WO1999064847A1 - Electrochemical probes for detection of molecular interactions and drug discovery - Google Patents

Electrochemical probes for detection of molecular interactions and drug discovery Download PDF

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Publication number
WO1999064847A1
WO1999064847A1 PCT/US1999/011848 US9911848W WO9964847A1 WO 1999064847 A1 WO1999064847 A1 WO 1999064847A1 US 9911848 W US9911848 W US 9911848W WO 9964847 A1 WO9964847 A1 WO 9964847A1
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Prior art keywords
binding pair
biological binding
electrochemical
reaction chamber
biological
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Application number
PCT/US1999/011848
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French (fr)
Inventor
Thomas W. Welch
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Xanthon, Inc.
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Publication date
Application filed by Xanthon, Inc. filed Critical Xanthon, Inc.
Priority to AU43185/99A priority Critical patent/AU4318599A/en
Publication of WO1999064847A1 publication Critical patent/WO1999064847A1/en

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54366—Apparatus specially adapted for solid-phase testing
    • G01N33/54373—Apparatus specially adapted for solid-phase testing involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
    • G01N33/5438—Electrodes

Definitions

  • the present invention relates to methods and apparatus for performing electrochemical analyses that depend on specific binding between members of a biological binding pair.
  • the invention provides an electrochemical analysis apparatus for performing amperometric, coulometric and potentiometric or voltammetric analyses for detecting specific binding between a first member of a biological binding pair in solution with a second member of a biological binding pair that is electrochemically labeled.
  • the second member of the biological binding pair is linked to an electrochemical catalyst, preferably an enzyme and most preferably a redox enzyme, in the presence of a substrate for the electrochemical catalyst.
  • apparatus for performing voltammetric analyses of current produced over a range of applied voltages in the presence of electrochemically labeled biologically active binding species are provided by the invention.
  • the invention also provides methods for performing high throughput screening assays for detecting inhibition of specific binding between the members of the biological binding pair for use in drug development, biochemical analysis and protein purification assays.
  • surrogate ligands for the biological binding species of the invention and methods for identifying surrogate ligands from complex biological mixtures including biologically-derived fluids.
  • U.S. Patent No. 5,198,367, issued March 30, 1993 to Aizawa et al. disclosed an amperometric immunoassay.
  • U.S. Patent No. 5,346,832, issued September 13, 1994 to Aizawa et al. disclosed an amperometric immunoassay.
  • Embree et al., 1990, J. Chromatogr. 526: 439-446 describes electrochemical detection of an electrochemically active derivative of digoxin.
  • Devlin et al., 1990, Science 249: 404-406 describes random peptide libraries.
  • Hirai & Varmus, 1990, Molec. Cell. Biol. K): 1307-1318 describes site-directed mutagenesis of src homology domain 3.
  • Lam et al., 1991 , Nature (London) 354: 82-84 describes random peptide libraries. Burrows et al., 1991 , Eur. J. Biochem. 202: 543-549 describes direct electrochemistry of proteins.
  • Wanatabe-Fukunaga et al., 1992, Nature (London) 356: 314-317 describes fas as an apoptotic factor.
  • Phizicky & Fields 1995, Microbiol Rev 59 94-123 describe methods for detecting and analyzing protein-protein interactions.
  • the present invention provides methods and apparatus for performing electrochemical analysis for detecting binding between a biological binding pair. These methods and apparatus are useful for performing direct binding and competition binding experiments for detecting and analyzing compounds capable of inhibiting binding between the biological binding pair, thereby identifying compounds capable of interacting with biologically-active portions of the species comprising the biological binding pair. The methods of the invention are useful for performing rapid, high throughput screening of biologically active compounds for use as drugs that interact with one of the members of the biological binding pair and thereby interfere with or affect its biological function.
  • the invention provides an apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair.
  • the apparatus comprises a first electrode, the electrode comprising a conducting or semiconducting material.
  • the apparatus also comprises a second, reference electrode, and a third, auxiliary electrode.
  • Each of the electrodes is electrically connected to a potentiostat, and the electrodes are all in electrical contact with a reaction chamber containing a solution of an electrochemically reactive liquid.
  • This electrochemically- reactive solution contains a first member of a biological binding pair.
  • the solution further comprises a second member of the biological binding pair, wherein said second member is electrochemically labeled with a chemical species capable of participating in a reduction or oxidation reaction with the electrode under conditions whereby an electrical potential is applied to the electrodes.
  • a current is produced in the apparatus when an electrical potential is applied to the electrodes; this current is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
  • either the first or the second member of the biological binding pair is present in the reaction chamber of the apparatus in concentration excess to the other member of the pair.
  • the first member of the biological binding pair is linked to a particle, most preferably a bead.
  • the electrochemical assay is a voltammetric, amperometric or coulometric assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry.
  • the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof.
  • the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof
  • the first member of the biological binding pair is a first protein or fragment thereof that specifically binds to a second protein
  • the second member of the biological bingmg pair is a hgand, and antigen or a protein that binds to the first member of the biological binding pair
  • the second member of the biological binding pair is a surrogate hgand for the first member of the biological binding pair, having a binding affinity of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar
  • the apparatus of the invention also includes embodiments wherein the apparatus further comprises a multiplicity of each of the electrodes and reaction chambers of the invention, wherein each reaction chamber contains an electrolyte and is m electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus, and each of the electrodes in electrochemical contact with each reaction chamber is elect ⁇ cally connected to a potentiostat
  • the apparatus of the invention also includes embodiments wherein the apparatus further comprises a multiplicity of each of the first and second members of the biological binding pair, wherein cun-ent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular elect ⁇ cal potential applied between the electrodes, wherein the current produced at each particular elect ⁇ cal potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair
  • the second member of the biological binding pair is electrochemically labeled with an organic or inorganic complex comp ⁇ sing a transition metal cation
  • the electrochemical label is a ruthenium complex, preferably a pentaamineruthenium compound such as ⁇ Ru(NH 3 ) 5 Cl ⁇ Cl, Ru(NH 3 ) 6 ⁇ or Ru(NH 3 ) 5 (H 2 O) 2 ⁇ .
  • the electrochemical label is an iron complex, most preferably
  • the invention also provides a kit comprising at least one second member of the biological binding pair, preferably comprising a surrogate ligand having binding specificity for the first member of the biological binding pair characterized by a dissociation constant (K d ) of from about from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar ( ⁇ M), and most preferably from about 1 OnM to about 10 ⁇ M, thus comprising an electrochemical probe.
  • K d dissociation constant
  • said second member of the biological binding pair is provided in an electrochemically labeled embodiment.
  • said second member of the biological binding pair is provided with reagents including an electrochemical label for preparing the electrochemically labeled embodiment by the user.
  • the kit also preferably provides a first member of the biological binding pair specific for the second member of the biological binding pair provided therewith. Additional and optional components of the kits of the invention include buffers, reagents and electrodes as described herein.
  • Methods of using the apparatus of the invention are also provided.
  • a method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to this aspect of the invention is provided.
  • the method comprises the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes of an apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes is electrically connected to a potentiostat; wherein the first reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber contains an electrochemically-labeled second member of the biological binding pair and an unrelated species that does not specifically bind to the second member of the biological binding pair, or the first member of the biological binding pair and an unrelated, electrochemically-labeled species that does not bind to the first member of the biological binding pair
  • the method further comp ⁇ ses the steps of.
  • the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulometric assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • a method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of this aspect of the invention the method composing the steps of a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes being elect ⁇ cally connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains a compound to be tested to determine its ability to inhibit binding of the second member of the biological binding pair to the first member of the biological binding pair
  • the method further comprises the steps of: b) performing an electrochemical assay in each of the first and second reaction chamber
  • the method comprises the steps of a) providing a reaction chamber m electrochemical contact with each of the electrodes of the apparatus according to the invention, wherein each of the electrodes is electrically connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair; and c) comparing the cuoent produced in the electrochemical assay in the presence of the inhibitor to the cuoent produced in the electrochemical assay in the absence of the inhibitor; wherein an inhibitor of
  • Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in the reaction chamber when an electrical potential is applied between the electrodes in the reaction chamber.
  • the level and amount of cuoent produced in the electrochemical assay in the presence of an inhibitor of binding between the members of the biological binding pair is compared with the level and amount of cuoent produced in the electrochemical assay in the reaction chamber in the absence of the inhibitor of binding of the first and second members of the biological binding pair.
  • the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
  • the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber.
  • the inhibitor is added to the reaction chamber together with the second member of the biological binding pair.
  • the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulometric assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry.
  • a method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of this aspect of the invention comp ⁇ sing the steps of a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes being electncally connected to a potentiostat, wherein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains a portion of the complex mixture comp ⁇ smg an inhibitor of binding of the second member of the biological binding pair, the method further comp ⁇ sing the steps of b) performing an electrochemical assay in each of the first
  • the method comp ⁇ ses the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes is elect ⁇ cally connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of a complex mixture comprising an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) comparing the cuoent produced in the electrochemical assay in the presence of the complex mixtuie to the cu
  • the complex mixture comprising the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
  • the complex mixture comp ⁇ sing the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber.
  • the complex mixture comp ⁇ sing the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
  • the electrochemical assays performed using the methods of the invention are voltammet ⁇ c, amperometric or coulomet ⁇ c assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • the method is used to isolate and identify an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair
  • the method comprises the additional steps of chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures, and performing the steps of the method on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair
  • the chemical fractionation includes chemical, biochemical, physical, and immunological methods for fractionation of chemical or biochemical species of inhibitor
  • the second member of a biological binding pair is an electrochemically labeled suoogate ligand characte ⁇ zed by a dissociation constant (K d ) for the first member of the biological binding pair of from about from about 50 picomolar (pM) to about 0 5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar ( ⁇ M), and most preferably from about lOnM to about 10 ⁇ M
  • the apparatus comprises a first electrode, wherein the electrode comp ⁇ ses a conducting or semiconducting surface, a second, reference electrode comp ⁇ sing a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comp ⁇ smg a conducting metal, wherein each of the electrodes is elect ⁇ cally connected to a potentiostat
  • the apparatus further comp ⁇ ses a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith
  • the solution further contains a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is bound to an electrochemical catalyst capable of participating in a reduction/oxidation reaction at the surface of the first electrode in the presence of a substrate for the electrochemical catalyst under conditions whereby an elect ⁇ cal potential is applied to the electrodes, and wherein the electrochemical catalyst
  • either the first or the second member of the biological binding pair is present in the reaction chamber of the apparatus in concentration excess to the other member of the pair
  • the first member of the biological binding pair is linked to a particle, most preferably a bead
  • the electrochemical assay is a voltammet ⁇ c, amperomet ⁇ c or coulomet ⁇ c assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof
  • the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof
  • the first member of the biological binding pair is a first protein or fragment thereof that specifically binds to a second protein
  • the second member of the biological bingmg pair is a ligand, and antigen or a protein that binds to the first member of the biological binding pair
  • first and second members of the biological binding pair e g , receptor/hgand, antigen/antibody, etc
  • the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair, having an affinity of binding of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar ( ⁇ M), and most preferably from about l OnM to about 10 ⁇ M
  • said suoogate ligand is electrochemically labeled, more preferably with a ruthenium compound
  • the electrochemical catalvst bound to the second member of the biological binding pair is an enzyme, most preferably horse radish peroxidase
  • the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus, most preferably a colored product
  • the apparatus of this aspect of the invention also includes embodiments wherein the apparatus further comp ⁇ ses a multiplicity of each of the electrodes and reaction chambers of the invention wherein each reaction chamber contains an electrolyte and is m electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus, and each of the electrodes in electrochemical contact with each reaction chamber is elect ⁇ cally connected to a potentiostat
  • the apparatus of this aspect of the invention also includes embodiments wherein the apparatus further comp ⁇ ses a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular electrical potential applied between the electrodes, wherein the cuoent produced at each particular elect ⁇ cal potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair
  • the second member of the biological binding pair is labeled with an electrochemical catalyst.
  • the electrochemical catalyst is an enzyme, most preferably a redox enzyme capable of catalysis of its substrate to product by an oxidation/reduction mechanism wherein either functional groups on the enzyme or bound cofactors are involved in the oxidation/reduction cycle.
  • the electrochemical catalyst is a peroxidase, for example horse radish peroxidase.
  • said cofactor is provided in the reaction chamber of the apparatus.
  • the apparatus of the invention comprises a second member of the biological binding pair chemically linked with a species, preferably an enzyme, that is capable of being oxidized or reduced at the surface of the first electrode and to participate in cyclic oxidation/reduction reactions at the surface of the electrode m the presence of a third species present m the solution, in embodiments wherein the electrochemical catalyst is an enzyme, the third species is a substrate for the enzyme. As a consequence of these reactions, an observable cuoent is produced in the apparatus of the invention.
  • a species preferably an enzyme
  • This third species cannot be directly oxidized or reduced at the surface of the first electrode
  • specific binding interactions between the members of the biological binding pair are detected by observation of an electrical cuoent.
  • Said elect ⁇ cal cuoent is produced at an electrode potential sufficient to activate (oxidize or reduce) the electrochemical catalyst attached to the second member of the biological binding pair
  • the electrochemical catalyst is reduced by (oxidized by) the first electrode, thereby activating the catalyst for its substrate.
  • the electrode potential permits cycles of oxidation/reduction of the electrochemical catalyst pair, thereby producing a cuoent related to catalysis of the substrate by the electrochemical catalyst.
  • the amount of cuoent produced by specific binding of the members of the biological binding pair is compared to the amount of cuoent produced before addition of the first member of the biological binding pair, or to the amount of cuoent produced upon addition of a known non-bmding first member (thereby providing a negative control).
  • Specificity of binding is determined by compa ⁇ son of the cuoent to that generated in the presence of a known inhibitor of binding. Additional comparisons of the extent, capacity or rate of binding inhibition, activation or competition can be determined by analysis of the extent of produced cuoent m the presence of putative inhibitors, competitors, activators or drug lead candidates, wherein specific details of the performance of such compansons will be understood by those with skill in the art and are more fully disclosed below.
  • the invention also provides a kit comprising at least one second member of the biological binding pair, preferably comp ⁇ sing a suoogate ligand having binding specificity for the first member of the biological binding pair characte ⁇ zed by a dissociation constant (K d ) of from about from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar ( ⁇ M), and most preferably from about 1 OnM to about 10 wM, thus comprising an electrochemical probe
  • said second member of the biological binding pair is provided in an embodiment wherein it is linked to an electrochemical catalyst
  • said second member of the biological binding pair is provided with reagents including an electrochemical catalyst label for preparing the electrochemical catalyst-linked embodiment by the user
  • the kit also provides a first member of the biological binding pair specific for the second member of the biological binding pair provided therewith.
  • kits of the invention include buffers, reagents, substrates for the electrochemical catalyst and electrodes as described herein.
  • Methods of using this embodiment of the apparatus of the invention are also provided.
  • a method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to this aspect of the invention is provided.
  • the method comp ⁇ ses the steps of: a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes of the apparatus being elect ⁇ cally connected to a potentiostat; wherein the each of the reaction chambers contains a substrate for the electrochemical catalyst and wherein the first reaction chamber comprises a first member of the biological binding pair and a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and wherein the second reaction chamber contains a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a chemical species that does not specifically bind to the second member of the biological binding pair, or vv herein the second reaction chamber contains a first member of a biological binding pair and a chemical species that does not specifically bind to the second member of the biological binding pair,
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the first reaction chamber than is produced in the second reaction chamber
  • the method comp ⁇ ses the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to the invention, and wherein each of the electrodes is elect ⁇ cally connected to a potentiostat, and wherein the reaction chamber contains an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing a
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected bv the production of a smaller amount of the detectable product in the second electrochemical assay than is produced m the first electrochemical assay
  • the electrochemical assays performed using the methods of the invention are voltammet ⁇ c, amperometric or coulomet ⁇ c assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • a method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to the invention comp ⁇ ses the steps of a) providing a first reaction chambei in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes of the apparatus being elect ⁇ cally connected to a potentiostat, wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, the method further comp ⁇ sing the steps of b) performing an electrochemical chambei in electrochemical contact with each of the electrodes of the apparatus of the invention,
  • the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the second reaction chamber than is produced in the first reaction chamber
  • the method comprises the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to this aspect of the invention, and wherein each of the electrodes is elect ⁇ cally connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) comparing the cuoent produced in the electrochemical assay in the presence of the inhibitor to the cu
  • the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber. In another prefeoed embodiment, the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber. In yet another prefeoed embodiment, the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the electrochemical assay performed in the presence of the inhibitor than is produced in the electrochemical assay performed m the absence of the inhibitor
  • the electrochemical assays performed using the methods of the invention are voltammet ⁇ c, amperometric or coulomet ⁇ c assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • a third embodiment of the methods of this aspect of the invention is provided a method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of the invention.
  • These methods comprise the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes being electrically connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains a portion of the complex mixture comprising an inhibitor of binding of the second member of the biological binding pair; the method further comprising the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of this aspect of the invention to produce a cuoent in the electrodes of the apparatus; and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in
  • Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in each reaction chamber when an electrical potential is applied between the electrodes in the chamber.
  • the level and amount of cuoent produced by specific binding of the first and second members of the biological binding pair in the first reaction chamber is compared with the level and amount of cuoent produced in the second reaction chamber in the presence of a complex chemical mixture comprising an inhibitor of specific binding.
  • the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the second reaction chamber than is produced m the first reaction chamber
  • a method for screening a complex chemical mixture for an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus comp ⁇ sing the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus wherein each of the electrodes is electrically connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and a substrate for the electrochemical catalyst, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of a complex mixture comp ⁇ sing an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) compa ⁇ ng the cuoent produced
  • Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in the reaction chamber when an elect ⁇ cal potential is applied between the electrodes in the reaction chamber.
  • the level and amount of cuoent produced in a first electrochemical assay in the presence of a complex chemical mixture comprising an inhibitor of specific binding between the members of the biological binding pair is compared with the level and amount of cuoent produced in a second electrochemical assay in the reaction chamber in the absence of a complex chemical mixture comprising an inhibitor of specific binding of the first and second members of the biological binding pair
  • the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
  • the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the electrochemical assay m the presence of a complex mixture comp ⁇ sing an inhibitor of specific binding than is produced in the electrochemical assay in the absence of the complex mixture comp ⁇ sing an inhibitor of specific binding between the members of the biological binding pair
  • the complex mixture comprising the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber In another prefeoed embodiment, the complex mixture comp ⁇ sing the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber In yet another prefeoed embodiment, the complex mixture comprising the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
  • the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulomet ⁇ c assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • the method is used to isolate and identify an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair
  • the method comp ⁇ ses the additional steps of d) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures, and e) performing the steps of the method on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair
  • the chemical fractionation includes chemical, biochemical, physical, and immunological methods for fractionation of chemical or biochemical species of inhibitor
  • the second member of a biological binding pair is an electrochemically labeled suoogate ligand characterized by a dissociation constant (K d ) for the first member of the biological binding pair of from about fiom about 50 picomolar (pM) to about 0 5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolai ( ⁇ M), and most preferably from about 1 OnM to about 10 ⁇ M
  • an electron donor species contained in the reaction chambers of the apparatus of the invention wherein the electron donor species is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode
  • oxidation/reduction of the electrochemical label at the surface of the first electrode is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair
  • Figure 1 is a schematic diagram illustrating the principle of diffusion limits on the rate of interfacial electrochemistry between an electrode surface and an electrochemically active species in solution.
  • Figure 2 is a graph showing cyclic voltammetric analysis of an electrochemically labeled peptide under the conditions described in Example 2.
  • Figure 3 is a graph showing the results of the experiment described in Example 3 and illustrating the decrease in collectable, Faradaic cuoent upon binding of a small, electrochemically labeled, biotinylated peptide to neutravidin.
  • Figure 4 is a graph showing the determination of the effective diffusion coefficent of a small, electochemically labeled, biotinylated peptide free in solution, in the presence of biotin-saturated neutravidin, and bound to a stoichiometric excess of neutravidin as described in Example 3.
  • Figure 5 is a graph illustrating the increase in collectable, Faradaic cuoent observed when a small electrochemically labeled species is displaced from a larger species by competitive binding of an unlabeled species as described in Example 4.
  • Figure 6 is a graph depicting the changes in peak anodic cuoent as a function of added competitor under the conditions described in Example 4.
  • the present invention provides apparatus and methods for detecting specific interactions, particularly including binding interactions, between members of a biological binding pair.
  • biological binding pair is intended to encompass any two biologically-derived or isolated molecules, or any chemical species that specifically interact therewith, that specifically bind with a chemical affinity measured by a dissociation constant of at least 50mM.
  • a biological binding pair proteins that interact with other proteins, including fragments thereof; proteins and peptides; proteins and ligands; proteins and co-factors; proteins and allosteric or cooperative regulators; proteins and nucleic acids; proteins and carbohydrates; antigens and antibodies; lipids, including fatty acids, triglycerides and polar lipids that interact with proteins or peptides; receptors and ligands, particularly cytokines; virus-receptor pairs; enzymes and substrates; and enzymes and inhibitors Also encompassed with this definition are any chemical compound or mixture that interacts with at least one member of a biological binding pair
  • the members of the biological binding pairs of the invention are intended to encompass molecules that are naturally-occur ⁇ ng, synthetic, or prepared by recombinant genetic means or biochemical isolation and extraction means Synthetic embodiments of a member of a biological binding pair will be understood to typically share structural simila ⁇ ty with at least a portion of any naturally-occur ⁇ ng analogue which they resemble
  • the apparatus of the invention comp ⁇ ses a first, conductive or semiconductive electrode
  • mate ⁇ als useful forprepa ⁇ ng the conductive or semiconductive electrodes of the invention include metallically-impregnated glass, such as tm-doped mdium oxide or fluorine-doped tin oxide glass, gold, carbon or platinum
  • the apparatus also includes an auxiliary electrode, comprised of any conducting metal, including for example, platinum (Pt)-w ⁇ re auxiliary electrodes, and a reference electrode, including silver wire electrodes, silver/sih er chloride (Ag/AgCl) reference electrodes, saturated calomel, and others know to those with skill m the art
  • the apparatus comp ⁇ ses one or a multiplicity of reaction chambers, each having one of each of these electrodes, and each of the electrodes being elect ⁇ cally connected to a potentiostat or other device that applies and maintains a constant potential under varying cuoent conditions
  • the term "electrically connected" is intended to mean, inter
  • Inorganic complexes such as Ru 2" 3+ -amme complexes, feoocenes, and osmium- or cobalt-polypy ⁇ dyl complexes are attached to the peptide via histidine or cysteine residues or at the amino terminus.
  • Redox-active organic molecules such as paraquat derivatives and quinones, are attached to peptides by conjugating the redox-active organic moiety via lysine or cysteine residues or at the amino terminus.
  • organic labels or the organic ligands of transition-metal complexes can include reactive substituents that allow direct incorporation of these complexes in the context of automated biopolymer synthesis.
  • prefeoed compounds comprising the second member of the biological binding pair are "suoogate" ligands to the first member of the specific binding pair.
  • the term "suoogate ligand" is intended to define a set of biologically-active compounds that specifically bind to any defined target comp ⁇ sing a first member of a biological binding pair
  • this definition is intended to encompass a variety of ligands of a target, particularly a target protein, comprising the first member of a biological binding pair, including a natural hgand.
