EP1268523A2 - Composes de fixation et procede d'identification de composes de fixation - Google Patents

Composes de fixation et procede d'identification de composes de fixation

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Publication number
EP1268523A2
EP1268523A2 EP01920642A EP01920642A EP1268523A2 EP 1268523 A2 EP1268523 A2 EP 1268523A2 EP 01920642 A EP01920642 A EP 01920642A EP 01920642 A EP01920642 A EP 01920642A EP 1268523 A2 EP1268523 A2 EP 1268523A2
Authority
EP
European Patent Office
Prior art keywords
molecule
chemokine receptor
binding
ccr5
library
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP01920642A
Other languages
German (de)
English (en)
Inventor
John J. Nestor, Jr.
Carol J. Wilson
Raymond H. See
Christina A. Tan Hehir
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Consensus Pharmaceuticals Inc
Original Assignee
Consensus Pharmaceuticals Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US09/813,653 external-priority patent/US20020064770A1/en
Priority claimed from US09/813,448 external-priority patent/US20020142346A1/en
Priority claimed from US09/813,651 external-priority patent/US20030018438A1/en
Application filed by Consensus Pharmaceuticals Inc filed Critical Consensus Pharmaceuticals Inc
Publication of EP1268523A2 publication Critical patent/EP1268523A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/18—Antivirals for RNA viruses for HIV
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • 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
    • 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
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
    • C07K14/7158—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for chemokines
    • 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
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6863—Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors
    • 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
    • G01N33/74—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving hormones or other non-cytokine intercellular protein regulatory factors such as growth factors, including receptors to hormones and growth factors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/72—Assays involving receptors, cell surface antigens or cell surface determinants for hormones
    • G01N2333/726—G protein coupled receptor, e.g. TSHR-thyrotropin-receptor, LH/hCG receptor, FSH
    • 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 generally to Cysteine-Cysteine Chemokine Receptor 5 ("CCR5" or "CC chemokine receptor 5"), and more particularly, to binding compounds for CC chemokine receptor 5.
  • Methods of the invention are useful for the treatment of disease by identifying and preparing therapeutic binding compounds for CC chemokine receptor 5.
  • Chemokines comprise a family of structurally related secreted proteins of about 70-110 amino acids that share the ability to induce migration and activation of specific types of blood cells. See Proost P., et al. (1996) Int. J. Clin. Lab. Rse. 26: 211-223; Premack, et al. (1996) Nature Medicine 2: 1174-1178; Yoshie, et al. (1997) J. Leukocyte Biol. 62: 634-644. Over 30 different human chemokines have been described to date.
  • CXC or ⁇ - chemokines While they are primarily responsible for the activation and recruitment of leukocytes, they vary in their specificities for different leukocyte types (neutrophils, monocytes, eosinophils, basophils, lymphocytes, dendritic cells, etc.), and in the types of cells and tissues where the chemokines are synthesized. Further analysis of this family of proteins has shown that it can be divided up into two further subfamilies of proteins. These have been termed CXC or ⁇ - chemokines, and the CC or ⁇ -chemoldnes based on the spacings of two conserved cysteine residues near the amino terminus of the proteins.
  • Chemokines are typically produced at sites of tissue injury or stress, where they promote the infiltration of leukocytes into tissues and facilitate an inflammatory response. Some chemokines act selectively on immune system cells such as subsets of T-cells or B lymphocytes or antigen presenting cells, and may thereby promote immune responses to antigens. In addition, some chemokines have the ability to regulate the growth or migration of hematopoietic progenitor and stem cells that normally differentiate into specific leukocyte types, thereby regulating leukocyte numbers in the blood.
  • chemokines are mediated by cell surface receptors that are members of a family of seven transmembrane ("7TM"), G-protein coupled receptors ("GPCR"). At least twelve different human chemokine receptors are l ⁇ iown, including CCRl, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CXCR1, CXCR2, CXCR3, and CXCR4. These receptors vary in their specificities for specific chemokines. Some receptors bind to a single known chemokine, while others bind to multiple chemokines.
  • 7TM seven transmembrane
  • GPCR G-protein coupled receptors
  • chemokine receptors such as CCR5
  • HAV Human Immunodeficiency Virus
  • Chemokines are important in medicine because they regulate the movement and biological activities of leukocytes in many disease situations, including, but not limited to: allergic disorders, autoimmune diseases, ischemia/reperfusion injury, development of atherosclerotic plaques, cancer (including mobilization of hematopoietic stem cells for use in chemotherapy or myeloprotection during chemotherapy), chronic inflammatory disorders, chronic rejection of transplanted organs or tissue grafts, chronic myelogenous leukemia, and infection by HIV and other pathogens.
  • CCR5 in particular, has been implicated in diseases such as multiple sclerosis and rheumatoid arthritis. See, e.g., Balashov et al., Proc. Nail. Acad. Sci, USA 96:6873-6878 (1999); and Mack, et al, Arthritis Rheum. 42(5):981-8 (1999).
  • Antagonists of chemokine receptors may be of benefit in many of these diseases by reducing excessive inflammation and immune system responses.
  • chemokines and antagonists that bind to HIV co-receptors may have utility in inhibiting viral entry into cells.
  • HIV causes Acquired hnmune Deficiency Syndrome ("AIDS"), which is one of the leading causes of death in the United States and throughout the world.
  • AIDS Acquired hnmune Deficiency Syndrome
  • HIV causes Acquired hnmune Deficiency Syndrome
  • AIDS Acquired hnmune Deficiency Syndrome
  • the severity of the immune system damage is measured by an absolute CD4 + lymphocyte count; a patient having a count of less than 200 cells/ ⁇ l is considered to have AIDS.
  • the CD4 protein is a glycoprotein of approximately 60,000 molecular weight and is expressed on the cell membrane of mature, thymus-derived (T) lymphocytes, and to a lesser extent on cells of the monocyte/macrophage lineage.
  • CD4 cells appear to function by providing an activating signal to B cells, by inducing T lymphocytes bearing the reciprocal CD8 marker to become cytotoxic/suppressor cells, and/or by interacting with targets bearing major histocompatibility complex (MHC) class II molecules.
  • MHC major histocompatibility complex
  • the host immune system will produce antibodies targeted against various antigenic sites, or determinants, of gpl20. Some of those antibodies will have a neutralizing effect and will inhibit HIV infectivity. It is believed that this neutralizing effect is due to the antibodies' ability to interfere with HIV's cellular attachment. It is also believed that this effect may explain in part, the rather long latency period between the initial seroconversion and the onset of clinical symptoms.
  • T-tropic T cell tropic
  • M-tropic macrophage tropic
  • T-tropic T cell tropic
  • chemokines could block the infectivity of M-tropic but not T-tropic HIV strains.
