per biomolecule is known, and the extinction coefficient of the dye molecule is known, then the absolute concentration of the biomolecule can also be determined from a measurement of optical density. As used herein, the term “biological system” is used to refer to any solution or mixture comprising one or more biomolecules in addition to the visually detectable biomolecule. Nonlimiting examples of such biological systems include cells, cell extracts, tissue samples, electrophoretic gels, assay mixtures, and hybridization reaction mixtures.
  • “Microparticle” is a type of solid support and refers to any of a number of small particles useful for attachment to compounds of the invention, including, but not limited to, glass beads, magnetic beads, polymeric beads, nonpolymeric beads, and the like. In certain embodiments, a microparticle comprises polystyrene beads.
  • “Base pairing moiety” refers to a heterocyclic moiety capable of hybridizing with a complementary heterocyclic moiety via hydrogen bonds (e.g., Watson-Crick base pairing). Base pairing moieties include natural and unnatural bases. Non-limiting examples of base pairing moieties are RNA and DNA bases such adenosine, guanosine, thymidine, cytosine and uridine and analogues thereof.
  • The invention disclosed herein is also meant to encompass all compounds of structure (I) being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number. Examples of isotopes that can be incorporated into the disclosed compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2H, 3H, 11C, 13C, 14C, 13N, 15N, 15O, 17O, 18O, 31P, 32P, 35S, 18F, 36Cl, 123I and 125I respectively.
  • Isotopically-labeled compounds of structure (I) can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described below and in the following Examples using an appropriate isotopically-labeled reagent in place of the non-labeled reagent previously employed.
  • “Stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
  • “Optional” or “optionally” means that the subsequently described event or circumstances may or may not occur, and that the description includes instances where said event or circumstance occurs and instances in which it does not. For example, “optionally substituted alkyl” means that the alkyl group may or may not be substituted and that the description includes both substituted alkyl groups and alkyl groups having no substitution.
  • “Salt” includes both acid and base addition salts.
  • “Acid addition salt” refers to those salts which are formed with inorganic acids such as, but not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4-acetamidobenzoic acid, camphoric acid, camphor-10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane-1,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, formic acid, fumaric acid, galactaric acid, gentisic acid, glucoheptonic acid, gluconic acid, glucuronic acid, glutamic acid, glutaric acid, 2-oxo-glutaric acid, glycerophosphoric acid, glycolic acid, hippuric acid, isobutyric acid, lactic acid, lactobionic acid, lauric acid, maleic acid, malic acid, malonic acid, mandelic acid, methanesulfonic acid, mucic acid, naphthalene-1,5-disulfonic acid, naphthalene-2-sulfonic acid, 1-hydroxy-2-naphthoic acid, nicotinic acid, oleic acid, orotic acid, oxalic acid, palmitic acid, pamoic acid, propionic acid, pyroglutamic acid, pyruvic acid, salicylic acid, 4-aminosalicylic acid, sebacic acid, stearic acid, succinic acid, tartaric acid, thiocyanic acid, p-toluenesulfonic acid, trifluoroacetic acid, undecylenic acid, and the like.
  • “Base addition salt” refers to those salts which are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like. Particularly preferred organic bases are isopropylamine, diethylamine, ethanolamine, trimethylamine, dicyclohexylamine, choline and caffeine.
  • Often crystallizations produce a solvate of the compound of the invention. The present invention includes all solvates of the described compounds. As used herein, the term “solvate” refers to an aggregate that comprises one or more molecules of a compound of the invention with one or more molecules of solvent. The solvent may be water, in which case the solvate may be a hydrate. Alternatively, the solvent may be an organic solvent. Thus, the compounds of the present invention may exist as a hydrate, including a monohydrate, dihydrate, hemihydrate, sesquihydrate, trihydrate, tetrahydrate and the like, as well as the corresponding solvated forms. The compounds of the invention may be true solvates, while in other cases the compounds of the invention may merely retain adventitious water or another solvent or be a mixture of water plus some adventitious solvent.
  • The compounds of the invention (e.g., compounds I-VII), or their salts, tautomers or solvates may contain one or more asymmetric centers and may thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids. The present invention is meant to include all such possible isomers, as well as their racemic and optically pure forms. Optically active (+) and (−), (R)- and (S)-, or (D)- and (L)-isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques, for example, chromatography and fractional crystallization. Conventional techniques for the preparation/isolation of individual enantiomers include chiral synthesis from a suitable optically pure precursor or resolution of the racemate (or the racemate of a salt or derivative) using, for example, chiral high pressure liquid chromatography (HPLC). When the compounds described herein contain olefinic double bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. Likewise, all tautomeric forms are also intended to be included.
  • A “stereoisomer” refers to a compound made up of the same atoms bonded by the same bonds but having different three-dimensional structures, which are not interchangeable. The present invention contemplates various stereoisomers and mixtures thereof and includes “enantiomers”, which refers to two stereoisomers whose molecules are nonsuperimposeable mirror images of one another.
  • A “tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule. The present invention includes tautomers of any said compounds. Various tautomeric forms of the compounds are easily derivable by those of ordinary skill in the art.
  • The chemical naming protocol and structure diagrams used herein are a modified form of the I.U.P.A.C. nomenclature system, using the ACD/Name Version 9.07 software program and/or ChemDraw Version 10.0 software naming program (CambridgeSoft). Common names familiar to one of ordinary skill in the art are also used.
  • “Bonding” refers to the process by which one molecule or atom associates with another atom or molecule. Bonding includes, ionic bonding, covalent bonding, chelation, association complexes, hydrogen bonding and the like. A moiety capable of bonding with an analyte molecule or solid support is moiety capable of associating with the analyte molecule or solid support by any of the above means. In one embodiments, the moiety binds with the analyte molecule or solid support by covalent bonding (i.e., the moiety is capable of forming a covalent bond with the analyte molecule or solid support).
  • As noted above, in one embodiment of the present invention, compounds useful as fluorescent and/or colored dyes in various analytical methods are provided.
  • In one embodiment, the compound has the following structure (I):
  • Figure US20240043455A1-20240208-C00003
  • or a salt or stereoisomer thereof, wherein:
      • M1 and Mz are, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • L1, L3, L4 L6, L7 and L8 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
      • R1 is, at each occurrence, independently H, alkyl or alkoxy;
      • R2 is an electron pair, H, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; or R2 is -L9-(L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R3 is H, OH, SH, —NH2, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, —Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, 0-phosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether; or R2 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R4 is, at each occurrence, independently O, S, OZ, SZ or N(R6)2, where Z is a cation and each R6 is independently H or alkyl;
      • R5 is, at each occurrence, independently oxo, thioxo or absent;
      • L9 and L11 are, at each occurrence, independently an optional linker;
      • L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
      • Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
      • n is an integer from 1 to 20;
      • q and w are each independently 0 or 1 for each integral value of n, wherein q is 1 for at least two integral values of n, or wherein q and w are each independently one for at least one integral value of n; and
      • z is an integer from 1 to 10,
      • provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In some embodiments, provided at least one of R2 or R3 is -L9-L10)z-L11-Q. In other embodiments, at least one of R2 or R3 is -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In some embodiments, q is 1 and w is 0 for each integral value of n.
  • In other embodiments of the foregoing, the compound has the following structure (Ia):
  • Figure US20240043455A1-20240208-C00004
  • wherein:
      • M1 is, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising four or more aryl or heteroaryl rings, or combinations thereof;
      • L1, L2 and L3 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
      • R1 is, at each occurrence, independently H, alkyl or alkoxy;