  • the suoogate ligands of the invention preferably comprise those ligands that specifically bind to the target protein with a chemical affinity measured by a dissociation constant (K d ) of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar ( ⁇ M), and most preferably from about lOnM to about 10 ⁇ M.
  • K d dissociation constant
  • suoogate ligands are prefeoed because they bind with sufficient affinity that the concentration of the electrochemical label at the surface of the first electrode of the apparatus of the invention is sufficient to produce an expenmentally-detectable cuoent, while at the same time the binding affinity is weak enough to be displaced by competitors and inhibitors at concentrations of these compounds that are economical and can be expe ⁇ mentally achieved.
  • Suoogate ligands therefore provide both the required degree of specificity and the required degree of easy dissociabihty to enable the methods and apparatus of the invention to detect binding inhibition by competitor species.
  • second members of the biological binding pair that are electrochemically-labeled suoogate ligands include, but are not limited to, peptides, nucleic acids, carbohydrates, and small molecules.
  • the peptides are preferably obtained from phage-displayed combinatorial peptide libraries (see co-owned and co-pending U.S. patent application, Serial No. 08/740,671, filed October 21, 1996, incorporated by reference herein) as well as other means, such as synthetic peptides prepared on pins or beads.
  • Peptides and proteins comprising the electrochemical probes and targets of the apparatus and methods of this invention can be prepared by synthetic methods, including solid phase peptide synthesis, biochemical isolation and modification techniques including partial proteolysis, and by recombinant genetic methods understood by those with skill in the art (see Sambrook et al, 1990, Molecular Cloning, 2d ed, Cold Spring Harbor Laboratory Press, N.Y.).
  • An example of a useful electrochemical labeling method is addition of a ruthenium group (Ru(NH 1 ) 5 (OH : ) 2 ⁇ ) to histidine residues within a peptide sequence.
  • Another example of a useful electrochemical labeling method is addition of a feoocene carboxylic acid to side chains of lysine residues via the use of selective deprotection strategies during automated peptide synthesis.
  • Feoocenes are also attractive labels because addition of substituents to the organic cyclopentadienyl- ligands can alter the redox potential by several hundred millivolts, thereby allowing observation of binding of multiple labels in one assay.
  • electrochemical labels can be added to the amino- or carboxyl termini of peptides or protein fragments post-synthetically, or to the reactive side chain thiol groups of a cysteine residue, the hydroxyl group of a serine or threonine residue (or on a carbohydrate moiety), or the amino group of a lysine residue of the peptide.
  • Fmoc derivatives of "unnatural" amino acids such as D- amino acids or amino acid analogues such as ⁇ -aminocaproic acid
  • cobalt or osmium complexes with polypyridyl ligands possessing carboxylic acid substituents can be coupled to the ⁇ -amine of lysine using standard peptide chemistry.
  • Table I Targets for which binding peptides have been identified from combinatorial libraries
  • Urokinase receptor 19 bFGF-R integrin Ilb/IIIa/avB 1 20-23
  • Hsc70 24 tissue factor Vila atrial naturiuretic peptide A receptor fibronectin 25
  • CD 1 -B2M complex 27 tissue-type plasminogen activator 28 core antigen of Hepatitis B virus 29
  • HIV-1 nucleocapsid protein NCp7 30 erythropoietin receptor 31 trypsin 32 chymotrypsin 33 interleukin- 1 receptor 34
  • nucleic acids e.g., RNA and DNA species, including poly- and oligonucleofides
  • aptamers can be electrochemically-labeled with a labeling group at either the 3 ' or 5' termini, or modified nucleotide triphosphate that binds an electrochemical labeling group can be incorporated into oligonucleofides by non-discriminating RNA or DNA polymerases during the in vitro generation of the aptamer.
  • cyclic AMP can be electrochemically-labeled without diminishing binding to protein kinase A, thereby providing a biological binding pair for electrochemical analysis of compounds that affect cAMP binding to protein kinase A.
  • Solutions of electrochemically-reactive liquids useful in the apparatus of the invention include any electrolyte solution at physiologically-relevant ionic strength (equivalent to about 0.15M NaCl) and neutral pH.
  • electrolyte solutions useful with the apparatus of the invention include phosphate buffered saline (PBS), HEPES buffered solutions, and sodium bicarbonate buffered ion solutions.
  • PBS phosphate buffered saline
  • HEPES buffered solutions sodium bicarbonate buffered ion solutions.
  • an electron donor species contained in the reaction chambers of the apparatus of the invention wherein the electron donor species is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode.
  • oxidation/reduction of the electrochemical label at the surface of the first electrode is accompanied by the production of detectable amount of chemilummescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair
  • the term "electron donor species” is intended to encompass any chemical species having a readily-oxidized electron pair, including but not limited to amines (such as t ⁇ ethylamine, tnpropylamme, t ⁇ ethanolamine), phosphmes, arsines and the like
  • the chemilummescence produced by oxidation/reduction of the electrochemical label in the presence of the electron donor species has a wavelength in the visible portion of the electromagnetic spectrum, although the invention encompasses detectable chemilummescence at any wavelength
  • the term "electrochemical assay” is intended to encompass any assay performed m an apparatus of the invention, wherein the oxidation/reduction of an electrochemical label attached to a second member of a biological binding pair is achieved at a first electrode on the invention upon application of an electric potential between the electrodes
  • the electrochemical assays of the invention include but are not limited a voltammetric, amperomet ⁇ c or coulomet ⁇ c assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
  • high-throughput screens of natural product and combinatorial chemical libraries for antagonists of protein-protein interactions Such low molecular weight chemical antagonists of specific protem-protein interactions are of value to the pharmaceutical industry as potential drug leads for developing therapeutic agents
  • each of the reaction chambers or microtitre sample wells in a representative experiment contain discrete combinatorial compounds or purified natural products (such as polyketides or fermentation broth components). After incubating the compounds in the presence of the electrode, voltammetric analysis of the cuoent produced in the reaction chamber is performed.
  • results of these analyses are compared for wells containing the electrochemically-labeled suoogate ligand in the presence and absence of the compound or mixture of compounds to be tested.
  • Compounds that inhibit the binding of the electrochemically-labeled suoogate ligand to the target protein on the electrode surface yield an increased amount of cuoent compared with compounds that do not bind to the target, which show no effect on suoogate ligand binding.
  • appropriate controls for detecting increase in observed cuoent due to target protein denaturation are included in each determination.
  • These controls include testing the target protein in a reaction chamber freshly prepared with a solution comprising an electrolyte and electrochemically-labeled suoogate ligand in the absence of the compounds to be tested, and by testing these compounds with unrelated target proteins.
  • the methods of the invention are practiced on a minimal volume of solution, either on a 96-well microtitre plate whereby 96 electrodes are configured to be utilized simultaneously, or in the context of emerging microfluidic technology.
  • the competition binding assays are performed to detect compounds that affect specific binding between the target protein and the electrochemically-labeled suoogate ligand by causing a confo national change in the target protein.
  • the target protein is first incubated with the electrochemically-labeled suoogate ligand, and then placed in a reaction chamber containing the compound or compounds to be tested.
  • Compounds that bind to an available site on the target and induce a confoonational or allosteric change in the target cause release of the electrochemically-labeled suoogate ligand, and are detected by the production of an increase in the observed cuoent in the reaction chamber as detected, for example, by cyclic voltammetric analysis.
  • appropriate control reactions are performed to detect loss of suoogate ligand binding due to target protein denaturation.
  • the invention also provides methods for measuring the binding affinity of interaction between members of a biological binding pair, such as protein-peptide and protein-protein interactions. These measurements are useful for determining the dissociation constant (K d ) of the interaction between the components of the biological binding pair.
  • K d dissociation constant
  • These methods provide an alternative to existing methods for measuring binding affinities and dissociation constants, such as surface plasmon resonance instruments (e.g., BIAcore*, Pharmacia).
  • the methods of the present invention are advantageous compared with such previously-disclosed technologies because the present methods are more rapid, less costly and require less biological material.
  • the methods of the invention constitute a homogeneous assay whereas the methods known in the prior art require immobilization of one member of the biological binding pair.
  • the methods of the present invention can be practiced using electrochemical probes and electrochemical ligands having molecular weights of 300 daltons or more.
  • the methods known in the prior art require ligands that are at least about 5 kilodaltons (kD) in size, since the signal strength using prior art methods is proportional to the size of the binding ligand.
  • This limitation prevents analysis of binding interaction properties of molecules having molecular weights less than the cutoff threshold, 5kD. This limitation is important, since small molecular weight compounds form a large percentage of potential drug lead compounds.
  • assay conditions using the methods and apparatus of this invention are more permissible than the assay conditions required using the methods of the prior art, including but not limited to conditions of probe concentration, salt concentration and assay performance in the presence of organic solvents.
  • the invention also provides methods and apparatus for determining the binding affinity and chemical "strength" of the interactions between members of a biological binding pair. Knowing the strength of the interaction between two members of a biological binding pair is important for determining whether the interaction has potential as a good target for drug discovery. The ability to detect these interactions with a rapid, inexpensive and convenient assay can greatly accelerate both target validation and screening.
  • the methods of the present invention provide the ability to screen any two members of a biological binding pair for the capacity to specifically bind or otherwise specifically interact.
  • the invention also provides methods for mapping region(s) of interaction between the members of the pair, using various truncated or altered forms of either or both members of the binding pair. For protein-protein interactions, there are several cuoently of interest in drug discovery, that are listed in Table II.
  • protein.-protein interaction methods are provided. Such interactions are difficult to detect or characterize using existing technology.
  • a particular target protein is incubated with an electrochemically- active solution containing an electrochemically-labeled suoogate ligand and a cell extract comprising a protein(s) that specifically interacts with the target protein.
  • binding of the interacting protein instead of the electrochemically-labeled suoogate ligand results in an increased amount of cuoent produced during electrochemical analysis, e.g., cyclic voltammetry.
  • This inventive method for detecting protein-protein interactions is advantageous compared with cuoently-available methods, as illustrated by a comparison with cuoent methods for assaying column fractions during protein purification.
  • the cuoently- available techniques include enzymatic assays of chromatographic column fractions that generate a radioactive product and that are only applicable to proteins having known enzymatic activity.
  • ELIS A assays For proteins with unknown enzymatic activity, ELIS A assays, band shift assays using a radiolabeled target, or co-immunoprecipitations (that require antibodies to a radiolabeled target) are used.
  • ELIS A assays band shift assays using a radiolabeled target, or co-immunoprecipitations (that require antibodies to a radiolabeled target) are used.
  • Each of these methods is time-consuming and tedious, and frequently require the use of radiochemical detection methods that are disadvantageous in terms of safety and regulatory concerns.
  • the methods of the cuoent invention are rapid, specific, and inexpensive.
  • An additional advantage of the electrochemical screening methods of the present invention is that such screening methods are able to detect weak protein-protein interactions that cannot be detected by existing techniques.
  • the methods of the present invention are also applicable to a variety of alternative embodiments of protein purification techniques, including analysis of chromatographic fractions, tissue distribution surveys for the presence of the target binding protein in tissue samples from tumors, for example, and for cell-cycle specific interactions, for example, by using extracts from synchronized cells. Table II Interactions of Interest
  • K-channel src various proteins WW domain containing proteins ptyr proteins SH2 domains, PTB domains, phosphatases
  • RNA RNA binding proteins concanavalin A lectins lipids lipoproteins fatty acids (FA) FA binding proteins steroids steroid hormone receptors cytomegalovirus DNA polymerase polymerase accessory factor
  • the methods and apparatus of the invention are advantageous over the analytical techniques and equipment known in the art for the following reasons.
  • the sensitivity of the methods of the invention permit detection of specific binding interactions between the members of a biological binding pair over 4-5 orders of magnitude of concentration (i.e., 10,000- to 100,000-fold).
  • This invention provides detection methods having the sensitivity of radiochemical detection methods without the health, safety and regulatory concerns that accompany radiochemically-based methods.
  • the invention also affords detection of biological binding interactions with high sensitivity over a wide range of binding affinities.
  • the assays are rapid, inexpensive and are performed in vitro.
  • the reagents used in the practice of the invention i.
  • the electrodes and electrochemically-labeled suoogate ligands are stable and have a relatively long shelf-life compared with, for example, radiochemical reagents.
  • structure-activity relationships can be determined quantitatively, based on the deteonination of changes in binding kinetics observed using cyclic voltammetry, for example.
  • the analyses can be multiplexed, that is, each reaction can be performed in a reaction chamber comprising more than one biological binding pair, wherein the electrochemical label of each of the second members of the binding pair present in the reaction chamber has a different redox potential, so that one or a mixture of potential drug lead compounds can be analyzed for binding to a variety of potential targets.
  • the methods and apparatuses of the invention are amenable to automation, including but not limited to the use of multiwell (such as 96-well microtitre) assay plates and robotic control of electrodes and electrochemical components of the reaction chambers thereof.
  • the sensitivity of the electrochemical assays of the invention permit detection of small amounts of either suoogate ligand, inhibitory compounds, or both, thereby increasing the efficiency of performing assays such as drug screenings.
  • these increases in efficiency result in higher throughput screening, addressing a maj or obstacle to drug development.
  • the invention provides methods for determining dissociation constants for biological binding pair interactions that are more rapid, less expensive and require less sample than known methods (including, for example, equilibrium dialysis, analytical ultracentrifugation, analytical microcalorimetry and
  • the assays provided by the present invention can be performed in the absence of any information on the identity of the binding partner for any target protein or suoogate ligand. This advantage eliminates the requirement that the biological activity of a target protein be known before the protein can be characterized. Eleventh, the assays of the invention are flexible, and allow analysis of binding or competition binding for any biological binding pair. Moreover, either of the binding pairs can be electrochemically-labeled, and under appropriate assay conditions, the diffusion behavior of both members of the biological binding pair in the electrochemically active solution can be observed and characterized.
  • a second member of a biological binding pair preferably a peptide or nucleic-acid suoogate ligand as defined herein, coupled to an electrochemical catalyst comprising an electrochemically activated catalytic species.
  • electrochemical catalysts are enzymes such as glucose oxidase and horseradish peroxidase, which effect the oxidation or reduction of their substrates and are electrochemically reactivated at potentials that are insufficient to effect direct electrochemistry of the substrate.
  • Such enzymes are understood in the art to achieve catalysis by lowering an electrochemical barrier in the redox chemistry of the substrate, so that judicious choice of electrode potential allows selective electrochemical detection of the enzyme-catalyzed reaction in the vicinity of the electrode.
  • several synthetic transition-metal complexes such as those of oxoruthenium(IV), oxoosmium(IV), oxomolybdenum(IV), dioxomolybdenum(VI) and dioxorhenium(VI) are capable of oxidizing or reducing a variety of organic functional groups in a substrate at potentials at which direct electrochemistry is impossible. (For examples, see Stultz et al, 1995, J. Am Chem. Soc.
  • binding of the second member of the biological binding pair to the first member of the biological binding pair results in codiffusion of the electrochemical catalyst and the target protein. Redox reactions between the electrochemical label, the substrate and the electrode results in cuoent flow at the electrode, due to transfer of redox equivalents to the substrate.
  • binding of the suoogate with the first member of a biological binding pair causes the horse radish peroxidase enzyme to be reduced at a rate limited by codiffusion with the target.
  • This reduced form of the enzyme is the active form, which can therefore act catalytically to transfer electrons to hydrogen peroxide in the solution, producing oxygen and water.
  • the enzyme is constitutively reduced by the electrode after each catalytic cycle and, as the entire process is repeated, the binding of the suoogate ligand-enzyme conjugate is detected and quantitated as decrease in cuoent flowing through the electrode to the solution.
  • the amount of cuoent produced is related to the amount and extent of binding between members of the biological binding pair.
  • the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus.
  • the term "detectable product” is intended to encompass a product that can be differentially detected in a solution containing the biological binding pairs, the electrochemical catalyst, and the substrate therefore.
  • a detectable label but not limited thereto is a colored product, that is, a product that absorbs electromagnetic radiation, preferably within that portion of the spectrum comprising visible light, so that the extent of the reaction can be monitored colorimetrically.
  • detectable product any product that can be detected spectrophotometrically, including for example differences in the oxidation state of the NAD T /NADH or NADP7NADPH redox pair, as well as other cofactors including for example riboflavin.
  • the detection of the detectable product can be used as a control for stability of the electrochemical catalyst, the substrate therefor or both, or for depletion of the substrate by the catalyst during the reaction (i.e., saturation), and can be used as a suoogate for cuoent production or as an internal validating control for the observed cuoent produced in the reaction chamber of the apparatus.
  • binding or lack of binding of the conjugate is used to determine the occupancy of the available binding sites by an electrochemically inactive species.
  • this species will be a single drug candidate from a large library of either natural products or combinatorially synthesized molecules. Binding of the drug candidate can be ascertained by at least three related techniques.
  • the first member of the biological binding pair comprising a target can be preincubated with the drug candidate to allow all possible binding interactions between the candidate drug and the first member of the biological binding pair to occur prior to adding the electrochemically-labeled suoogate ligand.
  • the increase in cuoent upon addition of the electrochemically-labeled suoogate ligand when compared with cuoent produced in the absence of the drug candidate, is a measure of the extent of occupancy of the available binding sites of the electrode-immobilized first member of the biological binding pair by the drug.
  • a drug candidate is added concuoently with an electrochemically-labeled suoogate ligand conjugate at different concentrations, and the effect of the presence of the drug candidate on the produced cuoent used to deteonine the inhibition constant of the drug for suoogate ligand binding.
  • the target can be saturated with electrochemically-labeled suoogate ligand prior to the addition of the drug, whereby loss of observable cuoent indicates the capacity of the drug candidate to displace suoogate ligand binding.
  • Electrochemically labeled peptides were prepared using art-recognized techniques (see Yocom et al, 1982, Proc. Natl Acad. Sci. USA 79: 7052 - 7055; Nocera et al, 1984, J. Amer. Chem. Soc. 106: 5145 - 5150).
  • the derivatized peptide EC-1 having the amino acid sequence:
  • An example of such a voltammogram is shown in Figure 2 and was acquired under the following conditions.
  • the reaction chamber of the apparatus of the invention contained 100 ⁇ M ECl peptide as disclosed in Example 1 dissolved in a buffered aqueous solution containing 10 mM Tris, 150 mM NaCl, and 0.05% Tween 20. Cyclic voltammetry was performed where the applied voltage was scanned at 50 mV sX The cyclic voltammogram shown in Figure 2 illustrates the electrochemical behavior of the ECl peptide in the absence of a first member of a biological binding pair that specifically binds to the peptide.
  • the electrochemical analysis apparatus and methods of the invention were used to detect and analyze the specific binding interaction between neutravidin and the biotinylated ECl peptide as follows. Cyclic voltammetry was performed using a solution in the reaction chamber as disclosed in Example 2 at applied voltage scan rates of 25, 50, 100, 200, and 400 mV s "1 . The voltammogram acquired at 50 mV s "1 is shown in Figure 3 (the curve designated "A"). Voltammograms were then acquired under identical peptide and scan-rate conditions in the presence of stoichiometric excesses of neutravidin (shown in Figure 3, the curve designated as "B") and biotin-saturated neutravidin.
  • the effective diffusion coefficients of EC-1 alone was determined to be approximately 3.8 x 10 "7 cm 2 s "1
  • biotin-saturated neutravidin was determined to be approximately 3.4 x 10 "7 cm 2 s "1 , respectively.
  • Electrochemical Assay for Screening Combinatorial Libraries An electrochemical assay of the invention is used to screen combinatorial chemical libraries to detect samples that perturb the electrochemical signal in cyclic voltammetry resulting from the interaction between a target protein and electrochemically-labeled binding peptide.
  • the conditions of the screen must not be easily perturbed, or the voltammetry output diminished thereby.
  • such a screening assay will function over a wide range of pH and salt concentrations, and is not sensitive to common contaminants (such as coupling reagents) that are frequently encountered in combinatorial chemical libraries.
  • Cyclic voltammograms were calculated assuming protein and suoogate ligand concentrations of 100 ⁇ M under conditions of increasing concentrations of a competitor with a target-binding affinity of 50 nM, using a theoretical microfluidic cell with electrode area of 8.5 x 10 "6 cm 2 and using a potential scan rate of 50 mV s "1 .
  • the electrochemical analysis methods of the invention are also useful for determining the K d of the interaction between a protein and specific binding peptides therefor, for example, the Src-SH3 domain and a number of short, proline-rich specific binding peptides.
  • the interaction of the Src SH3 domain with short, proline-rich peptides such as Arg-Pro-Leu-Pro-Pro-Leu-Pro (SEQ ID No.: 2) and Ala-Pro-Pro-Val- Pro-Pro-Arg (SEQ ID No.: 3) have been intensively studied, and K d values have been determined by validated means such as BIAcore 8 (Pharmacia, Upsalla).
  • the K d value for the interaction of GST-Src SH3 and SH3 binding peptides is determined using the electrochemical analysis methods of the invention to provide a compa ⁇ son with a pharmacologically-validated method
  • Solutions of the GST-Src SH3 fusion protein are mixed with electrochemically-labeled species of the prohne- ⁇ ch SH3- domain specific binding peptides shown above
  • Electrochemical signal is generated using cyclic voltammetry as desc ⁇ bed in Examples 2-4 above, and the signal is monitored over time as desc ⁇ bed in Example 4 above
  • Electrochemical signal data are collected at va ⁇ ous concentrations of the peptide, and the electrochemical signal is then used to calculate a K d value for the peptide K d values are also determined using the BIAcore* method as a validated control, and a comparison of the results between the tw o analytical methods used to validate the values determined using the electrochemical analysis assays of the invention
  • the electrochemical analytic methods and apparatus of the invention are used to detect protein peptide interactions in a complex mixture A variety of different target molecules and sources of specific binding peptides are used in these expe ⁇ ments Although it is usually possible to find a suoogate ligand for a protein by using phage display or by screening combinatorial libraries (see co-owned and co-pendmg L S patent application, Se ⁇ al No 08/740,671 , filed on October 31, 1996, incorporated herein by reference), the natural ligand for a protein is more difficult to identify
  • the electrochemical screening assays of the invention provide a relatively simple means for identifying natural ligands
  • the natural ligand for the Src SH3 domain in cell extracts is detected GST-Src SH3 domain fusion protein solutions are incubated with electrochemically-labeled Src-SH3 binding peptide to specifically "load" the SH3 domain with the electrochemically-labeled peptide
  • the solutions are
  • fractions are analyzed for the presence of a compound(s) that can displace binding of the electrochemically-labeled specific binding peptide as detected by cyclic voltammetry. Only those fractions containing such activity are caoied through subsequent steps of the biochemical fractionation. After several such biochemical purification steps, active fractions are analyzed by SDS-polyacrylamide gel electrophoresis to determine the relative purity of the fractions. Microsequencing of homogeneous protein-containing
  • bands is then used to isolate and identify the active protein(s) comprising the fraction having specific peptide displacement activity.
  • the methods of the invention thereby provide a sensitive method for detecting protein-protein interactions from heterogeneous mixtures of biological compounds.
  • the electrochemical analysis assays of the invention are also used to determine functions for orphan receptors isolated and identified by recombinant genetic methods. Frequently, DNA sequences are discovered encoding regions resembling receptor coding domains. When these sequences are discovered, it is presently quite difficult to determine the biological function or activity of the encoded receptor or the natural ligand of these receptors.
  • the extracellular domain of the receptor is expressed and used as the target for screening phage displayed peptide libraries to identify a suoogate ligand.
  • the suoogate ligand is then used in a number of ways. Electrochemical screens of combinatorial libraries are conducted to identify antagonists of the assay. These compounds are then used in model biosystems (for example, mammalian cells transformed with a recombinant expression construct encoding the receptor that express the receptor at the cell surface) to decipher the biological role of the receptor (for example, to determine if the receptor is linked to adenylate cyclase).
  • the suoogate ligands are also used in an electrochemical screening assay to identify the natural ligand.
  • Cell lysates, supernatants or tissue extracts are fractionated and assayed by the electrochemical screening assays of the invention to identify fractions containing a molecule that displaces the labeled suoogate ligand from the electrode-bound target.
  • Protein or peptide ligands isolated thereby can be then identified by sequencing.
  • Small molecule ligands may be identified by mass spectral analysis and other analytical systems.
  • Such assays systems can also be applied to molecules found in biological fluids (such as mammalian brain extracts) to indicate the existence of the natural ligand in such biological extracts.
  • electrochemical analysis assays of the invention is the identification of ligands for the fas receptor (see Hahne et al , 1996, Science 274: 1363; Nagata et al , 1995, Science 267: 1449, Takahashi et al , 1994, Cell 76: 969; Wanatabe-Fukunaga et al , 1992. Nature 356 314).
  • the fas receptor which is expressed in almost all cell types, t ⁇ ggers the apoptotic (programmed cell death) pathway when it is bound by its ligand.
  • the expression of the ligand for the fas receptor is much more restricted Apoptosis is t ⁇ ggered when the ligand on one cell interacts with the receptor on another cell This is a therapeutically useful target since it has recently been demonstrated that the expression of the fas ligand on the surface of some melanoma cells t ⁇ ggers apoptosis m body's immune cells, thereby allowing cancer cells to evade the host immune response
  • the extracellular domain of the fas receptor is expressed for use as a target m phage display to identify a suoogate ligand (using, for example, the methods disclosed in co-owned and co-pending U S patent application. Serial No 08/740.671, filed on October 31 , 1996, incorporated herein by reference) Suoogate ligands so identified are then electrochemically-labeled and incubated with the fas receptor extracellular domain.
  • Plasma cell supernatants are fractionated, and the fractions assayed by cyclic voltammetry and electrochemical screening as described herein to detect those fractions that contain activity capable of displacing the labeled suoogate ligand from the electrode.
  • the fas receptor ligand is detected
  • the function of the fas receptor is identified using the electrochemical analytic methods of the invention. In these assays, the extracellular domain of the fas receptor is used to obtain a suoogate ligand via phage display library as desc ⁇ bed above.
  • the labeled suoogate ligand is then used in an electrochemical screen to identify compounds from a combinato ⁇ al chemical library that displace or compete the labeled hgand from the fas receptor protein.
  • the identified compound may either be an agonist or an antagonist of fas receptor activity.
  • the compound(s) identified in this screen are tested m a model biological system to study receptor function. For example, the compound is added to cells in culture that express the fas receptor and the biological response of the cells observed A receptor antagonist blocks the apoptotic pathway in the presence of the fas ligand.
  • apoptosis provides a sensitive assay that can be used in conjunction with the electrochemical analysis assays of the invention to analyze fas receptor function
  • the electrochemical assay of the invention is used to screen combinato ⁇ al chemical libra ⁇ es to detect samples that perturb a chemilummescence signal resulting from the interaction betw een a target protein and an electrochemically labeled binding peptide
  • a variety of different target molecules and sources of specific binding suoogate ligands are used in these experiments

