WO2000069896A2 - Interactions moleculaires dans les cellules hematopoietiques - Google Patents

Interactions moleculaires dans les cellules hematopoietiques Download PDF

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WO2000069896A2
WO2000069896A2 PCT/US2000/013161 US0013161W WO0069896A2 WO 2000069896 A2 WO2000069896 A2 WO 2000069896A2 US 0013161 W US0013161 W US 0013161W WO 0069896 A2 WO0069896 A2 WO 0069896A2
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protein
pdz
cell
peptide
cells
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WO2000069896A3 (fr
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Peter S. Lu
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Arbor Vita Corporation
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Publication of WO2000069896A2 publication Critical patent/WO2000069896A2/fr
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    • 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
    • A—HUMAN NECESSITIES
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    • A—HUMAN NECESSITIES
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    • A61P21/00—Drugs for disorders of the muscular or neuromuscular system
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
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    • A—HUMAN NECESSITIES
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    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/07—Animals genetically altered by homologous recombination
    • A01K2217/075—Animals genetically altered by homologous recombination inducing loss of function, i.e. knock out
    • A—HUMAN NECESSITIES
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
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Definitions

  • the present invention relates to peptides and peptide analogues, and methods
  • the invention provides methods of modulating metabolism (e.g., activation) of hematopoietic cells (e.g., T cells and B cells) by antagonizing an interaction between a PDZ domain containing protein and a protein that binds a PDZ domain.
  • hematopoietic cells e.g., T cells and B cells
  • it relates to fusion peptides containing an amino acid sequence corresponding to the carboxyl terminus of
  • PDZ domains of proteins are named after three prototypical proteins: PSD95,
  • PDZ domain-containing proteins are involved in synapse formation by organizing transmembrane neurotransmitter receptors through intracellular interactions.
  • PDZ domains contain the signature sequence GLGF.
  • typical PDZ domain- containing proteins contain three PDZ domains, one SH3 domain and one guanylate kinase
  • intracellular PDZ domain-containing proteins include LIN-2, LIN-7 and LIN- 10 at the pre-synapse, and PSD95 at the post-synapse.
  • PDZ domains have been shown to bind the carboxyl termini of transmembrane proteins in neuronal cells.
  • Songyang et al. reported that proteins capable of binding PDZ domains contain a carboxyl terminal motif sequence of E-S/T-X-V/I (Songyang et al, 1997, Science 275:73).
  • X-ray crystallography studies have revealed the contact points between the motif sequence and PDZ domains (Doyle et al., 1996, Cell 88:1067-1076). While the interaction between PDZ domains and ion channels in neurons have been studied extensively, such interactions have had limited studies in other biological systems, especially the hematopoietic system.
  • the hematopoietic system is composed of different cell types that perform distinct functions. Many of its diverse function requires coordinated movement of cell surface receptors including ion channels, adhesion surface molecules to coordinate cell-cell interaction, and cytokine receptors. Despite their diverse functional activities, all hematopoietic cells are believed to develop from a multipotent bone marrow hematopoietic stem cell. Such stem cell has been shown to express a surface marker termed CD34. During differentiation, the stem cell gives rise to progenitor cells in each of several specific hematopoietic cell lineages. The progenitor cells then undergo a series of morphological and functional changes to produce mature functionally committed hematopoietic cells.
  • lymphocytes which include T cells, B cells and natural killer (NK) cells
  • monocytes and granulocytes i.e., neutrophils, basophils and eosinophils
  • lymphocytes, monocytes and granulocytes are collectively referred to as white blood cells or leukocytes.
  • other hematopoietic cells perform functions that are unrelated to the immune system. For example, erythrocytes are involved in gas transport, and cells of the thrombocytic series are involved in blood clotting.
  • T cells and B cells recognize antigens and generate an immune response.
  • T cells recognize antigens by heterodimeric surface receptors termed the T cell receptor (TCR).
  • TCR T cell receptor
  • the TCR is associated with a series of polypeptides collectively referred to as CD3 complex.
  • B cells recognize antigens by surface immunoglobulins (Ig), which are also secretory molecules.
  • Ig surface immunoglobulins
  • co-stimulatory surface receptors have been identified in T cells and B cells, which augment cellular activation during antigen-induced activation.
  • T cell antigen receptor/CD3 complex TCR/CD3
  • other molecules expressed by T cells which mediate an activation signal include but are not limited to, CD2, CD4, CD5, CD6, CD8, CD18, CD27, CD28, CD43, CD45, CD152 (CTLA-4), CD154, MHC class I, MHC class II, CDwl37 (4-1BB), CDwl50, and the like (Barclay et al., The Leucocyte Antigen Facts Book, 1997, Second edition, Academic Press; Leucocyte Typing, 1984, Bernard et al. (eds.), Springer- Verlag; Leukocyte Typing II, 1986, Reinherz et al.
  • T cell surface antigens include antigen-binding antibody derivatives such as variable domains, peptides, superantigens, and their natural ligands such as CD58 (LFA-3) for CD2, HIV gpl20 for CD4, CD27L for
  • Activation molecules expressed by B cells include but are not limited to, surface Ig, CD18, CD19, CD20, CD21, CD22, CD23, CD40, CD45, CD80, CD86 and ICAM1.
  • natural ligands of these molecules and antibodies directed to them as well as antibody derivatives may be used to deliver an activation signal to B cells.
  • the invention provides a method of modulating a biological function of a cell, e.g., an endothelial cell or hematopoietic cell (such as a a leukocyte, e.g., T cell or B cell), by introducing into the cell an antagonist that inhibits binding of a PDZ protein and a PL protein in the cell, or a agonist that enhances binding of a PDZ protein and a PL protein in the cell.
  • the PL protein is an adhesion protein, an adaptor protein, or an intracellular protein.
  • the PL protein is CD6, CD49E, CD49F, CD 138, Clasp- 1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM-1, CD83, CD44, CD4, CD97, CD3n, DOCK2, CD34, FceRIb, or FasLigand.
  • the PL protein is characterized by a carboxy- terminal amino acid motif that is X-S-X-A, X-A-D/E-V, X-V/l L-X*-V, or X-S/T-X-F (where X is any amino acid and X* is any non- aromatic amino acid).
  • the PL protein is expressed by T lymphocytes or B lymphocytes.
  • the PDZ protein is CASK, MPP1, DLG1, PSD95, NeDLG, SYNla, TAX43, LDP, LIM, LIMK, AF6, PTN-4, prILl ⁇ , 41.8, RGS12, DVL1, TAX 40, TIAM1, MINT1, K303, TAX2, or KIAA561.
  • the cell is a leukocyte and the biological function is cell activation, cell proliferation, maintenance of cell structure, cell metabolic activity, or cytokine production.
  • the method further includes detecting a change in leukocyte activation.
  • the antagonist is an agent that inhibits the binding of a PL peptide to a PDZ domain polypeptide in an "A" assay, in a "G” assay, or in both an A assay and a G assay.
  • the antagonist can be a polypeptide, such as a polypeptide having at the carboxyterminus at least two residues that are the same as the carboxy-terminal two residues of a PL protein, such as a PL protein is expressed in a hematopoietic or endothelial cell that is an adhesion protein, an adaptor protein, or an intracellular protein.
  • the carboxy-terminal four residues of the polypeptide are the same as the carboxy- terminal four residues of the PL protein.
  • the PL protein has a carboxy- terminal amino acid motif selected from X-S-X-A, X-A-D/E-V, X-V/I/L-X*-V, or X-S/T-X-F, where X is any amino acid and X* is any non-aromatic amino acid.
  • the PL protein is CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM- 1, CD83, CD44, CD97, CD3n, DOCK2, CD34, FceRIb, or FasLigand.
  • the antagonist is a peptide mimetic of a PL inhibitor sequence peptide.
  • the antagonist is a fusion polypeptide having a PL sequence and transmembrane transporter amino acid sequence (such as HIV tat, Drosophila antenapedia, herpes simplex virus VP22 or anti-DNA CDR 2 and 3).
  • the invention provides a method of determining whether a test compound is an inhibitor of binding between a PDZ protein and a PL protein by contacting a PDZ domain polypeptide having a sequence from the PDZ protein, and a PL peptide under conditions in which they form a complex, in the presence and in the absence of a test compound, and detecting the formation of the complex in the presence and absence of the test compound, where less complex formation in the presence of the test compound than in the absence of the compound indicates that the test compound is an inhibitor of a PDZ protein -PL protein binding.
  • the PL peptide has a sequence that includes the a C-terminal sequence of a PL protein, such as CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAMl, Clasp-2, CD95, DNAM-1, CD83, CD44, CD97, CD3n, DOCK2, CD34, FceRIb, or FasLigand.
  • a PL protein such as CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAMl, Clasp-2, CD95, DNAM-1, CD83, CD44, CD97, CD3n, DOCK2, CD34, FceRIb, or FasLigand.
  • the PDZ domain polypeptide is a fusion polypeptide.
  • the invention provides a method of determining whether a test compound is an agonist of binding between a PDZ protein and a PL protein by contacting a PDZ domain polypeptide, and a PL peptide under conditions in which they form a complex, in the presence and in the absence of a test compound, and detecting the formation of the complex in the presence and absence of the test compound, where more complex formation in the presence of the test compound than in the absence of the compound indicates that the test compound is an agonist of a PDZ protein -PL protein binding.
  • the invention further provides an inhibitor of binding of a PDZ protein and a PL protein.
  • the inhibitor is characterized in that it reduces binding of a peptide selected from the group consisting of a PL peptide selected from the group consisting of CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM-1, CD83, CD44, CD97, CD3n, DOCK2, CD34, FceRIb, and FasLigand and a PDZ domain polypeptide.
  • the inhibitor is a peptide comprising a sequence that is from 3 to about 20 residues of a C-terminal sequence of a PL protein selected from CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM-1, CD83, CD44, CD97, CD3n, DOCK2, CD34, FceRIb, and FasLigand; a peptide having a motif X-S-X-A, X- A-D/E-V, X-V/I/L-X*-V, or X-S/T-X-F, (where X is any amino acid and X* is any non- aromatic amino acid); a peptide mimetic,; or a small organic molecule.
  • the invention also provides a pharmaceutical composition containing the inhibitor.
  • the disease is characterized by an inflammatory or humoral immune response or is an autoimmune disease.
  • the invention further provides a method of reducing inflammation in a subject, by administering an agent that inhibits binding of a PDZ protein and a PL protein, where the PL protein is an adhesion protein, an adaptor protein, or an intracellular protein.
  • the invention also provides use of an inhibitor of the binding of a PDZ protein and a PL protein to inhibit leukocyte activation or to treat a disease mediated by hematopoietic cells, such as a disease is characterized by an inflammatory or humoral immune response.
  • the invention also provides use of an inhibitor of the binding of a PDZ protein and a PL protein in the preparation of a medicament for treatment of a disease mediated by hematopoietic cells.
  • the invention also provides a method of modulating a biological function of a hematopoietic cell, comprising introducing into the cell an antagonist that inhibits binding of a PDZ protein and a PL protein in the cell as deduced from Table 2, for example, where the PL protein is DNAM-1 and the PDZ protein is MPP1, MPP2, DLG1, NeDLG, PSD95, LIM, AF6,
  • the PL protein is LPAP and the PDZ protein is DLG1 or MINT1, or the PL protein is DNAM-1 and the PDZ protein is PSD95 or MPP2.
  • the present invention also relates to peptides and peptide analogues that bind PDZ domains in hematopoietic cells.
  • it relates to fusion peptides and peptide analogues containing a hematopoietic cell surface receptor carboxyl terminal sequence and a transmembrane transporter sequence which facilitates entry of the peptides into a target cell.
  • the invention also relates to methods of using such compositions in inhibiting leukocyte activation as measured by cytokine production, cell proliferation, apoptosis and cytotoxicity. It is an object of the invention to administer a therapeutically effective amount of the aforementioned fusion peptides or peptide analogues as pharmaceutical compositions to a subject to inhibit undesirable leukocyte-mediated events.
  • FIGURES 1A-1D show the results of exemplary assays in which the binding of biotinylated peptides having a sequence of the carboxyl-terminus ("c -terminus") of various leukocyte proteins to PDZ domains (i.e., GST-PDZ domain fusion proteins) was determined using the "G” assay described infra.
  • the PDZ domains are: PSD95 (Fig. 1 A ); NeDLG (Fig.
  • peptides 1-31 refer to the biotinylated PL peptide used in the assay, and are identified in the Key, infra. "Peptide IDs" are defined in
  • FIGURES 2A and 2B show the Apparent Affinity Determination for PDZ-
  • FIGURES 3A-3F show inhibition of PDZ - PL peptide interactions.
  • FIGURES 4A and 4B shows the results of introduction of a Tat-CD3 fusion peptide on T cell activation.
  • Antigen-specific T cell activation was measured by cytokine production.
  • Fusion peptides containing tat and a T cell surface molecule carboxyl terminus inhibited ⁇ -interferon (IFN) production by a T cell line in response to myelin basic protein (MBP) stimulation.
  • IFN ⁇ -interferon
  • MBP myelin basic protein
  • a “fusion protein” or “fusion polypeptide” as used herein refers to a composite protein, i.e., a single contiguous amino acid sequence, made up of two (or more) distinct, heterologous polypeptides which are not normally fused together in a single amino acid sequence.
  • a fusion protein can include a single amino acid sequence that contains two entirely distinct amino acid sequences or two similar or identical polypeptide sequences, provided that these sequences are not normally found together in the same configuration in a single amino acid sequence found in nature.
  • Fusion proteins can generally be prepared using either recombinant nucleic acid methods, i.e., as a result of transcription and translation of a recombinant gene fusion product, which fusion comprises a segment encoding a polypeptide of the invention and a segment encoding a heterologous protein, or by chemical synthesis methods well known in the art.
  • a "fusion protein construct” as used herein is a polynucleotide encoding a fusion protein.
  • PDZ domain refers to protein sequence (i.e., modular protein domain) of approximately 90 amino acids, characterized by homology to the brain synaptic protein PSD-95, the Drosophila septate junction protein Discs-Large (DLG), and the epithelial tight junction protein ZOl (ZOl).