  • a particular receptor was required for the activity of T-tropic strains. See e.g., Horuk R., Immunol Today 20(2):89-94 (1999); Doms RW, Peiper SC, Virology 235(2):179-90 (1997); Ward SG, Bacon K, Westwick J., Immunity 9(1):1-11 (1998); Berson JF, Doms RW., Semin Immunol 10(3):237-48 (1998).
  • CCR5 a 352-amino acid protein
  • TM transmembrane
  • TM1 residues 32-56
  • TM2 67-88
  • TM3 103-124
  • TM4 144-167
  • TM5 198-220
  • TM6 236-257
  • TM7 281- 301, putatively
  • M-tropic viruses are believed to interact with residues in the extracellular domains of CCR5, with the second loop being the most important.
  • TAK 779 antagonizes the binding of RANTES (regulated on activation, normal T cell expressed and secreted) to CCR5-expressing Chinese hamster ovary cells and blocked CCR5-mediated Ca 2+ signaling at nanomolar concentrations.
  • the inhibition of CC chemokine receptors by TAK-779 appears to be specific to CCR5.
  • TAK-779 displays highly potent and selective inhibition of R5 HIV-1 replication without showing cytotoxicity.
  • the compound appears to inhibit the replication of R5 HIV-1 clinical isolates as well as a laboratory strain at a concentration of 1.6-3.7 nM in peripheral blood mononuclear cells, but was inactive against a T-cell line-tropic HIV-1. See e.g. , Baba M, et al. , Proc Natl Acad Sci U S A 96(10):5698-703 (1999).
  • Aminooxypentane (AOP)-RANTES[2-68] is a chemically modified form of the chemokine RANTES.
  • AOP chemokine RANTES.
  • (AOP)-RANTES does not induce chemotaxis and is a subnanomolar antagonist of CCR5 function in monocytes. It potently inhibits the infection of macrophages by M-tropic HIV-1 strains. Thus, activation of cells by chemokines is not a prerequisite for the inhibition of viral uptake and replication. See e.g., Simmons G, et al, Science 276(5310):276-9 (1997). More recently, another chemically modified RANTES has been described as more potent: (NNY)-RANTES[2-68].
  • CCR5 As a result of the limitations of prior inhibitors of CCR5, a need still remains for effective HIV preventative and therapeutic agents, and methods for identifying candidates thereof. It has been demonstrated that HIV uses the CCR5 as a co-receptor for cellular entry that can be blocked by its natural ligands and this makes a high affinity ligand for CCR5 an important therapeutic target. GPCRs in general, and CCR5 in particular, are very difficult to solubilize and purify because they normally need to fold and be maintained in the presence of the native lipids of the cell membrane. Simple expression and precipitation with antibodies result routinely in denatured aggregates with little or no ability to specifically bind native ligands.
  • Such therapeutics may comprise peptides, peptidomimetics, or small molecules that can inhibit natural ligand binding to CCR5. Such methods and compositions are provided herein.
  • the present invention provides binding compounds for CCR5 and methods for identifying those binding compounds.
  • screening methods are provided to identify binding motifs for CCR5, as well as ligands capable of binding to CCR5.
  • the invention comprises the design and identification of therapeutic peptides, peptidomimetics, or small molecules suitable for use in the prevention or treatment of HIV and AIDS.
  • methods of the invention provide for the synthesis and purification of linear and cyclic peptide libraries useful for screening and identifying a binding motif for CCR5, as well as screening for potential ligands thereof.
  • Methods of the invention provide for the incorporation of unnatural amino acids and amino acids of the D configuration into linear or cyclic peptides for use in such libraries. Libraries comprising peptides having such amino acids demonstrate enhanced binding affinity and duration of action in vivo resulting from resistance to proteolysis.
  • the invention provides for the use of highly diverse libraries of peptide (linear and cyclic, natural and unnatural amino acids), peptidomimetic, and small molecule compounds for the lead ligand identification step.
  • ligands may be directly or indirectly agonistic or antagonistic to CCR5 binding activity.
  • the invention provides for the use of phage display methods for the identification of preliminary motif information, followed by additional rounds of affinity purification with purified receptor preparations and highly diverse libraries of the invention.
  • phage display technology is combined with the use of cyclic peptide and/or peptidomimetic libraries.
  • computer-aided design technology is used to virtually screen, identify, design, or validate lead compounds for agonistic or antagonistic potential with regard to CCR5 activity.
  • Such technology uses computer-generated, three- dimensional images based upon molecular and structural information of both the CCR5 and the potential binding partners by virtually aligning the protein with the binding partners.
  • potential leads are identified by prior screening of an actual library or through some other means.
  • One embodiment of the invention involves the screening of biologically appropriate drugs that relies on structure based rational drag design.
  • a three dimensional structure of the protein (or similar family member), peptide or molecule is determined and potential agonists and/or antagonists are designed with the aid of computer modeling.
  • the drug is contacted with CCR5, wherein a binding complex forms between the potential drug and CCR5.
  • the present invention provides for the use of partially purified CCR5 receptor protein as the agent for carrying out the selection, identification, and improvement of tight binding ligands in identifying therapeutically useful compounds.
  • the invention comprises the use of tagging methods to generate a modified CCR5 receptor protein that functions to facilitate purification and identification steps involved in the screening methods.
  • the invention comprises a nucleic acid sequence corresponding to the receptor CCR5 fused to tag sequences (i.e., GST, FLAG, 6xHis, dual tagged with FLAG-GST, C-MYC, MBP, V5, Xpress, CBP, HA) with appropriate specific protease sites engineered into the vector.
  • methods of the invention provide for solubilization and immobilization of CCR5 to facilitate ligand selection methods provided herein.
  • CCR5 may be derived from any source, such as, for example, cell membrane preparations and whole cell preparations.
  • the invention provides for a method of screening combinatorial libraries directly for general affinity determination using membranes from baculovirus expression systems or any other appropriate expression system.
  • partially purified CCR5 is used in carrying out the selection, identification, and improvement of tight binding ligands.
  • partially purified, tagged CCR5 is used in a sequestered form to screen diverse libraries (focused or highly diverse) for the affinity purification of a tight binding ligand.
  • the conditions for solubilization and immobilization of the appropriate ligand provides for the use of low salt, such as, for example, low magnesium or calcium concentrations; and no sodium chloride (“NaCl”) (0.0 nM NaCl).
  • low salt such as, for example, low magnesium or calcium concentrations
  • NaCl no sodium chloride
  • the invention comprises the step of eluting bound components of the libraries from the immobilized protein with specific N-terminally blocked peptides or other non-sequencable analogs.