Abstract

This invention relates to methods and apparatus for performing electrochemical analyses. The invention provides an electrochemical apparatus for performing amperometric, coulometric and potentiometric or voltametric analyses for detecting specific binding between members of a biological binding pair wherein one member is electrochemically labeled or linked to an electrochemical catalyst. Methods for using the apparatus of the invention for performing binding and competition binding assays are provided. The invention also provides methods for performing high throughput screening assays for detecting inhibition of specific binding between the members of the biological binding pair for use in drug development, biochemical analysis and protein purification assays.

Description

ELECTROCHEMICAL PROBES FOR DETECTION OF MOLECULAR INTERACTIONS AND DRUG DISCOVERY
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to methods and apparatus for performing electrochemical analyses that depend on specific binding between members of a biological binding pair. Specifically, the invention provides an electrochemical analysis apparatus for performing amperometric, coulometric and potentiometric or voltammetric analyses for detecting specific binding between a first member of a biological binding pair in solution with a second member of a biological binding pair that is electrochemically labeled. Alternatively, the second member of the biological binding pair is linked to an electrochemical catalyst, preferably an enzyme and most preferably a redox enzyme, in the presence of a substrate for the electrochemical catalyst. In particular, apparatus for performing voltammetric analyses of current produced over a range of applied voltages in the presence of electrochemically labeled biologically active binding species are provided by the invention. Also provided are methods for using the apparatus of the invention for performing binding and competition binding assays, specifically competition binding assays using complex mixtures of biologically active chemical species. The invention also provides methods for performing high throughput screening assays for detecting inhibition of specific binding between the members of the biological binding pair for use in drug development, biochemical analysis and protein purification assays. Also provided are surrogate ligands for the biological binding species of the invention and methods for identifying surrogate ligands from complex biological mixtures including biologically-derived fluids.
2. Background of the Prior Art
U.S. Patent No. 5,534,132, issued July 9, 1996 to Vreeke et al. disclosed an electrode for use in detecting an affinity reaction.
U.S. Patent No. 5,262,035, issued November 16, 1993 to Gregg et al. disclosed a biosensor electrode using redox enzymes.
U.S. Patent No. 5,198,367, issued March 30, 1993 to Aizawa et al. disclosed an amperometric immunoassay. U.S. Patent No. 5,346,832, issued September 13, 1994 to Aizawa et al. disclosed an amperometric immunoassay.
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Yocum et al, 1982, Proc. Natl. Acad. Sci. USA 79: 7052-7055 describes preparation of a pentaamineruthenium derivative of horse heart ferricytochrome c.
Nocera et al., 1984, J. Amer. Chem. Soc. 106: 5145-5150 describes kinetics of intramolecular electron transfer from Ru" to Feιπ in ruthenium-modified cytochrome c.
Wright et al., 1986, Anal. Chem. 58: 2995-2998 describes a homogeneous enzyme-linked immunoassay with electrochemical detection of an electroactive product.
Embree et al., 1990, J. Chromatogr. 526: 439-446 describes electrochemical detection of an electrochemically active derivative of digoxin. Devlin et al., 1990, Science 249: 404-406 describes random peptide libraries.
Hirai & Varmus, 1990, Molec. Cell. Biol. K): 1307-1318 describes site-directed mutagenesis of src homology domain 3.
Lam et al., 1991 , Nature (London) 354: 82-84 describes random peptide libraries. Burrows et al., 1991 , Eur. J. Biochem. 202: 543-549 describes direct electrochemistry of proteins.
Wanatabe-Fukunaga et al., 1992, Nature (London) 356: 314-317 describes fas as an apoptotic factor.
Salamon et al., 1992, Arch. Biochem. Biophys. 299: 193-198 describes direct electrochemistry of thioredoxins and glutathione.
Oldenburg et al., 1992, Proc. Natl. Acad. Sci. USA 89: 5393-5397 describes random peptide libraries.
Scott et al., 1992, Proc. Natl. Acad. Sci. USA 89: 5398-5402 describes random peptide libraries. Hammer et al., 1992, J. Exp. Med. 176: 1007-1013 describes random peptide libraries.
Tsai & Weber, 1992, Anal. Chem. 64: 2897-2903 describes the influence of tyrosine on detection of copper-protein complexes. O'Neil et al , 1992. Proteins Structure, Function & Genetics J.4 509-515 describes GPIIb/IIIa antagonists obtained using phage display libraries
Yu et al , 1992, Science 258 1665-1668 describes si c homology domain 3
Dedman etc// , 1993,./ Bwl Chem 268 23025-23030 describes random peptide libraries
Chen et al , 1993. J Amer Chem Soc U 5 12591-12592 describes src homology domain 3-bιndmg ligands using phage display libraries
Kay et al , 1993, Gene 128 59-65 describes random peptide libraries
Hammer et al , 1993, Cell 14 197-203 describes MHC-bmdmg peptides Rozakis-Adcock et al , 1993, Nature (London) 363 83-85 descπbes src SH3 domains
Salamon et α/ , 1993 Pi oc Natl Acad Sci USA 90 6420-6423 descπbes direct measurement of cyclic current-voltage responses using an electrode comprising an artificial hpid bilayer and integral membrane proteins Qureshi et al , 1993, Biomed Chromatog 7 251 -255 describes methods for detecting HPLC fractions containing biologically active peptides
Okada et α/ , 1993, J Biol Chem 268 18070-18075 describes SH3-deleted src mutants
Koivunen et α/ , 1993, J Biol Chem 268 20205-20210 describes phage display libraries
Koivunen et al , 1993, J Cell Biol Y2Λ 373-380 describes phage display libraries
Hiramatsu et al , 1994, J Biochem 1 15 584-589 describes electrochemical detection of polyamines Suzawa et al , 1994, Anal Chem 66 3889-3894 describes a homogeneous immunoassay with electrochemical detection
Johnston et al , 1994, Inorg Chem 33 6388-6390 descπbes rhenium-mediated electrocatalytic oxidation of DNA at mdium tin-oxide electrodes as a method for voltammetπc detection of DNA cleavage in solution Picksleyetα/ , 1994, Oncogene 9 2523-2529 descπbes binding between p53 and
MDM 2
Fong et al , 1994, Drug Develop Res 33 64-70 describes scanning whole cells with phage display hbraπes Yu et al., 1994, Cell 76: 933-945 describes src homology domain 3 fragments.
Uchida & Kawakishi, 1994, J. Biol. Chem. 269: 2405-2410 describes the identification of oxidized histidine at the active site of Cu, Zn superoxide dismutase.
Biachini & Wild, 1994, Toxicol. Lett. 72: 175-184 describes electrochemical detection of 7-methyldeoxyguanosine.
Cummings etα/., 1994,J. Chromatos. B 653: 192-203 describes electrochemical detection of neuropeptide growth factor antagonists.
Mitton & Trevithick, 1994, Methods Enzymol. 233: 523-539 describes electrochemical detection of HPLC fractions for detecting antioxidant compounds in vertebrate lens.
Daniels & Lane. 1994, J. Molec. Biol. 243: 639-652 describes random peptide libraries.
Sparks et al, 1994, J. Biol. Chem. 269: 23853-23856 describes src homology domain 3 fragments. Cheadle et al. , 1994, J. Biol. Chem. 269: 24034-24039 describes src homology domain 3 fragments.
Rickles et al., 1994, EMBO J. 13: 5598-5604 describes src homology domain 3-binding ligands using phage display libraries.
Iwabuchi et al., 1994, Proc. Natl. Acad. Sci. USA 91_: 6098-6102 describes p53 binding proteins.
Takahashi et al.. 1994. Cell 76: 969-976 describes fas as an apoptotic factor.
Goodson et al, 1994, Proc. Natl. Acad. Sci. USA 9j_: 7129-7133 describes urokinase receptor antagonists obtained using phage display libraries.
Scharfet α/., 1995, Biochem. Biophys. Res. Commun. 209: 1018-1025 describes electrochemical studies on nitrate reductase using a biosensor.
Abrams & Zhao, 1995, J. Biol. Chem. 270: 333-339 describes src homology domain 3.
Ivanenkov et al, 1995, J. Biol. Chem. 270: 14651-14658 describes random peptide libraries. Takenakaetα/., 1995, J. Biol Chem. 210: 19839- 19844 describes phage display libraries.
Martens eta , 1995, J. Biol. Chem. 210: 21 129-21 136 describes random peptide libraries. Dyson & Murray, 1995, Proc. Natl Acad Sci USA 92: 2194-2198 descπbes random peptide libraπes.
Chen & Sudol, 1995. Proc Natl Acad. Sci. USA 92 7819-7823 descπbes src homology domain 3. Nagata & Golstem, 1995, Science 267: 1449-1456 describes/αs as an apoptotic factor.
Saksela et al, 1995, EMBO J. 14: 484-491 describes src homology domain 3.
Sudol et al , 1995, FEBS Lett 369: 67-71 describes src homology domain 3.
Weng et al , 1995, Molec Cell Biol J 5 5627-5634 describes src homology domain 3.
Rickles et al , 1995, Proc Natl Acad Sci USA 92/ 10909-109 3 descπbes src homology domain 3-bιndιng ligands using phage display libraπes
Feng et al , 1995, Proc Natl Acad. Sci USA 92 12408-2415 describes src homology domain 3. Gold et al , 1995, Ann Rev Biochem. (A 763-797 describes aptamers.
Phizicky & Fields, 1995, Microbiol Rev 59 94-123 describe methods for detecting and analyzing protein-protein interactions.
Adey & Kay, 1996, Gene 169' 133-134 descπbes random peptide libraπes.
Sparks et al , 1996, Proc Natl Acad Sci USA 93 1540-1543 describes src homology domain 3 fragments
Yanofsky et al , 1996, Rroc Natl Acad Sci LSA 93 7381-7386 descπbes high affinity interleukin type I antagonists obtained using recombinant peptide libraπes.
Wπghton et al , 1996, Science 273 458-463 describes small peptides isolated from random peptide libraries as mimetics for erythropoietin. Holmes et al, 1996, Science 274:2089-2091 descπbes src SH3 domains.
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SUMMARY OF THE INVENTION
The present invention provides methods and apparatus for performing electrochemical analysis for detecting binding between a biological binding pair. These methods and apparatus are useful for performing direct binding and competition binding experiments for detecting and analyzing compounds capable of inhibiting binding between the biological binding pair, thereby identifying compounds capable of interacting with biologically-active portions of the species comprising the biological binding pair. The methods of the invention are useful for performing rapid, high throughput screening of biologically active compounds for use as drugs that interact with one of the members of the biological binding pair and thereby interfere with or affect its biological function. In a first aspect, the invention provides an apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair. The apparatus comprises a first electrode, the electrode comprising a conducting or semiconducting material. The apparatus also comprises a second, reference electrode, and a third, auxiliary electrode. Each of the electrodes is electrically connected to a potentiostat, and the electrodes are all in electrical contact with a reaction chamber containing a solution of an electrochemically reactive liquid. This electrochemically- reactive solution contains a first member of a biological binding pair. The solution further comprises a second member of the biological binding pair, wherein said second member is electrochemically labeled with a chemical species capable of participating in a reduction or oxidation reaction with the electrode under conditions whereby an electrical potential is applied to the electrodes. In the use of the apparatus, a current is produced in the apparatus when an electrical potential is applied to the electrodes; this current is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair. In prefeπed embodiments, either the first or the second member of the biological binding pair is present in the reaction chamber of the apparatus in concentration excess to the other member of the pair. In preferred embodiments, the first member of the biological binding pair is linked to a particle, most preferably a bead.
In preferred embodiments, the electrochemical assay is a voltammetric, amperometric or coulometric assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry.
In a preferred embodiment, the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof. In another preferred embodiment, the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof In yet another preferred embodiment, the first member of the biological binding pair is a first protein or fragment thereof that specifically binds to a second protein In preferred embodiments, the second member of the biological bingmg pair is a hgand, and antigen or a protein that binds to the first member of the biological binding pair One of ordinary skill in the art will recognize the appropπate choice of first and second members of the biological binding pair (e g , receptor/hgand, antigen/antibody, etc ) In particularly preferred embodiments of the invention, the second member of the biological binding pair is a surrogate hgand for the first member of the biological binding pair, having a binding affinity of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about lOnM to about 10 μM Preferably said surrogate hgand is electrochemically labeled, more preferably with a ruthenium compound
The apparatus of the invention also includes embodiments wherein the apparatus further comprises a multiplicity of each of the electrodes and reaction chambers of the invention, wherein each reaction chamber contains an electrolyte and is m electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus, and each of the electrodes in electrochemical contact with each reaction chamber is electπcally connected to a potentiostat
The apparatus of the invention also includes embodiments wherein the apparatus further comprises a multiplicity of each of the first and second members of the biological binding pair, wherein cun-ent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular electπcal potential applied between the electrodes, wherein the current produced at each particular electπcal potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair In preferred embodiments, the second member of the biological binding pair is electrochemically labeled with an organic or inorganic complex compπsing a transition metal cation In preferred embodiments, the electrochemical label is a ruthenium complex, preferably a pentaamineruthenium compound such as {Ru(NH3)5Cl}Cl, Ru(NH3)6 ~ or Ru(NH3)5(H2O)2τ. In other preferred embodiments, the electrochemical label is an iron complex, most preferably a ferrocene compound, or a cobalt or osmium complex.
The invention also provides a kit comprising at least one second member of the biological binding pair, preferably comprising a surrogate ligand having binding specificity for the first member of the biological binding pair characterized by a dissociation constant (Kd) of from about from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about 1 OnM to about 10 μM, thus comprising an electrochemical probe. In certain embodiments of the kits of the invention, said second member of the biological binding pair is provided in an electrochemically labeled embodiment. In certain other embodiments of the kits of the invention, said second member of the biological binding pair is provided with reagents including an electrochemical label for preparing the electrochemically labeled embodiment by the user. The kit also preferably provides a first member of the biological binding pair specific for the second member of the biological binding pair provided therewith. Additional and optional components of the kits of the invention include buffers, reagents and electrodes as described herein.
Methods of using the apparatus of the invention are also provided. In a first embodiment, a method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to this aspect of the invention is provided. In this embodiment, the method comprises the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes of an apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes is electrically connected to a potentiostat; wherein the first reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber contains an electrochemically-labeled second member of the biological binding pair and an unrelated species that does not specifically bind to the second member of the biological binding pair, or the first member of the biological binding pair and an unrelated, electrochemically-labeled species that does not bind to the first member of the biological binding pair The method further compπses the steps of. b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a current in the electrodes of the apparatus; and c) compaπng the current produced in the electrochemical assay in the first reaction chamber to the current produced in the electrochemical assay in the second reaction chamber wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller current in the first reaction chamber than is produced in the second reaction chamber Specific interaction between the members of the biological binding pair is detected by this compaπson of the electπcal current produced in each of the reaction chambers when an electrical potential is applied between the electrodes in each chamber Specific binding of the first and second members of the biological binding pair in the first reaction chamber produces a lower current output in the first reaction chamber than is produced in the second reaction chamber, where there is no specific interaction between the second member of the biological binding pair and the unrelated species in that chamber, or between the first member of the biological binding pair m the second reaction chamber and the unrelated, electrochemically-labeled species contained in the second reaction chamber In a preferred embodiment, the second member of the biological binding pair is a surrogate hgand for the first member of the biological binding pair In an alternative embodiment of the methods of the invention provided for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair, the method compπses the steps of: a) providing a reaction chamber in electrochemical contact with each of the electrodes of an apparatus of the invention, wherein each of the electrodes is electπcally connected to a potentiostat, and wherein the reaction chamber contains an electrochemically-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair, and b) performing a first electrochemical assay in the reaction chamber to produce a current in the electrodes of the apparatus, and c) adding to the reaction chamber a first member of the biological binding pair that is specifically bound by the electrochemically-labeled second member of the biological binding pair, and d) performing a second electrochemical assay in the reaction chamber to produce a current in the electrodes of the apparatus, and e) compaπng the current produced in the first electrochemical assay to the current produced m the second electrochemical assay, wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller current in the second electrochemical assay than is produced in the first electrochemical assay Specific interaction between the members of the biological binding pair is detected by a compaπson of the electπcal current produced in the reaction chamber when an electπcal potential is applied between the electrodes in the reaction chamber The level and amount ot cuπent produced m the first electrochemical assay in the presence of the second member of the biological binding pair and the absence of the first member of the biological binding pair in the reaction chamber is compared with the level and amount of current produced in the second electrochemical assay in the reaction chamber in the presence of both the first and second members of the biological binding pair In a preferred embodiment, the second member of the biological binding pair is a surrogate hgand for the first member of the biological binding pair
In preferred embodiments, the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulometric assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In a second embodiment of the methods of the invention is provided a method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of this aspect of the invention, the method composing the steps of a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes being electπcally connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains a compound to be tested to determine its ability to inhibit binding of the second member of the biological binding pair to the first member of the biological binding pair The method further comprises the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a current in the electrodes of the apparatus, and c) comparing the current produced in the electrochemical assay in the first reaction chamber to the current produced in the electrochemical assay in the second reaction chamber wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger current in the second reaction chamber than is produced m the first reaction chamber Specific interaction between the members of the biological binding pair is detected by a compaπson of the electrical current produced in the reaction chamber when an electπcal potential is applied between the electrodes in the chamber The level and amount of current produced by specific binding of the first and second members of the biological binding pair in the reaction chamber is compared with the lev el and amount of cuoent produced in the chamber in the presence of an inhibitor of specific binding In a preferred embodiment, the second member of the biological binding pair is a suoogate hgand for the first member of the biological binding pair.
In an alternative embodiment of the methods of the invention provided for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1, the method comprises the steps of a) providing a reaction chamber m electrochemical contact with each of the electrodes of the apparatus according to the invention, wherein each of the electrodes is electrically connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair; and c) comparing the cuoent produced in the electrochemical assay in the presence of the inhibitor to the cuoent produced in the electrochemical assay in the absence of the inhibitor; wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor. In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair.
Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in the reaction chamber when an electrical potential is applied between the electrodes in the reaction chamber. The level and amount of cuoent produced in the electrochemical assay in the presence of an inhibitor of binding between the members of the biological binding pair is compared with the level and amount of cuoent produced in the electrochemical assay in the reaction chamber in the absence of the inhibitor of binding of the first and second members of the biological binding pair. In a prefeoed embodiment, the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber. In another prefeoed embodiment, the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber. In yet another prefeoed embodiment, the inhibitor is added to the reaction chamber together with the second member of the biological binding pair.
In additional prefeoed embodiments, the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulometric assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry. In yet a third embodiment of the methods of the invention is provided a method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of this aspect of the invention, the method compπsing the steps of a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes being electncally connected to a potentiostat, wherein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains a portion of the complex mixture compπsmg an inhibitor of binding of the second member of the biological binding pair, the method further compπsing the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a cuoent in the electrodes of the apparatus, and c) compaπng the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein a complex mixture compπsing an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber Specific interaction between the members of the biological binding pair is detected by a compaπson of the electπcal cuoent produced in each reaction chamber when an electπcal potential is applied between the electrodes in the chamber The level and amount of cuoent produced by specific binding of the first and second members of the biological binding pair in the first reaction chamber is compared with the level and amount of cuoent produced in the second reaction chamber in the presence of a complex chemical mixture compπsing an inhibitor of specific binding In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair.
In an alternative embodiment of the methods of the invention provided for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1 , the method compπses the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, wherein each of the electrodes is electπcally connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of a complex mixture comprising an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) comparing the cuoent produced in the electrochemical assay in the presence of the complex mixtuie to the cuoent produced in the electrochemical assay in the absence of the complex mixture, wherein a complex mixture comprising an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the complex mixture than is produced in the electrochemical assay in the absence of the complex mixture Specific interaction between the members of the biological binding pair is detected by a compaπson of the electπcal cuoent produced in each reaction chamber when an electπcal potential is applied between the electrodes in the chamber The level and amount of cuoent produced by specific binding of the first and second members of the biological binding pair in the first reaction chamber is compared with the level and amount of cuoent produced in the second reaction chamber in the presence of a complex chemical mixture composing an inhibitor of specific binding In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