  • PDZ domains are also known as Discs-Large homology repeats ("DHRs") and GLGF repeats). PDZ domains generally appear to maintain a core consensus sequence (Doyle, D. A., 1996, Cell 85: 1067-1076).
  • PDZ domains are found in diverse membrane-associated proteins including members of the MAGUK family of guanylate kinase homologs, several protein phosphatases and kinases, neuronal nitric oxide synthase, and several dystrophin-associated proteins, collectively known as syntrophins.
  • PDZ domain-containing proteins and PDZ domain sequences are shown in TABLE 3.
  • the term "PDZ domain” also encompasses variants (e.g., naturally occuring variants) of the sequences of TABLE 3 (e.g., polymorphic variants, variants with conservative substitutions, and the like).
  • PDZ domains are substantially identical to those shown in TABLE 3, e.g., at least about 70%, at least about 80%, or at least about 90% amino acid residue identity when compared and aligned for maximum correspondence.
  • PDZ protein refers to a naturally occurring protein containing a PDZ domain, e.g., a human protein.
  • exemplary PDZ proteins include CASK, MPP1, DLG1, PSD95, NeDLG, TAX33, SYNla, TAX43, LDP, LIM, LIMK1, LIMK2, MPP2, NOS1, AF6, PTN-4, prILl ⁇ , 41.8kD, KIAA0559, RGS12, KIAA0316, DVL1, TAX40, TIAM1, MLNTl, KIAA0303, CBP, MINT3, TAX2, KIAA0561.
  • Exemplary PDZ proteins are listed in TABLE 2 and TABLE 3.
  • PDZ-domain polypeptide refers to a polypeptide containing a PDZ domain, such as a fusion protein including a PDZ domain sequence, a naturally occurring PDZ protein, or an isolated PDZ domain peptide.
  • PL protein or "PDZ Ligand protein” refers to a naturally occurring protein that forms a molecular complex with a PDZ-domain, or to a protein whose carboxy-terminus, when expressed separately from the full length protein (e.g., as a peptide fragment of 4-25 residues, e.g., 16 residues), forms such a molecular complex.
  • the molecular complex can be observed in vitro using the "A assay” or "G assay” described infra, or in vivo.
  • Exemplary PL proteins listed in TABLE 2 are demonstrated to bind specific PDZ proteins. This definition is not intended to include anti-PDZ antibodies and the like.
  • a "PL sequence” refers to the amino acid sequence of the C- terminus of a PL protein (e.g., the C-terminal 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 20 or 25 residues) ("C-terminal PL sequence") or to an internal sequence known to bind a PDZ domain (“internal PL sequence).
  • a "PL peptide” is a peptide of having a sequence from, or based on, the sequence of the C-terminus of a PL protein. Exemplary PL peptides (biotinylated) are listed in TABLE 4.
  • a "PL fusion protein” is a fusion protein that has a PL sequence as one domain, typically as the C-terminal domain of the fusion protein.
  • An exemplary PL fusion protein is a tat-PL sequence fusion.
  • PL inhibitor peptide sequence refers to PL peptide an amino acid sequence that (in the form of a peptide or PL fusion protein) inhibits the interaction between a PDZ domain polypeptide and a PL peptide (e.g., in an A assay or a G assay).
  • a "PDZ-domain encoding sequence” means a segment of a polynucleotide encoding a PDZ domain.
  • the polynucleotide is DNA
  • RNA single stranded or double stranded.
  • the terms "antagonist” and “inhibitor,” when used in the context of modulating a binding interaction are used interchangeably and refer to an agent that reduces the binding of the, e.g., PL sequence (e.g., PL peptide) and the, e.g., PDZ domain sequence (e.g., PDZ protein, PDZ domain peptide).
  • the terms "agonist” and “enhancer,” when used in the context of modulating a binding interaction are used interchangeably and refer to an agent that increases the binding of the, e.g., PL sequence (e.g., PL peptide) and the, e.g., PDZ domain sequence (e.g., PDZ protein, PDZ domain peptide).
  • PL sequence e.g., PL peptide
  • PDZ domain sequence e.g., PDZ protein, PDZ domain peptide
  • peptide mimetic As used herein, the terms “peptide mimetic, " “peptidomimetic,” and “peptide analog” are used interchangeably and refer to a synthetic chemical compound which has substantially the same structural and/or functional characteristics of an PL inhibitory or PL
  • the mimetic can be either entirely composed of synthetic, non-natural analogues of amino acids, or, is a chimeric molecule of partly natural peptide amino acids and partly non-natural analogs of amino acids.
  • the mimetic can also inco ⁇ orate any amount of natural amino acid conservative substitutions as long as such substitutions also do not substantially alter the mimetic's structure and/or inhibitory or binding activity.
  • a mimetic composition is within the scope of the invention if it is capable of binding to a PDZ domain and/or inhibiting a PL-PDZ interaction.
  • Polypeptide mimetic compositions can contain any combination of nonnatural structural components, which are typically from three structural groups: a) residue linkage groups other than the natural amide bond ("peptide bond") linkages; b) non-natural residues in place of naturally occurring amino acid residues; or c) residues which induce secondary structural mimicry, i.e., to induce or stabilize a secondary structure, e.g., a beta turn, gamma
  • a polypeptide can be characterized as a mimetic when all or some of its residues are joined by chemical means other than natural peptide bonds. Individual peptidomimetic residues can be joined by peptide bonds, other chemical bonds or coupling means, such as, e.g., glutaraldehyde, N-hydroxysuccinimide esters, bifunctional maleimides,
  • a polypeptide can also be characterized as a mimetic by containing all or some non-natural residues in place of naturally occurring amino acid residues.
  • Nonnatural residues are well described in the scientific and patent literature; a few exemplary nonnatural compositions useful as mimetics of natural amino acid residues and guidelines are described below.
  • Mimetics of aromatic amino acids can be generated by replacing by, e.g., D- or L- naphylalanine; D- or L- phenylglycine; D- or L-2 thieneylalanine; D- or L-l, -2, 3-, or 4- pyreneylalanine; D- or L-3 thieneylalanine; D- or L-(2-pyridinyl)-alanine; D- or L-(3- pyridinyl)-alanine; D- or L-(2-pyrazinyl)-alanine; D- or L-(4-isopropyl)-phenylglycine; D- (trifluoromethyl)-phenylglycine; D-(trifluoromethyl)-phenylalanine; D-p-fluorophenylalanine; D- or L-p-biphenylphenylalanine; K- or L-p-methoxybiphenylphenyla
  • Aromatic rings of a nonnatural amino acid include, e.g., thiazolyl, thiophenyl, pyrazolyl, benzimidazolyl, naphthyl, furanyl, pyrrolyl, and pyridyl aromatic rings.
  • Mimetics of acidic amino acids can be generated by substitution by, e.g., non- carboxylate amino acids while maintaining a negative charge; (phosphono)alanine; sulfated threonine.
  • Aspartyl or glutamyl can also be converted to asparaginyl and glutaminyl residues by reaction with ammonium ions.
  • Mimetics of basic amino acids can be generated by substitution with, e.g., (in addition to lysine and arginine) the amino acids ornithine, citrulline, or (guanidino)-acetic acid, or (guanidino)alkyl-acetic acid, where alkyl is defined above.
  • Nitrile derivative e.g., containing the CN-moiety in place of COOH
  • Asparaginyl and glutaminyl residues can be deaminated to the corresponding aspartyl or glutamyl residues.
  • Arginine residue mimetics can be generated by reacting arginyl with, e.g., one or more conventional reagents, including, e.g., phenylglyoxal, 2,3-butanedione, 1,2- cyclohexanedione, or ninhydrin, preferably under alkaline conditions.
  • one or more conventional reagents including, e.g., phenylglyoxal, 2,3-butanedione, 1,2- cyclohexanedione, or ninhydrin, preferably under alkaline conditions.
  • Tyrosine residue mimetics can be generated by reacting tyrosyl with, e.g., aromatic diazonium compounds or tetranitromethane. N-acetylimidizol and tetranitromethane can be used to form O-acetyl tyrosyl species and 3-nitro derivatives, respectively. Cysteine residue mimetics can be generated by reacting cysteinyl residues with, e.g., alpha-halo acetates such as 2-chloroacetic acid or chloroacetamide and corresponding amines; to give carboxymethyl or carboxyamidomethyl derivatives.
  • Cysteine residue mimetics can also be generated by reacting cysteinyl residues with, e.g., bromo-trifluoroacetone, alpha- bromo-beta-(5-imidozoyl) propionic acid; chloroacetyl phosphate, N-alkylmaleimides, 3-nitro- 2-pyridyl disulfide; methyl 2-pyridyl disulfide; p-chloromercuribenzoate; 2-chloromercuri-4 nitrophenol; or, chloro-7-nitrobenzo-oxa-l,3-diazole.
  • cysteinyl residues e.g., bromo-trifluoroacetone, alpha- bromo-beta-(5-imidozoyl) propionic acid
  • chloroacetyl phosphate N-alkylmaleimides
  • 3-nitro- 2-pyridyl disulfide methyl 2-pyridyl disulfide
  • Lysine mimetics can be generated (and amino terminal residues can be altered) by reacting lysinyl with, e.g., succinic or other carboxylic acid anhydrides. Lysine and other alpha-amino-containing residue mimetics can also be generated by reaction with imidoesters, such as methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trinitrobenzenesulfonic acid, O-methylisourea, 2,4, pentanedione, and transamidase-catalyzed reactions with glyoxylate.
  • imidoesters such as methyl picolinimidate, pyridoxal phosphate, pyridoxal, chloroborohydride, trinitrobenzenesulfonic acid, O-methylisourea, 2,4, pentanedione, and transamidase-catalyzed reactions with glyoxylate.
  • Mimetics of methionine can be generated by reaction with, e.g., methionine sulfoxide.
  • Mimetics of proline include, e.g., pipecolic acid, thiazolidine carboxylic acid, 3- or 4- hydroxy proline, dehydroproline, 3- or 4-methylproline, or 3,3,-dimethylproline.
  • Histidine residue mimetics can be generated by reacting histidyl with, e.g., diethylprocarbonate or para- bromophenacyl bromide.
  • mimetics include, e.g., those generated by hydroxylation of proline and lysine; phosphorylation of the hydroxyl groups of seryl or threonyl residues; methylation of the alpha-amino groups of lysine, arginine and histidine; acetylation of the N-terminal amme; methylation of main chain amide residues or substitution with N-methyl amino acids; or amidation of C-terminal carboxyl groups.
  • a component of a natural polypeptide can also be replaced by an amino acid (or peptidomimetic residue) of the opposite chirality.
  • an amino acid or peptidomimetic residue of the opposite chirality.
  • any amino acid naturally occurring in the L-configuration (which can also be referred to as the R or S, depending upon the structure of the chemical entity) can be replaced with the amino acid of the same chemical structural type or a peptidomimetic, but of the opposite chirality, generally referred to as the D- amino acid, but which can additionally be referred to as the R- or S- form.
  • the mimetics of the invention can also include compositions that contain a structural mimetic residue, particularly a residue that induces or mimics secondary structures, such as a beta turn, beta sheet, alpha helix structures, gamma turns, and the like.
  • a structural mimetic residue particularly a residue that induces or mimics secondary structures, such as a beta turn, beta sheet, alpha helix structures, gamma turns, and the like.
  • substitution of natural amino acid residues with D-amino acids; N-alpha-methyl amino acids; C-alpha-methyl amino acids; or dehydroamino acids within a peptide can induce or stabilize beta turns, gamma turns, beta sheets or alpha helix conformations.
  • Beta turn mimetic structures have been described, e.g., by Nagai (1985) Tet. Lett. 26:647-650; Feigl (1986) J. Amer. Chem. Soc.
  • Beta sheet mimetic structures have been described, e.g., by Smith (1992) J. Amer. Chem. Soc. 114:10672-10674.
  • a type VI beta turn induced by a cis amide surrogate, 1,5-disubstituted tetrazol is described by Beusen (1995) Biopolymers 36:181-200.
  • peptide variants and “conservative amino acid substitutions” refer to peptides that differ from a reference peptide (e.g., a peptide having the sequence of the c arboxy-terminus of a specified PL protein) by substitution of an amino acid residue having similar properties (based on size, polarity, hydrophobicity, and the like).
  • a reference peptide e.g., a peptide having the sequence of the c arboxy-terminus of a specified PL protein
  • substitution of an amino acid residue having similar properties based on size, polarity, hydrophobicity, and the like.
  • amino acids may be generally categorized into three main classes: hydrophilic amino acids, hydrophobic amino acids and cysteine-like amino acids, depending primarily on the characteristics of the amino acid side chain. These main classes may be further divided into subclasses.
  • Hydrophilic amino acids include amino acids having acidic, basic or polar side chains and hydrophobic amino acids include amino acids having aromatic or apolar side chains.
  • Apolar amino acids may be further subdivided to include, among others, aliphatic amino acids.
  • the definitions of the classes of amino acids as used herein are as follows:
  • Hydrophobic Amino Acid refers to an amino acid having a side chain that is uncharged at physiological pH and that is repelled by aqueous solution.
  • genetically encoded hydrophobic amino acids include He, Leu and Val.
  • non- genetically encoded hydrophobic amino acids include t-BuA.
  • Amino Acid refers to a hydrophobic amino acid having a side chain
  • aromatic group containing at least one ring having a conjugated ⁇ -electron system (aromatic group).
  • aromatic group may be further substituted with groups such as alkyl, alkenyl, alkynyl, hydroxyl, sulfanyl, nitro and amino groups, as well as others.
  • groups such as alkyl, alkenyl, alkynyl, hydroxyl, sulfanyl, nitro and amino groups, as well as others.
  • genetically encoded aromatic amino acids include Phe, Tyr and Trp.
  • Non-genetically encoded aromatic amino acids include phenylglycine, 2-naphthylalanine, ⁇ -2-thienylalanine, 10 l,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, 4-chloro-phenylalanine, 2- fluorophenylalanine, 3-fluorophenylalanine and 4-fiuorophenylalanine.
  • Apolar Amino Acid refers to a hydrophobic amino acid having a side chain that is generally uncharged at physiological pH and that is not polar.
