WO2006050262A2 - Compositions and methods for modification of biomolecules - Google Patents

Compositions and methods for modification of biomolecules Download PDF

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Publication number
WO2006050262A2
WO2006050262A2 PCT/US2005/039269 US2005039269W WO2006050262A2 WO 2006050262 A2 WO2006050262 A2 WO 2006050262A2 US 2005039269 W US2005039269 W US 2005039269W WO 2006050262 A2 WO2006050262 A2 WO 2006050262A2
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ester
azide
alkyl
molecule
group
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PCT/US2005/039269
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French (fr)
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WO2006050262A3 (en
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Carolyn R. Bertozzi
Nicholas J. Agard
Jennifer A. Prescher
Jeremy Michael Baskin
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The Regents Of The University Of California
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Priority to DK05823231.5T priority Critical patent/DK1812031T3/en
Priority to EP05823231.5A priority patent/EP1812031B1/en
Priority to ES05823231.5T priority patent/ES2545533T3/en
Publication of WO2006050262A2 publication Critical patent/WO2006050262A2/en
Publication of WO2006050262A3 publication Critical patent/WO2006050262A3/en

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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6842—Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
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    • A61K47/555—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound pre-targeting systems involving an organic compound, other than a peptide, protein or antibody, for targeting specific cells
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    • C07C59/40—Unsaturated compounds
    • C07C59/58—Unsaturated compounds containing ether groups, groups, groups, or groups
    • C07C59/72—Unsaturated compounds containing ether groups, groups, groups, or groups containing six-membered aromatic rings and other rings
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    • C07C63/00—Compounds having carboxyl groups bound to a carbon atoms of six-membered aromatic rings
    • C07C63/68—Compounds having carboxyl groups bound to a carbon atoms of six-membered aromatic rings containing halogen
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    • C07C69/67—Esters of carboxylic acids having esterified carboxylic groups bound to acyclic carbon atoms and having any of the groups OH, O—metal, —CHO, keto, ether, acyloxy, groups, groups, or in the acid moiety of saturated acids
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    • C07D207/00—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
    • C07D207/02—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D207/30—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having two double bonds between ring members or between ring members and non-ring members
    • C07D207/34—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having two double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D207/36—Oxygen or sulfur atoms
    • C07D207/40—2,5-Pyrrolidine-diones
    • C07D207/416—2,5-Pyrrolidine-diones with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to other ring carbon atoms
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    • C07D207/00—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
    • C07D207/02—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D207/44—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members
    • C07D207/444—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5
    • C07D207/448—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5 with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms, e.g. maleimide
    • C07D207/452—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having three double bonds between ring members or between ring members and non-ring members having two doubly-bound oxygen atoms directly attached in positions 2 and 5 with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms, e.g. maleimide with hydrocarbon radicals, substituted by hetero atoms, directly attached to the ring nitrogen atom
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    • C07D249/00—Heterocyclic compounds containing five-membered rings having three nitrogen atoms as the only ring hetero atoms
    • C07D249/16—Heterocyclic compounds containing five-membered rings having three nitrogen atoms as the only ring hetero atoms condensed with carbocyclic rings or ring systems
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    • C07D495/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms
    • C07D495/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having sulfur atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
    • C07D495/04—Ortho-condensed systems
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    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/58—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
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    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
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    • C07C2601/18—Systems containing only non-condensed rings with a ring being at least seven-membered

Definitions

  • the invention relates generally to covalent modification of molecules useful in, for example, modification of surfaces (including cell surfaces), and modification of molecules under physiological conditions (e.g., in a cellular environment).
  • the requisite phosphines are susceptible to air oxidation and their optimization for improved water solubility and increased reaction rate has proven to be synthetically challenging.
  • the azide group has an alternative mode of bioorthogonal reactivity: the [3+2] cycloaddition with alkynes described by Huisgen. In its classic form, this reaction has limited applicability in biological systems due to the requirement of elevated temperatures (or pressures) for reasonable reaction rates. Sharpless and coworkers surmounted this obstacle with the development of a copper(I)-catalyzed version, termed "click chemistry,” that proceeds readily at physiological temperatures and in richly functionalized biological environs. This discovery has enabled the selective modification of virus particles, nucleic acids, and proteins from complex tissue lysates.
  • the present invention provides modified cycloalkyne compounds; and method of use of such compounds in modifying biomolecules.
  • the present invention features a cycloaddition reaction that can be carried out under physiological conditions.
  • the invention involves reacting a modified cycloalkyne with an azide moiety on a target biomolecule, generating a covalently modified biomolecule.
  • the selectivity of the reaction and its compatibility with aqueous environments provide for its application in vivo ⁇ e.g., on the cell surface or intracellularly) and in vitro ⁇ e.g., synthesis of peptides and other polymers, production of modified ⁇ e.g., labeled) amino acids).
  • Figures IA and IB depict cycloaddition reactions.
  • Figure IA depicts Cu(I)-catalyzed
  • Figure IB depicts strain-promoted [3+2] cycloaddition of azides and cyclooctynes.
  • Figure 2 depicts labeling of azide-modified GIyCAM-Ig with alkyne probes.
  • Figures 3A-C depict cell surface labeling with a modified cyclooctyne compound.
  • Figure 4A schematically depicts labeling of cell-surface azides with cyclooctyne probes.
  • Figure 4B depicts cyclooctyne probe labeling of Jurkat cells that contain cell-surface azides.
  • Figure 5 depicts labeling of splenocytes with cyclooctyne-FLAG.
  • Figure 6 depicts in vivo labeling of mice with cyclooctyne-FLAG compounds.
  • reactive partner is meant a molecule or molecular moiety that specifically reacts with another reactive partner.
  • exemplary reactive partners are those of the reaction of the invention, i.e., an azide group of an azide-modified target molecule and the cycloalkyne group of a modified cycloalkyne moiety.
  • isolated is meant to describe a compound of interest that is in an environment different from that in which the compound naturally occurs. “Isolated” is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified.
  • substantially purified refers to a compound that is removed from its natural environment or its synthetic environment and is at least 60% free, at least 75% free, at least 90% free, at least 95% free, at least 98% free, or at least 99% free from other components with which it is naturally associated, or is at least 60% free, at least 75% free, at least 90% free, at least 95% free, at least 98% free, or at least 99% free from contaminants associated with synthesis of the compound.
  • the term "cell” in the context of the in vivo applications of the invention is meant to encompass eukaryotic and prokaryotic cells of any genus or species, with mammalian cells being of particular interest. "Cell” is also meant to encompass both normal cells and diseased cells, e.g. , cancerous cells. In many embodiments, the cells are living cells.
  • polypeptide and protein refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
  • the term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
  • physiological conditions is meant to encompass those conditions compatible with living cells, e.g., predominantly aqueous conditions of a temperature, pH, salinity, etc. that are compatible with living cells.
  • aryl as used herein means 5- and 6-membered single-aromatic radicals which may include from zero to four heteroatoms.
  • Representative aryls include phenyl, thienyl, furanyl, pyridinyl, (is)oxazoyl and the like.
  • lower alkyl generally means an acyclic alkyl radical containing from 1 to about 10, e.g., from 1 to about 8 carbon atoms, or from 1 to about 6 carbon atoms.
  • examples of such radicals include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl and the like.
  • aliphatic group means a saturated or unsaturated linear or branched hydrocarbon group and encompasses alkyl, alkenyl, and alkynyl groups, for example.
  • alkyl group means a substituted or unsubstituted, saturated linear or branched hydrocarbon group or chain (e.g., Ci to C 8 ) including, for example, methyl, ethyl, isopropyl, tert-butyl, heptyl, iso-propyl, n-octyl, dodecyl, octadecyl, amyl, 2-ethylhexyl, and the like.
  • Suitable substituents include carboxy, protected carboxy, amino, protected amino, halo, hydroxy, protected hydroxy, nitro, cyano, monosubstituted amino, protected monosubstituted amino, disubstituted amino, C 1 to C 7 alkoxy, Ci to C 7 acyl, Ci to C 7 acyloxy, and the like.
  • substituted alkyl means the above defined alkyl group substituted from one to three times by a hydroxy, protected hydroxy, amino, protected amino, cyano, halo, trifloromethyl, mono- substituted amino, di-substituted amino, lower alkoxy, lower alkylthio, carboxy, protected carboxy, or a carboxy, amino, and/or hydroxy salt.
  • substituted (cycloalkyl)alkyl and “substituted cycloalkyl” are as defined below substituted with the same groups as listed for a "substituted alkyl” group.
  • alkenyl group means an unsaturated, linear or branched hydrocarbon group with one or more carbon-carbon double bonds, such as a vinyl group.
  • alkynyl group means an unsaturated, linear or branched hydrocarbon group with one or more carbon-carbon triple bonds.
  • cyclic group means a closed ring hydrocarbon group that is classified as an alicyclic group, aromatic group, or heterocyclic group.
  • alicyclic group means a cyclic hydrocarbon group having properties resembling those of aliphatic groups.
  • aromatic group or aryl group means a mono- or polycyclic aromatic hydrocarbon group, and may include one or more heteroatoms, and which are further defined below.
  • heterocyclic group means a closed ring hydrocarbon in which one or more of the atoms in the ring are an element other than carbon (e.g., nitrogen, oxygen, sulfur, etc.), and are further defined below.
  • halo and halogen refer to the fluoro, chloro, bromo or iodo groups. There can be one or more halogen, which are the same or different.
  • haloalkyl refers to an alkyl group as defined above that is substituted by one or more halogen atoms.
  • the halogen atoms may be the same or different.
  • dihaloalkyl refers to an alkyl group as described above that is substituted by two halo groups, which may be the same or different.
  • trihaloalkyl refers to an alkyl group as describe above that is substituted by three halo groups, which may be the same or different.
  • perhaloalkyl refers to a haloalkyl group as defined above wherein each hydrogen atom in the alkyl group has been replaced by a halogen atom.
  • perfluoroalkyl refers to a haloalkyl group as defined above wherein each hydrogen atom in the alkyl group has been replaced by a fluoro group.
  • cycloalkyl means a mono-, bi-, or tricyclic saturated ring that is fully saturated or partially unsaturated. Examples of such a group included cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, cyclooctyl, cis- or trans decalin, bicyclo[2.2.1]hept-2-ene, cyclohex-1-enyl, cyclopent-1-enyl, 1 ,4-cyclooctadienyl, and the like.
  • (cycloalkyl)alkyl means the above-defined alkyl group substituted for one of the above cycloalkyl rings. Examples of such a group include (cyclohexyl)methyl, 3- (cyclopropyl)-n-propyl, 5-(cyclopentyl)hexyl, 6-(adamantyl)hexyl, and the like.
  • substituted phenyl specifies a phenyl group substituted with one or more moieties, and in some instances one, two, or three moieties, chosen from the groups consisting of halogen, hydroxy, protected hydroxy, cyano, nitro, trifluoromethyl, Ci to C 7 alkyl, Ci to C 7 alkoxy, Ci to C 7 acyl, Ci to C 7 acyloxy, carboxy, oxycarboxy, protected carboxy, carboxymethyl, protected carboxymethyl, hydroxymethyl, protected hydroxymethyl, amino, protected amino, (monosubstituted)amino, protected (monosubstituted)amino, (disubstituted)amino, carboxamide, protected carboxamide, N-(Ci to C 6 alkyl)carboxamide, protected N-( Ci to C 6 alkyl)carboxamide, N,N-di(Ci to C 6 alkyl)carboxamide, trifluoro
  • substituted phenyl includes a mono- or di(halo)phenyl group such as 2, 3 or 4-chlorophenyl, 2,6-dichlorophenyl, 2,5-dichlorophenyl, 3,4-dichlorophenyl, 2, 3 or 4-bromophenyl, 3,4-dibromophenyl, 3-chloro-4-fluorophenyl, 2, 3 or 4-fluorophenyl and the like; a mono or di(hydroxy)phenyl group such as 2, 3, or 4-hydroxyphenyl, 2,4- dihydroxyphenyl, the protected-hydroxy derivatives thereof and the like; a nitrophenyl group such as 2, 3, or 4-nitrophenyl; a cyanophenyl group, for example, 2, 3 or 4-cyanophenyl; a mono- or di(alkyl)phenyl group such as 2, 3, or 4-methylphenyl, 2,4-dimethylphenyl, 2, 3 or 4-
  • substituted phenyl represents disubstituted phenyl groups wherein the substituents are different, for example, 3 -methyl -4-hydroxyphenyl, 3-chloro-4-hydroxyphenyl, 2-methoxy-4-bromophenyl, 4-ethyl-2-hydroxyphenyl, 3-hydroxy- 4-nitrophenyl, 2-hydroxy-4-chlorophenyl and the like.
  • (substituted phenyl)alkyl means one of the above substituted phenyl groups attached to one of the above-described alkyl groups. Examples of include such groups as 2- phenyl-1-chloroethyl, 2-(4'-methoxyphenyl)ethyl, 4-(2',6'-dihydroxy phenyl)n-hexyl, 2-(5'- cyano-3'-methoxyphenyl)n-pentyl, 3-(2',6'-dimethylphenyl)n-propyl, 4-chloro-3-aminobenzyl, 6-(4'-methoxyphenyl)-3-carboxy(n-hexyl), 5-(4'-aminomethylphenyl)-3-(aminomethyl)n- pentyl, 5-phenyl-3-oxo-n-pent-l-yl, (4-hydroxynapth-2-yl)methyl and the
  • aromatic refers to six membered carbocyclic rings.
  • heteroaryl denotes optionally substituted five-membered or six-membered rings that have 1 to 4 heteroatoms, such as oxygen, sulfur and/or nitrogen atoms, in particular nitrogen, either alone or in conjunction with sulfur or oxygen ring atoms.
  • the above optionally substituted five-membered or six-membered rings can optionally be fused to an aromatic 5-membered or 6-membered ring system.
  • the rings can be optionally fused to an aromatic 5-membered or 6-membered ring system such as a pyridine or a triazole system, e.g., to a benzene ring.
  • heteroaryl thienyl, furyl, pyrrolyl, pyrrolidinyl, imidazolyl, isoxazolyl, triazolyl, thiadiazolyl, oxadiazolyl, tetrazolyl, thiatriazolyl, oxatriazolyl, pyridyl, pyrimidyl, pyrazinyl, pyridazinyl, oxazinyl, triazinyl, thiadiazinyl tetrazolo, l,5-[b]pyridazinyl and purinyl, as well as benzo-fused derivatives, for example, benzoxazolyl, benzthiazolyl, benzimidazolyl and indolyl.
  • Substituents for the above optionally substituted heteroaryl rings are from one to three halo, trihalomethyl, amino, protected amino, amino salts, mono-substituted amino, di- substituted amino, carboxy, protected carboxy, carboxylate salts, hydroxy, protected hydroxy, salts of a hydroxy group, lower alkoxy, lower alkylthio, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, (cycloalkyl)alkyl, substituted (cycloalkyl)alkyl, substituted (cycloalkyl)alkyl, phenyl, substituted phenyl, phenylalkyl, and (substituted phenyl)alkyl.
  • Substituents for the heteroaryl group are as heretofore defined, or in the case of trihalomethyl, can be trifluoromethyl, trichloromethyl, tribromomethyl, or triiodomethyl.
  • lower alkoxy means a Ci to C 4 alkoxy group
  • lower alkylthio means a Cj to C 4 alkylthio group.
  • (monosubstituted)amino refers to an amino group with one substituent chosen from the group consisting of phenyl, substituted phenyl, alkyl, substituted alkyl, Ci to C 4 acyl, C 2 to C 7 alkenyl, C 2 to C 7 substituted alkenyl, C 2 to C 7 alkynyl, C 7 to Ci 6 alkylaryl, C 7 to Ci 6 substituted alkylaryl and heteroaryl group.
  • the (monosubstituted) amino can additionally have an amino-protecting group as encompassed by the term "protected (monosubstituted)amino."
  • the term "(disubstituted)amino” refers to amino groups with two substituents chosen from the group consisting of phenyl, substituted phenyl, alkyl, substituted alkyl, Ci to C 7 acyl, C 2 to C 7 alkenyl, C 2 to C 7 alkynyl, C 7 to Ci 6 alkylaryl, C 7 to Cj 6 substituted alkylaryl and heteroaryl. The two substituents can be the same or different.
  • heteroaryl(alkyl) denotes an alkyl group as defined above, substituted at any position by a heteroaryl group, as above defined.
  • heterocyclo group optionally mono- or di- substituted with an alkyl group means that the alkyl may, but need not, be present, and the description includes situations where the heterocyclo group is mono- or disubstituted with an alkyl group and situations where the heterocyclo group is not substituted with the alkyl group.
  • isomers Compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed “isomers.” Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.” Stereoisomers that are not mirror images of one another are termed “diastereomers” and those that are non-superimposable mirror images of each other are termed “enantiomers.” When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible.
  • An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or (-)-isomers respectively).
  • a chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a "racemic mixture.”
  • the compounds of this invention may possess one or more asymmetric centers; such compounds can therefore be produced as individual (R)- or (S)- stereoisomers or as mixtures thereof. Unless indicated otherwise, the description or naming of a particular compound in the specification and claims is intended to include both individual enantiomers and mixtures, racemic or otherwise, thereof.
  • the methods for the determination of stereochemistry and the separation of stereoisomers are well-known in the art (see, e.g., the discussion in Chapter 4 of "Advanced Organic Chemistry", 4th edition J. March, John Wiley and Sons, New York, 1992).
  • the present invention features a strain-promoted [3+2] cycloaddition reaction that can be carried out under physiological conditions.
  • the invention involves reacting a modified cycloalkyne with an azide moiety on a biomolecule, generating a covalently modified biomolecule.
  • the selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).
  • the reaction is compatible with modification of living cells.
  • the invention provides methods and compositions for specifically and efficiently synthetically modifying cellular components in an aqueous environment, thus providing for modification of such cellular components on or in living cells.
  • the invention uses reactive partners that are completely abiotic and are chemically orthogonal to native cellular components, thus providing for extreme selectivity of the reaction.
  • the reaction can be carried out under physiological conditions, e.g. , a pH of about 7 within an aqueous environment, and at about 37°C.
  • the invention is based in part on the discovery of a means for carrying out a modified
  • Huisgen reaction that can be carried out in an aqueous, physiological environment. Because the reaction of the invention is highly selective and functions in aqueous solvents, the reaction can be used in a variety of applications both in vitro and in vivo.
  • the reaction is accomplished through use of a first molecule comprising a strained cycloalkyne moiety, and second molecule comprising an azide moiety.
  • the azide moiety on the second molecule reacts, in the absence of a catalyst, with the strained cycloalkyne moiety on the first molecule, forming a final conjugate product comprising fused azide/cycloalkyne ring.
  • the first molecule comprising the strained cycloalkyne moiety can further comprise a moiety that allows for subsequent reactions and/or which provides for detectable labeling of the product of the final reaction.
  • the reaction proceeds without the need for a catalyst. Instead, activation energy for the reaction is provided by azide group and the strained cycloalkyne group.
  • the invention takes advantage of the massive bond angle deformation of the acetylene group in the cycloalkyne moiety, which provides for ring strain. For example, the bond angle deformation of the acetylene group of cyclooctyne to 163° accounts for nearly 18 kcal/mol of ring strain. This destabilization of the ground state versus the transition state of the reaction provides a dramatic rate acceleration compared to unstrained alkynes.
  • the present invention provides modified cycloalkyne compounds; and compositions comprising the compounds.
  • a subject modified cycloalkyne is a compound of the formula:
  • X is a strained cycloalkyne group, or a heterocycloalkyne group, substituted with Ri 1 and in some embodiments one or more additional groups;
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
  • Ri is a substituted or unsubstituted aliphatic group, e.g., a substituted or unsubstituted alkyl; a substituted or unsubstituted alkenyl; or a substituted or unsubstituted alkynyl.
  • R 1 is a substituted or unsubstituted phenyl.
  • Y is a reactive group.
  • Suitable reactive groups include, but are not necessarily limited to, carboxyl, amine, (e.g., alkyl amine (e.g., lower alkyl amine), aryl amine), ester (e.g., alkyl ester (e.g., lower alkyl ester, benzyl ester), aryl ester, substituted aryl ester), thioester, sulfonyl halide, alcohol, thiol, succinimidyl ester, isothiocyanate, iodoacetamide, maleimide, hydrazine, and the like.
  • amine e.g., alkyl amine (e.g., lower alkyl amine), aryl amine
  • ester e.g., alkyl ester (e.g., lower alkyl ester, benzyl ester), aryl ester, substituted aryl ester
  • Y is a reactive group selected from a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
  • Y is a molecule of interest, where suitable molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like.
  • suitable molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like.
  • Y is a molecule of interest other than a linker, the molecule of interest is attached directly to Ri, or is attached through a linker.
  • the cycloalkyne is a strained cycloalkyne, e.g., the cycloalkyne increases the rate of reaction from about 2-fold to about 1000-fold, e.g., the cycloalkyne increases the rate of reaction at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, or at least about 1000-fold, compared to the rate of reaction between an azide and a linear alkyne having the same number of carbon atoms as the cycloalkyne.
  • the strained cycloalkyne will in some embodiments be a heterocycloalkyne, e.g., the cycloalkyne will in some embodiments comprise atoms other than carbon.
  • the cycloalkyne or heterocycloalkyne will be a 7-membered ring.
  • the cycloalkyne or heterocycloalkyne will be an 8-membered ring.
  • the cycloalkyne or heterocycloalkyne will be a 9-membered ring.
  • the strain on the cycloalkyne can be increased in a variety of ways, e.g., through the use of heteroatoms; the degree of unsaturation, or torsional strain; the use of electron- withdrawing groups, etc.
  • the cycloalkyne is a cyclooctyne.
  • the strained cycloalkyne is a compound in which one or more of the carbon atoms in the cycloalkyne ring, other than the two carbon atoms joined by a triple bond, is substituted with one or more electron-withdrawing groups, e.g., a halo (bromo, chloro, fluoro, iodo), a nitro group, a cyano group, or a sulfone group.
  • the electron-withdrawing group is a nitro group, a cyano group, or a sulfone group
  • the electron-withdrawing group is not directly linked to the cycloalkyne ring.
  • a subject modified cycloalkyne is of Formula I:
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons joined by the triple bond.
  • the modified cycloalkyne is of Formula I, wherein one or more of the carbon atoms in the cyclooctyne ring, other than the two carbon atoms joined by a triple bond, is substituted with one or more electron-withdrawing groups, e.g., a halo (bromo, chloro, fluoro, iodo), a nitro group, a cyano group, a sulfone group, or a sulfonic acid group.
  • a subject modified cycloalkyne is of Formula II:
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond.
  • a subject modified cycloalkyne is of Formula III:
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond.
  • a subject modified cycloalkyne is of Formula IV:
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
  • V can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond.
  • Exemplary, non-limiting examples of a subject halogenated cyclooctyne compound include:
  • Y is a molecule of interest.
  • Suitable molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like.
  • Y is a molecule of interest other than a linker, the molecule of interest is attached directly to Ri, or is attached through a linker.
  • the modified cycloalkyne comprises a molecule desired for delivery and conjugation to the azido-target substrate (azide-containing target molecule), which target substrate may be displayed on the cell surface, may reside within the cell membrane, or may be intracellular.
  • small molecule drugs e.g., cytotoxic molecules (e.g., drugs), lig
  • compositions and methods of the invention can be used to deliver a detectable label to a target molecule having an azide.
  • a subject modified cycloalkyne comprises a detectable label, covalently bound to the modified cycloalkyne either directly or through a linker.
  • Exemplary detectable labels include, but are not necessarily limited to, fluorescent molecules (e.g., autofluorescent molecules, molecules that fluoresce upon contact with a reagent, etc.), radioactive labels (e.g., 111 In, 125 I, 131 1, 212 B, 90 Y, 186 Rh, and the like); biotin (e.g., to be detected through reaction of biotin and avidin); fluorescent tags; imaging reagents (e.g., those described in U.S. Pat. No. 4,741,900 and U.S. Pat. No. 5,326,856), and the like.
  • fluorescent molecules e.g., autofluorescent molecules, molecules that fluoresce upon contact with a reagent, etc.
  • radioactive labels e.g., 111 In, 125 I, 131 1, 212 B, 90 Y, 186 Rh, and the like
  • biotin e.g., to be detected through reaction of biotin and avidin
  • fluorescent tags e.g., those
  • Detectable labels also include peptides or polypeptides that can be detected by antibody binding, e.g., by binding of a detectably labeled antibody or by detection of bound antibody through a sandwich-type assay.
  • quantum dots e.g., detectably labeled semiconductor nanocrystals, such as fluorescently labeled quantum dots, antibody-conjugated quantum dots, and the like. See, e.g., Dubertret et al. 2002 Science 298:759-1762; Chan et al. (1998) Science 281 :2016-2018; U.S. Patent No. 6,855,551; Bruchez et al. (1998) Science 281 :2013-2016
  • Suitable fluorescent molecules include, but are not limited to, fluorescein, fluorescein isothiocyanate, succinimidyl esters of carboxyfluorescein, succinimidyl esters of fluorescein, 5 -isomer of fluorescein dichlorotriazine, caged carboxyfiuorescein-alanine-carboxamide, Oregon Green 488, Oregon Green 514; Lucifer Yellow, acridine Orange, rhodamine, tetramethylrhodamine, Texas Red, propidium iodide, JC- 1 (5,5',6,6'-tetrachloro-l , 1 ',3,3'-tetraethylbenzimidazoylcarbocyanine iodide), tetrabromorhodamine 123, rhodamine 6G, TMRM (tetramethylrhodamine- , methyl ester), TM
  • Suitable fluorescent proteins and chromogenic proteins include, but are not limited to, a green fluorescent protein (GFP), including, but not limited to, a GFP derived from Aequoria victoria or a derivative thereof, e.g., a "humanized” derivative such as Enhanced GFP, which is available commercially, e.g., from Clontech, Inc.; a GFP from another species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem.