In a prefeoed embodiment, the complex mixture comprising the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber In another prefeoed embodiment, the complex mixture compπsing the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber In yet another prefeoed embodiment, the complex mixture compπsing the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
In additional prefeoed embodiments, the electrochemical assays performed using the methods of the invention are voltammetπc, amperometric or coulometπc assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In an additional aspect of this embodiment of the invention, the method is used to isolate and identify an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair In this embodiment, the method comprises the additional steps of chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures, and performing the steps of the method on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair In this aspect, it will be recognized that all of the steps of the methods of the invention according to this aspect can be repeatedly performed on chemically fractionated submixtures to yield submixtures compπsing increasingly purified preparations of the inhibitor In prefeoed embodiments, the chemical fractionation includes chemical, biochemical, physical, and immunological methods for fractionation of chemical or biochemical species of inhibitor
In prefeoed embodiments of each of the methods of the invention, the second member of a biological binding pair is an electrochemically labeled suoogate ligand characteπzed by a dissociation constant (Kd) for the first member of the biological binding pair of from about from about 50 picomolar (pM) to about 0 5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about lOnM to about 10 μM
In a second aspect of the invention is provided another apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair In this aspect of the invention, the apparatus comprises a first electrode, wherein the electrode compπses a conducting or semiconducting surface, a second, reference electrode compπsing a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode compπsmg a conducting metal, wherein each of the electrodes is electπcally connected to a potentiostat The apparatus further compπses a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith The solution further contains a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is bound to an electrochemical catalyst capable of participating in a reduction/oxidation reaction at the surface of the first electrode in the presence of a substrate for the electrochemical catalyst under conditions whereby an electπcal potential is applied to the electrodes, and wherein the electrolyte in the reaction chamber further contains a substrate for the electrochemical catalyst In the use of the apparatus of the invention, a cuoent is produced in the apparatus when an electπcal potential is applied to the electrodes and this cuoent is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair
In prefeoed embodiments, either the first or the second member of the biological binding pair is present in the reaction chamber of the apparatus in concentration excess to the other member of the pair In prefeoed embodiments, the first member of the biological binding pair is linked to a particle, most preferably a bead
In prefeoed embodiments, the electrochemical assay is a voltammetπc, amperometπc or coulometπc assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In a prefeoed embodiment, the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof In another prefeoed embodiment, the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof In yet another prefeoed embodiment, the first member of the biological binding pair is a first protein or fragment thereof that specifically binds to a second protein
In prefeoed embodiments, the second member of the biological bingmg pair is a ligand, and antigen or a protein that binds to the first member of the biological binding pair One of ordinary skill in the art will recognize the appropriate choice of first and second members of the biological binding pair (e g , receptor/hgand, antigen/antibody, etc )
In particularly prefeoed embodiments of the invention, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair, having an affinity of binding of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about l OnM to about 10 μM Preferably said suoogate ligand is electrochemically labeled, more preferably with a ruthenium compound
In a prefeoed embodiment, the electrochemical catalvst bound to the second member of the biological binding pair is an enzyme, most preferably horse radish peroxidase In additional prefeoed embodiments, the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus, most preferably a colored product
The apparatus of this aspect of the invention also includes embodiments wherein the apparatus further compπses a multiplicity of each of the electrodes and reaction chambers of the invention wherein each reaction chamber contains an electrolyte and is m electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus, and each of the electrodes in electrochemical contact with each reaction chamber is electπcally connected to a potentiostat The apparatus of this aspect of the invention also includes embodiments wherein the apparatus further compπses a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular electrical potential applied between the electrodes, wherein the cuoent produced at each particular electπcal potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair
As provided in this aspect of the invention, the second member of the biological binding pair is labeled with an electrochemical catalyst. In prefeoed embodiments, the electrochemical catalyst is an enzyme, most preferably a redox enzyme capable of catalysis of its substrate to product by an oxidation/reduction mechanism wherein either functional groups on the enzyme or bound cofactors are involved in the oxidation/reduction cycle. In particularly prefeoed embodiments, the electrochemical catalyst is a peroxidase, for example horse radish peroxidase. In aspects of the apparatus requiπng a oxidation/reduction of a bound cofactor, said cofactor is provided in the reaction chamber of the apparatus.
In the use of this embodiment of the invention, specific binding interactions between the members of the biological binding pair are detected by observation of an electrical cuoent The apparatus of the invention comprises a second member of the biological binding pair chemically linked with a species, preferably an enzyme, that is capable of being oxidized or reduced at the surface of the first electrode and to participate in cyclic oxidation/reduction reactions at the surface of the electrode m the presence of a third species present m the solution, in embodiments wherein the electrochemical catalyst is an enzyme, the third species is a substrate for the enzyme. As a consequence of these reactions, an observable cuoent is produced in the apparatus of the invention. This third species, however, cannot be directly oxidized or reduced at the surface of the first electrode In the use of this embodiment of the invention, specific binding interactions between the members of the biological binding pair are detected by observation of an electrical cuoent. Said electπcal cuoent is produced at an electrode potential sufficient to activate (oxidize or reduce) the electrochemical catalyst attached to the second member of the biological binding pair At said appropπate electrode potential, the electrochemical catalyst is reduced by (oxidized by) the first electrode, thereby activating the catalyst for its substrate. As substrate is consumed, the electrode potential permits cycles of oxidation/reduction of the electrochemical catalyst pair, thereby producing a cuoent related to catalysis of the substrate by the electrochemical catalyst. In the practice of the invention, the amount of cuoent produced by specific binding of the members of the biological binding pair is compared to the amount of cuoent produced before addition of the first member of the biological binding pair, or to the amount of cuoent produced upon addition of a known non-bmding first member (thereby providing a negative control). Specificity of binding is determined by compaπson of the cuoent to that generated in the presence of a known inhibitor of binding. Additional comparisons of the extent, capacity or rate of binding inhibition, activation or competition can be determined by analysis of the extent of produced cuoent m the presence of putative inhibitors, competitors, activators or drug lead candidates, wherein specific details of the performance of such compansons will be understood by those with skill in the art and are more fully disclosed below.
The invention also provides a kit comprising at least one second member of the biological binding pair, preferably compπsing a suoogate ligand having binding specificity for the first member of the biological binding pair characteπzed by a dissociation constant (Kd) of from about from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about 1 OnM to about 10 wM, thus comprising an electrochemical probe In certain embodiments of the kits of the invention, said second member of the biological binding pair is provided in an embodiment wherein it is linked to an electrochemical catalyst In certain other embodiments of the kits of the invention, said second member of the biological binding pair is provided with reagents including an electrochemical catalyst label for preparing the electrochemical catalyst-linked embodiment by the user The kit also provides a first member of the biological binding pair specific for the second member of the biological binding pair provided therewith.
Additional and optional components of the kits of the invention include buffers, reagents, substrates for the electrochemical catalyst and electrodes as described herein.
Methods of using this embodiment of the apparatus of the invention are also provided. In a first embodiment of these methods is provided a method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to this aspect of the invention. In this embodiment, the method compπses the steps of: a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes of the apparatus being electπcally connected to a potentiostat; wherein the each of the reaction chambers contains a substrate for the electrochemical catalyst and wherein the first reaction chamber comprises a first member of the biological binding pair and a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and wherein the second reaction chamber contains a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a chemical species that does not specifically bind to the second member of the biological binding pair, or vv herein the second reaction chamber contains a first member of a biological binding pair and a chemical species that does not specifically bind to the second member of the biological binding pair, bound to an electrochemical catalyst, the method further compπsing the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of the invention to produce a cuoent in the electrodes of the apparatus, and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced m the electrochemical assay m the second reaction chamber wherein binding of the second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the first reaction chamber than is produced in the second reaction chamber Specific interaction between the members of the biological binding pair is detected by this compaπson of the electrical cuoent produced in each of the reaction chambers when an electπcal potential is applied between the electrodes m each chamber Specific binding of the first and second members of the biological binding pair in the first reaction chamber produces a lower cuoent output in the first reaction chamber than is produced in the second reaction chamber, where there is no specific interaction between the second member of the biological binding pair and the unrelated species in that chamber, or between the first member of the biological binding pair and the unrelated, electrochemically-labeled species contained in the second reaction chamber
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the first reaction chamber than is produced in the second reaction chamber In an alternative embodiment of this method for detecting binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to this aspect of the invention, the method compπses the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to the invention, and wherein each of the electrodes is electπcally connected to a potentiostat, and wherein the reaction chamber contains an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing a first electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and c) adding to the reaction chamber a first member of the biological binding pair that is specifically bound by the electrochemical catalyst-labeled second member of the biological binding pair, and d) performing a second electiochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and e) comparing the cuoent produced in the first electrochemical assay to the cuoent produced in the second electrochemical assay, herein binding of the electrochemical catalvst-labeled second member of the biological binding pair with the fust member of the biological binding pair is detected by the production of a smaller cuoent in the second electrochemical assay than is produced in the first electrochemical assay Specific interaction between the members of the biological binding pair is detected by a compaπson of the electπcal cuoent produced in the reaction chamber when an electπcal potential is applied between the electrodes in the reaction chamber The level and amount of cuoent produced m the first electrochemical assay in the presence of the second member of the biological binding pair and the absence of the first member of the biological binding pair in the reaction chamber is compared with the level and amount of cuoent produced in the second electrochemical assay in the reaction chamber in the presence of both the first and second members of the biological binding pair In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected bv the production of a smaller amount of the detectable product in the second electrochemical assay than is produced m the first electrochemical assay
In prefeoed embodiments, the electrochemical assays performed using the methods of the invention are voltammetπc, amperometric or coulometπc assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In a second embodiment of the methods of this aspect of the invention is provided a method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to the invention In this embodiment, the method compπses the steps of a) providing a first reaction chambei in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes of the apparatus being electπcally connected to a potentiostat, wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, the method further compπsing the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus according to this aspect of the invention to produce a cuoent m the electrodes of the apparatus, and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay m the second reaction chamber wherein an inhibitor of binding of the second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber. Specific interaction between the members of the biological binding pair is detected by a compaπson of the electπcal cuoent produced in the reaction chamber when an electπcal potential is applied between the electrodes in the chamber The level and amount of cuoent produced by specific binding of the first and second members of the biological binding pair in the reaction chamber is compared with the level and amount of cuoent produced in the chamber in the presence of an inhibitor of specific binding. In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the second reaction chamber than is produced in the first reaction chamber
In an alternative embodiment of the methods of the invention for identifying an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to the invention, the method comprises the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to this aspect of the invention, and wherein each of the electrodes is electπcally connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) comparing the cuoent produced in the electrochemical assay in the presence of the inhibitor to the cuoent produced in the electrochemical assay in the absence of the inhibitor, wherein an inhibitor of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor.
Specific interaction between the members of the biological binding pair is detected by a compaπson of the electrical cuoent produced in the reaction chamber when an electπcal potential is applied between the electrodes in the reaction chamber The level and amount of cuoent produced in a first electrochemical assay in the presence of an inhibitor of binding between the members of the biological binding pair is compared with the level and amount of cuoent produced in a second electrochemical assay in the reaction chamber in the absence of the inhibitor of binding of the first and second members of the biological binding pair
In a prefeoed embodiment, the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber. In another prefeoed embodiment, the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber In yet another prefeoed embodiment, the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the electrochemical assay performed in the presence of the inhibitor than is produced in the electrochemical assay performed m the absence of the inhibitor In additional prefeoed embodiments, the electrochemical assays performed using the methods of the invention are voltammetπc, amperometric or coulometπc assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In yet a third embodiment of the methods of this aspect of the invention is provided a method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus of the invention. These methods comprise the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus of the invention, each of the electrodes being electrically connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains a portion of the complex mixture comprising an inhibitor of binding of the second member of the biological binding pair; the method further comprising the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of this aspect of the invention to produce a cuoent in the electrodes of the apparatus; and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein a complex mixture comprising an inhibitor of binding of the second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber. Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in each reaction chamber when an electrical potential is applied between the electrodes in the chamber. The level and amount of cuoent produced by specific binding of the first and second members of the biological binding pair in the first reaction chamber is compared with the level and amount of cuoent produced in the second reaction chamber in the presence of a complex chemical mixture comprising an inhibitor of specific binding. In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the second reaction chamber than is produced m the first reaction chamber
In an additional aspect of this embodiment of the invention is provided a method for screening a complex chemical mixture for an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to this aspect of the invention, the method compπsing the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus wherein each of the electrodes is electrically connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and a substrate for the electrochemical catalyst, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of a complex mixture compπsing an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) compaπng the cuoent produced in the electrochemical assay in the presence of the complex mixture to the cuoent produced in the electrochemical assay in the absence of the complex mixture, wherein a complex mixture compπsing an inhibitor of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the complex mixture than is produced m the electrochemical assay in the absence of the complex mixture
Specific interaction between the members of the biological binding pair is detected by a comparison of the electrical cuoent produced in the reaction chamber when an electπcal potential is applied between the electrodes in the reaction chamber. The level and amount of cuoent produced in a first electrochemical assay in the presence of a complex chemical mixture comprising an inhibitor of specific binding between the members of the biological binding pair is compared with the level and amount of cuoent produced in a second electrochemical assay in the reaction chamber in the absence of a complex chemical mixture comprising an inhibitor of specific binding of the first and second members of the biological binding pair In a prefeoed embodiment, the second member of the biological binding pair is a suoogate ligand for the first member of the biological binding pair
In prefeoed embodiments, the substrate for the electrochemical catalyst produces a detectable product, most preferably a colored product, and wherein inhibition of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a larger amount of the detectable product in the electrochemical assay m the presence of a complex mixture compπsing an inhibitor of specific binding than is produced in the electrochemical assay in the absence of the complex mixture compπsing an inhibitor of specific binding between the members of the biological binding pair
In a prefeoed embodiment, the complex mixture comprising the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber In another prefeoed embodiment, the complex mixture compπsing the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber In yet another prefeoed embodiment, the complex mixture comprising the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
In additional prefeoed embodiments, the electrochemical assays performed using the methods of the invention are voltammetric, amperometric or coulometπc assays, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry
In an additional aspect of this embodiment of the invention, the method is used to isolate and identify an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair In this embodiment, the method compπses the additional steps of d) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures, and e) performing the steps of the method on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair In this aspect, it will be recognized that all of the steps of the methods of the invention according to this aspect can be repeatedly performed on chemically fractionated submixtures to yield submixtures compπsing increasingly purified preparations of the inhibitor In prefeoed embodiments, the chemical fractionation includes chemical, biochemical, physical, and immunological methods for fractionation of chemical or biochemical species of inhibitor
In prefeoed embodiments of each of the methods of the invention, the second member of a biological binding pair is an electrochemically labeled suoogate ligand characterized by a dissociation constant (Kd) for the first member of the biological binding pair of from about fiom about 50 picomolar (pM) to about 0 5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolai (μM), and most preferably from about 1 OnM to about 10 μM
In additional prefeoed embodiments of the apparatus and methods of this invention are provided an electron donor species contained in the reaction chambers of the apparatus of the invention, wherein the electron donor species is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode In these embodiments of the apparatus and methods of the invention, oxidation/reduction of the electrochemical label at the surface of the first electrode is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair
Specific prefeoed embodiments of the present invention will become evident from the following more detailed description of certain prefeoed embodiments and the claims BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 is a schematic diagram illustrating the principle of diffusion limits on the rate of interfacial electrochemistry between an electrode surface and an electrochemically active species in solution. Figure 2 is a graph showing cyclic voltammetric analysis of an electrochemically labeled peptide under the conditions described in Example 2.
Figure 3 is a graph showing the results of the experiment described in Example 3 and illustrating the decrease in collectable, Faradaic cuoent upon binding of a small, electrochemically labeled, biotinylated peptide to neutravidin. Figure 4 is a graph showing the determination of the effective diffusion coefficent of a small, electochemically labeled, biotinylated peptide free in solution, in the presence of biotin-saturated neutravidin, and bound to a stoichiometric excess of neutravidin as described in Example 3.
Figure 5 is a graph illustrating the increase in collectable, Faradaic cuoent observed when a small electrochemically labeled species is displaced from a larger species by competitive binding of an unlabeled species as described in Example 4.