      • R2 is an electron pair, H, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, or R2 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R3 is H, OH, SH, —NH2, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, —Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, 0-phosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether; or R2 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R4 is, at each occurrence, independently O, S, OZ, SZ or N(R6)2, where Z is a cation and each R6 is independently H or alkyl;
      • R5 is, at each occurrence, independently oxo, thioxo or absent;
      • L9 and L11 are, at each occurrence, independently an optional linker;
      • L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
      • Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule;
      • n is an integer from 1 to 10; and
      • z is an integer from 1 to 10, provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In some other embodiments, the compound has the following structure (Ib):
  • Figure US20240043455A1-20240208-C00005
  • wherein:
      • R7, R8, R9, R10, R11 and R12 are, at each occurrence, independently H or alkyl; and
      • x1, y1 and z1 are, at each occurrence, independently an integer from 0 to 5.
  • In different embodiments, the compound has one of the following structures (Ic), (Id), (Ie) or (If):
  • Figure US20240043455A1-20240208-C00006
  • In yet more embodiments, w is 1 for at least one integral value of n. For example, in some embodiments the compound has the following structure (Ig):
  • Figure US20240043455A1-20240208-C00007
  • wherein:
      • R7, R8, R9, R10, R11 and R12 are, at each occurrence, independently H or x1, x2, y1, y2, z1 and z2 are, at each occurrence, independently an integer
  • In other embodiments of the foregoing, R5 is oxo and R4 is O− or OZ.
  • In some other embodiments, R2 is H or an electron pair, and R3 is -L9-(L10)z-L11-Q.
  • In some different embodiments, R2 is hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl or sulfhydrylalkylether, and R3 is -L9-(L10)z-L11-Q. For example, in some embodiments R2 has one of the following structures:
  • Figure US20240043455A1-20240208-C00008
  • wherein
      • R2a is —OH, —NH2, or —SH; and
      • a is an integer from 1 to 10.
  • In more embodiments of the foregoing, R3 is -L9-L10)z-L11-Q, and R2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R2 is optionally substituted with a substituent selected from —OH, —NH2 and —SH. For example, in some embodiments R2 has one of the following structures:
  • Figure US20240043455A1-20240208-C00009
    Figure US20240043455A1-20240208-C00010
  • wherein:
      • R2a is —OH, —SH, —NH2, phosphate or thiophosphate;
      • R4a and R4b are independently O, S, OZ or SZ, where Z is a cation;
      • R5a and R5b are independently oxo, or thioxo; and
      • a, b and c are each independently integers from 1 to 10.
  • In more embodiments of the foregoing, R2 is -L9-L10)z-L11-Q, and R3 is OH or phosphate.
  • In yet more embodiments of the foregoing, R2 is -L9-L10)z-L11-Q, and R3 is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH2 and —SH. For example, in some embodiments R3 has one of the following structures:
  • Figure US20240043455A1-20240208-C00011
  • wherein:
      • R3a is —OH, —SH, —NH2, phosphate or thiophosphate;
      • R4a and R4b are independently O, S, OZ or SZ, where Z is a cation;
      • R5a and R5b are independently oxo, or thioxo; and
      • b and c are each independently integers from 1 to 10.
  • In yet more embodiments of the foregoing, R2 is -L9-L10)z-L11-Q, and R3 is OH or phosphate.
  • In different embodiments, R4a and R4b are each O− and R5a and R5b are each oxo. In some other embodiments, R4a and R4b are each O− and R5a and R5b are each thioxo. In some different embodiments, R4a and R4b are each S− and R5a and R5b are each thioxo. In more different embodiments, R4a and R4b are each S− and R5a and R5b are each oxo.
  • In some other embodiments, at least one of a, b or c is 2. For example, in some embodiments each of a, b and c is 2.
  • In more embodiments of the foregoing, at least one of a, b or c is 6. For example, in some embodiments each of a, b and c is 6.
  • In other embodiments of the foregoing, n is an integer from 1 to 5. In some embodiments, n is an integer from 2 to 15. In some different embodiments, n is an integer from 2 to 10. In some other embodiments, n is an integer from 2 to 5.
  • Still other embodiments provide a compound having the following structure (II):
  • Figure US20240043455A1-20240208-C00012
  • or a salt or stereoisomer thereof, wherein:
      • M1 is, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • L1, L3, and L7 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
      • R1 is, at each occurrence, independently H, alkyl or alkoxy;
      • R2 is an electron pair, H, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; or R2 is -L9-(L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R3 is H, OH, SH, —NH2, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether; or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I)
      • R4 is, at each occurrence, independently O−, S−, OZ, SZ or N(R6)2, where Z is a cation and each R6 is independently H or alkyl;
      • R5 is, at each occurrence, independently oxo, thioxo or absent;
      • L9 and L11 are, at each occurrence, independently an optional linker;
      • L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene; Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
      • n is an integer from 1 to 20; and
      • z is an integer from 1 to 10,
      • provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In some embodiments, at least one of R2 or R3 is -L9-L10)z-L-Q. In different embodiments, at least one of R2 or R3 is-L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In other embodiments of the foregoing, R3 is -L9-(L10)z-L11-Q, and R2 is an electron pair or H.
  • In yet more embodiments of the foregoing, R3 is -L9-L10)z-L11-Q, and R2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R2 is optionally substituted with a substituent selected from —OH, —NH2 and —SH. For example, in some embodiments R2 has one of the following structures:
  • Figure US20240043455A1-20240208-C00013
    Figure US20240043455A1-20240208-C00014
  • wherein:
      • R2a is —OH, —SH, —NH2, phosphate or thiophosphate;
      • R4a and R4b are independently O, S, OZ or SZ, where Z is a cation;
      • R5a and R5b are independently oxo, or thioxo; and
      • a, b and c are each independently integers from 1 to 10.
  • In some different embodiments, R2 is -L9-L10)z-L11-Q, and R3 is OH or phosphate. In some other embodiments R2 is -L9-L10)z-L11-Q, and R3 is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH2, and —SH.
  • In other embodiments of the foregoing, R3 has one of the following structures:
  • Figure US20240043455A1-20240208-C00015
  • wherein
      • R3a is —OH, —SH, —NH2, phosphate or thiophosphate;
      • R4a and R4b are independently O, S, OZ or SZ, where Z is a cation;
      • R5a and R5b are independently oxo, or thioxo; and b and c are each independently integers from 1 to 10.
  • In various embodiments, R4 is O and R5 is oxo at each occurrence.
  • In different embodiments, L1, L3 and L7 are each alkylene linkers.
  • In some other different embodiments, L1 and L3 are each alkylene linkers and L7 is absent. In some of these embodiments, alkylene is methylene.
  • Other embodiments provide a compound having the following structure
  • Figure US20240043455A1-20240208-C00016
  • or a salt or stereoisomer thereof, wherein:
      • M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • R1 is H, alkyl or alkoxy;
      • R2 is H, an electron pair or a cation; or R2 is -L9-(L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R3 is H, phosphate or OH; or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
      • R4 is O—, S− OZ, SZ where Z is a cation;
      • R5 is oxo or thioxo;
      • R7, R8, R9, R10, R11 and R12 are, at each occurrence, independently H or alkyl;
      • L9 and L11 are, at each occurrence, independently an optional linker;
      • L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
      • Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support; and
      • x, y and z are, at each occurrence, independently an integer from 0 to 5; and
      • z is an integer from 1 to 10,
      • provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In some other embodiments, at least one of R2 or R3 is -L9-L10)z-L11-Q. In different embodiments, at least one of R2 or R3 is -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
  • In further embodiments, x, y and z are each 1.
  • In various other embodiments, x is 0 and y and z are each 1.
  • M1 is generally a visually detectable moiety or substance. For example, M1 may be visually detectable in the UV, visible or IR spectrum. In some of any of the foregoing, M1 is, at each occurrence, independently fluorescent or colored. For example, in some embodiments M1 is fluorescent.
  • In certain embodiments, M1 is not a purine or pyrimidine base, such as, but not limited to guanine, cytosine, thymidine and adenine. In other embodiments, M1 is not a porphyrin. In other embodiments, M1 is not one of the following:
  • Figure US20240043455A1-20240208-C00017
