Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/0004—Oxidoreductases (1.)
  • C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
  • C12N9/0083—Miscellaneous (1.14.99)
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70571—Receptors; Cell surface antigens; Cell surface determinants for neuromediators, e.g. serotonin receptor, dopamine receptor
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/70596—Molecules with a "CD"-designation not provided for elsewhere
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Y—ENZYMES
  • C12Y114/00—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14)
  • C12Y114/99—Miscellaneous (1.14.99)
  • C12Y114/99001—Prostaglandin-endoperoxide synthase (1.14.99.1), i.e. cyclooxygenase
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/566—Immunoassay; Biospecific binding assay; Materials therefor using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
  • C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2799/00—Uses of viruses
  • C12N2799/02—Uses of viruses as vector
  • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid
  • C12N2799/026—Uses of viruses as vector for the expression of a heterologous nucleic acid where the vector is derived from a baculovirus
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2500/00—Screening for compounds of potential therapeutic value
  • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2500/00—Screening for compounds of potential therapeutic value
  • G01N2500/20—Screening for compounds of potential therapeutic value cell-free systems

Definitions

• the invention relates to the fields of pharmacology and medicine. More specifically, the invention relates to the screening of hydrophobic proteins for the identification of the respective ligand molecules with particular relevance to the development of novel medicines and medical diagnostics.
• Hydrophobic proteins present a unique problem for the pharmaceutical industry in the development of agonists and antagonists of hydrophobic protein function.
• the difficulty arises from the fact that HPs are not easily purified and are difficult to work with in isolated form ( e . g. , solubility difficulties, etc.).
• HPs are not easily purified and are difficult to work with in isolated form ( e . g. , solubility difficulties, etc.).
• they may be found, inter alia , associated with the lipid bi-layer of a cell and the organelles therein.
• hydrophobic protein includes membrane proteins, integral membrane proteins, transmembrane proteins, monotopic membrane proteins, polytopic membrane proteins, pump proteins (a subclass of enzymes), channel proteins, receptor kinase proteins, G protein-coupled receptor proteins, membrane-associated enzymes, transporter proteins, etc. Frequently, these proteins play an important role in intra- and intercellular signaling and the general relation of a cell to its environment, e . g. , solute movement, etc. Thus, hydrophobic proteins are important targets for drug development .
• the human geneome project will provide an enormous amount of information about the structure and function of hydrophilic and hydrophobic proteins encoded therein. For example, it is estimated that 1,700-5,000 G protein-coupled receptor proteins (GPCRs) will be discovered in the human genome (Marchese, A., et al . (1999) Trends Pharmacol . Sci . 20:370; Henikoff, S., et al . (1997) Science 278:609). However, given the lack of suitable screening methodologies for the identification of ligands that bind hydrophobic proteins, hundreds of the GPCRs identified by the human genome project will be classified as orphan receptors, having no known ligand to advance their study.
• GPCRs G protein-coupled receptor proteins
• GPCRs are so important to the medical sciences that a separate database has been established to provide information on sequence data, mutant data, and ligand binding data, for example (Horn, F. et al . (1998) Nucleic Acids Research 26: 227-281). Thus, there is a need in the art for the development of screening methodologies, particularly high throughput methodologies, for HP ligand identification.
• HP targets are purified for screening.
• COX-2 purified in a detergent-solubilized form can be screened by monitoring its enzymatic activity in a homogeneous solution phase assay wherein small molecule inhibitors of enzymatic activity can be identified as drug leads (see Song, Y. , et al . (1999) J “ . Med. Chem . 42: 1151- 1160 and Barnett, J. , et al . (1994) Biochimica et Biophysica Acta 1209: 130-139 .
• the HP may be bound to a carrier for screening purposes (see Sklar, L.A. et al . (2000) Biotechniques 28: 976-985; Bieri, C. et al . (1999)
• Affinity selection to identify ligands to water-soluble proteins is known in the art.
• International Publication No. WO 99/35109 by Nash et al describes a method for producing mass-coded combinatorial libraries, which are useful in combination with affinity selection and the identification of the bound ligand by mass spectroscopy.
• International Patent Application No. WO 97/01755 by Jindal et al describes the affinity selection of ligands bound to a target molecule combined with the subsequent isolation of the ligand molecule by multidimensional chromatographic methodology.
• U.S. Patent No. 6,020,141 by Pantoliano et al describes a method of affinity selection combined with ligand identification by thermal shift assay.
• affinity ligand selection and ligand identification there still remains a fundamental challenge to apply affinity selection to non- water-soluble HP targets because of the hindering presence of excess amphiphile, which is required to maintain the pure HP in a biologically active conformation.
• HP is solvated through hydrophobic interactions between the hydrophobic parts of the HP and the hydrophobic moiety of the amphiphile.
• all buffer components are hydrophilic and solvate the protein either through hydration or by participating in electrostatic or ionic bonds.
• amphiphile in preparations of pure HP imparts a colloidal characteristic to the solution.
• HPs are purified in 100 to 10, 000-fold molar excess of detergent. These amphiphilic detergent molecules interact with both the HP and the drug molecules being screened.
• amphiphiles form macromolecular assemblies, like micelles or liposomes, that are just as large as most proteins. These macromolecular assemblies impart a colloidal characteristic to solutions of amphiphile- solublized HP, further distinguishing HP's from soluble proteins.
• buffers e.g. tris or Na-phosphate
• salt e.g. NaCl or KC1
• the invention provides an affinity selection-based HP screening method that can operate in the presence of an amphiphile without regard to the specific biological function of the HP target.
• the present invention solves problems associated with affinity selection of HP ligands by enabling detection of the specific binding of a small drug-like molecules to an HP in the presence of an amphiphile.
• the present invention also provides novel methods and compositions of matter for the production of purified HPs useful for screening purposes. These discoveries have been exploited to provide the present invention, which includes compositions and methods.
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a ligand molecule by affinity selection by exposing a hydrophobic target protein bound by an amphiphile to a multiplicity of molecules to promote the formation of at least one complex between the hydrophobic target protein and the ligand molecule; (b) separating the complex from the unbound molecules; and (c) identifying the ligand molecule.
• exposure of the hydrophobic target protein to a multiplicity of molecules occurs under homogeneous solution phase conditions. In certain embodiments of the first aspect, exposure of the hydrophobic target protein to a multiplicity of molecules occurs under heterogeneous solution phase conditions. In certain embodiments of the first aspect, selection of the ligand molecule is done using multidimensional chromatography.
• the hydrophobic target protein is selected from the group consisting of a membrane protein, an integral membrane protein, a transmembrane protein, a monotopic membrane protein, a polytopic membrane protein, a pump protein, a channel protein, a receptor kinase protein, a G protein- coupled receptor protein, a membrane-associated enzyme, and a transporter protein.
• the multiplicity of molecules is a mass coded library of molecules. In certain embodiments of the first aspect, the multiplicity of molecules is a library of molecules that is not mass coded. In certain embodiments of the first aspect, the amphiphile is selected from the group consisting of (a) a polar lipid, (b) an amphiphilic macromolecular polymer,
• ligand molecule identification is done by mass spectral analysis.
• the ligand molecule is deconvoluted by mass spectral analysis.
• separation of the complex from the unbound molecules is accomplished with solid phase chromatography media.
• the hydrophobic target protein comprises (a) at least one transmembrane domain sequence, (b) at least two tag sequences useful for affinity purification, and (c) a hydrophobic protein (HP) sequence.
• the hydrophobic protein sequence is selected from the group consisting of (a) a membrane protein, (b) an integral membrane protein, (c) a transmembrane protein, (d) a monotopic membrane protein, (e) a polytopic membrane protein, (f) a pump protein, (g) a channel protein, (h) a receptor kinase protein, (i) a G protein-coupled receptor protein, (j) a membrane-associated enzyme, and (k) a transporter protein.
• the tag sequences comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-COOH) (SEQ ID NO.-l), (b) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID N0-.2), (c) a hemagglutinin tag (NH2-YPYDVPDYA-C00H) (SEQ ID N0:3), (d) a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO : 4 ) , (e) an HSV tag (NH2-QPELAPEDPED-C00H) (SEQ ID NO:5) and (f) a rhodopsin tag (NH2
• the hydrophobic target protein comprises a sequence with an amino terminus to carboxy terminus order selected from the group consisting of (a) Tagl-Tag2-HP, (b) Tagl-HP-Tag2 , and
• the invention provides a method wherein the hydrophobic target protein is selected from the group consisting of (a) Myc tag-EE tag-Human m2 muscarinic acetylcholine receptor (mAChR) (SEQ ID NO: 7), (b) Flag tag-Human Beta 2 Adrenergic Receptor-EE tag (SEQ ID N0:8), (c) Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO:9), (d) Flag tag-Human ml mAChR-EE tag (SEQ ID NO:10), and (e) Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID N0:11).
• the invention provides a method wherein the hydrophobic target protein further comprises a heterologous signal sequence (SS) at the amino terminus.
• the heterologous signal sequence is selected from the group consisting of (a) the Mellitin signal sequence of NH2 -KFLVNVALVFMWYISYIYA-COOH (SEQ ID NO: 12), (b) the GP signal sequence of NH2-VRTAVLILLLVRFSEP- C00H (SEQ ID NO-.13), (c) the Hemagglutinin signal sequence of NH2-KTIIALSYIFCLVFA-COOH (SEQ ID NO:14), (d) the rhodopsin tag 1 signal sequence of NH2- MNGTEGPNFYVPFSNKTGWRSPFEAPQYYLAEP-COOH (SEQ ID NO: 15), and (e) the rhodopsin tag ID4 signal sequence of NH2- GKNPLGVR TETSQVAPA-COOH (SEQ ID NO:
• the tag sequences further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO: 18) .
• the hydrophobic target protein is selected from the group consisting of (a) GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO:19), (b) Mellitin SS-Flag tag-Human Beta 2 Adrenergic Receptor-EE tag(SEQ ID NO:20), (c) Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO:21), (d) Mellitin SS-Flag tag-Human ml mAChR-EE tag (SEQ ID NO-.22), and (e) Hemagglutinin SS-Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID NO: 23) .
• the invention provides a method of isolating a hydrophobic protein, the method comprising (a) purifying the hydrophobic protein by sucrose gradient ultracentrifugation, (b) purifying the hydrophobic protein by antibody affinity purification, and (c) purifying the hydrophobic protein by immobilized metal affinity chromatography.
• the hydrophobic protein comprises (a) at least one transmembrane domain sequence, (b) at least two tag sequences useful for affinity selection, and (c) a hydrophobic protein (HP) sequence.