  • Examples of genetically T r encoded apolar amino acids include Gly, Pro and Met.
  • Examples of non-encoded apolar amino acids include Cha.
  • Aliphatic Amino Acid refers to an apolar amino acid having a saturated or unsaturated straight chain, branched or cyclic hydrocarbon side chain.
  • Examples of genetically encoded aliphatic amino acids include Ala, Leu, Val and He.
  • Examples of non-encoded 20 aliphatic amino acids include Nle.
  • Hydrophilic Amino Acid refers to an amino acid having a side chain that is attracted by aqueous solution.
  • examples of genetically encoded hydrophilic amino acids include Ser and Lys.
  • examples of non-encoded hydrophilic amino acids include Cit and hCys.
  • Acidic Amino Acid refers to a hydrophilic amino acid having a side chain pK
  • Acidic amino acids typically have negatively charged side chains at physiological pH due to loss of a hydrogen ion.
  • Examples of genetically encoded acidic amino acids include Asp and Glu.
  • Basic Amino Acid refers to a hydrophilic amino acid having a side chain pK value of greater than 7.
  • Basic amino acids typically have positively charged side chains at physiological pH due to association with hydronium ion.
  • genetically encoded basic amino acids include Arg, Lys and His.
  • non-genetically encoded basic amino acids include the non-cyclic amino acids ornithine, 2,3-diaminopropionic acid, 2,4- diaminobutyric acid and homoarginine.
  • Poly Amino Acid refers to a hydrophilic amino acid having a side chain that is uncharged at physiological pH, but which has a bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms.
  • genetically encoded polar amino acids include Asx and Glx.
  • non-genetically encoded polar amino acids include citrulline, N-acetyl lysine and methionine sulfoxide.
  • cyste-Like Amino Acid refers to an amino acid having a side chain capable of forming a covalent linkage with a side chain of another amino acid residue, such as a disulfide linkage.
  • cysteine-like amino acids generally have a side chain containing at least one thiol (SH) group.
  • examples of genetically encoded cysteine-like amino acids include Cys.
  • non-genetically encoded cysteine-like amino acids include homocysteine and penicillamine.
  • cysteine has both an aromatic ring and a polar hydroxyl group.
  • cysteine has dual properties and can be included in both the aromatic and polar categories.
  • cysteine in addition to being able to form disulfide linkages, cysteine also has apolar character.
  • cysteine can be used to confer hydrophobicity to a peptide.
  • Certain commonly encountered amino acids which are not genetically encoded of which the peptides and peptide analogues of the invention may be composed include, but are not limited to, ⁇ -alanine (b-Ala) and other omega-amino acids such as 3-aminopropionic acid
  • Dap 2,3-diaminopropionic acid
  • Dpr 4-aminobutyric acid and so forth; ⁇ -aminoisobutyric acid (Aib); ⁇ -aminohexanoic acid (Aha); ⁇ -aminovalenc acid (Ava); N-methylglycine or sarcosine (MeGly); ornithine (Orn); citrulline (Cit); t-butylalanine (t-BuA); t-butylglycine
  • TABLE 1 is for illustrative purposes only and does not purport to be an exhaustive list of amino acid residues which may comprise the peptides and peptide analogues described herein.
  • Other amino acid residues which are useful for making the peptides and peptide analogues described herein can be found, e.g., in Fasman, 1989, CRC Practical Handbook of Biochemistry and Molecular Biology, CRC Press, Inc., and the references cited therein.
  • Amino acids not specifically mentioned herein can be conveniently classified into the above-described categories on the basis of known behavior and/or their characteristic chemical and/or physical properties as compared with amino acids specifically identified.
  • a "detectable label” has the ordinary meaning in the art and refers to an atom (e.g., radionuclide), molecule (e.g., fluorescein), or complex, that is or can be used to detect (e.g., due to a physical or chemical property), indicate the presence of a molecule or to enable binding of another molecule to which it is covalently bound or otherwise associated.
  • label also refers to covalently bound or otherwise associated molecules (e.g., a biomolecule such as an enzyme) that act on a substrate to produce a detectable atom, molecule or complex.
  • Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Labels useful in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., DynabeadsTM), fluorescent dyes (e.g., fluorescein, Texas red, rhodamine, green fluorescent protein, enhanced green fluorescent protein, and the like), radiolabels (e.g., 3H, 1251, 35S, 14C, or 32P), enzymes (e.g., hydrolases, particularly phosphatases such as alkaline phosphatase, esterases and glycosidases, or oxidoreductases, particularly peroxidases such as horse radish peroxidase, and others commonly used in ELISAs), substrates, cofactors, inhibitors, chemiluminescent groups, chromogenic agents, and colorimetric labels such as colloidal gold or
  • Patents teaching the use of such labels include U.S. Patent Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
  • Means of detecting such labels are well known to those of skill in the art.
  • radiolabels and chemiluminescent labels may be detected using photographic film or scintillation counters
  • fluorescent markers may be detected using a photodetector to detect emitted light (e.g., as in fluorescence-activated cell sorting).
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • a label is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • the label may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art.
  • Non-radioactive labels are often attached by indirect means.
  • a ligand molecule e.g., biotin
  • the ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal generating system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound.
  • a signal generating system such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound.
  • a number of ligands and anti-ligands can be used. Where a ligand has a natural anti-ligand, for example, biotin, thyroxine, and cortisol, it can be used in conjunction with the labeled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody.
  • the molecules can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore. Means of detecting labels are well known to those of skill in the art.
  • means for detection include a scintillation counter, photographic film as in autoradiography, or storage phosphor imaging.
  • the label is a fluorescent label
  • it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence.
  • the fluorescence may be detected visually, by means of photographic film, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like.
  • enzymatic labels may be detected by providing the appropriate substrates for the enzyme and detecting the resulting reaction product.
  • simple colorimetric labels may be detected by observing the color associated with the label. It will be appreciated that when pairs of fluorophores are used in an assay, it is often preferred that they have distinct emission patterns (wavelengths) so that they can be easily distinguished.
  • the term "substantially identical" in the context of comparing amino acid sequences means that the sequences have at least about 70%, at least about 80%, or at least about 90% amino acid residue identity when compared and aligned for maximum correspondence.
  • An algorithm that is suitable for determining percent sequence identity and sequence similarity is the FASTA algorithm, which is described in Pearson, W.R. & Lipman, D.J., 1988, Proc. Natl. Acad. Sci. U.S.A. 85: 2444. See also W. R. Pearson, 1996, Methods Enzymol 266: 227-258.
  • hematopoietic cells include leukocytes including lymphocytes (T cells, B cells and NK cells), monocytes, and granulocytes (i.e., neutrophils, basophils and eosinophils), macrophages, dendritic cells, megakaryocytes, reticulocytes, erythrocytes, and CD34 + stem cells.
  • the present inventors have discovered that interactions between PDZ proteins and PL proteins play an important and extensive role in the biological function of hematopoietic cells and other cells involved in the immune response.
  • PDZ-PL interactions were known in the nervous system (i.e., in neurons), their universal importance in hematopoietic cell function, especially in function of T cells and B cells, and their fundamental role in modulation of the immune response has not been recognized.
  • cell adhesion molecules that mediate cell-cell interaction in the hematopoietic system are PDZ-binding proteins (PL proteins) and bind to PDZ proteins.
  • biological function in the context of a cell, refers to a detectable biological activity normally carried out by the cell, e.g., a phenotypic change such as proliferation, cell activation (e.g., T cell activation, B cell activation, T-B cell conjugate formation), cytokine release, degranulation, tyrosine phosphorylation, ion (e.g., calcium) flux, metabolic activity, apoptosis, changes in gene expression, maintenance of cell structure, cell migration, adherance to a substrate, signal transduction, cell-cell interactions, and others described herein or known in the art.
  • a phenotypic change such as proliferation, cell activation (e.g., T cell activation, B cell activation, T-B cell conjugate formation), cytokine release, degranulation, tyrosine phosphorylation, ion (e.g., calcium) flux, metabolic activity, apoptosis, changes in gene expression, maintenance of cell structure, cell migration, adher
  • the present invention relates to peptides, peptide analogues or mimetics, pharmaceutical compositions, and methods of using such compositions to regulate the biological activities of hematopoietic cells, e.g. T cells and B cells, or other cells (e.g., endothelial cells) that necessary for immune function.
  • the invention further relates to methods of using the compositions to modulate hematopoietic cell activation and immune function, as well as assays for such inhibitors.
  • TABLE 2 summarizes an extensive analysis of protein interactions in T cells and B cells.
  • PDZ proteins the vast majority of which were not previously known to be expressed in immune system cells, are listed in the top row of TABLE 2.
  • the first column of the table lists PL proteins. Positions in the matrix denoted by the letter “A” or “G” indicate that an interaction between the PDZ protein and the PL has been detected in novel binding assays (described in detail in, e.g., Section 6.2, infra).
  • a blank cell indicates that no interaction was detected using the assays of the invention.
  • An asterisk (*) denotes a PL-PDZ interaction previously reported in the scientific literature.
  • the PDZ proteins listed in TABLE 2 are naturally 5 occurring proteins containing a PDZ domain.
  • the present invention is particularly directed to the detection and modulation of interactions between PDZ proteins and PL proteins in hematopoietic cells.
  • Exemplary PL proteins are listed in TABLE 2. Notably, as discussed infra, many of these PL proteins have not previously been recognized as such in any cell system.
  • a variety of PL protein classes are known, and the PL proteins described herein can be characterized as (1) "PL adhesion proteins” (2) "PL ion channel proteins” (3) "PL adaptor proteins” (4) "PL intracellular proteins” and (5) "PL cytokine receptor proteins.”
  • an adhesion protein is a cell surface protein involved in cell-cell interaction by direct contact with cell surface molecules (e.g., transmembrane proteins or surface proteins) on a different cell.
  • cell surface molecules e.g., transmembrane proteins or surface proteins
  • the PL adhesion protein localizes at the interface of the two cells and directly contacts a cell surface molecule on the second cell.
  • a cell-cell interface is a region where the plasma membranes of two different cells are in close (generally ⁇ 10 nm, often about 1 nm) apposition.
  • direct molecular contact means interaction of 20 molecules at distances where Van der Walls forces are significant, generally less than about 1 nm.
  • Exemplary PL adhesion proteins include CD6; CD49E (alpha-4); CD49F (a form, alpha ⁇ ); CD138 (syndecan); CLASP-1; CLASP-4; VCAM1; CLASP-2; DNAM-1; CD83; CD44 (long form); CD97; (CD55L); CD3n; DOCK2; CD34; and FceRIb.
  • CD6 CD49E (alpha-4); CD49F (a form, alpha ⁇ ); CD138 (syndecan); CLASP-1; CLASP-4; VCAM1; CLASP-2; DNAM-1; CD83; CD44 (long form); CD97; (CD55L); CD3n; DOCK2; CD34; and FceRIb.
  • CD6 CD49E (alpha-4); CD49F (a form, alpha ⁇ ); CD138 (syndecan); CLASP-1; CLASP-4; VCAM1; CLASP-2; DNAM-1; CD83; CD44 (long form); CD97; (CD55L); CD3n; DO
  • PL proteins of the invention are PL adhesion proteins.
  • the invention is PL adhesion proteins.
  • the inhibition or modulation occurs in a hematopoietic cell. In a related embodiment, the inhibition or modulation occurs in an endothelial cell. In a related embodiment, the inhibition or modulation occurs in an endothelial cell. In a related embodiment, the inhibition or modulation 30 occurs in an epithelial cells, keratinocytes, hepatocytes, cardiac myocytes.
  • an ion channel protein means a transmembrane protein that itself catalyzes the passage of an ion from aqueous solution on one side of a lipid bilayer membrane to aqueous solution on the other side (e.g., by forming a small pore in the membrane).
  • the PL proteins of the invention are PL ion channel proteins.
  • the invention provides methods and reagents, as detailed herein, for inhibiting interactions between PL ion channel proteins and
  • the inhibition or modulation occurs in a hematopoeitic cell. In a related embodiment, the inhibition or modulation occurs in an endothelial cell.
  • an intercellular (i.e., cytosolic) protein has the normal meaning in the art and refers to a protein that is not membrane bound, e.g., has no transmembrane domain.
  • the PL proteins of the invention are PL intercellular proteins.
  • Exemplary PL intercellular proteins include Glycophorin C and LPAP.
  • the invention provides methods and reagents, as detailed herein, for inhibiting interactions between PL cytoplasmic proteins and PDZ proteins to modulate an immune response.
  • the inhibition or modulation occurs in a hematopoeitic cell.
  • the inhibition or modulation occurs in an endothelial cell.
  • a cytokine receptor has the normal meaning in the art and refers to a membrane protein with an extracellular domain that specifically binds a cytokine.
  • exemplary PL cytokine receptor proteins include CDW125 (IL5R), CDW128A (IL8RA), and BRL-1.
  • the PL proteins of the invention are PL cytokine proteins.
  • the invention provides methods and reagents, as detailed herein, for inhibiting interactions between PL cytokine proteins and PDZ proteins to modulate an immune response.
  • the inhibition or modulation occurs in a hematopoeitic cell.
  • the inhibition or modulation occurs in an endothelial cell.
  • an adaptor protein means a molecule (e.g., protein) that contributes to the formation of a multimolecular complex by binding two or more other biomolecuics.
  • the binding of the two or more other molecules by the adaptor molecule/protem generally involves direct molecular contact between the adaptor protein and each of the two or more other moiccules.
  • One exemplary PL adaptor protein is LPAP.
  • the PL proteins of the invention are PL adaptor proteins.
  • the invention provides methods and reagents, as detailed herein, for inhibiting interactions between PL adaptor proteins and PDZ proteins to modulate an immune response.
  • the inhibition or modulation occurs in a hematopoeitic cell.
  • the inhibition or modulation occurs in an endothelial cell.
  • the PL proteins of the invention are characterized by specific C-terminal (i.e., PL domain) amino acid sequences or amino acid motifs, as described elsewhere in this disclosure.
  • the PL proteins of the invention bind a PDZ protein expressed in T lymphocytes, B lymphocytes, or both T and B lymphocytes. In an embodiment, the PL protein binds a PDZ protein expressed in endothelial cells. In various embodiments, the PL proteins and/or the PDZ protein to which it binds are not expressed in the nervous system (e.g., neurons).