  • GFP green fluorescent protein
  • Suitable epitope tags include, but are not limited to, hemagglutinin (HA; e.g., HA;
  • CYPYDVPDYA SEQ ID NO: 1
  • FLAG e.g., DYKDDDDK
  • FLAG-C e.g., DYKDDDDKC
  • c-myc e.g., CEQKLISEEDL; SEQ ID NO:4
  • metal ion affinity tag such as a polyhistidine tag (e.g., His 6 ), and the like.
  • Suitable imaging agents include positive contrast agents and negative contrast agents.
  • Suitable positive contrast agents include, but are not limited to, gadolinium tetraazacyclododecanetetraacetic acid (Gd-DOTA); Gadolinium- diethylenetriaminepentaacetic acid (Gd-DTPA); Gadolinium- 1,4, 7-tris(carbonylmethyl)- 10-(2'-hydroxypropyl)- 1 ,4,7, 10-tetraazacyclododecane (Gd-HP -DO3 A); Manganese(II)- dipyridoxal diphosphate (Mn-DPDP); Gd-diethylenetriaminepentaacetate- bis(methylamide) (Gd-DTPA-BMA); and the like.
  • Gd-DOTA gadolinium tetraazacyclododecanetetraacetic acid
  • Gd-DTPA Gadolinium- diethylenetriaminepentaacetic acid
  • Suitable negative contrast agents include, but are not limited to, a superparamagnetic iron oxide (SPIO) imaging agent; and a perfluorocarbon, where suitable perfluorocarbons include, but are not limited to, fluoroheptanes, fluorocycloheptanes, fluoromethylcycloheptanes, fiuorohexanes, fluorocyclohexanes, fluoropentanes, fluorocyclopentanes, fluoromethylcyclopentanes, fluorodimethylcyclopentanes, fluoromethylcyclobutanes, fluorodimethylcyclobutanes, fluorotrimethylcyclobutanes, fluorobutanes, fiuorocyclobutanse, fiuoropropanes, fluoroethers, fluoropolyethers, fluorotriethylamines, perfluorohexanes, perfluoropentanes, perfluorobutanes, perfluoropropanes, sulfur
  • a subject modified cycloalkyne comprises a member of a pair of binding partners
  • a member of a pair of binding partners is referred to herein as a "specific binding partner.”
  • Suitable specific binding partners include, but are not limited to, a member of a receptor/ligand pair; a member of an antibody/antigen pair; a member of a lectin/carbohydrate pair; a member of an enzyme/substrate pair; biotin/avidin; biotin/streptavidin; digoxin/antidigoxin; and the like.
  • Suitable specific binding partners include, but are not limited to a receptor ligand; a receptor for a ligand; a ligand-binding portion of a receptor; an antibody; an antigen-binding fragment of an antibody; an antigen; a hapten; a lectin; a lectin- binding carbohydrate; an enzyme substrate; an irreversible inhibitor of an enzyme (e.g., an irreversible inhibitor that binds a substrate binding site of an enzyme, e.g., a "suicide" substrate); and the like.
  • Suitable ligand members of receptor/ligand pairs include, but are not limited to, neurotransmitters such as opioid compounds, acetylcholine, and the like; viral proteins that bind to a cell surface receptor, e.g., human immunodeficiency virus gpl20, and the like; hormones; and the like.
  • Suitable antigen-binding antibody fragments include F(ab') 2 , F(ab) 2 , Fab', Fab, Fv, scFv, and Fd fragments, single-chain antibodies, and fusion proteins comprising an antigen- binding portion of an antibody and a non-antibody protein (e.g., an antigen-binding fragment of an antibody fused to an immunoglobulin constant region).
  • Suitable haptens include, but are not limited to, (4-hydroxy-3-nitrophenyl) acetyl; diethylenetriaminepentaacetic acid (DTPA) or one of its metal complexes; paranitrophenyl; biotin; fluorescein isothiocyanate; and the like.
  • Drugs include, but are not limited to, (4-hydroxy-3-nitrophenyl) acetyl; diethylenetriaminepentaacetic acid (DTPA) or one of its metal complexes; paranitrophenyl; biotin; fluorescein isothiocyanate; and the like.
  • Suitable drugs that can be attached to a modified cycloalkyne moiety include, but are not limited to, cytotoxic compounds (e.g., cancer chemotherapeutic compounds); antiviral compounds; biological response modifiers (e.g., hormones, chemokines, cytokines, interleukins, etc.); microtubule affecting agents; hormone modulators; steroidal compounds; and the like.
  • cytotoxic compounds e.g., cancer chemotherapeutic compounds
  • antiviral compounds e.g., antiviral compounds
  • biological response modifiers e.g., hormones, chemokines, cytokines, interleukins, etc.
  • microtubule affecting agents e.g., hormone modulators; steroidal compounds; and the like.
  • Suitable cancer chemotherapeutic compounds include, but are not limited to, non- peptidic (i.e., non-proteinaceous) compounds that reduce proliferation of cancer cells; peptidic compounds that reduce proliferation of cancer cells; anti-metabolite agents; cytotoxic agents; and cytostatic agents.
  • Non-limiting examples of chemotherapeutic agents include alkylating agents, nitrosoureas, antimetabolites, antitumor antibiotics, plant (vinca) alkaloids, and steroid hormones.
  • Suitable agents that act to reduce cellular proliferation include, but are not limited to, alkylating agents, such as nitrogen mustards, nitrosoureas, ethylenimine derivatives, alkyl sulfonates, and triazenes, including, but not limited to, mechlorethamine, cyclophosphamide (CytoxanTM), melphalan (L-sarcolysin), carmustine (BCNU), lomustine (CCNU), semustine (methyl-CCNU), streptozocin, chlorozotocin, uracil mustard, chlormethine, ifosfamide, chlorambucil, pipobroman, triethylenemelamine, triethylenethiophosphoramine, busulfan, dacarbazine, and temozolomide.
  • alkylating agents such as nitrogen mustards, nitrosoureas, ethylenimine derivatives, alkyl sulfonates, and triazenes, including, but
  • Suitable antimetabolite agents include folic acid analogs, pyrimidine analogs, purine analogs, and adenosine deaminase inhibitors, including, but not limited to, cytarabine (CYTOSAR-U), cytosine arabinoside, fluorouracil (5-FU), floxuridine (FudR), 6-thioguanine, 6-mercaptopurine (6-MP), pentostatin, 5 -fluorouracil (5-FU), methotrexate, 10-propargyl-5,8- dideazafolate (PDDF, CB3717), 5,8-dideazatetrahydrofolic acid (DDATHF), leucovorin, fludarabine phosphate, pentostatine, and gemcitabine.
  • CYTOSAR-U cytarabine
  • cytosine arabinoside including, but not limited to, fluorouracil (5-FU), floxuridine (FudR), 6-thioguanine
  • Suitable antiproliferative natural products and their derivatives include, but are not limited to, Ara-C, paclitaxel (Taxol®), docetaxel (Taxotere®), deoxycoformycin, mitomycin- C, L-asparaginase, azathioprine; brequinar; alkaloids, e.g. vincristine, vinblastine, vinorelbine, vindesine, etc.; podophyllotoxins, e.g. etoposide, teniposide, etc.; antibiotics, e.g.
  • anthracycline daunorubicin hydrochloride (daunomycin, rubidomycin, cerubidine), idarubicin, doxorubicin, epirubicin and morpholino derivatives, etc.; phenoxizone biscyclopeptides, e.g. dactinomycin; basic glycopeptides, e.g. bleomycin; anthraquinone glycosides, e.g. plicamycin (mithramycin); anthracenediones, e.g. mitoxantrone; azirinopyrrolo indolediones, e.g. mitomycin; macrocyclic immunosuppressants, e.g. cyclosporine, FK-506 (tacrolimus, prograf), rapamycin, etc. ; and the like.
  • phenoxizone biscyclopeptides e.g. dactinomycin
  • basic glycopeptides e.g.
  • Suitable anti-proliferative cytotoxic agents are navelbene, CPT-11, anastrazole, letrazole, capecitabine, reloxafine, cyclophosphamide, ifosamide, and droloxafine.
  • Suitable microtubule affecting agents that have antiproliferative activity include, but are not limited to, allocolchicine (NSC 406042), Halichondrin B (NSC 609395), colchicine (NSC 757), colchicine derivatives (e.g., NSC 33410), dolstatin 10 (NSC 376128), maytansine (NSC 153858), rhizoxin (NSC 332598), paclitaxel (Taxol®), Taxol® derivatives, docetaxel (Taxotere®), thiocolchicine (NSC 361792), trityl cysterin, vinblastine sulfate, vincristine sulfate, natural and synthetic epothilones including but not limited to, eopthilone A, epothilone B, discodermolide; estramustine, nocodazole, and the like.
  • Suitable hormone modulators and steroids include, but are not limited to, adrenocorticosteroids, e.g. prednisone, dexamethasone, etc.; estrogens and pregestins, e.g. hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrol acetate, estradiol, clomiphene, tamoxifen; etc.; and adrenocortical suppressants, e.g.
  • adrenocorticosteroids e.g. prednisone, dexamethasone, etc.
  • estrogens and pregestins e.g. hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrol acetate, estradiol, clomiphene, tamoxifen; etc.
  • adrenocortical suppressants e.g.
  • estradiosteroids may inhibit T cell proliferation.
  • chemotherapeutic agents include metal complexes, e.g. cisplatin (cis-
  • DDP dihydroxyurea
  • hydrazines e.g. N-methylhydrazine
  • epidophyllotoxin a topoisomerase inhibitor
  • procarbazine mitoxantrone
  • leucovorin tegafur
  • Other antiproliferative agents of interest include immunosuppressants, e.g.
  • mycophenolic acid mycophenolic acid, thalidomide, desoxyspergualin, azasporine, leflunomide, mizoribine, azaspirane (SKF 105685); Iressa® (ZD 1839, 4-(3-chloro-4-fluorophenylamino)-7-methoxy-6- (3-(4-morpholinyl)propoxy)quinazoline); etc.
  • Taxanes are also suitable for attachment to a cycloalkyne moiety.
  • “Taxanes” include paclitaxel, as well as any active taxane derivative or pro-drug.
  • “Paclitaxel” (which should be understood herein to include analogues, formulations, and derivatives such as, for example, docetaxel, TAXOLTM, TAXOTERETM (a formulation of docetaxel), 10-desacetyl analogs of paclitaxel and 3'N-desbenzoyl-3'N-t-butoxycarbonyl analogs of paclitaxel) may be readily prepared utilizing techniques known to those skilled in the art (see also WO 94/07882, WO 94/07881, WO 94/07880, WO 94/07876, WO 93/23555, WO 93/10076; U.S.
  • Paclitaxel should be understood to refer to not only the common chemically available form of paclitaxel, but analogs and derivatives (e.g., TaxotereTM docetaxel, as noted above) and paclitaxel conjugates (e.g., paclitaxel-PEG, paclitaxel-dextran, or paclitaxel-xylose).
  • analogs and derivatives e.g., TaxotereTM docetaxel, as noted above
  • paclitaxel conjugates e.g., paclitaxel-PEG, paclitaxel-dextran, or paclitaxel-xylose.
  • Taxane also included within the term “taxane” are a variety of known derivatives, including both hydrophilic derivatives, and hydrophobic derivatives.
  • Taxane derivatives include, but not limited to, galactose and mannose derivatives described in International Patent Application No. WO 99/18113; piperazino and other derivatives described in WO 99/14209; taxane derivatives described in WO 99/09021, WO 98/22451, and U.S. Patent No. 5,869,680; 6-thio derivatives described in WO 98/28288; sulfenamide derivatives described in U.S. Patent No. 5,821,263; and taxol derivative described in U.S. Patent No. 5,415,869.
  • Biological response modifiers that are suitable for attachment to a cycloalkyne moiety include, but are not limited to, (1) inhibitors of tyrosine kinase (RTK) activity; (2) inhibitors of serine/threonine kinase activity; (3) tumor-associated antigen antagonists, such as antibodies that bind specifically to a tumor antigen; (4) apoptosis receptor agonists; (5) inter leukin-2; (6) IFN- ⁇ ; (7) IFN- ⁇ (8) colony-stimulating factors; and (9) inhibitors of angiogenesis.
  • RTK tyrosine kinase
  • Suitable linkers include, but are not limited to, a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, a nitro, and a peptide linker.
  • Exemplary peptide linkers for use in linking a molecule of interest to a modified cycloalkyne will in some embodiments have a combination of glycine, alanine, proline and methionine residues, where suitable peptide linkers include, but are not limited to AAAGGM (SEQ ID NO:5); AAAGGMPP AAAGGM (SEQ ID NO:6); AAAGGM (SEQ ID NO:7); and PPAAAGGMM (SEQ ID NO: 8).
  • Any flexible linker generally having a length of from about 6 amino acids and about 40 amino acids is suitable for use.
  • Linkers may have virtually any sequence that results in a generally flexible peptide, including alanine-proline rich sequences.
  • compositions comprising a subject modified cycloalkyne compound.
  • a subject composition generally comprises a subject modified cycloalkyne compound; and at least one additional compound.
  • Suitable additional compounds include, but are not limited to: a salt, such as a magnesium salt, a sodium salt, etc., e.g., NaCl, MgCl, KCl, MgSO 4 , etc.; a buffering agent, e.g., a Tris buffer, N-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES), 2-(N- Morpholino)ethanesulfonic acid (MES), 2-(N-Morpholino)ethanesulfonic acid sodium salt (MES), 3-(N-Morpholino)propanesulfonic acid (MOPS), N-tris[Hydroxymethyl]methyl-3- aminopropane salt, etc.
  • a subject composition comprises a subject modified cycloalkyne compound; and a pharmaceutically acceptable excipient.
  • pharmaceutically acceptable excipients are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, A. Gennaro (2000) "Remington: The Science and Practice of Pharmacy," 20 th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C. Ansel et al., eds., 7 th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A.H. Kibbe et al., eds., 3 rd ed. Amer. Pharmaceutical Assoc.
  • the pharmaceutically acceptable excipients such as vehicles, adjuvants, carriers or diluents, are readily available to the public.
  • pharmaceutically acceptable auxiliary substances such as pH adjusting and buffering agents, tonicity adjusting agents, stabilizers, wetting agents and the like, are readily available to the public.
  • the present invention provides methods for chemoselective modification of a target molecule comprising an azide.
  • the methods generally involve reacting an azide in an azide- containing target molecule with a modified cycloalkyne.
  • the modified cycloalkyne has a structure as described above.
  • a subject method for synthetically modifying a cellular component generally involves: a) introducing an azide moiety into a cellular component, thereby generating an azide-modif ⁇ ed cellular component; and contacting the cell comprising the azide-modified cellular component with a reactive partner comprising a modified cycloalkyne, the contacting being under physiological conditions.
  • the contacting step results in reaction between the azide group of azide-modified cellular component and the cycloalkyne of the reactive partner, thereby synthetically and covalently modifying the cellular component.
  • the method is carried out on living cells in vitro. In other embodiments, the method is carried out on living cells ex vivo. In still other embodiments, the method is carried out on living cells in vivo.
  • the chemoselective ligation is designed for use in fully aqueous, physiological conditions and involves production of a stable, final product comprising a fused azide/cycloalkyne ring.
  • this embodiment involves reacting a first reactant comprising a strained cycloalkyne moiety with a second reactant comprising an azide, such that a covalent bond is formed between the first and second reactants by reaction of the strained cycloalkyne moiety with the azide group.
  • a first reactant comprises a strained cycloalkyne moiety that provides the energy for the reaction between the first and second reactants.
  • the first reactant is a modified cycloalkyne compound of the formula:
  • X is a cycloalkyne group substituted with Rj ;
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
  • R 1 is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
  • the first reactant is a modified cycloalkyne compound of any of Formulas I-IV, as described above.
  • Exemplary reactive groups include, but are not necessarily limited to, carboxyl, amine,
  • alkyl amine e.g., lower alkyl amine
  • aryl amine e.g., alkyl ester (e.g., lower alkyl ester, benzyl ester), aryl ester, substituted aryl ester), thioester, sulfonyl halide, alcohol, thiol, succinimidyl ester, isothiocyanate, iodoacetamide, maleimide, hydrazine, and the like.
  • Exemplary molecules of interest further include dyes (e.g., fluorescein or modified fluorescein, and the like), toxins (including cytotoxins), linkers, peptides, and the like.
  • the molecule of interest may be reacted directly with the reactive group or through a linker.
  • exemplary molecules of interest include, but are not necessarily limited to, a detectable label, a drug, a peptide, a member of a specific binding pair, and the like. Such molecules of interest are described in more detail above.
  • Y is a reactive group selected from a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
  • the cycloalkyne is a cyclooctyne.
  • the modified cycloalkyne is of Formula I:
  • Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
  • Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
  • the modified cycloalkyne is of any of Formulas II- IV, above.
  • the second reactant is a compound that comprises an azide such that a covalent bond is formed between the first and second reactants by reaction of the cycloalkyne moiety with the azide group.
  • the second reactant is of the formula: R 2 -N 3
  • R 2 is a target molecule, e.g., a biomolecule or other target molecule.
  • Target molecules of particular interest as the second reactant include, but are not necessarily limited to, amino acids and amino acid residues, polypeptides (including peptides and proteins), sugars or sugar residues, and the like, which contain or are modified to contain at least one azide.
  • the target molecules can be naturally occurring, or may be synthetically or recombinantly produced, and may be isolated, substantially purified, or present within the native milieu of the unmodified molecule upon which the azide-containing target molecule is based (e.g. , on a cell surface or within a cell, including within a host animal, e.g., a mammalian animal, such as a murine host ⁇ e.g., rat, mouse), hamster, canine, feline, bovine, swine, and the like).
  • the target molecule is present in vitro in a cell-free reaction.
  • the target molecule is present in a cell and/or displayed on the surface of a cell.
  • the target molecule is in a living cell; on the surface of a living cell; in a living organism, e.g., in a living multicellular organism.
  • Suitable living cells include cells that are part of a living multicellular organism; cells isolated from a multicellular organism; immortalized cell lines; and the like.
  • the target molecule is a polypeptide
  • the polypeptide may be composed of D- amino acids, L-amino acids, or both, and may be further modified, either naturally, synthetically, or recombinantly, to include other moieties.
  • the target polypeptide may be a lipoprotein, a glycoprotein, or other such modified protein.
  • the target molecule useful as the second reactant comprises at least one azide for reaction with modified cycloalkyne according to the invention, but may comprise 2 or more, 3 or more, 5 or more, 10 or more azides.
  • the number of azides that may be present in a target molecule will vary according to the intended application of the final product of the reaction, the nature of the target molecule itself, and other considerations which will be readily apparent to the ordinarily skilled artisan in practicing the invention as disclosed herein.
  • This embodiment of the invention is particularly useful in modification of a target molecule in vivo.
  • the target substrate is modified to comprise an azide group at the point at which linkage to the modified cycloalkyne reactant is desired.
  • the target substrate is a polypeptide
  • the polypeptide is modified to contain an N-terminal azide
  • the target substrate is a glycoprotein
  • a sugar residue of the glycoprotein can be modified to contain an azide.
  • a target molecule that is unmodified with an azide, but that is to be modified with an azide, is referred to herein as a "target substrate.”
  • a target molecule that is modified with an azide is referred to herein as "an azide-modified target molecule” or "an azide-containing target molecule.”
  • the target substrate can be generated in vitro and then introduced into the cell using any of a variety of methods well known in the art (e.g., microinjection, liposome or lipofectin- mediated delivery, electroporation, etc.), which methods will vary according to the nature of the substrate to be targeted for modification and can be readily and appropriately selected by the ordinarily skilled artisan.
  • the final target substrate can also be generated in vivo by exploiting a host cell's natural biosynthetic machinery.
  • the cell can be provided with a biocompatible azide-derivative of a substrate for synthesis of the desired target molecule, which substrate is processed by the cell to provide an azide-derivative of the desired final target substrate.
  • the cell can be provided with an azide derivative of a sugar residue found within the glycoprotein, which is subsequently processed by the cell through natural biosynthetic processes to produce a modified glycoprotein having at least one modified sugar moiety comprising an accessible azide group.
  • the target substrate can also be produced in vivo using methods well known in the art.
  • unnatural amino acids having azides can be incorporated into recombinant polypeptides expressed in E. coli (see, e.g., Kiick et al. (2000) Tetrahedron 56:9487). Such recombinantly produced polypeptides can be selectively reacted with a modified cycloalkyne reagent according to the invention.
  • an azide group is incorporated into the target molecule by providing a cell (e.g., a eukaryotic cell that glycosylates biopolymers such as proteins) with a synthetic building block for the desired biopolymer target substrate.
  • a cell e.g., a eukaryotic cell that glycosylates biopolymers such as proteins
  • the cell can be provided with a sugar molecule comprising an azide group to provide for incorporation of the azide group in a glycoprotein.
  • the glycoprotein is expressed on the cell surface.
  • the azide group can be incorporated into an amino acid, which is subsequently incorporated into a peptide or polypeptide synthesized by the cell.
  • the target molecule is a carbohydrate-containing molecule (e.g., a glycoprotein; a polysaccharide; etc.), and an azide group is introduced into the target molecule using a synthetic substrate.
  • the synthetic substrate is an azide derivative of a sugar utilized in production of a glycosylated molecule.
  • the synthetic substrate is an azide derivative of a sugar utilized in production of a cell surface molecule, e.g., in the glycoprotein biosynthetic pathway.
  • the host cell can be provided with a synthetic sialic acid azido-derivative, which is incorporated into the pathway for sialic acid biosynthesis, eventually resulting in the incorporation of the synthetic sugar residue in glycoproteins.
  • the glycoproteins are displayed on the cell surface.
  • the synthetic substrate is an azido derivative of mannosamine of the general formula:
  • n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and R 1 , R 2 , R 3 , and
  • R 4 are independently hydrogen or acetyl.
  • the synthetic substrate is an azido sugar derivative of a general formula of, for example:
  • n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and R 2 , R 3 , and R 4 are independently hydrogen or acetyl.
  • the synthetic substrate is an azido sugar derivative of a general formula of, for example:
  • Ri, R 2 , R 3 , and R 4 are independently hydrogen or acetyl, and where the synthetic substrate is incorporated into biosynthetic pathways involving fucose.
  • the synthetic substrate is an azido sugar derivative of a general formula of, for example:
  • n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and Ri, R 2 , R 3 , and
  • R 4 are independently hydrogen or acetyl, and which is incorporated into biosynthetic pathways involving galactose.
  • a subject method is used to modify the surface of a cell.
  • the invention features a method of modifying the surface of cell in vitro or in vivo.
  • the method generally involves reacting an azide group in a target molecule that comprises an azide group with a modified cycloalkyne to provide for chemoselective ligation at the cell surface.
  • the method comprises modifying a target molecule on a cell surface with an azide group; and reacting the azide group in the target molecule with a modified cycloalkyne.
  • an azido sugar is provided to a living cell, which azido sugar is incorporated into a glycoprotein that is displayed on the cell surface. Modification of an azide-modified target molecule with detectable labels, drugs, and other molecules
  • the present invention provides for attachment of a molecule of interest, e.g., a functional molecule, to an azide-modified target molecule.
  • the methods generally involve reacting an azide-modified target molecule with a subject modified cycloalkyne, where the modified cycloalkyne comprises a molecule of interest, as described above.
  • molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like. Attachment of target molecules to a support
  • the modified cycloalkyne can also comprise one or more hydrocarbon linkers (e.g., an alkyl group or derivative thereof such as an alkyl ester) conjugated to a moiety providing for attachment to a solid substratum (e.g., to facilitate assays), or to a moiety providing for easy separation (e.g., a hapten recognized by an antibody bound to a magnetic bead).
  • hydrocarbon linkers e.g., an alkyl group or derivative thereof such as an alkyl ester
  • a moiety providing for attachment to a solid substratum e.g., to facilitate assays
  • a moiety providing for easy separation e.g., a hapten recognized by an antibody bound to
  • a polypeptide having an azide at a selected site can be generated, and the methods and compositions of the invention used to deliver a tag or other moiety to the azide of the polypeptide.
  • the tag or other moiety can then be used as the attachment site for affixing the polypeptide to a support (e.g. , solid or semi-solid support, particular a support suitable for use as a microchip in high-throughput assays). Attachment of molecules for delivery to a target site
  • the modified cycloalkyne will in some embodiments comprise a small molecule drug, toxin, or other molecule for delivery to a cell.
  • the small molecule drug, toxin, or other molecule will in some embodiments provide for a pharmacological activity.
  • the small molecule drug, toxin, or other molecule will in some embodiments serve as a target for delivery of other molecules.
  • Small molecule drugs may be small organic or inorganic compounds having a molecular weight of more than 50 and less than about 2,500 daltons.
  • Small molecule drugs may comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and may include at least an amine, carbonyl, hydroxyl or carboxyl group, and may contain at least two of the functional chemical groups.
  • the drugs may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups.
  • Small molecule drugs are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
  • a subject modified cycloalkyne comprises one of a pair of binding partners (e.g., a ligand; a ligand -binding portion of a receptor; an antibody; an antigen- binding fragment of an antibody; an antigen; a hapten; a lectin; a lectin-binding carbohydrate; etc.).
  • the modified cycloalkyne can comprise a polypeptide that serves as a viral receptor and, upon binding with a viral envelope protein or viral capsid protein, facilitates attachment of virus to the cell surface on which the modified cycloalkyne is displayed.