• the hydrophobic protein sequence is selected from the group consisting of
• transmembrane protein a transmembrane protein
• a monotopic membrane protein a monotopic membrane protein
• a polytopic membrane protein a pump protein
• a pump protein a pump protein
• a channel protein a channel protein
• a receptor kinase protein a receptor kinase protein
• a G protein-coupled receptor protein a membrane-associated enzyme
• a transporter protein a transporter protein
• the tag sequences of the hydrophobic protein comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-C00H) (SEQ ID NO:l), (b) an EE tag (NH2- EEEEYMPME-COOH) (SEQ ID NO:2), (c) a hemagglutinin tag (NH2- YPYDVPDYA-COOH) (SEQ ID NO : 3 ) , (d) a myc tag (NH2- KHKLEQLRNSGA-COOH) (SEQ ID NO:4), (e) an HSV tag (NH2- QPELAPEDPED-COOH) (SEQ ID NO: 5) and (f) a rhodopsin tag
• the hydrophobic protein comprises a sequence with an amino terminus to carboxy terminus order selected from the group consisting of (a) Tagl-Tag2-HP, (b) Tagl-HP-Tag2 , and (c) HP-Tagl-Tag2.
• the hydrophobic protein is selected from the group consisting of (a) Myc tag-EE tag-Human m2 mAChR (SEQ ID NO:7), (b) Flag tag-Human Beta 2 Adrenergic Receptor-EE tag (SEQ ID NO: 8),
• the hydrophobic protein further comprises a heterologous signal sequence (SS ) at the amino terminus.
• the heterologous signal sequence is selected from the group consisting of (a) the Mellitin signal sequence of NH2-KFLVNVALVFMWYISYIYA- COOH (SEQ ID NO: 12), (b) the GP signal sequence of NH2- VRTAVLILLLVRFSEP-COOH (SEQ ID NO: 13), (c) the Hemagglutinin signal sequence of NH2-KTIIALSYIFCLVFA-COOH (SEQ ID NO:14),
• the tag sequences of the hydrophobic protein further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO: 18) .
• the hydrophobic target protein is selected from the group consisting of (a) GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO:19), (b) Mellitin SS-Flag tag-Human Beta 2 Adrenergic Receptor-EE tag(SEQ ID NO:20), (c) Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO:21), (d) Mellitin SS- Flag tag-Human ml mAChR-EE tag (SEQ ID NO:22), and (e) Hemagglutinin SS-Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID NO: 23) .
• the invention provides an isolated nucleic acid molecule suitable for hydrophobic protein expression, comprising (a) a vector polynucleotide sequence for protein expression in a eukaryotic cell, and (b) a polynucleotide sequence encoding an engineered hydrophobic protein comprising the following elements (i) an N-terminal methionine residue, (ii) a heterologous signal sequence
• the N-terminal methionine sequence and the heterologous signal sequence are selected from the group consisting of (a) MKFLVNVALVFMWYISYIYA (SEQ ID NO:24), (b) MVRTAVLILLLVRFSEP (SEQ ID N0:25), (c) MKTIIALSYIFCLVFA (SEQ ID NO: 26), (d) MMNGTEGPNFYVPFSNKTGWRSPFEAPQYYLAEP-COOH (SEQ ID NO: 27), and (e) MGKNPLGVRKTETSQVAPA-COOH (SEQ ID NO: 28).
• the tag sequences comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-COOH) (SEQ ID NO:l), (b) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID NO : 2 ) , (c) a hemagglutinin tag (NH2-YPYDVPDYA-COOH) (SEQ ID NO:3), (d) a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:4), and (e) an HSV tag (NH2 -QPELAPEDPED-COOH) (SEQ ID NO:5).
• the elements of the engineered hydrophobic protein are arrayed from an amino to carboxy terminus order selected from the group consisting of (a) SS-Tagl-Tag2-HP, (b) SS-Tagl-HP-
• the engineered hydrophobic protein is selected from the group consisting of (a) GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO:19), (b) Mellitin SS-Flag tag-Human Beta 2
• Adrenergic Receptor-EE tag SEQ ID NO:20
• the tag sequences further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO: 18).
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a hydrophobic target protein from the group consisting of (i) a membrane protein, (ii) an integral membrane protein, (iii) a transmembrane protein, (iv) a monotopic membrane protein, (v) a polytopic membrane protein, (vii) a pump protein, (viii) a channel protein, (iX)a receptor kinase protein, (X) a G protein-coupled receptor protein, Xii) a membrane-associated enzyme, and (Xiii) a transporter protein, wherein the hydrophobic protein is bound by amphiphile selected from the group consisting of (i) a polar lipid, (ii) an amphiphilic macromolecular polymer, (iii) a surfactant or detergent, and (iV) an amphiphilic polypeptide; (b) selecting a ligand molecule using
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a hydrophobic target protein from the group consisting of (i) a membrane protein, (ii) an integral membrane protein, (iii) a transmembrane protein, (iv) a monotopic membrane protein, (v) a polytopic membrane protein, (vii) a pump protein, (viii) a channel protein, (iX)a receptor kinase protein, (X) a G protein-coupled receptor protein, Xii) a membrane-associated enzyme, and (Xiii) a transporter protein, wherein the hydrophobic protein is bound by amphiphile selected from the group consisting of (i) a polar lipid, (ii) an amphiphilic macromolecular polymer, (iii) a surfactant or detergent, and (iV) an amphiphilic polypeptide; (b) selecting a ligand molecule using
• the invention provides a method of isolating a hydrophobic protein, the method comprising: (a) selecting a hydrophobic protein comprising: (i) at least one transmembrane domain sequence, (ii) at least two tag sequences useful for affinity selection selected from the group consisting of: (A) a FLAG tag (NH2-DYKDDDDK-C00H) (SEQ ID NO-.29), (B) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID N0:30), (C) a hemagglutinin tag (NH2-YPYDVPDYA-C00H) (SEQ ID NO:31), (D) a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:32), and (E) an HSV tag (NH2-QPELAPEDPED-COOH) (SEQ ID NO:33); (iii) a hydrophobic protein (HP) sequence selected from the group consisting of: (A) a FL
• the invention provides, an isolated nucleic acid molecule suitable for hydrophobic protein expression, comprising: (a) a vector polynucleotide sequence for protein expression in a eukaryotic cell, and (b) a polynucleotide sequence encoding an engineered hydrophobic protein comprising the following elements (i) an N-terminal methionine residue, (ii) a heterologous signal sequence (SS) , wherein the N-terminal methionine sequence and the heterologous signal sequence are selected from the group consisting of (1) MKFLVNVALVFMWYISYIYA (SEQ ID NO:24), (2) MVRTAVLILLLVRFSEP (SEQ ID NO:25), (3) MKTIIALSYIFCLVFA (SEQ ID NO-.26), (4)
• MMNGTEGPNFYVPFSNKTGWRSPFEAPQYYLAEP-COOH SEQ ID NO: 27
• MGKNPLGVRKTETSQVAPA-COOH SEQ ID NO:28
• tag sequences useful for affinity selection selected from the group consisting of (1) a FLAG tag (NH2-DY DDDDK-C00H) (SEQ ID NO:l), (2) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID N0:2),
• a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:4), and (5) an HSV tag (NH2 -QPELAPEDPED-COOH) (SEQ ID NO:5).
• a hydrophobic protein (HP) sequence selected from the group consisting of (1) a membrane protein, (2) an integral membrane protein, (3) a transmembrane protein, (4) a monotopic membrane protein, (5) a polytopic membrane protein, (6) a pump protein, (7) a channel protein, (8) a receptor kinase protein, (9) a G protein-coupled receptor protein, (10) a membrane-associated enzyme, and (11) a transporter protein.
• Figure 1 presents the amino acid sequence of the HP protein GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO: 19) .
• Figure 2 presents the amino acid sequence of the HP protein Mellitin-Flag Tag-Human Beta 2 Adrenergic Receptor- E ⁇ (SEQ ID NO -.20) .
• Figure 3 presents the amino acid sequence of the HP protein Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV-Myc (SEQ ID NO: 21) .
• Figure 4 presents the amino acid sequence of the HP protein Mellitin-Flag Tag-Human ml mAChR-EE (SEQ ID NO: 22) .
• Figure 5 presents the amino acid sequence of the HP protein Hemagglutinin SS-Rat m3 mAChR-HSV-OctaHis (SEQ ID ' NO: 23) .
• Figure 6 presents SEC chromatograms represented by a screenshot from a computer interface developed to monitor the performance of the ALIS screening system. Relative absorbance at 230 nm is plotted on the vertical axis versus elution time following sample injection after injection onto the SEC column.
• the view compiles separation profiles for the analysis of six different binding reaction mixtures. In each case the mixture is composed of 25 ⁇ M each indomethacin and meclofenamate, 10 ⁇ M COX-1, and 1 ⁇ M each for approximately 2500 individual screening compounds.
• the peaks eluting between 12-15 seconds correspond to the COX-1 containing SEC fractions that are sent to the mass spectrometer for analysis.
• the peaks eluting after 17 seconds corresponds to unbound library members.
• Figure 7 presents mass spectral analysis showing the estimated recovery of two known COX-1 ligands (NSAID LM, composed of inclomethacin and meclofenamate) extracted from test libraries as described in Fig. 1.
• NSAID LM composed of inclomethacin and meclofenamate
• Different COX-1 preparations from different days (10/15 and 10/18) bind the known ligands in the absence and presence of competing libraries (NGL-15-A-137, NGL-10-A-41, NGL-116-A-470, NGM-51, NGM-108, NGM-177) .
• the mass spectral analysis permits estimation of the pmol of each ligand recovered. Estimates were performed in triplicate for both indomethacin and meclofenamate .
• Figure 8 presents the structure of an example COX-1 ligand identified by ALIS.
• This compound termed NGL-177-A- 1128-A-2a, is one example of a compound identified as a COX- 1 ligand by ALIS screening.
• Figure 9 presents a bar graph demonstrating competition with meclofenamate for COX-1 binding.
• Selected COX-1 hit compounds each present at approximately 1 ⁇ M and identified by ten character names prefixed with NGL-x, were individually tested to determine whether they compete with 25 ⁇ M meclofenamate for binding to COX-1.
• the mass spectral response corresponding to the mass of either meclofenamate or the test ligand was quantified.
• the "ligand + competitor" response will be lower that the "ligand - competitor” response.
• the meclofenamate response will be lower for that "ligand + competitor” trial than in the "COX1 + 25 ⁇ M Meclofenamate trial.”
• the test compound represented by NGL-169-A-1151-A-4 is competitive with meclofenamate while the test compound represented by NGL-175-A-1127-A-1 is not significantly competitive.
• Figure 10 presents a bar graph demonstrating the extent of M2R1 ligand recovery quantified by the signal strength of the mass spectral analysis in accordance with the ALIS procedure.
• the x-axis is in relative units of mass spectrometric signal response for the respective masses of pirenzepine, QNB, and atropine.
• the invention relates to the fields of pharmacology and medicine. More specifically, the invention relates to the screening of hydrophobic proteins for the identification of the respective ligand molecules with particular relevance to the development of novel ⁇ medicines and medical diagnostics.
• the patent and scientific literature cited herein establishes the knowledge that is available to those with skill in the art.
• the issued U.S. patents, allowed applications, published foreign applications, and references cited herein are hereby incorporated by reference. Any conflicts between these sources and the present specification shall be resolved in favor of the latter.
• the invention provides an affinity selection-based HP screening method that can operate in the presence of an amphiphile without regard to the specific biological function of the HP target.