  • the nervous system e.g., neurons
  • the PL protein of the invention binds only one PDZ protein listed in TABLE 2. In other embodiment, the PL protein binds 1 to 3, 3 to 5, or more than 5 different PDZ proteins listed in TABLE 2.
  • the PL protein is expressed or upregulated upon cell activation (e.g., in activated B lymphocytes, T lymphocytes) or upon entry into mitosis (e.g., up-regulation in rapidly proliferating cell populations).
  • the PL protein is (i) a protein that mediates immune cell (e.g., hematopoietic cell) activation or migration, (ii) a protein that does not mediate apoptosis in a cell type (iii) a protein that is other than a G-protein coupled seven transmembrane helix receptor, (iv) a protein that is G-protein coupled seven transmembrane helix receptor but not a cytokine receptor or (v) a protein that is not a G-protein coupled seven transmembrane helix receptor and is a cytokine receptor.
  • PDZ proteins are expressed in immune system cells, and play a fundamental biological role in modulation of the immune response.
  • PDZ proteins DLG1 and TIAM-1 have been previously described to be in T cells. The present inventors discovered, using a BLAST search of the
  • the cells resuspension was mixed and after 5 minutes incubation at room temperature (RT), chloroform was added at 0.2 ml per ml TRIZOL. The resuspension was vigorously shaken and incubated for 3 more minutes at RT. Samples were then centrifuged at 12000 x g for 15 minutes at 4° C, the aqueous phase was recovered and RNA was precipitated with 2-propanol.
  • RT room temperature
  • the precipitate was collected by centrifugation at 12000 x g for 15 minutes at 4° C, washed with 75% ethanol, finally recollected by another spin at 12000 x g for 15 minutes at 4° C, air dried and resuspended in an appropriate volume of DEPC treated water.
  • RNA concentration and purity were determined by the measurement of 260/280 nm light absorption by the nucleic acid.
  • the SUPERSCRIPT II reverse transcriptase cDNA kit (GIBCO-BRL; Cat. # 18064-014) was used. RNA input per 200 ⁇ l cDNA reaction sample was 10 ⁇ g. Prior to cDNA synthesis RNA was treated with 1 unit/ ⁇ l DNAse I in 110 ⁇ l water at 37° C for 20 minutes. DNase I was then inactivated by a 10 minutes incubation at 70° C.
  • Random primer was used for cDNA priming; 10 ⁇ l of random hexamer primer (100 ng/ ⁇ l) was added, samples were heated to 70° C for 5 minutes and chilled on ice. Subsequently 40 ⁇ l SUPERSCRIPT II "first strand" buffer, 20 ⁇ l of 0.1 M DDT, 10 ⁇ l of a 10 mM of mix of deoxynucleotide triphosphates (dATP, dCTP, dGTP, dUTP) and 10 ⁇ l of SUPERSCRIPT II reverse transcriptase were added and cDNA synthesis was done for 45 minutes at 42 ° C. Reavtions were stopped by a 5 minutes incubation at 95 ° C and typically, 2-4 ⁇ l of such cDNA samples were used for PCR.
  • SUPERSCRIPT II "first strand" buffer 20 ⁇ l of 0.1 M DDT, 10 ⁇ l of a 10 mM of mix of deoxynucleotide triphosphates (dATP
  • telomere sequences encoding the various PDZ domains of interest were used for PCR.
  • PCR was conducted using primers designed to amplify specifically PDZ domain-containing regions of PDZ proteins of interest. Oligonucleotide primers were designed to amplify one or more PDZ-encoding domains.
  • Oligonucleotide primers were designed to amplify one or more PDZ-encoding domains.
  • GenBank accession number of the PDZ-domain containing proteins GenBank accession number of the PDZ-domain containing proteins.
  • the PCR primers included endonuclease restriction sequences at their ends to allow ligation with pGEX-3X cloning vector (Pharmacia, GenBank XXI13852 ) in frame with glutathione-S transferase (GST).
  • INADL2/3 (PDZ dom.), KIAA0316, and 26s subunit p27 were detected in T cells, but not B cells.
  • mCASK, KIAA0559, PTN-4, and XI 1 beta were detected in B cells, but not T cells.
  • MINT1, MINT3, MPP1, MPP2, NE-DLG, NOS1, novel serine protease, PTN-3, prIL 16, PSD95, RGS12, serine protease, SYNTENIN, SYNTR 1 alpha, TAXI, TAX2, TAX33, TAX40, Tax43 (SYN, Betal), TIAM ww ⁇ 3, and XI 1 prot. were detected in both T cells and B cells.
  • cDNA sequences representing the same gene have several database entries under different accession numbers and names. Accession numbers shown correspond to the gene name used in this description, and numbering of nucleotides and amino acids correlates to those Genbank entries. Amino acid sequences shown correspond to the cloned DNA portions of PDZ domain containing genes. Linker amino acid sequences (e.g., amino acids encoded by DNA flanking the cloning site of the pGEX-3X cloning vector), are in italics
  • sequence analysis of the PDZ clones revealed differences to the DNA and/or protein sequence as published in the databases, summarized in TABLE 3A.
  • A' and G Two complementary assays, termed “A' and "G,” were developed to detect binding between a PDZ-domain polypeptide and candidate PDZ ligand. In each of the two different assays, binding, is detected between a peptide having a sequence corresponding to the
  • a protein anticipated to bind to one or more PDZ domain i.e. a candidate PL peptide
  • a PDZ-domain polypeptide typically a fusion protein containing a PDZ domain
  • the candidate, PL peptide is immobilized and binding of a soluble PDZ- domain polypeptide to the immobilized peptide is detected (the "A”' assay is named for the fact that in one embodiment an avidin surface is used to immobilize the peptide).
  • the PDZ-domain polypeptide is immobilized and binding of a soluble PL peptide is detected (The "G” assay is named for the fact that in one embodiment a GST-binding surface is used to immobilize the PDZ-domain polypeptide).
  • GST-binding surface is used to immobilize the PDZ-domain polypeptide.
  • GST-PDZ domain fusion proteins were prepared for use in the assays of the invention. PCR products containing PDZ encoding domains (as described in ⁇ 6.1 supra) were
  • PCR products i.e., DNA fragments
  • PDZ domain encoding DNA was extracted from agarose gels using the "sephaglas" gel extraction system (Pharmacia) according to the
  • PCR primers were designed to include endonuclease restriction sites to facilitate ligation of PCR fragments into a GST gene fusion vector (pGEX-3X; Pharmacia, GenBank accession no. XXU13852) in-frame with the glutathione-S transferase coding sequence.
  • This vector contains a IPTG inducible lacZ promoter.
  • the pGEX-3X vector contains a IPTG inducible lacZ promoter.
  • the PDZ-encoding PCR fragment and linearized pG ⁇ X-3X vector were ethanol precipitated and resuspended in 10 ul standard ligation buffer. Ligation was performed for 4-10 hours at 7°C using T4 DNA ligase. It will be understood that some of the resulting constructs include very short linker sequences and that, when multiple PDZ domains were cloned, the constructs included some DNA located between individual PDZ domains.
  • the ligation products were transformed in DH5 ⁇ or BL-21 E.coli bacteria strains. Colonies were screened for presence and identity of the cloned PDZ domain containing DNA as well as for correct fusion with the glutathione S-transferase encoding DNA portion by PCR and by sequence analysis. Positive clones were tested in a small scale assay for expression of the GST/PDZ domain fusion protein and, if expressing, these clones were subsequently grown up for large scale preparations of GST/PDZ fusion protein. GST-PDZ domain fusion protein was overexpressed following addition of IPTG to the culture medium and purified.
  • IPTG isopropyl ⁇ -D-thiogalactopyranoside
  • l .OmM concentration of l .OmM
  • Bacteria were collect by centrifugation (4500 g) and resuspended in Buffer A- (50mM Tris, pH 8.0, 50mM dextrose, lmM EDTA, 200uM phenylmethylsulfonylfluoride).
  • Buffer A+ Buffer A-, 4mg/ml lysozyme
  • Buffer B (lOmM Tris, pH 8.0, 50mM KC1, lmM EDTA. 0.5% Tween-20, 0.5% NP40 (a.k.a. IGEPAL CA-630), 200uM phenylmethylsulfonylfluoride) was added and incubated for an additional 20 min.
  • the bacterial cell lysate was centrifuged (x20,000g), and supernatant was added to glutathione sepharose 4B (Pharmacia, cat no. 17-0765-01) previous swelled (rehydrated) in IX phosphate-buffered saline (PBS).
  • the supernatant-sepharose slurry was poured into a column and washed with at least 20 bed volumes of IX PBS.
  • GST fusion protein was eluted off the glutathione sepharose by applying 0.5-1.0 ml aliquots of 5mM glutathione and collected as separate fractions. Concentrations of fractions were determined using BioRadTrotein Assay (cat no. 500-0006) according to manufacturer's specifications. Those fractions containing the highest concentration of fusion protein were pooled and dialyzed against IX PBS/35% glycerol. Fusion proteins were assayed for size and quality by SDS gel electrophoresis (PAGE) as described in "Sambrook.” Fusion protein aliquots were stored at minus 80°C and at minus 20°C.
  • PDZ domains are known to be bound by the C-terminal residues of PDZ-binding proteins.
  • cell surface receptor proteins were identified and peptides having the sequence corresponding to the c-terminus of each protein were synthesized. TABLE 4 lists these proteins, and provides corresponding C- terminal sequences and GenBank accession numbers. "Clasp 1" is described in WO 00/20434 (published 13 April 2000). "Clasp 2" and “Clasp 4" are described in copending applications USSN 09/547276 (attorney docket No. 20054-000200) and 60/196527 (attorney docket No.20054-000400), both filed April 11 , 2000.
  • Synthetic peptides of defined sequence can be synthesized by any standard resin-based method (see, e.g., U. S. Pat. No. 4,108,846; see also, Caruthers et al., 1980, Nucleic Acids Res. Symp. Ser., 215-223; Horn et al., 1980, Nucleic Acids Res. Symp. Ser., 225-232; Roberge, et al., 1995, Science 269:202).
  • the peptides used in the assays described herein were prepared by the FMOC (see, e.g., Guy and Fields, 1997, Meth. Enz.
  • peptides were labeled with biotin at the amino-terminus by reaction with a four-fold excess of biotin methyl ester in dimethylsulfoxide with a catalytic amount of base.
  • the peptides were cleaved from the resin using a halide containing acid (e.g. trifluoroacetic acid) in the presence of appropriate antioxidants (e.g. ethanedithiol) and excess solvent lyophilized.
  • peptides can be redissolved and purified by reverse phase high performance liquid chromatography (HPLC).
  • HPLC solvent system involves a Vydac C-18 semi-preparative column running at 5 mL per minute with increasing quantities of acetonitrile plus 0.1% trifluoroacetic acid in a base solvent of water plus 0.1%) trifluoroacetic acid.
  • the identities of the peptides are confirmed by MALDI cation-mode mass spectrometry.
  • exemplary biotinylated peptides are provided in TABLE 4.
  • one binding partner of a PDZ-PL pair is immobilized, and the ability of the second binding partner to bind is determined.
  • These assays which are described infra, can be readily used to screen for hundreds to thousand of potential PDZ-ligand interactions in a few hours. Thus these assays can be used to identify yet more novel PDZ-PL interactions in hematopoietic cells. In addition, they can be used to identify antagonists of PDZ-PL interactions (see infra).
  • the invention provides an assay in which biotinylated candidate PL peptides are immobilized on an avidin coated surface. The binding of PDZ- domain fusion protein to this surface is then measured.
  • the PDZ- domain fusion protein is a GST/PDZ fusion protein and the assay is carried out as follows:
  • Avidin is bound to a surface, e.g. a protein binding surface.
  • avidin is bound to a polystyrene 96 well plate (e.g., Nunc Polysorb (cat #475094) by addition of 100 uL per well of 20 ug/mL of avidin (Pierce) in phosphate buffered saline without calcium and magnesium, pH 7.4 ("PBS", GibcoBRL) at 4°C for 12 hours.
  • PBS phosphate buffered saline without calcium and magnesium, pH 7.4
  • the plate is then treated to block nonspecific interactions by addition of 200 uL per well of PBS containing 2 g per 100 mL protease-free bovine serum albumin ("PBS/BSA”) for 2 hours at 4°C.
  • PBS/BSA protease-free bovine serum albumin
  • Biotinylated PL peptides (or candidate PL peptides, e.g. see TABLE 4) are immobilized on the surface of wells of the plate by addition of 50 uL per well of 0.4 uM peptide in PBS/BSA for 30 minutes at 4°C.
  • each different peptide is added to at least eight different wells so that multiple measurements (e.g. duplicates and also measurements using different (3ST/PDZ-domain fusion proteins and a GST alone negative control) can be made, and also additional negative control wells are prepared in which no peptide is immobilized.
  • the plate is washed 3 times with PBS.
  • GST/PDZ-domain fusion protein (prepared as described supra) is allowed to react with the surface by addition of 50 uL per well of a solution containing 5 ug/mL GST/PDZ-domain fusion protein in PBS/BSA for 2 hours at 4°C.
  • GST alone i.e. not a fusion protein
  • specified wells generally at least 2 wells (i.e. duplicate measurements) for each immobilized peptide. After the 2 hour reaction, the plate is washed 3 times with PBS to remove unbound fusion protein.
  • the binding of the GST/PDZ-domain fusion protein to the avidin- biotinylated peptide surface can be detected using a variety of methods, and detectors known in the art.
  • 50 uL per well of an anti-GST antibody in PBS/BSA e.g. 2.5 ug/mL of polyclonal goat-anti-GST antibody, Pierce
  • PBS/BSA polyclonal goat-anti-GST antibody, Pierce
  • HRP horseradish peroxidase
  • a specific or selective reaction will be at least twice background signal, more typically more than 5 times background, and most typically 10 or more times the background signal.
  • a statistically significant reaction will involve multiple measurements of the reaction with the signal and the background differing by at least two standard errors, more typically four standard errors, and most typically six or more standard errors.