  • the modified cycloalkyne comprises an antigen that is specifically bound by an antibody (e.g., monoclonal antibody), to facilitate detection and/or separation of host cells displaying the antigen on the cell surface.
  • an antibody e.g., monoclonal antibody
  • the modified cycloalkyne comprises a ligand binding portion of a receptor, or a receptor-binding portion of a ligand.
  • Subject modified cycloalkyne compounds, and subject modification methods are useful in a variety of applications, including research applications and diagnostic applications.
  • Research applications include research applications and diagnostic applications.
  • subject modified cycloalkyne compounds, and subject modification methods are useful in research applications.
  • Applications of interest include research applications, e.g., exploring functional and physical characteristics of a receptor; proteomics; metabolomics; and the like. Research applications also include drug discovery or other screening applications.
  • Proteomics aims to detect, identify, and quantify proteins to obtain biologically relevant information. Metabolomics is the detection, identification, and quantification of metabolites and other small molecules such as lipids and carbohydrates. Fiehn (2001) Comparative and Functional Genomics 2:155-168; and U.S. Patent No. 6,873,914.
  • Drug discovery applications include, but are not limited to, identifying agents that inhibit cancer cell viability and/or growth.
  • the instant invention provides methods of identifying an agent that inhibits cancer cell viability and/or growth. The methods generally involve modifying a component of the cell to comprise a first reactive partner comprising an azide; contacting the cell, in the presence of a test agent, with a second reactive partner comprising a modified cycloalkyne, the contacting being under physiological conditions; where the contacting results in reaction between the azide group of the first reactive partner and the cycloalkyne of the second reactive partner, thereby synthetically and covalently modifying the cellular component; and determining the effect, if any, of the test agent on the level of modification of the cell with the second reactive partner.
  • the method provides for identifying an agent that reduces growth and/or viability of the cancerous cell. Diagnostic and therapeutic applications
  • Applications of interest also include diagnostic applications, e.g., for detection of cancer; and the like, where a subject modified cycloalkyne comprising a detectable label is used to label an azide-modified target molecule, e.g., an azide-labeled target molecule present on a cancer cell.
  • Applications of interest also include therapeutic applications, where a drug or other therapeutic agent is delivered to an azide-modified target molecule, using a subject modified cycloalkyne that comprises a covalently linked drug or other therapeutic agent.
  • the present invention is used for in vivo imaging, e.g., to determine the metabolic or other state of a cell in an organism, e.g., an individual.
  • a subject method can be applied to in vivo imaging of cancer cells in an individual (e.g., a mammal, including rodents, lagomorphs, felines, canines, equines, bovines, ovines, caprines, non-human primates, and humans).
  • One exemplary, non-limiting application of a subject azide-alkyne cycloaddition is in the detection of metabolic change in cells that occur as they alter their phenotype.
  • altered glycosylation patterns are a hallmark of the tumor phenotype, consisting of both the under- and over-expression of naturally-occurring glycans as well as the presentation of glycans normally restricted to expression during embryonic development.
  • Examples of common antigens associated with transformed cells are sialyl Lewis a, sialyl Lewis x, sialyl T, sialyl Tn, and polysialic acid (PSA). J ⁇ rgensen et al. (1995) Cancer Res.
  • PSA is a homopolymer of sialic acid residues up to 50 units in length. Elevated levels of sialic acid are highly correlated with the transformed phenotype in many cancers, including gastric (Dohi et al. (1994) Cancer 73, 1552; and Yamashita et al. (1995) J. Natl. Cancer Inst. 87, 441-446), colon (Yamashita et al. (1995) J. Natl. Cancer Inst. 87, 441-446; Hanski et al. (1995) Cancer Res. 55, 928-933; Hanski et al. (1993) Cancer Res. 53, 4082-4088; Yang et al.
  • the collective display of multiple sialylated antigens on a single cancer cell can account for the fact that so many different tumor types share the high sialic acid phenotype without necessarily expressing an identical complement of antigens (Roth et al. (1988) supra). Consequently, diagnostic or therapeutic strategies that target cells on the basis of sialic acid levels have broad applicability to many cancers.
  • Introduction and incorporation of unnatural azidosugars (ManNAz, GaINAz) into living animals provides for detection of changes in metabolic state. Via the attachment of the appropriate epitope tag, the modified cyclooctyne labels these cells in a living organism, and consequently detects changes in metabolic state. Early detection of tumorigenic cells and subsequent intervention reduces the severity and increases survival rates for cancer patients.
  • Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c, subcutaneous(ly); and the like.
  • Example 1 Modification of biomolecules using a modified cyclooctyne MATERIALS AND METHODS
  • RPMI 1640 media and phosphate-buffered saline (PBS) were purchased from
  • Fetal calf serum was from Hyclone.
  • FITC-conjugated avidin and bovine serum albumin BSA
  • peroxidase- conjugated mouse anti-biotin HRP- ⁇ -biotin
  • HRP- ⁇ -Ig peroxidase-co ⁇ jugated donkey anti-human Ig
  • Precast Tris ⁇ Cl 4-15% polyacrylamide gels, nitrocellulose, and Tween 20 were purchased from BioRad.
  • RestoreTM Western blot stripping buffer and enhanced chemiluminescent substrate were obtained from Pierce.
  • Triethylamine (67 ⁇ L, 0.46 mmol) and compound 4 (104 mg 0.23 mmol) were added and the solution was stirred for 1 h.
  • GIyCAM-Ig samples (in PBS, pH 7.4 containing 0.7% DMF) were incubated with 250 ⁇ M 6, 2.5 mM TCEP, 250 ⁇ M tris- triazolyl ligand (from a 1.7 mM stock in 1 :4 DMSO:tert-butanol), and 2.5 mM CuSO 4 . Samples were vortexed and allowed to react at rt for 12 h. Prior to electrophoresis, samples were incubated with an equal volume of 100 mM 2-azidoethanol in 2 X SDS-PAGE loading buffer for 8 h at rt (to quench unreacted 5 or 6).
  • the quenched samples were boiled for 3 min and loaded onto pre-cast polyacrylamide gels. After electrophoresis, the samples were electroblotted to nitrocellulose membrane.
  • the membrane was blocked using 5% BSA in PBS (pH 7.4, containing 0.05% Tween 20 (blocking buffer A) for 1 h at rt, then incubated with a solution of blocking buffer A containing HRP- ⁇ -biotin (1 :250,000 dilution, 1 h at rt). The membrane was washed, and detection of membrane-bound anti-biotin-HRP was accomplished by chemiluminescence.
  • the membrane was rinsed with PBS (pH 7.4) containing 0.05% Tween (PBS-T) and placed in stripping buffer (15 min at RT) to remove bound anti-biotin Ig.
  • PBS-T 0.05% Tween
  • the membrane was thoroughly rinsed with PBS-T and probed for residual anti-biotin signal by chemiluminescence.
  • Jurkat cells human T-cell lymphoma
  • RPMI- 1640 media supplemented with 10% FCS, penicillin (100 units/mL) and streptomycin (0.1 mg/mL).
  • Cell densities were maintained between 1 x 10 5 and 1.6 x 10 6 cells/mL for all experiments.
  • Jurkat cells were seeded at a density of 1.5-2.0 x 10 5 cells/mL and incubated for 3 d in untreated media or media containing various concentrations of Ac 4 ManNAz. After growth in the presence of Ac 4 ManNAz, cells were distributed into a 96-well V-bottom tissue culture plate. The cells were pelleted (3500 rpm, 3 min) and washed twice with 200 ⁇ L of labeling buffer (PBS, pH 7.4 containing 1% FCS). Cells were then incubated with 5 or a biotinylated phosphine probe (Vocadlo et al. (2003) Proc. Natl. Acad. ScL U.S.A.
  • Cyclooctyne 3 was stable to mild acid (0.5 N HCl for 30 min), base (0.8 M NaOMe for 30 min), and prolonged exposure to biological nucleophiles such as thiols (120 mM 2- mercaptoethanol for 12 h).
  • Control samples of GIyCAM-Ig were expressed in the absence of azido sugar.
  • the purified GIyCAM-Ig samples were incubated with 250 ⁇ M 5 overnight, the unreacted cyclooctyne was quenched with excess 2-azidoethanol, and the samples were analyzed by Western blot probing with HRP- ⁇ -biotin (Fig. 2). Robust biotinylation was observed for GIyCAM-Ig modified with SiaNAz. Native GIyCAM-Ig lacking azides showed no background labeling, underscoring the extraordinarily of the strain-promoted cycloaddition.
  • the blot was stripped and reprobed with HRP-labeled anti-IgG antibody (HRP- ⁇ -IgG) to confirm equal protein loading.
  • HRP-labeled anti-IgG antibody HRP- ⁇ -IgG
  • consistently diminished anti-IgG immunoreactivity was observed for azide-modified GIyCAM-Ig labeled with 6 in the presence of copper. It is possible that the combination of triazole products and copper damages the epitope recognized by HRP- ⁇ -IgG.
  • GIyCAM-Ig was treated with buffer (-), 250 ⁇ M 5, or 250 ⁇ M 6 alone or in the presence (cat) of CuSO 4 , TCEP, and a triazolyl ligand, overnight at rt. Reaction mixtures were quenched with 2-azidoethanol and analyzed by Western blot probing with HRP- ⁇ -biotin (upper panel). The blot was then stripped and reprobed with HRP- ⁇ -Ig (lower panel).
  • FIGs 3A and 3B Cell surface labeling with compound 5.
  • Jurkat cells were incubated in the presence (+Az) or absence (-Az) of 25 ⁇ M Ac 4 ManNAz for 3 d.
  • Figure 3 A The cells were reacted with various concentrations of 5 for 1 h at rt and treated with FITC- avidin; mean fluorescence intensity (MFI) was determined by flow cytometry.
  • Figure 3B The cells were incubated with 250 ⁇ M 5 for various durations at rt and analyzed as in A.
  • C The cells were incubated with 100 ⁇ M probe for 1 h at rt and analyzed as in A. Error bars represent the standard deviation from three replicates.
  • AU arbitrary fluorescence units.
  • Example 2 Synthesis of additional cyclooctyne compounds and their use in labeling of living cells [00171] This example presents the synthesis of compounds 3a and 3b (shown below), the evaluation of their kinetic parameters in reactions with small organic azides, and their use in bioorthogonal labeling of living cells.
  • TEA 0.508 mL, 3.65 mmol
  • cyclooctyne 3b 0.200 g, 0.768 mmol
  • amine 13 (0.235 g, 0.875 mmol
  • O-(7- Azabenzotriazol-l-yl)-N,N,N',N-tetramethyluronium hexafluorophosphate HATU, 0.305 g, 0.802 mmol
  • HOBT 1-hydroxybenzotriazole
  • the kinetic data were derived by monitoring the change in integration of resonances corresponding to the benzylic protons in benzyl azide ( ⁇ ⁇ 4.2 ppm) compared to the corresponding resonances of the triazole products ( ⁇ ⁇ 5.0 to 5.5 ppm).
  • the kinetic data were derived from integration of the resonances corresponding to the more downfield pair of aromatic protons ( ⁇ ⁇ 7.9 ppm) in the cyclooctyne starting material compared to the corresponding resonances in the triazole products ( ⁇ ⁇ 7.7 to 7.8 ppm).
  • Second-order rate constants for the reaction were determined by plotting 1 /[benzyl azide] versus time in the case of the reactions of 3a and 3b with benzyl azide and by plotting l/[3a] versus time or l/[3b] versus time in the case of the reactions of 3a and 3b with 2- azidoethanol, and subsequent analysis by linear regression. Second-order rate constants correspond to one half of the determined slope (Table 1). Error bars represent standard deviations from three replicate experiments.
  • Jurkat cells human T-cell lymphoma
  • RPMI- 1640 media supplemented with 10% FCS, penicillin (100 units/mL), and streptomycin (0.1 mg/mL).
  • Cell densities were maintained between 1 x 10 5 and 1.6 x 10 6 cells/mL.
  • the cells were incubated for 3 d in untreated media or media containing 25 ⁇ M Ac 4 ManNAz. After growth in the presence of Ac 4 MaIiNAz, cells were distributed into a 96-well V-bottom tissue culture plate.
  • the cells were pelleted (3500 rpm, 3 min) and washed twice with 200 ⁇ L of labeling buffer (PBS, pH 7.4 containing 1% FCS). Cells were then incubated with 12b-FLAG or 1-FLAG in labeling buffer for 1 h at it. After incubation, cells were pelleted, washed twice with labeling buffer, and resuspended in the same buffer containing FITC-conjugated ⁇ -FLAG (1:3000 dilution of the Sigma stock). After a 30-min incubation on ice (in the dark), the cells were washed twice with 200 ⁇ L of cold labeling buffer and then diluted to a volume of 400 ⁇ L for flow cytometry analysis.
  • labeling buffer PBS, pH 7.4 containing 1% FCS
  • Azides were installed on the surfaces of Jurkat cells by metabolic labeling of sialic acid residues 10 . Briefly, cells fed peracetylated iV-azidoacetylmannosamine (Ac 4 ManNAz), an analog of N-acetylmannosamine (ManNAc), convert the azido sugar to the corresponding azido sialic acid (SiaNAz) within cell surface glycoproteins. Reaction of the cell-surface azides with phosphine or cyclooctyne probes containing the FLAG epitope was monitored by flow cytometry using visualization with a FITC-conjugated ⁇ -FLAG antibody ( Figure 4a).
  • the 12b-FLAG labels Jurkat cells in an azide-dependent fashion, similar to a previously studied FLAG-labeled phosphine probe capable of undergoing the Staudinger ligation (1-FLAG).
  • Compound 12b-FLAG labels cells in a dose-dependent manner. No toxicity was observed in any of these experiments,.
  • FIGS 4A and 4B Labeling of cell-surface azides with cyclooctyne probes
  • Light blue Cells incubated in the absence of Ac 4 ManNAz. Error bars indicate the standard deviation of three trials. a Mean fluorescence intensity.
  • Example 3 Synthesis of an aryl-less cyclooctyne compound and its use in labeling of living cells
  • This example describes synthesis of an "aryl-less" octyne (ALO; shown below) and the use of a conjugated ALO to label living cells in vivo.
  • ALO aryl-less octyne
  • the aryl-less octyne was synthesized; then a maleimide group was introduced.
  • the maleimide functionality allows for specific conjugation to the thiol of a cysteine containing peptides. Described below are the synthesis of the octyne, the octyne-linked maleimides, their conjugation to a FLAG peptide, and the subsequent use of these conjugates on cell surfaces and in living mice.
  • Compound 14 [00200] Compound 14. AgClO 4 (2.40 g, 11.6 mmol) was added to a solution of dibromobicycle 1 (1.00 g, 3.72 mmol) and methyl glycolate (6.0 ml, 78.2 mmol) dissolved in toluene (4 mL) in a flame-dried, aluminum-foil-wrapped flask. The reaction was stirred for 2 h, diluted with pentane (20 mL), and filtered to remove insoluble silver salts.
  • the reaction can be purified at this point to yield the free acid, but is most often taken on in crude form to give the activated pentafluorophenyl ester
  • the reaction mixture was dissolved in 5ml CH 2 Cl 2 , and to this solution was added Et 3 N (332 ⁇ L, 2.38 mmol) followed by pentafluorophenyltrifluoroacetate (409 ⁇ L, 2.38 mmol).
  • Et 3 N 332 ⁇ L, 2.38 mmol
  • pentafluorophenyltrifluoroacetate 409 ⁇ L, 2.38 mmol.
  • B6D2F1 mice were obtained from The Jackson Laboratory (Bar Harbor, ME). All animals were housed and monitored at the Northwest Animal Facility (Berkeley, CA), and experiments were performed according to guidelines established by the Animal Care and Use Committee at the University of California, Berkeley (protocol number R234-0504B). General protocol for compound administration
  • mice were administered daily doses of Ac 4 ManNAz (0-300 mg/kg in -200 ⁇ L of 70%
  • mice were injected i.p. with oct-FLAG (0-40 ⁇ mol in -200 ⁇ L H 2 O), Phos-FLAG (20 ⁇ mol in -200 ⁇ L H 2 O), or vehicle alone (H 2 O). After 3 h, the mice were anesthetized with isoflurane and sacrificed, and their splenocytes were isolated using a standard protocol. Labeling of splenocyte cell surface azides ex vivo
  • Splenocytes from one spleen were suspended in RPMI medium 1640 and distributed among wells of a 96-well V-bottom tissue culture plate (3 wells per treatment, -5 x 10 5 cells/well). The cells were pelleted (3500 rpm, 3 min), rinsed three times with labeling buffer (1% FBS in PBS, pH 7.4), and incubated with 0-500 ⁇ M oct-FLAG in labeling buffer, Phos- FLAG in labeling buffer, or labeling buffer alone.
  • labeling buffer 1% FBS in PBS, pH 7.4
  • the cells were rinsed three times with labeling buffer, treated with FITC- ⁇ -FLAG (1:900 dilution) or FITC- conjugated mouse IgGi isotype control (1 :200 dilution) in labeling buffer for 30 min on ice, rinsed, and analyzed by flow cytometry.
  • Splenocyte Labeling of FLAG conjugates Splenocytes grown in the presence of
  • Phosphine-FLAG serves as a positive control of ligation, and the three synthesized octynes all show bioorthogonality as demonstrated by increased labeling in the present of azide bearing cells. The degree of labeling is consistent with in vitro kinetic data within the octynes. The more hydrophobic octynes (F-oct(MOFO) and Oct (the first reported cyclooctyne) show some background.
  • mice were injected with azide labeled sugars as described in the procedures. They were subsequently injected with phosphine-FLAG or ALO-FLAG, sacrificed and their cells were analyzed for the presence of FLAG via flow cytometry. The results are shown in Figure 6.

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Abstract

The present invention provides modified cycloalkyne compounds; and method of use of such compounds in modifying biomolecules. The present invention features a cycloaddition reaction that can be carried out under physiological conditions. In general, the invention involves reacting a modified cycloalkyne with an azide moiety on a target biomolecule, generating a covalently modified biomolecule. The selectivity of the reaction and its compatibility with aqueous environments provide for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids).

Description

COMPOSITIONS AND METHODS FOR MODIFICATION OF BIOMOLECULES
CROSS-REFERENCE [0001] This application claims the benefit of U.S. Provisional Patent Application No.
60/624,202 filed November 1 , 2004, which application is incorporated herein by reference in its entirety.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
[0002] The U.S. government may have certain rights in this invention, pursuant to grant nos.
ROI GM58867 awarded by the National Institutes of Health.
FIELD OF THE INVENTION
[0003] The invention relates generally to covalent modification of molecules useful in, for example, modification of surfaces (including cell surfaces), and modification of molecules under physiological conditions (e.g., in a cellular environment).
BACKGROUND OF THE INVENTION [0004] Selective chemical reactions that are orthogonal to the diverse functionality of biological systems are now recognized as important tools in chemical biology. As relative newcomers to the repertoire of synthetic chemistry, these bioorthogonal reactions have inspired new strategies for compound library synthesis, protein engineering, functional proteomics, and chemical remodeling of cell surfaces. The azide has secured a prominent role as a unique chemical handle for bioconjugation. The Staudinger ligation has been used with phosphines to tag azidosugars metabolically introduced into cellular glycoconjugates. The Staudinger ligation can be performed in living animals without physiological harm; nevertheless, the Staudinger reaction is not without liabilities. The requisite phosphines are susceptible to air oxidation and their optimization for improved water solubility and increased reaction rate has proven to be synthetically challenging. [0005] The azide group has an alternative mode of bioorthogonal reactivity: the [3+2] cycloaddition with alkynes described by Huisgen. In its classic form, this reaction has limited applicability in biological systems due to the requirement of elevated temperatures (or pressures) for reasonable reaction rates. Sharpless and coworkers surmounted this obstacle with the development of a copper(I)-catalyzed version, termed "click chemistry," that proceeds readily at physiological temperatures and in richly functionalized biological environs. This discovery has enabled the selective modification of virus particles, nucleic acids, and proteins from complex tissue lysates. Unfortunately, the mandatory copper catalyst is toxic to both bacterial and mammalian cells, thus precluding applications wherein the cells must remain viable. Catalyst-free Huisgen cycloadditions of alkynes activated by electron-withdrawing substituents have been reported to occur at ambient temperatures. However, these compounds undergo Michael reaction with biological nucleophiles. [0006] There is a need in the field for additional mechanisms to modify biological molecules through a biocompatible reaction, particularly in a biological environment. The present invention addresses this need.
Literature [0007] Huisgen (1963) Angew. Chem. Int. Ed. 2:565-598; Shea and Kim. J. Am. Chem. Soc.
1992, 114, 4846-4855; Reese and Shaw (1970) Chem. Comm. 1172-1173; Wilbur et al.
Bioconj. Chem. 1996, 7, 689-702; Bistrup et al. J. Cell Biol. 1999, 145, 899-910; Saxon et al. J.
Am. Chem. Soc. 2002, 124, 14893-14902; Hang and Bertozzi. Ace. Chem. Res. 2001, 34, 727-
736; Link et al. Curr. Opin. Biotechnol. 2003, 14, 603-609; Lee et al. J Am. Chem. Soc.
2003, 125, 9588-9589; Wang et al. J Am. Chem. Soc, 2003, 125, 3192-3193; Kiick et al. Proc.
Natl. Acad. Sci. U.S.A. 2002, 99, 19-24; Speers and Cravatt. Chem. Biol. 2004, 11, 535-546;
Saxon and Bertozzi Science 2000, 287, 2007-2010; Link, A. J.; Tirrell, D. A. J. Am. Chem.
Soc. 2003, 125, 1164-1165; Dube and Bertozzi. Curr. Opin. Chem. Biol. 2003, 7, 616-625;
Vocadlo et al. Proc. Natl. Acad. Sci. U.S.A. 2003, 700, 9116-9121; Prescher et al.. Nature
2004, 430, 873-877; Seo et al. J. Org. Chem. 2003, 68, 609-612; Li et al. Tetrahedron Lett.
2004, 45, 3143-3146; Wittig and Krebs. Chem. Ber. 1961, 94, 3260-3275; Meier et al. Chem.
Ber. 1980, 113, 2398-2409; Turner et al.. J. Am. Chem. Soc. 1972, 95, 790-792.
SUMMARY OF THE INVENTION
[0001] The present invention provides modified cycloalkyne compounds; and method of use of such compounds in modifying biomolecules. The present invention features a cycloaddition reaction that can be carried out under physiological conditions. In general, the invention involves reacting a modified cycloalkyne with an azide moiety on a target biomolecule, generating a covalently modified biomolecule. The selectivity of the reaction and its compatibility with aqueous environments provide for its application in vivo {e.g., on the cell surface or intracellularly) and in vitro {e.g., synthesis of peptides and other polymers, production of modified {e.g., labeled) amino acids). BRIEF DESCRIPTION OF THE DRAWINGS
[0008] Figures IA and IB depict cycloaddition reactions. Figure IA depicts Cu(I)-catalyzed
Huisgen cycloaddition ("click chemistry"). Figure IB depicts strain-promoted [3+2] cycloaddition of azides and cyclooctynes.
[0009] Figure 2 depicts labeling of azide-modified GIyCAM-Ig with alkyne probes.
[0010] Figures 3A-C depict cell surface labeling with a modified cyclooctyne compound.
[0011] Figure 4A schematically depicts labeling of cell-surface azides with cyclooctyne probes. Figure 4B depicts cyclooctyne probe labeling of Jurkat cells that contain cell-surface azides.
[0012] Figure 5 depicts labeling of splenocytes with cyclooctyne-FLAG.
[0013] Figure 6 depicts in vivo labeling of mice with cyclooctyne-FLAG compounds.
DEFINITIONS
[0014] By "reactive partner" is meant a molecule or molecular moiety that specifically reacts with another reactive partner. Exemplary reactive partners are those of the reaction of the invention, i.e., an azide group of an azide-modified target molecule and the cycloalkyne group of a modified cycloalkyne moiety.
[0015] As used herein the term "isolated" is meant to describe a compound of interest that is in an environment different from that in which the compound naturally occurs. "Isolated" is meant to include compounds that are within samples that are substantially enriched for the compound of interest and/or in which the compound of interest is partially or substantially purified.
[0016] As used herein, the term "substantially purified" refers to a compound that is removed from its natural environment or its synthetic environment and is at least 60% free, at least 75% free, at least 90% free, at least 95% free, at least 98% free, or at least 99% free from other components with which it is naturally associated, or is at least 60% free, at least 75% free, at least 90% free, at least 95% free, at least 98% free, or at least 99% free from contaminants associated with synthesis of the compound.
[0002] As used herein, the term "cell" in the context of the in vivo applications of the invention is meant to encompass eukaryotic and prokaryotic cells of any genus or species, with mammalian cells being of particular interest. "Cell" is also meant to encompass both normal cells and diseased cells, e.g. , cancerous cells. In many embodiments, the cells are living cells.
[0003] The terms "polypeptide" and "protein," used interchangeably herein, refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
[0017] The term "physiological conditions" is meant to encompass those conditions compatible with living cells, e.g., predominantly aqueous conditions of a temperature, pH, salinity, etc. that are compatible with living cells.
[0018] The term "aryl" as used herein means 5- and 6-membered single-aromatic radicals which may include from zero to four heteroatoms. Representative aryls include phenyl, thienyl, furanyl, pyridinyl, (is)oxazoyl and the like.
[0019] The term "lower alkyl", alone or in combination, generally means an acyclic alkyl radical containing from 1 to about 10, e.g., from 1 to about 8 carbon atoms, or from 1 to about 6 carbon atoms. Examples of such radicals include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl and the like.