  • In still other embodiments of any of the foregoing, M1 comprises three or more aryl or heteroaryl rings, or combinations thereof, for example four or more aryl or heteroaryl rings, or combinations thereof, or even five or more aryl or heteroaryl rings, or combinations thereof. In some embodiments, M1 comprises six aryl or heteroaryl rings, or combinations thereof. In further embodiments, the rings are fused. For example in some embodiments, M1 comprises three or more fused rings, four or more fused rings, five or more fused rings, or even six or more fused rings.
  • In some embodiments, M1 is cyclic. For example, in some embodiments M1 is carbocyclic. In other embodiment, M1 is heterocyclic. In still other embodiments of the foregoing, M1, at each occurrence, independently comprises an aryl moiety. In some of these embodiments, the aryl moiety is multicyclic. In other more specific example, the aryl moiety is a fused-multicyclic aryl moiety, for example which may comprise at least 3, at least 4, or even more than 4 aryl rings.
  • In other embodiments of any of the foregoing compounds of structure (I), M1, at each occurrence, independently comprises at least one heteroatom. For example, in some embodiments, the heteroatom is nitrogen, oxygen or sulfur.
  • In still more embodiments of any of the foregoing, M1, at each occurrence, independently comprises at least one substituent. For example, in some embodiments the substituent is a fluoro, chloro, bromo, iodo, amino, alkylamino, arylamino, hydroxy, sulfhydryl, alkoxy, aryloxy, phenyl, aryl, methyl, ethyl, propyl, butyl, isopropyl, t-butyl, carboxy, sulfonate, amide, or formyl group.
  • In some even more specific embodiments of the foregoing, M1, at each occurrence, independently is a dimethylaminostilbene, quinacridone, fluorophenyl-dimethyl-BODIPY, his-fluorophenyl-BODIPY, acridine, terrylene, sexiphenyl, porphyrin, benzopyrene, (fluorophenyl-dimethyl-difluorobora-diaza-indacene)phenyl, (bis-fluorophenyl-difluorobora-diaza-indacene)phenyl, quaterphenyl, bi-benzothiazole, ter-benzothiazole, bi-naphthyl, bi-anthracyl, squaraine, squarylium, 9, 10-ethynylanthracene or ter-naphthyl moiety. In other embodiments, M1 is, at each occurrence, independently p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, or perylene amide or a derivative thereof. In still more embodiments, M1 is, at each occurrence, independently a coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-1,8-naphthalimide dye.
  • In still more embodiments of any of the foregoing, M1 at each occurrence is the same. In other embodiments, each M1 is different. In still more embodiments, one or more M1 is the same and one or more M1 is different.
  • In some embodiments, M1 is pyrene, perylene, perylene monoimide or 6-FAM or derivative thereof. In some other embodiments, M1 has one of the following structures:
  • Figure US20240043455A1-20240208-C00018
  • In some embodiments, M2 is selected from any one of the above described M1 moieties. In some embodiments, M1 and M2 are the same. In other embodiments, M1 and M2 are different.
  • In other embodiments, at least one occurrence of M2 is a base pairing moiety. For example, in some embodiments each occurrence of M2 is a base pairing moiety. In some of these embodiments, the base pairing moiety is a purine, a pyrimidine, a dihydropyrimidine or a derivative thereof. In further embodiments, the base pairing moiety has one of the following structures:
  • Figure US20240043455A1-20240208-C00019
  • The present invention includes monomeric compounds (e.g., n=1) as well as oligomeric compound (e.g., n is 2-20 or 2-10). In other of the foregoing embodiments, n is an integer from 1 to 5. For example, in some embodiments, n is an integer from 2 to 10, or 2 to 5, such as 3. In other embodiments n is 1. In more embodiments, n is 2. In other embodiments n is 3. In more embodiments, n is 4. In other embodiments n is 5. In more embodiments, n is 6. In other embodiments n is 7. In more embodiments, n is 8. In other embodiments n is 9. In more embodiments, n is 10.
  • Any number of methylene spacer units (i.e., x, y and z) can be included. In some embodiments x is 0. In other embodiments x is 1. In more embodiments, x is 2. In some embodiments x is 3. In other embodiments x is 4. In more embodiments, x is 5.
  • In some embodiments y is 0. In other embodiments y is 1. In more embodiments, y is 2. In some embodiments y is 3. In other embodiments y is 4. In more embodiments, y is 5.
  • In some embodiments z is 1-5. In some embodiments z is 0. In other embodiments z is 1. In more embodiments, z is 2. In some embodiments z is 3. In other embodiments z is 4. In more embodiments, z is 5.
  • In other embodiments, x is 1, y is 0 and z is 1. In other embodiments, x is 0, y is 1 and z is 1.
  • In various embodiments, L9 is present. For example, in some embodiments L9 is C1-C6 alkylene.
  • In various embodiments, L10 is selected from the group consisting of polyalkylenether, phospho and phosphoalkylene. For example, in some embodiments L10 is selected from the group consisting of
  • Figure US20240043455A1-20240208-C00020
  • wherein a is an integer from 1 to 6 and b is an integer from 2 to 10.
  • In various embodiments, (L10)z has one of the following structures:
  • Figure US20240043455A1-20240208-C00021
  • where b is an integer from 2-10, for example 5.
  • In various embodiments, L9 and L11 are each independently a C1-C6 alkylene linker. In some embodiments, L9 is a C2 alkylene linker. In other embodiments, L11 is a C6 alkylene linker.
  • In still other embodiments, Q is a moiety capable of bonding with an analyte molecule or a solid support. In certain embodiments, Q provides a means of connecting the compound of structure (I) to an analyte molecule or a solid support (e.g., by a covalent bond). For example, in some embodiments Q is a reactive group capable of forming a covalent bond with an analyte molecule or a solid support. In this regard the type of Q group and connectivity of the Q group to the remainder of the compound of structure (I) is not limited. In certain embodiments, the Q is a moiety which is not susceptible to hydrolysis under aqueous conditions, but is sufficiently reactive to form a bond with a corresponding group on an analyte molecule or solid support (e.g., an amine).
  • Certain embodiments of the compounds described herein comprise Q groups commonly employed in the field of bioconjugation. For example in some embodiments, Q is a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group. In some more specific embodiments, Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or a maleimide. In some embodiments, the activated ester is an N-succinimide ester, imidoester or polyflourophenyl ester. In other embodiments, the alkyne is an alkyl azide or acyl azide.
  • Exemplary Q moieties are provided in Table I below.
  • TABLE 1
    Exemplary Q Moieties
    Structure Class
    Figure US20240043455A1-20240208-C00022
         		Sulfhydryl
    Figure US20240043455A1-20240208-C00023
         		Isothio- cyanate
    Figure US20240043455A1-20240208-C00024
         		Imidoester
    Figure US20240043455A1-20240208-C00025
         		Acyl Azide
    Figure US20240043455A1-20240208-C00026
         		Activated Ester
    Figure US20240043455A1-20240208-C00027
         		Activated Ester
    Figure US20240043455A1-20240208-C00028
         		Activated Ester
    Figure US20240043455A1-20240208-C00029
         		Activated Ester
    Figure US20240043455A1-20240208-C00030
         		Activated Ester
    Figure US20240043455A1-20240208-C00031
         		Sulfonyl halide
    Figure US20240043455A1-20240208-C00032
         		Maleimide
    Figure US20240043455A1-20240208-C00033
         		Maleimide
    Figure US20240043455A1-20240208-C00034
         		α-haloimide
    Figure US20240043455A1-20240208-C00035
         		Disulfide
    Figure US20240043455A1-20240208-C00036
         		Phosphine
    Figure US20240043455A1-20240208-C00037
         		Azide
    Figure US20240043455A1-20240208-C00038
         		Alkyne
    Figure US20240043455A1-20240208-C00039
         		Biotin
    Figure US20240043455A1-20240208-C00040
         		Diene
    Figure US20240043455A1-20240208-C00041
         		Alkene/ dienophile
    Figure US20240043455A1-20240208-C00042
         		Alkene/ dienophile
    —NH2 Amino
  • In some embodiments, it is advantageous to employ compounds wherein Q is —SH since —SH can be readily conjugated to many analyte molecules, bifinctiponal linker groups and/or solid supports (e.g., by formation of a disulfide bond with a free sulfhydryl on the analyte molecule or solid support). However, for purposes of long term stability of the compounds, it may be desirous to store the compound in the form of a disulfide dimer. Accordingly, some embodiments provide such disulfide dimers. For example, in some embodiments at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I). “Compound of structure (I)” refers to any of the compounds described herein, which are encompassed by structure (I).
  • The dimer may be formed between any one of R2 or R3 and another one of R2 or R3. For ease of illustration, but limitation, an exemplary dimer, wherein the dimer is formed between two R2 groups is illustrated below (Ia′):
  • Figure US20240043455A1-20240208-C00043
  • or a salt thereof, wherein R1, R3, R4, R5, L1, L3, L7, L9, L10, L11 and z are each independently as defined for any of the foregoing embodiments.
  • The dimers are also illustrated as follows (Ia′):
  • Figure US20240043455A1-20240208-C00044
  • The disulfide linker between the two compounds of structure (I), i.e., -L9(L10)z-L11-S—S-L11-(L10)z-L9-, can have various structures. In some embodiments, -L9(L10)z-L11-S—S-L11-(L10)z-L9- has one of the following structures:
  • Figure US20240043455A1-20240208-C00045