  • a statistical test e.g. a T-test
  • comparing repeated measurements of the signal with repeated measurements of the background will result in a p- value ⁇ 0.05, more typically a p-value ⁇ 0.01, and most typically a p-value ⁇ 0.001 or less.
  • GST/PDZ-domain fusion protein to an avidin surface not exposed to (i.e. not covered with) the PL peptide is one suitable negative control (sometimes referred to as "B").
  • B suitable negative control
  • the signal from binding of GST polypeptide alone (i.e. not a fusion protein) to an avidin-coated surface that has been exposed to (i.e. covered with) the PL peptide is a second suitable negative control
  • the arithmetic mean (or, equivalently, average) of several measurements is used in determining the binding, and the standard error of the mean is used in determining the probable error in the measurement of the binding.
  • the standard error of the mean of N measurements equals the square root of the following: the sum of the squares of the difference between each measurement and the mean, divided by the product of (N) and (N-1).
  • specific binding of the PDZ protein to the plate-bound PL peptide is determined by comparing the mean signal ("mean S") and standard error of the signal (“SE”) for a particular PL-PDZ combination with the mean BI and/or mean B2.
  • binding was detected to be specific (denoted by an "A" in the matrix) when (1) the, mean S was at least twice the mean BI and at least twice the mean B2 and (2) the mean S was at least six standard errors (six SE) greater than both the mean BI and the mean B2.
  • an additional criterion was used to ensure that none of the interactions defined as specific arose from a combined tendency of both the particular PDZ fusion protein and PL peptide tested to each give a higher than usual background.
  • This criteria was that (3) the mean S was at least twenty times the product of the mean B 1 and the mean B2. The factor twenty times reflects that at least one of BI and B2 is generally less than 0.1 O.D.
  • the invention provides an assay in which a GST/PDZ fusion protein is immobilized on a surface ("G" assay). The binding of labeled PL peptide (as listed in TABLE 4) to this surface is then measured.
  • the assay is carried out as follows:
  • a PDZ-domain polypeptide is bound to a surface, e.g. a protein binding surface.
  • a GST/PDZ fusion protein containing one or more PDZ domains is bound to a polystyrene 96-well plate.
  • the GST/PDZ fusion protein can be bound to the plate by any of a variety of standard methods known to one of skill in the art, although some care must be taken that the process of binding the fusion protein to the plate does not alter the ligand-binding properties of the PDZ domain.
  • the GST/PDZ fusion protein is bound via an anti-GST antibody that is coated onto the 96-well plate. Adequate binding to the plate can be achieved when: a. 100 uL per well of 5 ug/mL goat anti-GST polyclonal antibody
  • PBS polystyrene 96-well plate
  • Nunc Polysorb a polystyrene 96-well plate
  • the plate is blocked by addition of 200 uL per well of PBS/BSA for 2 hours at 4°C.
  • c. The plate is washed 3 times with PBS.
  • 50 uL per well of 5 ug/mL GST/PDZ fusion protein) or, as a negative control, GST polypeptide alone (i.e. not a fusion protein) in PBS/BSA is added to the plate for 2 hours at 4°C. e. the plate is again washed 3 times with PBS.
  • Biotinylated PL peptides (or candidate PL peptides, e.g. as shown in TABLE 4) are allowed to react with the surface by addition of 50 uL per well of 20 uM solution of the biotinylated peptide in PBS/BSA for 10 minutes at 4°C, followed by an additional 20 minute incubation at 25°C. The plate is washed 3 times with ice cold PBS.
  • the binding of the biotinylated peptide to the GST/PDZ fusion protein surface can be detected using a variety of methods and detectors known to one of skill in the art.
  • 100 uL per well of 0.5 ug/mL streptavidin-horse radish peroxidase (HRP) conjugate dissolved in BSA/PBS is added and allowed to react for 20 minutes at 4°C.
  • the plate is then washed 5 times with 50 mM Tris pH 8.0 containing 0.2% Tween 20, and developed by addition of 100 uL per well of HRP-substrate solution (TMB, Dako) for 20 minutes at room temperature (RT).
  • TMB HRP-substrate solution
  • RT room temperature
  • the reaction of the HRP and its substrate is terminated by addition of 100 uL per well of I M sulfuric acid, and the optical density (O.D.) of each well of the plate is read at 450 um.
  • Specific binding of a PL peptide and a PDZ domain polypeptide is determined by comparing the signal from the well(s) in which the PL peptide and PDZ domain polypeptide are combined, with the background signal(s).
  • the background signal is the signal found in the negative control(s).
  • a specific or selective reaction will be at least twice background signal, more typically more than 5 times background, and most typically 10 or more times the background signal.
  • a statistically significant reaction will involve multiple measurements of the reaction with the signal and the background differing by at least two standard errors, more typically four standard errors, and most typically six or more standard errors.
  • a statistical test e.g.
  • the signal from binding of a given PL peptide to immobilized (surface bound) GST polypeptide alone is one suitable negative control
  • the arithmetic mean (or, equivalently, average.) of several measurements is used in determining the binding, and the standard error of the mean is used in determining the probable error in the measurement of the binding.
  • the standard error of the mean of N measurements equals the square root of the following: the sum of the squares of the difference between each measurement and the mean, divided by the product of (N) and (N-1).
  • specific binding of the PDZ protein to the platebound peptide is determined by comparing the mean signal ("mean S") and standard error of the signal (“SE”) for a particular PL-PDZ combination with the mean B 1.
  • the PDZ-PL detection assays can employ a variety of surfaces to bind the PL and PDZ-containing proteins.
  • a surface can be an "assay plate" which is formed from a material (e.g. polystyrene) which optimizes adherence of either the PL protein or PDZ- containing protein thereto.
  • the individual wells of the assay plate will have a high surface area to volume ratio and therefore a suitable shape is a flat bottom well (where the proteins of the assays are adherent).
  • Other surfaces include, but are not limited to, polystyrene or glass beads, polystyrene or glass slides, and alike.
  • the assay plate can be a "microtiter" plate.
  • microtiter microtiter
  • the assay plate 20 late when used herein refers to a multiwell assay plate, e.g., having between about 30 to 200 individual wells, usually 96 wells. Alternatively, high density arrays can be used Often, the individual wells of the microtiter plate will hold a maximum volume of about 250 ul.
  • the assay plate is a 96 well polystyrene plate (such as that sold by Becton Dickinson Labware, Lincoln Park, N.J.), which allows for automation and high throughput
  • the label can be detectable by itself (e.g., radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, can catalyze a chemical alteration of a substrate compound or composition which is detectable.
  • the preferred label is an enzymatic one which catalyzes
  • r a color change of a non-radioactive color reagent.
  • the label is indirectly conjugated with the antibody.
  • the antibody can be conjugated with biotin and any of the categories of labels mentioned above can be conjugated with avidin, or vice versa (see also "A” and “G” assay above).
  • Biotin binds selectively to avidin and thus, the label can be conjugated with the antibody in this indirect manner. See, Ausubel, supra, for a review of techniques involving biotin-avidin conjugation and similar assays.
  • the antibody is conjugated with a small hapten (e.g. digoxin) and one of the different types of labels mentioned above is conjugated with an anti-hapten antibody (e.g. anti-digoxin antibody).
  • a small hapten e.g. digoxin
  • an anti-hapten antibody e.g. anti-digoxin antibody
  • washing is meant exposing the solid phase to an aqueous solution (usually a buffer or cell culture media) in such a way that unbound material (e.g., non-adhering cells, non-adhering capture agent, unbound ligand, receptor, receptor construct, cell lysate, or HRP antibody) is removed therefrom.
  • a detergent e.g., Triton X
  • the aqueous washing solution is decanted from the wells of the assay plate following washing. Conveniently, washing can be achieved using an automated washing device. Sometimes, several washing steps (e.g., between about 1 to 10 washing steps) can be required.
  • blocking buffer refers to an aqueous, pH buffered solution containing at least one blocking compound which is able to bind to exposed surfaces of the substrate which are not coated with a PL or PDZ- containing protein.
  • the blocking compound is normally a protein such as bovme serum albumin (BSA), gelatin, casein or milk powder and does not cross-react with any of the reagents in the assay.
  • BSA bovme serum albumin
  • the block buffer is generally provided at a pH between about 7 to 7.5 and suitable buffering agents include phosphate and TRIS.
  • enzyme-substrate combinations include, for example:
  • HRPO Horseradish peroxidase
  • AP alkaline phosphatase
  • para-Nitrophenyl phosphate as chromogenic substrate.
  • ⁇ -D-galactosidase ( ⁇ D-Gal) with a chromogenic substrate (e.g. p- nitrophenyl- ⁇ -D-galactosidase) or fluorogenic substrate 4-methylumbelliferyl- ⁇ -D- galactosidase.
  • a chromogenic substrate e.g. p- nitrophenyl- ⁇ -D-galactosidase
  • fluorogenic substrate 4-methylumbelliferyl- ⁇ -D- galactosidase 4-methylumbelliferyl- ⁇ -D- galactosidase.
  • TABLE 2 shows the results of assays in which specific binding was detected using the "A” and "G” assays described herein.
  • the top row of the table specifies the source of the PDZ domain used in the GST-PDZ fusion proteins (see TABLE 3).
  • the first column lists the cell surface proteins from which C-terminal peptide sequences were derived and the second column ("code") identifies the peptide used in the assay (see TABLE 4).
  • code identifies the peptide used in the assay (see TABLE 4).
  • the third column, “Seq” provides the sequence of the four (4) C-terminal residues of the cell surface protein and peptide.
  • A indicates specific binding as detected in the "A” assay.
  • “G” indicates specific binding as shown in the "G” assay.
  • a blank indicates that no specific binding was detected using the "A” or “G” assays.
  • An asterisk (*) indicates that a pairwise interaction between the PDZ protein and the cell
  • MATRIX to detect binding between PDZ proteins and candidate PL peptides.
  • a number of u specific PDZ-PL interactions are identified by the MATRIX and key amino acids and positions important in PDZ binding ("PL motifs") are deduced from these results. Not only is the
  • the assay can further aid in the rapid discovery and characterization of novel PL proteins and PL motifs to help in rational drug design and synthesis of PL-PDZ interaction inhibitors. 5
  • PL motifs important in PDZ binding e.g., the C-terminal motifs S/T-X-V/I/L (for DLG1) and Y/F-Y/F-I L/F for MPP1 (see, Doyle et al., 1996, Cell 85, 1067; Songyang et al., 1997, Science 275, 73).
  • the reported motifs are not sufficiently specific (i.e. a large number of proteins meet these criteria yet are 5 not necessarily actual PDZ ligands) and cover only a small number of PDZ proteins (approximately 10).
  • the PRISM MATRIX can be used to determine ligand specificity and to deduce ligand binding motifs for any PDZ protein because it can precisely determine sequences of amino acids that do or do not result in specific PDZ binding.
  • the assay has revealed a significant of new PDZ domain binding motifs (i.e.
  • PL motifs C-terminal sequence 10 of CD6, ISAA; C- terminal sequence of CD49E, TSDA; C- terminal sequence of CD49F, TSDA; C-terminal sequence of Clasp-1, SAEV; C- terminal sequence of CLASP-4, YAEV; C- terminal sequence of CD44, KIGV; C-terminal sequence of IL5R, DSVF; C-terminal sequence of BLR- 1, LTTF.
  • PDZ-PL PDZ-PL
  • CD6 the C-terminal sequence of CD6, SAA and the C-terminal sequence of CD49E, SDA bind to the PDZ-domain polypeptide 20 41.8 while the related C-terminal sequence of CD166, TEA and C- terminal sequence of CD148, YIA do not.
  • Other novel motifs are described in TABLE 5A.
  • X* is any non-aromatic amino acid (any residue other than T, F or W).
  • TABLE 2 is arranged so that both the PDZ/GST fusion proteins and the PL peptide ligands are ordered with structurally similar molecules close to each other.
  • the PDZ domains of each of the GST-PDZ fusion proteins were ranked for amino acid sequence similarity using the CLUSTAL multiple sequence alignment software package. Proteins with greatest sequence similarity are closest to each other in the matrix.
  • the PL peptide ligands were also ordered on the basis of amino acid similarity, but with weight given to residues reported to be important in PDZ binding (Doyle et al., 1996, Cell 85, 1067).
  • peptides were first ordered based on the most C-terminal residue (zero position) in the following amino acid order: G, A, C, S, T, N, Q, D, E, H, K, R, V, I, L, M, P, F, Y, W.
  • the same ranking scheme was then applied to the next most important residue for peptide binding, the -2 position, followed by the -1 position and the -3 position.
  • the GST-PDZ fusions can also be arranged to give additional weight to residues known to be important for ligand binding when aligning the proteins.
  • Regions of the TABLE 1 matrix that are densely filled with significant binding interactions indicate that a particular ligand structure tends to bind to a particular family of PDZ domains.
  • the results indicate that PDZ domains with similar structures bind ligands with similar structures, as indicated by the presence in the matrix of some clusters of many significant binding interactions and other areas of few significant binding interactions.
  • These results reveal a number of structural relationships between different PDZ proteins and their ligands. The understanding of these structural relationships can be used to scan databases for probable ligands of specific PDZ proteins, facilitating the design of inhibitors of such novel interactions and the prediction of the side-effect profile of such inhibitors.
  • MPPl the closest relative to CASK in the ordering system used, bound a set of five different ligands, including neurexin. All of the MPPl ligands identified are structurally similar in that they terminate in valine (V) and have a charged amino acid (E or K) at the -3 position from the C-terminus ((C-terminal motif: E/K - X - X - V)
  • DLGl is closely related to two other proteins
  • All of these ligands terminate in A, V, I, or L, and four of five have serine (S) at the -2 position, defining the C-terminal ligand motif S - X - A/N/I/L for this PDZ domain.
  • X* is any non-aromatic amino acid.
  • one of these ligands also binds to KIAA 0561 's closest relative, TAX2.
  • the two ligands that bind to prIL16 both have a charged amino acid at the -3 position, a hydrophobic amino acid at the
  • X* is any non-aromatic amino acid.