  • the invention comprises the step of binding combinatorial libraries to a resin-immobilized protein.
  • the invention comprises a purified polypeptide with tag sequences, which may be immobilized onto an appropriate affinity resin for assay.
  • a further embodiment comprises the step of releasing or eluting tagged protein with its bound library with specific N-terminally blocked peptides or other non-sequencable analogs.
  • a method of the invention comprises the step of cleaving a tag from a protein of interest using a specific protease (as designed into the protein/vector) after immobilization onto an affinity resin and after the combinatorial library is bound to release the complex.
  • the target ligand is selected from a linear peptide library, a peptidomimetic library, a cyclic peptide library, or a focused library developed using an initial motif identified by phage display techniques or a library combining any of the foregoing.
  • a target ligand is eluted from the receptor preparation using a peptide or other ligand, or by using pH change or chaotropic agents, such as urea or guanidine hydrochloride, that can disrupt the hydrogen bonding structure of water and denature proteins in concentrated solutions by reducing the hydrophobic effect.
  • ligands for CCR5 identified using the methods disclosed herein.
  • protein sequencing techniques are used for the determination of the structure of the ligand identified by the affinity purification step.
  • the invention comprises therapeutic agents, such as, for example, a small molecule antagonist of CCR5 binding that are identified using methods of the invention appropriate for the treatment of a disease or disorder, such as, for example, HIV infection or AIDS.
  • a patient infected with HIV is treated with a therapeutic agent comprising a compound identified using methods of the invention or a small molecule antagonist of CCR5 binding.
  • a patient infected with HIV is treated through the use of combinations of therapeutics that include, for example, CCR5 inhibitors, reverse transcriptase protease inhibitors, and other anti-HIV therapeutics.
  • Figure 1 shows the gpl20 residues involved in CCR5 binding.
  • Figure 2 shows a peptide library with a fixed, non-degenerate lysine or arginine and eight degenerate positions consisting of eighteen amino acids in approximately equal proportion.
  • Figure 3 shows a peptide library screening using binding domains.
  • Figure 4 shows a CCR5 cDNA sequence.
  • Figure 5 shows a baculovirus transfer vector for CCR5-HIS.
  • Figure 6 shows a baculovirus transfer vector for CCR5-FLAG.
  • Figure 7 shows a baculovirus transfer vector for CCR5-GST.
  • Figure 8a is a chart showing the characterization of saturation binding of [ 125 I]-MIP- 1 ⁇ to
  • Figure 8b is a chart showing the characterization of displacement of [ 125 I]-MIP-l ⁇ binding to CCR5 by MlP-l ⁇ both in membrane preparations and immobilized on the column.
  • Figure 9 shows the immobilization of GPCRs for affinity purification from libraries.
  • Figure 10 shows the purification of CCR5-GST using glutathione-sepharose.
  • Figure 11 shows the screening of peptide libraries using CCR5 -containing membranes.
  • Figure 12 is a chart showing the % solubilization of CCR5 under exemplary conditions.
  • methods of the invention provide for the determination of a binding motif for CCR5. Further, methods of the invention provide for the identification of agonists or antagonists of the interaction of CCR5 with its natural ligand, thereby providing for the identification of therapeutic lead compounds.
  • Methods for library design and synthesis, and library screening that are particularly useful in the invention are described in the following patent and patent applications, the disclosure of each of which is incorporated by reference herein: Cantley et al, U.S. Patent No. 5,532,167; Cantley, et al, U.S.S.N. 08/369,643, filed December 17, 1998; Cantley, et al, U.S.S.N.
  • CCR5 is cloned and expressed, and tested for activity.
  • the CCR5 may be tagged on the C-terminus or on the N-terminus to facilitate the determination of the character of the CCR5's ligand-binding properties.
  • Exemplary tags include, without limitation, 6xHis, FLAG, GST, V5, Xpress, c-myc, HA, CBD, and MBP.
  • the tagged CCR5 is used in screening of libraries comprising, for example, linear and/or cyclic peptides having natural and/or unnatural amino acids, peptidomimetics and/or small molecules.
  • Such peptidomimetics and small molecules may comprise any natural or synthetic compound, composition, chemical, protein, or any combination or modification of any of the foregoing that is used to screen for binding compounds of CCR5.
  • an oriented degenerate peptide library method useful in methods of the invention uses soluble peptide libraries consisting of one or more amino acids in non-degenerate positions, known or suspected to be important for ligand binding, and eighteen amino acids in approximately equal proportions in degenerate positions. Cysteine and tryptophan may be omitted to avoid certain analytical difficulties on sequencing.
  • a library is shown in Figure 2, where X represents a degenerate position consisting of any of eighteen amino acids and a lysine or arginine is fixed at a non-degenerate position.
  • arginine or lysine as an orienting residue is based on the fact that basic residues of g l20 are important determinants in binding to CCR5.
  • Another aspect of the invention involves the selection of any amino acid as an orienting residue.
  • additional residues can be added to the N- terminal of the sequence shown in Figure 2 because there are often interfering substances present in the first and second sequencing cycles. Additional residues can be added at the C-terminal end to provide amino acids to better anchor the peptide to the filter in the sequencer cartridge.
  • Another aspect of the invention provides for the use of highly diverse libraries of peptide (linear and cyclic, natural and unnatural amino acids), peptidomimetic, and small molecule compounds for the lead identification step.
  • these ligands can be agonistic or antagonistic in their function on the receptor.
  • the invention uses partially purified CCR5 as the agent for carrying out the selection, identification, and improvement of tight binding ligands as a route to therapeutically useful compounds.
  • the invention provides for the development and use of solubilization and immobilization procedures that facilitate efficient ligand selection methods provided herein.
  • the optimal conditions for the solubilization and immobilization for efficient ligand selection comprise the use of low salt, such as, for example, low or no magnesium or calcium concentrations, and no NaCl concentrations (0.0 nM NaCl).
  • Low salt such as, for example, low or no magnesium or calcium concentrations, and no NaCl concentrations (0.0 nM NaCl).
  • Ligand selection methods using, for example, inactive, precipitated protein, cell membrane preparations, and whole cell preparations are further provided herein.
  • the screening step may comprise phage display technology.
  • phage display systems have been used to screen peptide libraries for binding to selected target molecules and to display functional proteins with the potential of screening these proteins for desired properties. More recent improvements of the display approach have made it possible to express enzymes as well as antibody fragments on the bacteriophage surface thus allowing for selection of specific properties by selecting with specific ligands. See e.g., Smith SF, et al, Methods Enzym. 217:228-257 (1993). Phage display methods may be used for the identification of preliminary motif information, and followed by additional rounds of affinity purification with purified receptor preparations of the invention and highly diverse libraries, especially cyclic peptide and peptidomimetic libraries.