Figure 6 is a graph depicting the changes in peak anodic cuoent as a function of added competitor under the conditions described in Example 4.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention provides apparatus and methods for detecting specific interactions, particularly including binding interactions, between members of a biological binding pair. For the purposes of this invention, the term "biological binding pair" is intended to encompass any two biologically-derived or isolated molecules, or any chemical species that specifically interact therewith, that specifically bind with a chemical affinity measured by a dissociation constant of at least 50mM. Specifically included in this definition of a biological binding pair are proteins that interact with other proteins, including fragments thereof; proteins and peptides; proteins and ligands; proteins and co-factors; proteins and allosteric or cooperative regulators; proteins and nucleic acids; proteins and carbohydrates; antigens and antibodies; lipids, including fatty acids, triglycerides and polar lipids that interact with proteins or peptides; receptors and ligands, particularly cytokines; virus-receptor pairs; enzymes and substrates; and enzymes and inhibitors Also encompassed with this definition are any chemical compound or mixture that interacts with at least one member of a biological binding pair The members of the biological binding pairs of the invention are intended to encompass molecules that are naturally-occurπng, synthetic, or prepared by recombinant genetic means or biochemical isolation and extraction means Synthetic embodiments of a member of a biological binding pair will be understood to typically share structural similaπty with at least a portion of any naturally-occurπng analogue which they resemble or are constructed to resemble or mimic These definitions are non-exclusive and non-hmitmg, and are intended to encompass any two biological or chemical species capable of specifically interacting with the defined chemical affinity
The apparatus of the invention compπses a first, conductive or semiconductive electrode Examples of mateπals useful forprepaπng the conductive or semiconductive electrodes of the invention include metallically-impregnated glass, such as tm-doped mdium oxide or fluorine-doped tin oxide glass, gold, carbon or platinum The apparatus also includes an auxiliary electrode, comprised of any conducting metal, including for example, platinum (Pt)-w ιre auxiliary electrodes, and a reference electrode, including silver wire electrodes, silver/sih er chloride (Ag/AgCl) reference electrodes, saturated calomel, and others know to those with skill m the art The apparatus compπses one or a multiplicity of reaction chambers, each having one of each of these electrodes, and each of the electrodes being electπcally connected to a potentiostat or other device that applies and maintains a constant potential under varying cuoent conditions For the purposes of this invention, the term "electrically connected" is intended to mean, inter aha, that the components are connected such that cuoent can flow through the electrodes The apparatus of the invention also provides a second member of a biological binding pair, wherein said second member is electrochemically labeled Electrochemical labels are defined as chemical species, either complexes of transition metals or organic species that are capable of participating in a reduction/oxidation (redox) reaction with the first electrode of the apparatus when an electπcal potential is applied between the electrodes in the reaction chamber of the apparatus Electrochemical labels include catiomc species such as transition metal cations including ruthenium, iron, osmium and cobalt Electrochemical labeling strategies include coordination of one or more nucleophilic atoms of a second member species to form a transition-metal complex For second members of a biological binding pair compπsing a peptide, electrochemical labels are attached to the peptide via reactive functional groups including but not limited to histidine, lysme or cysteine side chains or the ammo terminus. Inorganic complexes such as Ru2" 3+-amme complexes, feoocenes, and osmium- or cobalt-polypyπdyl complexes are attached to the peptide via histidine or cysteine residues or at the amino terminus. Redox-active organic molecules, such as paraquat derivatives and quinones, are attached to peptides by conjugating the redox-active organic moiety via lysine or cysteine residues or at the amino terminus. Alternatively, organic labels or the organic ligands of transition-metal complexes can include reactive substituents that allow direct incorporation of these complexes in the context of automated biopolymer synthesis. The choice of the electrochemical label is optimized for detection of the label to the exclusion of other redox couples present in the solution and for possible interference of the label with the specific binding of the second member of the biological binding pair with a first member of a biological binding pair In the practice of the invention, prefeoed compounds comprising the second member of the biological binding pair are "suoogate" ligands to the first member of the specific binding pair. For the purposes of this invention, the term "suoogate ligand" is intended to define a set of biologically-active compounds that specifically bind to any defined target compπsing a first member of a biological binding pair Although this definition is intended to encompass a variety of ligands of a target, particularly a target protein, comprising the first member of a biological binding pair, including a natural hgand. the suoogate ligands of the invention preferably comprise those ligands that specifically bind to the target protein with a chemical affinity measured by a dissociation constant (Kd) of from about 50 picomolar (pM) to about 0.5 mM, more preferably from about 1 nanomolar (nM) to about 100 micromolar (μM), and most preferably from about lOnM to about 10 μM. Such suoogate ligands are prefeoed because they bind with sufficient affinity that the concentration of the electrochemical label at the surface of the first electrode of the apparatus of the invention is sufficient to produce an expenmentally-detectable cuoent, while at the same time the binding affinity is weak enough to be displaced by competitors and inhibitors at concentrations of these compounds that are economical and can be expeπmentally achieved. Suoogate ligands therefore provide both the required degree of specificity and the required degree of easy dissociabihty to enable the methods and apparatus of the invention to detect binding inhibition by competitor species. Some of the targets for which binding peptides have been identified are listed in Table I.
In the practice of the methods of the invention, second members of the biological binding pair that are electrochemically-labeled suoogate ligands include, but are not limited to, peptides, nucleic acids, carbohydrates, and small molecules. In embodiments of the methods of the invention using peptides as second members of the biological binding pair, the peptides are preferably obtained from phage-displayed combinatorial peptide libraries (see co-owned and co-pending U.S. patent application, Serial No. 08/740,671, filed October 21, 1996, incorporated by reference herein) as well as other means, such as synthetic peptides prepared on pins or beads. Such peptides that contain only naturally-occuoing amino acids must be electrochemically-labeled, because they lack sufficient redox potential under the voltage conditions tolerated by the first member of the biological binding pair. Peptides and proteins comprising the electrochemical probes and targets of the apparatus and methods of this invention can be prepared by synthetic methods, including solid phase peptide synthesis, biochemical isolation and modification techniques including partial proteolysis, and by recombinant genetic methods understood by those with skill in the art (see Sambrook et al, 1990, Molecular Cloning, 2d ed, Cold Spring Harbor Laboratory Press, N.Y.).
An example of a useful electrochemical labeling method is addition of a ruthenium group (Ru(NH1)5(OH:)2^) to histidine residues within a peptide sequence.
Another example of a useful electrochemical labeling method is addition of a feoocene carboxylic acid to side chains of lysine residues via the use of selective deprotection strategies during automated peptide synthesis. Feoocenes are also attractive labels because addition of substituents to the organic cyclopentadienyl- ligands can alter the redox potential by several hundred millivolts, thereby allowing observation of binding of multiple labels in one assay. Alternatively, electrochemical labels can be added to the amino- or carboxyl termini of peptides or protein fragments post-synthetically, or to the reactive side chain thiol groups of a cysteine residue, the hydroxyl group of a serine or threonine residue (or on a carbohydrate moiety), or the amino group of a lysine residue of the peptide. In addition, Fmoc derivatives of "unnatural" amino acids (such as D- amino acids or amino acid analogues such as ε-aminocaproic acid) that can be incorporated during peptide synthesis can be used. For example, cobalt or osmium complexes with polypyridyl ligands possessing carboxylic acid substituents can be coupled to the ε-amine of lysine using standard peptide chemistry. Table I. Targets for which binding peptides have been identified from combinatorial libraries
Targets References
Streptavidin 1, 2, 3
HLA-DR 4, 5 concanavalin A 6, 7 calmodulin 8, 9
S100 10 p53 1 1
SH3 domains 12-18
Urokinase receptor 19 bFGF-R integrin Ilb/IIIa/avB 1 20-23
Hsc70 24 tissue factor Vila atrial naturiuretic peptide A receptor fibronectin 25
E-selectin 26
CD 1 -B2M complex 27 tissue-type plasminogen activator 28 core antigen of Hepatitis B virus 29
HIV-1 nucleocapsid protein NCp7 30 erythropoietin receptor 31 trypsin 32 chymotrypsin 33 interleukin- 1 receptor 34 References: 1. Devlin et al, 1990, Science 249: 404; 2. Lam et al, 1991 , Nature 354:
82; 3. Fowlkes, 1993, Gene 128: 59; 4. Hammer et al, 1992, J. Exp. Med. 116: 1007; 5. Hammer et al, 1993, Cell 74: 197; 6. Scott et al., 1992, Proc. Natl. Acad. Sci. USA 89: 5398; 7. Oldenburg et al, 1992, Proc. Natl. Acad. Sci. USA 89: 5393; 8. Dedman et al, 1993, J. Biol. Chem. 268: 23025; 9. Adey et al, 1996, Gene 169: 133; 10. Ivanenkov et α/., 1995, J. Biol. Chem. 210: 14651 ; 11. Daniels et al, 1994, J. Mol Biol.
243: 639; 12. Sparks et al, 1996, Proc. Natl. Acad. Sci. USA 93: 1540; 13. Sparks etal, 1994, J. Biol. Chem. 269: 23853; 14. Cheadle et al, 1994, J. Biol Chem. 269: 24034; 15. Rickles et al, 1994, EMBOJ. U: 5598; 16. Rickles et al, 1995, Proc. Natl. Acad. Sci. USA 92: 10909; 17. Chen et al, 1993, J. Amer. Chem. Soc. U5: 12591 ; 18. Yu et al, 1994, Cell 76: 933; 19. Goodson et al, 1994, Proc. Natl. Acad. Sci. USA 9Λ : 7129;
20. O'Neill et al, 1992, Proteins 14: 509; 21. Fong et al., 1994, DrugDev. Res. 33: 64; 22. Koivunen et al, 1993, J Biol Chem. 268: 20205; 23. Koivunen et al, 1993, J. Cell Biol. 124: 373; 24. Takenaka et al, 1995, J. Biol Chem. 19839; 25. J. Cell Biol. 130: 1189; 26. Martens et al, 1995, J. Biol. Chem. 270: 21129; 27. Science 269: 223; 28. Proc. Natl. Acad. Sci. USA 92: 7627; 29. Dyson et al, 1995, Proc. Natl. Acad. Sci. USA
92: 2194; 30. FEBSLett. 361: 85; 31. Wrighton et al, 1996, Science 273: 458; 32. Fang et al, 1996, Biochem. Biophys. Res. Commun. 220: 53; 33. J. Chromatography 711: 1 19; 34. Yanofsky et al, 1996, Proc. Natl. Acad. Sci. USA 93: 7381. In addition, a variety of non-peptide suoogate ligands can be adapted to this electrode system. For example, nucleic acids (e.g., RNA and DNA species, including poly- and oligonucleofides) that specifically bind to a target molecule can be obtained from combinatorial nucleic acid libraries; these molecules have been termed "aptamers" (as disclosed in Gold et al, 1995, Ann. Rev. Biochem. 64: 763). Such aptamers can be electrochemically-labeled with a labeling group at either the 3 ' or 5' termini, or modified nucleotide triphosphate that binds an electrochemical labeling group can be incorporated into oligonucleofides by non-discriminating RNA or DNA polymerases during the in vitro generation of the aptamer. Finally, certain small molecules can be electrochemically-labeled in a way that does not destroy their binding activity. For example, cyclic AMP (cAMP) can be electrochemically-labeled without diminishing binding to protein kinase A, thereby providing a biological binding pair for electrochemical analysis of compounds that affect cAMP binding to protein kinase A.
Solutions of electrochemically-reactive liquids (also termed electrolyte solutions herein) useful in the apparatus of the invention include any electrolyte solution at physiologically-relevant ionic strength (equivalent to about 0.15M NaCl) and neutral pH. Nonlimiting examples of electrolyte solutions useful with the apparatus of the invention include phosphate buffered saline (PBS), HEPES buffered solutions, and sodium bicarbonate buffered ion solutions. In the practice of the methods of the invention, when an appropriate potential is applied to the electrode, electrons are transfeoed to or from the electrochemical label from or to the electrode. The efficiency of electron transfer is proportional to the square root of the species' diffusion coefficient which, in turn, is inversely proportional to the species' radius. Therefore, codiffusion of the suoogate ligands with the larger target protein slows the frequency with which the electrochemical labels encounter the electrode with the result that less cuoent is produced. This schema is illustrated in Figure 1.
In prefeoed embodiments of the apparatus and methods of this invention are provided an electron donor species contained in the reaction chambers of the apparatus of the invention, wherein the electron donor species is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode. In these embodiments of the apparatus and methods of the invention, oxidation/reduction of the electrochemical label at the surface of the first electrode is accompanied by the production of detectable amount of chemilummescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair For the purpose of this invention, the term "electron donor species" is intended to encompass any chemical species having a readily-oxidized electron pair, including but not limited to amines ( such as tπethylamine, tnpropylamme, tπethanolamine), phosphmes, arsines and the like Preferably, the chemilummescence produced by oxidation/reduction of the electrochemical label in the presence of the electron donor species has a wavelength in the visible portion of the electromagnetic spectrum, although the invention encompasses detectable chemilummescence at any wavelength
The invention provides methods of using the apparatus described herein to perform electrochemical assays For the purposes of this invention, the term "electrochemical assay" is intended to encompass any assay performed m an apparatus of the invention, wherein the oxidation/reduction of an electrochemical label attached to a second member of a biological binding pair is achieved at a first electrode on the invention upon application of an electric potential between the electrodes In prefeoed embodiments, the electrochemical assays of the invention include but are not limited a voltammetric, amperometπc or coulometπc assay, most preferably cyclic voltammetry, chronoamperometry, or chronocoulometry In one application of the methods of the invention are provided high-throughput screens of natural product and combinatorial chemical libraries for antagonists of protein-protein interactions Such low molecular weight chemical antagonists of specific protem-protein interactions are of value to the pharmaceutical industry as potential drug leads for developing therapeutic agents In the practice of these methods of the invention, a target protein compπsing a first member of a biological binding pair is dissolved in an appropπate electrolyte The first electrode is placed in a reaction chamber of the apparatus of the invention, preferably a microtiter plate well, said reaction chamber containing the target protein, an electrochemically-labeled suoogate ligand. and a compound or mixture of compounds to be tested for the ability to inhibit binding of the suoogate ligand to the target protein (It will be understood that fragments of biologically-active proteins retaining the specific binding properties thereof are also encompassed withm the scope of the target proteins of the electrodes of the invention ) For example, each of the reaction chambers or microtitre sample wells in a representative experiment contain discrete combinatorial compounds or purified natural products (such as polyketides or fermentation broth components). After incubating the compounds in the presence of the electrode, voltammetric analysis of the cuoent produced in the reaction chamber is performed. The results of these analyses are compared for wells containing the electrochemically-labeled suoogate ligand in the presence and absence of the compound or mixture of compounds to be tested. Compounds that inhibit the binding of the electrochemically-labeled suoogate ligand to the target protein on the electrode surface yield an increased amount of cuoent compared with compounds that do not bind to the target, which show no effect on suoogate ligand binding. In the practice of this invention, appropriate controls for detecting increase in observed cuoent due to target protein denaturation are included in each determination. These controls include testing the target protein in a reaction chamber freshly prepared with a solution comprising an electrolyte and electrochemically-labeled suoogate ligand in the absence of the compounds to be tested, and by testing these compounds with unrelated target proteins. Optimally, the methods of the invention are practiced on a minimal volume of solution, either on a 96-well microtitre plate whereby 96 electrodes are configured to be utilized simultaneously, or in the context of emerging microfluidic technology.
Alternatively, the competition binding assays are performed to detect compounds that affect specific binding between the target protein and the electrochemically-labeled suoogate ligand by causing a confo national change in the target protein. In these embodiments of the methods of the invention, the target protein is first incubated with the electrochemically-labeled suoogate ligand, and then placed in a reaction chamber containing the compound or compounds to be tested. Compounds that bind to an available site on the target and induce a confoonational or allosteric change in the target cause release of the electrochemically-labeled suoogate ligand, and are detected by the production of an increase in the observed cuoent in the reaction chamber as detected, for example, by cyclic voltammetric analysis. As above, appropriate control reactions are performed to detect loss of suoogate ligand binding due to target protein denaturation.
The invention also provides methods for measuring the binding affinity of interaction between members of a biological binding pair, such as protein-peptide and protein-protein interactions. These measurements are useful for determining the dissociation constant (Kd) of the interaction between the components of the biological binding pair. These methods provide an alternative to existing methods for measuring binding affinities and dissociation constants, such as surface plasmon resonance instruments (e.g., BIAcore*, Pharmacia). The methods of the present invention are advantageous compared with such previously-disclosed technologies because the present methods are more rapid, less costly and require less biological material. In addition the methods of the invention constitute a homogeneous assay whereas the methods known in the prior art require immobilization of one member of the biological binding pair. In addition, the methods of the present invention can be practiced using electrochemical probes and electrochemical ligands having molecular weights of 300 daltons or more.
In contrast, the methods known in the prior art require ligands that are at least about 5 kilodaltons (kD) in size, since the signal strength using prior art methods is proportional to the size of the binding ligand. This limitation prevents analysis of binding interaction properties of molecules having molecular weights less than the cutoff threshold, 5kD. This limitation is important, since small molecular weight compounds form a large percentage of potential drug lead compounds. In addition, assay conditions using the methods and apparatus of this invention are more permissible than the assay conditions required using the methods of the prior art, including but not limited to conditions of probe concentration, salt concentration and assay performance in the presence of organic solvents.
The invention also provides methods and apparatus for determining the binding affinity and chemical "strength" of the interactions between members of a biological binding pair. Knowing the strength of the interaction between two members of a biological binding pair is important for determining whether the interaction has potential as a good target for drug discovery. The ability to detect these interactions with a rapid, inexpensive and convenient assay can greatly accelerate both target validation and screening. The methods of the present invention provide the ability to screen any two members of a biological binding pair for the capacity to specifically bind or otherwise specifically interact. The invention also provides methods for mapping region(s) of interaction between the members of the pair, using various truncated or altered forms of either or both members of the binding pair. For protein-protein interactions, there are several cuoently of interest in drug discovery, that are listed in Table II.
In yet another embodiment of the methods of the invention are provided methods for detecting specific binding and other interactions between members of biological binding pairs in complex mixtures of chemical and biochemical molecules. In one embodiment, protein.-protein interaction methods are provided. Such interactions are difficult to detect or characterize using existing technology. Using the methods of the present invention, a particular target protein is incubated with an electrochemically- active solution containing an electrochemically-labeled suoogate ligand and a cell extract comprising a protein(s) that specifically interacts with the target protein. As described with other embodiments of competition binding experiments using the methods of the invention, binding of the interacting protein instead of the electrochemically-labeled suoogate ligand results in an increased amount of cuoent produced during electrochemical analysis, e.g., cyclic voltammetry.
This inventive method for detecting protein-protein interactions is advantageous compared with cuoently-available methods, as illustrated by a comparison with cuoent methods for assaying column fractions during protein purification. The cuoently- available techniques include enzymatic assays of chromatographic column fractions that generate a radioactive product and that are only applicable to proteins having known enzymatic activity. For proteins with unknown enzymatic activity, ELIS A assays, band shift assays using a radiolabeled target, or co-immunoprecipitations (that require antibodies to a radiolabeled target) are used. Each of these methods is time-consuming and tedious, and frequently require the use of radiochemical detection methods that are disadvantageous in terms of safety and regulatory concerns.
In contrast, the methods of the cuoent invention are rapid, specific, and inexpensive. An additional advantage of the electrochemical screening methods of the present invention is that such screening methods are able to detect weak protein-protein interactions that cannot be detected by existing techniques. The methods of the present invention are also applicable to a variety of alternative embodiments of protein purification techniques, including analysis of chromatographic fractions, tissue distribution surveys for the presence of the target binding protein in tissue samples from tumors, for example, and for cell-cycle specific interactions, for example, by using extracts from synchronized cells. Table II Interactions of Interest
Molecule 1 Molecule 2 fibronectin integrin antigen antibody calmodulin -20 effector molecules tubulin microtubule associated proteins actin actin binding proteins, Dnase I p53 MDM2 cdk cyclin, p21 ras raf fos jun
TBP RNA polymerases
Sos Grb2 p53 p53BP2
K-channel src various proteins WW domain containing proteins ptyr proteins SH2 domains, PTB domains, phosphatases
UGI UDG regulatory subunit PKA catalytic subunit PKA enhancer elements enhancer binding proteins
DNA transcription factors
RNA RNA binding proteins concanavalin A lectins lipids lipoproteins fatty acids (FA) FA binding proteins steroids steroid hormone receptors cytomegalovirus DNA polymerase polymerase accessory factor
BPTI trypsin
Rb E2F, E 1 A, SV40 T antigen
References: Iwabuchi et al, 1994, Proc. Natl Acad. Sci. USA 9J_: 6098; Holmes et al, 1996, Science 274: 2089; Rozakis-Adcock et al, 1993, Nature 363: 83; Phizicky et al, 1995, Microbiol. Rev. 59: 94; Chan et al, 1996, EMBO J. 15: 1045; Chen et al, 1995, Proc. Natl. Acad. Sci. USA 92: 7819; Sudol et al, 1995, FEBS Lett. 369: 67.
The methods and apparatus of the invention are advantageous over the analytical techniques and equipment known in the art for the following reasons. First, the sensitivity of the methods of the invention permit detection of specific binding interactions between the members of a biological binding pair over 4-5 orders of magnitude of concentration (i.e., 10,000- to 100,000-fold). This invention provides detection methods having the sensitivity of radiochemical detection methods without the health, safety and regulatory concerns that accompany radiochemically-based methods. The invention also affords detection of biological binding interactions with high sensitivity over a wide range of binding affinities. Second, the assays are rapid, inexpensive and are performed in vitro. Third, the reagents used in the practice of the invention (i. e., the electrodes and electrochemically-labeled suoogate ligands) are stable and have a relatively long shelf-life compared with, for example, radiochemical reagents. Fourth, structure-activity relationships can be determined quantitatively, based on the deteonination of changes in binding kinetics observed using cyclic voltammetry, for example. Fifth, the analyses can be multiplexed, that is, each reaction can be performed in a reaction chamber comprising more than one biological binding pair, wherein the electrochemical label of each of the second members of the binding pair present in the reaction chamber has a different redox potential, so that one or a mixture of potential drug lead compounds can be analyzed for binding to a variety of potential targets. Sixth, the methods and apparatuses of the invention are amenable to automation, including but not limited to the use of multiwell (such as 96-well microtitre) assay plates and robotic control of electrodes and electrochemical components of the reaction chambers thereof. Seventh, the sensitivity of the electrochemical assays of the invention permit detection of small amounts of either suoogate ligand, inhibitory compounds, or both, thereby increasing the efficiency of performing assays such as drug screenings. Eighth, these increases in efficiency result in higher throughput screening, addressing a maj or obstacle to drug development. Ninth, the invention provides methods for determining dissociation constants for biological binding pair interactions that are more rapid, less expensive and require less sample than known methods (including, for example, equilibrium dialysis, analytical ultracentrifugation, analytical microcalorimetry and