  • the "A” and “G” assays of the invention can be used to determine the "apparent affinity" of binding of a PDZ ligand peptide to a PDZ-domain polypeptide. Apparent affinity is determined based on the concentration of one molecule required to saturate the binding of a second molecule (e.g., the binding of a ligand to a receptor). Two particularly useful approaches for quantitation of apparent affinity of PDZ-ligand binding are provided infra. (1) A GST/PDZ fusion protein, as well as GST alone as a negative control, are bound to a surface (e.g., a 96-well plate) and the surface blocked and washed as described supra for the "G” assay.
  • a surface e.g., a 96-well plate
  • a solution of biotinylated PL peptide (e.g. as shown in TABLE 4) is added to the surface in increasing concentrations in PBS/BSA (e.g. at 0.1 uM, 0.33 uM, 1 uM, 3.3 uM, 10 uM, 33 uM, and 100 uM).
  • the PL peptide is allowed to react with the bound GST/PDZ fusion protein (as well as the GST alone negative control) for 10 minutes at 4 C followed by 20 minutes at 25 C.
  • the plate is washed 3 times with ice cold PBS to remove unbound labeled peptide.
  • the net binding signal is determined by subtracting the binding of the peptide to GST alone from the binding of the peptide to the GST/PDZ fusion protein.
  • the net binding signal is then plotted as a function of ligand concentration and the plot is fit (e.g. by using the Kaleidagraph software package curve fitting algorithm) to the following equation, where "Signal [ligand] " is the net binding signal at PL peptide concentration "[ligand],” “Kd” is the apparent affinity of the binding event, and "Saturation Binding” is a constant determined by the curve fitting algorithm to optimize the fit to the experimental data:
  • FIGURE 2 shows varying concentrations of biotinylated CLASP-2 (FIG. 2A) or Fas
  • FIG. 2B C-terminal peptides reacted with immobilized (plate bound) GST polypeptide or
  • GST/PDZ fusion proteins (GST/DLG1, GST/NeDLG, and GDT/PSD95) in duplicate.
  • the signals were normalized, plotted and fit to a saturation binding curve, yielding an apparent affinity of 21 uM for DLGl -CLASP-2 interaction, 7.5 uM for NeDLG-CLASP-2 interaction,
  • NeDLG-Fas interaction and 85 uM for PSD95-Fas interaction.
  • a fixed concentration of a PDZ-domain polypeptide and increasing concentrations of a labeled PL peptide (labeled with, for example, biotin or fluorescein, see
  • TABLE 4 for representative peptide amino acid sequences are mixed together in solution and allowed to react.
  • preferred peptide concentrations are 0.1 uM, 1 uM, 10 uM, 100 uM, 1 mM.
  • appropriate reaction times can range from 10 minutes to 2 days at temperatures ranging from 4 C to 37 C.
  • the identical reaction can also be carried out using a non-PDZ domain-containing protein as a control (e.g., if the PDZ-domain polypeptide is fusion protein, the fusion partner can be used).
  • (2) PDZ-ligand complexes can be separated from unbound labeled peptide using a variety of methods known in the art.
  • the complexes can be separated using higb performance size-exclusion chromatography (HPSEC, gel filtration) (Rabinowitz et al., 1998, Immunity 9:699), affinity chromatography(e.g. using glutathione sepharose beads), and affinity absorption (e.g., by binding to an anti-GST-coated plate as described supra).
  • higb performance size-exclusion chromatography HPSEC, gel filtration
  • affinity chromatography e.g. using glutathione sepharose beads
  • affinity absorption e.g., by binding to an anti-GST-coated plate as described supra.
  • the PDZ-ligand complex is detected based on presence of the label on the peptide ligand using a variety of methods and detectors known to one of skill in the art. For example, if the label is fluorescein and the separation is achieved using HPSEC, an in-line fluorescence detector can be used. The binding can also be detected as described supra for the G assay.
  • the PDZ-ligand binding signal is plotted as a function of ligand concentration and the plot is fit. (e.g., by using the Kaleidagraph software package curve fitting algorithm) to the following equation, where "Signal [h d] " is the binding signal at PL peptide concentration "[ligand],” "Kd” is the apparent affinity of the binding event, and "Saturation Binding” is a constant determined by the curve fitting algorithm to optimize the fit to the experimental data:
  • PDZ-domain polypeptides and PL proteins the assays described supra and other assays can also be used to identify the binding of other molecules (e.g., peptide mimetics, small molecules, and the like) to PDZ domain sequences.
  • other molecules e.g., peptide mimetics, small molecules, and the like
  • combinatorial and other libraries of compounds can be screened. Screening of libraries can be accomplished by any of a variety of commonly known methods. See, e.g., the following references, which disclose screening of peptide libraries: Parmley and Smith, 1989, Adv. Exp. Med. Biol. 251 :215-218; Scott and Smith, 1990, Science 249:386-390; Fowlkes et al., 1992;
  • screening can be carried out by contacting the library members with a hematopoietic cell PDZ-domain polypeptide immobilized on a solid support (e.g. as described supra in the "G” assay) and harvesting those library members that bind to the protein.
  • a solid support e.g. as described supra in the "G” assay
  • panning techniques are described by way of example in Parmley and Smith, 1988, Gene 73:305-318; Fowlkes et al., 1992, BioTechniques 13:422-427; PCT Publication No. WO 94/18318; and in references cited hereinabove.
  • the two-hybrid system for selecting interacting proteins in yeast can be used to identify molecules that specifically bind to a PDZ domain- containing protein. Furthermore, the identified molecules are further tested for their ability to inhibit transmembrane receptor interactions with a PDZ domain.
  • antagonists of an interaction between a PDZ protein and a PL protein are identified. In one embodiment, a modification of the "A" assay described supra is used to identify antagonists. In one embodiment, a modification of the "G" assay described supra is used to identify antagonists.
  • screening assays are used to detect molecules that specifically bind to PDZ domains in hematopoietic cells.
  • Such molecules are useful as agonists or antagonists of PDZ-protein-mediated cell function (e.g., cell activation, e.g., T cell activation, vesicle transport, cytokine release, growth factors, transcriptional changes, cytoskeletin rearrangement, cell movement, chemotaxis, and the like).
  • cell activation e.g., T cell activation, vesicle transport, cytokine release, growth factors, transcriptional changes, cytoskeletin rearrangement, cell movement, chemotaxis, and the like.
  • such assays are performed to screen for leukocyte activation inhibitors for drug development.
  • the invention thus provides assays to detect molecules that specifically bind to PDZ domain- containing proteins in hematopoietic cells.
  • recombinant cells expressing PDZ domain-encoding nucleic acids can be used to produce PDZ domains in these assays and to screen for molecules that bind to the domains.
  • Molecules are contacted with the PDZ domain (or fragment thereof) under conditions conducive to binding, and then molecules that specifically bind to such domains are identified.
  • Methods that can be used to carry out the foregoing are commonly known in the art.
  • diversity libraries such as random or combinatorial peptide or non-peptide libraries can be screened for molecules that specifically bind to PDZ domains in hematopoietic cells.
  • Many libraries are known in the art that can be used, e.g., chemically synthesized libraries, recombinant (e.g., phage display libraries), and in vitro translation-based libraries.
  • phage display libraries are described in Scott and Smith, 1990, Science 249:386-390; Devlin et al, 1990, Science, 249:404-406; Christian, R.B., et al., 1992, J. Mol. Biol 227:711-718); Lenstra, 1992, J Immunol Meth. 152:149-157; Kay et al., 1993, Gene 128:59-65; and PCT Publication No. WO 94/18318 dated August 18, 1994.
  • In vitro translation-based libraries include but are not limited to those described in PCT Publication No. WO 91/05058 dated April 18, 1991; and Mattheakis et al., 1994, Proc. Natl. Acad. Sci. USA 91:9022-9026.
  • a benzodiazepine library see e.g., a benzodiazepine library (see e.g., a benzodiazepine library (see e.g., a benzodiazepine library (see e.g., a benzodiazepine library (see e.g., a benzodiazepine library (see e.g., a benzodiazepine library (see e.g.,
  • Bunin et al., 1994, Proc. Natl. Acad. Sci. USA 91 :4708-4712) can be adapted for use.
  • Peptoid libraries (Simon et al, 1992, Proc. Natl. Acad. Sci. USA 89:9367-9371) can also be used.
  • antagonists are identified by conducting the A or G assays in the presence and absence of a known or candidate antagonist. When decreased binding is observed in the presence of a compound, that compound is identified as an antagonist. Increased binding in the presence of a compound signifies that the compound is an agonist.
  • a test compound in one assay, can be identified as an inhibitor (antagonist) of binding between a PDZ protein and a PL protein by contacting a PDZ domain polypeptide and a PL peptide in the presence and absence of the test compound, under conditions in which they would (but for the presence of the test compound) form a complex, and detecting the formation of the complex in the presence and absence of the test compound. It will be appreciated that less complex formation in the presence of the test compound than in the absence of the compound indicates that the test compound is an inhibitor of a PDZ protein -PL protein binding.
  • the PL peptide comprises an amino acid sequence substantially identical to the C-terminal sequence of a PL protein (e.g., CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM-1, CD83, CD44, CD4, CD97, Neurexin, CD3n, DOCK2, CD34, FceRIb, or FasLigand).
  • a PL protein e.g., CD6, CD49E, CD49F, CD138, Clasp-1, Clasp-4, VCAM1, Clasp-2, CD95, DNAM-1, CD83, CD44, CD4, CD97, Neurexin, CD3n, DOCK2, CD34, FceRIb, or FasLigand.
  • the "G” assay is used in the presence or absence of an candidate inhibitor. In one embodiment, the "A” assay is used in the presense or absence of a candiate inhibitor.
  • one or more PDZ domain- containing GST-fusion proteins are bound to the surface of wells of a 96-well plate as described 20 supra (with appropriate controls including nonfusion GST protein). All fusion proteins are bound in multiple wells so that appropriate controls and statistical analysis can be done.
  • a test compound in BSA/PBS typically at multiple different concentrations is added to wells.
  • 30 uL of a detectably labeled (e.g., biotinylated) peptide known to bind to the relevant PDZ domain is added in each of the wells at a final
  • ⁇ 7 J concentration of, e.g., between about 2 uM and about 40 uM, typically 5 uM, 15 uM, or 25 uM.
  • This mixture is then allowed to react with the PDZ fusion protein bound to the surface for 10 minutes at 4°C followed by 20 minutes at 25°C.
  • the surface is washed free of unbound peptide three times with ice cold PBS and the amount of binding of the peptide in the presence and absence of the test compound is determined.
  • the level of binding is measured for each 30 set of replica wells (e.g. duplicates) by subtracting the mean GST alone background from the mean of the raw measurement of peptide binding in these wells.
  • the A assay is carried out in the presence or absence of an test candidate to identify inhibitors of PL-PDZ interactions.
  • a test compound is determined to be a specific inhibitor of the binding of the PDZ domain (P) and a PL (L) sequence when, at a test compound concentration of less than or equal to 1 mM (e.g., less than or equal to: 500 uM, 100 uM, 10 uM, 1 uM, 100 nM or 1 nM) the binding of P to L in the presence of the test compound less than about 50% of the binding in the absence of the test compound, (in various embodiments, less than about 25%o, less than about 10%, or less than about l%o).
  • the net signal of binding of P to L in the presence of the test compound plus six (6) times the standard error of the signal in the presence of the test compound is less than the binding signal in the absence of the test compound.
  • assays for an inhibitor are carried out using a single PDZ protein-PL protein pair (e.g., a PDZ domain fusion protein and a PL peptide).
  • the assays are carried out using a plurality of pairs, such as a plurality of different pairs listed in TABLE 2.
  • These antagonists can be identified by carrying out a series of assays using a candidate inhibitor and different PL-PDZ pairs (e.g., as shown in the matrix of TABLE 2) and comparing the results of the assays. All such pairwise combinations are contemplated by the invention (e.g., test compound inhibits binding of PL, to PDZ, to a greater degree than it inhibits binding of PL, to PDZ 2 or PL 2 to PDZ 2 ).
  • test compound inhibits binding of PL, to PDZ, to a greater degree than it inhibits binding of PL, to PDZ 2 or PL 2 to PDZ 2 ).
  • the PDZ binding moieties and PDZ protein -PL protein binding antagonists of the invention are used to modulate biological activities or ructions of cells (e.g., hematopoietic cells, such as T cells and B cells and the like), endothelial cells, and other immune system cells, as described herein, and for treatment of diseases and conditions in human and nonhuman animals (e.g., experimental models). Exemplary biological acitivities are listed supra.
  • the compounds of the invention are useful for treating (ameliorating symptoms of) a variety of diseases and conditions, including diseases characterized by inflammatory and humoral immune responses, e.g., inflammation, allergy (e.g., systemic anaphylaxis, hypersensitivity responses, drug allergies, insect sting allergies; inflammatory bowel diseases, ulcerative colitis, ileitis and enteritis; psoriasis and inflammatory dermatoses, scleroderma; respiratory allergic diseases such as asthma, allergic rhinitis, hypersensitivity lung diseases, and the like vasculitis, rh incompatibility, transfusion reactions, drug sensitivities, PIH, atopic dermatitis, eczema, rhinnitis; autoimmune diseases, such as arthritis (rheumatoid and psoriatic), multiple sclerosis, systemic lupus erythematosus, insulin-dependent diabetes,
  • inflammatory and humoral immune responses e.g., inflammation, allergy (e
  • PL proteins and PDZ proteins listed in TABLE 2 are well characterized, and one of skill, guided by this disclosure (including the discovery of the interactions between PL proteins and PDZ proteins described herein), will recognize many uses for modulators (e.g., enhancers or inhibitors) of PDZ-PL interactions such as those described in TABLE 2.
  • modulators e.g., enhancers or inhibitors
  • PDZ-PL interactions such as those described in TABLE 2.
  • CD6 binds PDZ protein 41.8.
  • CD6 is expressed on thymocytes, T cells, and B cell chronic lymphocytic leukemias. CD6 plays a role in T cell co- stimulation and CD6 negative T cells are less autoreactive than CD6 positive T cells. Inhibition of CD6 and CD6/41.8 interactions is predicted to reduce the symptoms of graft- versus-host disease (GVHD) or psoriasis.
