WO2001006250A2 - Thermo-chemical sensors and uses thereof - Google Patents
Thermo-chemical sensors and uses thereof Download PDFInfo
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- WO2001006250A2 WO2001006250A2 PCT/US2000/019383 US0019383W WO0106250A2 WO 2001006250 A2 WO2001006250 A2 WO 2001006250A2 US 0019383 W US0019383 W US 0019383W WO 0106250 A2 WO0106250 A2 WO 0106250A2
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- library
- target
- ligand
- protein
- virus
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N25/00—Investigating or analyzing materials by the use of thermal means
- G01N25/20—Investigating or analyzing materials by the use of thermal means by investigating the development of heat, i.e. calorimetry, e.g. by measuring specific heat, by measuring thermal conductivity
- G01N25/48—Investigating or analyzing materials by the use of thermal means by investigating the development of heat, i.e. calorimetry, e.g. by measuring specific heat, by measuring thermal conductivity on solution, sorption, or a chemical reaction not involving combustion or catalytic oxidation
- G01N25/4846—Investigating or analyzing materials by the use of thermal means by investigating the development of heat, i.e. calorimetry, e.g. by measuring specific heat, by measuring thermal conductivity on solution, sorption, or a chemical reaction not involving combustion or catalytic oxidation for a motionless, e.g. solid sample
Definitions
- thermo-chemical sensor e.g., a calorimeter
- Ligands can be divided into two main categories: binding ligands, which bind and form stable complexes with target biomolecules; and substrates, which interact with target biomolecules and become chemically modified.
- Ligands for a biomolecular target can be identified by their ability to physically associate with the target biomolecule.
- the processes of binding and substrate turnover are typically probed by assays that indicate if complex formation or chemical reactivity has occurred or not. These assays often depend on changes in, for example, spectroscopic or chromatographic properties of the complex or ligands of interest.
- screening assays measure the interaction between a compound and a target in a way that limits the scope of the compounds that can be tested. For example, although many proteins have multiple functions, most assays are capable of detecting only one of such functions. Such assays limit the scope of the compounds that can be tested.
- Additional limitations to currently available screening assays include: (i) length and/or costly separation steps that are often necessary in non-homogeneous assays; (ii) problems of optical detection associated with assays that cannot effectively detect the activities of colored compounds or suspensions or turbid extracts; (iii) the tedious and cumbersome testing of even a small subset of possible compounds when the assays are not high-throughput assays; (iv) the expense and difficulty of assays that require the use of cell lines and/or animals; and (v) the absence of information obtained in most currently available assays about the strength of an interaction between the test compound and the target. Accordingly, there is a need for relatively inexpensive, large-scale assays which enable the detection of an interaction between a target and a test compound, without significantly limiting the scope of the target functions that can be detected.
- methods of the invention detect a change in heat generated upon conversion of a test substrate(s) into a product(s) or, where the target and interactor are ligand and counter-ligand, upon binding.
- the absorption or evolution of heat is a universal property of chemical reactions, thus the power of the methods of the invention can transcend that of methods which make overly constraining limiting assumptions about the nature of the target or its interactions with other molecules.
- Some embodiments of the invention require no assumptions about the -nature of the target and its interaction with its interactor, e.g., its naturally occurring ligand, substrate, or binding partner.
- Other methods of the invention incorporate knowledge of or assumptions about the target (and/or interactor) to guide in the choice of potential interactors.
- embodiments of the invention use genomic, or other bioinformatic analyses of the target to optimize and prioritize the choice of interactors against which to test the target.
- the invention features, a method of analyzing a target, e.g., a protein.
- a target e.g., a protein
- the method includes:
- Putative function can be assigned by any means, e.g., by the identification of a characteristic possessed (or in some cases not possessed) by the target.
- exemplary characteristics include: a structural characteristic, e.g., in the case of a protein, a preselected level of sequence identity with another protein; possession of a sequence or motif, or a protein fold; similarities in 3-dimensional structure between the target and another molecule, e.g., a protein of known function; promoter structure or other 3', 5', or other regulatory structure; chromosomal location or other genetic properties such as suppressor, auxotroph, permease, drug resistance, drug sensitivity, or other similar activities or properties; expression profile, e.g., tissue specificity, disease, or disorder specific expression, temporal expression pattern; source, e.g., the species from which the target is derived.
- the identification of a characteristic shared (or in some cases not shared) by the target and a molecule, e.g., a protein, of known function can allow assignment of the, or an, activity of the molecule, e.g., protein, of known function to the target.
- putative function can be assigned, e.g., by comparing the sequence of the protein, or a nucleic acid which encodes it, to a reference sequence, (e.g., determining if the target protein includes a preselected sequence, e.g., a preselected motif, e.g., a consensus sequence), or by comparing the sequence of the protein to another protein with known 3-dimensional structure (e.g., determining the presence or absence of a protein fold); or by comparing the 3-dimensional structure of a crystal of the target protein to other proteins of known function; (2) providing a library of interaction candidates, e.g., a library of potential substrates, or binding ligands, for a protein.
- a reference sequence e.g., determining if the target protein includes a preselected sequence, e.g., a preselected motif, e.g., a consensus sequence
- a preselected sequence e.g., a preselected motif, e.g.
- the library will include at least one, and more preferably a plurality of members, each of which is known to interact with a protein having the assigned putative function.
- a library can contain a plurality of protease substrates. Assignment of putative function can optimize screening strategy, e.g., by guiding the choice of a particular library of interactors.); (3) providing a reaction mixture which includes the target, e.g., protein:
- (6) optionally, comparing the value for heat change obtained with a predetermined value, thereby analyzing the target, e.g., protein, e.g., by identifying a library member which is a substrate or a ligand of the target, e.g., protein.
- a library member which is a substrate or a ligand of the target, e.g., protein.
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Borrelia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, My
- Mycobacterium tuberculosis Sanger Mycoplasma mycoides, Neisseria meningitidis strain, Streptomyces coelicolor, Actinobacillus actinomyce, Chlamydia trachomatis, Halobacterium sp., Mycoplasma capricolum, Neisseria gonorrhea, Pseudomonas aeruginosa, Aspergillus nidulans, Candida albicans, Leishmania major, Neurospora crassa, Pneumocystis carinii, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma cruzi, Trypanosoma brucei, Abelson murine leukemia virus, Adeno-associated virus 2 or -3, Dengue virus type 1, 2 or 3, Hepatitis A-G virus, Hepatitis GB virus B, Human
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster,
- the target is produced by a human.
- the target e.g., a protein
- an organelle e.g., the mitochondria
- the target e.g., the protein
- the target has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the protein has a known first activity and it is tested against a library which includes an interactor which interacts with the protein by way of a second activity, e.g., an unknown activity.
- the target is a naturally occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the protein has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- a plurality of library members is tested simultaneously, e.g., in the same reaction mixture, which can allow for an increase in the throughput of the method.
- a plurality of library members e.g., one which provides a positive result
- One or more library members from the plurality or from a smaller group, e.g., one which provides a positive result, can be tested individually.
- the method further includes repeating one or more steps, e.g., one or both of steps (4) and (5), under a different condition, e.g., at a different salt concentration, different pH, or in the presence of a different cofactor.
- the method further includes repeating at least one step, e.g., steps (3)-(6) with a second or subsequent member or members of the library.
- a plurality of library members e.g., candidate substrates or test ligands, is tested.
- the plurality of library members includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 compounds.
- the prefe ⁇ ed embodiment includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 of the library members share a structural or functional characte ⁇ stic.
- the library includes a plurality of members having a common characteristic, e.g., all members of the plurality are enzyme cofactors; substrates for, e.g., biosynthetic or degradative enzymes (e.g., protease substrates), including carbohydrates, nucleoside/nucleotides, amino acids, lipids; vitamins; hormones; nucleic acids; e.g., DNA molecules; or natural products, e.g., bacterial natural products.
- the library can include any metabolite, precursor, or intermediate of the members listed above.
- the library is: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA, library; or a natural product library, e.g., a bacterial natural product library.
- a library member (a potential or candidate interactor) is a species which has potential to interact with a target, e.g., a target protein.
- a library member is a candidate substrate or a test ligand.
- a library member is selected from the group consisting of: an enzyme substrate, a metabolite, a cofactor, a natural product (e.g., a bacterial natural product), a carbohydrate, a polysaccharide, a nucleic acid (e.g., a nucleoside or nucleotide precursor, a double- stranded (ds) or single-stranded (ss) DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L-amino acid or a precursor thereof), a vitamin, a hormone, a lipid, a small organic molecule, a metals, a peptide, a protein, a lipid, a glycoprotein, a glycolipid, a transition state analog and combinations thereof.
- a natural product e.g., a bacterial natural product
- a carbohydrate e.g., a polysacchari
- the method further includes testing the protein against at least one member of a second library.
- two, or more, libraries are tested simultaneously.
- the target can be tested against each (or some) members of a first library, e.g., a cofactor library, and each (or some) members of a second library, e.g., a library of potential substrates.
- a first library e.g., a cofactor library
- a second library e.g., a library of potential substrates.
- the target is tested against all or a plurality of the novel combinations, e.g., against (first], secondi), (first] second 2 ) ... (first], second 5 o), and so on.
- a library member is a member of a combinatorial library.
- the target interacts with, e.g., binds, and preferably modifies, the test compound.
- Modify includes making or breaking a bond, e.g., a non- covalent or covalent bond, in the test compound or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing the target structure or function, e.g., analyzing the physical properties of the target; analyzing the target in vitro or in vivo activity; analyzing the target sequence (e.g., amino acid or nucleotide sequence) for the presence of, e.g., conserved amino acid domains, thereby predicting the target structure or function.
- the analysis of the target structure or function is performed prior to contacting the target with the library.
- the method further includes: selecting a library member, e.g., candidate substrate or test ligand based on its interaction with the target; and confirming that the candidate substrate or test ligand is a substrate or a ligand, respectively.
- a library member e.g., candidate substrate or test ligand based on its interaction with the target.
- the method further includes: selecting a library member based on its interaction with the target; and contacting the library member with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the library member has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes selecting an interactor (e.g., a library member) on the basis of its interaction with the target and: purifying the library, e.g., a candidate substrate or test ligand; crystallizing a library member, e.g., a candidate substrate or test ligand; evaluating a physical property of a library member, e.g., a candidate substrate or test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the library member can be crystallized by itself, or as complexed with the target.
- the method further includes using a library member selected for interacting with the target to identify, e.g., by binding to or interacting with the selected library member, an agent which modulates an interaction between the target and the selected library member.
- the method further includes selecting an interactor (e.g., a library member) on the basis of its interaction with the target and: optimizing a property of a chosen library member, e.g., candidate substrate or test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- an interactor e.g., a library member
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the protein and a member of the library, e.g., kc at , K M , or ko-
- the method can include the use of a linking reaction, e.g., a surrogate ligand, as described elsewhere herein.
- a linking reaction e.g., a surrogate ligand
- the invention features, a method of purifying or isolating an interactor (or a target) from a mixture.
- an interactor e.g. a substrate or counter ligand
- the interactor can be, e.g., a ligand, receptor, counter ligand, cofactor, or substrate, which interacts with a target, e.g., a protein.
- the mixture can be a complex biological sample, e.g., whole cells, a cell homogenate or lysate, a tissue sample, a sample of a biological fluid.
- a target e.g., other macromolecules, e.g., nucleic acids
- the method includes: (1) providing a mixture; (2) partitioning the mixture into to a plurality of fractions including a first and a second fraction, e.g., a soluble and a membrane fraction: (3) contacting the target with the first fraction to form a first reaction mixture;
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Bo ⁇ elia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, My
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- the target is produced by a human.
- the target e.g., a protein
- an organelle e.g., the mitochondria
- the target e.g., a protein
- the target has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the target e.g., a protein
- the target is a naturally-occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the target e.g., a protein, has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- the method further includes repeating one or more steps, e.g., one or both of steps (4) and (5), under a different condition, e.g., at a different salt concentration, different pH, or in the presence of an exogenous cofactor.
- the target interacts with, e.g., binds, and preferably modifies, the interactor.
- Modify includes making or breaking a bond, e.g., a non-covalent or covalent bond, in the test compound or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing the interactor structure or function, e.g., analyzing the physical properties of the interactor.
- the method further includes: selecting a interactor, e.g., based on its interaction with the target; and confirming that the interactor is, e.g., a substrate or a ligand.
- the method further includes: contacting the purified or isolated interactor with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if purified or isolated interactor has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes selecting an interactor (e.g., a library member) on the basis of its interaction with the target and: purifying the purified or isolated interactor; crystallizing purified or isolated interactor; evaluating a physical property of the purified or isolated interactor.
- an interactor e.g., a library member
- the method further: optimizing a property of a purified or isolated interactor, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the target and purified or isolated interactor, e.g., k cat , K , or k D .
- the method can include the use of a linking reaction, e.g., a su ⁇ ogate ligand, as described elsewhere herein.