BIAcore®-analysis). Tenth, the assays provided by the present invention can be performed in the absence of any information on the identity of the binding partner for any target protein or suoogate ligand. This advantage eliminates the requirement that the biological activity of a target protein be known before the protein can be characterized. Eleventh, the assays of the invention are flexible, and allow analysis of binding or competition binding for any biological binding pair. Moreover, either of the binding pairs can be electrochemically-labeled, and under appropriate assay conditions, the diffusion behavior of both members of the biological binding pair in the electrochemically active solution can be observed and characterized.
In these embodiments of the apparatus of the invention are also comprised a second member of a biological binding pair, preferably a peptide or nucleic-acid suoogate ligand as defined herein, coupled to an electrochemical catalyst comprising an electrochemically activated catalytic species. Examples of such electrochemical catalysts are enzymes such as glucose oxidase and horseradish peroxidase, which effect the oxidation or reduction of their substrates and are electrochemically reactivated at potentials that are insufficient to effect direct electrochemistry of the substrate. Such enzymes are understood in the art to achieve catalysis by lowering an electrochemical barrier in the redox chemistry of the substrate, so that judicious choice of electrode potential allows selective electrochemical detection of the enzyme-catalyzed reaction in the vicinity of the electrode. Also, several synthetic transition-metal complexes such as those of oxoruthenium(IV), oxoosmium(IV), oxomolybdenum(IV), dioxomolybdenum(VI) and dioxorhenium(VI) are capable of oxidizing or reducing a variety of organic functional groups in a substrate at potentials at which direct electrochemistry is impossible. (For examples, see Stultz et al, 1995, J. Am Chem. Soc. 117: 2520; Cheng et al, \995, JAm. Chem. Soc. 117: 2970, Neyhart et al. 1993, J. Am Chem. Soc. U5: 4423; Schultz et al, 1993, J. Am Chem. Soc. U5: 4244; Thorp et al, 1989, Inorg. Chem. 28: 889). In the use of this embodiment of the invention, binding of the second member of the biological binding pair to the first member of the biological binding pair results in codiffusion of the electrochemical catalyst and the target protein. Redox reactions between the electrochemical label, the substrate and the electrode results in cuoent flow at the electrode, due to transfer of redox equivalents to the substrate. For example, using a suoogate ligand linked chemically to horseradish peroxidase, binding of the suoogate with the first member of a biological binding pair causes the horse radish peroxidase enzyme to be reduced at a rate limited by codiffusion with the target. This reduced form of the enzyme is the active form, which can therefore act catalytically to transfer electrons to hydrogen peroxide in the solution, producing oxygen and water. The enzyme is constitutively reduced by the electrode after each catalytic cycle and, as the entire process is repeated, the binding of the suoogate ligand-enzyme conjugate is detected and quantitated as decrease in cuoent flowing through the electrode to the solution. Thus, under the appropriate conditions of substrate concentration and applied potential at the electrode, the amount of cuoent produced is related to the amount and extent of binding between members of the biological binding pair.
In particularly prefeoed embodiments of this aspect of the invention, the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus. For the purposes of this invention, the term "detectable product" is intended to encompass a product that can be differentially detected in a solution containing the biological binding pairs, the electrochemical catalyst, and the substrate therefore. Exemplary of a detectable label, but not limited thereto is a colored product, that is, a product that absorbs electromagnetic radiation, preferably within that portion of the spectrum comprising visible light, so that the extent of the reaction can be monitored colorimetrically. Also within the meaning of the term "detectable product" is any product that can be detected spectrophotometrically, including for example differences in the oxidation state of the NADT/NADH or NADP7NADPH redox pair, as well as other cofactors including for example riboflavin. In this aspect, the detection of the detectable product can be used as a control for stability of the electrochemical catalyst, the substrate therefor or both, or for depletion of the substrate by the catalyst during the reaction (i.e., saturation), and can be used as a suoogate for cuoent production or as an internal validating control for the observed cuoent produced in the reaction chamber of the apparatus.
In another application of the invention, binding or lack of binding of the conjugate is used to determine the occupancy of the available binding sites by an electrochemically inactive species. Typically, this species will be a single drug candidate from a large library of either natural products or combinatorially synthesized molecules. Binding of the drug candidate can be ascertained by at least three related techniques. In a first embodiment, the first member of the biological binding pair comprising a target can be preincubated with the drug candidate to allow all possible binding interactions between the candidate drug and the first member of the biological binding pair to occur prior to adding the electrochemically-labeled suoogate ligand. The increase in cuoent upon addition of the electrochemically-labeled suoogate ligand, when compared with cuoent produced in the absence of the drug candidate, is a measure of the extent of occupancy of the available binding sites of the electrode-immobilized first member of the biological binding pair by the drug. In a second embodiment, a drug candidate is added concuoently with an electrochemically-labeled suoogate ligand conjugate at different concentrations, and the effect of the presence of the drug candidate on the produced cuoent used to deteonine the inhibition constant of the drug for suoogate ligand binding. In a third embodiment, the target can be saturated with electrochemically-labeled suoogate ligand prior to the addition of the drug, whereby loss of observable cuoent indicates the capacity of the drug candidate to displace suoogate ligand binding. Those of ordinary skill will recognize the utility of these methods for characterizing the binding and inhibitory properties of drug candidates for any biological binding pair of interest. Additional features of the invention are more fully illustrated in the following
Examples. These Examples illustrate certain aspects of the above-described method and advantageous results. These Examples are shown by way of illustration and not by way of limitation.
EXAMPLE 1
Preparation of Electrochemically Labeled Peptides
Electrochemically labeled peptides were prepared using art-recognized techniques (see Yocom et al, 1982, Proc. Natl Acad. Sci. USA 79: 7052 - 7055; Nocera et al, 1984, J. Amer. Chem. Soc. 106: 5145 - 5150). In one example, the derivatized peptide EC-1, having the amino acid sequence:
Lys(ε-biotin)-Ser-Lvs(ε-feooceneacetic acid)-Ser-NH,
(SEQ ID No.: 1) was synthesized as follows. The first (underlined) lysine incorporated was protected as an α-Fmoc-, ε-Boc- derivative. After removal of the Boc- group, feooceneacetic acid was coupled to the ε-amine via standard benzotriazolyl-N-oxy- tris(dimethylamino)phosphonium hexafluorophosphate/ hydroxy-benzotriazole (BOP/HOBt) chemistry. The remainder of the peptide was synthesized via standard procedures. EXAMPLE 2 Cyclic Voltammetry
Cyclic voltammograms were collected using a BAS 100B potentiostat/galvanostat (BAS, West Lafayette, IN) with a single compartment voltammetric cell equipped with a glassy carbon (GC) working electrode (area = 0.032 cm2), platinum (Pt)-wire auxiliary electrode and silver/silver chloride (Ag/AgCl) reference electrode (see Johnston etal, 1994, Inorg. Chem. 33: 6388-6390). An example of such a voltammogram is shown in Figure 2 and was acquired under the following conditions. The reaction chamber of the apparatus of the invention contained 100 μM ECl peptide as disclosed in Example 1 dissolved in a buffered aqueous solution containing 10 mM Tris, 150 mM NaCl, and 0.05% Tween 20. Cyclic voltammetry was performed where the applied voltage was scanned at 50 mV sX The cyclic voltammogram shown in Figure 2 illustrates the electrochemical behavior of the ECl peptide in the absence of a first member of a biological binding pair that specifically binds to the peptide.
EXAMPLE 3 Electrochemical Assay for Detecting Specific Binding
The electrochemical analysis apparatus and methods of the invention were used to detect and analyze the specific binding interaction between neutravidin and the biotinylated ECl peptide as follows. Cyclic voltammetry was performed using a solution in the reaction chamber as disclosed in Example 2 at applied voltage scan rates of 25, 50, 100, 200, and 400 mV s"1. The voltammogram acquired at 50 mV s"1 is shown in Figure 3 (the curve designated "A"). Voltammograms were then acquired under identical peptide and scan-rate conditions in the presence of stoichiometric excesses of neutravidin (shown in Figure 3, the curve designated as "B") and biotin-saturated neutravidin. These results showed that the presence of neutravidin resulted in binding between the neutravidin and the biotinylated ECl peptide, and that this binding reduced the cuoents observed in the cyclic voltammograms. This reduction in the observed cuoents was used to deteonine the effective diffusion coefficients of the peptide-neutravidin complexes formed in the reaction chamber. The effective diffusion coefficient of the peptide under these conditions was calculated via a plot of peak anodic cuoent versus the square root of scan rate according to the Randles-Sevcik equation : ip = 269000n3/2v"2CADl/2 where i is the peak cuoent, n is the number of electrons transfeoed, v is the square root of scan rate in V s"', C is concentration in moles/cm3, A is electrode area in cm2, and D is the diffusion coefficient in cm2 s"1. These plots are shown in Figure 4. The effective diffusion coefficients of EC-1 alone was determined to be approximately 3.8 x 10"7 cm2 s"1, and in the presence of biotin-saturated neutravidin was determined to be approximately 3.4 x 10"7 cm2 s"1, respectively. These results were consistent with experimental expectations, since the neutravidin-biotin binding affinity is sufficiently high that dissociation of neutravidin-biotin and complex formation between the freed neutravidin and biotinylated EC-1 peptide was considered highly unlikely. In the presence of neutravidin, the diffusion coefficient calculated from the observed cuoent was reduced to approximately 6.8 x 10"8 cm2 s"1, consistent with a loss of approximately 50 percent of the Faradaic cuoent. These results demonstrated that the peptide codiffused with the 60 kD neutravidin protein only when specific interaction of the biotin label of the EC-1 peptide with the biotin-binding site of neutravidin occuoed. These results thus demonstrated that specific binding between the first member of a biological binding pair (neutravidin) with an electrochemically-labeled second member of a biological binding pair (the EC-1 peptide) could be detected using the methods and apparatus of the invention, and that the observed cuoent reduction could be used to characterize the biological binding pair.
EXAMPLE 4 Electrochemical Assay for Screening Combinatorial Libraries An electrochemical assay of the invention is used to screen combinatorial chemical libraries to detect samples that perturb the electrochemical signal in cyclic voltammetry resulting from the interaction between a target protein and electrochemically-labeled binding peptide. For the electrochemical assay to be useful for screening libraries of chemical compounds for compounds that disrupt the target : peptide interaction, the conditions of the screen must not be easily perturbed, or the voltammetry output diminished thereby. Optimally, such a screening assay will function over a wide range of pH and salt concentrations, and is not sensitive to common contaminants (such as coupling reagents) that are frequently encountered in combinatorial chemical libraries.
To evaluate the validity of the electrochemical analysis assay for screening combinatorial libraries, theoretical cyclic voltammograms were calculated using the BAS DigiSim cyclic voltammetry computer simulation software. The mathematical model assumes a target protein with a diffusion coefficient of 2.0 x 10" cm2 s"1 bound to an electrochemically-labeled suoogate ligand which, unbound, has a diffusion coefficient of 4.0 x 10"6 cm2 s"' . Binding of the suoogate ligand and protein is governed by a dissociation constant of 1.0 x 1 'b M and the binding reaction rate constant is fixed at a diffusion-controlled value of l .Ox 109 M"1 s"' . Cyclic voltammograms were calculated assuming protein and suoogate ligand concentrations of 100 μM under conditions of increasing concentrations of a competitor with a target-binding affinity of 50 nM, using a theoretical microfluidic cell with electrode area of 8.5 x 10"6 cm2 and using a potential scan rate of 50 mV s"1.
The cyclic voltammograms are shown in Figure 5; a plot of peak anodic cuoent versus concentration of added competitor (Figure 6) demonstrates that the suoogate ligand is displaced from the target at inhibitor concentrations of -10 to 100 μM, consistent with stoichiometric displacement of the suoogate ligand by a higher-affinity species.
EXAMPLE 5
Electrochemical Analysis for Determining the Ktl for a Known Protein: Peptide
Interaction
The electrochemical analysis methods of the invention are also useful for determining the Kd of the interaction between a protein and specific binding peptides therefor, for example, the Src-SH3 domain and a number of short, proline-rich specific binding peptides. The interaction of the Src SH3 domain with short, proline-rich peptides such as Arg-Pro-Leu-Pro-Pro-Leu-Pro (SEQ ID No.: 2) and Ala-Pro-Pro-Val- Pro-Pro-Arg (SEQ ID No.: 3) have been intensively studied, and Kd values have been determined by validated means such as BIAcore8 (Pharmacia, Upsalla). On average, these peptides have been shown to bind to the Src SH3 domain with aKd of 5μM. These data provide a solid basis for comparison of the ability of the electrochemical assay of the invention to provide an accurate Kd value for the same interaction.
The Kd value for the interaction of GST-Src SH3 and SH3 binding peptides is determined using the electrochemical analysis methods of the invention to provide a compaπson with a pharmacologically-validated method Solutions of the GST-Src SH3 fusion protein are mixed with electrochemically-labeled species of the prohne-πch SH3- domain specific binding peptides shown above Electrochemical signal is generated using cyclic voltammetry as descπbed in Examples 2-4 above, and the signal is monitored over time as descπbed in Example 4 above Electrochemical signal data are collected at vaπous concentrations of the peptide, and the electrochemical signal is then used to calculate a Kd value for the peptide Kd values are also determined using the BIAcore* method as a validated control, and a comparison of the results between the tw o analytical methods used to validate the values determined using the electrochemical analysis assays of the invention
EXAMPLE 6 Electrochemical Analysis for Detecting Protein:Peptide Interactions in Complex
Mixtures
The electrochemical analytic methods and apparatus of the invention are used to detect protein peptide interactions in a complex mixture A variety of different target molecules and sources of specific binding peptides are used in these expeπments Although it is usually possible to find a suoogate ligand for a protein by using phage display or by screening combinatorial libraries (see co-owned and co-pendmg L S patent application, Seπal No 08/740,671 , filed on October 31, 1996, incorporated herein by reference), the natural ligand for a protein is more difficult to identify The electrochemical screening assays of the invention provide a relatively simple means for identifying natural ligands To demonstrate this aspect of the electrochemical analytic methods of the invention, the natural ligand for the Src SH3 domain in cell extracts is detected GST-Src SH3 domain fusion protein solutions are incubated with electrochemically-labeled Src-SH3 binding peptide to specifically "load" the SH3 domain with the electrochemically-labeled peptide The solutions are then incubated with whole cell extracts from about 107 - 10s HeLa cells and cyclic voltammetry performed Data analysis is performed to determine the extent of increase in the electrochemical signal resulting from displacement of the electrochemically-labeled peptide by compound(s) present in the HeLa cell extract The cell extract is then fractionated using conventional biochemical fractionation techniques, including a variety of chromatographic methods (such as anion exchange chromatography using DEAE Sepharose, cation exchange chromatography using carboxymethyl Sepharose, and size exclusion chromatography using Sephadex and Sepharose). After each fractionation, fractions are analyzed for the presence of a compound(s) that can displace binding of the electrochemically-labeled specific binding peptide as detected by cyclic voltammetry. Only those fractions containing such activity are caoied through subsequent steps of the biochemical fractionation. After several such biochemical purification steps, active fractions are analyzed by SDS-polyacrylamide gel electrophoresis to determine the relative purity of the fractions. Microsequencing of homogeneous protein-containing
"bands" is then used to isolate and identify the active protein(s) comprising the fraction having specific peptide displacement activity. The methods of the invention thereby provide a sensitive method for detecting protein-protein interactions from heterogeneous mixtures of biological compounds. The electrochemical analysis assays of the invention are also used to determine functions for orphan receptors isolated and identified by recombinant genetic methods. Frequently, DNA sequences are discovered encoding regions resembling receptor coding domains. When these sequences are discovered, it is presently quite difficult to determine the biological function or activity of the encoded receptor or the natural ligand of these receptors. For an unknown receptor sequence, the extracellular domain of the receptor is expressed and used as the target for screening phage displayed peptide libraries to identify a suoogate ligand. The suoogate ligand is then used in a number of ways. Electrochemical screens of combinatorial libraries are conducted to identify antagonists of the assay. These compounds are then used in model biosystems (for example, mammalian cells transformed with a recombinant expression construct encoding the receptor that express the receptor at the cell surface) to decipher the biological role of the receptor (for example, to determine if the receptor is linked to adenylate cyclase).
The suoogate ligands are also used in an electrochemical screening assay to identify the natural ligand. Cell lysates, supernatants or tissue extracts are fractionated and assayed by the electrochemical screening assays of the invention to identify fractions containing a molecule that displaces the labeled suoogate ligand from the electrode-bound target. Protein or peptide ligands isolated thereby can be then identified by sequencing. Small molecule ligands may be identified by mass spectral analysis and other analytical systems. Such assays systems can also be applied to molecules found in biological fluids (such as mammalian brain extracts) to indicate the existence of the natural ligand in such biological extracts. An example of such use of the electrochemical analysis assays of the invention is the identification of ligands for the fas receptor (see Hahne et al , 1996, Science 274: 1363; Nagata et al , 1995, Science 267: 1449, Takahashi et al , 1994, Cell 76: 969; Wanatabe-Fukunaga et al , 1992. Nature 356 314). The fas receptor, which is expressed in almost all cell types, tπggers the apoptotic (programmed cell death) pathway when it is bound by its ligand. The expression of the ligand for the fas receptor is much more restricted Apoptosis is tπggered when the ligand on one cell interacts with the receptor on another cell This is a therapeutically useful target since it has recently been demonstrated that the expression of the fas ligand on the surface of some melanoma cells tπggers apoptosis m body's immune cells, thereby allowing cancer cells to evade the host immune response
The extracellular domain of the fas receptor is expressed for use as a target m phage display to identify a suoogate ligand (using, for example, the methods disclosed in co-owned and co-pending U S patent application. Serial No 08/740.671, filed on October 31 , 1996, incorporated herein by reference) Suoogate ligands so identified are then electrochemically-labeled and incubated with the fas receptor extracellular domain.
Plasma cell supernatants are fractionated, and the fractions assayed by cyclic voltammetry and electrochemical screening as described herein to detect those fractions that contain activity capable of displacing the labeled suoogate ligand from the electrode. After a series of fractionations by conventional chromatographic techniques, the fas receptor ligand is detected In addition, the function of the fas receptor is identified using the electrochemical analytic methods of the invention. In these assays, the extracellular domain of the fas receptor is used to obtain a suoogate ligand via phage display library as descπbed above. The labeled suoogate ligand is then used in an electrochemical screen to identify compounds from a combinatoπal chemical library that displace or compete the labeled hgand from the fas receptor protein. The identified compound may either be an agonist or an antagonist of fas receptor activity. The compound(s) identified in this screen are tested m a model biological system to study receptor function. For example, the compound is added to cells in culture that express the fas receptor and the biological response of the cells observed A receptor antagonist blocks the apoptotic pathway in the presence of the fas ligand. while a receptor agonist mimics the fas ligand and results in stimulation of the apoptotic pathway Thus, detection of apoptosis provides a sensitive assay that can be used in conjunction with the electrochemical analysis assays of the invention to analyze fas receptor function
EXAMPLE 7
Electochemiluminescence Detection of Codiffusion of Members of a Biological Binding Pair
The electrochemical assay of the invention is used to screen combinatoπal chemical libraπes to detect samples that perturb a chemilummescence signal resulting from the interaction betw een a target protein and an electrochemically labeled binding peptide A variety of different target molecules and sources of specific binding suoogate ligands are used in these experiments
Although it is accurate to descπbe an electrochemical cuoent as a sum of ohmic, capacitive, and Faradaic components, it can be in practice difficult to account accurately and precisely for the relativ e contributions from each source An advantageous feature of some electrochemical reactions is the production of a photon from a luminescent product If the rate of the electrochemical reaction is governed by diffusion, then it becomes possible to measure this diffusion rate as a function of the quantity of light emitted For example, oxidation of both a tπsbipyπdme ruthenium (II) complex and tπethanolamme occurs at a potential of +1 0 V versus a Ag/AgCl reference electrode The two oxidized products then react to yield a luminescent ruthenium (II) species
Because the bimolecular rate constant is a function of the sum of the diffusion coefficients of the two species, the yield of photons is a direct measure of these diffusion coefficients Thus, if the ruthenium complex is attached to the suoogate hgand, codiffusion with the larger member of the biological binding pair will result in a decrease in the signal from electrochemiluminescence In this embodiment of electrochemical drug screening assays as provided by the invention, compounds that displace the suoogate ligand from the target will effect faster diffusion of the prelummescent species resulting in a larger amount of photons emitted It should be understood that the foregoing disclosure emphasizes certain specific embodiments of the invention and that all modifications or alternatives equivalent thereto are within the spirit and scope of the invention as set forth in the appended claims.