  • GVHD graft- versus-host disease
  • GVHD graft- versus-host disease
  • GVHD graft- versus-host disease
  • CD6-PDZ interaction inhibitors will improve overall survival of transplantation patients (e.g., leukemia patients).
  • CD49e binds to the PDZ-domain-containing protein41.8kD.
  • CD49e is a 110 kD transmembrane membrane protein of the integrin alpha family (integrin alpha 5). Paired with the integrin beta- 1 subunit it forms VLA-5.
  • VLA-5 is expressed predominantly on hematopoietic and lymphoid lineage cells including monocytes, basophils, T cells, and activated B cells.
  • VLA-5 is the receptor for the ubiquitously-expressed adhesion molecule fibronectin. Tissue injury such as myocardial infarction releases soluble fragments of fibronectin.
  • Binding of these soluble fragments to VLA-5 results in chemotaxis of immune cells including monocytes to the source of fibronectin, as well as down-modulation of VLA-5 expression on these cells.
  • Such ligand- induced down-modulation is a common and required feature of chemotaxic receptors.
  • the 41.8/CD49e interaction is believed to be necessary for proper membrane distribution of CD49e and/or recycling of CD49e such that when it is disrupted, the migration and adherence to fibronectin -containing surfaces is similarly disrupted, resulting in an inability of immune system cells to effectively migrate toward a fibronectin source and adhere to fibronectin-containing surfaces.
  • Such disruption would therefore result in desirable reduced inflammatory processes, including reduced post-myocardial infarction inflammation.
  • Other diseases to be treated include but are not limited to joint inflamation, psoriasis, contact allergy, Crohn's Disease, inflammatory bowel disease, eczema, atopic dermatitis.
  • CD49F VLA-6 ⁇ subunit
  • CD49F binds PDZ protein 41.8.
  • CD49f is known as an mtegnn subunit that pairs either with the ⁇ l integrin subunit (CD29), forming VLA-6, or with
  • CD 104 ( ⁇ 4 integrin subunit).
  • the integrin supergene family consists of a number of cell surface ⁇ heterodimers important for many different physiologic processes, including embryogenesis, thrombosis, wound healing, tumorigenesis and immune responses. Each ⁇ chain can pair with various ⁇ chains.
  • Both VLA-6 and CD49f CD104 are widely expressed on epithelia in non-lymphoid tissues. VLA-6 is also expressed on platelets, monocytes, thymocytes and T lymphocytes, with an increased expression on activated and resting memory T cells.
  • Inhibition of interactions between VLA-6 and 41.8 has a number of therapeutic functions such as the prevention and treatment of metastatic cancers, and treatment of overactive immunity.
  • VLA-6 is associated with invasivion of prostrate carcinoma and plays a role in the metastasis of breast cancer. Blockage of VLA-6 function combined with conventional treatment for prostrate cancer, would be a more effective treatment by preventing metastatic disease (see, Cress et al., 1995, Cancer Metastasis R). Blockage of CD49f through PDZ interaction may also treat Rh incompatibility by blunting memory response or in the treatment of keloids.
  • CD138 is a transmembrane proteoglycan receptor with the extracellular domain functioning as a ligand binding domain for various extracellular matrix components and the intracellular portion functioning to alter cytoskeleton and transduce intracellular signals. CD138 also binds FGF2 and may be a co-receptor for FGF receptor (Yayon et al., 1991).
  • CD138 interacts with 41.8kD protein and TIAM1.
  • the c- terminus of CD 138 has also been reported to bind the PDZ domains of syntenin and human CASK (Cohen et al., 1998, J. Cell. Biol. 142:129-138; Grootjans et al., 1997, PNAS 94:13683- 13688; Hsueh et al., 1998, J. Cell. Biol. 142:139-151).
  • CD138 is expressed in pre-B cells, immature B cells, plasma cells, neural cells, the basolateral surface of epithelial cells, embryonic mesenchymal cells, vascular smooth muscle cells, endothelial cells and neural cells but not mature circulating B cells.
  • CD 138 The interaction between CD 138 and the PDZ domains of the 41.8kD protein and TIAM1 proteins is believed to be necessary for the proper distribution of CD 138 on the cell surface. Disruption of the interaction by administration of an effective amount of an antagonist is expected to interfere with the migration and adherence of cells to the extracellular matrix, resulting in reduced inflammatory and humoral immune responses.
  • Inhibition of CD 138 may be used to treat without limitation diseases such as post-myocardial infarction inflamatory damage, joint injury, rheumatoid arthritis, vasculitis, drug reaction, scleraderma, SLE, Hashimoto thyroiditis, Goodpasture's syndrome, juvenile insulin-dependent diabetes, psoriasis.
  • diseases such as post-myocardial infarction inflamatory damage, joint injury, rheumatoid arthritis, vasculitis, drug reaction, scleraderma, SLE, Hashimoto thyroiditis, Goodpasture's syndrome, juvenile insulin-dependent diabetes, psoriasis.
  • CD98 interacts with MPP2.
  • CD98 is expressed at high levels on monocytes and at low levels on T cells, B cells, splenocytes, NK cells, and granulocytes.
  • CD98 plays roles in adhesion, fusion and is a L-type amino acid transporter.
  • CD98 is also involved in virus-mediated cell fusion (e.g. paramyoviruses: parainfluenza virus type 2, Newcastle disease virus, and rubulaviruses)and antagonism of CD98 function is expected to treat )viral infections and limit viral spread.
  • CD98 inhibitors can be an antiviral agent for, but not limited to paramyovirus, parainfluenza, Newcastle disease and rubula. Other roles include treatment for acute leukemias.
  • CLASP-1 interacts with DLGl, PSD95, and NeDLG.
  • CLASP- 1 is a member of a superfamily of immune-cell associated proteins with similar motifs (see PCT/US99/22996 published as WO 00/20434).
  • CLASP-1 functions in the maintenance of the immune synapse.
  • the CLASP-1 transcript is present in lymphoid organs and neural tissue, and the protein is expressed by T and B lymphocytes and macrophages in the MOMA-1 subregion of the marginal zone of the spleen, an area known to be important in T:B cell interaction.
  • CLASP-1 staining of individual T and B cells exhibits a preactivation structural polarity, being organized as a "ball” or “cap” structure in B cells, and forming a "ring", "ball” or “cap” structure in T cells. The placement of these structures is adjacent to the microtubule-organizing center ("MTOC").
  • MTOC microtubule-organizing center
  • CLASP-1 antibody staining indicates that CLASP-1 is at the interface of T-B cell conjugates that are fully committed to differentiation. Antibodies to the extracellular 0 domain of CLASP-1 also block T-B cell conjugate formation and T cell activation.
  • CLASP-1 agonists/antagonists include, but is not limited to, rheumaotoid arthritis, juvenile diabetes, organ rejection, graft-versus-host
  • CLASP-4 interacts with DLGl, PSD95, NeDLG, LDP, AF6,
  • CLASP-4 is a member of a superfamily of immune-cell associated 0 proteins with similar motifs (see copending U.S.Pat. Application 60/196,527 filed April 11,
  • CLASP-4 protein is expressed primarily in peripheral blood lymphocytes.
  • CLASP-4 agonists/antagonists include, but is not limited to, rheumaotoid arthritis, juvenile diabetes, organ rejection, graft-versus-host disease, scleroderma, multiple sclerosis, acute leukemias, leukemic blast crisis, post-infarction inflamation (cardiac, etc.), atherosclerosis.
  • VCAM-1 The vascular cell adhesion molecule- 1 (VCAM-1, CD 106) is predominantly expressed by vascular endothelium (i.e.,, endothelial cells) but has been detected in macrophages, dendritic cells, bone marrow-derived cells, fibroblasts, cortical thymic epithelial cells, vascular smooth muscle cells, myoblasts and myotubes.
  • VCAM-1 mediates adhesion through interacting with an integrin ligand, VLA-4, which is expressed by lymphocytes, monocytes and eosinophils.
  • VCAM-1 and VLA-4 The interaction between VCAM-1 and VLA-4 is important for activation, flattening and extravasation of VLA-4 expressing cells when the endothelium itself has become activated due to inflammation or injury (Salomon et al., 1997, Blood 89:2461- 2471; St-Pierre et al., 1996, Eur. J. Immunol. 26:2050-2055; Bell et al, 1995, Int. Immunol. 7:1861-1871).
  • VCAM-1 is a ligand for the PDZ domains of MPPl, DLGl, NeDLGl, LDP, 41.8 protein, TIAM1 and K303. These interactions are believed to mediate the function of endothelial cell interactions with integrin expressing leukocytes. When the PDZ-PL interactions are disrupted, the adherence of leukocytes to the endothelium will similarly be disrupted, resulting in, e.g., reduction of inflammation.
  • VCAM-1 binding to PDZ proteins is useful for reducing abnormal VCAM-1 inflammatory responses and associated pathologies such as (but not limited to) renal allograft rejection, insulin-dependent diabetes, rheumatoid arthritis, post-myocardial infarction complications and systemic lupus erythematosus (Pasloske et al., 1994, Ann Rev Med 45:283;
  • CLASP-2 interacts with PSD-95, NeDLG, and DLGl.
  • CLASP-2 is a member of a superfamily of immune-cell associated proteins with similar motifs (see copending U.S. Pat. 09/547,276 filed April 11, 2000; WO 00/10158 filed April 11, 2000;
  • CLASP-2 transcript is present most strongly in placenta followed by lung, kidney and heart and the protein is expressed in T and B cells, and kidney epithelial cells.
  • CLASP-2 Inhibition of the interaction of CLASP-2 and PDZ domains will interfere with CLASP-2 function resulting in interference with T and B cell function (e.g., T and B cell activation), signal transduction, cell-cell interactions, and membrane organization.
  • T and B cell function e.g., T and B cell activation
  • signal transduction e.g., T and B cell interactions
  • membrane organization e.g., T and B cell interactions
  • blocking CLASP-2 function or expression can selectively block immune responses in the heart (for example, to selectively stop immune response in the heart compartment, e.g., following cardiac transplant rejection or post-MI inflammation, without compromising immunity elsewhere).
  • Other diseases to be treatment by CLASP-1 agonists/antagonists include, but is not limited to, rheumaotoid arthritis, juvenile diabetes, organ rejection, graft-versus-host disease, scleroderma, multiple sclerosis.
  • CD95 Fas/Apo-1
  • FasL Fas ligand
  • CD95 binds the PDZ domains DLGl, PSD95, NeDLG, and 41.8. Inhibition of the interaction of CD95 and PDZ domains.
  • K. KV1.3 (Shaker Type Kvl.3 Potassium Channel) As shown supra, Kvl.3 binds DLGl, PSD95, NeDLG, LIMK, 41.8, RGS12,
  • Kvl.3 is a Shaker-related channel protein that is involved in modulating the membrane potential of T lymphocytes (Lewis and Cahalan, 1995, Ann. Rev. Immunol.
  • DNAM-1 is associated with Fyn constitutively but required the presence of pervanadate (a tyrosine phosphatase inhibitor) (see Shibuya, et al. 1999, Immunity. 11:615-623).
  • pervanadate a tyrosine phosphatase inhibitor
  • DNAM-1 Upon stimulation with anti-CD3 (or DNAM-1), DNAM-1 is phosphorylated at Serine 329 (Shibuya, et al. 1998, J. Immun. 161:1671-1676.) and associates with LFA-1.
  • Fyn becomes associated with DNAM-1 independent of pervanadate. Fyn phosphorylates DNAM-1 at Y 322, but does not require Y322 to continue binding to DNAM-1.
  • DNAM-1 itself does not have a SH3 binding domain but only has the Src phosphorylation site at Y322, an adaptor molecule must be present to bridge DNAM-1 and Fyn.
  • DLGl has been described in the literature to be present in T cells (Hanada, et al. 1997. J Biol Chem 272:26899), but does not bind Fyn.
  • PSD95 does not have a SH3 binding site.
  • several of the other PDZ proteins do have SH3 binding domains including but not limited to NeDLG, RGS12, MPP2 and can fulfill this function.
  • the Y139 is a candidate phosphorylation site to control association of Fyn to DNAM-1 and the adaptor PDZ.
  • inhibition of PDZ association with DNAM-1 using the reagents of the invention will inhibit Fyn association with DNAM-1 and the subsequent Y322 phosphorylation and activation of cytotoxic T cells.
  • Diseases that can be treated include but are not limited to Crohn's Disease, multiple sclerosis, ulcerative colitis, inflammatory bowel disease, graft-versus-host, juvenile diabetes, Hashimoto's disease.
  • CD83 is a transmembrane glycoprotein, expressed predominantly on activated dendritic cells (DCs), Langerhans cells in the skin, with some weak expression detected on activated peripheral lymphocytes, and interdigitating reticulum cells within the T cell zones of lymphoid organs (Zhou and Tedder, 1995, J. Immunol. 154:3821-3835; Zhou et al, 1992, J. Immunol 149:735-742). CD83 is up-regulated de novo upon activation of an immature DCs, and is the major discriminating marker and characteristic for activated, mature DCs
  • DCs function as antigen presenting cells
  • APCs Upregulation and expression of CD83 thus appears to be required for DCs to mature and function as APCs.
  • CD83 binds to the PDZ domains of DLGl, PSD95, and NeDLG. These interactions between CD83 and PDZ domains, and between CD83 and DLGl, PSD95, and NeDLG are believed to be important for proper distribution and recycling of CD83. Disruption of CD83 and PDZ proteins with agonists and antagonist can be used to treat, but not limited to, psoriasis, cancers, allergies, autoimmune diseases such as multiple sclerosis, system lupus erythematosis.
  • CD44 phagocytic glycoprotein 1, lymphocyte homing receptor, p85 and HCAM
  • CD44 is single pass transmembrane protein that has several different isoforms due to alternative splicing. It has a broad pattern of expression being detected on both hematopoietic and non-hematopoietic cell types including epithelial, endothelial, mesenchymal and neuronal cells.
  • CD44H is a major isoform that is expressed in lymphoid, myeloid and erythroid cells (reviewed in Barclay et al., 1997, The Leukocyte Antigen Facts Book, 2ed, Academic Press).