- a linking reaction e.g., a su ⁇ ogate ligand
- the invention features, a method of analyzing a target, e.g., discovering an interactor, e.g., a substrate or a ligand of a protein.
- the method includes: (a) providing a reaction mixture which includes a target:
- a candidate interactor e.g., a candidate substrate or a test ligand
- the interactor e.g., the substrate or ligand
- the interactor is identified by a change in the heat of the reaction mixture, e.g., change which is greater than a predetermined value.
- a plurality, e.g., a library, of candidate interactors, e.g., candidate substrates or test ligands is tested.
- the plurality, e.g., a library, of candidate substrates or test ligands includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 , or 10 candidate substrates or test ligands.
- method includes: (a) providing a reaction mixture which includes a first interactor of the plurality and the target;
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Borrelia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, My
- Streptomyces coelicolor Actinobacillus actinomyce, Chlamydia trachomatis, Halobacterium sp., Mycoplasma capricolum, Neisseria gono ⁇ hea, Pseudomonas aeruginosa, Aspergillus nidulans, Candida albicans, Leishmania major, Neurospora crassa, Pneumocystis carinii, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma cruzi, Trypanosoma brucei, Abelson murine leukemia virus, Adeno-associated virus 2 or -3, Dengue virus type 1, 2 or 3, Hepatitis A-G virus, Hepatitis GB virus B, Human T-cell lymphotropic virus type 1 or 2, Human T-cell lymphotropic virus type I, Human adenovirus type 12 or 2, Human
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- the target is produced by a human.
- the target e.g., a protein
- an organelle e.g., the mitochondria
- the target has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the target has a known first activity and it is tested against a library which includes an interactor which interacts with the target by way of a second activity, e.g., an unknown activity.
- the target is a naturally-occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the target e.g., a protein, has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- a nucleic acid e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- a plurality of candidate interactors e.g., library members
- a plurality of library members e.g., one which provides a positive result
- a plurality of library members can be subdivided into smaller groups and those smaller groups tested.
- One or more library members from the plurality or from a smaller group, e.g., one which provides a positive result, can be tested individually.
- the method further includes repeating one or more under a different condition, e.g., at a different salt concentration, different pH, or in the presence of a different cofactor.
- the method further includes repeating at least one step with a second or subsequent member or members of the library of candidate interactors.
- a plurality of candidate interactors e.g., library members
- the plurality of candidate interactors includes at least 10, 10 2 ,
- 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 compounds In a prefe ⁇ ed embodiment includes at least 10, 10 2 , 10 3 ,
- 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 of the library members share a structural or functional characteristic.
- the library of candidate interactors includes a plurality of members having a common characteristic, e.g., all members of the plurality are enzyme cofactors; substrates for, e.g., biosynthetic or degradative enzymes (e.g., protease substrates), including carbohydrates, nucleoside/nucleotides, amino acids, lipids; vitamins; hormones; nucleic acids; e.g., DNA molecules; or natural products, e.g., bacterial natural products.
- the library can include any metabolite, precursor, or intermediate of the members listed above.
- the library of candidate interactors is: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA library; or a natural product library, e.g., a bacterial natural product library.
- the candidate interactor is a species which has potential to interact with a target, e.g., a target protein.
- the candidate interactor is a candidate substrate or a test ligand.
- the candidate interactor is selected from the group consisting of: an enzyme substrate, a metabolite, a cofactor, a natural product (e.g., a bacterial natural product), a carbohydrate, a polysaccharide, a nucleic acid, (e.g., a nucleoside or nucleotide precursor, a ds or ss DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L- amino acid or a precursor thereof), a vitamin, a hormone, a lipid, a small organic molecule, a metals, a peptide, a protein, a lipid, a glycoprotein
- the method further includes testing the candidate interactor against at least one member of a second library.
- two, or more, libraries of candidate interactors are tested simultaneously.
- the target can be tested against each (or some) members of a first library, e.g., a cofactor library, and each (or some) members of a second library, e.g., a library of potential substrates.
- a first library e.g., a cofactor library
- a second library e.g., a library of potential substrates.
- the target is tested against all or a plurality of the novel combinations, e.g., against (first], second]), (first] second 2 ) ... (first], second 50 ), and so on.
- the member of the library of candidate interactors is a member of a combinatorial library.
- the target interacts with, e.g., binds to, and preferably modifies, the candidate interactor.
- Modify includes making or breaking a bond, e.g., a non- covalent or covalent bond, in the candidate interactor or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing the target structure or function, e.g., analyzing the physical properties of the target; analyzing the target in vitro or in vivo activity; analyzing the target sequence (e.g., amino acid or nucleotide sequence) for the presence of, e.g., conserved amino acid domains, thereby predicting the target structure or function.
- the analysis of the target structure or function is performed prior to contacting the target with the candidate interactor.
- the method further includes: selecting a candidate interactor, e.g., a library member, based on its interaction with the target; and confirming that the candidate interactor interacts with the target, e.g., is a substrate or a ligand of the target, respectively.
- a candidate interactor e.g., a library member
- the method further includes: selecting a candidate interactor, e.g., library member, based on its interaction with the target; and contacting the library member with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the library member has an effect on the cell or animal.
- a candidate interactor e.g., library member
- the method further includes selecting a candidate interactor (e.g., a library member) on the basis of its interaction with the target and: purifying the library, e.g., a candidate substrate or test ligand; crystallizing a library member, e.g., a candidate substrate or test ligand; evaluating a physical property of a library member, e.g., a candidate substrate or test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- a candidate interactor e.g., a library member
- the method further includes using a library member selected for interacting with the target to identify, e.g., by binding to or interacting with the selected library member, an agent which modulates an interaction between the target and the selected library member.
- the method further includes selecting a candidate interactor (e.g., a library member) on the basis of its interaction with the target and: optimizing a property of a chosen library member, e.g., candidate substrate or test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- a candidate interactor e.g., a library member
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the protein and a member of the library, e.g., k cat , K M , or kp.
- the method can include the use of a linking reaction, e.g., a surrogate ligand, as described elsewhere herein.
- a linking reaction e.g., a surrogate ligand
- Embodiments of the method can include the use of a linking interaction, e.g., a surrogate ligand, as is described herein.
- a linking interaction e.g., a surrogate ligand
- one or more steps, e.g., step (b) further includes the inclusion of a su ⁇ ogate ligand and a signal-generating entity, and the interaction of the su ⁇ ogate ligand, e.g., displaced su ⁇ ogate ligand, and the signal-generating entity, as described elsewhere herein.
- the invention features, a method of modifying, e.g., optimizing, the structure of a compound.
- the parameter optimized can be, e.g., the ability of the compound to interact with a target, e.g., for the ability to bind or modify the target.
- the method includes:
- the method includes: (a) providing a target;
- the method can further include one or more cycles of the following steps:
- (h) optionally, comparing the value determined in (g) with a predetermined value, and if the value and the predetermined value manifest a predetermined relationship, e.g., if the former is equal to or less than the latter, then
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Borrelia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, My
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- the target is produced by a human.
- the target e.g., a protein
- an organelle e.g., the mitochondria
- the target e.g., protein has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the target e.g., a protein
- the target is a naturally-occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the target e.g., a protein, has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- a nucleic acid e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- the test compound (a potential or candidate interactor) is a species which has potential to interact with a target, e.g., a target protein.
- a target protein e.g., a target protein.
- the test compound is a candidate substrate or a test ligand.
- the test compound is a member of a library that includes a plurality of members having a common characteristic, e.g., all members of the plurality are enzyme cofactors; substrates for, e.g., biosynthetic or degradative enzymes (e.g., protease substrates), including carbohydrates, nucleoside/nucleotides, amino acids, lipids; vitamins; hormones; nucleic acids; e.g., DNA molecules; or natural products, e.g., bacterial natural products.
- the library can include any metabolite, precursor, or intermediate of the members listed above.
- the test compound is a member of a library selected from the group consisting of: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA library; or a natural product library, e.g., a bacterial natural product library.
- a library selected from the group consisting of: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA library; or a natural product library, e.g., a bacterial natural product library.
- the test compound is selected from the group consisting of: an enzyme substrate, a metabolite, a cofactor, a natural product (e.g., a bacterial natural product), a carbohydrate, a polysaccharide, a nucleic acid, (e.g., a nucleoside or nucleotide precursor, a ds or ss DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L- amino acid or a precursor thereof), a vitamin, a hormone, a lipid, a small organic molecule, a metals, a peptide, a protein, a lipid, a glycoprotein, a glycolipid, a transition state analog and combinations thereof.
- a natural product e.g., a bacterial natural product
- a carbohydrate e.g., a polysaccharide
- a nucleic acid e.g.,
- a test compound is a member of a combinatorial library.
- the target interacts with, e.g., binds, and preferably modifies, the test compound.
- Modify includes making or breaking a bond, e.g., a non- covalent or covalent bond, in the test compound or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing the test compound, or modified test compound structure or function, e.g., analyzing the physical properties of the the test compound or modified test compound; analyzing the test compound or modified test compound in vitro or in vivo activity.
- the method further includes: selecting a test compound or modified test compound, and contacting it with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the test compound or modified test compound has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes selecting test compound or modified test compound, e.g., on the basis of its interaction with the target and: purifying the test compound or modified test compound; crystallizing test compound or modified test compound; evaluating a physical property of a test compound or modified test compound, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes purifying the test compound or modified test compound, e.g., on the basis of its interaction with the target and: optimizing a property of test compound or modified test compound, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the target and the test compound or modified test compound, e.g., k cat , K M , or k D .
- the method can include the use of a linking reaction, e.g., a surrogate ligand, as described elsewhere herein.
- a linking reaction e.g., a surrogate ligand
- the invention features, a method of comparing two interactors, e.g., ligands, e.g., an initial ligand structure and a modification thereof.
- the interactors can be compared, e.g., for the ability to interact with a target, e.g., for the ability to bind or modify the target.
- the method includes:
- modified interactor e.g., modified ligand, i.e., a ligand molecule in which one or more changes have been made;
- step (g) comparing the measurements made in (c) and (f), thereby comparing two interactors or ligands, e.g., an initial structure and a modification thereof.
- the steps can be performed in any order, e.g., (a-c) on the one hand, can be performed first, and (d-f) on the other hand, subsequently.
- (a-c) on the one hand, and (d-f) on the other hand can be performed completely or partly simultaneously.
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Bo ⁇ elia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, My
- Mycobacterium tuberculosis Sanger Mycoplasma mycoides, Neisseria meningitidis strain, Streptomyces coelicolor, Actinobacillus actinomyce, Chlamydia trachomatis, Halobacterium sp., Mycoplasma capricolum, Neisseria gono ⁇ hea, Pseudomonas aeruginosa, Aspergillus nidulans, Candida albicans, Leishmania major, Neurospora crassa, Pneumocystis carinii, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma cruzi,
- Trypanosoma brucei Abelson murine leukemia virus, Adeno-associated virus 2 or -3, Dengue virus type 1, 2 or 3, Hepatitis A-G virus, Hepatitis GB virus B, Human T-cell lymphotropic virus type 1 or 2, Human T-cell lymphotropic virus type I, Human adenovirus type 12 or 2, Human he ⁇ esvirus 1-4, Human immunodeficiency virus type 1-2, Human parainfluenza virus 3, Human respiratory syncytial virus, Infectious hematopoietic necrosis virus, Influenza A virus, Influenza B virus, Influenza C virus and Measles virus. Additional examples of species that produce the targets tested using the methods of the invention are described below.
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- the target is produced by a human.
- the target e.g., a protein
- an organelle e.g., the mitochondria
- the target e.g., a protein
- the target has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the target is a naturally occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the target e.g., a protein, has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- a nucleic acid e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- the method further includes repeating one or more steps under a different condition, e.g., at a different salt concentration, different pH, or in the presence of a different cofactor.
- the target interacts with, e.g., binds, and preferably modifies, the interactor.
- Modify includes making or breaking a bond, e.g., a non-covalent or covalent bond, in the test compound or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. " Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing an interactor structure or function, e.g., analyzing the physical properties of an interactor; analyzing an interactor in vitro or in vivo activity
- the method further includes: selecting an interactor, e.g., based on its interaction with the target; and contacting an interactor with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if interactor has an effect on the cell or animal.
- the method further includes selecting an interactor, e.g., on the basis of its interaction with the target and: an interactor; an interactor; evaluating a physical property of an interactor, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- an interactor e.g., on the basis of its interaction with the target and: an interactor; an interactor; evaluating a physical property of an interactor, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes selecting an interactor on the basis of its interaction with the target and: optimizing a property of the interactor, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the protein and an interactor, e.g., k ⁇ t, KM, or ko-
- the method can include the use of a linking reaction, e.g., a surrogate ligand, as described elsewhere herein.
- a linking reaction e.g., a surrogate ligand
- the invention features, a method of comparing a subject molecule and a modification thereof, e.g., an initial structure and a modification thereof. The method includes:
- the steps can be performed in any order, e.g., (a-c) on the one hand, can be performed first and (d-f) on the other hand, subsequently or, (a-c) on the one hand, and (d-f) on the other hand, can be performed completely or partly simultaneously.