  • In still other embodiments, Q is an analyte molecule or solid support. For example, in some embodiments the analyte molecule is a biomolecule. In some embodiments, the biomolecule is a nucleic acid, amino acid or a polymer thereof. In other embodiments the biomolecule is a nucleic acid, peptide, carbohydrate, lipid, enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer, antigen or prion.
  • In different embodiments, the analyte molecule is a drug, vitamin or small molecule.
  • In various other embodiments, R7, R8, R9, R10, R11 and R12, when present, are each H.
  • In some other different embodiments, x1, y1 and z1 are each 1.
  • In more different embodiments, each x1 is 0 and each y1 and z1 are 1.
  • In some different embodiments, each x2 is 1 and each y2 and z2 are 0.
  • Other embodiments are directed to a compound having the following structure (IV):
  • Figure US20240043455A1-20240208-C00046
  • or a salt or stereoisomer thereof, wherein:
      • M1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
      • R20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, C1-C6 alkyl or C1-C6 hydroxylalkyl; and
      • each x′, y′ and z′ is independently an integer from 0 to 10.
  • In some of these embodiments, M1 is as defined in any one of the foregoing embodiments. For example, in some embodiments, M1 is perylene.
  • In other embodiments, Q is as defined in any one of the foregoing embodiments. For example, in some embodiments, Q is —SH.
  • In various embodiments, each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • In some other different embodiments, R20 is phosphate, —CH2OPO3 2— or CH2OH.
  • In some embodiments, the compound has the following structure:
  • Figure US20240043455A1-20240208-C00047
  • Other embodiments provide a compound having one of the following structures:
  • Figure US20240043455A1-20240208-C00048
    Figure US20240043455A1-20240208-C00049
  • where Q is an analyte molecule.
  • Other embodiments are directed to a disulfide dimer having the following structure (V):
  • Figure US20240043455A1-20240208-C00050
  • or a salt or stereoisomer thereof, wherein:
      • M1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • R20 is, at each occurrence, independently H, phosphate, alkylphosphate, C1-C6 alkyl or C1-C6 hydroxylalkyl; and
      • each x′, y′ and z′ is independently an integer from 0 to 10.
  • In some of these embodiments, M1 is as defined in any one of the foregoing embodiments. For example, in some embodiments, M1 is perylene.
  • In various embodiments, each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • In some other different embodiments, R20 is phosphate, CH2OPO3 2— or CH2OH.
  • In various other embodiments, the disulfide dimer has the following structure:
  • Figure US20240043455A1-20240208-C00051
  • In further embodiments of the foregoing, M1 has the following structure:
  • Figure US20240043455A1-20240208-C00052
  • In various other embodiments, a compound having the following structure (VI) is provided:
  • Figure US20240043455A1-20240208-C00053
  • or a salt or stereoisomer thereof, wherein:
      • M1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
      • R20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, C1-C6 alkyl or C1-C6 hydroxylalkyl; and each x′, y′ and z′ is, at each occurrence, independently an integer from 0 to 10.
  • In some of these embodiments, M1 is as defined in any one of the foregoing embodiments. For example, in some embodiments, M1 is perylene.
  • In other embodiments, Q is as defined in any one of the foregoing embodiments. For example, in some embodiments, Q is —SH.
  • In various embodiments, each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • In some other different embodiments, R20 is phosphate, CH2OPO3 2— or CH2OH.
  • In some embodiments, the compound has the following structure:
  • Figure US20240043455A1-20240208-C00054
  • In further embodiments of the foregoing, M1 has the following structure:
  • Figure US20240043455A1-20240208-C00055
  • Other embodiments provide a disulfide dimer having the following structure (VII):
  • Figure US20240043455A1-20240208-C00056
  • or a salt or stereoisomer thereof, wherein:
      • M1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
      • R20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, C1-C6 alkyl or C1-C6 hydroxylalkyl; and
      • each x′, y′ and z′ is, at each occurrence, independently an integer from 0 to 10.
  • In some of these embodiments, M1 is as defined in any one of the foregoing embodiments. For example, in some embodiments, M1 is perylene.
  • In various embodiments, each y′ is 0. In some different embodiments, each z′ is 1. In yet more embodiments of the foregoing, each x′ is independently an integer from 2-6.
  • In some other different embodiments, R20 is phosphate, CH2OPO3 2— or CH2OH.
  • In some embodiment, the disulfide dimer has the following structure:
  • Figure US20240043455A1-20240208-C00057
  • For example, in some embodiments of the foregoing M1 has the following structure:
  • Figure US20240043455A1-20240208-C00058
  • For ease of illustration, various compounds comprising phosphorous moieties (e.g., phosphate and the like) are depicted in the anionic state (e.g., —OPO3 2—) One of skill in the art will readily understand that the charge is dependent on pH and the uncharged (e.g., protontated or salt, such as sodium or other cation) forms are also included in the scope of the invention.
  • Compositions comprising any of the foregoing compounds and one or more biomolecules are provided in various other embodiments. In some embodiments, use of such compositions in analytical methods for detection of the one or more biomolecules are also provided.
  • In still other embodiments, the compounds are useful in various analytical methods. For example, in certain embodiments the disclosure provides a method of staining a sample, the method comprising adding to said sample a compound of structure (I), wherein R2 is -L9-L10)z-L11-Q, Q is a moiety capable of bonding with an analyte molecule and R3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
  • In some embodiments of the foregoing methods, R2 is a linker comprising a covalent linkage to a biomolecule. For example, a nucleic acid, amino acid or a polymer thereof (e.g., polynucleotide or polypeptide). In still more embodiments, the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
  • In yet other embodiments of the foregoing method, R2 comprises a linker comprising a covalent linkage to a microparticle. For example, in some embodiments the microparticle is a polymeric bead or nonpolymeric bead.
  • In even more embodiments, said optical response is a fluorescent response.
  • In other embodiments, said sample comprises cells, and some embodiments further comprise observing said cells by flow cytometry.
  • In still more embodiments, the method further comprises distinguishing the fluorescence response from that of a second fluorophore having detectably different optical properties.
  • In other embodiments, the disclosure provides a method for visually detecting a biomolecule, comprising:
      • (a) providing a compound of structure (I), wherein R2 is -L9-L10)z-L11-Q, Q is a moiety capable of bonding with the biomolecule and R3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; and
      • (b) detecting the compound by its visible properties.
  • For example, a nucleic acid, amino acid or a polymer thereof (e.g., polynucleotide or polypeptide). In still more embodiments, the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
  • In other embodiments, a method for visually detecting a biomolecule is provided, the method comprising:
      • (a) admixing any of the foregoing compounds with one or more biomolecules; and
      • (b) detecting the compound by its visible properties.
  • It is understood that any embodiment of the compounds of structure (I), as set forth above, and any specific choice set forth herein for a R1, R2, R3, R4, R5, L1, L3, L4, L6, L7, L8, M1, M2, q, w and n variable in the compounds of structure (I), as set forth above, may be independently combined with other embodiments and/or variables of the compounds of structure (I) to form embodiments of the inventions not specifically set forth above. In addition, in the event that a list of choices is listed for any particular R or M group in a particular embodiment and/or claim, it is understood that each individual choice may be deleted from the particular embodiment and/or claim and that the remaining list of choices will be considered to be within the scope of the invention.
  • It is understood that in the present description, combinations of substituents and/or variables of the depicted formulae are permissible only if such contributions result in stable compounds.
  • It will also be appreciated by those skilled in the art that in the process described herein the functional groups of intermediate compounds may need to be protected by suitable protecting groups. Such functional groups include hydroxy, amino, mercapto and carboxylic acid. Suitable protecting groups for hydroxy include trialkylsilyl or diarylalkylsilyl (for example, t-butyldimethylsilyl, t-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl, benzyl, and the like. Suitable protecting groups for amino, amidino and guanidino include t-butoxycarbonyl, benzyloxycarbonyl, and the like. Suitable protecting groups for mercapto include —C(O)—R11 (where R11 is alkyl, aryl or arylalkyl), p-methoxybenzyl, trityl and the like. Suitable protecting groups for carboxylic acid include alkyl, aryl or arylalkyl esters. Protecting groups may be added or removed in accordance with standard techniques, which are known to one skilled in the art and as described herein. The use of protecting groups is described in detail in Green, T. W. and P. G. M. Wutz, Protective Groups in Organic Synthesis (1999), 3rd Ed., Wiley. As one of skill in the art would appreciate, the protecting group may also be a polymer resin such as a Wang resin, Rink resin or a 2-chlorotrityl-chloride resin.