[0020] The term "aliphatic group" means a saturated or unsaturated linear or branched hydrocarbon group and encompasses alkyl, alkenyl, and alkynyl groups, for example. The term "alkyl group" means a substituted or unsubstituted, saturated linear or branched hydrocarbon group or chain (e.g., Ci to C8 ) including, for example, methyl, ethyl, isopropyl, tert-butyl, heptyl, iso-propyl, n-octyl, dodecyl, octadecyl, amyl, 2-ethylhexyl, and the like. Suitable substituents include carboxy, protected carboxy, amino, protected amino, halo, hydroxy, protected hydroxy, nitro, cyano, monosubstituted amino, protected monosubstituted amino, disubstituted amino, C1 to C7 alkoxy, Ci to C7 acyl, Ci to C7 acyloxy, and the like. The term "substituted alkyl" means the above defined alkyl group substituted from one to three times by a hydroxy, protected hydroxy, amino, protected amino, cyano, halo, trifloromethyl, mono- substituted amino, di-substituted amino, lower alkoxy, lower alkylthio, carboxy, protected carboxy, or a carboxy, amino, and/or hydroxy salt. As used in conjunction with the substituents for the heteroaryl rings, the terms "substituted (cycloalkyl)alkyl" and "substituted cycloalkyl" are as defined below substituted with the same groups as listed for a "substituted alkyl" group. The term "alkenyl group" means an unsaturated, linear or branched hydrocarbon group with one or more carbon-carbon double bonds, such as a vinyl group. The term "alkynyl group" means an unsaturated, linear or branched hydrocarbon group with one or more carbon-carbon triple bonds. The term "cyclic group" means a closed ring hydrocarbon group that is classified as an alicyclic group, aromatic group, or heterocyclic group. The term "alicyclic group" means a cyclic hydrocarbon group having properties resembling those of aliphatic groups. The term "aromatic group" or "aryl group" means a mono- or polycyclic aromatic hydrocarbon group, and may include one or more heteroatoms, and which are further defined below. The term "heterocyclic group" means a closed ring hydrocarbon in which one or more of the atoms in the ring are an element other than carbon (e.g., nitrogen, oxygen, sulfur, etc.), and are further defined below.
[0021] The terms "halo" and "halogen" refer to the fluoro, chloro, bromo or iodo groups. There can be one or more halogen, which are the same or different.
[0022] The term "haloalkyl" refers to an alkyl group as defined above that is substituted by one or more halogen atoms. The halogen atoms may be the same or different. The term "dihaloalkyl " refers to an alkyl group as described above that is substituted by two halo groups, which may be the same or different. The term "trihaloalkyl" refers to an alkyl group as describe above that is substituted by three halo groups, which may be the same or different. The term "perhaloalkyl" refers to a haloalkyl group as defined above wherein each hydrogen atom in the alkyl group has been replaced by a halogen atom. The term "perfluoroalkyl" refers to a haloalkyl group as defined above wherein each hydrogen atom in the alkyl group has been replaced by a fluoro group.
[0023] The term "cycloalkyl" means a mono-, bi-, or tricyclic saturated ring that is fully saturated or partially unsaturated. Examples of such a group included cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, cyclooctyl, cis- or trans decalin, bicyclo[2.2.1]hept-2-ene, cyclohex-1-enyl, cyclopent-1-enyl, 1 ,4-cyclooctadienyl, and the like.
[0024] The term "(cycloalkyl)alkyl" means the above-defined alkyl group substituted for one of the above cycloalkyl rings. Examples of such a group include (cyclohexyl)methyl, 3- (cyclopropyl)-n-propyl, 5-(cyclopentyl)hexyl, 6-(adamantyl)hexyl, and the like.
[0025] The term "substituted phenyl" specifies a phenyl group substituted with one or more moieties, and in some instances one, two, or three moieties, chosen from the groups consisting of halogen, hydroxy, protected hydroxy, cyano, nitro, trifluoromethyl, Ci to C7 alkyl, Ci to C7 alkoxy, Ci to C7 acyl, Ci to C7 acyloxy, carboxy, oxycarboxy, protected carboxy, carboxymethyl, protected carboxymethyl, hydroxymethyl, protected hydroxymethyl, amino, protected amino, (monosubstituted)amino, protected (monosubstituted)amino, (disubstituted)amino, carboxamide, protected carboxamide, N-(Ci to C6 alkyl)carboxamide, protected N-( Ci to C6 alkyl)carboxamide, N,N-di(Ci to C6 alkyl)carboxamide, trifluoromethyl, N-(( Ci to C6 alkyl)sulfonyl)amino, N-(phenylsulfonyl)amino or phenyl, substituted or unsubstituted, such that, for example, a biphenyl or naphthyl group results. [0026] Examples of the term "substituted phenyl" includes a mono- or di(halo)phenyl group such as 2, 3 or 4-chlorophenyl, 2,6-dichlorophenyl, 2,5-dichlorophenyl, 3,4-dichlorophenyl, 2, 3 or 4-bromophenyl, 3,4-dibromophenyl, 3-chloro-4-fluorophenyl, 2, 3 or 4-fluorophenyl and the like; a mono or di(hydroxy)phenyl group such as 2, 3, or 4-hydroxyphenyl, 2,4- dihydroxyphenyl, the protected-hydroxy derivatives thereof and the like; a nitrophenyl group such as 2, 3, or 4-nitrophenyl; a cyanophenyl group, for example, 2, 3 or 4-cyanophenyl; a mono- or di(alkyl)phenyl group such as 2, 3, or 4-methylphenyl, 2,4-dimethylphenyl, 2, 3 or 4- (iso-propyl)phenyl, 2, 3, or 4-ethylphenyl, 2, 3 or 4-(n-propyl)phenyl and the like; a mono or di(alkoxy)phenyl group, for example, 2,6-dimethoxyphenyl, 2, 3 or 4-(isopropoxy)phenyl, 2, 3 or 4-(t-butoxy)phenyl, 3-ethoxy-4-methoxyphenyl and the like; 2, 3 or 4- trifluoromethylphenyl; a mono- or dicarboxyphenyl or (protected carboxy)phenyl group such as 2, 3 or 4-carboxyphenyl or 2,4-di(protected carboxy)phenyl; a mono- or di(hydroxymethyl)phenyl or (protected hydroxymethyl)phenyl such as 2, 3 or 4-(protected hydroxymethyl)phenyl or 3,4-di(hydroxymethyl)phenyl; a mono- or di(aminomethyl)phenyl or (protected aminomethyl)phenyl such as 2, 3 or 4-(aminomethyl)phenyl or 2,4-(protected aminomethyl)phenyl; or a mono- or di(N-(methylsulfonylamino))phenyl such as 2, 3 or 4-(N- (methylsulfonylamino))phenyl. Also, the term "substituted phenyl" represents disubstituted phenyl groups wherein the substituents are different, for example, 3 -methyl -4-hydroxyphenyl, 3-chloro-4-hydroxyphenyl, 2-methoxy-4-bromophenyl, 4-ethyl-2-hydroxyphenyl, 3-hydroxy- 4-nitrophenyl, 2-hydroxy-4-chlorophenyl and the like.
[0027] The term "(substituted phenyl)alkyl" means one of the above substituted phenyl groups attached to one of the above-described alkyl groups. Examples of include such groups as 2- phenyl-1-chloroethyl, 2-(4'-methoxyphenyl)ethyl, 4-(2',6'-dihydroxy phenyl)n-hexyl, 2-(5'- cyano-3'-methoxyphenyl)n-pentyl, 3-(2',6'-dimethylphenyl)n-propyl, 4-chloro-3-aminobenzyl, 6-(4'-methoxyphenyl)-3-carboxy(n-hexyl), 5-(4'-aminomethylphenyl)-3-(aminomethyl)n- pentyl, 5-phenyl-3-oxo-n-pent-l-yl, (4-hydroxynapth-2-yl)methyl and the like.
[0028] As noted above, the term "aromatic" or "aryl" refers to six membered carbocyclic rings.
Also as noted above, the term "heteroaryl" denotes optionally substituted five-membered or six-membered rings that have 1 to 4 heteroatoms, such as oxygen, sulfur and/or nitrogen atoms, in particular nitrogen, either alone or in conjunction with sulfur or oxygen ring atoms.
[0029] Furthermore, the above optionally substituted five-membered or six-membered rings can optionally be fused to an aromatic 5-membered or 6-membered ring system. For example, the rings can be optionally fused to an aromatic 5-membered or 6-membered ring system such as a pyridine or a triazole system, e.g., to a benzene ring. [0030] The following ring systems are examples of the heterocyclic (whether substituted or unsubstituted) radicals denoted by the term "heteroaryl": thienyl, furyl, pyrrolyl, pyrrolidinyl, imidazolyl, isoxazolyl, triazolyl, thiadiazolyl, oxadiazolyl, tetrazolyl, thiatriazolyl, oxatriazolyl, pyridyl, pyrimidyl, pyrazinyl, pyridazinyl, oxazinyl, triazinyl, thiadiazinyl tetrazolo, l,5-[b]pyridazinyl and purinyl, as well as benzo-fused derivatives, for example, benzoxazolyl, benzthiazolyl, benzimidazolyl and indolyl.
[0031] Substituents for the above optionally substituted heteroaryl rings are from one to three halo, trihalomethyl, amino, protected amino, amino salts, mono-substituted amino, di- substituted amino, carboxy, protected carboxy, carboxylate salts, hydroxy, protected hydroxy, salts of a hydroxy group, lower alkoxy, lower alkylthio, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, (cycloalkyl)alkyl, substituted (cycloalkyl)alkyl, phenyl, substituted phenyl, phenylalkyl, and (substituted phenyl)alkyl. Substituents for the heteroaryl group are as heretofore defined, or in the case of trihalomethyl, can be trifluoromethyl, trichloromethyl, tribromomethyl, or triiodomethyl. As used in conjunction with the above substituents for heteroaryl rings, "lower alkoxy" means a Ci to C4 alkoxy group, similarly, "lower alkylthio" means a Cj to C4 alkylthio group.
[0032] The term "(monosubstituted)amino" refers to an amino group with one substituent chosen from the group consisting of phenyl, substituted phenyl, alkyl, substituted alkyl, Ci to C4 acyl, C2 to C7 alkenyl, C2 to C7 substituted alkenyl, C2 to C7 alkynyl, C7 to Ci6 alkylaryl, C7 to Ci6 substituted alkylaryl and heteroaryl group. The (monosubstituted) amino can additionally have an amino-protecting group as encompassed by the term "protected (monosubstituted)amino." The term "(disubstituted)amino" refers to amino groups with two substituents chosen from the group consisting of phenyl, substituted phenyl, alkyl, substituted alkyl, Ci to C7 acyl, C2 to C7 alkenyl, C2 to C7 alkynyl, C7 to Ci6 alkylaryl, C7 to Cj6 substituted alkylaryl and heteroaryl. The two substituents can be the same or different.
[0033] The term "heteroaryl(alkyl)" denotes an alkyl group as defined above, substituted at any position by a heteroaryl group, as above defined.
[0034] "Optional" or "optionally" means that the subsequently described event, circumstance, feature, or element may, but need not, occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. For example, "heterocyclo group optionally mono- or di- substituted with an alkyl group" means that the alkyl may, but need not, be present, and the description includes situations where the heterocyclo group is mono- or disubstituted with an alkyl group and situations where the heterocyclo group is not substituted with the alkyl group. [0035] Compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed "isomers." Isomers that differ in the arrangement of their atoms in space are termed "stereoisomers." Stereoisomers that are not mirror images of one another are termed "diastereomers" and those that are non-superimposable mirror images of each other are termed "enantiomers." When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or (-)-isomers respectively). A chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a "racemic mixture."
[0036] The compounds of this invention may possess one or more asymmetric centers; such compounds can therefore be produced as individual (R)- or (S)- stereoisomers or as mixtures thereof. Unless indicated otherwise, the description or naming of a particular compound in the specification and claims is intended to include both individual enantiomers and mixtures, racemic or otherwise, thereof. The methods for the determination of stereochemistry and the separation of stereoisomers are well-known in the art (see, e.g., the discussion in Chapter 4 of "Advanced Organic Chemistry", 4th edition J. March, John Wiley and Sons, New York, 1992).
[0037] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
[0038] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention. [0039] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
[0040] It must be noted that as used herein and in the appended claims, the singular forms "a,"
"and," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a modified cycloalkyne" includes a plurality of such modified cycloalkynes and reference to "the target molecule" includes reference to one or more target molecules and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a "negative" limitation.
[0041] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
DETAILED DESCRIPTION OF THE INVENTION
[0042] The present invention features a strain-promoted [3+2] cycloaddition reaction that can be carried out under physiological conditions. In general, the invention involves reacting a modified cycloalkyne with an azide moiety on a biomolecule, generating a covalently modified biomolecule. The selectivity of the reaction and its compatibility with aqueous environments provides for its application in vivo (e.g., on the cell surface or intracellularly) and in vitro (e.g., synthesis of peptides and other polymers, production of modified (e.g., labeled) amino acids). The reaction is compatible with modification of living cells.
[0043] The invention provides methods and compositions for specifically and efficiently synthetically modifying cellular components in an aqueous environment, thus providing for modification of such cellular components on or in living cells. The invention uses reactive partners that are completely abiotic and are chemically orthogonal to native cellular components, thus providing for extreme selectivity of the reaction. Furthermore, the reaction can be carried out under physiological conditions, e.g. , a pH of about 7 within an aqueous environment, and at about 37°C.
[0044] The invention is based in part on the discovery of a means for carrying out a modified
Huisgen reaction that can be carried out in an aqueous, physiological environment. Because the reaction of the invention is highly selective and functions in aqueous solvents, the reaction can be used in a variety of applications both in vitro and in vivo. The reaction is accomplished through use of a first molecule comprising a strained cycloalkyne moiety, and second molecule comprising an azide moiety. The azide moiety on the second molecule reacts, in the absence of a catalyst, with the strained cycloalkyne moiety on the first molecule, forming a final conjugate product comprising fused azide/cycloalkyne ring. The first molecule comprising the strained cycloalkyne moiety can further comprise a moiety that allows for subsequent reactions and/or which provides for detectable labeling of the product of the final reaction. The reaction proceeds without the need for a catalyst. Instead, activation energy for the reaction is provided by azide group and the strained cycloalkyne group. The invention takes advantage of the massive bond angle deformation of the acetylene group in the cycloalkyne moiety, which provides for ring strain. For example, the bond angle deformation of the acetylene group of cyclooctyne to 163° accounts for nearly 18 kcal/mol of ring strain. This destabilization of the ground state versus the transition state of the reaction provides a dramatic rate acceleration compared to unstrained alkynes. MODIFIED CYCLOALKYNE COMPOUNDS
[0045] The present invention provides modified cycloalkyne compounds; and compositions comprising the compounds. A subject modified cycloalkyne is a compound of the formula:
[0046] Y-R1-X
[0047] where:
[0048] X is a strained cycloalkyne group, or a heterocycloalkyne group, substituted with Ri1 and in some embodiments one or more additional groups;
[0049] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
[0050] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. In some embodiments, Ri is a substituted or unsubstituted aliphatic group, e.g., a substituted or unsubstituted alkyl; a substituted or unsubstituted alkenyl; or a substituted or unsubstituted alkynyl. In some embodiments, R1 is a substituted or unsubstituted phenyl.
[0051] In some embodiments, Y is a reactive group. Suitable reactive groups include, but are not necessarily limited to, carboxyl, amine, (e.g., alkyl amine (e.g., lower alkyl amine), aryl amine), ester (e.g., alkyl ester (e.g., lower alkyl ester, benzyl ester), aryl ester, substituted aryl ester), thioester, sulfonyl halide, alcohol, thiol, succinimidyl ester, isothiocyanate, iodoacetamide, maleimide, hydrazine, and the like. In some embodiments, Y is a reactive group selected from a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
[0052] In some embodiments, Y is a molecule of interest, where suitable molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like. Where Y is a molecule of interest other than a linker, the molecule of interest is attached directly to Ri, or is attached through a linker.
[0053] The cycloalkyne is a strained cycloalkyne, e.g., the cycloalkyne increases the rate of reaction from about 2-fold to about 1000-fold, e.g., the cycloalkyne increases the rate of reaction at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 500-fold, or at least about 1000-fold, compared to the rate of reaction between an azide and a linear alkyne having the same number of carbon atoms as the cycloalkyne. The strained cycloalkyne will in some embodiments be a heterocycloalkyne, e.g., the cycloalkyne will in some embodiments comprise atoms other than carbon. In some embodiments, the cycloalkyne or heterocycloalkyne will be a 7-membered ring. In other embodiments, the cycloalkyne or heterocycloalkyne will be an 8-membered ring. In other embodiments, the cycloalkyne or heterocycloalkyne will be a 9-membered ring. The strain on the cycloalkyne can be increased in a variety of ways, e.g., through the use of heteroatoms; the degree of unsaturation, or torsional strain; the use of electron- withdrawing groups, etc. In some embodiments of particular interest, the cycloalkyne is a cyclooctyne. In some embodiments, the strained cycloalkyne is a compound in which one or more of the carbon atoms in the cycloalkyne ring, other than the two carbon atoms joined by a triple bond, is substituted with one or more electron-withdrawing groups, e.g., a halo (bromo, chloro, fluoro, iodo), a nitro group, a cyano group, or a sulfone group. Where the electron-withdrawing group is a nitro group, a cyano group, or a sulfone group, the electron-withdrawing group is not directly linked to the cycloalkyne ring.
[0054] In some embodiments, a subject modified cycloalkyne is of Formula I:
Figure imgf000013_0001
[0055] where:
[0056] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
[0057] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons joined by the triple bond.
[0058] In some embodiments, the modified cycloalkyne is of Formula I, wherein one or more of the carbon atoms in the cyclooctyne ring, other than the two carbon atoms joined by a triple bond, is substituted with one or more electron-withdrawing groups, e.g., a halo (bromo, chloro, fluoro, iodo), a nitro group, a cyano group, a sulfone group, or a sulfonic acid group. Thus, e.g., in some embodiments, a subject modified cycloalkyne is of Formula II:
Figure imgf000013_0002
Formula II
[0059] where:
[0060] each of X and X' is independently: (a) H; (b) one or two halogen atoms (e.g., bromo, chloro, fluoro, iodo); (c) -W-(CH2),,-Z (where: n is an integer from 1-4 (e.g., n = 1, 2, 3, or 4); W, if present, is O, N, or S; and Z is nitro, cyano, sulfonic acid, or a halogen); (d) -(CH2)n-W- (CH2)m-Z (where: n and m are each independently 1 or 2; W is O, N, S, or sulfonyl; if W is O, N, or S, then Z is nitro, cyano, or halogen; and if W is sulfonyl, then Z is H); or (e) -(CH2)n-Z (where: n is an integer from 1-4 (e.g., n = 1, 2, 3, or 4); and Z is nitro, cyano, sulfonic acid, or a halogen);
[0061] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
[0062] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond. [0063] In some embodiments, a subject modified cycloalkyne is of Formula III:
Figure imgf000014_0001
Formula III
[0064] where:
[0065] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
[0066] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond.
[0067] In some embodiments, a subject modified cycloalkyne is of Formula IV:
Figure imgf000014_0002
Formula IV
[0068] where:
[0069] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
[0070] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. Ri
V can be at any position on the cyclooctyne group other than at the two carbons linked by the triple bond.
[0071] Exemplary, non-limiting examples of a subject halogenated cyclooctyne compound include:
Figure imgf000015_0001
Figure imgf000015_0002
and
Figure imgf000015_0003
Molecules of interest
[0072] In some embodiments, Y is a molecule of interest. Suitable molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like. Where Y is a molecule of interest other than a linker, the molecule of interest is attached directly to Ri, or is attached through a linker.
[0073] Where Y is a molecule of interest, the modified cycloalkyne comprises a molecule desired for delivery and conjugation to the azido-target substrate (azide-containing target molecule), which target substrate may be displayed on the cell surface, may reside within the cell membrane, or may be intracellular. Molecules that may be desirable for delivery include, but are not necessarily limited to, detectable labels (e.g., spin labels, fluorescence resonance energy transfer (FRET)-type dyes, e.g., for studying structure of biomolecules in vivo), small molecule drugs, cytotoxic molecules (e.g., drugs), ligands for binding by a target receptor (e.g., to facilitate viral attachment, attachment of a targeting protein present on a liposome, etc.), tags to aid in purification by, for example, affinity chromatography (e.g., attachment of a FLAG epitope), and molecules to facilitate selective attachment of the polypeptide to a surface, and the like. Specific, non-limiting examples are provided below. Detectable labels
[0074] The compositions and methods of the invention can be used to deliver a detectable label to a target molecule having an azide. Thus, in some embodiments, a subject modified cycloalkyne comprises a detectable label, covalently bound to the modified cycloalkyne either directly or through a linker.
[0075] Exemplary detectable labels include, but are not necessarily limited to, fluorescent molecules (e.g., autofluorescent molecules, molecules that fluoresce upon contact with a reagent, etc.), radioactive labels (e.g., 111In, 125I, 1311, 212B, 90Y, 186Rh, and the like); biotin (e.g., to be detected through reaction of biotin and avidin); fluorescent tags; imaging reagents (e.g., those described in U.S. Pat. No. 4,741,900 and U.S. Pat. No. 5,326,856), and the like. Detectable labels also include peptides or polypeptides that can be detected by antibody binding, e.g., by binding of a detectably labeled antibody or by detection of bound antibody through a sandwich-type assay. Also suitable for use are quantum dots (e.g., detectably labeled semiconductor nanocrystals, such as fluorescently labeled quantum dots, antibody-conjugated quantum dots, and the like). See, e.g., Dubertret et al. 2002 Science 298:759-1762; Chan et al. (1998) Science 281 :2016-2018; U.S. Patent No. 6,855,551; Bruchez et al. (1998) Science 281 :2013-2016
[0076] Suitable fluorescent molecules (fluorophores) include, but are not limited to, fluorescein, fluorescein isothiocyanate, succinimidyl esters of carboxyfluorescein, succinimidyl esters of fluorescein, 5 -isomer of fluorescein dichlorotriazine, caged carboxyfiuorescein-alanine-carboxamide, Oregon Green 488, Oregon Green 514; Lucifer Yellow, acridine Orange, rhodamine, tetramethylrhodamine, Texas Red, propidium iodide, JC- 1 (5,5',6,6'-tetrachloro-l , 1 ',3,3'-tetraethylbenzimidazoylcarbocyanine iodide), tetrabromorhodamine 123, rhodamine 6G, TMRM (tetramethylrhodamine- , methyl ester), TMRE (tetramethylrhodamine, ethyl ester ), tetramethylrosamine, rhodamine B and 4- dimethylaminotetramethylrosamine, green fluorescent protein, blue-shifted green fluorescent protein, cyan-shifted green fluorescent protein, red-shifted green fluorescent protein, yellow- shifted green fluorescent protein, 4-acetamido-4'-isothiocyanatostilbene-2,2'disulfonic acid; acridine and derivatives: acridine, acridine isothiocyanate; 5-(2'- aminoethyl)aminonaphthalene-l -sulfonic acid (EDANS); 4-amino-N-[3- vinylsulfonyl)phenyl]naphth- alimide-3,5 disulfonate; N-(4-anilino-l-naphthyl)maleimide; anthranilamide; 4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a diaza-S-indacene-S-propioni-c acid BODIPY; cascade blue; Brilliant Yellow; coumarin and derivatives: coumarin, 7-amino-4- methylcoumarin (AMC, Coumarin 120),7-amino-4-trifluoromethylcoumarin (Coumarin 151); cyanine dyes; cyanosine; 4',6-diaminidino-2-phenylindole (DAPI); 5',5"-dibromopyrogallol- sulfonaphthalein (Bromopyrogallol Red); 7-diethylamino-3-(4'-isothiocyanatophenyl)-4- methylcoumarin; diethylenetriaamine pentaacetate; 4,4'-diisothiocyanatodihydro-stilbene-2- ,2'-disulfonic acid; 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid; 5- (dimethylamino]naphthalene-l-sulfonyl chloride (DNS, dansyl chloride); 4- dimethylaminophenylazophenyl-4'-isothiocyanate (DABITC); eosin and derivatives: eosin, eosin isothiocyanate, erythrosin and derivatives: erythrosin B, erythrosin, isothiocyanate; ethidium; fluorescein and derivatives: 5-carboxyfluorescein (FAM),5-(4,6-dichlorotriazin-2- yl)amino- -fluorescein (DTAF), 2',7'dimethoxy-4'5'-dichloro-6-carboxyfluorescein (JOE), fluorescein, fluorescein isothiocyanate, QFITC, (XRITC); fluorescamine; IRl 44; IRl 446; Malachite Green isothiocyanate; 4-methylumbelli-feroneortho cresolphthalein; nitrotyrosine; pararosaniline; Phenol Red; B-phycoerythrin; o-phthaldialdehyde; pyrene and derivatives: pyrene, pyrene butyrate, succinimidyl 1 -pyrene; butyrate quantum dots; Reactive Red 4 (Cibacron™ Brilliant Red 3B-A) rhodamine and derivatives: 6-carboxy-X-rhodamine (ROX), 6-carboxyrhodamine (R6G), lissamine rhodamine B sulfonyl chloride rhodamine (Rhod), rhodamine B, rhodamine 123, rhodamine X isothiocyanate, sulforhodamine B, sulforhodamine 101, sulfonyl chloride derivative of sulforhodamine 101 (Texas Red); N,N,N',N'-tetramethyl-6- carboxyrhodamine (TAMRA); tetramethyl rhodamine; tetramethyl hodamine isothiocyanate (TRITC); riboflavin; 5-(2'-aminoethyl) aminonaphthalene-1 -sulfonic acid (EDANS), 4-(4'- dimethylaminophenylazo)benzoic acid (DABCYL), rosolic acid; CAL Fluor Orange 560; terbium chelate derivatives; Cy 3; Cy 5; Cy 5.5; Cy 7; IRD 700; IRD 800; La Jolla Blue; phthalo cyanine; and naphthalo cyanine, coumarins and related dyes, xanthene dyes such as rhodols, resorufins, bimanes, acridines, isoindoles, dansyl dyes, aminophthalic hydrazides such as luminol, and isoluminol derivatives, aminophthalimides, aminonaphthalimides, aminobenzofurans, aminoquinolines, dicyanohydroquinones, and fluorescent europium and terbium complexes; and the like. Fluorophores of interest are further described in WO 01/42505 and WO 01/86001. Suitable fluorescent proteins and chromogenic proteins include, but are not limited to, a green fluorescent protein (GFP), including, but not limited to, a GFP derived from Aequoria victoria or a derivative thereof, e.g., a "humanized" derivative such as Enhanced GFP, which is available commercially, e.g., from Clontech, Inc.; a GFP from another species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem. 20:507-519; "humanized" recombinant GFP (hrGFP) (Stratagene); any of a variety of fluorescent and colored proteins from Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973; and the like.