- the method further includes: selecting a modified molecule which interacts with the target; and confirming that the modified molecule interacts with, e.g., binds, to the target in a second test, e.g., one in which the surrogate ligand is not present.
- the method further includes: selecting a modified molecule which interacts with the target; and confirming that the modified molecule interacts with, e.g., binds, to the target by contacting the modified molecule with the target in vitro, e.g., in the absence of the su ⁇ ogate modified molecule.
- the method further includes: selecting a modified molecule which interacts with the target; and contacting the ligand with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the ligand has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes: purifying a test ligand; crystallizing a test ligand; evaluating a physical property of a test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes: optimizing a property of a chosen test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein,
- the change in heat is measured with a microcalorimeter.
- the invention features, a method of analyzing a compound, e.g., a protein or nucleic acid, e.g., a structured RNA, or other target.
- a compound e.g., a protein or nucleic acid, e.g., a structured RNA, or other target.
- the method includes:
- a denaturant e.g., guanidine hydrochloride, urea, or a similar agent
- the measurement is made with a microcalorimeter.
- the method includes: (a) providing reaction mixture which includes a target;
- the target is a protein or polypeptide, a nucleic acid, e.g., an RNA. It can be purified, partially purified, or in a crude state.
- a denaturant e.g., guanidine hydrochloride, urea, or a similar agent, is added to the reaction mixture.
- one or more conditions e.g., the concentration of the denaturant and the target, or the temperature, is chosen such the presence of a ligand that binds the relatively more compactly folded state results in a relatively large change in heat, e.g., by driving the target molecules into the folded state.
- the change in heat is measured with a microcalorimeter.
- the target e.g., a protein
- a pathogen e.g., a prokaryotic or a eukaryotic pathogen, including a bacterium, a protozoan, a virus, e.g., phage, or a fungus.
- the protein can be a protein produced by any of the following species: i
- Aquifex aeolicus Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Borrelia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Saccharomyces cerevisiae, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp., Pseudomonas aeruginosa, Ureaplasma urealyticum, Pyrobaculum aerophilum, Pyrococcus furiosus, Mycobacterium tuberculosis, Mycobacterium tuberculosis, Neisseria gonorrhea, Neisseria mening
- Neisseria meningitides Pseudomonas putida, Po ⁇ hyromonas gingivalis, Salmonella typhimurium, Shewanella putrefaciens, Streptococcus pneumoniae, Vibrio cholerae, Clostridium acetobutylicum, Campylobacter jejuni, Halobacterium salinarium Institute, Listeria monocytogenes, Mycobacterium tuberculosis Sanger, Mycoplasma mycoides, Neisseria meningitidis strain, Streptomyces coelicolor, Actinobacillus actinomyce, Chlamydia trachomatis, Halobacterium sp., Mycoplasma capricolum, Neisseria gonorrhea, Pseudomonas aeruginosa, Aspergillus nidulans, Candida albicans, Leishmania major, Neurospora crassa, P
- the target e.g., a protein
- a eukaryotic organism e.g., a single-celled or a multicellular organism.
- eukaryotic organisms include: Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- the target is produced by a human.
- the target, e.g., a protein is produced by an organelle, e.g., the mitochondria, of an organism.
- the target e.g., the protein
- the target has no known activity (e.g., enzymatic activity), or has an activity which is difficult to measure.
- the target e.g., protein
- the target has a known first activity and it is tested against a library which includes an interactor which interacts with the protein by way of a second activity, e.g., an unknown activity.
- the target is a naturally occurring protein or fragment thereof; a protein of unknown function and/or structure; a protein for which the hgand, substrate, or other interacting molecule is not known.
- the target e.g., the protein, has at least one enzymatic activity.
- the target is a nucleic acid, e.g., a DNA or RNA (e.g., structured
- RNA e.g., a ribozyme
- a plurality of library members is tested simultaneously, e.g., in the same reaction mixture, which can allow for an increase in the throughput of the method.
- a plurality of library members e.g., one which provides a positive result
- One or more library members from the plurality or from a smaller group, e.g., one which provides a positive result, can be tested individually.
- the method further includes repeating one or more steps under a different condition, e.g., at a different salt concentration, different pH, or in the presence of a different cofactor.
- the method further includes repeating at least one with a second or subsequent member or members of the library.
- a plurality of library members e.g., candidate substrates or test ligands, is tested.
- the plurality of library members includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 compounds.
- the plurality of library members includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 of the library members share a structural or functional characteristic.
- the library includes a plurality of members having a common characteristic, e.g., all members of the plurality are enzyme cofactors; substrates for, e.g., biosynthetic or degradative enzymes (e.g., protease substrates), including carbohydrates, nucleoside/nucleotides, amino acids, lipids; vitamins; hormones; nucleic acids; e.g., DNA molecules; or natural products, e.g., bacterial natural products.
- the library can include any metabolite, precursor, or intermediate of the members listed above.
- the library is: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA library; or a natural product library, e.g., a bacterial natural product library.
- a library member (a potential or candidate interactor) is a species which has potential to interact with a target, e.g., a target protein.
- a library member is a candidate substrate or a test ligand.
- a library member is selected from the group consisting of: an enzyme substrate, a metabolite, a cofactor, a natural product (e.g., a bacterial natural product), a carbohydrate, a polysaccharide, a nucleic acid, (e.g., a nucleoside or nucleotide precursor, a ds or ss DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L- amino acid or a precursor thereof), a vitamin, a hormone, a lipid, a small organic molecule, a metals, a peptide, a protein, a lipid, a glycoprotein, a glycolipid, a transition state analog and combinations thereof.
- a natural product e.g., a bacterial natural product
- a carbohydrate e.g., a polysaccharide
- a nucleic acid e.g.
- the method further includes testing the protein against at least one member of a second library.
- two, or more, libraries are tested simultaneously.
- the target can be tested against each (or some) members of a first library, e.g., a cofactor library, and each (or some) members of a second library, e.g., a library of potential substrates.
- a first library e.g., a cofactor library
- a second library e.g., a library of potential substrates.
- the target is tested against all or a plurality of the novel combinations, e.g., against (first], second]), (first] second 2 ) ... (first], secondso), and so on.
- a library member is a member of a combinatorial library.
- the target interacts with, e.g., binds, and preferably modifies, the library member.
- Modify includes making or breaking a bond, e.g., a non- covalent or covalent bond, in the test compound or the target. Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include changes in activity, e.g., enzymatic activity, physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: analyzing library member structure or function, e.g., analyzing the physical properties of the target; analyzing library member in vitro or in vivo activity.
- the method further includes: selecting a library member, e.g., candidate substrate or test ligand based on its interaction with the target; and confirming that the candidate substrate or test ligand is a substrate or a ligand, respectively.
- a library member e.g., candidate substrate or test ligand based on its interaction with the target.
- the method further includes: selecting a library member based on its interaction with the target; and contacting the library member with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the library member has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes selecting an interactor (e.g., a library member) on the basis of its interaction with the target and: purifying the library, e.g., a candidate substrate or test ligand; crystallizing a library member, e.g., a candidate substrate or test ligand; evaluating a physical property of a library member, e.g., a candidate substrate or test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- an interactor e.g., a library member
- the method further includes using a library member selected for interacting with the target to identify, e.g., by binding to or interacting with the selected library member, an agent which modulates an interaction between the target and the selected library member.
- the method further includes selecting an interactor (e.g., a library member) on the basis of its interaction with the target and: optimizing a property of a chosen library member, e.g., candidate substrate or test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein.
- an interactor e.g., a library member
- the change in heat output is measured with a microcalorimeter.
- the method further includes determining a physical constant of an interaction between the protein and a member of the library, e.g., kcat, KM, or ko-
- the invention features, a method of analyzing an interactor, e.g., a substrate, e.g., discovering a target molecule which modifies the substrate.
- the method includes: providing a reaction mixture which includes the interactor, e.g., substrate: contacting the interactor with a candidate target; evaluating a change in heat the reaction mixture; optionally, comparing the value for heat change obtained with a predetermined value, thereby of analyzing a interactor, e.g., discovering a target for the interactor.
- the interactor is identified by a change in the heat of the reaction mixture, e.g., change which is greater than a predetermined value.
- a plurality of candidate targets are tested.
- the plurality of candidate targets includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 candidate targets.
- the target interacts with, e.g., binds, and preferably modifies, the substrate.
- Modify includes making or breaking a bond, e.g., a non-covalent or covalent bond, in the surrogate ligand (or in the signal-generating entity itself).
- Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include physical changes in phase, changes in aggregation, or polymerization.
- the method further includes: selecting a candidate target; and confirming that candidate target modified the target.
- the method further includes: selecting a candidate target; and contacting the candidate target with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the candidate target has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes: purifying a candidate target; crystallizing a candidate target; evaluating a physical property of a candidate target, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes: optimizing a property of a chosen candidate target, e.g., optimizing affinity for the substrate, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein, In- a prefe ⁇ ed embodiment, the change in heat is measured with a microcalorimeter.
- the invention features, a method of analyzing a target, e.g., analyzing an interaction of a target and a second entity.
- the method includes: providing a reaction mixture containing the target, allowing the interaction to proceed, wherein the interaction is linked to a linking interaction, e.g., a linking reaction, e.g., the release of a su ⁇ ogate-ligand or a change in conformation; allowing a product of the linking reaction to enter a second reaction, e.g., the cleavage or degradation of a surrogate ligand; and measuring the heat change from the second reaction, thereby analyzing an interaction of the target.
- a linking interaction e.g., a linking reaction, e.g., the release of a su ⁇ ogate-ligand or a change in conformation
- a product of the linking reaction to enter a second reaction, e.g., the cleavage or degradation of a surrogate ligand
- the linking reaction or the second reaction can include a change in phase.
- one or more additional reactions can be inte ⁇ osed between the linking reaction and the second reaction.
- the interaction of the target can be, e.g., an interaction between the target and another molecule, e.g., a ligand or a solute molecule, or an interaction of a first moiety of the target with a second moiety of the target, e.g., autophosphorylation, or a change in the conformation of the target, e.g., the secondary, tertiary, or quartenary, structure of the target.
- the reaction mixture is not transparent; the reaction mixture is colored; the reaction mixture is turbid; the reaction mixture contains a substance which interferes with fluorescent or colorimetric detection; the reaction mixture is not a pure solution, e.g., it contains products other than the target.
- the reaction mixture contains: a substance which interferes with radioactive analysis; a substance which interferes with spectrophotometric analysis, e.g., NMR analysis.
- a prefe ⁇ ed embodiment the change in heat is measured with a microcalorimeter.
- the invention features, a method of analyzing a test ligand, target, or an interaction between the two.
- the method includes: providing a reaction mixture containing a su ⁇ ogate ligand and a target, contacting the reaction mixture with the test ligand and with a signal-generating entity; wherein the signal-generating entity is present with the su ⁇ ogate ligand under conditions which allow it to interact with su ⁇ ogate ligand, e.g., with surrogate ligand which has been displaced from the target by binding of the test ligand to the target; and measuring the change in heat in the reaction mixture, thereby analyzing a test ligand, target, or an interaction between the two.
- the su ⁇ ogate hgand exhibits negative heterotropic linkage with respect to a test ligand which can bind the target, (i.e., it is displaced upon binding of the test ligand to the target).
- a test ligand which can bind the target, (i.e., it is displaced upon binding of the test ligand to the target).
- the invention also includes embodiments wherein the surrogate ligand binds the target upon binding of the test ligand, thereby reducing the level of free surrogate ligand and thereby providing less surrogate ligand to interact with the signal-generating entity.
- the interaction between the signal-generating entity and the su ⁇ ogate ligand occurs more readily between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand.
- the interaction between the signal-generating entity and free (as opposed to target-bound) surrogate ligand occurs at least 2, 5, 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 fold more readily between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand.
- the invention also includes embodiments wherein the interaction between the signal-generating entity and the surrogate ligand occurs more readily between the signal-generating entity and target-bound (as opposed to free) surrogate ligand.
- the interaction between the signal-generating entity and target-bound (as opposed to free) surrogate ligand occurs at least 2, 5, 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 fold more readily between the signal-generating entity and target-bound (as opposed to free) su ⁇ ogate ligand.
- the su ⁇ ogate ligand is an ion, e.g., a proton.
- the signal-generating entity is a buffer molecule, e.g., with a relatively large heat of ionization, e.g., Tris HCL.
- the su ⁇ ogate ligand is factor which modulates, e.g., increases or decreases, the activity of the signal-generating entity.
- the surrogate ligand can be a metal ion which activates (or inhibits) an enzyme which is the signal-generating entity.
- the signal-generating entity interacts with, e.g., binds, and preferably modifies, su ⁇ ogate ligand, e.g., free su ⁇ ogate ligand.
- Modify includes making or breaking a bond, e.g., a non-covalent or covalent bond, in the su ⁇ ogate ligand (or in the signal-generating entity itself).
- Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can also include physical changes in phase, changes in aggregation, or polymerization.
- the target is a protein or polypeptide
- the su ⁇ ogate ligand is a nucleic acid
- the signal-generating entity is an enzyme which cleaves a bond in a nucleic acid, e.g., a nuclease.
- the method further includes: selecting a ligand which interacts with the target; and confirming that the ligand interacts with, e.g., binds, to the target, in a second test, e.g., one in which the surrogate ligand is not present.
- the method further includes: selecting a test ligand which interacts with the target; and confirming that the test ligand interacts with, e.g., binds, to the target by contacting the ligand with the target in vitro, e.g., in the absence of the surrogate ligand.
- the method further includes: selecting a ligand which interacts with the target; and contacting the ligand with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the ligand has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes: purifying a test ligand; crystallizing a test ligand; evaluating a physical property of a test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes: optimizing a property of a chosen test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein,
- the su ⁇ ogate ligand e.g., a su ⁇ ogate ligand, e.g., a nucleic acid
- the su ⁇ ogate ligand is amplified, e.g., with PCR or more preferably with an isothermal amplification method, prior to interaction with the signal-generating entity.
- the change in heat is measured with a microcalorimeter.
- the signal-generating entity interacts directly with the surrogate hgand. In other embodiments is interacts indirectly, e.g., it interacts with an amplification product generated from the surrogate ligand or it acts on the product of a reaction between the surrogate ligand and another entity.
- the invention features, a method of analyzing a target, a test ligand, or the interaction between the two.
- the method includes: providing a reaction mixture containing a surrogate ligand and the target; contacting the reaction mixture with the test ligand and with a signal-generating entity; wherein the signal-generating entity is present with the su ⁇ ogate ligand under conditions which allow it to interact with free su ⁇ ogate ligand, e.g., with surrogate ligand which has been displaced from the target by binding of the test ligand; and measuring the change in heat in the reaction mixture, thereby analyzing a test ligand, target, or an interaction between the two.
- the su ⁇ ogate ligand exhibits negative heterotropic linkage with respect to a test ligand which can bind the target, (i.e., it is displaced upon binding of the test ligand to the target). This is the prefe ⁇ ed embodiment and the subject of most of the discussion herein.
- the invention also includes embodiments wherein the su ⁇ ogate ligand binds the target upon binding of the test ligand, thereby reducing the level of free su ⁇ ogate ligand and thereby providing less su ⁇ ogate ligand to interact with the signal-generating entity.
- the interaction between the signal-generating entity and the surrogate ligand occurs more readily between the signal-generating entity and free (as opposed to target-bound) surrogate ligand.
- the interaction between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand occurs at least 2, 5, 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 fold more readily between the signal-generating entity and free (as opposed to target-bound) surrogate ligand.
- the invention also includes embodiments wherein the interaction between the signal-generating entity and the surrogate ligand occurs more readily between the signal-generating entity and target-bound (as opposed to free) surrogate ligand.
- the interaction between the signal-generating entity and target-bound (as opposed to free su ⁇ ogate hgand occurs at least 2, 5, 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 fold more readily between the signal-generating entity and target-bound (as opposed to free) surrogate ligand.
- the signal-generating entity interacts with, e.g., binds, and preferably modifies, free surrogate ligand.
- Modify includes making or breaking a bond, e.g., a non-covalent or covalent bond, in the surrogate ligand (or in the signal-generating entity itself).
- Modification includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation labeling, ligation, synthesis, and similar reactions. Modification can include physical changes in phase, changes in aggregation, or polymerization.
- the signal-generating entity is a degradative enzyme.
- the su ⁇ ogate ligand is a nucleic acid and the signal-generating entity is an enzyme which modifies a nucleic acid, or uses the nucleic acid for a substrate or template, e.g., the signal-generating entity an enzyme, e.g., a nuclease, e.g., a DNAse, e.g., an endonuclease or an exonuclease, a polymerase, e.g., a DNA polymerase: the signal-generating entity modifies a protein, e.g., by making or breaking a covalent or non-covalent bond in the su ⁇ ogate ligand (or itself) e.g., it cleaves a peptide bond, e.g., is a protease, and the su ⁇ ogate ligand includes a peptide bond,
- the method further includes: selecting a ligand which interacts with the target; and confirming that the test ligand interacts with, e.g., binds, to the target in a second test, e.g., one in which the su ⁇ ogate ligand is not present.
- the method further includes: selecting a test ligand which interacts with the target; and confirming that the ligand interacts with, e.g., binds, to the target by contacting the test ligand with the target in vitro, e.g., in the absence of the surrogate ligand.
- the method further includes: selecting a test ligand which interacts with the target; and contacting the test ligand with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the test ligand has an effect on the cell or animal.
- a cell e.g., a cultured cell, or an animal
- the method further includes: purifying a test ligand; crystallizing a test ligand; evaluating a physical property of a test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes: optimizing a property of a chosen test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein,
- the reaction mixture is not transparent; the reaction mixture is colored; the reaction mixture is turbid; the reaction mixture contains a substance which interferes with fluorescent or colorimetric detection; the reaction mixture is not a pure solution, e.g., it contains products other than the target.
- the reaction mixture contains: a substance which interferes with radioactive analysis; a substance which interferes with spectrophotometric analysis, e.g., NMR analysis.
- the surrogate ligand e.g., a nucleic acid
- is amplified e.g., with PCR or more preferably with an isothermal amplification method, prior to interaction with the signal-generating entity.
- the change in heat is measured with a microcalorimeter.
- the signal-generating entity interacts directly with the surrogate hgand. In other embodiments is interacts indirectly, e.g., it interacts with an amplification product generated from the surrogate ligand or it acts on the product of a reaction between the surrogate ligand and another entity.
- the invention features, a method of analyzing a target, a test ligand, or the interaction between the two.
- the method includes: providing a reaction mixture containing a su ⁇ ogate ligand, which is a nucleic acid, and the target; contacting the reaction mixture with the test ligand and with a signal-generating entity, which is a molecule which makes or breaks a bond, e.g., a covalent or non-covalent bond, in the su ⁇ ogate ligand; wherein the signal-generating entity is present with the su ⁇ ogate ligand under conditions which allow it to interact with free surrogate ligand, e.g., with surrogate ligand which has been displaced from the target by binding of the test ligand; and measuring the change in heat in the reaction mixture, thereby analyzing a test ligand, target, or an interaction between the two.
- the su ⁇ ogate hgand exhibits negative heterotropic linkage with respect to a test ligand which can bind the target, (i.e., it is displaced upon binding of the test ligand to the target).
- the interaction between the signal-generating entity and the surrogate ligand occurs more readily between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand.
- the interaction between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand occurs at least 2, 5, 10, 10 2 , 10 3 , 10 4 , 10 , 10 , 10 , or 10 fold more readily between the signal-generating entity and free (as opposed to target-bound) su ⁇ ogate ligand.
- the signal-generating entity is a degradative enzyme.
- the signal-generating entity is an enzyme which modifies a nucleic acid, or uses the nucleic acid for a substrate or template, e.g., the signal-generating entity an enzyme, e.g., a nuclease, e.g., an endonuclease or an exonuclease, a polymerase, e.g., a DNA polymerase.
- an enzyme e.g., a nuclease, e.g., an endonuclease or an exonuclease
- a polymerase e.g., a DNA polymerase.
- the method further includes: selecting a test ligand which interacts with the target; and confirming that the test ligand interacts with, e.g., binds, to the target in a second test, e.g., one in which the su ⁇ ogate ligand is not present.
- the method further includes: selecting a ligand which interacts with the target; and confirming that the test ligand interacts with, e.g., binds, to the target by contacting the test ligand with the target in vitro, e.g., in the absence of the surrogate ligand.
- the method further includes: selecting a test ligand which interacts with the target; and contacting the test ligand with a cell, e.g., a cultured cell, or an animal, and, optionally, determining if the ligand has an effect on the cell or animal.
- a test ligand which interacts with the target
- a cell e.g., a cultured cell, or an animal
- the method further includes: purifying a test ligand; crystallizing a test ligand; evaluating a physical property of a test ligand, e.g., molecular weight, isoelectric point, sequence (where relevant), or crystal structure.
- the method further includes: optimizing a property of a chosen test ligand, e.g., optimizing affinity for the target, altering molecular weight, e.g., decreasing molecular weight, or altering, e.g., increasing, solubility. Optimization can be performed using known methods or methods disclosed herein,
- the su ⁇ ogate ligand is amplified, e.g., with PCR or more preferably with an isothermal amplification method, e.g., prior to interaction with the signal- generating entity.
- the change in heat is measured with a microcalorimeter.
- the signal-generating entity interacts directly with the su ⁇ ogate ligand. In other embodiments is interacts indirectly, e.g., it interacts with an amplification product generated from the surrogate ligand or it acts on the product of a reaction between the su ⁇ ogate ligand and another entity.
- the invention features a library of interaction candidates, e.g., a library of candidate substrates or test ligands as described herein.
- the library includes at least one member which is known to interact with a target.
- the library is: a substrate library; a cofactor library; a carbohydrate biosynthesis and/or degradation library; a purine and pyrimidine biosynthesis and/or degradation library; an amino acid biosynthesis and/or degradation library; a lipid biosynthesis and/or degradation library; a vitamin and/or hormone library; a nucleic acid, e.g., DNA library; or a natural product library, e.g., a bacterial natural product library.
- a library member is a species which has potential to interact with a target, e.g., a target protein.
- a library member is a candidate substrate or a test ligand.
- a library member is selected from the group consisting of: an enzyme substrate, a metabolite, a cofactor, a natural product (e.g., a bacterial natural product), a carbohydrate, a polysaccharide, a nucleic acid (e.g., a nucleoside or nucleotide precursor, a double- stranded (ds) or single-stranded (ss) DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L-amino acid or a precursor thereof), a vitamin, a hormone, a lipid, a small organic molecule, a metals, a peptide, a protein, a lipid, a glycoprotein, a glycolipid, a transition state analog and combinations thereof.
- a natural product e.g., a bacterial natural product
- a carbohydrate e.g., a polysacchari
- the library includes a plurality of members having a common characteristic, e.g., all members of the plurality are enzyme cofactors; substrates for, e.g., biosynthetic or degradative enzymes (e.g., protease substrates), including carbohydrates, nucleoside/nucleotides, amino acids, lipids; vitamins; hormones; nucleic acids; e.g., DNA molecules; or natural products, e.g., bacterial natural products.
- the library can include any metabolite, precursor, or intermediate of the members listed above.
- the library can include any combination of members having different characteristics.
- a library of cofactors can be combined with a library of substrates for biosynthetic or degradative enzymes.
- the library includes at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 compounds.
- the library includes at least 10, 10 , 10 , 10 , 10 , 10 , 10 , or 10 8 of the library members which share a structural or functional characteristic.
- the library can include combinations of members sharing structural or functional characteristics.
- the library can include at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 s of the library members which share a structural or functional characteristic and at least 10, 10 2 , 10 3 , 10 4 , 10 5 , 10 6 , 10 7 , or 10 8 of the library members which share a different structural or functional characteristic.
- a combination of two, or more, libraries is tested with a target simultaneously.
- the target can be tested against each (or some) members of a first library, e.g., a cofactor library, and each (or some) members of a second library, e.g., a library of potential substrates.
- a first library e.g., a cofactor library
- a second library e.g., a library of potential substrates.
- the target is tested against all or a plurality of the novel combinations, e.g., against (first], second]), (first] second 2 ) ... (first], second 50 ), and so on.
- Figure I depicts a schematic diagram of the target-mediated conversion of a test substrate(s) into a product(s). Such conversion generates a heat signal.
- This method measures the heat output generated from the interaction between a test substrate and a target (e.g., a target protein).
- a target e.g., a target protein
- the target-mediated conversion of a test substrate(s) into a product(s) generates a heat signal.
- the heat signal can be detected calorimetrically.
- FIG. 2 depicts a schematic diagram of the molecular detection switch to detect binding of a test ligand.
- This method uses the generation of a heat signal to identify the interaction of a test ligand with a target (e.g., a target protein).
- a su ⁇ ogate ligand is incubated in the presence of the target such that an interaction (e.g., binding) occurs.
- the surrogate ligand is displaced.
- the free su ⁇ ogate ligand i.e., the displaced su ⁇ ogate ligand
- serves as a substrate for a signal-generating entity e.g., an enzyme, in such a manner that a heat signal is generated.
- a signal-generating entity e.g., an enzyme
- Figures 3A-3B depict a read-out of the rate of heat generated ( ⁇ cal/sec) during a substrate screen with hexokinase with respect to time (sec).
- Figure 3A shows the heat flow in the presence of a substrate, which reaches a maximum soon after the addition of enzyme to the reaction cell and then decays to the baseline as the level of substrate is depleted.
- Figure 3B shows a control (carbohydrate library minus substrate)
- Figure 4 depicts the experimental flow chart for the substrate screen with hexokinase.