• hydrophobic protein refers to any purified protein that is prepared with amphiphile.
• the term may also refer to any protein for which, when purified to greater than 1% purity or purified to greater than 10% purity or purified to greater than 25% purity or purified to greater than 50% purity, either requires or benefits from the presence of an amphiphile for functional assays, to enhance stability
• the hydrophobic protein of the invention is a mammalian hydrophobic protein. In a particularly preferred embodiment, the hydrophobic protein of the invention is a human hydrophobic protein.
• hydrophobic protein is also meant to include proteins identified by bioinformatics-assisted means through the use of the following non-limiting examples of algorithms designed for the identification of hydrophobic proteins: (a) DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) M. Cserzo, E. Wallin, I. Simon, G. von Heijne and A. Elofsson: Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the Dense Alignment Surface method; Prot. Eng. vol. 10, no.
• a method of identifying a ligand for a hydrophobic protein is synonymous with a method of screening for a ligand that binds a small molecule.
• screening refers to a procedure used to detect the interaction between polypeptide, for example a hydrophobic protein, and a small molecule; it is useful for discriminating between ligands that bind to proteins with a Kd ⁇ 200 ⁇ M from large ensembles of ligands that either do not bind to the protein or bind only weakly with a Kd > 200 ⁇ M.
• the present invention utilizes mass spectrometry (MS) in the identification of hydrophobic protein ligands.
• MS mass spectrometry
• the MS technique is only rarely performed to analyze samples containing hydrophobic proteins because these samples contain detergent amphiphiles. Detergents suppress analyte ion formation, a critical phenomenon for MS, and so significantly hamper MS, that reports of successful MS analysis of hydrophobic proteins are few. Nevertheless, several labs have tried to perform MS analysis of purified hydrophobic proteins by identifying methods to remove the detergent prior to MS analysis. All of these labs use matrix-assisted laser desorption ionization (MALDI) to present the protein sample to the detector.
• MALDI matrix-assisted laser desorption ionization
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a ligand molecule by affinity selection by exposing a hydrophobic target protein bound by an amphiphile to a multiplicity of molecules to promote the formation of at least one complex between the hydrophobic target protein and the ligand molecule; (b) separating the complex from the unbound molecules; and (c) identifying the ligand molecule.
• the affinity screening methods of the invention are to be distinguished from functional selection methodologies.
• Functional selection methodologies involve ligand selection based on criteria that identify some specific protein-ligand or protein-protein interaction as significant; such ligand selection depends on either an action assignable to the protein (e . g. , chemical catalysis for enzymes) or identification of some interaction between the protein and some other molecule (e.g., interaction between a protein and a known small molecule ligand in the case of non-enzymes) .
• these screening methodologies are generally based on enzymatic or biofunctional assays or ligand displacement assays.
• Various embodiments of the method of the invention may utilize an automated ligand identification system (ALIS) for the discovery of novel drug leads.
• ALIS selects ligands based on the affinity of the compound for its target protein and identifies the ligands by mass spectrometry (see International Patent Application WO 99/35109) .
• the invention herein provides for the application of ALIS to amphiphile complexed HPs.
• affinity selection means a ligand selection based on the affinity of one molecule for a selected protein target; such ligand selection is independent of the functional activity of the protein of interest other than for the fact the protein binds the small molecule .
• amphiphile is used to mean any molecule generally with the properties of a detergent, phospholipid, or surfactant that enhances the water solubility of hydrophobic polypeptides; specifically any molecule known to assume an association colloid in aqueous solution; non-limiting examples of such amphiphiles would include phospholipids and other polar lipids (exemplified by phosphatidylcholines, lysophospholipids, cholesterols, lecithins, ceramides, etc); amphiphilic macromolecular polymers (exemplified by the work of Christophe Tribet and Jean-Luc Popot (Tribet, C. et al . J.L. Natl. Acad.' Sci. USA
• surfactants including alkyl saccharides, alkyl thioglycosides, alkyl dimethylamine oxides, bile acid derivatives like cholate and the CHAPS series, FOS-CHOLINETM series, CYMALTM or CYGLUTM series, glucamides, and alkyl polyoxyethylenes, etc; or polypeptides known to adopt amphipathic structures (exemplified by work of C.E. Schafmeister and R.M. Stroud (Schafmeister, C.E. et al . , RM Science (1993) 262:734-8).
• the term "multiplicity of molecules” refers to a plurality of molecules to be tested for the property of specific binding to a hydrophobic target protein.
• molecule is meant, any compound in the size range of 150 to 5000 atomic mass units (amu) .
• Such compounds may be generated by any means known in the art . Particularly favored methods of generating the multiplicity of molecules is through the use of combinatorial chemistry.
• a “combinatorial library” refers to a plurality of molecules or compounds which are formed by combining, in every possible way for a given compound length, a set of chemical or biochemical building blocks which may or may not be related in structure.
• the term can refer to a plurality of chemical or biochemical compounds which are formed by selectively combining a particular set of chemical building blocks. For example, twenty amino acids randomly combined into hexameric peptides will produce no less than 64 million compounds. With the "combinatorial library" approach, as many different compounds as possible are made, and then candidate compounds are selected by screening them for binding activity against the target molecule of interest, e . g. , a hydrophobic protein.
• exposure of the hydrophobic target protein to a multiplicity of molecules occurs under homogeneous solution phase conditions. In certain embodiments of the first aspect, exposure of the hydrophobic target protein to a multiplicity of molecules occurs under heterogeneous solution phase conditions. In certain embodiments of the first aspect, selection of the ligand molecule is done using multidimensional chromatography.
• homogeneous solution phase means a protein preparations whereby a protein is combined with (a) ligand (s) with the intent to facilitate possible protein-ligand interactions; such preparations are found as sols in the temperature range of -40 to 60 °C such that neither protein nor ligand are bound to a supporting element; these preparations would either pass through a semipermeable membrane with a size cut-off of 5.0 ⁇ M or behave as though they a sedimentation coefficient of less than 500 Svedbergs or both; examples of such preparations would include combinations of ligand (s) with proteins that are solubilized in amphiphile, proteins incorporated into proteoliposomes, proteins incorporated into cell-derived virus-like particles, etc.
• heterogeneous solution phase means a protein preparations whereby a protein is combined with (a) ligand (s) with the intent to facilitate possible protein-ligand interactions; such preparations are found as mixtures in the temperature range of -40 to 60 °C such that either the protein or the ligand is bound to a supporting element; these preparations would either fail to pass through a semipermeable membrane with a size cut-off of 5.0 ⁇ M or they would behave as though they have a sedimentation coefficient of greater than 500 Svedbergs or both; examples of such preparations would include combinations of ligand (s) with proteins that are presented on the surface of a bead/stationary element whereby the protein is attached to the bead/stationary element through either a covalent or non-covalent linkage or a linkage dependent upon the self- association of amphiphiles or combinations of proteins with ligands that are fixed to a stationary phase.
• multi-dimensional chromatography means a procedure for processing a sample involving more than one chromatographic method in tandem.
• Representative types of chromatographic methods include: (1) solid phase chromatography media: any of a variety of materials including small particles ( ⁇ 5 ⁇ M) , solid porous castings, filters, or semipermeable membranes that may commonly be referred to as resins, gels, immobilized artificial membranes, stationary phase elements, or otherwise, and are used with the intent of providing stationary surfaces over which or through which solubilized analytes are passed or with which solubilized analytes interact as in chromatographic or electrophoretic separations or fractionations; and (2) solution phase chromatography media: solutions or fluids suitable for use in electrophoretic separations or fractionations when used in combination with stationary phase chromatography media.
• the hydrophobic target protein is selected from the group consisting of a membrane protein, an integral membrane protein, a transmembrane protein, a monotopic membrane protein, a polytopic membrane protein, a pump protein, a channel protein, a receptor kinase protein, a G protein- coupled receptor protein, a membrane-associated enzyme, and a transporter protein.
• the multiplicity of molecules is a mass coded library of molecules. In certain embodiments of the first aspect, the multiplicity of molecules is a library of molecules that is not mass coded.
• the term "mass-coded library” refers to a mass coded combinatorial library.
• the compounds of the mass-coded combinatorial library are of the general formula X(Y) n , wherein X is a scaffold, each Y is a peripheral moiety and n is an intsger greater than 1, typically from 2 to about 6.
• the term "scaffold”, as used herein, refers to a molecular fragment to which two or more peripheral moieties are attached via a covalent bond.
• the scaffold is a molecular fragment which is common to each member of the mass-coded set of compounds.
• peripheral moiety refers to a molecular fragment which is bonded to a scaffold.
• Each member of the set of mass-coded compounds will include a combination of n peripheral moieties bonded to the scaffold and this set of compounds forms a mass-coded combinatorial library. More details of mass-coded libraries are provided in the patent application WO9935109A1, which is incorporated herein by reference.
• the phrase "a library of molecules that is not mass-coded” means any plurality of molecules or compounds that are not produced by a mass-coded combinatorial process.
• the term includes any and all other methods of producing a combinatorial library.
• the term also includes compounds constructed by "Structure Based Drug Design” methodology, which seeks to design a drug based on the structure of the target protein, and natural libraries of compounds obtained from body fluids, tissues or cells.
• the amphiphile is selected from the group consisting of (a) a polar lipid, (b) an amphiphilic macromolecular polymer, (c) a surfactant or detergent, and (d) an amphiphilic polypeptide.
• ligand identification is done by mass spectral analysis.
• the ligand molecule is deconvoluted by mass spectral analysis.
• separation of the complex from the unbound molecules is accomplished with solid phase chromatography media.
• the hydrophobic target protein comprises (a) at least one transmembrane domain sequence, (b) at least two tag sequences useful for affinity selection, and (c) a hydrophobic protein (HP) sequence.
• the hydrophobic protein sequence is selected from the group consisting of (a) a membrane protein, (b) an integral membrane protein, (c) a transmembrane protein, (d) a monotopic membrane protein, (e) a polytopic membrane protein, (f) a pump protein, (g) a channel protein, (h) a receptor kinase protein, (i) a G protein-coupled receptor protein, (j) a membrane-associated enzyme, and (k) a transporter protein.
• the tag sequences comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-COOH) (SEQ ID NO:l), (b) an EE tag (NH2-EEEEYMPME-COOH) (SEQ ID NO:2), (c) a hemagglutinin tag (NH2-YPYDVPDYA-C00H) (SEQ ID N0:3), (d) a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:4), (e) an HSV tag (NH2 -QPELAPEDPED-COOH) (SEQ ID NO: 5) and (f) a rhodopsin tag (NH2GTEGPNFYVPFSNKTGWRSPFEAPQYYLAEPWQFSM- COOH) (SEQ ID NO: 6) .
• the hydrophobic target protein comprises a sequence with an amino terminus to carboxy terminus order selected from the group consisting of (a) Tagl-Tag2-HP, (b) Tagl-HP-Tag2 , and (c) HP-Tagl-Tag2.