[0078] Suitable epitope tags include, but are not limited to, hemagglutinin (HA; e.g.,
CYPYDVPDYA; SEQ ID NO: 1), FLAG (e.g., DYKDDDDK; SEQ ID NO:2), FLAG-C (e.g., DYKDDDDKC; SEQ ID NO:3, c-myc (e.g., CEQKLISEEDL; SEQ ID NO:4), a metal ion affinity tag such as a polyhistidine tag (e.g., His6), and the like.
[0079] Suitable imaging agents include positive contrast agents and negative contrast agents.
Suitable positive contrast agents include, but are not limited to, gadolinium tetraazacyclododecanetetraacetic acid (Gd-DOTA); Gadolinium- diethylenetriaminepentaacetic acid (Gd-DTPA); Gadolinium- 1,4, 7-tris(carbonylmethyl)- 10-(2'-hydroxypropyl)- 1 ,4,7, 10-tetraazacyclododecane (Gd-HP -DO3 A); Manganese(II)- dipyridoxal diphosphate (Mn-DPDP); Gd-diethylenetriaminepentaacetate- bis(methylamide) (Gd-DTPA-BMA); and the like. Suitable negative contrast agents include, but are not limited to, a superparamagnetic iron oxide (SPIO) imaging agent; and a perfluorocarbon, where suitable perfluorocarbons include, but are not limited to, fluoroheptanes, fluorocycloheptanes, fluoromethylcycloheptanes, fiuorohexanes, fluorocyclohexanes, fluoropentanes, fluorocyclopentanes, fluoromethylcyclopentanes, fluorodimethylcyclopentanes, fluoromethylcyclobutanes, fluorodimethylcyclobutanes, fluorotrimethylcyclobutanes, fluorobutanes, fiuorocyclobutanse, fiuoropropanes, fluoroethers, fluoropolyethers, fluorotriethylamines, perfluorohexanes, perfluoropentanes, perfluorobutanes, perfluoropropanes, sulfur hexafluoride, and the like. Specific binding partners
[0080] In another embodiment, a subject modified cycloalkyne comprises a member of a pair of binding partners A member of a pair of binding partners is referred to herein as a "specific binding partner."
[0081] Suitable specific binding partners include, but are not limited to, a member of a receptor/ligand pair; a member of an antibody/antigen pair; a member of a lectin/carbohydrate pair; a member of an enzyme/substrate pair; biotin/avidin; biotin/streptavidin; digoxin/antidigoxin; and the like. Suitable specific binding partners include, but are not limited to a receptor ligand; a receptor for a ligand; a ligand-binding portion of a receptor; an antibody; an antigen-binding fragment of an antibody; an antigen; a hapten; a lectin; a lectin- binding carbohydrate; an enzyme substrate; an irreversible inhibitor of an enzyme (e.g., an irreversible inhibitor that binds a substrate binding site of an enzyme, e.g., a "suicide" substrate); and the like.
[0082] Suitable ligand members of receptor/ligand pairs include, but are not limited to, neurotransmitters such as opioid compounds, acetylcholine, and the like; viral proteins that bind to a cell surface receptor, e.g., human immunodeficiency virus gpl20, and the like; hormones; and the like.
[0083] Suitable antigen-binding antibody fragments include F(ab')2, F(ab)2, Fab', Fab, Fv, scFv, and Fd fragments, single-chain antibodies, and fusion proteins comprising an antigen- binding portion of an antibody and a non-antibody protein (e.g., an antigen-binding fragment of an antibody fused to an immunoglobulin constant region).
[0084] Suitable haptens include, but are not limited to, (4-hydroxy-3-nitrophenyl) acetyl; diethylenetriaminepentaacetic acid (DTPA) or one of its metal complexes; paranitrophenyl; biotin; fluorescein isothiocyanate; and the like. Drugs
[0085] Suitable drugs that can be attached to a modified cycloalkyne moiety include, but are not limited to, cytotoxic compounds (e.g., cancer chemotherapeutic compounds); antiviral compounds; biological response modifiers (e.g., hormones, chemokines, cytokines, interleukins, etc.); microtubule affecting agents; hormone modulators; steroidal compounds; and the like.
[0086] Suitable cancer chemotherapeutic compounds include, but are not limited to, non- peptidic (i.e., non-proteinaceous) compounds that reduce proliferation of cancer cells; peptidic compounds that reduce proliferation of cancer cells; anti-metabolite agents; cytotoxic agents; and cytostatic agents. Non-limiting examples of chemotherapeutic agents include alkylating agents, nitrosoureas, antimetabolites, antitumor antibiotics, plant (vinca) alkaloids, and steroid hormones.
[0087] Suitable agents that act to reduce cellular proliferation include, but are not limited to, alkylating agents, such as nitrogen mustards, nitrosoureas, ethylenimine derivatives, alkyl sulfonates, and triazenes, including, but not limited to, mechlorethamine, cyclophosphamide (Cytoxan™), melphalan (L-sarcolysin), carmustine (BCNU), lomustine (CCNU), semustine (methyl-CCNU), streptozocin, chlorozotocin, uracil mustard, chlormethine, ifosfamide, chlorambucil, pipobroman, triethylenemelamine, triethylenethiophosphoramine, busulfan, dacarbazine, and temozolomide. [0088] Suitable antimetabolite agents include folic acid analogs, pyrimidine analogs, purine analogs, and adenosine deaminase inhibitors, including, but not limited to, cytarabine (CYTOSAR-U), cytosine arabinoside, fluorouracil (5-FU), floxuridine (FudR), 6-thioguanine, 6-mercaptopurine (6-MP), pentostatin, 5 -fluorouracil (5-FU), methotrexate, 10-propargyl-5,8- dideazafolate (PDDF, CB3717), 5,8-dideazatetrahydrofolic acid (DDATHF), leucovorin, fludarabine phosphate, pentostatine, and gemcitabine.
[0089] Suitable antiproliferative natural products and their derivatives, (e.g., vinca alkaloids, antitumor antibiotics, enzymes, lymphokines, and epipodophyllotoxins), include, but are not limited to, Ara-C, paclitaxel (Taxol®), docetaxel (Taxotere®), deoxycoformycin, mitomycin- C, L-asparaginase, azathioprine; brequinar; alkaloids, e.g. vincristine, vinblastine, vinorelbine, vindesine, etc.; podophyllotoxins, e.g. etoposide, teniposide, etc.; antibiotics, e.g. anthracycline, daunorubicin hydrochloride (daunomycin, rubidomycin, cerubidine), idarubicin, doxorubicin, epirubicin and morpholino derivatives, etc.; phenoxizone biscyclopeptides, e.g. dactinomycin; basic glycopeptides, e.g. bleomycin; anthraquinone glycosides, e.g. plicamycin (mithramycin); anthracenediones, e.g. mitoxantrone; azirinopyrrolo indolediones, e.g. mitomycin; macrocyclic immunosuppressants, e.g. cyclosporine, FK-506 (tacrolimus, prograf), rapamycin, etc. ; and the like.
[0090] Other suitable anti-proliferative cytotoxic agents are navelbene, CPT-11, anastrazole, letrazole, capecitabine, reloxafine, cyclophosphamide, ifosamide, and droloxafine.
[0091] Suitable microtubule affecting agents that have antiproliferative activity include, but are not limited to, allocolchicine (NSC 406042), Halichondrin B (NSC 609395), colchicine (NSC 757), colchicine derivatives (e.g., NSC 33410), dolstatin 10 (NSC 376128), maytansine (NSC 153858), rhizoxin (NSC 332598), paclitaxel (Taxol®), Taxol® derivatives, docetaxel (Taxotere®), thiocolchicine (NSC 361792), trityl cysterin, vinblastine sulfate, vincristine sulfate, natural and synthetic epothilones including but not limited to, eopthilone A, epothilone B, discodermolide; estramustine, nocodazole, and the like.
[0092] Suitable hormone modulators and steroids (including synthetic analogs) include, but are not limited to, adrenocorticosteroids, e.g. prednisone, dexamethasone, etc.; estrogens and pregestins, e.g. hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrol acetate, estradiol, clomiphene, tamoxifen; etc.; and adrenocortical suppressants, e.g. aminoglutethimide; 17α-ethinylestradiol; diethylstilbestrol, testosterone, fluoxymesterone, dromostanolone propionate, testolactone, methylprednisolone, methyl-testosterone, prednisolone, triamcinolone, chlorotrianisene, hydroxyprogesterone, aminoglutethimide, estramustine, medroxyprogesterone acetate, leuprolide, Flutamide (Drogenil), Toremifene (Fareston), and Zoladex®. Estrogens stimulate proliferation and differentiation, therefore compounds that bind to the estrogen receptor are used to block this activity. Corticosteroids may inhibit T cell proliferation.
[0093] Other suitable chemotherapeutic agents include metal complexes, e.g. cisplatin (cis-
DDP), carboplatin, etc.; ureas, e.g. hydroxyurea; and hydrazines, e.g. N-methylhydrazine; epidophyllotoxin; a topoisomerase inhibitor; procarbazine; mitoxantrone; leucovorin; tegafur; etc.. Other antiproliferative agents of interest include immunosuppressants, e.g. mycophenolic acid, thalidomide, desoxyspergualin, azasporine, leflunomide, mizoribine, azaspirane (SKF 105685); Iressa® (ZD 1839, 4-(3-chloro-4-fluorophenylamino)-7-methoxy-6- (3-(4-morpholinyl)propoxy)quinazoline); etc.
[0094] Taxanes are also suitable for attachment to a cycloalkyne moiety. "Taxanes" include paclitaxel, as well as any active taxane derivative or pro-drug. "Paclitaxel" (which should be understood herein to include analogues, formulations, and derivatives such as, for example, docetaxel, TAXOL™, TAXOTERE™ (a formulation of docetaxel), 10-desacetyl analogs of paclitaxel and 3'N-desbenzoyl-3'N-t-butoxycarbonyl analogs of paclitaxel) may be readily prepared utilizing techniques known to those skilled in the art (see also WO 94/07882, WO 94/07881, WO 94/07880, WO 94/07876, WO 93/23555, WO 93/10076; U.S. Pat. Nos. 5,294,637; 5,283,253; 5,279,949; 5,274,137; 5,202,448; 5,200,534; 5,229,529; and EP 590,267), or obtained from a variety of commercial sources, including for example, Sigma Chemical Co., St. Louis, Mo. (T7402 from Taxus brevifolia; or T-1912 from Taxus yannanensis).
[0095] Paclitaxel should be understood to refer to not only the common chemically available form of paclitaxel, but analogs and derivatives (e.g., Taxotere™ docetaxel, as noted above) and paclitaxel conjugates (e.g., paclitaxel-PEG, paclitaxel-dextran, or paclitaxel-xylose).
[0096] Also included within the term "taxane" are a variety of known derivatives, including both hydrophilic derivatives, and hydrophobic derivatives. Taxane derivatives include, but not limited to, galactose and mannose derivatives described in International Patent Application No. WO 99/18113; piperazino and other derivatives described in WO 99/14209; taxane derivatives described in WO 99/09021, WO 98/22451, and U.S. Patent No. 5,869,680; 6-thio derivatives described in WO 98/28288; sulfenamide derivatives described in U.S. Patent No. 5,821,263; and taxol derivative described in U.S. Patent No. 5,415,869. It further includes prodrugs of paclitaxel including, but not limited to, those described in WO 98/58927; WO 98/13059; and U.S. Patent No. 5,824,701. [0097] Biological response modifiers that are suitable for attachment to a cycloalkyne moiety include, but are not limited to, (1) inhibitors of tyrosine kinase (RTK) activity; (2) inhibitors of serine/threonine kinase activity; (3) tumor-associated antigen antagonists, such as antibodies that bind specifically to a tumor antigen; (4) apoptosis receptor agonists; (5) inter leukin-2; (6) IFN-α; (7) IFN-γ (8) colony-stimulating factors; and (9) inhibitors of angiogenesis. Linkers
[0098] Suitable linkers include, but are not limited to, a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, a nitro, and a peptide linker.
[0099] Exemplary peptide linkers for use in linking a molecule of interest to a modified cycloalkyne will in some embodiments have a combination of glycine, alanine, proline and methionine residues, where suitable peptide linkers include, but are not limited to AAAGGM (SEQ ID NO:5); AAAGGMPP AAAGGM (SEQ ID NO:6); AAAGGM (SEQ ID NO:7); and PPAAAGGMM (SEQ ID NO: 8). Any flexible linker, generally having a length of from about 6 amino acids and about 40 amino acids is suitable for use. Linkers may have virtually any sequence that results in a generally flexible peptide, including alanine-proline rich sequences. Compositions
[00100] The present invention further provides compositions, including pharmaceutical compositions, comprising a subject modified cycloalkyne compound. A subject composition generally comprises a subject modified cycloalkyne compound; and at least one additional compound. Suitable additional compounds include, but are not limited to: a salt, such as a magnesium salt, a sodium salt, etc., e.g., NaCl, MgCl, KCl, MgSO4, etc.; a buffering agent, e.g., a Tris buffer, N-(2-Hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES), 2-(N- Morpholino)ethanesulfonic acid (MES), 2-(N-Morpholino)ethanesulfonic acid sodium salt (MES), 3-(N-Morpholino)propanesulfonic acid (MOPS), N-tris[Hydroxymethyl]methyl-3- aminopropanesulfonic acid (TAPS), etc.; a solubilizing agent; a detergent, e.g., a non-ionic detergent such as Tween-20, etc.; a protease inhibitor; and the like.
[00101] In some embodiments, a subject composition comprises a subject modified cycloalkyne compound; and a pharmaceutically acceptable excipient. A wide variety of pharmaceutically acceptable excipients are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, A. Gennaro (2000) "Remington: The Science and Practice of Pharmacy," 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C. Ansel et al., eds., 7th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A.H. Kibbe et al., eds., 3rd ed. Amer. Pharmaceutical Assoc.
[00102] The pharmaceutically acceptable excipients, such as vehicles, adjuvants, carriers or diluents, are readily available to the public. Moreover, pharmaceutically acceptable auxiliary substances, such as pH adjusting and buffering agents, tonicity adjusting agents, stabilizers, wetting agents and the like, are readily available to the public. METHODS OF MODIFYING A TARGET BIOMOLECULE
[00103] The present invention provides methods for chemoselective modification of a target molecule comprising an azide. The methods generally involve reacting an azide in an azide- containing target molecule with a modified cycloalkyne. The modified cycloalkyne has a structure as described above. Thus, in many embodiments, a subject method for synthetically modifying a cellular component generally involves: a) introducing an azide moiety into a cellular component, thereby generating an azide-modifϊed cellular component; and contacting the cell comprising the azide-modified cellular component with a reactive partner comprising a modified cycloalkyne, the contacting being under physiological conditions. The contacting step results in reaction between the azide group of azide-modified cellular component and the cycloalkyne of the reactive partner, thereby synthetically and covalently modifying the cellular component. In some embodiments, the method is carried out on living cells in vitro. In other embodiments, the method is carried out on living cells ex vivo. In still other embodiments, the method is carried out on living cells in vivo.
[00104] In one embodiment, the chemoselective ligation is designed for use in fully aqueous, physiological conditions and involves production of a stable, final product comprising a fused azide/cycloalkyne ring. In general, this embodiment involves reacting a first reactant comprising a strained cycloalkyne moiety with a second reactant comprising an azide, such that a covalent bond is formed between the first and second reactants by reaction of the strained cycloalkyne moiety with the azide group. First reactant
[00105] A first reactant comprises a strained cycloalkyne moiety that provides the energy for the reaction between the first and second reactants. The first reactant is a modified cycloalkyne compound of the formula:
[00106] Y-R1-X
[00107] where:
[00108] X is a cycloalkyne group substituted with Rj ; [00109] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
[00110] R1 is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro. In some embodiments, the first reactant is a modified cycloalkyne compound of any of Formulas I-IV, as described above.
[00111] Exemplary reactive groups include, but are not necessarily limited to, carboxyl, amine,
(e.g., alkyl amine (e.g., lower alkyl amine), aryl amine), ester (e.g., alkyl ester (e.g., lower alkyl ester, benzyl ester), aryl ester, substituted aryl ester), thioester, sulfonyl halide, alcohol, thiol, succinimidyl ester, isothiocyanate, iodoacetamide, maleimide, hydrazine, and the like. Exemplary molecules of interest further include dyes (e.g., fluorescein or modified fluorescein, and the like), toxins (including cytotoxins), linkers, peptides, and the like.
[00112] The molecule of interest may be reacted directly with the reactive group or through a linker. Exemplary molecules of interest include, but are not necessarily limited to, a detectable label, a drug, a peptide, a member of a specific binding pair, and the like. Such molecules of interest are described in more detail above.
[00113] In some embodiments, Y is a reactive group selected from a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
[00114] In some embodiments, the cycloalkyne is a cyclooctyne.
[00115] In some embodiments, the modified cycloalkyne is of Formula I:
Figure imgf000024_0001
Formula I
[00116] where
[00117] Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
[00118] Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
[00119] In other embodiments, the modified cycloalkyne is of any of Formulas II- IV, above. Second reactant
[00120] The second reactant is a compound that comprises an azide such that a covalent bond is formed between the first and second reactants by reaction of the cycloalkyne moiety with the azide group. In general, the second reactant is of the formula: R2-N3
[00121] where R2 is a target molecule, e.g., a biomolecule or other target molecule.
Target molecules
[00122] Molecules comprising an azide and suitable for use in the present invention, as well as methods for producing azide-comprising molecules suitable for use in the present invention, are well known in the art. Target molecules of particular interest as the second reactant include, but are not necessarily limited to, amino acids and amino acid residues, polypeptides (including peptides and proteins), sugars or sugar residues, and the like, which contain or are modified to contain at least one azide.
[00123] The target molecules can be naturally occurring, or may be synthetically or recombinantly produced, and may be isolated, substantially purified, or present within the native milieu of the unmodified molecule upon which the azide-containing target molecule is based (e.g. , on a cell surface or within a cell, including within a host animal, e.g., a mammalian animal, such as a murine host {e.g., rat, mouse), hamster, canine, feline, bovine, swine, and the like). In some embodiments, the target molecule is present in vitro in a cell-free reaction. In other embodiments, the target molecule is present in a cell and/or displayed on the surface of a cell. In many embodiments of interest, the target molecule is in a living cell; on the surface of a living cell; in a living organism, e.g., in a living multicellular organism. Suitable living cells include cells that are part of a living multicellular organism; cells isolated from a multicellular organism; immortalized cell lines; and the like.
[00124] Where the target molecule is a polypeptide, the polypeptide may be composed of D- amino acids, L-amino acids, or both, and may be further modified, either naturally, synthetically, or recombinantly, to include other moieties. For example, the target polypeptide may be a lipoprotein, a glycoprotein, or other such modified protein.
[00125] In general, the target molecule useful as the second reactant comprises at least one azide for reaction with modified cycloalkyne according to the invention, but may comprise 2 or more, 3 or more, 5 or more, 10 or more azides. The number of azides that may be present in a target molecule will vary according to the intended application of the final product of the reaction, the nature of the target molecule itself, and other considerations which will be readily apparent to the ordinarily skilled artisan in practicing the invention as disclosed herein. [00126] This embodiment of the invention is particularly useful in modification of a target molecule in vivo. In this embodiment, the target substrate is modified to comprise an azide group at the point at which linkage to the modified cycloalkyne reactant is desired. For example, where the target substrate is a polypeptide, the polypeptide is modified to contain an N-terminal azide. Where the target substrate is a glycoprotein, a sugar residue of the glycoprotein can be modified to contain an azide. A target molecule that is unmodified with an azide, but that is to be modified with an azide, is referred to herein as a "target substrate." A target molecule that is modified with an azide is referred to herein as "an azide-modified target molecule" or "an azide-containing target molecule." Azide modification of a target molecule
[00127] The target substrate can be generated in vitro and then introduced into the cell using any of a variety of methods well known in the art (e.g., microinjection, liposome or lipofectin- mediated delivery, electroporation, etc.), which methods will vary according to the nature of the substrate to be targeted for modification and can be readily and appropriately selected by the ordinarily skilled artisan. The final target substrate can also be generated in vivo by exploiting a host cell's natural biosynthetic machinery. For example, the cell can be provided with a biocompatible azide-derivative of a substrate for synthesis of the desired target molecule, which substrate is processed by the cell to provide an azide-derivative of the desired final target substrate. For example, where the target substrate is a cell surface glycoprotein, the cell can be provided with an azide derivative of a sugar residue found within the glycoprotein, which is subsequently processed by the cell through natural biosynthetic processes to produce a modified glycoprotein having at least one modified sugar moiety comprising an accessible azide group.
[00128] The target substrate can also be produced in vivo using methods well known in the art.
For example, unnatural amino acids having azides can be incorporated into recombinant polypeptides expressed in E. coli (see, e.g., Kiick et al. (2000) Tetrahedron 56:9487). Such recombinantly produced polypeptides can be selectively reacted with a modified cycloalkyne reagent according to the invention.
[00129] In one example, an azide group is incorporated into the target molecule by providing a cell (e.g., a eukaryotic cell that glycosylates biopolymers such as proteins) with a synthetic building block for the desired biopolymer target substrate. For example, the cell can be provided with a sugar molecule comprising an azide group to provide for incorporation of the azide group in a glycoprotein. In some embodiments, the glycoprotein is expressed on the cell surface. Alternatively, the azide group can be incorporated into an amino acid, which is subsequently incorporated into a peptide or polypeptide synthesized by the cell. Several methods are available for incorporating unnatural building blocks into biopolymers; one need not be restricted to cell surface oligosaccharides as target molecules. See, e.g., vanHest et al. (1998) FEBS Lett. 428:68; and Nowak et α/.(1995) Science 268:439.
[00130] In one embodiment, the target molecule is a carbohydrate-containing molecule (e.g., a glycoprotein; a polysaccharide; etc.), and an azide group is introduced into the target molecule using a synthetic substrate. In some embodiments, the synthetic substrate is an azide derivative of a sugar utilized in production of a glycosylated molecule. In some embodiments, the synthetic substrate is an azide derivative of a sugar utilized in production of a cell surface molecule, e.g., in the glycoprotein biosynthetic pathway. For example, the host cell can be provided with a synthetic sialic acid azido-derivative, which is incorporated into the pathway for sialic acid biosynthesis, eventually resulting in the incorporation of the synthetic sugar residue in glycoproteins. In some embodiments, the glycoproteins are displayed on the cell surface.
[00131] In one example, the synthetic substrate is an azido derivative of mannosamine of the general formula:
Figure imgf000027_0001
[00132] where n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and R1, R2, R3, and
R4 are independently hydrogen or acetyl. In some embodiments, the substrate is JV- azidoacetylmannosamine (n = 1) or an acetylated derivative thereof, or JV- azidopropanoylmannosamine (n=2) or an acetylated form thereof.
[00133] In another embodiment, the synthetic substrate is an azido sugar derivative of a general formula of, for example:
Figure imgf000028_0001
Figure imgf000028_0002
[00134] either of which can be incorporated into the sialic acid biosynthesis pathway, and where n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and R2, R3, and R4 are independently hydrogen or acetyl.
[00135] In another embodiment, the synthetic substrate is an azido sugar derivative of a general formula of, for example:
Figure imgf000028_0003
[00136] where Ri, R2, R3, and R4 are independently hydrogen or acetyl, and where the synthetic substrate is incorporated into biosynthetic pathways involving fucose.