- Figure 5a(i) shows the heat released upon binding of hexokinase to glucose over time. As time proceeds, the fixed amount of hexokinase in the cell is bound, so additional glucose produces less heat. 5 ⁇ l injections of a 5 ⁇ M solution of glucose were titrated into the calorimetric cell containing 2 ml of a 50 nM solution of hexokinase. Because no ATP is present, the glucose merely binds to the protein. The heat released from each injection was measured and the binding constant calculated from those measurments.
- Figure 5a(ii) shows heat released as hexokinase phosphorylates glucose in the presence of ATP, converting ATP to ADP.
- a single 5 ⁇ l injection of a 20 ⁇ M solution of hexokinase was titrated into the calorimetric cell containing 2 ml of a solution of 100 ⁇ M glucose and 1 mM ATP.
- a large negative heat is observed as the hexokinase acts on the glucose.
- Figure 5b compares rates of reaction of glucose and ATP catalyzed by hexokinase measured by two different techniques: UV spectrophotometry and calorimetry.
- the heat output of the reaction from figure 5 a (ii) is plotted with respect to time.
- the reaction was also measured using a second assay, both methods give the same rates for the reaction (within experimental error).
- Figure 6 compares rates of reaction of thrombin-catalyzed cleavage of a labeled peptide substrate (SAR-PRO-ARG-parantroanilide) with UV spectrophotometry and calorimetry.
- the PNA paranitronalide
- Figures 7A-7D demonstrate the use of the present invention to deconvolute a mixture of compounds.
- Hexokinase and glucose were present in each test.
- Various mixtures of cofactors were added to each test. Only when ATP was present in the mixture was a significant amount of heat generated.
- 5 ⁇ l injections of a 20 ⁇ M solution of hexokinase were titrated into a solution of 100 ⁇ M glucose and one or more "cofactors", all at 1 mM concentration. In the initial experiment with the entire library of 15 cofactors present, enzymatic turnover was observed (as
- Figure 8 demonstrates calorimetric measurement of hexokinase-catalyzed glucose phosphorylation in the presence of a complex mixture of natural products.
- 5 ⁇ l injections of a 20 ⁇ M solution of hexokinase were titrated into solutions of 100 ⁇ M glucose and 1 mM ATP and increasing concentrations of tea.
- Tea solutions can simulate natural product extracts, i.e., complex mixtures.
- Significant enzymatic activity (turnover) was observed at all but the highest concentrations of tea.
- Figure 9 demonstrates the use of calorimetry to aid in determining function of cryptic proteins.
- E. coli protein YJ ⁇ Q binds to GTP analog GTP-gamma-S.
- a K d of 115 ⁇ M was determined.
- 5 ⁇ l injections of an 11 mM GTP-gamma-S solution were titrated into 2 ml of a solution containing 385 ⁇ M of an E. coli protein for which no function was previously known.
- the experiment shows that the protein binds this molecule (an analog of GTP), allowing us to putatively assign GTP-binding properties to this protein.
- the abso ⁇ tion or evolution of heat is a universal property of chemical reactions.
- Methods described herein link an interaction, e.g., binding, of a test compound or an interactor, e.g., a test ligand or a candidate substrate, with a target (e.g., a target macromolecule, e.g., a target protein or nucleic acid) to a change in heat.
- a target e.g., a target macromolecule, e.g., a target protein or nucleic acid
- the heat output is detected by calorimetry. This allows analysis of the interaction without imposing sha ⁇ ly constraining limitations on the type, range, or specific identity of the activity of the target.
- an interactor e.g., a substrate
- methods of the invention detect a change in heat generated upon conversion of a test substrate(s) into a produces) or, where the target and interactor are ligand and counter-ligand, upon binding.
- Some embodiments of the invention require no assumptions about the nature of the target and its interaction with its interactor, e.g., its naturally occurring ligand, substrate, or binding partner.
- Other methods of the invention inco ⁇ orate knowledge of or assumptions about the target (and/or interactor) to guide in the choice of potential interactors.
- embodiments of the invention use genomic, or other bioinformatic analyses of the target to optimize and/or prioritize the choice of interactors against which to test the target.
- Libraries of interaction candidates e.g., a library of candidate substrate or test ligands as described herein, are also within the scope of the present invention.
- the methods and compositions, e.g., libraries, of the present application can be used for diagnostic testing, for
- Agents e.g., pharmaceutical agents, identified using the methods described herein are also within the scope of the present invention.
- test compound also refe ⁇ ed to as an “interactor” is a species which has potential to interact with a target, e.g., a target macromolecule, (e.g., a protein or nucleic acid).
- a target e.g., a target macromolecule, (e.g., a protein or nucleic acid).
- the test compound can be a candidate substrate or a test ligand.
- a test compound can be any agent, including without limitation small organic molecules, metals, peptides, proteins, lipids, glycoproteins, glycolipids, carbohydrates, polysaccharides, nucleic acids (e.g., a nucleoside or nucleotide precursor, a ds or ss DNA molecule, a circular nucleic acid, a super-coiled nucleic acid), an amino acid, (e.g., a D- or L-amino acid or a precursor thereof), a vitamin, a hormone, enzyme substrates, metabolites, transition state analogs, cofactors, natural products (e.g., bacterial natural products) and combination thereof.
- a library can comprise a plurality of test compounds.
- a “mixture” or “reaction mixture” can be a complex combination of substances, e.g., impure samples, such as suspensions, natural product extracts, cell homogenates, cell lysates or cell extracts, whole cells, reconstituted systems, biochemical mixtures, biological samples, tissue samples, biological fluids, or colored solutions, which may include more than one test compound.
- impure samples such as suspensions, natural product extracts, cell homogenates, cell lysates or cell extracts, whole cells, reconstituted systems, biochemical mixtures, biological samples, tissue samples, biological fluids, or colored solutions, which may include more than one test compound.
- a “candidate substrate” is a substance which gives rise to a different chemical entity when acted on.
- Exemplary candidate substrates include an enzyme substrate; a metabolite; a cofactor (e.g., a group transfer and energy coupling molecule); a natural product, e.g., a bacterial natural product; a carbohydrate; a polysaccharide; a nucleic acid, e.g., a nucleoside or nucleotide precursor, a double-stranded (ds) or single-stranded (ss) DNA molecule; an amino acid, e.g., a D- or L-amino acid or a precursor thereof; a vitamin; a hormone; a lipid, among others.
- a "test ligand” is a member of a combinatorial library; is a drug candidate; is from a library of compounds; a library of natural compounds, e.g., fungal products or fermentation products; organic synthesis libraries.
- the hgand is: a polypeptide which has been expressed from a nucleic acid from a population of nucleic acids, e.g., from a cDNA library, a differentially expressed cDNA library, a genomic library, a library
- a "library” is a collection substances which can potentially interact with a target.
- the library includes at least one member which is known to interact with a target.
- a “substrate library” is a collection of compounds for which targets, e.g., proteins, e.g., those of unknown function (also refe ⁇ ed to herein as "unknowns") can be screened against for potential interaction, e.g., enzymatic activity. Interaction, e.g., enzymatic activity will result in a change in heat output which will be detected by the calorimeter.
- the term "target” refers to any molecule of interest.
- the target is a protein or polypeptide, e.g., a naturally occurring protein or fragment thereof; a protein of unknown function; a protein for which the ligand, substrate, or other interacting molecule is not known.
- the target can be nucleic acid, e.g., a DNA or RNA (e.g., structured RNA, e.g., a ribozyme).
- Targets include molecules (e.g., peptides, proteins or nucleic acids), having known or unknown structure or function.
- the target is a protein without a catalytic activity, with no known catalytic activity, or has a catalytic activity which is difficult to measure.
- a target can also be a carbohydrate, a polysaccharide, and a glycoprotein, among others.
- the term "su ⁇ ogate ligand” refers to an agent that interacts with (e.g., binds to) a target, e.g., a target protein.
- the surrogate ligand can be naturally associated with the target, or not naturally associated with the target.
- the su ⁇ ogate ligand has a K D for the target of at least lO '1 , 10 ⁇ 2 , 10 '4 . 10 "6 , 10 '8 , 10 "10 , 10 '12 , 10 '15 , 10 "20 , 10 "25 , lO ⁇ M '1 .
- the surrogate ligand meets the following criteria: (1) the surrogate ligand exhibits a heterotropic linkage with respect to a test ligand (i.e., it must be displaced upon binding of a test ligand (negative heterotropic linkage), or its binding to a target is enabled with respect to the test ligand (positive heterotropic linkage); and 2) the surrogate ligand in its "free" or displaced form serves as a switch to generate an amplified signal.
- the displaced su ⁇ ogate ligand serves as a substrate for an enzyme.
- the su ⁇ ogate ligand can interact with (e.g., bind
- the su ⁇ ogate ligand can catalytically alter the target, or alter the functional activity of the target.
- su ⁇ ogate ligands include anions, cations, protons, water and other solution phase components are found in association with a target.
- non-naturally occurring surrogate ligands include synthetic protein, a peptide and nucleic acid sequences (e.g., a DNA or an RNA molecule).
- a surrogate ligand of the invention is not limited to an agent that interacts with (e.g., binds to) a recognized functional region of the target protein, e.g. the active site of an enzyme, the antigen-combining site of an antibody, the hormone-binding site of a receptor, a cofactor-binding site, and the like.
- the su ⁇ ogate ligand is a nucleic acid molecule (also refe ⁇ ed to herein as a "su ⁇ ogate nucleic acid ligand").
- nucleic acid molecule refers to DNA, RNA, single-stranded or double-stranded and any chemical modifications thereof. Exemplary modifications include, but are not limited to, those which provide other chemical groups that inco ⁇ orate additional charge, polarizability, hydrogen bonding, and electrostatic interaction to the nucleic acid.
- Such modifications include, but are not limited to, 2'-position sugar modifications, 5-position pyrimidine modifications, 8-position purine modifications, modifications at exocyclic amines, substitutions of 4-thiouridine, substitution of 5-bromo or 5-iodo-uracil, backbone modifications, methylations, base-pairing combinations such as the isobases isocytidine and isoguanidine, as well as 3' and 5' modifications such as capping.
- the term "su ⁇ ogate nucleic acid ligand" includes a nucleic acid molecule comprising two to forty nucleotides, preferably ten to thirty nucleotides, more preferably, fifteen to twenty-five nucleotides, and most preferably, twenty nucleotides. Accordingly, in preferred embodiments, the surrogate ligand is an oligonucleotide. In one embodiment, the surrogate nucleic acid ligand is identified using the SELEX procedure as described in detail below, and in Gold et al. (1995) Annu. Rev. Biochem.
- the term "signal-generating entity” is an entity which interacts with a surrogate ligand in a non-isothermal process, preferably an exothermic process.
- the signal-generating entity amplifies a signal generated by a test ligand.
- the signal-generating entity may interact with (e.g., binds to) and preferably, modify a surrogate ligand in a manner that gives rise to a signal, e.g., heat output.
- a typical signal-generating entity is an enzyme which undergoes an exothermic or endothermic reaction with a su ⁇ ogate ligand.
- the signal-generating entity interacts more readily with a free surrogate ligand, as opposed to a su ⁇ ogate ligand bound to a target.
- the signal-generating entity modifies the free (as opposed to target-bound) su ⁇ ogate ligand by, e.g., forming or breaking a covalent or a non-covalent bond.
- the modification step may involve cleavage, degradation, phosphorylation, polymerization, or any other event that generates a signal, e.g., a heat signal.
- the signal-generating entity can be a degradative enzyme (e.g., a nuclease or a protease).
- the signal-generating entity can be a polymerizing enzyme, e.g., a polymerase.
- the signal-generating entity can be a nuclease, such as a staphylococcal nuclease (SNase), Serratia marcescens nuclease (SNase), bovine pancreatic nuclease (DNase I), or human (type IV) nuclease.
- the signal-generating entity can be a polymerase, e.g., a Tac polymerase.
- the signal-generating entity can be a ribonuclease (e.g., an RNAse).
- the signal-generating entity can be a protease.
- Exemplary proteases include, but are not limited to, trypsin, chymotrypsin, V8 protease, elastase, carboxypeptidase, proteinase K, thermolysin, papain and subtilisin.
- an enzyme requiring the metal for activation can be used as the signal-generating entity.
- the signal-generating entity can be a solution (e.g., a buffer solution) that amplifies the molecular events which occur when a test ligand binds to a target (e.g., a target protein).
- a target e.g., a target protein
- many target proteins release or bind a large number of protons when they bind to a test ligand. These release or absorbtion events are said to be "linkage" events.
- the linkage process can be amplified by introducing in the solution a buffer molecule with a large heat
- the signal-generating entity can be a change in phase, or an aggregation or polymerization of material.
- the interaction of a first molecule with a second can include a change in the association of the two molecules, e.g., an increase or decrease, in the binding of the two molecules or a modification of either or both of the molecules.
- modification includes, making or breaking a bond, e.g., a non-covalent or covalent bond. It includes cleavage, degradation, hydrolysis, a change in the level of phosphorylation, labeling, ligation, synthesis, and similar reactions.