  • the phage display methods allow the identification of motifs of natural amino acids.
  • Information derived from phage display can be taken into affinity purification methods using, for example, synthetic libraries containing novel amino acid analogs or cyclic peptides to select ligands that have enhanced pharmaceutical characteristics.
  • the use of initial, secondary and tertiary libraries allows a more complete definition of the specificity of the binding site. Secondary libraries may be sequenced incorporating information from the initial library. With the first library, some degenerate positions may yield high preferences for specific amino acids and these may become non- degenerate positions consisting of the preferred amino acid in a second library. See e.g. , Wu R, J Biol Chem 271(27): 15934-41 (1996).
  • computer-aided design technology may be used in the screening and/or designing of peptides, peptidomimetics, and small molecules.
  • computer aided design technology may virtually screen, identify, design and validate potential compounds with regards to their CCR5 activity.
  • Computer programs that may be used to aid in the design of appropriate peptides, peptidomimetics and small molecules include, for example, Dock, Frodo and Insight.
  • An example of a method for screening of biologically appropriate drugs relies on structure based rational drug design.
  • a three dimensional structure of the protein, peptide or molecule is determined (or modeled after a close family member) and potential agonists and/or antagonists are designed with the aid of computer modeling.
  • potential agonists and/or antagonists are designed with the aid of computer modeling. See e.g., Butt et al, Scientific American, December 92-98 (1993); West et al, TIPS, 16:67-74 (1995); Dunbrack et al, Folding & Design, 2:27-42 (1997).
  • the drug is contacted with CCR5, wherein a binding complex forms between the potential drug and CCR5.
  • Methods of contacting the drug to CCR5 are generally understood by anyone having skill in the art of drug development.
  • the screening step may be performed in solution phase, or with the CCR5 immobilized on affinity columns.
  • other forms of sequestration can be used to perform the affinity purification of select ligands from libraries. These include, but are not limited to the following examples.
  • the receptor and bound library components can be separated from non-bound library components using equilibrium dialysis.
  • the tagged receptor can be bound to specific affinity membranes, which are in the form of plates or are separate.
  • the libraries can then be incubated with the membrane and easily washed to remove non-specific binding components. Size exclusion methodology can be used to separate a purified receptor bound library complex from unbound components after pre-incubating the receptor with the library.
  • micellar complex containing the receptor (which may or may not incorporate lipids as well as detergent) can be separated after binding select affinity components from a library by differential centrifugation.
  • the high affinity ligand can be released using low pH or high salt conditions and the structure identified by sequencing as described herein.
  • peptide libraries were screened to determine each library's respective inhibition binding. In general, a greater than 10% inhibition at 100 ⁇ M was significant for continued evaluation of the sequence via affinity purification.
  • a high preference value is greater than 1. The value is determined by subtracting the control value from the sample value and dividing by the reference value. In a preferred embodiment of the invention, the preference value is greater than 1.2. In a highly preferred embodiment of the invention, the preference value is greater than 2.
  • the peptide is purified by, for example, High Performance Liquid Chromatography ("HPLC") and compositions are confirmed by Matrix- Assisted Laser Desorption Ionization- Time of Flight Mass Spectrometer (“MALDI-TOF MS”) and Edman Sequencing. Generally, relative affinities may be measured by modifying the radiolabel binding assay used in receptor purification.
  • HPLC High Performance Liquid Chromatography
  • MALDI-TOF MS Matrix- Assisted Laser Desorption Ionization- Time of Flight Mass Spectrometer
  • Edman Sequencing Edman Sequencing.
  • relative affinities may be measured by modifying the radiolabel binding assay used in receptor purification.
  • the bound components of the libraries can be eluted from the immobilized protein with specific N-terminally blocked peptides or other non-sequencable analogs.
  • the release/elution of the tagged CCR5 with its bound library can be accomplished using specific N-terminally blocked peptides or other non-sequencable analogs. This can be done using acetylated FLAG peptide to elute CCR5-FLAG receptor from the resin.
  • the bound peptide may be eluted directly using an N-terminally blocked peptide or ligand, or other non- sequenceable analog using, for example, (AOP)-RANTES.
  • the tag from CCR5 may be cleaved using a specific protease (as designed into the protein/vector; either entero inase or thrombin) after immobilization onto the affinity resin and after the combinatorial library is bound to release the complex.
  • libraries can be prescreened for their ability to bind to the receptor (using significantly less protein) by a binding assay using CCR5-containing membranes from, for example, Sf9 (Spodopterafrugiperda) or High Five (Trichoplusia ni) cells (both obtained from Invitrogen) in a single assay or in an array assay.
  • This screening may be performed using CCR5 and a number of linear and cyclic libraries to determine their effectiveness in inhibiting the natural ligand to bind.
  • Methods of the invention further comprise the design of therapeutic agents comprising peptides, peptidomimetics, and/or small molecules that are antagonistic to CCR5 activity appropriate for the treatment of patients with a disease, such as AIDS.
  • Binding compounds for CCR5 and the identification of optimal synthesis and purification thereof provides for an effective treatment of AIDS and HIV infection.
  • the small peptide ligand binding compounds of the invention both cyclic and linear peptide ligands, will have enhanced binding affinity and action, and are resistant to proteolysis.
  • Compounds that exhibited enhanced affinity and action include, for example, M-A-R-S-L-I-W-R-P-A-K-A-K-K-A, K-K-K-A-R-S-L-I-W-R- P-A-K-A-K-K-K, and cyclo(M-Y-A-T-R-W-K-N).
  • Amino acids and peptides are abbreviated and designated following the rules of the IUPAC-IUB Commission of Biochemical Nomenclature in J. Biol. Chem. 247, 977-983 (1972). Amino acid symbols denote the L- configuration unless indicated otherwise.
  • amino acids from the residues of gpl20 that are crucial for viral uptake may be used to specify fixed, or non-degenerate positions in the peptide libraries for use in the oriented peptide library method described below and in U.S. Patent 5,532,167, the disclosure of which is incorporated by reference herein. See e.g. , Rizzuto CD, et al. , Science 280(5371 ) : 1949- 53 (1998). See also Figure 1.
  • CCR5 vectors were prepared for the baculovirus expression system containing epitope tags using standard techniques known by those skilled in the art that allowed for easier purification of the receptor.
  • Tags may be incorporated at the N- or C-terminus of the proteins.
  • tags were incorporated at the C-terminus of the receptor to determine the character of the receptor's ligand-binding properties that are in the N-terminal or extracellular region of the molecule.
  • the construction of a C-terminal 6xHis tagged and C-terminal FLAG construct are provided below as examples.