• the invention provides a method wherein the hydrophobic target protein is selected from the group consisting of (a) Myc tag-EE tag-Human m2 mAChR (SEQ ID NO: 6), (b) Flag tag-Human Beta 2 Adrenergic Receptor-EE tag (SEQ ID NO:7), (c) Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO: 9), (d) Flag tag-Human ml mAChR-EE tag (SEQ ID NO:10), and (e) Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID NO: 11) .
• the invention provides a method wherein the hydrophobic target protein further comprises a heterologous signal sequence (SS) at the amino terminus.
• the heterologous signal sequence is selected from the group consisting of (a) the
• VRTAVLILLLVRFSEP-COOH (SEQ ID NO: 13), (c) the Hemagglutinin signal sequence of NH 2 -KTIIALSYIFCLVFA-COOH (SEQ ID NO: 14),
• the rhodopsin tag ID4 signal sequence of NH 2 - GKNPLGVRKTETSQVAPA-COOH (e) the rhodopsin tag ID4 signal sequence of NH 2 - GKNPLGVRKTETSQVAPA-COOH (SEQ ID NO: 16).
• the tag sequences further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO: 18) .
• the hydrophobic target protein is selected from the group consisting of (a) GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO: 19), (b) Mellitin SS-Flag tag-Human Beta 2 Adrenergic Receptor-EE tag(SEQ ID NO:20), (c) Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO:21), (d) Mellitin SS-Flag tag-Human ml mAChR-EE tag (SEQ ID NO:22), and (e) Hemagglutinin SS-Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID NO: 23) .
• the invention provides a method of isolating a hydrophobic protein, the method comprising (a) purifying the hydrophobic protein by sucrose gradient ultracentrifugation, (b) purifying the hydrophobic protein by antibody affinity purification, and (c) purifying the hydrophobic protein by immobilized metal affinity chromatography.
• the hydrophobic protein comprises (a) at least one transmembrane domain sequence, (b) at least two tag sequences useful for affinity selection, and (c) a hydrophobic protein (HP) sequence.
• the hydrophobic protein sequence is selected from the group consisting of (a) a membrane protein, (b) an integral membrane protein, (c) a transmembrane protein, (d) a monotopic membrane protein, (e) a polytopic membrane protein, (f) a pump protein, (g) a channel protein, (h) a receptor kinase protein, (i) a G protein-coupled receptor protein, (j) a membrane-associated enzyme, and (k) a transporter protein.
• the tag sequences of the hydrophobic protein comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-C00H) (SEQ ID NO:l), (b) an EE tag (NH2- EEEEYMPME-COOH) (SEQ ID NO:2), (c) a hemagglutinin tag (NH2- YPYDVPDYA-COOH) (SEQ ID NO : 3 ) , (d) a myc tag (NH2-
• the hydrophobic protein comprises a sequence with an amino terminus to carboxy terminus order selected from the group consisting of (a) Tagl-Tag2-HP, (b) Tagl-HP-Tag2 , and (c) HP-Tagl-Tag2.
• the hydrophobic protein is selected from the group consisting of
• the hydrophobic protein further comprises a heterologous signal sequence (SS) at the amino terminus.
• SS heterologous signal sequence
• the heterologous signal sequence is selected from the group consisting of (a) the Mellitin signal sequence of NH2-KFLVNVALVFMWYISYIYA- COOH (SEQ ID NO: 12), (b) the GP signal sequence of NH2- VRTAVLILLLVRFSEP-COOH (SEQ ID NO: 13), (c) the Hemagglutinin signal sequence of NH2-KTIIALSYIFCLVFA-COOH (SEQ ID NO:14),
• the tag sequences of the hydrophobic protein further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO: 18) .
• the hydrophobic target protein is selected from the group consisting of (a) GP67 SS-Myc tag-EE tag-Human m2 mAChR (SEQ ID NO:19), (b) Mellitin SS-Flag tag-Human Beta 2 Adrenergic Receptor-EE tag(SEQ ID NO:20), (c) Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV tag-Myc tag (SEQ ID NO:21), (d) Mellitin SS-Flag tag-Human ml mAChR-EE tag (SEQ ID NO:22), and (e) Hemagglutinin SS-Rat m3 mAChR-HSV tag-OctaHis tag (SEQ ID NO: 23) .
• the invention provides an isolated nucleic acid molecule suitable for hydrophobic protein expression, comprising (a) a vector polynucleotide sequence for protein expression in a eukaryotic cell, and (b) a polynucleotide sequence encoding an engineered hydrophobic protein comprising the following elements (i) an N-terminal methionine residue, (ii) a heterologous signal sequence (SS) , (iii) at least one transmembrane domain sequence, (iv) at least two tag sequences useful for affinity purification, and (v) a hydrophobic protein (HP) sequence.
• SS heterologous signal sequence
• HP hydrophobic protein
• a vector polynucleotide sequence for protein expression in a eukaryotic cell is meant any polynucleotide sequence comprising an origin of replication allowing replication in a eukaryotic cell, a selectable marker, e . g. , antibiotic resistance marker, and a promoter sequence element to promote transcription of the structural gene, which may be viral, prokaryotic or eukaryotic in origin.
• the origin of the vector polynucleotide sequence may be viral, prokaryotic or eukaryotic or a combination thereof.
• the vector sequence while being designed for expression in a eukaryotic cell may optionally contain a prokaryotic origin of replication.
• Non-limiting examples of suitable vector polynucleotide sequences include the following: baculovirus vectors such as pVL1392 (Pharmingen, San Diego, CA) and pBAC-1 (Novagen, Madison, WI) and mammalian expression vectors such as pcDNA 3.1 (Invitrogen, San Diego, CA) and pTriEx-1 (Novagen, Madison, WI) .
• baculovirus vectors such as pVL1392 (Pharmingen, San Diego, CA) and pBAC-1 (Novagen, Madison, WI)
• mammalian expression vectors such as pcDNA 3.1 (Invitrogen, San Diego, CA) and pTriEx-1 (Novagen, Madison, WI) .
• the appropriate DNA sequence may be inserted into the vector by a variety of procedures.
• the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art.
• the present invention relates to host cells containing the above-described constructs.
• the host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell.
• Introduction of the construct into the host cell can be effected by any means known in the art, including but not limited to transduction or transformation or transfection or electroporation. Examples of a suitable heterologous signal sequences
• SS include the honey bee mellitin SS (NH2-
• GKNPLGVRKTETSQVAPA-COOH (SEQ ID NO: 16).
• suitable SSs will be less that 75 aa long.
• These signal sequences may or may not be cleaved from the protein upon expression in animal cells.
• the rhodopsin tag 1 is not cleaved off of the protein when presented by the cell to the plasma membrane, whereas rhodopsin tag ID4 signal sequence is cleaved off.
• Non-limiting examples of a suitable epitope affinity tags include FLAG (NH2-DYKDDDDK-C00H) (SEQ ID NO:29), "EE"
• HSV herpes simplex virus tag
• QPELAPEDPED-COOH (SEQ ID NO: 33). These design elements of the hydrophobic protein are arrayed from amino to carboxy terminus in one of the following permutations: (1) SS-Tagl-Tag2-HP; (2) SS-Tagl-HP- Tag2; (3) SS-HP-Tagl-Tag2.
• the N-terminal methionine sequence and the heterologous signal sequence are selected from the group consisting of (a)
• the tag sequences comprise epitope tag sequences selected from the group consisting of (a) a FLAG tag (NH2-DYKDDDDK-COOH) (SEQ ID NO:l), (b) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID NO:2), (c) a hemagglutinin tag (NH2-YPYDVPDYA-COOH) (SEQ ID NO:3), (d) a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:4), (e) an HSV tag (NH2 -QPELAPEDPED-COOH) (SEQ ID NO:5), and (f) a rhodopsin tag (NH2 MNGTEGP, a FLAG tag (NH2-DYKDDDDK-COOH) (SEQ ID NO:l), (b) an EE tag (NH2-EEEEYMPME-C00H) (SEQ ID NO:2), (c) a hemagglutin
• the elements of the engineered hydrophobic protein are arrayed from an amino to carboxy terminus order selected from the group consisting of (a) SS-Tagl-Tag2-HP, (b) SS-Tagl-HP- Tag2, and (c) SS-HP-Tagl-Tag2.
• the engineered hydrophobic protein is selected from the group consisting of (a) GP67-Myc-EE-Human m2 mAChR (SEQ ID NO.-19), (b) Mellitin-Flag Tag-Human Beta 2 Adrenergic Receptor-EE (SEQ ID N0:20) , and (c) Hemagglutinin SS-Human Neurokinin 3 Receptor-HSV-Myc (SEQ ID NO: 21) .
• the tag sequences further comprise a hexahistidine sequence (SEQ ID NO: 17) and a decahistidine sequence (SEQ ID NO:18).
• the engineered hydrophobic protein is selected from the group consisting of (a) GP67- Myc-EE-Human m2 mAChR (SEQ ID NO:19), (b) Mellitin-Flag Tag- Human ml mAChR-EE (SEQ ID NO:20), and (c) Hemagglutinin SS- Rat m3 mAChR-HSV-OctaHis (SEQ ID NO: 21) .
• the HP sequence of the isolated polynucleotide may be any polynucleotide encoding a protein that is isolated with amphiphile present.
• the term may also refer to any polynucleotide encoding a protein for which, when purified to greater than 1% purity or purified to greater than 10% purity or purified to greater than 25% purity or purified to greater than 50-99% purity, either requires or benefits from the presence of an amphiphile for functional assays, to enhance stability (shelf-life or ability to withstand freeze-thaw cycles) , or to retain conformational integrity as observed by common laboratory techniques including ligand binding assays, circular dichroism, hydrodynamic assessments of mean size, shape, or density, interaction with conformation-specific antibodies.
• the hydrophobic protein of the invention is a mammalian hydrophobic protein.
• the hydrophobic protein of the invention is a human hydrophobic protein.
• the HP sequence of the isolated polynucleotide may include polynucleotides encoding proteins that are identified by bioinformatics-assisted means through the use of the following non-limiting examples of algorithms designed for the identification of hydrophobic proteins: (a) DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University) Cserzo, M. et al . (1997) Pro . Eng. 10:673- 676; (b) HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences) G.E Tusnady and I. Simon (1998) J " . Mol . Biol .