- Modification can include physical changes in phase, changes in aggregation, or polymerization. In the case of the interaction with a signal-generating entity the modification is not isothermal, and is preferably exothermic.
- the phrase "analyzing a ligand” can include one or more of: determining if the ligand binds to the target; evaluating the affinity of a test ligand for a target.
- the targets used in the methods of the present invention can be any molecule of interest.
- the target is a protein or polypeptide (also referred to herein as a "target protein"), e.g., a naturally occurring protein or fragment thereof; a protein of unknown function; a protein for which the ligand, substrate, or other interacting molecule is not known.
- target proteins include, without limitation, receptors, enzymes, oncogene products, tumor suppressor gene products, transcription factors, and infectious proteins (e.g., proteins obtained from an infectious organism, e.g., viral, parasitic, bacterial, and/or fungal proteins).
- target proteins may comprise wild type proteins, or, alternatively, mutant or variant proteins, including those with altered stability, activity, or other variant properties, or hybrid proteins to which foreign amino acid sequences, e.g. sequences that facilitate purification have been added (e.g., a glutathione S- transferase (GST) moiety).
- GST glutathione S- transferase
- the target proteins can be either in purified form or in impure form (e.g., as part of a complex mixture of proteins and other compounds as described herein).
- the target protein can be a recombinant protein or a biochemical isolate.
- the target can be any protein encoded by a gene isolated from a prokaryotic or eukaryotic organism. The isolated gene can be cloned into an expression vector, and introduced into a suitable host cell under
- Vectors can be, e.g., plasmids, viral vectors, among others.
- the vectors are modified, e.g., by linking the gene encoding the target protein to appropriate regulatory sequences, such that appropriate expression of the target protein is obtained.
- regulatory sequences include promoters, enhancers and other expression control elements (e.g., poly-adenylation signals) (see e.g., Goeddel; (1990) Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA).
- Targets may be obtained from a prokaryotic or a eukaryotic organism, such as microorganisms (e.g., bacteria, viruses, parasites), vertebrate or invertebrate animals (e.g., mammals, e.g., humans).
- microorganisms e.g., bacteria, viruses, parasites
- vertebrate or invertebrate animals e.g., mammals, e.g., humans.
- Exemplary prokaryotic organisms include: Aquifex aeolicus, Pyrococcus horikoshii, Bacillus subtilis, Treponema pallidum, Bo ⁇ elia burgdorferi, Hehcobacter pylori, Archaeoglobus fulgidus, Methanobacterium thermo., Escherichia coli, Mycoplasma pneumoniae, Synechocystis sp. PCC6803, Methanococcus jannaschii, Mycoplasma genitalium, Haemophilus influenzae, Rickettsia prowazekii, Pyrococcus abyssii, Bacillus sp.
- Exemplary eukaryotic organisms include: Aspergillus nidulans, Candida albicans, Leishmania major, Neurospora crassa, Pneumocystis carinii, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma cruzi, Trypanosoma brucei, Tetrahymena sp., Cryptosporidium parvum, Arabidopsis thaliana M, Brugia malayi, Caenorhabditis elegans, Drosophila melanogaster, Shistosoma mansoni, Shistosoma japonicum, and mammals, e.g., humans.
- Targets can be produced by an organelle of a eukaryotic organism.
- the target can be a mitochondrial enzyme.
- the organisms for which the genomes of organelles are known include: Chlorarachnion, GuiUardia theta, Cyanophora paradoxa, Epifagus virginiana, Euglena gracilis, GuiUardia theta, Marchantia polymo ⁇ ha, Nicotiana tabacum, Odontella sinensis, Oryza sativa, Po ⁇ hyra pu ⁇ urea, Pinus thunbergiana, Acanthamoeba castellanii, Allomyces macrogynus, Bos Taurus, cafeteria roenbergensis, Chrysodidymus synuroideus, Chondrus crispus, Chlamydomonas reinhardtii, Drosophila melanogaster, Drosophila yakuba, Equus asinus, Homo sapiens, Mus musculus,
- Targets can also be produced by phage, including without limitation, Acholeplasma bacteriophage, Acholeplasma phage/virus, Bacteriophage bIL67, Bacteriophage Cp-1, Bacteriophage G4, Bacteriophage HP1, Bacteriophage IKe, Bacteriophage lambda, Bacteriophage MS2, Bacteriophage PRDl , Bacteriophage PZA, Bacteriophage T4 and Lactococcus bacteriophage C2.
- phage including without limitation, Acholeplasma bacteriophage, Acholeplasma phage/virus, Bacteriophage bIL67, Bacteriophage Cp-1, Bacteriophage G4, Bacteriophage HP1, Bacteriophage IKe, Bacteriophage lambda, Bacteriophage MS2, Bacteriophage PRDl , Bacteriophage PZA, Bacteriophage T4 and Lactococcus bacteriophage C2.
- Targets may also be viral proteins.
- viruses that can produce the target include: Abelson murine leukemia virus, Adeno-associated virus 2, Adeno-associated virus 3, African swine fever virus, Alfalfa mosaic virus, Apple chlorotic leaf spot virus, Apple stem grooving virus, Arabis mosaic virus satellite, Arctic ground squirrel hepatitis B virus, Artichoke mottled crinkle virus, Autographa califomica nuclear polyhedrosis virus, Avian carcinoma virus,
- Pepper huasteco vims Pepper mottle vims, Plum pox vims, Polyomavims strain a2, Polyomavims strain a3, Potato leaf roll vims, Potato mop-top vims, Potato vims A, Potato vims M, Potato vims X, Potato vims Y, Punta Toro vims, Rabbit hemo ⁇ hagic disease vims, Rabies vims, Rice tungro spherical vims, Rice yellow mottle vims, Ross River vims, Rous sarcoma vims, Rubella vims, Saccharomyces cerevisiae vims La, Saguaro cactus vims, Satellite tobacco necrosis vims, Sendai vims, Simian foamy vims, Simian immunodeficiency vims, Simian sarcoma vims, Simian vims 40, Sindbis vims, Sindbis-like vims, Son
- a putative or predicted function is assigned to the target, preferably, prior to testing the target with a test compound.
- a putative function e.g., protein
- several bioinformatic techniques can be used.
- the identification of a characteristic shared (or in some cases not shared) by the target and a molecule, e.g., a protein, of known function can allow assignment of the, or an, activity of the molecule, e.g., protein, of known function to the target.
- Examples of the methods cu ⁇ ently used to predict protein functions include: sequence-based searches, fold recognition techniques (including threading algorithms and neural networks), homology modeling, and structure-based analyses.
- BLOCKS matches sequences against a full ungapped multiple sequence alignment of the conserved region not just the consensus sequence, and can therefore be highly sensitive at picking out distantly related sequences.
- the target amino acid sequence can also be analyzed for the presence or absence of protein folds using the Class, Architecture, Topology (fold family) and Homologous superfamily (CATH) database [http://www.biochem.ucl.ac.uk/bsm/cath1. Cu ⁇ ently, more than 670 different types of protein folds are represented in this database.
- CATH Homologous superfamily
- the ability to predict these stmctural motifs from primary sequence can be improved through the use of threading techniques (i.e. fitting the amino acid sequence of a protein of interest along a known 3-dimensional protein stmcture) (Bryant, SH et al. (1993) Proteins 16: 92-112).
- neural networks can also be used to predict the fold of proteins (Bohr, H. et al. (1990) FEBS Lett. 261, 43-46).
- Additional predictions of the accuracy of the function of a target protein which is homologous to another protein of known function can be obtained by homology modeling.
- Homology modeling Johnson, MS et al. (1994) Crit. Rev. Biochem. Mol. Biol. 29:1-68) involves the use of computational algorithms to compare the amino acid sequence of a protein of interest with that of another related protein with known 3-dimensional stmcture.
- stmcture-based determination of protein function can be used to infer a biological function for a target.
- the crystal stmcture of a target protein is determined, and its 3-dimensional stmcture is then compared with other proteins of known function. If there is a match, a biological function for a target can be predicted based on the known functions of the other protein.
- This approach was recently used to identify a novel NTPase from Methanococcus jannaschii (Hwang, KY et al. (1999) Nat. Struct. Biol. 6: 691-696).
- test compound is a chemical compound, molecule or complex, which is can be tested for its ability to interact with (e.g., bind to) a target, e.g., a target protein.
- the test compound is a small organic molecule, e.g., a synthetic or a naturally- occurring non-proteinaceous molecules.
- the test compound can be designed such that it interacts with a target, or it can be selected from a library of diverse compounds (e.g., a substrate library or a
- 58 combinatorial library based on a desired activity, e.g., random dmg screening based on a desired activity (e.g., its ability to interact with a target).
- libraries Method of the invention use libraries as sources of candidate interactors, e.g., agents which are candidates to be tested for the ability to interact with a target.
- a library can include a plurality of structurally or functionally related members. Library members can, however, be unrelated by stmcture or function.
- a library which includes a plurality of members which are functionally or structurally related can be useful, particularly when the target can be assigned an activity or a putative activity.
- a nuclease substrate library can be tested against the target.
- a nuclease substrate library can include a range of substrates or putative substrates.
- Libraries can be directed to broad target "activities". Examples of libraries are discussed below.
- the substrate requirements of newly discovered enzymes can be determined by dividing the substrate library in a systematic manner. This methodology will be referred to herein as substrate profiling.
- Cofactor libraries can include any of: group transfer and energy coupling molecules, coenzyme, e.g., ATP, GTP, TTP, CTP, UTP, NADH, NADPH, NAD, NADP, FAD, FADH, phosphoenolpyruvate ,Coenzyme A, lipoamide, S-adenosylmethionine, Thiamine pyrophosphate, Biotin, tetrahydrofolate, Uridine diphosphate glucose, Cytodine diphosphate diacylglycerol, and all known CoA modifying molecules such as succinyl-CoA. These group of molecules, called, cofactors are involved in vast number of diverse enzymatic reactions.
- coenzyme e.g., ATP, GTP, TTP, CTP, UTP, NADH, NADPH, NAD, NADP, FAD, FADH
- phosphoenolpyruvate phosphoenzyme A
- lipoamide S-adenosyl
- Example 5 An example of a cofactor library is disclosed and tested in Example 5 below, and includes the following members: ATP, GTP, CTP, TTP, UTP, NADH, NADPH, NAD, NADP, FAD, Flavin, Thiamine Monophosphate Chloride, Pyrodoxal 5 '-phosphate, Coenzyme A, and Cocarboxylase.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein. In many cases a cofactor library will be tested together with another library, for
- a cofactor library can be tested in combination with a carbohydrate library (see Example 5, below).
- Carbohydrate metabolism libraries can be used to screen for carbohydrate modifying enzymes. They can include carbohydrates, e.g., those involved in known biochemical pathways including long, short and single unit carbohydrates and modified carbohydrates from known biochemical pathways such as phosphorylated carbohydrates.
- a library of this type can include carbohydrates or modified carbohydrates not yet known to be substrates for any enzymes. Examples of the carbohydrates that can be used include: Glucose, Fmctose, Arabinose, Xylose, Mannose, Galactose, Lactose, Sucrose, and Ribose.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the carbohydrate library can be tested in combination with other libraries, e.g., a cofactor library.
- Example 5 An example of a carbohydrate library is disclosed and tested in Example 5 below, and includes the following members: D-glucose, arabinose, sucrose, ribose, lactose, galactose, maltose, and xylose tested.
- Purine and pyrimidine metabolism libraries can include nucleoside/nucleotide precursors and can be used to screen for enzymes involved in purine and pyrimidine biosynthesis or degradation.
- Examples of the purine and pyrimidine compounds that can be used include: Glycinamide-ribose-phosphate, Urea, Formyl glycinamide- RP, 5-Aminoimidazol carboxylate-RP, Inosine-P, Formylamido-imidazle-carboxamide-RP. Additional examples of substrates which can be used in the purine and pyrimidine library are provided in the Metabolic Pathway Chart, 1997, 20 th edition, from Sigma- Aldrich. In a prefe ⁇ ed embodiment, the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the purine and pyrimidine metabolism library can be tested in combination with other libraries, e.g., a cofactor library.
- Amino acid metabolism libraries can include amino acids, both D and/or L form, and precursors of the amino acids. It can include peptides with known protease domains to serve as substrates for all the cu ⁇ ently known proteases. This library will also contain some non-enzymatic proteins such as BSA to test for proteolytic activity not yet discovered or catogorised, allowing the discovery of new classes of proteases.
- amino acids that can be used in the amino acid metabolism library include: Alanine, Aspartate, Cysteine, Histidine, Glycine, and Isoleucine.
- substrates which can be used in the amino acid metabolism library are provided in the Metabolic Pathway Chart, 1997, 20 th edition, from Sigma- Aldrich.
- a peptide to be used as protease substrates include acetyl-ser-gln-asn-tyr-pro-val-val amide (from Sigma, page 1132, catalogue number A0806, 1999 edition) and Ser-pro-Arg also from Sigma.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the amino acid metabolism library can be tested in combination with other libraries, e.g., a cofactor library.