[00137] In another embodiment, the synthetic substrate is an azido sugar derivative of a general formula of, for example:
Figure imgf000028_0004
[00138] where n is from 1 to 6, generally from 1 to 4, more usually 1 to 2, and Ri, R2, R3, and
R4 are independently hydrogen or acetyl, and which is incorporated into biosynthetic pathways involving galactose. Cell surface modification
[00139] In some embodiments, a subject method is used to modify the surface of a cell. Thus, in one aspect, the invention features a method of modifying the surface of cell in vitro or in vivo. The method generally involves reacting an azide group in a target molecule that comprises an azide group with a modified cycloalkyne to provide for chemoselective ligation at the cell surface. In many embodiments, the method comprises modifying a target molecule on a cell surface with an azide group; and reacting the azide group in the target molecule with a modified cycloalkyne. For example, as described above, an azido sugar is provided to a living cell, which azido sugar is incorporated into a glycoprotein that is displayed on the cell surface. Modification of an azide-modified target molecule with detectable labels, drugs, and other molecules
[00140] In some embodiments, the present invention provides for attachment of a molecule of interest, e.g., a functional molecule, to an azide-modified target molecule. The methods generally involve reacting an azide-modified target molecule with a subject modified cycloalkyne, where the modified cycloalkyne comprises a molecule of interest, as described above. As described above, molecules of interest include, but are not limited to, a detectable label; a toxin (including cytotoxins); a linker; a peptide; a drug; a member of a specific binding pair; an epitope tag; and the like. Attachment of target molecules to a support
[00141] The modified cycloalkyne can also comprise one or more hydrocarbon linkers (e.g., an alkyl group or derivative thereof such as an alkyl ester) conjugated to a moiety providing for attachment to a solid substratum (e.g., to facilitate assays), or to a moiety providing for easy separation (e.g., a hapten recognized by an antibody bound to a magnetic bead). In one embodiment, the methods of the invention are used to provide for attachment of a protein (or other molecule that contains or can be modified to contain an azide) to a chip in a defined orientation. For example, a polypeptide having an azide at a selected site (e.g., at or near the N-terminus) can be generated, and the methods and compositions of the invention used to deliver a tag or other moiety to the azide of the polypeptide. The tag or other moiety can then be used as the attachment site for affixing the polypeptide to a support (e.g. , solid or semi-solid support, particular a support suitable for use as a microchip in high-throughput assays). Attachment of molecules for delivery to a target site
[0004] The modified cycloalkyne will in some embodiments comprise a small molecule drug, toxin, or other molecule for delivery to a cell. The small molecule drug, toxin, or other molecule will in some embodiments provide for a pharmacological activity. The small molecule drug, toxin, or other molecule will in some embodiments serve as a target for delivery of other molecules.
[0005] Small molecule drugs may be small organic or inorganic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Small molecule drugs may comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and may include at least an amine, carbonyl, hydroxyl or carboxyl group, and may contain at least two of the functional chemical groups. The drugs may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Small molecule drugs are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
[00142] In another embodiment, a subject modified cycloalkyne comprises one of a pair of binding partners (e.g., a ligand; a ligand -binding portion of a receptor; an antibody; an antigen- binding fragment of an antibody; an antigen; a hapten; a lectin; a lectin-binding carbohydrate; etc.). For example, the modified cycloalkyne can comprise a polypeptide that serves as a viral receptor and, upon binding with a viral envelope protein or viral capsid protein, facilitates attachment of virus to the cell surface on which the modified cycloalkyne is displayed. Alternatively, the modified cycloalkyne comprises an antigen that is specifically bound by an antibody (e.g., monoclonal antibody), to facilitate detection and/or separation of host cells displaying the antigen on the cell surface. In another example, the modified cycloalkyne comprises a ligand binding portion of a receptor, or a receptor-binding portion of a ligand. UTILITY
[00143] Subject modified cycloalkyne compounds, and subject modification methods, are useful in a variety of applications, including research applications and diagnostic applications. Research applications
[00144] In some embodiments, subject modified cycloalkyne compounds, and subject modification methods, are useful in research applications. Applications of interest include research applications, e.g., exploring functional and physical characteristics of a receptor; proteomics; metabolomics; and the like. Research applications also include drug discovery or other screening applications. [00145] Proteomics aims to detect, identify, and quantify proteins to obtain biologically relevant information. Metabolomics is the detection, identification, and quantification of metabolites and other small molecules such as lipids and carbohydrates. Fiehn (2001) Comparative and Functional Genomics 2:155-168; and U.S. Patent No. 6,873,914.
[00146] Drug discovery applications include, but are not limited to, identifying agents that inhibit cancer cell viability and/or growth. Thus, in some embodiments, the instant invention provides methods of identifying an agent that inhibits cancer cell viability and/or growth. The methods generally involve modifying a component of the cell to comprise a first reactive partner comprising an azide; contacting the cell, in the presence of a test agent, with a second reactive partner comprising a modified cycloalkyne, the contacting being under physiological conditions; where the contacting results in reaction between the azide group of the first reactive partner and the cycloalkyne of the second reactive partner, thereby synthetically and covalently modifying the cellular component; and determining the effect, if any, of the test agent on the level of modification of the cell with the second reactive partner.
[00147] Where the cancer cell is one that produces a higher amount of a carbohydrate than a normal (non-cancerous) cell of the same cell type, the method provides for identifying an agent that reduces growth and/or viability of the cancerous cell. Diagnostic and therapeutic applications
[00148] Applications of interest also include diagnostic applications, e.g., for detection of cancer; and the like, where a subject modified cycloalkyne comprising a detectable label is used to label an azide-modified target molecule, e.g., an azide-labeled target molecule present on a cancer cell. Applications of interest also include therapeutic applications, where a drug or other therapeutic agent is delivered to an azide-modified target molecule, using a subject modified cycloalkyne that comprises a covalently linked drug or other therapeutic agent.
[00149] In some embodiments, the present invention is used for in vivo imaging, e.g., to determine the metabolic or other state of a cell in an organism, e.g., an individual. As one non- limiting example, a subject method can be applied to in vivo imaging of cancer cells in an individual (e.g., a mammal, including rodents, lagomorphs, felines, canines, equines, bovines, ovines, caprines, non-human primates, and humans).
[00150] One exemplary, non-limiting application of a subject azide-alkyne cycloaddition is in the detection of metabolic change in cells that occur as they alter their phenotype. As one example, altered glycosylation patterns are a hallmark of the tumor phenotype, consisting of both the under- and over-expression of naturally-occurring glycans as well as the presentation of glycans normally restricted to expression during embryonic development. Examples of common antigens associated with transformed cells are sialyl Lewis a, sialyl Lewis x, sialyl T, sialyl Tn, and polysialic acid (PSA). Jørgensen et al. (1995) Cancer Res. 55, 1817-1819; Sell (1990) Hum. Pathology 21, 1003-1019; Taki et al. (1988) J. Biochem. 103, 998-1003; Gabius (1988) Angew. Chem. Int. Ed. Engl. 27, 1267-1276; Feizi (1991) Trends Biochem. Sci. 16, 84- 86; Taylor-Papadimitriou and Epenetos (1994) Trends Biotech. 12, 227-233; Hakomori and Zhang (1997) Chem. Biol. 4, 97-104; Dohi et al. (1994) Cancer 73, 1552. These antigens share an important feature - they each contain terminal sialic acid. PSA is a homopolymer of sialic acid residues up to 50 units in length. Elevated levels of sialic acid are highly correlated with the transformed phenotype in many cancers, including gastric (Dohi et al. (1994) Cancer 73, 1552; and Yamashita et al. (1995) J. Natl. Cancer Inst. 87, 441-446), colon (Yamashita et al. (1995) J. Natl. Cancer Inst. 87, 441-446; Hanski et al. (1995) Cancer Res. 55, 928-933; Hanski et al. (1993) Cancer Res. 53, 4082-4088; Yang et al. (1994) Glycobiology 4, 873-884; Saitoh et al. (1992) J. Biol. Chem. 267, 5700-5711), pancreatic (Sawada et al. (1994) Int. J. Cancer 57, 901-907), liver (Sawada et al.(1994) J. Biol. Chem. 269, 1425-1431), lung (Weibel et al. (1988) Cancer Res. 48, 4318-4323), prostate (Jørgensen et al. (1995) Cancer Res. 55, 1817- 1819), kidney (Roth et al. (1988) Proc. Natl. Acad. Sci. USA 85, 2999-3000), and breast cancers (Cho et al. (1994) Cancer Res. 54, 6302-6305), as well as several types of leukemia (Joshi et al. (1987) Cancer Res. 47, 3551-3557; Altevogt et al. (1983) Cancer Res. 43, 5138- 5144; Okada et al. (1994) Cancer 73, 1811-1816). A strong correlation between the level of cell surface sialic acid and metastatic potential has also been observed in several different tumor types (Kakeji et al. (1995) Brit. J. Cancer 71, 191-195; Takano et al. (1994) Glycobiology 4, 665-674). The collective display of multiple sialylated antigens on a single cancer cell can account for the fact that so many different tumor types share the high sialic acid phenotype without necessarily expressing an identical complement of antigens (Roth et al. (1988) supra). Consequently, diagnostic or therapeutic strategies that target cells on the basis of sialic acid levels have broad applicability to many cancers. Introduction and incorporation of unnatural azidosugars (ManNAz, GaINAz) into living animals provides for detection of changes in metabolic state. Via the attachment of the appropriate epitope tag, the modified cyclooctyne labels these cells in a living organism, and consequently detects changes in metabolic state. Early detection of tumorigenic cells and subsequent intervention reduces the severity and increases survival rates for cancer patients. EXAMPLES
[00152] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c, subcutaneous(ly); and the like.
Example 1 : Modification of biomolecules using a modified cyclooctyne MATERIALS AND METHODS
[00153] All chemical reagents were purchased from Aldrich and used without further purification. All solvents were distilled under a N2 atmosphere. CH2Cl2, toluene, and pyridine were dried over CaH2. Thin layer chromatography was carried out on Analtech Uniplate silica gel plates. Flash chromatography was performed using Merck 60 A 230-400 mesh silica gel. All 1H and 13C NMR spectra were acquired on Bruker AVB-400® or DRX-500® as noted. 1H chemical shifts are reported as δ referenced to solvent and coupling constants (J) are reported in Hz. Compounds 1 and 4 have been previously reported. Skattebol and Solomon (1973) Organic Syntheses 5/Coll. Volumes:306-310; and Wilbur et al. (1996) Bioconj. Chem. 7:689-702.
[00154] RPMI 1640 media and phosphate-buffered saline (PBS) were purchased from
Invitrogen Life Technologies. Fetal calf serum (FCS) was from Hyclone. FITC-conjugated avidin and bovine serum albumin (BSA) were purchased from Sigma, and peroxidase- conjugated mouse anti-biotin (HRP-α-biotin) and peroxidase-coηjugated donkey anti-human Ig (HRP-α-Ig) were from Jackson ImmunoResearch Laboratories, Inc. Precast TrisΗCl 4-15% polyacrylamide gels, nitrocellulose, and Tween 20 (non-ionic detergent) were purchased from BioRad. Restore™ Western blot stripping buffer and enhanced chemiluminescent substrate were obtained from Pierce. For cell-labeling experiments, a Coulter Z2 cell counter was used to determine cell densities. Flow cytometry data were acquired on a BD Biosciences FACSCalibur flow cytometer equipped with a 488-nm argon laser, and live cells were analyzed as determined by granularity and size. For all flow cytometry experiments, data points were collected in triplicate. Synthesis of Compounds:
Figure imgf000034_0001
Compound 2
[00155] Compound 2. AgClO4 (1.16 g, 5.61 mmol) was added to a solution of compound 1
(500 mg, 1.87 mmol) and methyl 4-hydroxymethylbenzoate (4.66 g, 28.1 mmol) dissolved in toluene (8 mL) in a flame-dried, aluminum-foil-wrapped flask. The reaction was stirred for 2 h, diluted with pentane (20 mL), and filtered to remove insoluble silver salts. The solution was concentrated and purified by silica gel chromatography (4-8% EtOAc: pet ether; Rf (8% EtOAc: pet ether) = 0.32) to yield 2 as a colorless oil (660 mg 1.86 mmol, 99%). 1H NMR (500 MHz, CDCl3) δ 8.02 (d, 2 H, J= 8.0 Hz), 7.47 (d, 2 H, J= 8.0 Hz), 6.21 (dd, 1 H, J= 4.0, 11.5 Hz), 4.72 (d, 1 H, J= 12.5 Hz), 4.39 (d, 1 H, J= 12.5 Hz), 3.95-3.91 (m, 4 H), 2.81 (app dq, 1 H, J= 5.5, 12..0), 2.32 (m, 1 H), 2.05-1.88 (m, 4 H), 1.75 (m, 1 H), 1.49 (app dq, 1 H, J = 5.0, 8.0), 1.35 (m, 1 H), 0.79 (m, 1 H); 13C NMR (125 MHz, CDCl3) δ 166.93, 143.20, 132.60, 132.09, 129.66, 129.34, 127.65, 84.22, 69.61, 52.04, 39.48, 36.46, 33.31, 28.09, 26.29; IR (cm" l) 2931, 2856, 1724, 1614, 1434, 1279, 1109; FAB HRMS calcd. for CnH23O3Br [M+H]+ 353.0752, found 353.0744.
Figure imgf000034_0002
Compound 3
[00156] Compound 3. A suspension of NaOMe (119 mg, 2.20 mmol) in anhydrous DMSO (8 mL) was added to compound 2 (650 mg, 1.84 mmol) dissolved in anhydrous DMSO (16 mL). The reaction was stirred 20 min and additional NaOMe (110 mg, 1.10 mmol in 1.5 mL of DMSO) was added. The reaction was stirred until the starting material was completely consumed as determined by TLC (20 min). The reaction was acidified with 1 M HCl (100 mL) and extracted twice with EtOAc (40 mL). The combined organic layers were washed with brine (40 mL) and concentrated. The resulting film was dissolved in 20% H2O/dioxane (15 mL), LiOH (220 mg, 9.0 mmol) was added, and the reaction was stirred for 24 h. The reaction was acidified with 1 M HCl (100 mL) and extracted twice with EtOAc (40 mL). The combined organic extracts were dried over MgSO4, filtered, and purified by silica gel chromatography (10:90:1 EtOAc: pet ether: AcOH - 25:75:1 EtOAc: pet ether: AcOH; Rf (25:75:1) = 0.38) to yield 3 (350 mg, 1.36 mmol, 74%) as a white solid. 1H NMR (500 MHz, CDCl3) δ 8.09 (d, 1 H, J= 8.50 Hz), 7.47 (d, 1 H, J= 8.0 Hz), 4.77 (d, 1 H, J= 12.5 Hz), 4.49 (d, 1 H, J= 13 Hz), 4.26 (m, 1 H), 2.32-2.26 (m, 1 H), 2.22-2.13 (m, 2 H), 2.08-2.03 (m, 1 H), 1.97-1.92 (m, 1 H), 1.89-1.83 (m, 2 H), 1.73-1.62 (m, 2 H) 1.52-1.44 (m, 1 H); 13C NMR (125 MHz, CDCl3) δ 171.52, 144.50, 130.27, 128.29, 127.46, 100.69, 92.40, 72.11, 70.39, 42.31, 34.26, 29.68, 26.31, 20.70; IR (cm"1) 2924, 2852, 2672, 2561, 1685, 1429, 1323, 1294, 1086; FAB HRMS calcd. for C16Hj8O3Li [M+Li]+ 265.1416, found 265.1422.
Figure imgf000035_0001
Compound 5
[00157] Compound 5. Pentafluorophenyl trifluoroacetate (Pfp-TFA) (40 μL, 0.23 mmol) was added to compound 3 in anhydrous pyridine (1 mL). The reaction was stirred for 4 h, diluted with CH2Cl2 (30 mL), and extracted with 1 M HCl (3 x 20 mL) and sat. NaHCO3 solution (2 x 20 mL). The organic layer was dried over MgSO4, filtered, and concentrated. The crude ester was dissolved in CH2Cl2 (2 mL). Triethylamine (67 μL, 0.46 mmol) and compound 4 (104 mg 0.23 mmol) were added and the solution was stirred for 1 h. The solution was concentrated and crude product purified by silica gel chromatography (80:15:5 EtOAc:MeOH:H2O, Rf = 0.40) to yield 5 (68 mg, 0.099 mmol, 51%) as a clear oil. 1H NMR (400 MHz, CD3CN) δ 7.80 (d, 2 H, J= 8.4 Hz), 7.42 (m, 3 H), 6.62 (br s, 1 H), 5.51 (s, 1 H), 5.19 (s, 1 H), 4.66 (d, 1 H, J = 12.0 Hz), 4.45-4.40 (m, 2 H), 4.29-4.26 (m, 2 H), 3.62-3.56 (m, 8 H), 3.52-3.49 (m, 2 H), 3.47-3.42 (m, 4 H), 3.22-3.13 (m, 3 H), 2.91-2.87 (m, 2 H), 2.66 (d, 1 H, J= 12.8 Hz), 2.32- 2.19 (m, 6 H), 1.89-1.79 (m, 4 H), 1.75-1.34 (m, 10 H); 13C NMR (125 MHz, CD3CN) δ 172.64, 166.56, 162.93, 141.82, 134.15, 127.47, 127.05, 100.31, 92.63, 71.94, 70.12, 69.94, 69.83, 69.16, 68.75, 61.37, 59.80, 55.36, 42.14, 40.18, 37.53, 36.56, 35.45, 34.12, 29.56, 29.32, 29.26, 28.02, 27.98, 26.18, 25.46, 20.13; FAB HRMS calcd. for C36H55N4O7S [M+H]+ 687.3791, found 687.3798.
Figure imgf000036_0001
Compound 6
[00158] Compound 6. Compound 4 (46 mg, 0.10 mmol), pentynoic acid (15 mg, 0.15 mmol) and HATU (59 mg, 0.15 mmol) were dissolved in anhydrous DMF (1 mL). Triethyl amine (22 μL, 0.15 mmol) was added to the solution and the reaction was stirred for 14 h. Purification by silica gel chromatography (15:2:1 EtOAc:MeOH:H2O to 9:2:1 EtOAc: MeOH: H2O Rf (9:2:1) = 0.30) yielded 6 (25 mg, 0.047 mmol, 46%) as a yellow oil. 1H NMR (400 MHz, CD3CN) δ 6.77 (br s, 2 H), 5.74 (s, 1 H), 5.38 (s, 1 H), 4.44 (app t, 1 H, J= 7.6 Hz), 4.27 (m, 1 H), 3.61- 3.54 (m, 8 H), 3.51 (t, 4 H, J= 6.4 Hz), 3.25-3.16 (m, 5 H), 2.91 (dd, 1 H, J= 4.8, 12.4 Hz), 2.68 (d, 1 H, J= 12.8 Hz), 2.47 (m, 2 H), 2.35-2.30 (m, 6 H), 2.22 (t, 1 H, J= 2.8 Hz), 2.17 (t, 2 H, J= 7.2 Hz), 1.75-1.53 (m, 8 H), 1.44-1.37 (m, 2 H); 13C NMR (100 MHz, CD3CN) δ 172.79, 170.74, 163.21, 83.53, 70.10, 69.82, 69.10, 68.71, 68.60, 61.46, 59.87, 55.41, 40.18, 36.49, 35.47, 34.69, 29.32, 29.29, 28.07, 28.01, 25.48, 14.32; FAB LRMS calcd. for C25H43N4O6S [M+H]+ 527.4, found 527.4. Western blot analysis of an azide-labeled GIyCAM-Ig
[00159] For Western blot analysis of azide-labeled and unlabeled GIyCAM-Ig, samples were incubated with 5 (250 μM final concentration in PBS, pH 7.4 containing 0.7% DMF), 6 (250 μM final concentration in PBS, pH 7.4 containing either 0.7% DMF) or left untreated for 12 h. To verify that 6 could react with azide-labeled GIyCAM-Ig via copper-mediated [3+2] cycloaddition, we employed a modified version of the method reported by Speers and Cravatt. Speers and Cravatt (2004) Chem. Biol. 11 :535-46. Briefly, GIyCAM-Ig samples (in PBS, pH 7.4 containing 0.7% DMF) were incubated with 250 μM 6, 2.5 mM TCEP, 250 μM tris- triazolyl ligand (from a 1.7 mM stock in 1 :4 DMSO:tert-butanol), and 2.5 mM CuSO4. Samples were vortexed and allowed to react at rt for 12 h. Prior to electrophoresis, samples were incubated with an equal volume of 100 mM 2-azidoethanol in 2 X SDS-PAGE loading buffer for 8 h at rt (to quench unreacted 5 or 6). The quenched samples were boiled for 3 min and loaded onto pre-cast polyacrylamide gels. After electrophoresis, the samples were electroblotted to nitrocellulose membrane. The membrane was blocked using 5% BSA in PBS (pH 7.4, containing 0.05% Tween 20 (blocking buffer A) for 1 h at rt, then incubated with a solution of blocking buffer A containing HRP-α-biotin (1 :250,000 dilution, 1 h at rt). The membrane was washed, and detection of membrane-bound anti-biotin-HRP was accomplished by chemiluminescence. Following detection, the membrane was rinsed with PBS (pH 7.4) containing 0.05% Tween (PBS-T) and placed in stripping buffer (15 min at RT) to remove bound anti-biotin Ig. The membrane was thoroughly rinsed with PBS-T and probed for residual anti-biotin signal by chemiluminescence.
[00160] The membrane was washed and re-blocked with 5% low-fat dry powdered milk
(blocking buffer B) for 1 h at rt. The membrane was then incubated with HRP-α-Ig (1 :5000 in blocking buffer B) for 1 h at rt. The membrane was washed again with PBS-T, and detection of membrane bound anti-human Ig was accomplished as for peroxidase-coηjugated anti-biotin. Control samples were treated in an identical manner, except that specific reagents were replaced by buffer where appropriate. Cell culture conditions
[00161] Jurkat cells (human T-cell lymphoma) were maintained in a 5% CO2, water-saturated atmosphere and grown in RPMI- 1640 media supplemented with 10% FCS, penicillin (100 units/mL) and streptomycin (0.1 mg/mL). Cell densities were maintained between 1 x 105 and 1.6 x 106 cells/mL for all experiments. Cell surface azide labeling and detection
[00162] Jurkat cells were seeded at a density of 1.5-2.0 x 105 cells/mL and incubated for 3 d in untreated media or media containing various concentrations of Ac4ManNAz. After growth in the presence of Ac4ManNAz, cells were distributed into a 96-well V-bottom tissue culture plate. The cells were pelleted (3500 rpm, 3 min) and washed twice with 200 μL of labeling buffer (PBS, pH 7.4 containing 1% FCS). Cells were then incubated with 5 or a biotinylated phosphine probe (Vocadlo et al. (2003) Proc. Natl. Acad. ScL U.S.A. 100:9116-21) in labeling buffer containing 2.8% DMF or labeling buffer plus 2.8% DMF alone. After incubation, cells were pelleted, washed twice with labeling buffer and resuspended in the same buffer containing FITC-avidin (1:500 dilution of the Sigma stock). Following a 10-min incubation on ice (in the dark), cells were washed with 200 μL of cold labeling buffer and the FITC-avidin staining procedure was repeated. The cells were washed twice with cold labeling buffer, then diluted to a volume of 400 μL for flow cytometry analysis. RESULTS
[00163] Biotinylated cyclooctyne 5 as synthesized as shown in Scheme 1. Scheme 1
Figure imgf000038_0001
[00164] Construction of the substituted cyclooctyne core was achieved essentially as described by Reese and Shaw. Reese and Shaw (1970) Chem. Comm. 1172-1173. Briefly, compound 1 (Skattebol and Solomon, supra) was treated with silver perchlorate to effect electrocyclic ring opening to the trans-allylic cation, which was captured with methyl hydroxymethylbenzoate to afford bromo-trafts-cyclooctene 2. Base-mediated elimination of the vinyl bromide followed by saponification yielded versatile intermediate 3, to which any biological probe can be attached. Finally, compound 3 was coupled to biotin analog 4 (Wilbur et al. (1996) Bioconj. CTze/w.7:689-702) bearing a PEG linker, providing target 5. Cyclooctyne 3 was stable to mild acid (0.5 N HCl for 30 min), base (0.8 M NaOMe for 30 min), and prolonged exposure to biological nucleophiles such as thiols (120 mM 2- mercaptoethanol for 12 h).
[00165] Model reactions were performed with compound 3 and 2-azidoethanol, benzylazide or
N-butyl α-azidoacetamide. In all cases, the only products observed were the two regioisomeric triazoles formed in approximately equal amounts. The reaction was then applied for covalent labeling of biomolecules. The recombinant glycoprotein GIyCAM-Ig (Bistrup et al. (1999) J Cell Biol. 145:899-910) was expressed in CHO cells in the presence of peracetylated N- azidoacetylmannosamine (Ac4ManNAz), leading to metabolic incorporation of the corresponding iV-azidoacetyl sialic acid (SiaNAz) into its glycans. Control samples of GIyCAM-Ig were expressed in the absence of azido sugar. The purified GIyCAM-Ig samples were incubated with 250 μM 5 overnight, the unreacted cyclooctyne was quenched with excess 2-azidoethanol, and the samples were analyzed by Western blot probing with HRP-α-biotin (Fig. 2). Robust biotinylation was observed for GIyCAM-Ig modified with SiaNAz. Native GIyCAM-Ig lacking azides showed no background labeling, underscoring the exquisite selectivity of the strain-promoted cycloaddition.
[00166] As a point of comparison, similar reactions were performed with biotin-modified terminal alkyne 6 (Scheme 1). In the absence of reagents for copper catalysis, no glycoprotein labeling was observed (Fig. 2). As expected based on previous reports (Sharpless and Finn (2003) J Am. Chem. Soc. 125:3192-3193; and Speers and Cravatt ((2004) Chem. Biol. 11 :535- 546), addition of CuSO4, TCEP and a triazolyl ligand resulted in facile labeling of the azide- modified glycoprotein. The blot was stripped and reprobed with HRP-labeled anti-IgG antibody (HRP-α-IgG) to confirm equal protein loading. Interestingly, consistently diminished anti-IgG immunoreactivity was observed for azide-modified GIyCAM-Ig labeled with 6 in the presence of copper. It is possible that the combination of triazole products and copper damages the epitope recognized by HRP-α-IgG.