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a hydrophobic target protein from the group consisting of (i) a membrane protein, (ii) an integral membrane protein, (iii) a transmembrane protein, (iv) a monotopic membrane protein, (v) a polytopic membrane protein, (vii) a pump protein, (viii) a channel protein, (iX)a receptor kinase protein, (X) a G protein-coupled receptor protein, Xii) a membrane-associated enzyme, and (Xiii) a transporter protein, wherein the hydrophobic protein is bound by amphiphile selected from the group consisting of (i) a polar lipid, (ii) an amphiphilic macromolecular polymer, (iii) a surfactant or detergent, and (iV) an amphiphilic polypeptide; (b) selecting a ligand molecule using
• the invention provides a method for identifying a ligand for a hydrophobic protein, the method comprising (a) selecting a hydrophobic target protein from the group consisting of (i) a membrane protein, (ii) an integral membrane protein, (iii) a transmembrane protein, (iv) a monotopic membrane protein, (v) a polytopic membrane protein, (vii) a pump protein, (viii) a channel protein, (iX)a receptor kinase protein, (X) a G protein-coupled fl rti -—,
• the invention provides, an isolated nucleic acid molecule suitable for hydrophobic protein expression, comprising: (a) a vector polynucleotide sequence for protein expression in a eukaryotic cell, and (b) a polynucleotide sequence encoding an engineered hydrophobic protein comprising the following elements (i) an N-terminal methionine residue, (ii) a heterologous signal sequence (SS) , wherein the N-terminal methionine sequence and the heterologous signal sequence are selected from the group consisting of (1) MKFLVNVALVFMWYISYIYA (SEQ ID NO: 24), (2) MVRTAVLILLLVRFSEP (SEQ ID NO: 25), (3) MKTIIALSYIFCLVFA (SEQ ID NO:26), (4) MMNGTEGPNFYVPFSNKTGWRSPFEAPQYYLAEP-COOH (SEQ ID NO: 27) and (5) MGKNPLGVRKTETSQVAPA-COOH (S)
• a myc tag (NH2-KHKLEQLRNSGA-COOH) (SEQ ID NO:4), and (5) an HSV tag (NH2 -QPELAPEDPED-COOH) (SEQ ID N0:5)
• a hydrophobic protein (HP) sequence selected from the group consisting of (1) a membrane protein, (2) an integral membrane protein, (3) a transmembrane protein, (4) a monotopic membrane protein, (5) a polytopic membrane protein, (6) a pump protein, (7) a channel protein, (8) a receptor kinase protein, (9) a G protein-coupled receptor protein, (10) a membrane-associated enzyme, and (11) a transporter protein.
• IDENTIFICATION BY ALIS Purified ovine COX-1 (>95% by SDS-PAGE) from Cayman Chemical Company (Ann Arbor, MI) was prepared for screening by exchanging the detergent . To remove the detergent in which the protein was supplied, Tween-20, ion exchange chromatography was conducted.
• COX-1 Target Protein (2X, stored at -80 degrees) 1.3 mg/mL (20 ⁇ M) in 80 mM Tris/240 ⁇ M DBM BlacB Control Protein (6X, stored at 4 degrees) 5.5 mg/mL (-150 ⁇ M) BlacB in IX SEC Library (40X, stored at 80 degrees) lOOmM in DMSO Discrete Ligands (40X, stored at -80 degrees) 40 ⁇ M in DMSO
• This sample prep SOP yields binding assays that combine COX- 1 with mass-encoded combinatorial libraries made of approximately 2500 small drug-like molecules, each member at a concentration of 1 ⁇ M.
• the sample was incubated 30- minutes at 4°C. As the total volume was 12 ⁇ L, the sample thus contained 240 pmol protein and 12 pmol of each library component.
• an unrelated membrane protein, diacyl glycerol kinase (Calbiochem, Inc.; San Diego, CA) , was also prepared in the same buffer at 20 ⁇ M and incubated with the same 2500-member library and treated similarly.
• the mixtures were individually subjected to ALIS Analysis. If any ligand of suitably high affinity was bound to the COX at the time its fraction was collected, the mass spectral analysis would identify its mass. By virtue of the mass-coding, the precise combination of building blocks and core molecule can be identified (see U.S. Patent No. 6,147,344) . If the same compound failed to appear in the diacyl glycerol kinase control experiment, the compound may then be identified as a specific ligand of the COX-1.
• the mixtures were then individually subjected to modified ALIS analysis as follows.
• the large detergent- solubilized protein was separated from the small drug-like molecules by size exclusion chromatography (SEC) over a 4.6mm x 50 mm x 5 ⁇ m SEC column at 0°C using a running buffer of TBS (80 mM tris," pH 8.0, 150 mM NaCl, 2.5% DMSO) at a flowrate of 2 mL/minute .
• SEC size exclusion chromatography
• TBS 80 mM tris
• pH 8.0 pH 8.0
• the eluting SEC fraction- containing protein was identified by UV-VTS detection monitoring at 230 nm and transferred by way of a sample loop to a low-flow (100 ⁇ L/minute) reverse-phase chromatography (RPC) system.
• RPC reverse-phase chromatography
• the RPC column (Higgins C-18; 1 mm x 50 mm x 5 ⁇ m) is maintained at 60 °C to promote dissociation of ligands from the complex. From this RPC column, the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 5 minute. If any ligand of suitably high affinity was bound to the COX at the time its fraction was collected, the mass spectral analysis will identify its mass. By virtue of the mass encoding the precise combination of building blocks and core can be identified (see U.S. Patent No.
• a gene construct encoding the m2 subtype of the muscarinic acetylcholine receptor (m2R) was cloned into a baculovirus expression vector according to conventional cloning methods (see e . g. , Baculovirus Expression Vector System, 6th Edition, 1999, Pharmingen, San Diego, CA) .
• the gene construct encoded a polypeptide with an amino terminal methionine followed immediately in frame by the melittin signal sequence (SEQ ID NO: 12) followed immediately in frame by the FLAG Ml epitope tag (SEQ ID NO:l) followed immediately in frame by the sequence for the m2 muscarinic acetylcholine receptor (NCBI Accession No. X04708) .
• the full-length polypeptide sequence therefore was:
• the mellitin signal sequence is cleaved after Ala(21) revealing an amino terminal FLAG epitope which is bound specifically by the FLAG Ml antibody resin (Sigma; St. Louis, MO).
• This baculovirus expression vector was used to generate baculovirus that directed the expression of the above polypeptide in insect cells according the conventional methods (Baculovirus Expression Vector System, 6th Edition, 1999, Pharmingen, San Diego, CA).
• To purify FLAG-tagged m2R 60 g of insect cells expressing the above polypeptide were suspended in 0.6 L of TBS [50 mM Tris-CL, pH 7.4, 100 mM NaCl), and the sample was homogenized by nitrogen cavitation. The homogenate was subjected to centrifugation at 500 x g for 30 minutes at 4 C to removed non-homogenized cells.
• the pellet was discarded and the supernatant was subjected to ultracentrifugation at 100,000 x g for 45 minutes at 4 C.
• the ultracentrifugation supernatant was discarded and the pelleted cell membranes were resuspended in TBS containing 0.5% (w/v) digitonin (TBS-D buffer) to a protein concentration of 2.5 mg/mL.
• TBS-D buffer 0.5% (w/v) digitonin
• the soluble supernatant was applied to a 5 mL column of the FLAG Ml antibody resin pre-equilibrated with TBS-D buffer at a flow rate of OJ mL/min for antibody affinity purification.
• the column was washed with 50 mL of TBS-D buffer and then the FLAG-tagged m2R protein was eluted from the column with TBS-D buffer containing 100 ⁇ g/mL of FLAG peptide (Sigma; St. Louis, MO). Eluted column fractions containing purified FLAG-tagged m2R were identified by SDS-PAGE.
• This m2R preparation consisted of 6 ⁇ M m2R in TBS-D with 100 ⁇ g/mL of FLAG peptide. Each m2R polypeptide is reversibly associated with a multiplicity of digitonin molecules, creating a membrane protein-detergent complex with a stoichiometry of m2R:digitonin of 1:5-500.
• This preparation was designated as Stock m2R for use in ALIS sample preparation according to the sample preparation protocol outlined below.
• Stock cyclooxygenase 1 was prepared according to the method in Example 1 to yield a concentration of 6 ⁇ M COX in TBS.
• Stock discrete ligands Sigma; St.Louis, MO
• QNB quinuclidinyl benzylate
• atropine were prepared to 400 ⁇ M in TBS.
• Four combinatorial chemical libraries were prepared in dimethyl sulphoxide (DMSO) constituting on average 2500- 5000 small drug-like molecules each at a concentration of 400 ⁇ M. These four drug libraries were designated NMG-66, NGM-41, NGL-10-A-41, and NGL-116-A-470.
• Binding reactions were prepared that combined protein (either m2R test protein or COX control protein) with ligand (either QNB alone, atropine alone, pirenzepine alone, atropine plus drug library, or QNB plus drug library) or protein with DMSO as a control.
• ligand either QNB alone, atropine alone, pirenzepine alone, atropine plus drug library, or QNB plus drug library
• protein with DMSO as a control.
• 38 ⁇ L of Premix Buffer was dispensed into polypropylene tubes containing 2 ⁇ L of DMSO or DMSO-solubilized ligands, mixed by vortexing, and centrifuged at 8,000 x g for 10 minutes at room temperature to remove insoluble material.
• the clarified supernatants (2 ⁇ L) containing either aqueous DMSO alone or aqueous DMSO- solubilized ligands (with or without drag libraries) were transferred to polypropylene tubes at 4 C.
• Target protein (8 ⁇ L) m2R or control (8 ⁇ L) protein COX was added to the supernatants, mixed well by pipetting, and incubated at 4 C for 60 minutes.
• binding reaction preparations were then subjected to ALIS analysis.
• the binding reaction preparations combine 4.8 ⁇ M target membrane protein (m2R) or 4.8 ⁇ M control membrane protein (COX) with a multiplicity of approximately 2500 small drug like molecules each at a concentration of 1-10 ⁇ M in a manner that established equilibrium binding conditions.
• High affinity ligands (Ki ⁇ 100 ⁇ M) to the proteins are then identified by ALIS.
• Small molecule ligands of the target protein m2R that do not also bind to the control protein COX are considered as specific ligands of the target protein.
• binding reactions were also prepared combining m2R or COX with individual (discrete) m2R ligands.
• This ALIS Analysis proceeded as described below with a series of size exclusion chromatography (SEC), followed by reverse phase chromatography (RPC), followed by mass spectrometric (MS) analysis.
• SEC size exclusion chromatography
• RPC reverse phase chromatography
• MS mass spectrometric
• the large detergent-solubilized molecules were separated from the unbound small drug-like molecules by SEC over a 4.6 mm x 50 mm x 5 ⁇ m SEC column at 4°C using a running buffer of 50 mM Tris-Cl, pH 7.5, 150 mM NaCl, 2.5% DMSO at a flowrate of 2 mL/minute.
• the protein containing fraction was identified with ultraviolet electronic absorption spectrometry monitoring at 230 nm.
• the protein-containing fraction was transferred by way of a sample loop to a low flowrate (100 ⁇ L/min RPC system.
• the RPC column (Higgins C-18; 1 mm x 50 m x 5 ⁇ m) is maintained at 60 C to promote ligand dissociation from the complex. From this
• RPC column the ligand in eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 5 minutes.
• Mass analyzed ligands collected with the protein-containing SEC fraction by virtue of its high affinity for the protein-detergent m2R complex were identified by fore-knowledge of their precise mass.
• m2 mAChR is purified according to the method of Peterson et al . (Peterson, G.L. et al .
• a library of mass-coded compounds is added to the m.2 mAChR/pirenzepine mixture, and the sample is analyzed to determine if a library compound displaces pirenzepine from the HP protein. Displacement of pirenzepine indicates that the library compound binds more tightly and at the same site as pirenzepine itself.