- Lipid metabolism libraries can include fatty acids, fatty acid precursors, steroids and steroid precursors, both those already discovered as substrates for known enzymes as well as fatty acids and steroids not yet discovered or categorized as substrates for enzymes.
- This library can be used to screen for enzymes involved in fatty acid metabolism.
- the substrates that can be used in the lipid metabolism libraries include: cholesterol, desmosterol, Zymosterol, Lanosterol, choline, lecitin, cephalin, linoleate, cardiolipin, and acetylcholine.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the lipid metabolism library can be tested in combination with other libraries, e.g., a cofactor library.
- This class of library can include vitamins and hormones as well as their metabolic precursors and can be used to screen for enzymes involved in the synthesis, breakdown or modification of hormones of vitamins.
- the substrates that can be used in the vitamin and hormone library include: retinoate, metarhodopsin, rhodopsin, vitamin K, opsin, and vitamin E. Additional examples of substrates which will be used in the vitamin and hormone library are given in the Metabolic Pathway Chart, 1997, 20 th edition, from Sigma- Aldrich.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the vitamin and hormone library can be tested in combination with other libraries, e.g., a cofactor library.
- This class of library can be used to screen for DNA modifying enzymes. It can include ds and ss DNA molecules, as well as partially ds DNA molecules, and DNA of random sequence, such as calf thymus DNA. It can include covalently closed circular DNA, both supercoiled and relaxed. These DNA molecules can be obtained from commercial vendors such as Sigma, Amersham, and Biorad. In a prefe ⁇ ed embodiment, the library includes at least 1, 2, 5 or 10 of the members disclosed herein. The DNA molecule library can be tested in combination with other libraries, e.g., a cofactor library.
- Natural product libraries e.g., bacterial natural product library can contain the natural products of an organism, e.g., a bacterium. They can be used to screen for unknown enzymatic activity amongst the unknowns.
- the substrate requirements of the natural product library can be determined by the deconvolution of the natural products by chromatographic methods.
- the library includes at least 1, 2, 5 or 10 of the members disclosed herein.
- the natural product library can be tested in combination with other libraries, e.g., a cofactor library.
- the natural product e.g., the bacterial natural product
- auxotroph which accumulates a given metabolite when grown at non-permissive conditions, e.g., at non-permissive temperature, or in the absence of an essential nutrient.
- the accumulated metabolite can be then purified from the organism prior to testing.
- Each of the different substrate libraries can be incubated with the target protein/proteins with the cofactor library at several different pH values and a common mixture of different salts in solution. Any enzymatic activity can be detected as a change in the heat output detected by the calorimeter. This will allow us to immediately categorize the broad type of enzymatic activity the new protein has. The precise substrate requirements can then be determined by dividing the substrate library systematically. Finally the substrate requirements and solution conditions for the newly discovered enzymes can be optimized, and important parameters such as the k ⁇ t , k M and/or ko can be determined.
- the test compound can be a member of a combinatorial library.
- Combinatorial libraries can be synthesized using methods known in the art and as reviewed in, see, e.g., E.M. Gordon et al, J. Med. Chem. (1994) 37:1385-1401 ; DeWitt, S. H.; Czamik, A. W. Ace. Chem. Res. (1996) 29:114; Armstrong, R. W.; Combs, A. P.; Tempest, P. A.; Brown, S. D.; Keating, T. A. Ace. Chem. Res. (1996) 29:123; Ellman, J. A. Ace. Chem. Res. (1996) 29:132; Gordon, E. M.; Gallop, M.
- test ligands can be prepared according to a variety of methods known in the art.
- a "split-pool" strategy can be implemented in the following way: beads of a functionalized polymeric support are placed in a plurality of reaction vessels; a variety of polymeric supports suitable for solid-phase peptide synthesis are known, and some are commercially available (for examples, see, e.g., M. Bodansky "Principles of Peptide Synthesis", 2nd edition, Springer-Verlag, Berlin (1993)).
- a solution of a different activated amino acid To each aliquot of beads is added a solution of a different activated amino acid, and the reactions are allow to proceed to yield a plurality of immobilized amino acids, one in each reaction vessel.
- each synthesis cycle can be randomly selected; alternatively, residues can be selected to provide a "biased" library. It will be appreciated that a wide variety of peptidic, peptidomimetic, or non- peptidic compounds can be readily generated in this way.
- a "diversomer library” is created by the method of Hobbs DeWitt et al. (Proc. Natl Acad. Sci. U.S.A. 90:6909 (1993)).
- Other synthesis methods including the "tea-bag” technique of Houghten (see, e.g., Houghten et al, Nature 354:84-86 (1991)) can also be used to synthesize libraries of compounds according to the subject invention.
- Combinatorial libraries of compounds can be synthesized with "tags" to encode the identity of each member of the library (see, e.g., W.C. Still et al, U.S. Patent No. 5,565,324 and PCT Publication Nos. WO 94/08051 and WO 95/28640).
- this method features the use of inert, but readily detectable, tags, that are attached to the solid support or to the compounds.
- an active compound is detected (e.g., by one of the techniques described above)
- the identity of the compound is determined by identification of the unique accompanying tag.
- This tagging method permits the synthesis of large libraries of compounds which can be identified at very low levels. Such a tagging scheme can be useful to identify compounds released from the beads.
- the libraries of test ligands contain at least 30 compounds, more preferably at least 100 compounds, and still more preferably at least 500 compounds. In preferred embodiments, the libraries of test ligands contain fewer than 10 ⁇ compounds, more preferably fewer than 10& compounds, and still more preferably fewer than 10 ⁇ compounds.
- the methods taught herein can be performed in a number of physical formats.
- the measurement is performed in an isothermal titration calorimeter.
- the calorimeter e.g., an isothermal titration calorimeter
- the target is immobilized in the flow cell.
- Samples can be introduced into a flow cell from a multi-compartment sample holder, e.g., a multi-well plate such as a microtitre plate, e.g., a 96 well plate. Samples can be pre-mixed in the compartments of the sample holder.
- a multi-compartment sample holder e.g., a multi-well plate such as a microtitre plate, e.g., a 96 well plate, in which each compartment includes a thermopyle, and each is a calorimetric cell can be used. Channels for fluid delivery to the compartments can be included.
- a method can be performed on a microchip, in which the appropriate wells channels, and other components have been formed, e.g., by etching or deposition. Fluids could be pumped or moved by electrokinetic methods.
- the reaction mixture can include a single target or multiple targets.
- one, or more, ligand can be added to a reaction mixture. It may be useful to multiplex one or both of these elements in order, e.g., to screen large numbers of species. E.g., where a large number of ligands are to be evaluated, the initial group of candidates can be pooled, and if a pool shows a promising result, members of the pool evaluated. Likewise in methods for evaluating substrates, candidates can be pooled. For large scale screening, calorimetry can be combined with a high-throughput screening format.
- the experimental conditions described above are adjusted to achieve a threshold proportion of test ligands identified as "positive" compounds or ligands from among the total compounds screened.
- this threshold is set according to two criteria. First, the number of positive compounds should be manageable in practical terms. Second, the number of positive compounds should reflect ligands with an appreciable affinity towards the target protein. A prefe ⁇ ed threshold is achieved when 0.1% to 1% of the total test ligands are shown to be ligands of a given target.
- ITCs are commercially available and are used routinely by skilled artisans. See e.g., US 5,873,763 issued to Plotnikov, V.V. on September 29, 1998; Indyk et al. (1998) Meth. Enzymol. 295:350-364; Brandts et al. (1990) American Laboratory 30-41.
- the ITC is a twin-cell differential device. It operates at a fixed temperature, while the liquid in the sample is continuously stirred. This instmment measures the heat that is evolved or absorbed as a result of the binding of the test ligand to the target.
- a differential scanning microcalorimeter can be used to detect the heat output.
- DSCs are commercially available and are used routinely by skilled artisans. See e.g., US 5,873,763 issued to Plotnikov, V.V.; and Freire (1995) Meth. Mol Bio. 40:191-218.
- the differential scanning microcalorimeter automatically raises or lowers the temperature at a given rate while monitoring the temperature differential between cells. From the temperature differential information, small differences in the heat capacities between the sample cell and the reference cell can be determined and attributed to the test substance.
- the reaction mixture is not transparent; the reaction mixture is colored; the reaction mixture is turbid; the reaction mixture contains a substance which interferes with fluorescent or colorimetric detection; the reaction mixture is not a pure solution, e.g., it contains products other than the target.
- the reaction mixture contains: a substance which interferes with radioactive analysis; a substance which interferes with spectrophotometric analysis, e.g., NMR analysis.
- a complex mixtures of substances e.g., an impure sample, such as a suspension, natural product extract, cell extract, biochemical mixture, or colored solution, which may include more than one test compounds, is tested.
- a surrogate ligand can be a nucleic acid (e.g., an oligonucleotide).
- the SELEX procedure can be used to identify a su ⁇ ogate ligand. Using the SELEX procedure (Gold et al. (1995) supra), a large number of random sequence oligonucleotides can be tested for their ability to bind with high affinity to a target, e.g., a target protein. The larger the library of nucleotides, the greater the chance of finding at least one sequence which binds to the target with a dissociation constant in the picomolar to nanomolar range.
- the ligand is about 20 nucleotides in length, as longer oligonucleotides will presumably only bind using a fraction of their length, leaving some residues vulnerable to degradation or processing by a signal-generating entity, even while the ligand is bound to the target.
- longer oligonucleotide sequence may lead to background hydrolysis when a DNase is used.
- the target used in the methods of the invention is a protein (e.g., a target protein).
- the target protein can be identified and purified, using standard biochemical techniques such as HPLC and ion-exchange or size-exclusion chromatography.
- a highly purified sample of the target protein is obtained.
- the SELEX method is employed to identify a single-stranded oligonucleotide (DNA) ligand which binds to the protein with high (>nM) affinity.
- the first step in this process entails the generation of a random oligonucleotide library of 10 14 -10 15 single-stranded DNA sequences which having the stmcture from the 5' to the 3' end shown below:
- Fixed A and B refer to constant sequences present at the 5' and the 3' ends of each member of the library. These constant sequences flank a random sequence and allow transcription and subsequent pool amplification after each round of the SELEX process (see Tuerk &Gold (1990) Science 249:505-510).
- the random sequences should not range beyond 20 nucleotides in length, (as larger ligands may only bind to the target using a central span of their residues, thus leaving their termini exposed to the activity of the DNase even while they are still bound to the target protein).
- the library is mixed with the target protein and then partitioned by passage through a nitrocellulose membrane. Those DNA sequences bound to the filter by the protein are then eluted and amplified with the polymerase chain reaction (PCR) for subsequent transcription of the (now- modified) library for a second round of SELEX. The process is repeated until a ligand which binds with the desired affinity is obtained.
- PCR polymerase chain reaction
- the selectivity of the SELEX process can be increased by using lower amounts of the target (e.g., target protein) in the later rounds, when the high-affinity ligands have been enriched enough to survive the competitive binding situation.
- the process has been tried with over 30 proteins and in almost all cases oligonucleotide ligands were found which bound with greater than nM affinity (Gold et al., 1995, supra).
- a suitable signal-generating entity which has high specific activity against the surrogate ligand.
- the signal-generating entity interacts (e.g., binds) more readily with a free su ⁇ ogate ligand, as opposed to a surrogate ligand bound to a target.
- such interaction amplifies a signal, e.g., generates a heat
- the signal-generating entity modifies the free surrogate ligand by, e.g., forming or breaking a covalent or a non-covalent bond.
- the modification step may involve cleavage, degradation, phosphorylation, polymerization, or any other event that generates a signal, e.g., a heat signal.
- the signal-generating entity can be a degradative enzyme (e.g., a nuclease or a protease).
- the signal-generating entity can be a polymerizing enzyme, e.g., a polymerase.
- the signal-generating entity can be immobilized, e.g., attached to a solid support, or crosslinked.
- the enzyme can be cross-linked to form a crystalline enzyme.
- the signal-generating entity can be a nuclease.
- Exemplary nucleases that can be used include without limitation staphylococcal nucleases (SNase), Serratia marcescens nucleases (SNase), bovine pancreatic nucleases (DNase I), or human (type IV) nucleases.
- the optimal DNase may be chosen.
- Optimal solution conditions may also be chosen, e.g., pH, temperature, and solvent conditions.
- the activity of a particular DNase for a specific su ⁇ ogate ligand can be assayed using methods described in Friedhoff et al. (1996) Eur. J. Biochem. 241 :572- 580 and Friedhoff et al. (1999) FEBSLett. 443:209-214.
- Several exemplary DNases are listed in the table below, along with their activities against particular substrates. The table is by no means complete, and it is not intended to limit the scope of the present invention.
- the signal-generating entity can also be a polymerase, e.g., a Tac polymerase.
- the signal-generating entity can be a ribonuclease (e.g., an RNAse).
- the signal-generating entity can be a protease.