[00167] Finally, the utility of the strain-promoted reaction for live cell labeling was investigated. Jurkat cells were incubated with 25 μM Ac4ManNAz for 3 d in order to introduce SiaNAz residues into their cell surface glycoproteins. Saxon and Bertozzi (2000) Science 287:2007-2010; and Saxon et al. 92002) J Am. Chem. Soc. 124:14893-14902. The cells were reacted with various concentrations of 5 for 1.5 h at rt, then stained with FITC- avidin and analyzed by flow cytometry. As shown in Fig. 3A, cells displaying azides showed a dose-dependent increase in fluorescence upon treatment with the cyclooctyne probe. No detectable labeling of cells lacking azides was observed. The cell surface reaction was also dependent on duration of incubation with 5 (Fig. 3B) and the density of cell-surface azides. No negative effects on cell viability were observed.
[00168] Figure 2. Labeling of azide-modified GIyCAM-Ig with alkyne probes. Purified
GIyCAM-Ig was treated with buffer (-), 250 μM 5, or 250 μM 6 alone or in the presence (cat) of CuSO4, TCEP, and a triazolyl ligand, overnight at rt. Reaction mixtures were quenched with 2-azidoethanol and analyzed by Western blot probing with HRP-α-biotin (upper panel). The blot was then stripped and reprobed with HRP-α-Ig (lower panel).
[00169] Figures 3A and 3B. Cell surface labeling with compound 5. Jurkat cells were incubated in the presence (+Az) or absence (-Az) of 25 μM Ac4ManNAz for 3 d. Figure 3 A. The cells were reacted with various concentrations of 5 for 1 h at rt and treated with FITC- avidin; mean fluorescence intensity (MFI) was determined by flow cytometry. Figure 3B. The cells were incubated with 250 μM 5 for various durations at rt and analyzed as in A. C. The cells were incubated with 100 μM probe for 1 h at rt and analyzed as in A. Error bars represent the standard deviation from three replicates. AU = arbitrary fluorescence units. [00170] The above example demonstrates that [3+2] cycloaddition of azides and cyclooctyne derivatives (modified cyclooctynes) according to a subject method occurs readily under physiological conditions in the absence of auxiliary reagents; and that the selective chemical modification of living cells using a subject method occurs without any apparent toxicity.
Example 2: Synthesis of additional cyclooctyne compounds and their use in labeling of living cells [00171] This example presents the synthesis of compounds 3a and 3b (shown below), the evaluation of their kinetic parameters in reactions with small organic azides, and their use in bioorthogonal labeling of living cells.
Figure imgf000040_0001
3a, X = H 3b, X = F
MATERIALS AND METHODS
[00172] All chemical reagents were of analytical grade, obtained from commercial suppliers, and used without further purification unless otherwise noted. With the exception of reactions performed in aqueous media, all reaction vessels were flame-dried prior to use. Reactions were performed in a N2 atmosphere, except in the case of reactions performed in aqueous media, and liquid reagents were added with a syringe unless otherwise noted. Tetrahydrofuran (THF) was distilled under N2 from Na/benzophenone immediately prior to use, and CH2Cl2 was distilled from CaH2 immediately prior to use. Chromatography was carried out with Merck 60 230-400 mesh silica gel according to the procedure described by Still. J. Org. Chem. (1978) 43:2923- 2925. Reactions and chromatography fractions were analyzed with Analtech 250 micron silica gel G plates, and visualized by staining with eerie ammonium molybdate or by absorbance of UV light at 245 nm. When an Rf is reported for a compound, the solvent that was used was the chromatography solvent unless otherwise noted. Organic extracts were dried over MgSO4 and solvents were removed with a rotary evaporator at reduced pressure (20 torr), unless otherwise noted. IR spectra were of thin films on NaCl plates. Unless otherwise noted, 1H, 13C, and 19F NMR spectra were obtained with 300 MHz or 400 MHz Bruker spectrometers. Chemical shifts are reported in δ ppm referenced to the solvent peak for 1H and 13C and relative to CFCl3 for 19F. Coupling constants (J) are reported in Hz. Low- and high-resolution fast atom bombardment (FAB) and electron impact (EI) mass spectra were obtained at the UC Berkeley Mass Spectrometry Facility, and elemental analyses were obtained at the UC Berkeley Micro- Mass Facility. Melting points were determined using a Mel-Temp 3.0 melting point apparatus and are uncorrected. Synthetic Procedures
Figure imgf000041_0001
Compound 6
[00173] (Cyclooct-l-enyloxyj-trimethylsilane (6). To a solution of cyclooctanone (40.0 g, 316 mmol) in 200 mL of anhydrous DMF were added triethylamine (TEA, 93.0 mL, 666 mmol) and chlorotrimethylsilane (84.0 mL, 666 mmol). The reaction was heated to reflux. After 15 h, the reaction was quenched with 20 mL of H2O and the DMF was removed on a rotary evaporator. The residue was diluted with hexanes (300 mL), washed with H2O (3 x 100 mL) and brine (1 x 50 mL), and dried over MgSO4. Distillation under reduced pressure (20 torr) yielded 58.1 g (93%) of the desired product as a colorless oil, bp 108 0C (20 torr) (lit. 106 °C at 25 torr). Nakamura ,et al. J Am. Chem. Soc. (1976) 98, 2346-2348. IR: 2926, 2851, 1661 cm"1. 1H NMR (CDCl3, 300 MHz): δ 0.20 (s, 9H), 1.39-1.58 (m, 8H), 2.02 (m, 2H), 2.19 (m, 2H), 4.75 (t, IH, J= 9.0 Hz). (Lit: 1H NMR (CDCl3, 600 MHz): δ 0.16 (s, 9H), 1.46 (m, 4H), 1.49 (m, 2H), 1.55 (m, 2H), 1.97 (m, 2H), 2.14 (m, 2H), 4.70 (t, IH, J= 8.0 Hz) (Frimer et al. J Org. Chem. (2000) 65, 1807-1817.) 13C NMR (CDCl3, 75 MHz): δ 0.4, 25.5, 26.3, 26.4, 27.8, 30.9, 31.0, 105.41, 152.99. (Lit: 13C NMR (CDCl3, 150 MHz): δ 0.45, 25.52, 26.36, 26.40, 27.83, 30.98, 31.05, 105.45, 153.05) Frimer et al. (2000) supra) FAB-HRMS: Calcd. for CnH23OSi+ [M+H]+: 199.1518, found 199.1520.
Figure imgf000041_0002
Compound 5b
[00174] 2-Fluorocyclooctanone (5b). To a solution of silyl enol ether 6 (57.8 g, 291 mmol) in
DMF (350 mL) was added a solution of Selectfluor (124 g, 349 mmol) in DMF (150 mL) over 1 h at rt. The solution was allowed to stir for 12 h. The reaction was quenched with 30 mL of H2O, and the DMF was removed on a rotary evaporator. The residue was diluted with hexanes (500 mL), washed with H2O (3 x 200 mL) and brine (1 x 50 mL), and dried over MgSO4. Following column chromatography (30:1 to 15:1 pentane/ether), a white solid was isolated (38.4 g, 91%, Rf = 0.30 in 9:1 pentane/ether), mp 48.1-49.8 °C. IR: 3429, 2932, 2859, 1721, 1709 cm'1. (Lit: 1710 cm'1) (Rozen and Menahem. J. Fluorine Chem. (1980), 16, 19-31). 1H NMR (CDCl3, 400 MHz): δ 1.25 (m, IH), 1.38-1.55 (m, 4H), 1.61 (m, IH), 1.73 (m, IH), 2.05 (m, 3H), 2.30 (m, IH), 2.55 (m, IH), 4.86 (ddd, IH, J= 49.6, 6.4, 2.8 Hz). (Lit: 1H NMR (CDCl3, 250 MHz): δ 1.36-2.7 (m, 12H), 4.9 (dm, IH, J= 49.5 Hz) (Chambers and Hutchinson J. Fluorine Chem. (1998) 89, 229-232) 13C NMR (CDCl3, 100 MHz): δ 20.3 (d, J= 4.0 Hz), 24.4 (d, J= 6.0 Hz), 24.5, 26.9, 32.2 (d, J= 11.0 Hz), 39.3, 94.7 (d, J= 185.0 Hz), 213.4 (d, J = 21.0 Hz). (Lit: 13C NMR (CDCl3, 50 MHz): δ 20.5 (d, J= 3.6 Hz), 24.6 (d, J= 3.7 Hz), 24.7, 27.2, 32.7 (d, J= 21.0 Hz), 39.6, 91.5 (d, J= 184.7 Hz), 213.9 (d, J= 20.9 Hz) (Chambers and Hutchinson (1998) supra) 19F NMR (CDCl3, 376 MHz): δ -190.7 (m). (Lit: 19F NMR (CDCl3, 235 MHz): δ -191.6 (m) (Chambers and Hutchinson (1998) supra)
Figure imgf000042_0001
Compound 4b
[00175] 4-(l-Fluoro-2-oxo-cycIooctyImethyl)benzoic acid methyl ester (4b). To a solution of
LDA (34 mL, 61 mmol, 1.8 M solution in heptane/THF/ethylbenzene) in THF (50 mL) at -78 °C was added a solution of 2-fluorocyclooctanone (5b) (7.38 g, 51.2 mmol) in THF (50 mL) over 2 h using a syringe pump. After 1 h, a solution of methyl 4-bromomethylbenzoate (17.6 g, 76.8 mmol) in THF (50 mL) was added and the reaction was allowed to warm to rt. After 1 h, the reaction mixture was quenched with H2O (50 mL) and the THF was removed on a rotary evaporator. The residue was diluted with EtOAc (200 mL), washed with H2O (3 x 100 mL) and brine (1 x 50 mL), and dried over MgSO4. Following column chromatography (50:1 to 15:1 hexanes/EtOAc), a white solid was isolated (6.45 g, 43%, Rf = 0.35 in 9:1 hexanes/EtOAc), mp 53.5-55.2 °C. IR: 2931, 2858, 1721 cm'1. 1H NMR (CDCl3, 400 MHz): δ 1.08 (m, IH), 1.35- 1.65 (m, 7H), 1.86 (m, 2H), 2.04 (app d, 2H, J= 9.0 Hz), 2.90 (dd, IH, J = 20.1, 14.1 Hz), 3.14 (dd, IH, J= 28.2, 14.1 Hz), 3.78 (s, 3H), 7.15 (d, 2H, J= 7.8 Hz), 7.83 (d, 2H, J= 8.4 Hz). 13C NMR (CDCl3, 100 MHz): 5 21.1, 24.7, 25.3, 27.6, 38.7 (d, J= 22.0 Hz), 40.0, 43.4 (d, J= 21.0 Hz), 51.9, 102.3 (d, J= 189.0 Hz), 128.7, 129.3, 130.5, 140.3, 166.8, 216.0 (d, J = 26.0 Hz). 19F NMR (CDCl3, 376 MHz): δ -166.0 (m). FAB-HRMS: Calcd. for CnH22O3F+ [M+H]+: 293.1553, found: 293.1560.
Figure imgf000043_0001
Compound 7b
[00176] 4-(l-Fluoro-2-trifluoromethanesulfonyloxy-cyclooct-2-enylmethyl)-benzoic acid methyl ester (7b). To a solution of ketone 4b (4.62 g, 15.8 mmol) in THF (50 mL) at -78 °C was added Potassium hexamethyldisilazide (KHMDS, 35.0 mL, 17.5 mmol, 0.50 M solution in toluene). After 1 h, a solution of N-Phenylbistrifluoromethanesulfonimide (Tf2NPh, 6.18 g, 17.3 mmol) in THF (25 mL) was added and the reaction was allowed to warm to rt. After 30 min, the reaction mixture was concentrated on a rotary evaporator and the product was purified by column chromatography (20:1 to 12:1 hexanes/EtOAc) to yield the desired product (4.90 g, 73%, Rf = 0.30 in 9:1 hexanes/EtOAc) as a colorless oil. IR: 3424, 2952, 1723, 1646 cm"1. 1H NMR (CDCl3, 400 MHz): δ 1.38-1.67 (m, 4H), 1.74-1.97 (m, 4H), 1.97-2.18 (m, 2H), 3.16 (app d, IH, J= 3.2 Hz), 3.20 (s, IH), 3.91 (s, 3H), 5.86 (t, IH, J= 9.6 Hz), 7.26 (d, 2H, J= 8.0 Hz), 7.96 (d, 2H, J= 8.4 Hz). 13C NMR (CDCl3, 100 MHz): δ 22.0, 22.1, 23.1, 25.2, 35.1 (d, J = 22.0 Hz), 44.3 (d, J= 26.0 Hz), 52.0, 95.7 (d, J= 177.0 Hz), 118.4 (q, J= 317.0 Hz), 123.8, 129.1, 129.4, 130.5, 139.7 (d, J= 8.0 Hz), 148.2 (d, J= 21.0 Hz), 166.8. 19F NMR (CDCl3, 376 MHz): δ -73.7 (app d, 3H, J= 3.8 Hz), -144.3 (app d, IH, J= 3.8 Hz). FAB-HRMS: Calcd. for Ci8H2IO5F4S+ [M+H]+: 425.1046, found: 425.1046.
Figure imgf000044_0001
Compound 8b
[00177] 4-(l-Fluoro-cyclooct-2-ynyImethyl)benzoic acid methyl ester (8b). To a solution of vinyl triflate 7b (14.3 g, 33.5 mmol) in THF (100 niL) at 0 °C was added LDA (23.5 mL, 35.2 mmol, 1.8M in heptane/THF/ethyl benzene) drop wise, using a syringe pump, over 3 h. LDA was added until the starting material was consumed. The reaction was quenched with 20 mL of H2O and the THF was removed on a rotary evaporator. The residue was diluted with EtOAc (300 mL), washed with H2O (3 x 100 mL) and brine (1 x 50 mL), and dried over MgSO4. After silica gel chromatography (50:1 to 25:1 hexanes/EtOAc), a colorless oil was isolated (5.41 g, 59%, Rf = 0.40 in 9:1 hexanes/EtOAc). IR: 3421, 2930, 2854, 2223, 1721, 1613 cm"1. 1H NMR (CDCl3, 300 MHz): δ 1.35 (m, IH), 1.66-1.76 (m, 2H), 1.76-2.07 (m, 4H), 2.07-2.33 (m, 3H), 3.03 (app d, IH, J= 2.1 Hz), 3.10 (s, IH), 3.90 (s, 3H), 7.37 (d, 2H, J= 8.1 Hz), 7.98 (d, 2H, J = 8.1 Hz). 13C NMR (CDCl3, 75 MHz): δ 20.5, 26.0 (d, J= 1.5 Hz), 29.4, 34.0, 44.7 (d, J= 26.0 Hz), 48.8 (d, J= 25.0 Hz), 51.9, 90.5 (d, J= 32.0 Hz), 95.2 (d, J= 175.0 Hz), 104.5 (d, J = 11.0 Hz), 128.6, 129.3, 130.3, 141.2, 167.0. 19F NMR (CDCl3, 376 MHz): δ -139.0 (m). FAB-HRMS: Calcd. for C17H20O2F+ [M+H]+: 275.1447, found: 275.1442.
Figure imgf000044_0002
Compound 3b
[00178] 4-(l-Fluoro-cyclooct-2-ynylmethyl)benzoic acid (3b). To a solution of cyclooctyne
8b (1.8 g, 6.6 mmol) in dioxane (30 mL) and H2O (7.5 mL) was added finely crushed LiOH (3.1 g, 130 mmol). The suspension was heated to 50 °C and stirred for 3 h. The dioxane was removed on a rotary evaporator and the reaction mixture was diluted with CH2Cl2 (100 mL).
The organic layer was washed with 1 N HCl (2 x 100 mL), H2O (3 x 100 mL), and brine (1 x 25 mL), and dried over MgSO4, yielding a white solid (1.7 g, 98%, Rf = 0.30 in 27:3:1 hexane/EtOAc/AcOH), mp 132.0-132.5 0C (dec). IR: 3442, 2926, 2851, 2674, 2557, 2224, 1686, 1611 cm-1. 1H NMR (DMSO-J6, 400 MHz): δ 1.39 (app quintet, IH, J= 7.6 Hz), 1.64 (m, 2H), 1.76 (m, 2H), 2.10 (m, 5H), 3.07 (s, IH), 3.11 (d, IH5 J= 8.0 Hz), 7.38 (d, 2H, J= 8.0 Hz), 7.87 (d, 2H, J= 8.4 Hz), 12.9 (br s, IH). 13C NMR (DMSO-J6, 100 MHz): δ 19.8, 25.7, 29.0, 33.7, 43.7 (d, J= 25.0 Hz), 47.6 (d, J= 25.0 Hz), 90.7 (d, J= 32.0 Hz), 95.4 (d, J= 173.0 Hz), 104.5 (d, J= 10.0 Hz), 129.0, 129.2, 130.4, 141.2, 167.2. 19F NMR (CD3CN, 376 MHz): δ -139.4 (m). FAB-HRMS: Calcd. for C16H18O2F+ [M+H]+: 261.1291, found: 261.1291. Anal, calcd. for Ci6Hi7O2F: C, 79.31; H, 7.49. Found: C, 79.07; H, 7.26.
Figure imgf000045_0001
Compound 13 [00179] 3-(2,5-Dioxo-2,5-dihydro-pyrrol-l-yl)-propylammonium trifluoroacetate (13). To a solution of maleimide (3.12 g, 32.2 mmol) and PPh3 (8.29 g, 31.6 mmol) in THF (150 mL) was added 7V-(t-butoxycarbonyl)propanolamine (5.00 mL, 29.3 mmol) and then diisopropyl azodicarboxylate (6.80 mL, 35.1 mmol). The solution was stirred at rt for 48 h, concentrated on a rotary evaporator, and purified by column chromatography (4:1 to 2:1 hexanes/EtOAc) to yield 10.3 g of a mixture of the 7V-Boc protected product and diisopropyl hydrazinedicarboxylate. The mixture was dissolved in a solution Of CH2Cl2 (60 mL) and H2O (5 mL), and then trifluoroacetic acid (TFA, 35 mL) was added. The reaction was stirred for 5 h at rt and then diluted with CH2Cl2 (50 mL) and H2O (50 mL). The aqueous layer was washed with CH2Cl2 (3 x 50 mL) and then concentrated to yield the desired product as a yellow oil (7.51 g, 96%). IR: 3435, 2959, 2917, 2849, 1707, 1683 cm"1. 1H NMR (DMSO-J6, 400 MHz): δ 1.76 (app q, 2H, J= 7.2 Hz), 2.78 (m, 2H), 3.45 (t, 2H, J= 6.8 Hz), 7.02 (s, 2H), 7.79 (br s, 3H). 13C NMR (DMSO-J6, 100 MHz): δ 26.7, 34.6, 37.0, 116.0 (q, 289.0 Hz), 134.7, 158.9 (q, J= 36.0 Hz), 171.3. 19F NMR (DMSO-J6, 376 MHz): δ -72.9 (s). FAB-HRMS: Calcd. for C7HnN2O2 + [M+H]+: 155.0821, found: 155.0824.
Figure imgf000046_0001
Compound 12b [00180] N-[3-(2,5-Dioxo-2,5-dihydro-pyrrol-l-yl)-propyl]-4-(l-fluorocycIooct-2- ynylmethyl)benzamide (12b). TEA (0.508 mL, 3.65 mmol) was added to a solution of cyclooctyne 3b (0.200 g, 0.768 mmol), amine 13 (0.235 g, 0.875 mmol), O-(7- Azabenzotriazol-l-yl)-N,N,N',N-tetramethyluronium hexafluorophosphate (HATU, 0.305 g, 0.802 mmol), and 1-hydroxybenzotriazole (HOBT, 0.123 g, 0.802 mmol) in CH2Cl2 (3 mL) at rt. The reaction was stirred for 15 min at rt, quenched with H2O (10 mL), and diluted with CH2Cl2 (50 mL). The organic layer was washed with 1 N HCl (3 x 50 mL), saturated NaHCO3 (3 x 50 mL), and brine (2 x 25 mL) and dried over MgSO4. Chromatography of the crude product (2:1 to 1 :1 hexanes/EtOAc) yielded the desired product as a white solid (0.198 g, 65%, Rf = 0.30 in 1:1 hexanes/EtOAc), mp 122.0-124.0 °C (dec). IR: 3413, 2931, 2854, 2222, 1705, 1640 cm"1. 1U NMR (CDCl3, 400 MHz): δ 1.39 (m, IH), 1.74 (m, 2H), 1.81-2.06 (m, 6H), 2.14-2.32 (m, 3H), 3.05 (d, IH, J= 2.8 Hz), 3.09 (s, IH), 3.40 (q, 2H, J= 6.4 Hz), 3.67 (t, 2H, J= 6.0 Hz), 6.75 (s, 2H), 6.93 (m, IH), 7.41 (d, 2H, J= 8.0 Hz), 7.81 (d, 2H, J= 8.0 Hz). 13C NMR (CDCl3, 100 MHz): δ 20.5, 26.0, 28.1, 29.4, 34.0, 34.8, 36.2, 44.6 (d, J= 25.0 Hz), 47.8 (d, J= 24.0 Hz), 90.7 (d, J= 32.0 Hz), 95.3 (d, J= 174.0 Hz), 104.5 (d, J= 10.0 Hz), 126.7, 130.5, 132.9, 134.2, 139.6, 167.1, 171.1. 19F NMR (CDCl3, 376 MHz): δ -139.0 (m). FAB- HRMS: Calcd. for C23H26N2O3F+ [M+H]+: 397.1927, found: 397.1920.
Figure imgf000046_0002
Compound 4a
[00181] 4-(2-Oxo-cyclooctylmethyl)benzoic acid methyl ester (4a). To a stirring solution of cyclooctanone (1.76 g, 14.0 mmol) in THF (30 mL) at -78 0C was added LDA (8.54 mL, 15.4 mmol, 1.8 M in heptane/THF/ethylbenzene). After 1 h, a solution of methyl 4- bromomethylbenzoate (3.53 g, 15.4 mmol) in THF (10 mL) was added and the reaction mixture was allowed to warm to rt. After 30 min, the reaction was quenched with H2O (10 mL) and the THF was removed on a rotary evaporator. The residue was diluted with EtOAc (100 mL), washed with H2O (3 x 100 mL) and brine (1 x 50 mL), and dried over MgSO4. Chromatography of the crude product (50:1 to 9:1 hexanes/EtOAc) yielded the desired product as a colorless oil (3.08 g, 80%, Rf = 0.30, 9:1 hexanes/EtOAc). IR: 3426, 2929, 2856, 1721, 1700, 1657, 1611 crn 1. 1H NMR (CDCl3, 300 MHz): δ 1.10-1.28 (m, IH), 1.28-1.42 (m, IH), 1.42-1.80 (m, 6H), 1.80-1.90 (m, IH), 1.90-2.08 (m, IH), 2.08-2.18 (m, IH), 2.22-2.35 (m, IH), 2.64 (dd, IH, J= 12.6, 6.0 Hz), 3.01 (m, 2H), 3.89 (s, 3H), 7.20 (d, 2H, J= 8.1 Hz), 7.93 (d, 2H, J= 8.4 Hz). 13C NMR (CDCl3, 75 MHz): δ 24.5, 24.6, 25.1, 27.7, 32.9, 38.1, 43.2, 51.5, 52.0, 128.1, 129.0, 129.7, 145.6, 167.0, 218.9. FAB-HRMS: Calcd. for C17H23O3 + [M+H]+: 275.1647, found: 275.1648.
Figure imgf000047_0001
Compound 7a
[00182] 4-(2-Trifluoromethanesulfonyloxy-cyclooct-2-enylmethyl)-benzoic acid methyl ester (7a). To a solution of ketone 4a (2.17 g, 7.91 mmol) in THF (50 mL) at -78 °C was added KHMDS (17.4 mL, 8.70 mmol, 0.50 M solution in toluene). After 1 h, a solution of Tf2NPh (3.11 g, 8.70 mmol) in THF (25 mL) was added and the reaction was allowed to warm to rt. After 30 min, the reaction mixture was concentrated on a rotary evaporator and the product was purified directly by column chromatography (20:1 to 12:1 hexanes/EtOAc) to yield the desired product (2.19 g, 68%, Rf = 0.35 in 9:1 hexanes/EtOAc) as a colorless oil. The product was isolated as a 9:1 mixture of regioisomers. IR: 2932, 2856, 1723, 1410 cm"1. 1H NMR (CDCl3, 400 MHz): δ 1.25-1.38 (m, IH), 1.38-1.52 (m, IH), 1.52-1.71 (m, 4H), 1.71- 1.85 (m, 2H), 1.98-2.11 (m, IH), 2.15-2.25 (m, IH), 2.73 (dd, IH5 J= 14.0, 6.8 Hz), 2.99 (dd, IH, J= 13.6, 8.0 Hz), 3.13 (m, IH), 3.73 (s, 3H), 5.76 (t, IH, J= 8.8 Hz), 7.27 (d, 2H, J= 8.0 Hz), 7.98 (d, 2H, J= 8.0 Hz). 13C NMR (CDCl3, 100 MHz): δ 25.2, 25.9, 26.5, 29.8, 33.3, 37.4, 39.8, 52.0, 118.5 (q, J= 318.0 Hz), 121.3, 128.4, 128.8, 129.8, 144.8, 151.0, 167.0. 19F NMR (CDCl3, 376 MHz): δ -73.8 (s). FAB-HRMS: Calcd. for C18H22O5F3S+ [M+H]+:
407.1140, found: 407.1133.