  • Alternative tags may include, for example, GST, V5, Xpress, c- myc, HA, CBD, and MBP. These constructs were made by analogous procedures using standard techniques known by those skilled in the art.
  • the 6xHis tag enables a one-step purification using nickel chelation.
  • the cDNA for CCR5 was obtained from Receptor Biology (Beltsville, MD). To create a C-terminal tag, the CCR5 was digested out of the commercial vector, pcDNA3, and ligated into an E. coli vector, pET30a, with a C-terminal 6xHis tag. The newly created CCR5-6xHis was then excised and ligated into pBlueBac, a baculovirus transfer vector (Invitrogen, Carlsbad, CA).
  • the construct was analyzed using both restriction digestion and sequencing, and then transfected into Sf9 insect cells (Pharmingen, San Diego, CA) for expression as typically done by those skilled in the art of protein expression.
  • a C-terminal bacterial FLAG construct was obtained from Sigma (pFLAG-CTC).
  • the CCR5 was excised from pcDNA3, ligated with a similarly digested pFLAG-CTC plasmid, then excised with the C-terminal FLAG tag and ligated into the digested pBlueBac vector.
  • the construct was analyzed using both restriction digestion and sequencing, and transfected into Sf9 or High Five (obtained from Invitrogen) insect cells for expression.
  • the pBlueBac vector containing the CCR5 insert was cotransfected with Bac-N-Blue DNA using cationic liposome mediated transfection using standard techniques.
  • the CCR5 was inserted into the baculovirus genome by homologous recombination. Cells were monitored from 24 hours post-transfection to 4-5 days. After about 72 hours, the transfection supernatant was assayed for recombinant plaques using a standard plaque assay. Cells which have the recombinant virus produced blue plaques when grown in the presence of X-gal (5-bromo-4-chloro-3-indoyl- ⁇ -D-galactoside).
  • PCR Polymerase Chain Reaction
  • Sf9 or High Five cells were maintained both as adherent and suspension cultures using standard techniques known to those skilled in the art.
  • the adherent cells were grown to confluence and passaged using the sloughing technique at a ratio of 1 :5.
  • Suspension cells were maintained in spinner flasks with 0.1% pluronic F-68 (to minimize shearing) for 2-3 months by sub-culturing to a density of 1 x 10 6 cells/ml.
  • a time course after infection with recombinant virus was used to define optimal growth conditions for expression using standard techniques. Aliquots of cells from spinner flasks were taken for this time course, centrifuged at 800 x g for 10 minutes at 4°C and both supernatant and pellet assayed by SDS-PAGE/Western blot analysis. The CCR5 was expected to be in the membrane fraction (pellet). All viable systems were assayed in this fashion for levels of expression. Systems were assayed for activity using a standard binding assay on a membrane preparation using MlP-l ⁇ (Calbiochem, San Diego, CA) and [ 125 I]-MIP-l ⁇ (New England Nuclear, "NEN", Boston, MA).
  • the membrane fraction was isolated by first pelleting the whole Sf9 cells (800 x g for 10 minutes at 4°C), then resuspending the pellet in a lysis buffer with homogenization.
  • Typical lysis buffer is around neutral pH and contains a cocktail of protease inhibitors, both of which are standard techniques for those skilled in the art. Membranes were pelleted. Solubilization was also conducted using varying NaCl concentrations. Despite conventional thinking, the step of solubilization using low salt, for example, low calcium and magnesium concentrations substantially in the absence of NaCl provided unexpected optimal conditions for solubilization when compared for quantity and activity.
  • solubilization of the receptor by different detergents such as, for example, ⁇ -dodecylmaltoside, n-octyl-glucoside, CHAPS, deoxycholate, NP-40, Triton X-100, Tween-20, digitonin, Zwittergents, CYMAL, lauroylsarcosine, etc., was compared for quantity and activity.
  • a candidate for isolation was carried through for purification as described below.
  • CCR5 was purified from the membrane fraction.
  • the exact purification scheme will depend on the construct chosen, which is subject to activity and ease of solubilization.
  • the membrane fraction was loaded onto a Ni-NTA column (Qiagen, Valencia, CA) in the presence of detergent, washed extensively, and eluted with imidazole.
  • Purification of the FLAG-tagged CCR5 was performed using the anti-FLAG M2 affinity matrix (Sigma, St. Louis, MO) in the presence of NP-40 at 0.3% concentration for solubilization and 0.1 % concentration for immobilization and eluted with glycine. The purification was performed in the presence of NP-40.
  • Activity of the purified receptor was assessed using a standard binding/displacement assay using MlP-l ⁇ and [ I]- MlP-l ⁇ .
  • tBu was used for the protection of side-chains of Asp, Glu, Ser, Thr, and Tyr, tert.-butyloxycarbonyl ("Boc") for Lys and Trp, 2,2,4,6,7- pentamethyldihydrobenzofuran-5-sulfonyl ("Pbf ') for Arg, and triphenylmethyl ("trityl", “Trt”) for Cys, His, Asn and Gin.
  • the scale of the synthesis was 0.20 mmol.
  • the resin was initially washed with N-methylpyrrolidinone (" ⁇ MP") followed by a 1 x 3 minutes and 1 x 7.6 minutes treatment of piperidine: ⁇ MP (1:4) for N ⁇ -Fmoc removal.
  • the resin was filtered and rinsed six times with a total of 90 ml of ⁇ MP and the cycle was repeated.
  • a batch of resin was allowed to react with mixtures of the combinatorial amino acids without any partitioning of the resin.
  • Adjusting the concentrations of the amino acids in the starting mixture controls the relative coupling rates, thereby ensuring equal incorporation of the amino acids in the library.
  • the optimization of a mixture of natural Boc and Fmoc protected amino acids for the one pot synthesis has been previously described (see e.g., U.S. Patent No.
  • Fmoc-Asp(OH)-ODmab (Dmab, 4-[N-(l-(4,4-dimethyl-2,6- dioxoxcyclohexylidene)-3-methylbutyl)amino]-benzyl) was side-chain anchored to Rink amide resin followed by chain elongation as described above. Following linear assembly, removal of the Dmab and Fmoc group was accomplished by treatments with hydrazine:DMF (1 :49) for 7 minutes and piperidine: ⁇ MP (1 :4) for 6 x 3 minutes, respectively. The resin was transferred to a syringe containing a polypropylene frit for manual cyclization.
  • On-resin head-to-tail cyclization was performed using 7-azabenzotriazol- 1 -yloxy)-tris(pyrrolidino)phosphonium hexafluorophosphate ("PyAOP"):DIEA (1:2, 4 equiv) in a solution containing 1% Trition X in NMP:DMF:dichloromethane, methylene chloride, DCM) (1 :1:1) for 2 hours at 55°C.