• the displacement assay is conducted as follows.
• the mixture of m2 mAChR, 1 ⁇ m pirenzepine, and 1 ⁇ M of each library compound are subjected to ALIS Analysis.
• MS signal corresponding to the mass of pirenzepine is monitored, while the mass of the library compounds are ignored. If the library compound quantitatively reduces the MS signal corresponding to the mass of pirenzepine, it is inferred that the library compound displaced pirenzepine from the HP protein, in this case mAChR protein. If incubation with the library compounds does not alter the MS signal corresponding to the mass of pirenzepine, the library compounds are considered not to contain an m2 mAChR ligand.
• EXAMPLE 4 AFFINITY SELECTION OF m2 itiACHR MASS-CODED LIGANDS AND IDENTIFICATION BY ALIS
• m2 mAChR is purified according to the method of Peterson et al . (Peterson, G.L. (1995) J.
• the protein is adjusted to 20 ⁇ M in a buffer of TBS-AGD is incubated with a 2500 -member library of mass-coded compounds, each member at a concentration of 1 ⁇ M. After a 30 minute incubation at 22°C, the sample was chilled at 4°C pending ALIS analysis.
• an unrelated membrane protein, glycophorin is also prepared in TBS-AGD at 20 ⁇ M and incubated with the mass-coded library. To determine if the compound specifically binds to the mAChR, the mAChR-compound mixture is analyzed by ALIS Analysis.
• COX-1 protein was purified from ram seminal vesicles according to the method of Johnson et al . (Johnson, J.L. (1995) Arch . Biochem . Biophys . 324:26-
• the COX-1 sample is adjusted to 20 ⁇ M in TBS-AGD (50 mM tris, pH 8.0, 150 mM NaCl, 800 mM dodecyl ⁇ -D-maltoside, 2.5% DMSO) is mixed and incubated with a 2500-member library of mass-coded compounds, each member at a concentration of 1 ⁇ M. After a 30 minute incubation at 22°C, the sample was chilled at 4°C pending ALIS analysis. As the total volume is 12 ⁇ L, the sample thus contains 240 pmol protein and 12 pmol of each library component. As a control test, an unrelated membrane protein, glycophorin, is also prepared in TBS-AGD at 20 ⁇ M and incubated with the same 2500-member library and treated similarly.
• TBS-AGD 50 mM tris, pH 8.0, 150 mM NaCl, 800 mM dodecyl ⁇ -D-maltoside, 2.5% DMSO
• the large detergent- solubilized protein is separated from the small drug-like molecules by size exclusion chromatography (SEC) over a 4.6mm x 50 mm x 5 ⁇ m SEC column at 0°C using a running buffer of TBS (50 mM tris, pH 8.0, 150 mM NaCl, 2.5% DMSO) at a flowrate of 2 mL/minutes .
• SEC size exclusion chromatography
• TBS 50 mM tris, pH 8.0, 150 mM NaCl, 2.5% DMSO
• the eluting SEC fraction containing protein is identified by on-line fluorescence detection exciting at 240-250 nm and monitoring emission at 340 nm and transferred by way of a sample loop to a low-flow
• the RPC column (Higgins C-18; 1 mm x 50 mm x 5 ⁇ m) is maintained at 60°C to promote dissociation of ligands from the complex. From the RPC column, the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 5 minutes. Ligand of suitably high affinity bound to the COX-1 at the time its fraction is collected, and the mass of the ligand is identified by mass spectral analysis.
• EXAMPLE 6 AFFINITY SELECTION OF COX-1 LIGANDS AND IDENTIFICATION BY MODIFIED ALIS WITH ON-LINE
• COX-1 protein was purified from ram seminal vesicles according to the method of Johnson et al . (Johnson, J.L. (1995) Arch . Biochem . Biophys . 324:26- 34) .
• the COX-1 sample is adjusted to 20 ⁇ M in TBS-AGD (50 mM tris, pH 8.0, 150 mM NaCl, 800 mM dodecyl ⁇ -D-maltoside, 2.5% DMSO) is mixed and incubated with a 2500-member library of mass-coded compounds, each member at a concentration of 1 ⁇ M. After a 30 minute incubation at 22°C, the sample is chilled at 4°C pending modified ALIS analysis.
• the sample contains 240 pmol protein and 12 pmol of each library component.
• an unrelated membrane protein, glycophorin is also prepared in TBS-AGD at 20 ⁇ M and incubated with the same 2500-member library and treated similarly.
• the large detergent-solubilized protein is separated from the small drug-like molecules by size exclusion chromatography (SEC) over a 4.6mm x 50 mm x 5 ⁇ m SEC column at 0°C using a running buffer of TBS (50 mM tris, pH 8.0, 150 mM NaCl, 2.5% DMSO) at a flowrate of 2 mL/minute.
• SEC size exclusion chromatography
• TBS 50 mM tris, pH 8.0, 150 mM NaCl, 2.5% DMSO
• the eluting SEC fraction containing protein is identified by on-line light scattering detection and transferred by way of a sample loop to a low-flow (100 ⁇ L/minute) reverse-phase chromatography (RPC) system.
• RPC reverse-phase chromatography
• the RPC column (Higgins C-18; 1 mm x 50 mm x 5 ⁇ m) is maintained at 60°C to promote dissociation of ligands from the complex. From the RPC column, the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over
• COX-1 protein at the time its fraction is collected and the mass of the ligand is identified by mass spectral analysis.
• EXAMPLE 7 HETEROGENEOUS SOLUTION PHASE SCREENING FOR
• HP ligands may also be screened by utilizing a heterogeneous solution phase screening method in which a tagged target sequence is immobilized on a solid support.
• a heterogeneous solution phase screening method in which a tagged target sequence is immobilized on a solid support.
• anti-flag antibody-loaded protein A agarose beads are prepared for use as a sedimentable stationary element in an immunoprecipitation (IP) -based screening protocol.
• TBS-AG 50 mM tris, pH 8.0, 150 mM NaCl, 800 mM dodecyl ⁇ -D-maltoside
• 100 ⁇ L of 50% v/v slurry of protein A agarose (Santa Cruz Biotechnology, St. Louis, MO.) are washed in a 1.5 mL eppendorf tube with three room temperature cycles of: (1) combining the beads with 1 mL TBS-AG; (2) mixing the sample by tumbling for 20 minutes; and (3) centrifugation at lOOOOxg, followed by a careful removal of the supernatant that leaves the pelleted agarose beads in the bottom of the tube .
• the 50 ⁇ L pellet of beads is brought up in 1.0 mL TBS-AG.
• 50 ⁇ L of 1 mg/mL ⁇ -galactosidase in TBS-AG buffer is added and the mixture is incubated at 4°C for 60 minutes to block non- specific binding of protein to the beads.
• 10 ⁇ L of 1.0 ⁇ g/mL anti-flag antibody (Sigma, St. Louis, Montana) , and the mixture is incubated at 4°C for 60 minutes.
• another preparation of control agarose beads handled similarly is treated with 10 ⁇ L of TBS-AG instead of the anti-flag antibody.
• the anti-flag loaded beads and the control beads are then washed to remove excess antibody and protein and, finally, resuspended in 0.10 mL of TBS-AG buffer and transferred to 0.5 mL eppendorf tubes .
• CHO cells expressing an m2 mAChR-flag tag-His tag protein are cultured, lysed, and homogenized.
• the m2 mAChR- containing membranes of the cells are purified by sucrose step-gradient ultracentrifugation. This sucrose step- gradient ultracentrifugation step removes most non-membrane proteins and cell debris.
• the ultracentrifugation step also has the potential of isolating specific populations of membranous cellular substructures.
• the mAChR-enriched membranes are solubilized with detergent (dodecyl- ⁇ - maltoside, D ⁇ M or CYMAL-7; (Anatrace; Maumee, OH)) and subjected to three steps of affinity purification.
• detergent dodecyl- ⁇ - maltoside, D ⁇ M or CYMAL-7; (Anatrace; Maumee, OH)
• MCAQ metal chelate affinity chromatography
• affinity purification over a column of immobilized mAChR ligand 3- (2 ' -aminobenzhydryloxy) -tropane (ABT) , followed by a desalting step will yield a final enrichment of active m.2 mAChR protein.
• the sample is adjusted to 20 ⁇ M m2 mAChR protein in a buffer of TBS-AGD and is incubated with a 2500-member library of mass-coded compounds, each member at a concentration of 1 ⁇ M.
• the reaction is done in a volume of 40 ⁇ L. After a 30 minute incubation at 22°C, the sample is chilled at 4°C pending MS analysis.
• ⁇ -galactosidase is similarly prepared in TBS-AGD at 20 ⁇ M and incubated with the mass-coded library.
• the m2 mAChR protein-compound mixtures are prepared for analysis by MS analysis with the following procedure.
• the purified protein-library mixtures are each split into two 20 ⁇ L volumes.
• one volume is combined with the anti-flag beads (anti- flag/protein A agarose ) for IP and the other volume is subjected to a mock IP by combination with the control agarose beads (buffer/protein A agarose beads) .
• the ⁇ -galactosidase mixture one 20 ⁇ L volume is combined with the anti-flag beads for a control IP and the other 20 ⁇ L volume is subjected to a mock IP by combination with the control agarose beads.
• IPs proceed, mixed by tumbling, for 60 minutes at 4°C .
• each IP is washed with three room temperature cycles of: (1) combining the beads with 1 mL TBS-AG, (2) mixing by tumbling for 2 minutes, and (3) centrifugation at 10,000 g, followed by a careful removal of the supernatant that leaves the pelleted agarose beads in the bottom of the tube.
• each 50 ⁇ L bed volume bead preparation is then resuspended in an additional 50 ⁇ L of TBS (50 mM tris, pH 8.0, 150 mM NaCl) and kept at 4°C.
• Each 100 ⁇ L bead preparation is combined with 50 ⁇ L of 30% acetonitrile in water heated to 60°C for 5 minutes to dissociate bound ligands from the protein. Then the mixture is centrifuged at 10,000 x g to pellet the beads, and the dissociated protein in the supernatant is transferred to a new tube .
• the IP procedure allows both an affinity selection of a ligand and the physical separation of the m2mAChR-ligand complex from unbound library members.
• These supernatants contain 50 mM tris, pH 8.0, 150 mM NaCl, 80 mM dodecyl ⁇ -D- maltoside, and 10% acetonitrile.
• Approximately 60 ⁇ L of these supernatant samples are injected individually into a low-flow (100 ⁇ L/minutes) reverse-phase chromatography (RPC) system.
• the RPC column Higgins C-18; 1 mm x 50 mm x 5 ⁇ m) is maintained at 60°C.
• the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 5 minutes.
• m2 mAChR-ligands are identified by observing a mass corresponding to one compounds from the 2500-member mass- coded library in the supernatant of the m2mAChR protein beads and not from the supernatant of the m2mAChR protein control, ⁇ -lac library, or ⁇ -lac control beads.
• the structure of the mass-coded compounds selected in the procedure are easily identified (see U.S. Patent No.