Claims

What is claimed is:
1. An apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair, the apparatus comprising a first electrode, wherein the electrode comprises a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, a third, auxiliary electrode comprising a conducting metal wherein each of the electrodes is electrically connected to a potentiostat, and wherein the apparatus further comprises a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith, the solution further containing a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode under conditions whereby an electrical potential is applied to the electrodes wherein a cuoent is produced in the apparatus when an electrical potential is applied to the electrodes and wherein the cuoent is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
2. The apparatus of claim 1 wherein the first member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the second member of the biological binding pair.
3. The apparatus of claim 1 wherein the second member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the first member of the biological binding pair.
4. The apparatus of claim 1 wherein the first member of the biological binding pair is linked to a particle.
5. An apparatus according to claim 1 , wherein the electrochemical assay is a voltammetπc, amperometric or coulometπc assay
6. An apparatus according to claim 5, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
7. An apparatus according to claim 1, wherein the apparatus further comprises a multiplicity of each of the electrodes and a multiplicity of reaction chambers, wherein each reaction chamber contains an electrolyte solution and is in electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus
8. An apparatus according to claim 1 , wherein the apparatus further compπses a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular electrical potential applied betw een the electrodes, wherein the cuoent produced at each particular electπcal potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
9 An apparatus according to claim 1, wherein the second member of the biological binding pair is electrochemically labeled with a transition metal complex.
10 An apparatus according to claim 9, wherein the transition metal complex contains a transition metal ion that is ruthenium, cobalt, iron or osmium.
11. An apparatus according to claim 1 , wherein the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof and the second member of the biological binding pair is a ligand that specifically binds to the receptor protein.
12. An apparatus according to claim 1 , wherein the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof and the second member of the biological binding pair is an antigen that specifically binds to the antibody.
13 An apparatus according to claim 1, wherein the first member of the biological binding pair is a first protein or fragment thereof and the second member of the biological binding pair is a second protein or fragment thereof that specifically binds to the first protein.
14 A kit for using the apparatus of Claim 1 to perform an electrochemical analysis, wherein the kit comprises a first member of a biological binding pair, a second member of the biological binding pair, an electrochemical label and a reagent for electrochemically labeling the second member of the biological binding pair with the electrochemical label
15 A kit for using the apparatus of Claim 1 to perform an electrochemical analysis, wherein the kit comprises a first member of a biological binding pair, and an electrochemically labeled second member of the biological binding pair
16 An electrochemically labeled suoogate ligand comprising a second member of a biological binding pair having a binding affinity of from about 1 nanomolar (nM) to about 100 micromolar (μM) for a first member of a biological binding pair.
17 An electrochemically labeled suoogate ligand according to claim 16, labeled with a transition metal complex
18 An electrochemically labeled suoogate ligand according to claim 17, wherein the transition metal is a ruthenium complex, a cobalt complex, an iron complex or an osmium complex
19. A method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1 , the method comprising the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to claim 1 , and a second reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to claim 1, wherein each of the electrodes is electrically connected to a potentiostat; wherein the first reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber contains an electrochemically-labeled second member of the biological binding pair and an unrelated species that does not specifically bind to the second member of the biological binding pair, or the first member of the biological binding pair and an unrelated, electrochemically-labeled species that does not bind to the first member of the biological binding pair; the method further comprising the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a cuoent in the electrodes of the apparatus; and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber. wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the first reaction chamber than is produced in the second reaction chamber
20. A method for detecting binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1 , the method comprising the steps of: a) providing a reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to claim 1 , wherein each of the electrodes is electπcally connected to a potentiostat, and wherein the reaction chamber contains an electrochemically-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair, and b) performing a first electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and c) adding to the reaction chamber a first member of the biological binding pair that is specifically bound by the electrochemically-labeled second member of the biological binding pair, and d) performing a second electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and e) comparing the cuoent produced m the first electrochemical assay to the cuoent produced in the second electrochemical assay, wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the second electrochemical assay than is produced in the first electrochemical assay
21 The method of Claim 19 wherein the electrochemical assay is a voltammetπc. amperometric or coulometπc assay
22 The method of Claim 19, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
23 The method of Claim 20 wherein the electrochemical assay is a voltammetπc, amperometπc or coulometπc assay
24 The method of Claim 20, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
25 A method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1 , the method comprising the steps of: a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus according to claim 1 , and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 1 , wherein each of the electrodes being electπcally connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains an inhibitoi of binding of the second member of the biological binding pair to the first member of the biological binding pair; the method further comprising the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a cuoent in the electrodes of the apparatus; and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber
26. A method for identifying an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1 , the method compπsing the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 1 , wherein each of the electrodes is electπcally connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) comparing the cuoent produced in the electrochemical assay in the presence of the inhibitor to the cuoent produced m the electrochemical assay in the absence of the inhibitor, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor
27 A method accoiding to claim 26 wherein the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber
28 A method according to claim 26 wherein the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber
29 A method according to claim 26 wherein the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
30 The method of Claim 25, wherein the electrochemical assay is a voltammetπc, amperometric or coulometric assay
31 The method of Claim 25, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
32 The method of Claim 26 wherein the electrochemical assay is a voltammetπc, amperometric or coulometric assay 33 The method of Claim 26, wherein the electrochemical assay is cyclic v oltammetry, chronoamperometry, or chronocoulometry
34 A method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1, the method compπsing the steps of a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 1, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 1 , wherein each of the electrodes being electrically connected to a potentiostat. w herein each of the reaction chambers contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and wherein the second reaction chamber further contains a portion of the complex mixture compπsing an inhibitor of binding of the second member of the biological binding pair, the method further comprising the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 1 to produce a cuoent in the electrodes of the apparatus, and c) compaπng the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein a complex mixture having an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber
35 A method for screening a complex chemical mixture for an inhibitor of binding of an electrochemically labeled second member of a biological binding pair with a first member of a biological binding pair using an apparatus according to claim 1, the method compπsing the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 1 , wherein each of the electrodes is electrically connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus presence and absence of a complex mixture compπsing an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) compaπng the cuoent produced m the electrochemical assay in the presence of the complex mixture to the cuoent produced in the electrochemical assay in the absence of the complex mixture, wherein a complex mixture having an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the complex mixture than is produced in the electrochemical assay in the absence of the complex mixture
36 A method according to claim 35 wherein the complex mixture compπsing the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber
37 A method according to claim 35 wherein the complex mixture compπsing the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber
38 A method according to claim 35 wherein the complex mixture compπsing the inhibitor is added to the reaction chamber together with the second member of the biological binding pair 39 A method according to claim 19 wherein the second member of the biological binding pair is an electrochemically labeled suoogate ligand
40 A method according to claim 20 wherein the second member of the biological binding pair is an electrochemically labeled suoogate hgand
41 A method according to claim 25 wherein the second member of the biological binding pair is an electrochemically labeled suoogate ligand
42 A method according to claim 26 wherein the second member of the biological binding pair is an electrochemically labeled suoogate ligand
43 A method according to claim 34 wherein the second member of the biological binding pair is an electrochemically labeled suoogate ligand
44 A method according to claim 35 wherein the second member of the biological binding pair is an electrochemically labeled suoogate ligand
45 The method of Claim 34 wherein the electrochemical assay is a voltammetπc, amperometric or coulometπc assay
46 The method of Claim 34, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
47 The method of Claim 35, wherein the electrochemical assay is a voltammetπc, amperometπc or coulometπc assay
48 The method of Claim 35, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry
50 A method according to 34 compπsing the additional steps of d) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures; and e) performing steps (a) through (c) of the method of claim 34 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair.
51. A method according to 35 compπsing the additional steps of b) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures, and c) performing steps (a) through (c) of the method of claim 35 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair
52 An apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair, the apparatus compπsing a first electrode, wherein the electrode compπses a conducting or semiconducting surface, a second, reference electrode compπsing a conducting metal in contact with an aqueous electrolyte solution, a third, auxiliary electrode compπsing a conducting metal wherein each of the electrodes is electrically connected to a potentiostat, and wherein the apparatus further comprises a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith, the solution further containing a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is bound to an electrochemical catalyst capable of participating m a reduction/oxidation reaction at the surface of the first electrode in the presence of a substrate for the electrochemical catalyst under conditions whereby an electrical potential is applied to the electrodes, wherein the electrolyte in the reaction chamber further contains a substrate for the electrochemical catalyst wherein a cuoent is produced in the apparatus when an electrical potential is applied to the electrodes and wherein the cuoent is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
53. The apparatus of claim 52 wherein the first member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the second member of the biological binding pair.
54. The apparatus of claim 52 wherein the second member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the first member of the biological binding pair.
55. An apparatus according to claim 52, wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
56. An apparatus according to claim 52, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
57. An apparatus according to claim 52, wherein the apparatus further comprises a multiplicity of each of the electrodes and a multiplicity of reaction chambers, wherein each reaction chamber contains an electrolyte and is in electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus.
58. An apparatus according to claim 52, wherein the apparatus further comprises a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemical catalyst-labeled second members of the biological binding pairs at a particular electrical potential applied between the electrodes, wherein the cuoent produced at each particular electrical potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
59. An apparatus according to claim 52, wherein the electrochemical catalyst bound to the second member of the biological binding pair is an enzyme.
60. An apparatus according to claim 59, wherein the enzyme is horse radish peroxidase.
61. An apparatus according to claim 52, wherein the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus.
62. An apparatus according to Claim 61 , wherein the detectable product is a colored product.
63. An apparatus according to claim 52, wherein the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof and the second member of the biological binding pair is a ligand that specifically binds to the receptor protein.
64. An apparatus according to claim 52, wherein the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof and the second member of the biological binding pair is an antigen that specifically binds to the antibody.
65. An apparatus according to claim 52, wherein the first member of the biological binding pair is a first protein or fragment thereof and the second member of the biological binding pair is a second protein or fragment thereof that specifically binds to the first protein. 66 A method for detecting binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 52, the method compπsing the steps of a) providing a first reaction chamber m electrochemical contact with each of the electrodes of the apparatus according to claim 52, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 52, wherein each of the electrodes being electπcally connected to a potentiostat, wherein the each of the reaction chambers contains a substrate for the electrochemical catalyst and a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and wherein the second reaction chamber contains an electrochemically-labeled second member of the biological binding pair and an unrelated species that does not specifically bind to the second member of the biological binding pair, or the first member of the biological binding pair and an unrelated, electrochemically-labeled species that does not bind to the first member of the biological binding pair, the method further compπsing the steps of b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 52 to produce a cuoent the electrodes of the apparatus, and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein binding of the second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the first reaction chamber than is produced in the second reaction chamber
67 A method for detecting binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 52, the method compπsing the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of an apparatus according to claim 52, wherein each of the electrodes is electrically connected to a potentiostat, and wherein the reaction chamber contains an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing a first electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and c) adding to the reaction chamber a first member of the biological binding pair that is specifically bound by the electrochemical catalyst-labeled second member of the biological binding pair, and d) performing a second electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus, and e) comparing the cuoent produced in the first electrochemical assay to the cuoent produced in the second electrochemical assay, wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the second electrochemical assay than is produced m the first electrochemical assay
68 The method of Claim 66, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the second reaction chamber than is produced in the first reaction chamber
69 The method of Claim 68, wherein the detectable product is a colored product
70 The method of Claim 67, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the second electrochemical assay than is produced in the first electrochemical assay.
71. The method of Claim 70, wherein the detectable product is a colored product.
72. The method of Claim 66 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
73. The method of Claim 66, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
74. The method of Claim 67 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
75. The method of Claim 67, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
76. A method for identifying an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 52, the method comprising the steps of: a) providing a first reaction chamber in electrochemical contact with each of the electrodes according to claim 52, and a second reaction chamber in electrochemical contact with each of the electrodes according to claim
52, wherein each of the electrodes being electrically connected to a potentiostat; wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair; the method further compπsing the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 52 to produce a cuoent m the electrodes of the apparatus; and c) compaπng the cuoent produced in the electrochemical assay m the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein an inhibitor of binding of the second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber.
77 A method for identifying an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 52, the method comprising the steps of a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 52, wherein each of the electrodes is electπcally connected to a potentiostat and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair and a substrate for the electrochemical catalyst, and b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, and c) compaπng the cuoent produced in the electrochemical assay m the presence of the inhibitor to the cuoent produced in the electrochemical assay in the absence of the inhibitor, wherein an inhibitor of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor.
78. The method of Claim 76 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
79. The method of Claim 76, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
80. The method of Claim 77 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
81. The method of Claim 77, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
82. A method according to claim 77 wherein the inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
83. A method according to claim 77 wherein the inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber.
84. A method according to claim 77 wherein the inhibitor is added to the reaction chamber together with the second member of the biological binding pair
85. The method of Claim 76, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is ftirther detected by the production of a smaller amount of the detectable product in the second reaction chamber than is produced in the first reaction chamber. 86 The method of Claim 85, wherein the detectable product is a colored product.
87 The method of Claim 77, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the second electrochemical assay than is produced in the first electrochemical assay
88 The method of Claim 87, wherein the detectable product is a colored product
89 A method for screening a complex chemical mixture for an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 52, the method compπsmg the steps of a) providing a first reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 52, and a second reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 52, wherein each of the electrodes being electπcally connected to a potentiostat, wherein each of the reaction chambers contains a first member of a biological binding pair, a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, bound to an electrochemical catalyst, and a substrate for the electrochemical catalyst, and wherein the second reaction chamber further contains a portion of the complex mixture compπsing an inhibitor of binding of the second member of the biological binding pair; the method further compπsing the steps of: b) performing an electrochemical assay in each of the first and second reaction chambers of the apparatus of claim 52 to produce a cuoent in the electrodes of the apparatus; and c) comparing the cuoent produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber wherein a complex mixture having an inhibitor of binding of the second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the second reaction chamber than is produced in the first reaction chamber.
90. The method of Claim 89 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
91. The method of Claim 89, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
92. A method according to claim 89 wherein the complex mixture comprising an inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
93. A method according to claim 89 wherein the complex mixture comprising an inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber.
94. A method according to claim 89 wherein the complex mixture comprising an inhibitor is added to the reaction chamber together with the second member of the biological binding pair
95. A method for screening a complex chemical mixture for an inhibitor of binding of a second member of a biological binding pair that is labeled with an electrochemical catalyst with a first member of a biological binding pair using an apparatus according to claim 1, the method comprising the steps of: a) providing a reaction chamber in electrochemical contact with each of the electrodes of the apparatus according to claim 43, wherein each of the electrodes is electrically connected to a potentiostat, and wherein the reaction chamber contains a first member of a biological binding pair and an electrochemical catalyst-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, and a substrate for the electrochemical catalyst, b) performing an electrochemical assay in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of a complex mixture comprising an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair; and c) comparing the cuoent produced in the electrochemical assay in the presence of the complex mixture to the cuoent produced in the electrochemical assay in the absence of the complex mixture; wherein a complex mixture having an inhibitor of binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger cuoent in the electrochemical assay in the presence of the complex mixture than is produced in the electrochemical assay in the absence of the complex mixture.
96. The method of Claim 95 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
97. The method of Claim 95, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
98. A method according to claim 95 wherein the complex mixture comprising an inhibitor is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
99. A method according to claim 95 wherein the complex mixture comprising an inhibitor is added to the reaction chamber before the second member of the biological binding pair is added to the reaction chamber.
100. A method according to claim 95 wherein the complex mixture comprising an inhibitor is added to the reaction chamber together with the second member of the biological binding pair
101. The method of Claim 95, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the second reaction chamber than is produced in the first reaction chamber.
102. The method of Claim 101, wherein the detectable product is a colored product.
103. The method of Claim 95, wherein the substrate for the electrochemical catalyst produces a detectable product, and wherein binding of the electrochemical catalyst-labeled second member of the biological binding pair with the first member of the biological binding pair is further detected by the production of a smaller amount of the detectable product in the second electrochemical assay than is produced in the first electrochemical assay.
104. The method of Claim 103, wherein the detectable product is a colored product.
105. A method according to claim 66 wherein the second member of the biological binding pair is a suoogate ligand.
106. A method according to claim 67 wherein the second member of the biological binding pair is a suoogate ligand.
107. A method according to claim 76 wherein the second member of the biological binding pair is a suoogate ligand.
108. A method according to claim 77 wherein the second member of the biological binding pair is a suoogate ligand.
109. A method according to claim 89 wherein the second member of the biological binding pair is a suoogate ligand.
110. A method according to claim 95 wherein the second member of the biological binding pair is a suoogate ligand.
1 11. A method according to claim 89 comprising the additional steps of: d) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures; and e) performing steps (a) through (c) of the method of claim 76 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair.
112. A method according to claim 95 comprising the additional steps of: d) chemically fractionating the complex mixture having an inhibitor of binding of the second member of the biological binding pair to the first member of the biological binding pair, to produce fractionated submixtures; and e) performing steps (a) through (c) of the method of claim 95 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair.
113. An apparatus according to Claim 1 , wherein the reaction chamber further comprises an electron donor species that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair.
114. A kit according to Claim 15 further comprising an electron donor species and wherein the electrochemical label produces chemiluminescence upon oxidation/reduction.
115. A method according to Claim 19, the method further comprising the step of : d) providing an electron donor species in the first and second reaction chambers that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; and e) comparing the chemiluminescence produced in the first reaction chamber with the chemiluminescence produced in the second reaction chamber, wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller amount of chemiluminescence in the first reaction chamber than is produced in the second reaction chamber.
116. A method according to Claim 20, the method further comprising the step of : d) providing an electron donor species in the reaction chamber that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; e) performing the first and second electrochemical assays; and f) comparing the chemiluminescence produced in the first electrochemical assay with the chemiluminescence produced in the second electrochemical assay, wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller amount of chemiluminescence in the second electrochemical assay than is produced in the first electrochemical assay.