Figure imgf000048_0001
Compound δa [00183] 4-Cyclooct-2-ynylmethylbenzoic acid methyl ester (8a). To a solution of vinyl triflate 7a (2.14 g, 5.28 mmol) in THF (30 mL) at 0 0C was added LDA (3.52 mL, 5.28 mmol, 1.8 M in heptane/THF/ethyl benzene) dropwise by syringe pump, over 3 h. LDA was added until the starting material was consumed. The reaction was quenched with H2O (10 mL) and the THF was removed on a rotary evaporator. The residue was diluted with EtOAc (100 mL), washed with H2O (3 x 100 mL) and brine (1 x 50 mL), and dried over MgSO4. After silica gel chromatography (3:1 :0 to 30:10:2 hexanes/toluene/EtOAc), a colorless oil was isolated (0.310 g, 23%, Rf = 0.20 in 30:10: 1 hexanes/toluene/EtOAc). IR: 2930, 2857, 1720 cm"1. 1H NMR (CDCl3, 300 MHz): δ 1.42 (m, 2H), 1.62 (m, IH), 1.71-1.88 (m, 3H), 1.88-1.98 (m, IH), 2.00- 2.10 (m, IH), 2.11-2.23 (m, 2H), 2.63-2.80 (m, 3H), 3.90 (s, 3H), 7.29 (d, 2H, J= 8.0 Hz), 7.97 (d, 2H, J= 8.4 Hz). 13C NMR (CDCl3, 100 MHz): δ 20.8, 28.4, 30.0, 34.8, 36.5, 40.3, 41.7, 51.9, 94.9, 96.1, 128.1, 128.9, 129.6, 145.7, 167.1. FAB-HRMS: Calcd. for CnH2IO2 + [M+H]+: 257.1542, found: 257.1536.
Figure imgf000048_0002
Compound 3a
[00184] 4-Cyclooct-2-ynyImethylbenzoic acid (3a). To a solution of cyclooctyne 8a (283 mg,
1.11 mmol) in dioxane (12 mL) and H2O (3 mL) was added finely crushed LiOH (530 mg, 22.1 mmol). The suspension was heated to 50 °C and stirred for 3 h. The dioxane was removed on a rotary evaporator. The residue was diluted with EtOAc (50 mL), washed with 1 N HCl (3 x 50 mL), H2O (3 x 50 mL), and brine (2 x 50 mL), and dried over MgSO4 to yield a white solid (254 mg, 95%, Rf = 0.25 in 27:3:1 hexane/EtOAc/AcOH), mp 112.0-113.9 °C (dec). IR: 3071, 2922, 2846, 1680 cm'1. 1H NMR (CD3CN, 400 MHz): δ 1.35-1.48 (m, 2H), 1.56-1.66 (m, IH), 1.66-1.95 (m, 4H), 2.01-2.17 (m, 3H), 2.70 (d, IH5 J= 5.2 Hz), 2.71 (d, IH, J= 1.2 Hz), 2.76 (m, IH), 7.33 (d, 2H, J= 8.4 Hz), 7.91 (d, 2H, J= 8.4 Hz), 9.40 (br s, IH). 13C NMR (CD3CN, 100 MHz): δ 21.2, 29.2, 30.8, 35.6, 37.3, 40.8, 42.5, 95.7, 97.1, 128.9, 130.1, 130.5, 147.4, 167.8. EI-HRMS: Calcd. for C16Hi8O2 M+: 242.1307, found: 242.1307. Anal. Calcd. for Ci6H18O2: C, 79.31; H, 7.49. Found: C, 79.07; H, 7.26.
Figure imgf000049_0001
Compound 12a [00185] 4-Cyclooct-2-ynylmethyl)-iV-[3-(2,5-dioxo-2,5-dihydro-pyrrol-l- yl)propyl]benzamide (12a). TEA (0.184 niL, 0.396 mmol) was added to a solution of cyclooctyne 3a (64 mg, 0.26 mmol), amine 13 (106 mg, 0.396 mmol), and HATU (111 mg, 0.291 mmol) in CH2Cl2 (2 mL) at rt. The reaction was stirred for 15 min at rt, quenched with H2O (10 mL), and diluted with CH2Cl2 (50 mL). The organic layer was washed with 1 N HCl (3 x 50 mL), saturated NaHCO3 (3 x 50 mL), and brine (2 x 25 mL), and dried over MgSO4. Chromatography of the crude product (2:1 to 1 :1 hexanes/EtOAc) yielded the desired product as a colorless oil (69 mg, 69%, Rf = 0.30 in 1 :1 hexanes/EtOAc). IR: 3411, 3099, 2925, 2849, 1704, 1639 cm-1. 1H NMR (CDCl3, 400 MHz): δ 1.42 (m, 2H), 1.61 (m, IH), 1.70-1.97 (m, 6H), 2.00-2.09 (m, IH), 2.09-2.22 (m, 2H), 2.62-2.78 (m, 3H), 3.38 (q, 2H, J= 6.4 Hz), 3.65 (t, 2H, J= 6.0 Hz), 6.74 (s, 2H), 6.93 (m, IH), 7.29 (d, 2H, J= 8.0 Hz), 7.78 (d, 2H, J= 8.0 Hz). 13C NMR (CDCl3, 100 MHz): δ 20.8, 28.2, 28.4, 29.9, 34.7, 34.8, 36.1, 36.5, 40.0, 41.6, 94.9, 96.2, 126.9, 129.0, 132.2, 134.2, 144.0, 167.1, 171.2. FAB-HRMS: Calcd. for C23H27N2O3 + [M+H]+: 379.2022, found: 379.2014.
Figure imgf000049_0002
Compounds lib and lie
[00186] Compounds lib and lie. Cyclooctyne 3b (0.20 g, 0.77 mmol) and 2-azidoethanol (NJ.
Agard, unpublished results, 461 μL, 3.84 mmol) were dissolved in CH3CN (7.2 mL) and Dulbecco's phosphate-buffered saline (IX, pH 7.4, 5.9 mL). The reaction was stirred at rt for 12 h and concentrated on a rotary evaporator. Chromatography of the crude product (95:4:1 to 90:9:1 CH2Cl2ZMeOHZAcOH) afforded a 20:1 mixture of llbilla (99 mg, 37%, Rf = 0.30 in 90:9:1 CH2Cl2ZMeOHZAcOH) and lie (144 mg, 54%, Rf = 0.15 in 90:9:1 CH2Cl2ZMeOHZAcOH) as colorless oils.
[00187] Compound lib: mp 175.0-178.0 0C. IR: 3442, 2103, 1644 cm"1. 1H NMR (CD3OD,
400 MHz): δ 1.39 (m, 3H), 1.55 (m, IH), 1.68 (m, IH), 1.79 (m, IH), 2.15 (m, 2H), 2.30 (m, IH), 2.82 (ddd, IH, J= 14.8, 4.4, 4.4 Hz), 3.38 (app t, IH, J= 12.4 Hz), 3.48 (app t, IH, J = 14.4 Hz), 4.02 (m, IH), 4.09 (m, IH), 4.46 (dt, IH, J= 14.0, 5.2 Hz), 4.62 (ddd, IH, J= 14.0, 8.0, 5.6 Hz), 7.05 (d, 2H, J= 8.4 Hz), 7.86 (d, 2H, J= 8.4 Hz). 13C NMR (CD3OD, 100 MHz): δ 22.9, 25.4, 27.4, 28.4, 38.3 (d, J= 22.0 Hz), 48.1 (d, J= 26.0 Hz), 53.9 (d, J= 7.0 Hz), 62.1, 97.0 (d, J= 174.0 Hz), 130.7, 131.2, 132.0, 135.2 (d, J= 23.0 Hz), 141.6 (d, J= 8.0 Hz), 145.7 (d, J= 5.0 Hz), 169.8. 19F NMR (CD3OD, 376 MHz): δ -145.7 (m). FAB-HRMS: Calcd. for C18H23FN3O3 + [M+H]+: 348.1723, found: 348.1722.
[00188] Compound lie: mp 183.0-184.6 0C. IR: 3423, 2068, 1643 cm"1. 1H NMR (CD3OD, 400
MHz): δ 1.31 (m, IH), 1.40-1.68 (m, 4H), 1.74 (m, IH), 1.92 (m, 2H), 2.39 (m, IH), 2.95 (m, IH), 3.32 (app q, 2H, J= 12.8 Hz), 3.88 (t, 2H, J= 5.6 Hz), 4.34 (m, 2H), 7.05 (d, 2H, J= 8.0 Hz), 7.82 (d, 2H, J= 8.0 Hz). 13C NMR (CD3OD, 100 MHz): δ 21.7, 23.8, 25.9, 28.1, 38.9, 51.1, 51.2, 55.0, 62.2, 130.3, 130.9, 132.0, 135.7, 144.2, 149.9, 170.8. FAB-HRMS: Calcd. for C18H24N3O4 + [M+H]+: 346.1767, found: 346.1764. Kinetic evaluation of cyclooctyne probes
[00189] Stock solutions of cyclooctynes 3a and 3b (50 mM), benzyl azide (500 mM) and 2- azidoethanol (500 mM) were made in either CD3CN or a 55:45 mixture of CD3CN and deuterated Dulbecco's phosphate-buffered saline (pH 7.4, made with D2O). Gentle heating andZor sonication in a H2O bath was required to fully dissolve 3a and 3b. An NMR tube was charged with 450 μL of either 3a or 3b, and 50 μL of either benzyl azide or 2-azidoethanol, and the reaction was monitored over time using 1H NMR spectroscopy.
[00190] In the case of the reactions of 3a and 3b with benzyl azide, the kinetic data were derived by monitoring the change in integration of resonances corresponding to the benzylic protons in benzyl azide (δ ~4.2 ppm) compared to the corresponding resonances of the triazole products (δ ~5.0 to 5.5 ppm). In the case of the reactions of 3a and 3b with 2-azidoethanol, the kinetic data were derived from integration of the resonances corresponding to the more downfield pair of aromatic protons (δ ~7.9 ppm) in the cyclooctyne starting material compared to the corresponding resonances in the triazole products (δ ~7.7 to 7.8 ppm). [00191] Second-order rate constants for the reaction were determined by plotting 1 /[benzyl azide] versus time in the case of the reactions of 3a and 3b with benzyl azide and by plotting l/[3a] versus time or l/[3b] versus time in the case of the reactions of 3a and 3b with 2- azidoethanol, and subsequent analysis by linear regression. Second-order rate constants correspond to one half of the determined slope (Table 1). Error bars represent standard deviations from three replicate experiments.
Table 1. Kinetic comparison of azido-ligations".
Figure imgf000051_0001
[00192] " Second-order rate constants for the [3+2] cycloaddition were determined at 22 0C using 1H
NMR (see experimental section for a full description of the experimental setup). h Agard, N. J., Prescher, J.A., Bertozzi, CR. J. Am. Chem. Soc. 2004, 126, 15046-15047. c Lin, F. L., Hoyt, H.M., van Halbeek, H., Bergman, R.G., Bertozzi, CR. J. Am. Chem. Soc. 2005, 127, 2686-95. Cell surface labeling ofJurkat cells with Hb-FLAG
[00193] Jurkat cells (human T-cell lymphoma) were maintained in a 5% CO2, water-saturated atmosphere and grown in RPMI- 1640 media supplemented with 10% FCS, penicillin (100 units/mL), and streptomycin (0.1 mg/mL). Cell densities were maintained between 1 x 105 and 1.6 x 106 cells/mL. The cells were incubated for 3 d in untreated media or media containing 25 μM Ac4ManNAz. After growth in the presence of Ac4MaIiNAz, cells were distributed into a 96-well V-bottom tissue culture plate. The cells were pelleted (3500 rpm, 3 min) and washed twice with 200 μL of labeling buffer (PBS, pH 7.4 containing 1% FCS). Cells were then incubated with 12b-FLAG or 1-FLAG in labeling buffer for 1 h at it. After incubation, cells were pelleted, washed twice with labeling buffer, and resuspended in the same buffer containing FITC-conjugated α-FLAG (1:3000 dilution of the Sigma stock). After a 30-min incubation on ice (in the dark), the cells were washed twice with 200 μL of cold labeling buffer and then diluted to a volume of 400 μL for flow cytometry analysis. RESULTS
[00194] To test the specificity of the cycloaddition reaction in a biological context, 3a and 3b were further derivatized with FLAG-C (SEQ ID NO:3), a short peptide epitope for which a fluorescently labeled antibody is commercially available (Scheme 6). Maleimide derivatives 12a and 12b were prepared by the HATU-mediated coupling of 3a and 3b with amino- maleimide 13. Cysteine-terminated FLAG peptides were ligated to maleimides 12a and 12b using standard conditions and the resulting probes (12a-FLAG and 12b-FLAG) were purified by HPLC for use in cell labeling experiments.
Figure imgf000052_0001
Figure imgf000052_0002
12a-FLAG, X = H 12b-FLAG, X = F
Scheme 6
[00195] Scheme 6: (a) O-(7-Azabenzotriazol-l-yl)-iV:7V;N',N'-tetramethyluronium hexafluorophosphate (HATU), 1-hydroxybenzotriazole (HOBT), TEA, CH2Cl2, 69 % (12a), 65 % (12b); (b) H2N-DYKDDDDKC-CO2H (SEQ ID NO:3), DMF/H20.
[00196] Azides were installed on the surfaces of Jurkat cells by metabolic labeling of sialic acid residues10. Briefly, cells fed peracetylated iV-azidoacetylmannosamine (Ac4ManNAz), an analog of N-acetylmannosamine (ManNAc), convert the azido sugar to the corresponding azido sialic acid (SiaNAz) within cell surface glycoproteins. Reaction of the cell-surface azides with phosphine or cyclooctyne probes containing the FLAG epitope was monitored by flow cytometry using visualization with a FITC-conjugated α-FLAG antibody (Figure 4a).
[00197] As shown in Figure 4b, the 12b-FLAG labels Jurkat cells in an azide-dependent fashion, similar to a previously studied FLAG-labeled phosphine probe capable of undergoing the Staudinger ligation (1-FLAG). Agard et al. (2004). J. Am. Chem. Soc. 126, 15046-15047. Compound 12b-FLAG labels cells in a dose-dependent manner. No toxicity was observed in any of these experiments,.
[00198] Figures 4A and 4B. Labeling of cell-surface azides with cyclooctyne probes, (a) Jurkat cells were incubated with azido sugars for 3 d and then labeled with various concentrations of 1-FLAG or 12b-FLAG. Detection of the FLAG peptide was achieved using a FITC- conjugated α-FLAG antibody, followed by analysis by flow cytometry, (b) Dark blue: Cells incubated with 25 μM Ac4ManNAz for 3 d. Light blue: Cells incubated in the absence of Ac4ManNAz. Error bars indicate the standard deviation of three trials. a Mean fluorescence intensity.
Example 3 : Synthesis of an aryl-less cyclooctyne compound and its use in labeling of living cells
[00199] This example describes synthesis of an "aryl-less" octyne (ALO; shown below) and the use of a conjugated ALO to label living cells in vivo. The aryl-less octyne was synthesized; then a maleimide group was introduced. The maleimide functionality allows for specific conjugation to the thiol of a cysteine containing peptides. Described below are the synthesis of the octyne, the octyne-linked maleimides, their conjugation to a FLAG peptide, and the subsequent use of these conjugates on cell surfaces and in living mice.
Figure imgf000053_0001
MATERIALS AND METHODS
Synthesis of ALO
Figure imgf000053_0002
Compound 14 [00200] Compound 14. AgClO4 (2.40 g, 11.6 mmol) was added to a solution of dibromobicycle 1 (1.00 g, 3.72 mmol) and methyl glycolate (6.0 ml, 78.2 mmol) dissolved in toluene (4 mL) in a flame-dried, aluminum-foil-wrapped flask. The reaction was stirred for 2 h, diluted with pentane (20 mL), and filtered to remove insoluble silver salts. The solution was concentrated and purified by silica gel chromatography (5-10% EtOAc: pet ether; Rf (10% EtOAc: pet ether) = 0.32) to yield 2 as a colorless oil (330 mg 1.19mmol, 22%). 1H NMR (300 MHz, CD3Cl) δ 6.20 (dd, IH, J = 3.9, 11.7) 4.23 (d, IH, J= 16.5), 4.11 (m, IH) 3.96 (d, IH, J = 16.5), 3.73 (s, IH), 2.70 (m, IH), 2.25 (m, IH), 0.8-2.1 (m, 8H). EI LRMS calculated CnH18O3Br [M+H]+ 278.2 found 278.1.
Figure imgf000054_0001
Compound 15
[00201] Compound 15. A suspension of NaOMe (128 mg, 2.38 mmol) in anhydrous DMSO (2 mL) was added to compound 2 (330 mg, 1.19 mmol) dissolved in anhydrous DMSO (3 mL). The reaction was stirred 20 min and additional NaOMe (250 mg, 4.8 mmol in 1.5 mL of DMSO) was added. The reaction was stirred until the starting material was completely consumed as determined by TLC (20 min). Water (1 ml) was added to the reaction and it was stirred overnight. The reaction was acidified with 1 M HCl (75 mL) and extracted twice with EtOAc (50 mL). The combined organic extracts were dried over MgSO4, filtered, and solvent was removed in vacuo. (The reaction can be purified at this point to yield the free acid, but is most often taken on in crude form to give the activated pentafluorophenyl ester) The reaction mixture was dissolved in 5ml CH2Cl2, and to this solution was added Et3N (332 μL, 2.38 mmol) followed by pentafluorophenyltrifluoroacetate (409 μL, 2.38 mmol). The reaction was stirred 3 h at it, solvent was removed in vacuo, and the product was purified by silica gel chromatography (1.5-3% EtOAc: petroleum ethers; Rf (3% EtOAc) = 0.30) to yield 3 as a clear oil (274 mg, 0.78 mmol, 66%).. 1H NMR (400 MHz, CD3Cl) δ 4.42 (m, 1 H), 4.25 (d, 1 H, J= 15.2), 4.13 (d, 1 H, J= 15.2), 1.5-2.3 (m, 10 H) EI LRMS calcd. for C16H14O3F5 [M+H]+ 349.3, found 349.0. Synthesis ofmaleimide octynes
Figure imgf000054_0002
Compound 16 Compound 17
[00202] Compounds 16 and 17 were synthesized as follows. TEA (1.5 eq) was added to a solution of cyclooctyne-PFP (1 eq.), and amine 13 (1.5 eq.), in CH2Cl2 at rt. The reaction was stirred for 2 h at rt, quenched with H2O, and diluted with CH2Cl2. The organic layer was washed with 1 N HCl (x 3) saturated NaHCO3 (x 3), and brine (x 2), and dried over MgSO4. Chromatography of the crude product (hexanes/EtOAc) yielded the desired product as a colorless oil.
Synthesis of oct-FLAG conjugates
[00203] Octyne-maleimide (1 eq) was added to a solution of FLAG-C (DYKDDDDKC; SEQ
ID NO:3) prepared by standard solid-phase peptide synthesis) (1.2 eq) in 1 :1 DMF:H2O and stirred overnight. The crude reaction mixture was concentrated and purified via reversed- phase HPLC (Varian Dynamax HPLC system with 254-nm detection, on a Microsorb C- 18 preparative column at a flow rate of 20 mL/min). All HPLC runs used the following gradient: 5-25% acetonitrile in water over 10 min, followed by 35-50% acetonitrile in water over 30 min. Mice
[00204] B6D2F1 mice were obtained from The Jackson Laboratory (Bar Harbor, ME). All animals were housed and monitored at the Northwest Animal Facility (Berkeley, CA), and experiments were performed according to guidelines established by the Animal Care and Use Committee at the University of California, Berkeley (protocol number R234-0504B). General protocol for compound administration
[00205] Mice were administered daily doses of Ac4ManNAz (0-300 mg/kg in -200 μL of 70%
DMSO, from a stock solution of 50 mg/mL) intraperitoneally (i.p.) for 7 days. Twenty-four hours after the final Ac4ManNAz injection, mice were injected i.p. with oct-FLAG (0-40 μmol in -200 μL H2O), Phos-FLAG (20 μmol in -200 μL H2O), or vehicle alone (H2O). After 3 h, the mice were anesthetized with isoflurane and sacrificed, and their splenocytes were isolated using a standard protocol. Labeling of splenocyte cell surface azides ex vivo
[00206] Splenocytes from one spleen were suspended in RPMI medium 1640 and distributed among wells of a 96-well V-bottom tissue culture plate (3 wells per treatment, -5 x 105 cells/well). The cells were pelleted (3500 rpm, 3 min), rinsed three times with labeling buffer (1% FBS in PBS, pH 7.4), and incubated with 0-500 μM oct-FLAG in labeling buffer, Phos- FLAG in labeling buffer, or labeling buffer alone. After incubation at rt for 1 h, the cells were rinsed three times with labeling buffer, treated with FITC-α-FLAG (1:900 dilution) or FITC- conjugated mouse IgGi isotype control (1 :200 dilution) in labeling buffer for 30 min on ice, rinsed, and analyzed by flow cytometry. RESULTS
[00207] Splenocyte Labeling of FLAG conjugates: Splenocytes grown in the presence of
Ac4ManNAz were labeled as described in the procedures. The results are shown in Figure 5. Phosphine-FLAG ("Phos-FLAG") serves as a positive control of ligation, and the three synthesized octynes all show bioorthogonality as demonstrated by increased labeling in the present of azide bearing cells. The degree of labeling is consistent with in vitro kinetic data within the octynes. The more hydrophobic octynes (F-oct(MOFO) and Oct (the first reported cyclooctyne) show some background.
[00208] In vivo labeling of mice: Mice were injected with azide labeled sugars as described in the procedures. They were subsequently injected with phosphine-FLAG or ALO-FLAG, sacrificed and their cells were analyzed for the presence of FLAG via flow cytometry. The results are shown in Figure 6. ALO-FLAG, but not F-oct-FLAG or Oct-FLAG, demonstrates the ability to perform this strain-promoted cycloaddition in a living animal.
[00209] While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

CLAIMSWhat is claimed is:
1. A compound of the formula:
Figure imgf000057_0001
where
Ri is a linker group; and
Y is H; a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest.
2. The compound of claim 1, wherein Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, a nitro, and a peptide linker.
3. The compound of claim 1, wherein Ri is an alkyl ester.
4. The compound of claim 1 , wherein Y is a reactive group selected from the group consisting of a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
5. The compound of claim 1, wherein Y is a detectable label, a drug, a toxin, a peptide, a polypeptide, an epitope tag, or a member of a specific binding pair.
6. The compound of claim 5, wherein Y is a fluorophore.
7. A compound of the formula:
Figure imgf000058_0001
wherein: each of X and X' is independently:
(a) H;
(b) one or two halogen atoms (e.g., bromo, chloro, fluoro, iodo);
(c) -W-(CH2)n-Z, wherein n is an integer from 1-4; wherein W, if present, is O, N, or S; and wherein Z is nitro, cyano, sulfonic acid, or a halogen;
(d) -(CH2),,- W-(CH2)m-Z, wherein n and m are each independently 1 or 2; wherein W is O, N, S, or sulfonyl; with the proviso that if W is O, N, or S, then Z is nitro, cyano, or halogen; and with the proviso that if W is sulfonyl, then Z is H; or
(e) -(CH2)n-Z, wherein n is an integer from 1-4; and wherein Z is nitro, cyano, sulfonic acid, or a halogen;
Y is H; a moiety that comprises a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest; and
Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
8. A method for chemoselective modification of a target molecule comprising an azide, the method comprising: reacting an azide of a target molecule with a modified cycloalkyne, the modified cycloalkyne having the formula
Y-Ri-X where
Y is H; a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
X is a cycloalkyne that is substituted with R1; and Ri is a linker; wherein said reacting produces a conjugate between the azide of the target molecule and the modified cycloalkyne.
9. The method of claim 8, wherein Ri is selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
10. The method of claim 8, wherein the target molecule is a sugar.
11. The method of claim 10, wherein the sugar is a substrate of sialic acid biosynthesis.
12. The method of claim 10, wherein the sugar is mannosamine or acetylated mannosamine.
13. The method of claim 8, wherein the target molecule is an amino acid.
14. The method of claim 8, wherein Y is a reactive group selected from the group consisting of a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
15. The method of claim 8, wherein Y comprises a linker group.
16. The method of claim 15, wherein the linker group provides for attachment of a detectable label, a drug, a toxin, a peptide, a polypeptide, a ligand, or a receptor.
17. The method of claim 8, wherein said reacting is performed in aqueous conditions.
18. The method of claim 8, wherein said reacting is performed under physiological conditions.
19. The method of claim 8, wherein the target molecule comprising the azide is expressed on a cell surface.
20. The method of claim 8, wherein X is a cyclooctyne.
21. A method for synthetically modifying a cellular component, the method comprising: introducing an azide moiety into a cellular component, thereby generating an azide- modified cellular component; and contacting the cell comprising the azide-modified cellular component with a reactive partner comprising a modified cycloalkyne, said contacting being under physiological -> conditions; wherein said contacting with said reactive partner results in reaction between the azide group of azide-modified cellular component and the cycloalkyne of the reactive partner, thereby synthetically and covalently modifying the cellular component.
22. The method of claim 21 , wherein cellular component is a polypeptide.
23. The method of claim 21 , wherein the modified cycloalkyne has the formula: Y-Ri-X where
Y is H; a reactive group that facilitates covalent attachment of a molecule of interest; or a molecule of interest;
X is a cycloalkyne that is substituted with Ri ; and
Ri is a linker selected from a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, an amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, an alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro.
24. The method of claim 23, wherein Y is a reactive group selected from a carboxyl, an amine, an ester, a thioester, a sulfonyl halide, an alcohol, a thiol, a succinimidyl ester, an isothiocyanate, an iodoacetamide, a maleimide, and a hydrazine.
25. The method of claim 23, wherein Ri is an alkyl ester.
26. The method of claim 25, wherein the alkyl ester is a methyl ester.
27. The method of.claim 21, wherein said contacting is in vivo.
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US20110213123A1 (en) 2011-09-01
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US8461298B2 (en) 2013-06-11
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