• EXAMPLE 9 HETEROGENEOUS SOLUTION PHASE SCREENING FOR
• Flag-tagged m2 mAChR protein is purified as outlined herein above and resuspended at a concentration of 20 ⁇ M in a buffer of TBS-AGD.
• the protein is incubated with a 2500- member library of mass-coded compounds, each member at a concentration of 1 ⁇ M and with 1 ⁇ M pirezepine, a known ligand for m2 mAChR protein, in a volume of 40 ⁇ L. After a 30 minute incubation at 22°C, the sample was chilled at 4°C pending MS analysis.
• ⁇ - galactosidase is similarly prepared in TBS-AGD at 20 ⁇ M and incubated with the mass-coded library and pirezepine.
• the purified protein-library-pirenzepine mixtures from either the m2 mAChR protein or ⁇ -galactosidase trials, are each split into two 20 ⁇ L volumes.
• one volume is combined with the anti-flag beads (anti-flag/protein A agarose) for IP and the other volume is subjected to a mock IP by combination with the control agarose beads (buffer/protein A agarose beads) .
• Protein A agarose beads are prepared as previously described herein.
• one 20 ⁇ L volume is combined with the anti-flag beads for a control IP and the other 20 ⁇ L volume is subjected to a mock IP by combination with the control agarose beads.
• These IPs proceed, mixed by tumbling, for 60 minutes at 4°C. Then each IP is washed with three room temperature cycles of: (1) combining the beads with 1 mL TBS-AG; (2) mixing by tumbling for 2 minutes; and (3) centrifugation at 10,000 x g, followed by a careful removal of the supernatant that leaves the pelleted agarose beads in the bottom of the tube.
• each 50 ⁇ L bed volume bead preparation is then resuspended in an additional 50 ⁇ L of TBS (50 mM tris, pH 8.0, 150 M NaCl) and kept at 4°C.
• TBS 50 mM tris, pH 8.0, 150 M NaCl
• four heterogeneous bead preparations are made: (1) m2 mAChR/anti-flag/protein A agarose (m2 beads) ; (2) m2 mAChR/buffer/protein A agarose beads (m2 control beads) ; (3) ⁇ -galactosidase/anti-flag/protein A agarose beads ( ⁇ - galactosidase beads) , and (4) ⁇ -galactosidase/buffer/protein A agarose beads ( ⁇ -galactosidase control beads) .
• bead-based preparations constitute heterogeneous solution phase systems useful for screening in the following manner.
• Each 100 ⁇ L bead preparation is combined with 50 mL of 30% acetonitrile in water heated to 60°C for 5 minutes to dissociate any bound pirenzepine from the protein.
• the mixture is centrifuged at 10,000 x g to pellet the beads, and dissociated protein in the supernatant is transferred to a new tube.
• the IP procedure allows both an affinity selection of the ligand and the physical separation of the m2 mAChR-ligand complex from unbound library members.
• These supernatants contain 50 mM tris, pH 8.0, 150 mM NaCl, 80 mM dodecyl ⁇ -D-maltoside, 10% acetonitrile, and ⁇ 50 pmol of pirenzepine. Approximately 60 ⁇ L of these supernatants " are injected into low-flow (100 ⁇ L/minute) reverse-phase chromatography (RPC) system. The RPC column (Higgins C-18; 1 mm x 50 mm x 5 ⁇ m) is maintained at 60°C.
• the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 5 minutes.
• the mass corresponding to pirenzepine from the supernatant of the m2 mAChR protein control, ⁇ - galactosidase library test, or ⁇ -galactosidase control beads should be higher than the pirenzepine mass response in the MS analysis of the m2 mAChR protein beads. It is then inferred that the 2500-member mass-coded library contains a ligand that binds to the m2 mAChR protein with an affinity greater than that of pirenzepine. Libraries that contain hits can thus be detected and selected from among other libraries that do not contain hits.
• HPs are multiplexed in the preparation of screening samples. Multiplexing is defined to mean any method of preparation wherein the target protein is combined with some known molar equivalent of one or more accessory proteins (APs) .
• APs accessory proteins
• the target HP is observed to bind a known agonist with greater affinity than without the AP(s) present; (2) in the presence of the AP(s) , the target HP is observed to bind a known antagonist with greater affinity than without the AP(s) present; (3) in the presence of the AP(s), the HP is shown to have greater functional activity as assayed by enzymatic, in vi tro, or cell-based assays; (4) in the presence of the AP(s), the HP is shown to alter its state of multimerization; and (5) in the presence of the AP(s), the HP is shown to have greater conformational stability or uniformity.
• a method for multiplexed screening of m2 mAChR with G ail p lY2 -Guanosine-diphosphate (GDP) as a heterotrimeric AP is presented.
• G ail p i 2 --GDP complex was identified as an AP for the m2 mAChR because its presence enhanced the affinity of the m2 mAChR for an antagonist, N- methylscapolamine (NMS) by 5 -fold as demonstrated by the following method.
• NMS N- methylscapolamine
• the human K opioid receptor was identified as an AP for the human ⁇ opioid receptor because its presence caused the multimerization state of the human ⁇ opioid receptor to change from monomer to heterodimer as demonstrated by the method of Jordan and Devi (Jordan, B.A. and Devi, L.A., (1999) Nature 399:697-708).
• Human K-opioid receptor is purified and dialyzed into TBS-AG at a concentration of 50 ⁇ M.
• Human ⁇ -opioid receptor is purified and dialyzed into TBS-AG at a concentration of 50 ⁇ M. Equal volumes of these two preparations were combined to allow them to dimerize.
• heterodimerized opioid receptor complex is then screened for ligand binding according to any of the methods utilizing affinity selection and ALIS or modified ALIS presented herein.
• the detergent micelle solubilization is exchanged for solubilization in defined proteoliposomes meeting the following criteria: (1) the lipid composition of the PL is defined and characterized as having no more than six discrete lipid entities making up 90% of the lipid content of the PL; (2) 90% of the HP-PL preparation has a defined, unimodal size distribution of particles spanning no more than three orders of magnitude and wherein mean particle size is in the range of 5-10000 nm; (c) the PL preparation yields >50 nM HP.
• the crude protein-lipid mixture is then incubated for 3 hours at 8°C with 5 minute, 22°C bath sonication at 30 minute intervals (6 times) .
• This mixture is then subjected to 11 passages through a 100 nm polycarbonate membranes in a small volume extruder according to the manufacturer's protocol (Avanti Polar Lipids, Alabaster, AL) at 20°C.
• the crude PL preparation is passed through a 10.0 mL desalting (G-50 sephadex column) previously equilibrated with TBS at 4°C.
• TBS at 4°C is used to elute the material from the column.
• This desalting procedure is conducted with a flow rate of 0.5 mL/minute .
• the protein concentration is estimated by combining a 10 ⁇ L sample with 10 ⁇ L of 0.2% Triton X-100 and using that mixture in a Bio-Rad colorimetric protein assay (Bio-Rad Inc., Hercules, CA) . The concentration is then adjusted by dilution with TBS to 10 ⁇ M.
• the size distribution is defined using a Coulter N4 submicron particle analyzer following the manufacturer's protocols.
• An independent assessment of size distribution and mean particle size is accomplished by analytical SEC by injecting 20 ⁇ L onto an analytical SEC column with a running buffer TBS at a flow rate of 1.0 mL/minute (G2000 SWXL , 5 x 300 mm, 5 ⁇ m; ToSo-Haas) , fitted with a UV detector monitoring at 280 nm, and chilled to 12°C.
• a single peak eluting at 8.23 minutes identified the retention time of the GPCR-PL's which was compared to standard curve of molecular size marker elution times and indicated that the mean apparent size was comparable to that of a 940,000 dalton protein.
• Proteoliposomes may also be prepared with HPs complexed with APs.
• detergent micelle solubilization is exchanged with solubilization in defined proteoliposomes meeting the following criteria: (1) the lipid composition of the PL was defined and characterized as having no more than six discrete lipid entities making up 90% of the lipid content of the PL; (2) 90% of the HP-PL preparation has a defined, unimodal size distribution of particles spanning no more than three orders of magnitude and wherein mean particle size is in the range of 5-10000 nm; (3) the PL preparation yields >50 nM HP; (4) the PL preparation included at least one other protein designated the accessory protein (AP) , the presence of which supports the maintenance of a favorable conformation for the target HP.
• AP accessory protein
• 50 ⁇ M G c.il p lY2 was prepared by combining equal volumes of 100 ⁇ M G ⁇ n with 100 ⁇ M Gp lY2 purified as described (ref) and dialyzed into TBSM plus 800 mM DbM (TBSM-AG) .
• To the lipid mixture is added 0.2 mL 50 ⁇ M m.2 mAChR prepared as described in Peterson, G.L. et al . (Peterson, G.L. et al . (1995) J. Biol . Chem. 270: 17808) and 0.2 mL 50 ⁇ M G ail p lY2 .
• To this mixture is added 10 ⁇ L of 50 mM GDP. This yields a crude mixture of lipid, HP, and AP.
• the crude HP/AP-lipid mixture is then incubated for 3 hours at 8°C with 5 minute, 22°C bath sonication at 30 minute intervals (6 times) .
• This mixture is then subjected to 11 passages through a 100 nm polycarbonate membranes in a small volume extruder according to the manufacturer's protocol
• the crude PL preparation is passed through a 10.0 mL desalting (G-50 sephadex column) previously equilibrated with TBS at 4°C.
• TBS at 4°C is used to elute the material from the column.
• This desalting procedure is conducted with a flow rate of 0.5 mL/minute.
• the protein concentration is estimated by combining a 10 ⁇ L sample with 10 ⁇ L of 0.2% Triton X-100 and using that mixture in a Bio-Rad colorimetric protein assay following the manufacture's instructions. The concentration is then adjusted by dilution with TBS to 20 ⁇ M.
• a Coulter N4 submicron particle analyzer is used according to the manufacturers protocol.
• An independent assessment of size distribution and mean particle size is accomplished by analytical SEC by injecting 20 ⁇ L onto an analytical SEC column with a running buffer TBS at a flow rate of 1.0 mL/minute (G2000 SWXL , 5 x 300 mm, 5 ⁇ m; ToSo-Haas) , fitted with a UV detector monitoring at 280 nm, and chilled to 12°C.
• a single peak eluting at 8.23 minutes post-injection identified the retention time of the HP/AP-PL's which is compared to standard curve of molecular size marker elution times.
• the resultant mean apparent size is comparable to that of' a 940,000 dalton protein.
• Control AP-PLs for use as screening controls are made to meet the following criteria: (1) the lipid composition of the PL was defined and characterized as having no more than six discrete lipid entities making up 90% of the lipid content of the PL; (2) 90% of the HP-PL preparation has a defined, unimodal size distribution of particles spanning no more than three orders of magnitude and wherein mean particle size is in the range of 5-10000 nm; (3) the PL preparation is designed to exactly mimic the analogous HP/AP-PL except no target HP is present.