117. A method according to Claim 25, the method further comprising the step of : d) providing an electron donor species in the first and second reaction chambers that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; and e) comparing the chemiluminescence produced in the first reaction chamber with the chemiluminescence produced in the second reaction chamber, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a smaller amount of chemiluminescence in the first reaction chamber than is produced in the second reaction chamber.
118. A method according to Claim 26, the method further comprising the step of : d) providing an electron donor species in the reaction chamber that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode oxidation/reduction of the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; e) performing the first and second electrochemical assays; and f) comparing the chemiluminescence produced in the first electrochemical assay with the chemiluminescence produced in the second electrochemical assay, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger amount of chemiluminescence in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor.
119. A method according to Claim 34, the method further comprising the step of : d) providing an electron donor species in the first and second reaction chambers that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; and e) comparing the chemiluminescence produced in the first reaction chamber with the chemiluminescence produced in the second reaction chamber, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a smaller amount of chemiluminescence in the first reaction chamber than is produced in the second reaction chamber.
120. A method according to Claim 35 , the method further comprising the step of : d) providing an electron donor species in the reaction chamber that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair; e) performing the first and second electrochemical assays; and f) comparing the chemiluminescence produced in the first electrochemical assay with the chemiluminescence produced in the second electrochemical assay, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is identified by the production of a larger amount of chemiluminescence in the presence of the inhibitor than is produced in the electrochemical assay in the absence of the inhibitor.
121. An apparatus according to Claim 52, wherein the reaction chamber further comprises an electron donor species that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair.
AMENDED CLAIMS
[received by the International Bureau on 01 October 1999 (01.10.99); original claims 34, 35, 62, 66-112 and 115-120 cancelled; original claims 14, 15, 19-33, 36- 48 , 50, 51, 113, 114 and 121 amended; new claims 122-134 added; remaining claims unchanged (14 pages)]
1. An apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair, the apparatus comprising a first electrode, wherein the electrode comprises a conducting or semiconducting
5 surface. a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution. a third, auxiliary electrode comprising a conducting metal wherein each of the electrodes is electrically connected to a potentiostat. and wherein the
10 apparatus further comprises a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith, the solution further containing a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is
15 electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode under conditions whereby an electrical potential is applied to the electrodes wherein a current is produced in the apparatus when an electrical potential is applied to the electrodes and wherein the current is reduced upon binding of the second member of the
20 biological binding pair to the first member of the biological binding pair.
2. The apparatus of claim 1 wherein the first member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the second member of the biological binding pair.
25
3. The apparatus of claim 1 wherein the second member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the first member of the biological binding pair.
30 4. The apparatus of claim 1 wherein the first member of the biological binding pair is linked to a particle.
5. An apparatus according to claim 1 , wherein the electrochemical assay is a voltammetric. amperometric or coulometric assay.
35
6. An apparatus according to claim 5, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
7. An apparatus according to claim 1, wherein the apparatus further comprises a multiplicity of each of the electrodes and a multiplicity of reaction chambers, wherein each reaction chamber contains an electrolyte solution and is in electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus.
8. An apparatus according to claim 1 , wherein the apparatus further comprises a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemically labeled second members of the biological binding pairs at a particular electrical potential applied between the electrodes, wherein the current produced at each particular electrical potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
9. An apparatus according to claim 1, wherein the second member of the biological binding pair is electrochemically labeled with a transition metal complex.
10. An apparatus according to claim 9. wherein the transition metal complex contains a transition metal ion that is ruthenium, cobalt, iron or osmium.
1 1. An apparatus according to claim 1, wherein the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof and the second member of the biological binding pair is a ligand that specifically binds to the receptor protein.
12. An apparatus according to claim 1, wherein the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof and the second member of the biological binding pair is an antigen that specifically binds to the antibody.
13. An apparatus according to claim 1 , wherein the first member of the biological binding pair is a first protein or fragment thereof and the second member of the biological binding pair is a second protein or fragment thereof that specifically binds to the first protein.
14. A kit for using the apparatus of claim 1 to perform an electrochemical analysis, wherein the kit comprises a first member of a biological binding pair, a second member of the biological binding pair, an electrochemical label and a reagent for electrochemically labeling the second member of the biological binding pair with the electrochemical label.
15. A kit for using the apparatus of claim 1 to perform an electrochemical analysis, wherein the kit comprises a first member of a biological binding pair, and an electrochemically labeled second member of the biological binding pair.
16. An electrochemically labeled surrogate ligand comprising a second member of a biological binding pair having a binding affinity of from about 1 nanomolar (nM) to about 100 micromolar (μM) for a first member of a biological binding pair.
17. An electrochemically labeled suoogate ligand according to claim 16, labeled with a transition metal complex.
18. An electrochemically labeled suoogate ligand according to claim 17, wherein the transition metal is a ruthenium complex, a cobalt complex, an iron complex or an osmium complex.
19. A method for determining the presence of a first member of a biological pair in a sample, by detecting binding of a second member of said biological binding pair with said first member of the biological binding pair, comprising the steps of: a) providing a first reaction chamber and a second reaction chamber, each of said reaction chambers in electrochemical contact with a first electrode comprising a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comprising a conducting metal, wherein each of the electrodes is electrically connected to a potentiostat; wherein the first reaction chamber comprises the sample and said second member of the biological binding pair that specifically binds to the first member of the biological binding pair, said second member being electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode when an electrical potential is applied to the electrodes, and wherein the second reaction chamber comprises said electrochemically-labeled second member of the biological binding pair and a control sample that does not contain the first member of the biological binding pair, or the sample as a control; the method further comprising the steps of: b) performing an electrochemical assay in said solution in each of the first and second reaction chambers to produce a current in the electrodes; and c) comparing the current produced in the electrochemical assay in the first reaction chamber to the current produced in the electrochemical assay in the second reaction chamber, wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller current in the first reaction chamber than is produced in the second reaction chamber, wherein the chemical species is a transition metal complex, and wherein the amount of cuoent produced by participation in the reduction/oxidation reaction is due to the amount of transition metal complex at the electrode surface.
20. A method for determining the presence of a first member of a biological pair in a sample, by detecting binding of an electrochemically labeled second member of a biological binding pair with the first member of a biological binding pair comprising the steps of: a) providing a reaction chamber in electrochemical contact with a first electrode comprising a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comprising a conducting metal, wherein each of the electrodes is electrically connected to a potentiostat; and wherein the reaction chamber comprises an electrochemically-labeled second member of the biological binding pair that specifically binds to a first member of the biological binding pair, said second member being electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode when an electrical potential is applied to the electrodes; b) performing a first electrochemical assay in said solution in the reaction chamber to produce a current in the electrodes; c) adding the sample to the reaction chamber; d) performing a second electrochemical assay in said solution in the reaction chamber to produce a cuoent in the electrodes; and e) comparing the cuoent produced in the first electrochemical assay to the cuoent produced in the second electrochemical assay; wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller cuoent in the second electrochemical assay than is produced in the first electrochemical assay. wherein the chemical species is a transition metal complex, and wherein the amount of cuoent produced by participation in the reduction/oxidation reaction is due to the amount of transition metal complex at the electrode surface.
21. The method of claim 19 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
22. The method of claim 19. wherein the electrochemical assay is cyclic voltammetry, chronoamperometry. or chronocoulometry.
23. The method of claim 20 wherein the electrochemical assay is a voltammetric. amperometric or coulometric assay.
24. The method of claim 20, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
25. A method for determining the presence of an inhibitor in a sample, comprising the steps of: a) providing a first reaction chamber and a second reaction chamber, each of said reaction chambers in electrochemical contact with a first electrode comprising a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comprising a conducting metal, wherein each of the electrodes is electrically connected to a potentiostat; wherein each of the reaction chambers comprises a first member of a biological binding pair and a second member of the biological binding pair that specifically binds to the first member of the biological binding pair, said second member of the biological binding pair being electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode when an electrical potential is applied to the electrodes, and wherein the second reaction chamber further comprises the sample; the method further comprising the steps of: b) performing an electrochemical assay in said solution in each of the first and second reaction chambers to produce a current in the electrodes of the apparatus; and c) comparing the current produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber, wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair in the sample is identified by the production of a larger current in the second reaction chamber than is produced in the first reaction chamber, wherein the chemical species is a transition metal complex, and wherein the amount of cuoent produced by participation in the reduction/oxidation reaction is due to the amount of transition metal complex at the electrode surface.
26. A method for determining the presence of an inhibitor in a sample, comprising the steps of: a) providing a reaction chamber in electrochemical contact with a first electrode comprising a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comprising a conducting metal, wherein each of the electrodes is electrically connected to a potentiostat and wherein the reaction chamber comprises a first member of a biological binding pair and an electrochemically-labeled second member of the biological binding pair that specifically binds to the first member of the biological binding pair, said second member being electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode when an electrical potential is applied to the electrodes, b) performing an electrochemical assay in said solution in the reaction chamber to produce a cuoent in the electrodes of the apparatus in the presence and absence of the sample: and c) comparing the current produced in the electrochemical assay in the presence of the sample to the current produced in the electrochemical assay in the absence of the sample; wherein an inhibitor of binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is determined to be present in the sample by the production of a larger current in the electrochemical assay in the presence of the sample than is produced in the electrochemical assay in the absence of the sample, wherein the chemical species is a transition metal complex, and wherein the amount of cuoent produced by participation in the reduction/oxidation reaction is due to the amount of transition metal complex at the electrode surface.
5 27. The method according to claim 25 wherein the sample is added to the reaction chamber after the second member of the biological binding pair is added to the reaction chamber.
28. The method according to claim 25 wherein the sample is added to the reaction chamber before the second member of the biological binding pair is added to the reaction
10 chamber.
29. The method according to claim 25 wherein the sample is added to the reaction chamber together with the second member of the biological binding pair.
I _> 30. The method of claim 25. wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
31. The method of claim 25, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry. 0
32. The method of claim 26 wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
33. The method of claim 26, wherein the electrochemical assay is cyclic voltammetry, _> chronoamperometry, or chronocoulometry.
36. The method according to claim 122 wherein the complex mixture is added to the second reaction chamber after the second member of the biological binding pair is added to the second reaction chamber. 0
37. The method according to claim 122 wherein the complex mixture is added to the second reaction chamber before the second member of the biological binding pair is added to the second reaction chamber.
38. The method according to claim 122 wherein the complex mixture is added to the second reaction chamber together with the second member of the biological binding pair.
39. The method according to claim 19 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
40. The method according to claim 20 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
41. The method according to claim 25 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
42. The method according to claim 26 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
43. The method according to claim 122 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
44. The method according to claim 123 wherein the second member of the biological binding pair is an electrochemically labeled surrogate ligand.
45. The method of claim 122 wherein the electrochemical assay is a voltammetric. amperometric or coulometric assay.
46. The method of claim 122, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
47. The method of claim 123, wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
48. The method of claim 123, wherein the electrochemical assay is cyclic voltammetry, chronoamperometry, or chronocoulometry.
50. The method according to claim 122 comprising the additional steps of: d) chemically fractionating the complex mixture, to produce fractionated submixtures; and e) performing steps (a) through (c) of the method of claim 25 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair.
51. The method according to claim 123 comprising the additional steps of: d) chemically fractionating the complex mixture, to produce fractionated submixtures; and e) performing steps (a) through (c) of the method of claim 26 on each of the fractionated submixtures to identify the submixtures that have an inhibitor of binding of the biological binding pair.
52. An apparatus for performing an electrochemical assay for detecting binding between members of a biological binding pair, the apparatus comprising a first electrode, wherein the electrode comprises a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, a third, auxiliary electrode comprising a conducting metal wherein each of the electrodes is electrically connected to a potentiostat, and wherein the apparatus further comprises a reaction chamber containing a solution of an electrolyte, wherein each of the electrodes is in electrochemical contact therewith, the solution further containing a first member of a biological binding pair, and a second member of the biological binding pair, wherein said second member is bound to an electrochemical catalyst capable of participating in a reduction/oxidation reaction at the surface of the first electrode in the presence of a substrate for the electrochemical catalyst under conditions whereby an electrical potential is applied to the electrodes, wherein the electrolyte in the reaction chamber further contains a substrate for the electrochemical catalyst wherein a cuoent is produced in the apparatus when an electrical potential is applied to the electrodes and wherein the current is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
53. The apparatus of claim 52 wherein the first member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the second member of the biological binding pair.
54. The apparatus of claim 52 wherein the second member of the biological binding pair is present in the reaction chamber at a concentration greater than the concentration of the first member of the biological binding pair.
55. An apparatus according to claim 52. wherein the electrochemical assay is a voltammetric, amperometric or coulometric assay.
56. An apparatus according to claim 52. wherein the electrochemical assay is cyclic voltammetry, chronoamperometry. or chronocoulometry.
57. An apparatus according to claim 52, wherein the apparatus further comprises a multiplicity of each of the electrodes and a multiplicity of reaction chambers, wherein each reaction chamber contains an electrolyte and is in electrochemical contact with one each of the three electrodes among the multiplicity of electrodes in the apparatus.
58. An apparatus according to claim 52, wherein the apparatus further comprises a multiplicity of each of the first and second members of the biological binding pair, wherein cuoent is produced in the apparatus by participation in a reduction/oxidation reaction at the surface of the first electrode by each of the electrochemical catalyst-labeled second members of the biological binding pairs at a particular electrical potential applied between the electrodes, wherein the current produced at each particular electrical potential is reduced upon binding of the second member of the biological binding pair to the first member of the biological binding pair.
59. An apparatus according to claim 52, wherein the electrochemical catalyst bound to the second member of the biological binding pair is an enzyme.
60. An apparatus according to claim 59, wherein the enzyme is horse radish peroxidase.
61. An apparatus according to claim 52, wherein the substrate of the electrochemical catalyst produces a detectable product upon undergoing an oxidation/reduction reaction with the electrochemical catalyst at the surface of the first electrode of the apparatus.
62. An apparatus according to claim 61 , wherein the detectable product is a colored product.
63. An apparatus according to claim 52, wherein the first member of the biological binding pair is a receptor protein or ligand binding fragment thereof and the second member of the biological binding pair is a ligand that specifically binds to the receptor protein.
64. An apparatus according to claim 52, wherein the first member of the biological binding pair is an antibody protein or antigen binding fragment thereof and the second member of the biological binding pair is an antigen that specifically binds to the antibody.
65. An apparatus according to claim 52, wherein the first member of the biological binding pair is a first protein or fragment thereof and the second member of the biological binding pair is a second protein or fragment thereof that specifically binds to the first protein.
1 13. An apparatus according to claim 1 , wherein the reaction chamber further comprises an electron donor species that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair.
1 14. A kit according to claim 15 further comprising an electron donor species and wherein the electrochemical label produces chemiluminescence upon oxidation/reduction.
121. An apparatus according to claim 52, wherein the reaction chamber further comprises an electron donor species that is oxidized with transfer of an electron to the electrochemical label at the surface of the first electrode and is accompanied by the production of a detectable amount of chemiluminescence that is diminished upon binding of the second member of the biological binding pair with the first member of the biological binding pair.
122. The method of claim 25, wherein the sample comprises a complex chemical mixture.
123. The method of claim 26, wherein the sample comprises a complex chemical mixture.
124. The method of claim 19, wherein the electrochemical assay comprises a time of inteoogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
125. The method of claim 20, wherein the electrochemical assay comprises a time of inteoogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
126. The method of claim 25, wherein the electrochemical assay comprises a time of interrogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
127. The method of claim 26, wherein the electrochemical assay comprises a time of interrogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
128. The method of claim 122, wherein the electrochemical assay comprises a time of interrogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
129. The method of claim 123, wherein the electrochemical assay comprises a time of inteoogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
130. The method according to claim 19, wherein the transition metal complex is a ruthenium complex.
131. The method according to claim 20, wherein the transition metal complex is a ruthenium complex.
132. The method according to claim 25, wherein the transition metal complex is a ruthenium complex.
133. The method according to claim 26, wherein the transition metal complex is a ruthenium complex.
134. A method for determining the presence of a first member of a biological pair in a sample, by detecting binding of a second member of said biological binding pair with said first member of the biological binding pair, comprising the steps of: a) providing a first reaction chamber and a second reaction chamber, each of said reaction chambers in electrochemical contact with a first electrode comprising a conducting or semiconducting surface, a second, reference electrode comprising a conducting metal in contact with an aqueous electrolyte solution, and a third, auxiliary electrode comprising a conducting metal, wherein each of the electrodes is electrically connected to a potentiostat; wherein the first reaction chamber comprises the sample and said second member of the biological binding pair that specifically binds to the first member of the biological binding pair, said second member being electrochemically labeled with a chemical species capable of participating in a reduction/oxidation reaction at the surface of the first electrode when an electrical potential is applied to the electrodes, and wherein the second reaction chamber comprises said electrochemically-labeled second member of the biological binding pair and control sample that does not contain the first member of the biological binding pair, or the sample as a control; the method further comprising the steps of: b) performing an electrochemical assay in said solution in each of the first and second reaction chambers to produce a cuoent in the electrodes; and c) comparing the current produced in the electrochemical assay in the first reaction chamber to the cuoent produced in the electrochemical assay in the second reaction chamber. wherein binding of the electrochemically labeled second member of the biological binding pair with the first member of the biological binding pair is detected by the production of a smaller current in the first reaction chamber than is produced in the second reaction chamber, wherein the chemical species is a transition metal complex, and wherein the amount of cuoent produced by participation in the reduction/oxidation reaction is due to the amount of transition metal complex at the electrode surface, and wherein the electrochemical assay comprises a time of inteoogation sufficient to detect a difference in diffusion when there is specific binding between the first and second members of the binding pair.
STATEMENT UNDER ARTICLE 19
In response to the International Search Report dated July 27, 1999 for the above- identified International Patent Application, this Statement is submitted under the provisions of the Patent Cooperation Treaty Article 19(1 ) in explanation of the amendments effected by the enclosed new substitute pages.
Support for changes in terminology in the replacement claims submitted b\ amendment herewith is primarily in the claims as originally filed. In addition, support for the amended claims in the specification is found at page 8. lines 5-10, page 32. linel 10 to page 33. line 1. page 43, lines 18-24) and the electrochemical assay is performed in the solution (supported by the specification at page 1. lines 7-12: page 6, lines 16-28; page 16. line 25 to page 17. line 13: page 36. lines 13-24; page 46. line 24 to page 47, iine 27: and page 49. lines 1 1-14.
Thus, the claims as amended are fully consistent with and supported by the as-filed disclosure of the application.
PCT/US1999/011848 1998-06-08 1999-05-28 Electrochemical probes for detection of molecular interactions and drug discovery WO1999064847A1 (en)

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US6383754B1 (en) 1999-08-13 2002-05-07 Yale University Binary encoded sequence tags
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WO2006043095A2 (en) * 2004-10-22 2006-04-27 E2V Biosensors Limited Monitoring enzyme-substrate reactions

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Cited By (9)

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US6261782B1 (en) 1999-04-06 2001-07-17 Yale University Fixed address analysis of sequence tags
US6677121B2 (en) 1999-04-06 2004-01-13 Agilix Corporation Fixed address analysis of sequence tags
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US6773886B2 (en) 1999-08-13 2004-08-10 Yale University Binary encoded sequence tags
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US7403017B2 (en) 2003-01-20 2008-07-22 Universal Biosensors Pty Limited Methods of measuring barrier formation
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WO2006043095A2 (en) * 2004-10-22 2006-04-27 E2V Biosensors Limited Monitoring enzyme-substrate reactions
WO2006043095A3 (en) * 2004-10-22 2006-07-06 E2V Biosensors Ltd Monitoring enzyme-substrate reactions

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