- Proteases useful in practicing the present invention include without limitation trypsin, chymotrypsin, V8 protease, elastase, carboxypeptidase, proteinase K, thermolysin and subtilisin (all of which can be obtained from Sigma Chemical Co., St. Louis, Mo.).
- the most important criterion in selecting a protease or proteases for use in practicing the present invention is that the protease(s) must be capable of digesting the particular target protein under the chosen incubation conditions.
- protease particularly proteases with different enzymatic mechanisms of action
- cofactors that are required for the activity of the protease(s) are provided in excess, to avoid false positive results due to test ligands that may sequester these factors.
- a surrogate ligand e.g., a su ⁇ ogate nucleic acid ligand
- a solution of the target protein and the su ⁇ ogate nucleic acid ligand is prepared in a 1 :1 ratio (concentrations approximately 10 mM) and allowed to equilibrate inside the microcalorimetry cell for several minutes, along with a much smaller concentration of a signal- generating entity.
- a specific deoxyribonuclease DNAse
- One assumption in the present invention is that while the surrogate nucleic acid ligand is bound to the target protein, it is prevented from undergoing as rapid a degradation by the DNAse as the free surrogate nucleic acid ligand.
- the target protein, surrogate nucleic acid ligand, and specific nuclease are then combined together in solution to form a reaction mixture.
- the target protein and surrogate nucleic acid ligand can both be present at approximately 1 ⁇ M, while the nuclease is present at approximately 1 nM.
- the total sample volume is approximately 1 ml.
- the sample is incubated in the microcalorimetry cell (e.g., the cell of an isothermal titration calorimeter).
- the twin cells are housed in an insulated container. The container is cooled, so heat energy is required to maintain the cells and their contents at the experimental temperature. The two cells are kept at thermal equilibrium with each other.
- test ligand that potentially binds to the target protein is then added to the sample cell. If the test ligand binds to the target protein with significant affinity (relative to the oligonucleotide), it will release some fraction of the surrogate ligand into solution, depending on the magnitudes of the respective binding constants. This newly- liberated su ⁇ ogate ligand will then begin to be hydrolyzed by the nuclease present in the solution, thus generating a heat output (power output) much larger than that produced by the initial competitive binding of the test compound. The heat output can be recorded for approximately 1 minute.
- the total heat output for a given trial can be related to (e.g., is proportional to) the ratio of the affinities of the surrogate ligand and the test ligand for the target protein.
- the conformational change of a target upon test ligand binding can be measured.
- Protein targets and structured RNA targets e.g., ribozymes
- test ligand binds to the more compact form of the target protein or RNA, then it will inhibit the conformational change thereby allowing for a difference in heat output to be detected as compared to a control solution with no test ligand. A detailed description of this detection is provided in Examples 3 and 4.
- the methods can also be used to analyze (e.g., identify) agents that bind to a target where the target is present on the surface of a cell, e.g., a bacterial cell wall component.
- the methods can be used to identify agents that interact with (e.g., bind to) cell surface molecules.
- the interaction among the target and the surrogate ligand, test ligand, and/or substrate can occur in vitro (e.g., in a cell-free system), or in vivo (e.g., in a cell, e.g., a prokaryotic or an eukaryotic cell).
- this interaction can be tested by adding these compounds to cells, e.g., living cells, placed inside of a calorimeter.
- EXAMPLE 1 SCREENING FOR COMPOUNDS CAPABLE OF BINDING TO
- a single-stranded oligonucleotide of DNA is identified which binds to the target protein of interest with high affinity.
- the protein and the oligonucleotide ligand are mixed together, each with a concentration of 10 ⁇ M.
- a minute amount (1 nM) of a deoxyribonuclease known to have high activity against the ligand is added (total volume of the solution 500 ⁇ l).
- the binding reaction between the target protein (P) and the ligand (L) can be written as follows:
- [PL] is equal to 0.99 ⁇ M, which means that 1% of the ligand is free in solution (from equation 3). This small fraction will begin to be hydrolyzed once the protein-ligand solution is combined with the DNase (giving some baseline heat output: 70 ⁇ cal/sec x 10 sec "1 - 700 ⁇ cal sec). After the initial solution of target protein, ligand, and nuclease is allowed to equilibrate in the sample cell, a test compound is added, at a final concentration of 10 ⁇ M.
- the test compound will eventually compete off one-half of the DNA, leaving it to be degraded by the DNase.
- the measure of activity of an enzymatic reaction is directly proportional to the differential power output in the calorimetric cell resulting from catalyzed conversion of substrate to product.
- the detection signal (power) for an enzyme reaction, as monitored by a calorimeter, is equal to the substrate turnover per second times the heat of the reaction, as given by the following equation:
- the change in power output of the calorimeter need be no greater than 0.5 ⁇ cal/sec. This power change would result from substrate turnover of 5 x 10 " ! 1 moles/sec assuming a typical heat of reaction of 10 kcal/mol of substrate. Since tumover numbers for enzymes are in the range from 10 to 10,000 per second, one would only require as little as picomoles or femtomoles of enzyme in the calorimeter to perform each dmg screening assay. To optimize the calorimetric assay to ensure maximum signal change, it is helpful to consider the following. A simple form of the equation relating velocity of an enzyme to the concentration of substrate and inhibitor is:
- V Vmax ⁇ 1 + K S [1 + I/Ki] ⁇ "1
- K[ is the inhibitor dissociation constant and K m is the Michaelis-Menton parameter for substrate.
- K m values vary predominantly in the range from 10"* to 10" ⁇ M.
- the enzyme activity is most sensitive to changes in small concentrations of inhibitor when the substrate concentration equals the K m . Addition of an inhibitor at a concentration equal to Kj, to a solution of enzyme with substrate concentration K m reduces the velocity of the enzyme (and hence the power output) by 34%.
- a solution of a buffered solution is denaturant such as Guanidine hydrochloride or urea is introduced into the calorimetric reaction cell. Then a syringe is filled with protein at a specified concentration (- 100
- test ligand In order to detect if a test ligand binds to the protein, one can repeat the above experiment, modifying it so that the test ligand is introduced into the denaturant solution and the protein solution at equal concentrations. If the test ligand binds to the compact state of the protein, then a smaller amount of the protein will convert to the less compact state upon being injected into the calorimeter, leading to a change in the overall heat output.
- the injection process could easily be automated by coupling a flow injection system to a tite ⁇ late, so that each sample is introduced into the same larger volume of denaturant.
- a buffered solution containing a purified target (e.g., a target protein of interest) is introduced into the differential scanning calorimeter reaction cell. Heat is added by increasing the temperature of the solution. When the protein undergoes its conformational change to a less compact form, heat is released. The apparent specific heat capacity curve is integrated to obtain the apparent specific heat output due to the conformational transition. The experiment is repeated with a fresh solution of protein to which some test ligand has been added. If the test ligand binds to the protein, the apparent specific heat output obtained by integrating the apparent specific heat capacity curve between the same two temperature points as the previous experiment, will be less. This difference serves as a convenient signal to indicate which ligands bind to the protein.
- a purified target e.g., a target protein of interest
- This example shows the monitoring of the rate of heat production resulting from the phosphorylation of glucose by hexokinase using isothermal titration calorimetry (ITC).
- Hexokinase type F-300 from Bakers yeast was purchased from Sigma and used without further purification.
- ATP and the carbohydrate and coenzyme kits used for substrate profiling were also obtained from Sigma. All reagents were suspended in a solution containing lOOmM HEPES (pH 8.0), 10 mM MgCl2, lOmM KC1 and ImM in ATP (reaction buffer).
- reaction buffer lOOmM HEPES
- 10 mM MgCl2, lOmM KC1 10 mM MgCl2, lOmM KC1 and ImM in ATP (reaction buffer).
- Hexokinase was prepared as a 50-unit/ml stock solution in reaction buffer. Reaction enthalpies reflecting enzyme turnover were obtained from thermograms collected with a VP-ITC microcalorimeter (MicroCal Inc., Northampton, MA). The VP-ITC instmment directly measures the heat evolved or absorbed in liquid samples as a result of injecting precise amounts of reactants into a thermally equilibrated reaction cell. The reaction cell volume is approximately 1.7 mis and is enclosed with an identical reference cell in an adiabatic inner shield inside an adiabatic outer shield. Once the instmment has been completely assembled with a spinning syringe it is brought to the desired experimental temperature.
- DP signal differential power
- DP signal differential power
- An injection which results in the chemical evolution (exothermic) or abso ⁇ tion of heat (endothermic) within the sample cell causes a negative change in the DP signal for an exothermic reaction and a positive change in the DP signal for an endothermic reaction. Since these chemical changes result in heats that deflect the initial (electrically equilibrated) DP signal away from equilibrium the instemper's DP feedback readministers power back into the cell compensating for these changes.
- the DP signal display has units of power ( ⁇ cal/sec) and the time integral of the peak yields a measurement of thermal energy, ⁇ H.
- the reaction conditions for the hexokinase substrate profiling were as follows: the sample cell was filled with 2 mis of the substrate/coenzyme solution described above. The assay was initiated by injecting 6 ⁇ L of 50-Unit/ml hexokinase solution into the sample cell. The temperature during each calorimetric assay was held constant throughout each experiment at 25°. Under the conditions of the experiments represented here, heats of dilution and mixing (as measured by the heat evolved in the absence of substrate) were less than 5% of the total heat measured for the enzymatic reaction (see Figures 3B). Throughout the enzymatic reaction the rate of heat generated was monitored continuously as shown in Figures 3A-3B.
- the heat flow reaches a maximum soon after the addition of enzyme to the reaction cell and then decays to the baseline as the level of substrate is depleted (see Figure 3A). As can be seen from Figures 3A and 3B, the amount of heat generated directly reflects whether substrate is present or not.
- the actual experimental protocol is summarized by the flow chart shown in Figure 4.
- hexokinase is injected into the complete carbohydrate library.
- the carbohydrate library used contained: D-glucose, arabinose, sucrose, ribose, lactose, galactose, maltose, and xylose tested in the presence of a cofactor library, which included, ATP, GTP, CTP, TTP, UTP, NADH, NADPH, NAD, NADP, FAD, Flavin, Thiamine Monophosphate Chloride, Pyrodoxal 5 '-phosphate, Coenzyme A, and Cocarboxylase.
- a heat signal is observed similar to that shown in Figure 3 A. This signal is indicative of enzyme tumover and hence the presence of substrate.
- the complete carbohydrate library is divided into two - one with substrate (Carbohydrate library 2A) the other without (Carbohydrate library 2B) ( Figure 4). The experiment is repeated as before and this time only one sample generates a heat signal, that of Carbohydrate library 2 A. Since no detectable heat signal is observed for Carbohydrate library 2B (see Figure 4) this collection is discarded.
Abstract
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JP2001510836A JP2003504641A (en) | 1999-07-19 | 2000-07-18 | Thermochemical sensors and uses thereof |
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WO2002021125A2 (en) * | 2000-09-05 | 2002-03-14 | The Althexis Company, Inc. | Drug discover employing calorimetric target triage |
JP2008224686A (en) * | 2001-08-10 | 2008-09-25 | Symyx Technologies Inc | Apparatus and method for creating and testing pre-formulation, and system therefor |
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AU2003231879A1 (en) * | 2002-05-28 | 2003-12-12 | The Trustees Of The University Of Pennsylvania | Methods, systems, and computer program products for computational analysis and design of amphiphilic polymers |
US7745161B2 (en) * | 2003-12-19 | 2010-06-29 | Palo Alto Research Center Incorporated | Amplification of enzymatic reactions for use with an enthalpy array |
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- 2000-07-18 CA CA002380283A patent/CA2380283A1/en not_active Abandoned
- 2000-07-18 WO PCT/US2000/019383 patent/WO2001006250A2/en not_active Application Discontinuation
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- 2000-07-18 EP EP00947428A patent/EP1194767A2/en not_active Withdrawn
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US3789662A (en) * | 1971-10-26 | 1974-02-05 | Instrumentation Labor Inc | Calorimetry |
US4021307A (en) * | 1974-06-07 | 1977-05-03 | Lkb-Produkter Ab | Method and apparatus for measuring temperature changes generated by enzyme activity |
WO1990000203A1 (en) * | 1988-06-27 | 1990-01-11 | Boehringer Mannheim Corporation | Improved biosensor and the method of its use |
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Cited By (4)
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---|---|---|---|---|
WO2002021125A2 (en) * | 2000-09-05 | 2002-03-14 | The Althexis Company, Inc. | Drug discover employing calorimetric target triage |
WO2002021125A3 (en) * | 2000-09-05 | 2002-07-04 | Althexis Company Inc | Drug discover employing calorimetric target triage |
JP2008224686A (en) * | 2001-08-10 | 2008-09-25 | Symyx Technologies Inc | Apparatus and method for creating and testing pre-formulation, and system therefor |
US7549978B2 (en) | 2001-08-10 | 2009-06-23 | Symyx Technologies, Inc. | Needle assembly |
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CA2380283A1 (en) | 2001-01-25 |
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