• Synthetic lipids (Avanti Polar Lipids, Alabaster, AL) D-ribo-phytospingosine-1-phosphate and ceramide-C18 : 0 each in chloroform are combined in a volume of 1 mL each at 5 mM in a glass test tube and the chloroform is evaporated at room temperature under a stream of argon for 24 hours. The lipid residue is then wetted with 0.40 mL of TBS plus 2 mM MgCl 2 (TBSM) , sonicated for 30 minutes at 28°C, and mixture transferred to a 1.5 mL polypropylene tube.
• Synthetic lipids Alabaster, AL
• 50 ⁇ M G a ...p.. Y .- was prepared by combining equal volumes of 100 ⁇ M G ⁇ il with 100 ⁇ M Gp lY2 purified as described Hou, Y. et al . , J. Biol . Chem. (2000) 275:38961-6 and dialyzed into TBSM plus 800 mM DbM (TBSM-AG) .
• To the lipid mixture is added 0.2 mL TBS-AG and 0.2 mL 50 ⁇ M G ⁇ il p lY2 .
• To this mixture is added 10 ⁇ L of 50 mM GDP. This yields a crude mixture of lipid and AP.
• the protein concentration is estimated by combining a 10 ⁇ L sample with 10 ⁇ L of 0.2% Triton X-100 and using that mixture in a Bio-Rad colorimetric protein assay following the instructions of the manufacturer. The concentration is then adjusted by dilution with TBS to 10 ⁇ M.
• This crude AP-lipid mixture is then incubated for 3 hours at 8°C with 5 minute, 22°C bath sonication at 30 minute intervals (6 times) .
• This mixture is then subjected to 11 passages through a 100 nm polycarbonate membranes in a small volume extruder according to the manufacturer's protocol
• a Coulter N4 submicron particle analyzer is used according to the manufacturers protocol.
• An independent assessment of size distribution and mean particle size is accomplished by analytical SEC by injecting 20 ⁇ L onto an analytical SEC column with a running buffer TBS at a flow rate of 1.0 mL/minute (G2000 SWXL , 5 x 300 mm, 5 ⁇ m; ToSo-Haas) , fitted with a UV detector monitoring at 280 nm, and chilled to 12°C.
• a single peak eluting at 8.23 minutes identified the retention time of the AP-PL's which is compared to standard curve of molecular size marker elution times.
• the resultant mean apparent size is comparable to that of a 940,000 dalton protein.
• the proteoliposomes described herein are then screened for ligand binding according to any of the methods utilizing affinity selection and ALIS or modified ALIS presented herein.
• nucleic acid sequences encoding the tagged HP proteins of the invention is well within the skill of those in the art, utilizing routing procedures common in the art of nucleic acid cloning.
• Tagged-HPs e . g. , Mellitin-Flag Tag-Human ml mAChR-EE- tag protein or Mellitin-Flag Tag-Human Beta 2 Adrenergic Receptor-EE-tag protein, are produced from a recombinant baculovirus following the methodology provided by the manufacturer of the viral expression system (Pharmingen, San Diego, CA) .
• recombinant virus is selected based on its ability to direct the expression of the recombinant protein (s) .
• Protein expression is confirmed by western blot analysis of detergent-solubilized cell lysates of the infected insect cells. Using primary antibodies that recognize either the Flag epitope, the EE epitope, or the HP protein itself, the western blot reveals whether or not, and to what degree, the HP proteins are expressed. If possible, a functional assay is performed to determine that the expressed protein is functional.
• a cell- based 3 H-N-methylscapolamine binding analyses is performed by the method of Rinken and Haga (Rinken, A. and Haga, T. (1993) Arch . Biocehm. Biophys . 301 : 158-164) confirmed that the virus-directed protein expression was functional, indicating a Bmax of 0.5xl0 5 receptors per cell and a Kd of 0.10 nM.
• This baculovirus was then amplified by to a high titer of 2.0xl0 8 pfu/mL by conventional methods (Pharmingen, San Diego, CA) .
• the cell pellets from all ten bioreactor production runs are combined, and the cell pellets are suspended in 500 mL of ice cold TBS buffer plus 1 mM EDTA, 10 ⁇ g/ml pepstatin and 1 ⁇ g/ml pmethylsulfonylfluoride, and 20 mM dodecyl- ⁇ -D- maltoside (DbM) .
• This cell slurry is subjected to 50 strokes in a pestle A dounce homogenizer at 4°C to break open the cells and solubilize the membrane proteins. To clarify this suspension, the material is centrifuged for 60 minutes at 40000xg at 4°C to remove insoluble material.
• the supernatant is then collected and used as a source of soluble Mellitin-Flag Tag-Human ml mAChR-EE protein.
• the honey bee mellitin signal sequence is cleaved off by cellular proteases in the process of expression and trafficking to the plasma membrane of the insect cell. From this point on the solubilized protein is referred to as Flag Tag-Human ml mAChR-EE.
• Each solubilized recombinant HP is then purified with two rounds of affinity purification over an antibody affinity column.
• Both the anti-EE-tag and anti-Flag-tag columns are prepared similarly. Briefly, 35 mg of purified anti-epitope antibody is dialyzed into coupling buffer and coupled to 10 mL CNBr-activated sepharose beads according the manufacturers protocol (Amersham Pharmacia, Piscataway, NJ) . The resin is then transferred to a 1.2 x 15 cm polypropylene column, and the epitope affinity columns are then equilibrated with TBS-AG at 4°C .
• solubilized HP protein e . g. , FlagTag- Human ml mAChR-EE
• HP protein e . g. , FlagTag- Human ml mAChR-EE
• the column was then washed with 5 column volumes of TBS-AG at the same flow rate.
• the specifically-bound HP is then eluted from the column with a bolus of excess EE peptide (NH2-EEEEYMPME- COOH; Sigma-Genosys, St. Louis, MO) solubilized in a volume of 15 mL in TBS-AG at 10 mM.
• the eluant is then applied similarly to the anti-Flag-tag affinity column, similarly washed, and eluted from the column with excess anti-FLAG peptide (NH2-DYKDDDDK-C00H; Sigma-Genosys, St. Louis, MO) .
• This material is then dialyzed with two exchanges into a 100 fold volume of TBS-AG overnight at 4°C.
• Sucrose gradient ultracentrifugation is then used to remove misfolded polypeptide.
• the material is applied to a discontinuous step gradient of 5%-25% sucrose in TBS-AG and centrifuged in a Beckman SW Ti.50 rotor at 1000OOxg for 4 hours at 4°C .
• the properly conformed HP, e . g. , FlagTag-Human ml mAChR-EE, material is collected at the 5%-25% interface. This material is then subjected to a final dialysis with two exchanges into a 100 fold volume of TBS-AG overnight at 4°C.
• the protein concentration of the HP solution is determined by colorimetric protein assay (Bio-Rad Laboratories, Inc., Hercules, CA) and adjusted as necessary, by dilution or concentration in a stirred ultrafiltration cell (Millipore, Bedford, MA) , to 50 ⁇ M.
• the detergent concentration is also determined by RPC-UV using a Higgins C-18 column whereupon 50 ⁇ L of the mixture the ligand is eluted into a high-resolution mass spectrometer for analysis using a gradient of 5%-95% acetonitrile (0.1% formic acid counterion) in water (w/ 0.1% formic acid) over 20 minutes.
• the Rt of the DbM is determined by a separate control experiments under identical conditions.
• the area under the DbM peak from the protein sample is compared to a standard curve generated from multiple RPC runs with identical conditions assaying the DbM peak heighth for DbM samples of known concentration. If the detergent concentration is estimated to be below 0.48 mM (4x cmc) , it is adjusted with the addition of a small amount of concentrated DbM in TBS .
• EXAMPLE 13 EPITOPE AFFINITY AND METAL CHELATE AFFINITY
• HPs are also constructed with an epitope affinity tag and a metal chelate affinity tag, as represented, for example, by Hemagglutinin SS-Rat m.3 mAChR-HSV-OctaHis.
• an isolated nucleic acid molecule encoding Hemagglutinin SS-Rat m3 mAChR-HSV-OctaHis is used in the production of a recombinant baculovirus following methods provided by the manufacturer (Pharmingen, San Diego, CA) .
• Virus production, the large-scale insect cell culture and expression of protein, the preparation of epitope affinity columns, the preparation of solubilized HP, and epitope affinity purification were all performed as previosly described herein except that anti-HSV antibody replaces the anti-FLAG antibody in the preparation of the HSV epitope affinity column and the HSV peptide (NH2 -QPELAPEDPED-COOH; Sigma-Genosys) is used to elute the Hemagglutinin SS-Rat m3 mAChR-HSV-OctaHis protein from the column instead of the FLAG peptide.
• anti-HSV antibody replaces the anti-FLAG antibody in the preparation of the HSV epitope affinity column and the HSV peptide (NH2 -QPELAPEDPED-COOH; Sigma-Genosys) is used to elute the Hemagglutinin SS-Rat m3 mAChR-HSV-OctaHis protein from
• the Hemagglutininin SS-Rat m3 mAChR-HSV-OctaHis protein since there is no EE epitope on the Hemagglutinin SS-Rat m3 mAChR-HSV-OctaHis protein, no epitope affinity purification using the EE epitope is used.
• the Hemagglutinin SS signal sequence may be cleaved off in some cell lines by cellular proteases in the process of expression and trafficking to the plasma membrane of the insect cell. From this point on the solubilized protein is referred to as Rat m.3 mAChR-HSV-OctaHis.
• Rat m3 mAChR- HSV-OctaHis is applied, at a flow rate of 0.2 mL/minutes, to a MCAC column prepared by loading 10 mL of Ni-NTA resin (Qiagen) into a 1.2 x 15 cm polypropylene column and equilibrating the column with 100 mL of TBS-AG at 4°C at a flow rate of 0.2 mL/minutes.
• the Rat m.3 mAChR-HSV- OctaHis is bound to the column, the column is washed with 100 mL of TBS-AG containing 5 mM imidazole.
• the column is developed with a 50 mL linear gradient of 5 mM-350 mM imidazole in TBS-AG at the same flow rate, collecting 0.5 mL fractions.
• This material is then dialyzed with three exchanges into a 100 fold volume of TBS-AG overnight at 4°C to remove excess imidazole.
• the material is then subjected to sucrose gradient ultracentrifugation and the concentrations of protein and detergent are estimated and adjusted as previously described herein.
• each sample is subjected to SDS-PAGE analysis on 5-12% Novex (Invitrogen, San Diego, CA) gels according to the manufacturer's instructions. Ten ⁇ g of sample are loaded per gel lane, and the protein samples are visualized by silver staining (Peterson, G.L. et al . (1995) J. Biol . Chem. 270: 17808). The specific activities of the mAChR proteins prepared according to these methods are determined according the method of Peterson, G.L. et al .
• the specific activity of the proteins is determined to be in the range of 11-16 nmol of specific ligand binding per mg mAChR protein.
• Ligand affinity chromatography is another measure by which the HPs of the invention may be evaluated for specific activity.
• the mAChR purified by the methods described herein may be subjected to known ligand affinity chromatography over a column of immobilized mAChR ligand 3- (2' -aminobenzhydryloxy) -tropane (ABT) .

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