  • the unreacted linear precursor was treated with Fmoc-Nva-OH/PyAOP/DIEA ("Nva", "norvaline”)(l:l:2, 4 equiv) in DMF for 1 x 18 hours and 1 x 3 hours.
  • Peptides and peptide libraries were characterized by HPLC, MALDI-TOF MS (Louisiana State University), and Edman degradation.
  • MALDI-TOF MS analysis is capable of detecting the presence of high-molecular weight impurities due to incomplete deprotection, deblocking, or re- alkylation.
  • Edman degradation provides quantitative information about the amount of each amino acid in each degenerate position in a library.
  • the initial libraries synthesized had single, non-degenerate orienting amino acids (i.e., M-X-X-X-X-R-X-X-X-X-A, where X is a degenerate equimolar mixture of all amino acids except cysteine).
  • Cyclic libraries (head-to-tail) were also prepared with single, non-degenerate orienting amino acids. Through the use of these initial libraries, the optimal residues at some degenerate positions become defined and secondary libraries were made fixing these positions.
  • the head to tail cyclized library cyclo(M-X-X-X-X-R-X-X-X-N) indicated that the -4 position (from the fixed R) should be lysine, the -2 position should be aspartate, the -1 position should be histidine, and the +3 position should be lysine so the secondary library was cyclo(M-K-X-D-H-R-X-X-K-N).
  • the initial library used a single, non-degenerate basic amino acid (i.e., M-A-X-X-X-X-R- X-X-X-X).
  • M-A-X-X-X-X-R- X-X-X-X The initial library used a single, non-degenerate basic amino acid (i.e., M-A-X-X-X-X-R- X-X-X).
  • libraries can be made with additional non-degenerate amino acids taken from sequence 1 or sequence 2 of the gpl20 loop binding CCR5, see Figure 1. Examples are X-X-R-I-X-Q-X-X based on sequence 1 or P-P-X-R-X-X-X-X based on sequence 2. The dash indicates that the residue is not involved. Secondary libraries were made fixing optimal residues found at some degenerate positions. Through the use of these initial libraries, the motifs become defined.
  • M-A-X-X-X-X-X-R-X-X-X-X indicated that the -4 position should be proline so the secondary library would be M-A-W-X-X-X-R-X-X-X-X.
  • the receptor was exposed to the library, and separation of free and bound peptides was accomplished by pelleting the membranes by centrifugation.
  • the GST tagged CCR5 purified receptor was incubated with a peptide library, about 1 ⁇ mole of peptide and about 1 nmole of binding sites.
  • receptor with bound peptide was separated from unbound peptides by centrifugation (receptor*peptide complex in the pellet, unbound peptide in the supernatant). Nonspecifically bound peptides were removed by exhaustive washing, and resuspension of the pellet in low pH ( ⁇ 2.5) was used to remove the bound peptide. This peptide was sequenced to determine the consensus sequence.
  • the receptor was immobilized on an anti-FLAG M2 affinity matrix (St. Louis, MO).
  • An additional purification approach used the CCR5-GST construct and immobilized glutathione (Pierce, Rockford, IL).
  • Both the bound peptide mixture and the starting peptide library were sequenced using standard techniques. The amounts of each amino acid, as a function of position, were determined. Preference values for each amino acid at each position were calculated by comparing the amounts of amino acids present in the starting library and bound fraction of peptides. These procedures were used to generate preferred sequences of peptides interacting with many binding domains and have been described in Table 1.
  • phage display technology is also used to identify preliminary binding motifs.
  • the phage display method provides for the identification of motifs of natural amino acids.
  • Phage display technology involves the insertion of DNA sequences into a gene coding for one of the phage coat proteins. The gene is inserted in a particular location so that the expressed protein insert can interact with other molecules. As a result, the encoded peptide or protein sequence will be presented on the surface of the phage and exposed for binding. By inserting degenerate nucleotides, each phage can express a different peptide sequence ("a phage library").
  • CCR5 cDNA correlating to GenBank Accession #U57840 may be used in the vector pCDNA3.
  • the only difference between CCR5 cDNA from Receptor Biology and CCR5 cDNA correlating to GenBank Accession #U57840 is a point mutation at base 180 that changes Leucine to a Glutamine in the amino acid sequence.
  • CCR5-HIS construct was derived from this system. PCR was performed using CCR5/pcDNA3 (from Receptor Biology) as the template and primers 5-Age His and 5-Spe His. The first primer introduced a unique Spe I site just before the initiator ATG of CCR5. The second primer mutated the stop codon of CCR5 into an Age I site in-frame with the histidine tag of pIZT/V5-His (Invitrogen, Carlsbad, CA). The PCR product was digested with Spe I and Age I, then ligated into similarly digested pIZT/V5-His. This construct is identified as CCR5-His- PIZT.
  • CCR5-His-PIZT was digested with Hae II and Spe I, then filled in with Klenow fragment.
  • the fragment containing CCR5-His was ligated into pBluebac 4.5 (Invitrogen,) that was previously digested with N7ze I and blunted with Klenow.
  • the construct was checked for correctness of orientation. This is called CCR5-HIS.
  • the construct was confirmed by restriction digestion and sequencing using standard techniques. This construct has been used for expression and has been determined to be expressed sufficiently and in active form for use in the affinity purification screening.
  • CCR5 with C-Terminal FLAG Tag PCR using standard techniques was performed using CCR5/pcDNA3 (from Receptor Biology) as the template and the primers 5-Xho pFLAG and 5-Sal pFLAG.
  • the PCR product was digested -with Xho I and Sal I and ligated into similarly digested pFLAG-CTC (a bacterial expression vector). This construct is called CCR5-FLAG-CTC.
  • CCR5-FLAG was then digested with Xho I and Sea I, and filled in with Klenow fragment.
  • the fragment containing CCR5- FLAG-CTC was ligated into pBluebac 4.5 that was first digested with Nhe I then blunted with Klenow.
  • This final construct is identified as CCR5-FLAG.
  • the construct was confirmed by restriction digestion and sequencing using standard techniques. This construct has been used for expression and has been determined to be expressed sufficiently and in active form for use in affinity purification screening.
  • CCR5 with C-Terminal GST Tag
  • PCR was performed using CCR5/pcDNA3 (from Receptor Biology) as the template and primers GST-BamHl and GST- Ndel .
  • the first primer mutated the stop codon of CCR5 into a BamH I restriction site (in-frame with the FLAG/GST tag of pESP-3).
  • the second primer introduced a unique Nde I site at the initiator codon of CCR5.
  • the PCR product was digested with BamH I and Nde I and ligated into similarly digested pESP-3 (a yeast expression vector.) This construct is called pCP8.