  • Furthermore, all compounds of the invention which exist in free base or acid form can be converted to their salts by treatment with the appropriate inorganic or organic base or acid by methods known to one skilled in the art. Salts of the compounds of the invention can be converted to their free base or acid form by standard techniques.
  • The following Reaction Schemes illustrate exemplary methods of making compounds of this invention. It is understood that one skilled in the art may be able to make these compounds by similar methods or by combining other methods known to one skilled in the art. It is also understood that one skilled in the art would be able to make, in a similar manner as described below, other compounds of structure (I) not specifically illustrated below by using the appropriate starting components and modifying the parameters of the synthesis as needed. In general, starting components may be obtained from sources such as Sigma Aldrich, Lancaster Synthesis, Inc., Maybridge, Matrix Scientific, TCI, and Fluorochem USA, etc. or synthesized according to sources known to those skilled in the art (see, for example, Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th edition (Wiley, December 2000)) or prepared as described in this invention.
  • Figure US20240043455A1-20240208-C00059
  • Reaction Scheme I illustrates and exemplary method for preparing compounds of structure I. R2′ and R3′ represent R2 and R3 moieties as defined herein, or precursors to R2 and R3 moieties or protected derivatives thereof which can be converted to the desired R2 and R3 moieties using techniques known in the art and provided in the examples below. Referring to Reaction Scheme 1, compounds of structure a can be purchased or prepared by methods well-known to those of ordinary skill in the art. Reaction of a with M1-X, where x is a halogen such as bromo, under Suzuki coupling conditions known in the art results in compounds of structure b. Compounds of structure b can be modified to obtain number of other compounds of structure I. For example, compounds of structure b can be oligomerized to obtain other compounds of structure I (i.e., where n is greater than 1, such as 2-10). Exemplary methods for oligomerization include methods analogous to phosphoramadite-based solid-phase oligonucleotide synthesis, which is well known in the art.
  • Figure US20240043455A1-20240208-C00060
  • Reaction Scheme II illustrates an alternative method for preparation of compounds of structure I. R2′ and R3′ represent R2 and R3 moieties as defined herein, or precursors to R2 and R3 moieties or protected derivatives thereof which can be converted to the desired R2 and R3 moieties using techniques known in the art and provided in the examples below. In this approach, a compound of structure c, which can be purchased or prepared by well-known techniques, is reacted with M1-Z to yield compounds of structure d. Here, Y and Z represent function groups having complementary reactivity (i.e., functional groups which react to form a covalent bond). Z may be pendant to M1 or a part of the structural backbone of M, for example a cyclic anhydride. Y may be any number of functional groups, such as amino.
  • Compounds of structure (I) comprising ribose moieties are prepared according to analogous procedures or purchased from commercial sources (e.g., as phosphoramadites).
  • In certain embodiments, the compounds of structure I are oligomers comprising from 2-10 repeating units. Such oligomers can be prepared using methods analogous to well-known automated DNA synthesis methods. DNA synthesis methods are well-known in the art. Briefly, two alcohol groups are functionalized with a dimethoxytrityl (DMT) group and a 2-cyanoethyl-N,N-diisopropylamino phosphoramidite group, respectively. The phosphoramidite group is coupled to an alcohol group, typically in the presence of an activator such as tetrazole, followed by oxidation of the phosphorous atom with iodine. The dimethoxytrityl group can be removed with acid (e.g., chloroacetic acid) to expose the free alcohol, which can be reacted with a phosphoramidite group. The 2-cyanoethyl group can be removed after oligomerization by treatment with aqueous ammonia.
  • Preparation of the phosphoramidites used in the oligomerization methods is also well-known in the art. For example, a primary alcohol (e.g., R3) can be protected as a DMT group by reaction with DMT-Cl. A secondary alcohol (e.g., R2) is then functionalized as a phosphoramidite by reaction with an appropriate reagent such as 2-cyanoethyl N,N-dissopropylchlorophosphoramidite. Methods for preparation of phosphoramidites and their oligomerization are well-known in the art and described in more detail in the examples.
  • The following examples are provided for purposes of illustration, not limitation.
    • EXAMPLES
  • General Methods 1H and 31P NMR spectra were obtained on a JEOL400 MHz spectrometer. 31P NMR spectra were referenced against 85% aqueous phosphoric acid and 1H spectra were referenced against TMS. Reverse phase HPLC dye analysis was performed using a Waters Acquity UHPLC system with a 2.1 mm×50 mm Acquity BEH-C18 column held at 45° C. Mass spectral analysis was performed on a Waters/Micromass Quattro micro MS/MS system (in MS only mode) using MassLynx 4.1 acquisition software. Mobile phase used for LC/MS on dyes was 100 mM 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), 8.6 mM triethylamine (TEA), pH 8.
  • Phosphoramidites and precursor molecules were analyzed using an Agilent Infinity 1260 UHPLC system with a diode array detector and High Performance Autosampler using an Aapptec® Spirit™ Peptide C18 column (4.6 mm×100 mm, 5 μm particle size). Excitation and emission profiles experiments were recorded on a Cary Eclipse spectra photometer.
  • All reactions were carried out in oven dried glassware under a nitrogen atmosphere unless otherwise stated. Commercially available DNA synthesis reagents were purchased from Glen Research (Sterling, VA). Anhydrous pyridine, toluene, dichloromethane, diisopropylethyl amine, triethylamine, acetic acid, pyridine, and THE were purchased from Aldrich. All other chemicals were purchased from Aldrich or TCI and were used as is with no additional purification.
  • All oligomer dyes were synthesized on an ABI 394 DNA synthesizer using standard protocols for the phosphoramidite-based coupling approach. The chain assembly cycle for the synthesis of oligomers was the following: (i) detritylation, 3% trichloroacetic acid in dichloromethane, 1 min; (ii) coupling, 0.1 M phosphoramidite and 0.45 M tetrazole in acetonitrile, 10 min; (iii) capping, 0.5 M acetic anhydride in THF/lutidine, 1/1, v/v 15 s; (iv) oxidation, 0.1 M iodine in THF/pyridine/water, 10/10/1, v/v/v, 30 s.
  • Chemical steps within the cycle were followed by acetonitrile washing and flushing with dry argon for 0.2-0.4 min. Cleavage from the support and removal of base and phosphoramidate protecting groups was achieved by treatment with ammonia for 1 hour at room temperature. Oligomer dyes were then analyzed by reverse phase HPLC as described above.
    • Example 1 Synthesis of Soluble Dye with Activated Ester Moiety
  • Example 1 exemplifies a water soluble dye substance, modified to contain an activated ester group (2 and 3), which can be conjugated to macromolecules having primary amine functional groups. In this example a dye sequence (1) containing a disulfide linker is reduced with tris(2-carboxyethyl)phosphine (TCEP) to release two smaller dye sequences, each with a Fluor and a free thiol terminus. These products are then reacted with the maleimido portion of N-Maleimido-6-Aminocaproyl 1-Hydroxy-2-Nitro-4-Benzenesulfonic acid Ester (Mal-Sac-HNSA), placing an activated ester group on each dye sequence which is resistant to H2O mediated hydrolysis, yet still subject to nucleophilic attack by molecules containing primary amines. Compound 1 was prepared according to the general procedures described herein, including methods analogous to solid-phase DNA phosphoramidite chemistry known in the art.
  • Figure US20240043455A1-20240208-C00061
  • A 5 mL micropipettor was used to add 3.88 mL of H2O to 10 mg of dry COMPOUND 1 in a 50 mL conical tube. The dissolved COMPOUND 1 was mixed for approximately 5 minutes using a Vortex mixer and a slight non-dye related precipitate appeared. The tube and its contents were spun in a centrifuge at its maximum speed (3280 RCF) for 5 minutes, and then the COMPOUND 1 supernatant was removed with care not to disturb the pellet. The clarified COMPOUND 1 was transferred to a new conical tube, and a sample was removed for quantification and HPLC analysis. HPLC-MS demonstrated that compound 1 was 52% pure and had a mass of 1648 Daltons (Da).
  • 5 mL of compound 1 was sampled from clarified solution using a micropipettor and diluted 20-fold in H2O. A blank measurement was performed on the NanoDrop using H2O, and then the absorbance of the diluted compound 1 was measured at 443 nm. Equation 1 was used to calculate the molar concentration of compound 1:

  • Molar concentration of COMPOUND1={A 443/(L*e COMPOUND 1)}*Dilution Factor   Equation 1:
      • eCOMPOUND 1=38,000 M−1 cm−1
      • Lnanodrop=0.1 cm
      • A443=0.614 AU
      • Dilution Factor=20

  • Molar concentration of COMPOUND 1=3.23×10−03 M COMPOUND 1.
  • A stock solution of TCEP (tris(2-carboxyethyl)phosphine), HCl salt was made by weighing 47.7 mg of TCEP and adding it to a 15 mL conical tube. 1.5 mL of H2O was added to the tube and the TCEP was dissolved using a vortex mixer to mix the solution thoroughly for approximately 5 minutes. The resulting solution was 31.8 mg/mL TCEP, or 0.111 MTCEP. Moles of COMPOUND 1 were calculated using Equation 2:

  • moles of COMPOUND 1={M COMPOUND 1*(V COMPOUND 1-mL/1000)}  Equation 2:

  • M COMPOUND 1=3.23×10−03 M  (Eq. 1)
      • VCOMPOUND 1=3.88 mL

  • Moles of COMPOUND 1 to be reduced=1.23×10−05 moles COMPOUND 1.
  • Equation 3 was used to calculate the moles of TCEP required to achieve a 11.3:1 molar ratio of TCEP to COMPOUND 1.

  • moles of TCEP=MolesCOMPOUND 1*11.3  Equation 3:

  • Moles COMPOUND1=1.23×10−05  (Eq. 2)
      • Molar Excess: 11.3

  • Moles of TCEP required=1.39×10−04 moles TCEP.
  • Equation 4 was used to calculate the volume of TCEP to add to COMPOUND 1:

  • Volume (mL) of TCEP Required={(MolesTCEP /M TCEP)*1000}  Equation 4:
      • MolesTCEP=1.39×10−04 (Eq. 3)
      • MTCEP=0.111 M
      • Volume of TCEP required=1.28 mL of TCEP.
  • The HCl salt of TCEP is acidic and reduction of the COMPOUND 1 needs to occur at slightly acidic to neutral pH (e.g. pH 6-7). The NaPO4 buffer should be in approximately 5-fold or higher molar excess maintain a pH of 6.5. Since the molarity of 0.6 M NaPO4 stock solution is 5.45-fold higher than the 0.111 M TCEP stock solution, an equal volume of the stock added to TCEP is sufficient to buffer the reaction.
  • Volumes of Reagents Required:

  • 3.23×10−03 M COMPOUND1=3.88 mL
      • 0.6 M NaPO4=1.28 mL
      • 0.111 M TCEP=1.28 mL
  • Using a micropipettor, 1.28 mL NaPO4 buffer was added to 3.88 mL COMPOUND 1. 1.28 mL TCEP was added to the COMPOUND 1-NaPO4 solution for a final reaction volume of 6.44 mL. The reaction was incubated at room temperature (˜23° C.). After 2 hours a sample was removed for HPLC-MS. HPLC analysis demonstrated that the reduction reaction under these conditions was partially completed (perhaps due to oxidized TCEP).
  • There are two reduced COMPOUND 1 products: the 5′-ECC-SH species which has an expected mass of 785 Daltons and the HS-CCE-3′ species which has an expected mass of 865 Daltons.
  • Despite only partial reduction in this example, the mixture containing the two intended products was reacted with N-Maleimido-6-Aminocaproyl 1-Hydroxy-2-Nitro-4-Benzenesulfonic acid Ester (MSH).
  • Using an analytical balance, 37 mg of dry MSH was weighed out and transferred to a 15 mL conical tube. 3.7 mL of H2O was added to the tube using a 5 mL micropipettor, making a 10 mg/mL (0.023 M) solution of MSH. 3.1 mL of this MSH solution was added to the tube containing 6.44 mL of COMPOUND 1 reduction mixture, and the volume of the resulting solution was brought to 10 mL by adding 0.46 mL H2O. The reaction was incubated at room temperature for 30 minutes.
  • The final concentration of the reactants was calculated for the final 10 mL volume:

  • (3.23×10−03 M COMPOUND 1)×(3.88 mL COMPOUND1)/10 mL=1.25×10−03 M COMPOUND1  COMPOUND 1:

  • TCEP: (0.111 MTCEP)*(1.28 mL TCEP)/10 mL=0.014 M TCEP

  • MSH: (0.023 M MSH)*(3.1 mL MSH)/10 mL=7.13×10−0 M MSH

  • NaPO4:(0.6M NaPO4*1.28 mL NaPO4)/10 mL=0.077M NaPO4
  • A sample was removed for HPLC-MS analysis, which showed that the maleimide functional group of the MSH was added to both the 5′-ECC-SH and the HS-CCE-3′ species, and that the products are compounds 2 and 3.
  • Semi-preparative reverse phase chromatography was used to isolate the products from the reaction mixture as follows:
    • Equipment
      • HPLC: Akta Purifier 100 Column
      • Phenomenex Gemini C18 (5 mm, 110 Å, 10×250 mm), part #00G-4435-NO
    Method 1:
      • Flow-rate: 2 mL/minute
      • Mobile Phase:
        • A=0.1 M TEAA, 5% Acetonitrile in H2O
        • B=100% Acetonitrile
      • Injection: 5 mL Reactants
      • Elution: 0-55% Mobile Phase B, 5 CV, Column Clean: 100% Mobile Phase B, 1 CV
      • Monitored traces:
        • Conductivity
        • UV absorbance at 445 nm and 310 nm
      • Fractionation: Threshold triggered by UV445 at 50 mAU, 1.25 mL per fraction collected in 15 mL
        • Collected in 15 mL conical tubes
        • Fractions analyzed by HPLC to confirm purity
  • The foregoing HPLC method was used to purify compound 3, however further HPLC purification was performed on compound 2 as follows: Equipment
      • HPLC: Akta Purifier 100
    Column
      • Phenomenex Gemini C18 (5 mm, 110 Å, 10×250 mm), part #00G-4435-NO
    Method 2:
      • Flow-rate: 2 mL/minute
      • Mobile Phase:
        • A=0.1 M TEAA, 5% methanol in H2O
        • B=100% methanol
      • Injection: 5 mL HNSA-S-CCE-3′+unreacted COMPOUND 1 (fraction B11)
      • Elution: 0-55% Mobile Phase B, 5 CV, Column Clean: 100% Mobile Phase B, 1 CV
      • Monitored traces:
        • Conductivity
        • UV absorbance at 445 nm and 310 nm
      • Fractionation: Threshold triggered by UV445 at 50 mAU, 1.25 mL per fraction collected in 15 mL
        • Collected in 15 mL conical tubes
        • Fractions analyzed by HPLC to confirm purity
        • Fraction C10 was confirmed to be the purified compound 2
  • 10 mL H2O was added to each of the collected product (i.e., compound 2 and 3) fractions to dilute the organic modifier to less than 15%. The samples were flash frozen in a dry-ice/ethanol bath, placed on a Labconco FreeZone 4.5 lyophilizer and allowed to freeze-dry overnight to remove moisture, solvent and TEAA buffer components.
  • Compounds 2 and 3 were reacted with TRIS (a molecule containing a primary amine) to simulate conjugation of a dye to a primary amine containing macromolecule such as a protein or antibody. 300 ml H2O was added to each component to completely dissolve. 50 ml aliquots of each component were treated with either 50 μL of water or 50 μL of 1 M Tris (pH 8.5) and allowed to react at room temperature for 15 minutes. Samples of each were submitted for HPLC analysis (see FIGS. 8a and 8b).
  • HPLC-MS analysis showed HNSA activated dye sequences were somewhat subject to degradation via either buffer-related methanol addition or hydration at the HNSA ester position of the molecule, but also showed that intact COMPOUND 1-HNSA reacted predictably with TRIS. Only the results for the 5′-ECC—S-HNSA product are shown.
    • Example 2 Synthesis of Maleimide-Containing Dye
  • Figure US20240043455A1-20240208-C00062
  • A water soluble dye with a functional maleimide group was synthesized by reacting a water soluble dye containing a terminal primary amine (compound 4) with the N-Hydroxysuccinimidyl group of Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (Sulfo-SMCC).
  • Determine the Molar Concentration of compound 4 by measuring its absorbance using a Nanodrop and Beer's Law. Using H2O as a diluent, make two 10-fold dilutions of compound 4 (a 100-fold final dilution). Perform a blank measurement on the NanoDrop using H2O. Measure the absorbance of compound 4 at 443 nm. Use Equation 1 to calculate the molar concentration of compound 4 from the absorbance.

  • Molar concentration of SND215={A 443/(L*e compound 45)}*Dilution Factor  Equation 1 (Beer's Law):
      • e compound 45=38,000 M−1 cm-1
      • Lnanodrop=0.1 cm
      • A443=0.372
      • Dilution Factor=100

  • Molar concentration of SND215=9.79×10−03 M compound 4.
  • Make a stock solution of Sulfo-SMCC. Weigh 28 mg of Sulfo-SMCC and add it to a 15 ml conical tube. Add 2.8 ml of H2O to the tube. Dissolve the Sulfo-SMCC using a Vortex mixer for approximately 5 minutes. This is a 10 mg/ml Sulfo-SMCC solution. Calculate that the molarity of Sulfo-SMCC is 0.023 MSuWo-SMCC.

  • moles of SND215={M compound 45*(V compound 4−ml/1000)}  Equation 2:

  • M compound 4=9.79×10−03 M  (Eq. 1)
      • V compound 4=0.65 ml

  • Moles of compound 4 to be reacted with Sulfo-SMCC=6.36×10−06 moles compound 4.
  • Use Equation 3 to calculate the moles of Sulfo-SMCC required to achieve a 10:1 Sulfo-SMCC to compound 4 molar ratio.

  • moles of Sulfo-SMCC=Moles compound 4*10  Equation 3:

  • Moles compound 4=6.36×10−06  (Eq. 2)
      • Molar Excess: 10

  • Moles of Sulfo-SMCC required=6.36×10−05 moles Sulfo-SMCC.
  • Use Equation 4 to calculate the volume of Sulfo-SMCC that will be added to compound 4.

  • Volume (ml) of Sulfo-SMCC Required={(MoleSulfo-SMCC /M SULFO-SMCC)*1000}  Equation 4:

  • MolesSULFO-sMCC=6.36×10−05  (Eq.3)
      • MSulfo-SMCC=0.023 M
      • Volume of Sulfo-SMCC required=2.765 ml of Sulfo-SMCC.
  • Sulfo-SMCC is acidic and addition of the compound 4 should occur at slightly basic to neutral pH (e.g. pH 7.5-8.5). The NaPO4 buffer should be approximately equi-molar to Sulfo-SMCC to maintain the pH of 7.5. Used 0.45 M NaPO4 (pH=8.0) to buffer the reaction.
  • Using the following volumes (see below) add the reactants to a 5 ml conical tube.

  • 9.79×10−03 M compound 4=0.65 ml
      • 0.45 M NaPO4=1.15 ml
      • 0.023 M Sulfo-SMCC=2.75 ml
      • H2O=0.45 ml
  • The final concentration of the reactants where the final volume is 5 ml is calculated as follows:

  • (9.79×10−03 M compound 4)×(0.65 ml compound 4)/5 ml=1.27×10−03 M compound 4  compound 4:

  • Sulfo-SMCC: (0.023M Sulfo-SMCC)*(3.1 ml Sulfo-SMCC)/5 ml=0.013M Sulfo-SMCC

  • NaPO4: (0.45 M NaPO4*1.15 ml NaPO4)/5 ml=0.104 M NaPO4
  • The pH of the reaction was approximately 7.5 using litmus paper. Incubate the reaction overnight at lab room temperature (approximately 23° C.). Calculate the final concentrations of the reactants for the reaction. Measure the pH of the reaction using litmus paper that spans a pH range of 7-14. Remove a sample for HPLC/MS analysis before reaction and once the reaction is complete. M.S. analysis of compound 4 before reaction: Calculated MW is 888.4. MW found is 887.2. M.S. analysis of compound 5 before reaction: Calculated MW is 1107.2. MW found is 1106.4.
  • Compound 5 was purified to an overall purity of 78% from the crude reaction mixture as follows:
    • Equipment
      • HPLC: Akta Purifier 100
    Column
      • Waters Spherisorb C6 (5 mm, 80 Å, 10×250 mm), part #PSS831085
    Method 1:
      • Flow-rate: 2 mL/minute
      • Mobile Phase:
        • A=0.1 M TEAA, 5% Acetonitrile in H2O
        • B=100% Acetonitrile
      • Injection: 5 mL Reactants
      • Elution: 0-55% Mobile Phase B, 5 CV, Column Clean: 100% Mobile Phase B, 1 CV
      • Monitored traces:
        • Conductivity
        • UV absorbance at 445 nm and 310 nm
      • Fractionation: Threshold triggered by UV445 at 50 mAU, 1.25 mL per fraction collected in 15 mL
        • Collect fractions B6 and B5 in 15 mL conical tubes
        • Pool fractions and analyzed by HPLC to confirm purity
  • Purified compound 5 was lyophilized as follows:
  • Dilute purified compound 5 to a final volume of 25 ml with H2O. Flash Freeze diluted compound 5 in a Dry-ice/Ethanol bath. After it was frozen, place the compound 5 into chamber a pre-chilled Labconco FreeZone 4.5 lyophilizer. Apply vacuum and let compound 5 freeze dry overnight. Using a needle scrape out a small amount of the material and reconstitute it in H2O. Analyze the reconstituted compound 5 by HPLC. Store the remaining dry SND215-Maleimide was stored in a −20° C. freezer.
  • The ability of compound 5 to form a covalent bond with an analyte molecule was tested as follows:
    • Reagents:
      • L-cysteine hydrochloride monohydrate (CAS 7048-04-6, FW 175.6, Thermo Scientific)
      • 0.1 M phosphate buffer (+0.15M NaCl), pH 6.5
      • Aqueous stock (0.15 mM) of SND215+MSH Procedure:
  • A 5 mM solution of L-cysteine in water was created by dissolving 12.5 mg solid in 14.2 mL water. The reaction between L-cysteine and a maleimido group should be carried out in slightly acidic conditions, so samples were prepared as shown and pH level was checked for pH 6-7:
      • Blank: 45 μL water+50 μL buffer+5 μL L-cysteine stock
      • Untreated sample: 45 μL SND215, 50 μL buffer, 5 μL water
      • Treated sample: 45 μL SND215, 50 μL buffer, 5 μL L-cysteine stock
  • Samples were well mixed and allowed to react at room temperature for 3 hours. Analysis was performed on 10 μL injections of each test sample using LC/MS. Results indicated that compound 5 reacted with cysteine to form a covalent bond as expected.
  • All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification, including U.S. provisional patent application Ser. No. 62/121,415, filed Feb. 26, 2015, are incorporated herein by reference, in their entireties to the extent not inconsistent with the present description.
  • From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims.

Claims (20)

What is claimed is:
1. A compound having the following structure (II):
Figure US20240043455A1-20240208-C00063
or a salt or stereoisomer thereof, wherein:
M1 is, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
L1, L3, and L7 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
R1 is, at each occurrence, independently H, alkyl or alkoxy;
R2 is an electron pair, H, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; or R2 is -L9-(L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
R3 is H, OH, SH, —NH2, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, —Oalkylphospho, —Oalkylthiophospho, alkyletherphospho, alkyletherthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho phosphoalkyl, phosphoalkylether, thiophosphoalkyl, thiophosphoalkylether, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether; or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I)
R4 is, at each occurrence, independently O−, S−, OZ, SZ or N(R6)2, where Z is a cation and each R6 is independently H or alkyl;
R5 is, at each occurrence, independently oxo, thioxo or absent;
L9 and L11 are, at each occurrence, independently an optional linker;
L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
n is an integer from 1 to 20; and
z is an integer from 1 to 10,
provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
2. The compound of claim 1, wherein R3 is -L9-(L10)z-L11-Q, and R2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R2 is optionally substituted with a substituent selected from —OH, —NH2 and —SH.
3. The compound of claim 2, wherein R2 has one of the following structures:
Figure US20240043455A1-20240208-C00064
Figure US20240043455A1-20240208-C00065
wherein:
R2a is —OH, —SH, —NH2, phosphate or thiophosphate;
R4a and R4b are independently O−, S− OZ or SZ, where Z is a cation;
R5a and R5b are independently oxo, or thioxo; and
a, b and c are each independently integers from 1 to 10.
4. The compound of claim 1, wherein R2 is -L9-L10)z-L11-Q, and R3 is OH or phosphate.
5. The compound of claim 1, wherein R2 is -L9-(L10)z-L11-Q, and R3 is, phosphate, thiophosphate, phospho, thiophospho, —Oalkylphospho, —Oalkylthiophospho, —Oalkyletherphospho, —Oalkyletherthiophospho, —Ophosphoalkyl, —Ophosphoalkylether, —Othiophosphoalkyl or —Othiophosphoalkylether optionally substituted with a substituent selected from —OH, —NH2 and —SH.
6. The compound of claim 5, wherein R3 has one of the following structures:
Figure US20240043455A1-20240208-C00066
wherein:
R3a is —OH, —SH, —NH2, phosphate or thiophosphate;
R4a and R4b are independently O−, S− OZ or SZ, where Z is a cation;
R5a and R5b are independently oxo, or thioxo; and
b and c are each independently integers from 1 to 10.
7. The compound of claim 6, wherein R4 is O− and R5 is oxo at each occurrence.
8. The compound of claim 7, wherein L1, L3 and L7 are each alkylene linkers.
9. The compound of claim 7, wherein L1 and L3 are each alkylene linkers and L7 is absent.
10. The compound of claim 8, wherein alkylene is methylene.
11. A method for visually detecting a biomolecule, the method comprising:
(a) admixing the compound of claim 1 with one or more biomolecules; and
(b) detecting the compound by its visible properties.
12. A compound having the following structure (III):
Figure US20240043455A1-20240208-C00067
or a salt or stereoisomer thereof, wherein:
M1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
R1 is H, alkyl or alkoxy;
R2 is H, an electron pair or a cation; or R2 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
R3 is H, phosphate or OH; or R3 is -L9-(L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I);
R4 is O, S, OZ, SZ where Z is a cation;
R5 is oxo or thioxo;
R7, R8, R9, R10, R11 and R12 are, at each occurrence, independently H or alkyl;
L9 and L11 are, at each occurrence, independently an optional linker;
L10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene, aminoalkylene, hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support; and
x, y and z are, at each occurrence, independently an integer from 0 to 5; and
z is an integer from 1 to 10,
provided at least one of R2 or R3 is -L9-L10)z-L11-Q or -L9-(L10)z-L11-S—S-L11-(L10)z-L9-I, where I represents, independently, a further compound of structure (I).
13. The compound of claim 12, wherein x, y and z are each 1.
14. The compound of claim 12, wherein x is 0 and y and z are each 1.
15. The compound of claim 12, wherein L9 is present and is C1-C6 alkylene.
16. The compound of claim 12, wherein (L10)z has one of the following structures:
Figure US20240043455A1-20240208-C00068
wherein b is an integer from 2 to 10.
17. The compound of claim 12, wherein M1 has one of the following structures:
Figure US20240043455A1-20240208-C00069
18. The compound of claim 12, wherein M1, at each occurrence, independently comprises at least one substituent, wherein the substituent is a fluoro, chloro, bromo, iodo, amino, alkylamino, arylamino, hydroxy, sulfhydryl, alkoxy, aryloxy, phenyl, aryl, methyl, ethyl, propyl, butyl, isopropyl, t-butyl, carboxy, sulfonate, amide, or formyl group.
19. The compound of claim 12, wherein Q is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, α-haloamide, biotin, amino or a maleimide.
20. A method for visually detecting a biomolecule, the method comprising:
(a) admixing the compound of claim 12 with one or more biomolecules; and
(b) detecting the compound by its visible properties.
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