  • pCP8 was then digested with Nde I and Sma I, and filled in with Klenow fragment.
  • the fragment containing CCR5-GST was ligated into pBluebac 4.5 that was first digested with Bgl II then blunted with Klenow. This final construct is identified as pCPlO. When describing the protein, the construct is identified as CCR5-GST. The construct was confirmed by restriction digestion and sequencing using standard techniques. This construct has been used for expression and has been determined to be expressed sufficiently and in active form for use in affinity purification screening.
  • Plasmid maps for these vectors can be found in Figures 5-7.
  • the vectors for the three new constructs were used to co-transfect Sf9 cells for the production of a viral stock of each. These viral stocks were purified using a standard plaque assay and then used in experiments to infect for the optimization of expression of CCR5 with its various C-terminal tags. High Five cells (Invitrogen) were also transfected with these CCR5 tagged constructs and tested for expression of CCR5. All constructs were determined to express the appropriately tagged receptor. Expression levels after 72 hours were as much as 5 times greater in High Five cells than those for Sf9 cells. All of the above described experiments were done using standard techniques known to those skilled in the art.
  • a fourth construct for the expression of CCR5 was made from the starting vector pBlueBac 4.5 (Invitrogen) to remove the thrombin and enterokinase cleavage sites in the previously described vectors.
  • the GST tag was added into the multiple cloning site by using PCR to generate the GST tag, then ligating into the digested vector (Smal/EcoRI) using standard procedures known to those skilled in the art.
  • the vector was made compatible with the Gateway technology from Lifetech for ease of manipulation. This was done by ligating into the Smal site the cassette containing the recombination sites required for this technology (from Lifetech).
  • CCR5 was amplified using PCR with primers to extend the gene to contain the attachment sites for recombination.
  • the PCR product was incorporated into the baculovirus vector using BP clonase (the enzyme required for homologous recombination) to make a vector for baculovirus expression containing CCR5 with a C-terminal GST tag without the enterokinase or thrombin cleavage sites.
  • This vector was cotransfected into Sf9 cells for preparation of the virus stock necessary for expression.
  • the virus was plaque purified, and a PCR and sequence checked clone was used for expression of CCR5. A time course with this construct showed that less proteolysis of the protein was observed and less time was necessary to obtain maximal expression of the receptor.
  • CCR5-GST, CCR5-FLAG, and CCR5-HIS were expressed in Sf9 and High Five cells, as described in Example 1.
  • Whole cells from Sf9 and High Five cell lines were lysed using hypotonic buffers (10 mM Tris, pH 7.4, 5 mM EDTA), and membrane preparations were made by homogenization and centrifugation using standard techniques known to those skilled in the art.
  • Membrane preparations for CCR5-GST, CCR5- FLAG, and CCR5-HIS were assayed using a standard radioligand binding assay respectively. Binding assays were performed with 5 ⁇ g of membranes in 50 mM Hepes, pH 7.5, 1% BSA.
  • FIG. 8 generally shows charts exemplifying the characterization of CCR5 receptor binding. Specifically, the K d for binding was measured using saturation experiments by adding increasing amounts of [ 125 I]-MIP-l ⁇ to CCR5 as seen in Figure 8a.
  • Solubilization of the tagged versions of CCR5 have been performed using many different combinations of detergents (NP-40, Triton X-100, ⁇ -D- maltoside, n-octylglucoside, CYMAL, Zwittergents, Tween-20, lysophosphatidyl chorine, CHAPS, etc.), salts (NaCl, CaCl 2 , MgCl 2 , MnCl 2 , KC1, etc.), buffers (Tris, Hepes, Hepps, Pipes, Mes, Mops, acetate, phosphate, imidazole, etc.), and various pH's (range 6.8-8.2).
  • detergents NP-40, Triton X-100, ⁇ -D- maltoside, n-octylglucoside, CYMAL, Zwittergents, Tween-20, lysophosphatidyl chorine, CHAPS, etc.
  • salts NaCl,
  • CCR5-GST and CCR5-FLAG were immobilized onto affinity columns for purification and for use as active proteins for screening of peptide libraries.
  • a schematic diagram showing the immobilization of GPCRs for affinity purification from libraries is shown in Figure 9.
  • CCR5-GST was bound and immobilized onto glutathione-agarose (Pierce) and glutathione-sepharose (Amersham Pharmacia Biotech) and CCR5-FLAG was immobilized onto a specific antibody column that recognizes the FLAG epitope (M2 column, Sigma).
  • the immobilization of the functional protein was accomplished by first solubilizing the receptor in 0.3% NP-40, 10 mM Hepes (or Pipes), pH 7.5, then binding it to the glutathione-sepharose resin in 0.1% NP-40, 10 mM Hepes (or Pipes), pH 7.5, 3 mM CaCl 2 , 15 mM MgCl 2 .
  • the activity of the immobilized receptor was determined by incubation for 1 hour at 4°C with the radiolabeled MlP-l ⁇ (as with the membrane assay above) and competition with cold MlP-l ⁇ . Uninfected cells have been used as controls for this activity, as well as the column alone.
  • FIG. 10 shows the eluant analyzed by SDS-PAGE and western blot for the purified receptor (coomassie stained) in Lane 1 and the ⁇ -GST antibody developed western blot of the solubilized CCR5-GST.
  • Purification of the CCR5-GST was done using glutathione-sepharose.
  • CCR5-GST was bound to glutathione-sepharose after solubilization with 0.3% NP-40.
  • NP-40 was diluted to 0.1%) before binding by rotation at 4°C for 2 hours with the resin.
  • the initial libraries used a single, non-degenerate basic amino acid (i.e., M-X-X-X-X- W-X-X-X-X-A-K-K-K). Through the use of these initial libraries, the optimal residues at some or all degenerate positions became defined. Secondary libraries were made if all of the positions were not defined, thereby fixing the defined positions. F. Screening of Peptide Libraries Using Immobilized CCR5
  • a membrane binding assay was developed to use with the peptide libraries.
  • Each peptide library (100 ⁇ M final concentration, average molecular weight) was incubated with the receptor (in membranes obtained as described herein) and the ability of the peptides in the library to inhibit [ 125 I]-MIP-l ⁇ binding was determined. Percent inhibition was calculated. Peptide libraries with the highest percent inliibition were assayed first. Specifically, as shown in Figure 11, binding inhibition assays were performed using 5 ⁇ g membranes, 0.5 nM [125I]-MIP-l ⁇ and a 100 ⁇ M aliquot of each peptide library. Results are shown in Figure 11 as %> inhibition.
  • CPI- 10070 M-A-X-X-X-X-X-R-X-X-X-X-A
  • CPI-10020 M-X-X-X-R-X-X-X.
  • the libraries include both linear and cyclic peptide libraries with various fixed orienting residues.
  • Table 2 Summary of results from CCR5 affinity purifications using peptide libraries.
  • immobilized functional CCR5 was used to isolate phage that bind to CCR5 using standard teclmiques known to those skilled in the art. Subtraction of the background from the glutathione-sepharose beads, BSA, and MIP1 ⁇ used in the assay was performed by incubation of the phage library with the mixture of these components. After incubating subtracted phage libraries (i.e., NEB, PhD C7C) with the receptor, bound phage were eluted both with the natural CCR5 ligand (MlPl ⁇ ) and with glycine, pH 2.2. PhD C7C is a particular phage library with 7 random amino acids between disulfides, and may be obtained from New England Biolabs. Multiple rounds of screening were performed. Both conditions have provided specific sequences which bind to CCR5 and may inhibit ligand binding.
  • subtracted phage libraries i.e., NEB, PhD C7C
  • MlPl ⁇ natural CCR5 ligand
  • Methods of preventing and treating AIDS and HIV infection comprise the step of administering a composition comprising such a compound capable of inhibiting CCR5 binding as described herein.
  • Administration may be by any compatible route.
  • administration may include oral or parenteral, including intravenous and intraperitoneal routes of administration.
  • a particularly preferred method is by controlled-release injection of a suitable formulation.
  • administration may be by periodic injections of a bolus of a composition, or may be made more continuous by intravenous or intraperitoneal administration from a reservoir that is external (e.g., an intravenous bag) or internal (e.g., a bioerodable implant).
  • a reservoir that is external (e.g., an intravenous bag) or internal (e.g., a bioerodable implant).
  • compositions contemplated by the present invention may be provided to an individual by any suitable means, directly (e.g., locally, as by injection, implantation or topical administration to a tissue locus) or systemically (e.g., parenterally or orally).
  • parenterally such as by intravenous, subcutaneous, intramolecular, ophthalmic, intraperitoneal, intramuscular, buccal, rectal, vaginal, intraorbital, intracerebral, intracranial, intraspinal, intraventricular, intrathecal, intracisternal, intracapsular, intranasal or by aerosol administration
  • the composition may comprise part of an aqueous or physiologically compatible fluid suspension or solution.
  • the carrier or vehicle is physiologically acceptable so that in addition to delivery of the desired composition to the patient, it does not otherwise adversely affect the patient's electrolyte and/or volume balance.
  • Useful solutions for parenteral administration may be prepared by any of the methods well known in the pharmaceutical art, described, for example, in REMINGTON'S PHARMACEUTICAL SCIENCES (Gennaro, A., ed.), Mack Pub., 1990.
  • Formulations of the therapeutic agents of the invention may include, for example, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, hydrogenated naphthalenes, and the like.
  • Formulations for direct administration in particular, may include glycerol and other compositions of high viscosity to help maintain the agent at the desired locus.
  • Biocompatible, preferably bioresorbable, polymers including, for example, hyaluronic acid, collagen, tricalcium phosphate, polybutyrate, lactide, and glycolide polymers and lactide/glycolide copolymers, may be useful excipients to control the release of the agent in vivo.
  • the concept of a controlled release injectable formulation for peptide drugs is well-accepted and offers several advantages.
  • bioavailabilities are high.
  • treatment regimens can consist of once per month or per three months (like Abbott's Leupron®), or once per year (e.g. Alza's Viadur®).
  • controlled release injectable formulations substantially reduces the doses that can be used (the Leupron injection dose is 1 mg/day but the 90 day formulationuses is 11.25 mg total). Also, increased efficacy can be achieved if the therapeutic is present continuously to prevent infectivity. This consideration is particularly important in view of the need to approach a cure for this disease by preventing the reformation of slow-to-clear deposits of infection such as the memory T cell compartment. See e.g., Lee, V., ed. Peptide and Protein Drug Delivery. Marcel Dekker, Inc., NY (1991).
  • Formulations for inhalation administration contain as excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or oily solutions for administration in the form of nasal drops, or as a gel to be applied intranasally.
  • Formulations for parenteral administration may also include glycocholate for buccal administration, methoxysalicylate for rectal administration, or cutric acid for vaginal administration.

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Abstract

L'invention concerne des compositions de composés de fixation du récepteur 5 de CC chimiokine ainsi que des procédés permettant d'identifier de tels composés dudit récepteur. L'invention concerne enfin des agents thérapeutiques renfermant de tels composés.
EP01920642A 2000-03-21 2001-03-21 Composes de fixation et procede d'identification de composes de fixation Withdrawn EP1268523A2 (fr)

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US19099600P 2000-03-21 2000-03-21
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US190946P 2000-03-21
US09/813,653 US20020064770A1 (en) 2000-03-21 2001-03-20 Binding compounds and methods for identifying binding compounds
US813653 2001-03-20
US813448 2001-03-20
US09/813,448 US20020142346A1 (en) 2000-03-21 2001-03-20 Binding compounds and methods for identifying binding compounds
US09/813,651 US20030018438A1 (en) 2000-03-21 2001-03-20 Binding compounds and methods for identifying binding compounds
US813651 2001-03-20
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WO2005056581A2 (fr) * 2003-12-10 2005-06-23 Universite De Lausanne Peptide susceptible de se lier specifiquement a un recepteur de chimiokine et son utilisation
CA2579678A1 (fr) * 2004-10-04 2006-04-13 Alchemia Limited Inhibiteurs selectifs
GB0724860D0 (en) * 2007-12-20 2008-01-30 Heptares Therapeutics Ltd Screening
JP5952816B2 (ja) * 2010-08-19 2016-07-13 プロビオドルグ エージー グルタミニルシクラーゼの結晶構造

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US5532167A (en) * 1994-01-07 1996-07-02 Beth Israel Hospital Substrate specificity of protein kinases

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EP1268521A1 (fr) 2003-01-02
AU2001253870A1 (en) 2001-10-03
WO2001071346A2 (fr) 2001-09-27
CA2403784A1 (fr) 2001-09-27
WO2001070765A1 (fr) 2001-09-27
WO2001071346A3 (fr) 2002-09-12
WO2001070768A3 (fr) 2002-03-14
AU2001247674A1 (en) 2001-10-03
AU2001247675A1 (en) 2001-10-03
WO2001070768A2 (fr) 2001-09-27
EP1268520A2 (fr) 2003-01-02
CA2404139A1 (fr) 2001-09-27
CA2403788A1 (fr) 2001-09-27
JP2003528319A (ja) 2003-09-24
WO2001070765A9 (fr) 2003-02-06
JP2004502134A (ja) 2004-01-22

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