  • CD44 is a receptor for hyaluronate (HA), which is a constituent of the 0 extracellular matrix (ECM).
  • CD44 functions as an adhesion molecule on the surface of leukocytes and erythrocytes that binds HA polymers in the ECM, and it can also act as a signaling receptor when HA becomes soluble during inflammatory reactions or tissue damage.
  • the cytoplasmic region of CD44 has been shown to bind or be associated with the actin cytoskeleton through interactions with spectrin and members of the ERM (ezrin, -; radixm, and meosin) family (reviewed in Lesley et al., 1993; Bajorath, 2000, Proteins 39:103-
  • CD44 is associated with the non-receptor tyrosine kinase p56Lck (Taher et al., 1996, J. Biol Chem. 271:2863-2867. CD44 has been shown to be a co-stimulatory molecule with CD3/TCR engagement to activate T cells (reviewed in Aruffo, 1996, J. Clin.
  • CD44 is a ligand for the PDZ domain contained in MPPl, prIL-16 and MINT1. It is believed that the interactions of CD44 with PDZ domains, and between CD44 with MPPl, prIL-16 and MINT1 function in maintenance of leukocyte structure and in leukocyte signaling. Thus, when a 5 CD44-PDZ interaction is disrupted, CD44 will fail to transduce proper intracellular signals, and maintain proper distribution of CD44 on the surface, which will prevent adhesion of leukocytes to the endothelium during inflammation and tissue damage.
  • agonists/antagonists of this interaction will thus result in, but not limited to, reduced inflammatory responses during tissue ischemia and cell lysis (e.g., rhabdomyosis), vascular insufficiencies (e.g. frostbite), psoriasis, eczema, graft-versus-host disease, granuloma annulare, scleroderma.
  • CD97 binds the PDZ domains of DLGl and 41.8.
  • CD97 is a 79.7 kD seven-span transmembrane protein expressed on granulocytes and monocytes and at low levels on resting T cells and B cells.
  • T or B cell activation expression levels of CD97 in T cells and B cells increases rapidly (Eichler et al., 1994, Scand. J. Immunol 39, 111- 115; Pickl et al., 1995, Leukocyte Typing :l 151-1153).
  • CD97 When expressed on COS cells, CD97 confers adhesion to lymphocytes and to erythrocytes.
  • the interaction of CD97 with DLGl and the 41.8 kd protein can be altered to interfere with proper membrane distribution of CD97 and/or recycling of CD97. Such modulation will affect CD97 dependent adherence of cells with therapeutic benefit.
  • agonists and antagonists of CD97-PDZ protein interaction can be used to treat rheumatoid arthritis, osteoarthritis, Crohn's Disease, Ulcerative colitis, psoriasis.
  • Glycophorin C interacts with the PDZ domains of human DLG, PSD95, NeDLG, MMP2, AF6, 41.8, and MINT1 (with Mint-1 described previously).
  • Glycophorin C is an integral membrane protein expressed in erythroid cells, thymus, stomach, breast, adult and fetal liver, monocytes, T and B cells (Le Van Kim et al., 1989, J. Biol. Chem. 264:20407-20414) and is known for its role in human erythrocytes where it interacts with MPPl and protein 4.1 to regulate the shape, integrity and mechanical stability of red cells (Marfatia et al., 1997, J. Biol. Chem. 272:24191-24197; Reid et al., 1987,
  • MMP2, AF6, 41.8, and MINT1 are believed necessary for maintenance of the physical integrity of cells in which they are expressed. Modulation of GC-PDZ interactions will alter with the function of these and can be utilized to treat, but not limited to, polycythemia vera, spherocytosis.
  • CDwl28A IL8RA
  • CDW128A binds to the PDZ domains of DLGl and
  • IL-8 receptor There are two forms for the IL-8 receptor, IL-8RA (CDwl28A) and IL-8RB (CDwl28B) both of which are members of the G protein-coupled receptor superfamily and chemokine receptor branch of rhodopsin family.
  • CDwl28A and CDwl28B both bind IL-8 with the same affinity but only CDwl28B, binds three other IL-8-related CXC chemokines: melanoma growth-stimulating activity (GRO/MGS A), neutrophil-activating peptide 2 (NAP-2) and ENA-78. See, e.g., Ahuja, SK. And Murphy, PM. 1996. J Biol Chem 271:20545-50.
  • CDwl28A is expressed on all granulocytes, a subset of T cells, monocytes, endothelial cells, keratinocytes, erythrocytes, and melanoma cells.
  • IL-8 induces chemotaxis of neutrophils, basophils, and T lymphocytes and increases neutrophil and monocyte adhesion to endothelial cells.
  • the binding of IL-8 to IL8RA induces a transient increase in intracellular calcium levels, activation of phospholipase D, a respiratory burst of neutrophils and chemotaxis. This pro-inflammatory response is effective in normal immune responses.
  • Inhibitors of CDwl28A are useful for treatment of psoriasis, rheumatoid arthritis, polyarthritis, and for control of angiogenesis-dependent disorders such as melanomas and breast cancer.
  • CD3- ⁇ is a splice variant of CD3 zeta and a component of the CD3/TCR complex, which is required for antigen recognition, signal transduction and activation of T cells
  • CD3- ⁇ is a ligand for the PDZ domains of MINT1, 41.8 protein, DLGl, and PSD95.
  • the interactions of CD3- ⁇ with PDZ domains, and of CD3- ⁇ with MINT1, 41.8 protein, DLGl, and PSD95 are believed to be important activation of T cells, which is required for all cellular immune responses. Modulation of this interaction by agonists and antogonists can be used to treat, but is not limited to, acute and chronic allograft rejection, multiple sclerosis, graft- versus-host disease, rheumatoid arthritis.
  • LPAP is a transmembrane protein expressed on resting and activated T- and B- cells. LPAP has been shown to bind to CD45, a protein that is part of the T-cell receptor complex and has been found to co-localize with CD4, CD2 and Thy-1. LPAP has also been co- immune precipitated with p56(lck) and ZAP-70. The actual function of LPAP is unknown, but it has been suggested that it is an assembly molecule for the CD45 complex.
  • LPAP binds to DLG-1 and MINT-1.
  • DLG-1 and MINT-1 are both expressed in T-cells. It has also been shown that DLG-1 co-precipitates with p56(lck) in T-cells.
  • the assays described herein also demonstrated that DLG-1 binds to CD95 and KV1.3, and binding of MINT-1 to KV1.3. All of these molecules are involved in signaling by the TCR.
  • LPAP is believed to function in organizing the signaling by CD45 in T-cell activation, possibly by recruiting p56(lck) as a substrate for CD45. Blocking the function of CD45 has been shown to severely impair the T-cell response.
  • Inhibiting the interaction between LPAP and PDZ proteins is expected to alter the CD45 -mediated path from the rest of the immune response.
  • Agonists and antagonists of PL - PDZ binding can be used to treat, but is not limited to, rheumatoid arthritis, transplant rejection, multiple sclerosis, scleroderma, graft-versus-host disease.
  • CD46 Complement membrane cofactor protein (MCP)
  • CD46 is a membrane protein expressed on all nucleated cells, but not on erythrocytes. CD46 is a member of the regulator of complement activation protein family. Its primary function is the protection of cells from complement attack by inactivating membrane deposited C3b/C4b complement (Liszewski, et al., 1999, Adv. Immunol. 61:201-283). CD46 exists in more than 8 isoforms that are generated by differential splicing, with molecular weights ranging from 45 to 70 kD. In addition to the above function, CD46 also serves as the receptor for the measles virus and for other pathogenic microorganisms (e.g. Streptococcus pyogenes) (Manchester et al, 1994, Proc. Natl Acad. Sci. USA 91:2161; Okada et al., 1995,
  • Streptococcus pyogenes Manchester
  • CD46 also appears to be over-expressed on certain tumors (Jurianz et al., 1999, Mol Immunol 36:929-939) thus rendering tumor cells insensitive to the action of complement. See, Barclay et al, (1997) The Leucocyte antigen facts book,
  • CD46 binds DLGl, PSD95 and Ne-DLG. This interaction is believed to be necessary for proper membrane distribution of CD46 and/or recycling of CD46. Alteration of the CD46-PDZ interaction can reduce the ability of measles virus and other pathogens to enter cells, renders CD46-expressing tumors susceptible to attack by complement.
  • CD46-PDZ interaction agonists and antagonists are useful for the treatment of , but not limited to, cancers and viral infectious diseases.
  • CDwl28B binds to the PDZ domains of DLGl, NeDLG, PSD95, and 41.8 in the assays described supra.
  • IL-8 receptor IL- 8RA
  • IL-8RB CDwl28B
  • CDwl28A and CDwl28B both binds IL-8 with equal affinity but only CDwl28B, also binds three other IL-8-related CXC chemokines: melanoma growth-stimulating activity (GRO/MGSA), neutrophil-activating peptide 2 (NAP-2) and ENA-78. See, e.g., Ahuja, SK and Murphy, PM. 1996. J Biol Chem 271:20545-50.
  • CDwl28B is expressed on all granulocytes, a subset of T cells, monocytes, endothelial cells, keratinocytes, erythrocytes, and melanoma cells.
  • IL-8 induces chemotaxis of neutrophils, basophils, and T lymphocytes but diminished relative to IL8RA and increases neutrophil and monocyte adhesion to endothelial cells.
  • the binding of IL-8A to its receptor induces a transient increase in intracellular calcium levelsand granule release but does not induce activation of phospholipase D or a respiratory burst in neutrophils. This pro- inflammatory response is effective in normal immune responses.
  • Inhibitors of CDwl28B are useful for treatment of psoriasis, rheumatoid arthritis, polyarthritis, and for control of angiogenesis-dependent disorders such as melanomas and breast cancer.
  • the DOCK family are a group of morphogenetic transmembrane proteins that interacts with cytoskeleton to affect cell shape changes. Members of this new family include
  • Drosophila myoblast city mbc
  • DOCK180 DOCK2
  • DOCK3 DOCK3
  • CED5 KIAA0209
  • DOCK1 or DOCK180 is the human homolog of C. elegans gene, CED5 which is involved in the engulfment and phagacytosis by macrophages of apoptotic cells.
  • DOCK2 is found in peripheral blood lymphocytes and can convert a flatten cell into a rounded morphology upon transfection (Nagase, et. al. 1996. DNA Res 3:321-329,
  • DOCK2 is a PL and binds to PDZ proteins.
  • DOCK2 complexes with A,B,C to control cell shape in preparation for transit of lymphocytes for vascular circulation.
  • Modulation of DOCK2 by agonists and antagonists of its PDZ protein interaction can be used to treat, but is not limited to, acute leukemia, blast crisis, post-myocardial infarction inflammation, post-traumatic inflammation.
  • CD34 binds DLGl, PSD95, and NeDLG.
  • CD34 is expressed on a small subpopulation of bone marrow cells which includes hematopoietic stem cells. CD34 is also present on bone marrow stomal cells and on endothelial cells.
  • the selectins CD62L (L-selectin) and CD62E (E-selectin) bind CD34.
  • CD34 mediates attachment and rolling of leukocytes.
  • the hematopoietic stem cell properties of CD34 include myeloid differentiation of stem cells. Modulation of the CD34-PDZ interaction with agonists and/or antagonists can be used to treat, but is not limited to, myelodysplasia, leukemias, post-traumatic inflammation, post-myocardial infarction inflammation.
  • the high affinity receptor for human IgE is composed of an ⁇ , ⁇ , and disulfide-linked ⁇ homodimer.
  • the ⁇ -chain binds the Fc portion of IgE, whereas the ⁇ -chain serves to amplify signals that are transduced through the ⁇ -chain homodimer.
  • the Fc ⁇ R ⁇ l is a PDZ ligand and is a member of the CD20/ Fc ⁇ R ⁇ l receptor family. As is shown supra, Fc ⁇ R ⁇ l binds MINT 1.
  • Fc ⁇ RI on basophils and mast cells plays a central role in the initiation of allergic responses. Signaling through the Fc ⁇ RI begins by crosslinking of a multivalent allergen bound to IgE. The result is vesicular degranulation, release of histamine, leukotrienes and pro-inflammatory cytokines (IL-6 and TNF ⁇ ), factors responsible for the symptoms of immediate hypersensitivity.
  • IL-6 and TNF ⁇ pro-inflammatory cytokines
  • Alteration of signaling by targeting PL/PDZ interaction with agonists and antagonists can be used to treat, but is not limited to, asthma, atopic dermatitis, eczema, drug reaction, mastocytosis, urticaria, eosinophilia myalgia syndrome (Turner, H., et. al., 1999, Nature 402 SUPP:B24).
  • CD95 Fas/Apo-1
  • FasL Fas ligand
  • CD95 and Fas ligand are a receptor-ligand pair critically involved in lymphocyte homeostasis and peripheral tolerance. Binding of Fas by its ligand results in apoptotic cell death, an important major mechanism for safe clearance of unwanted cell during resolution of the acute inflammatory response. FasL is mainly restricted to activated T lymphocytes and is rapidly induced. Fas ligand is frequently up-regulated in breast cancer, as compared with normal breast epithelial cells and benign breast disease. As is shown supra, FasL binds the KIAA0561 PDZ domain.
  • the PDZ-PL modifiers are useful for treatment of, but not limited to, tumors, e.g., tumors unresponsive to conventional chemotherapy.
  • CDW125 binds PTN-4 and RGS12.
  • CDW125 is an IL-5 receptor expressed on eosinophils and basophils. IL5 promotes growth and differentiation of eosinophil precursors and actives mature eosinophils (Takatsu et al 1994, Adv. Immunol 57:145-190).
  • the secreted form of CDwl25 has antagonistic properties and is able to inhibit IL-5-induced eosinophil proliferation and differentiation. Modulation of CDW125 binding to PDZ domains may be used to treat, but is not limited to, asthma, atopic dermatitis, eczema, drug reaction, urticaria, mastocytosis, eosinophilia.
  • BLR-1 Burkitt's lymphoma receptor-1
  • BLR-1 is a transmembrane receptor detected primarily on B cells, and shown to be upregulated in stimulated T cells (Dobner et al., 1992, Eur J. Immunol. 22:2795-2799.;
  • BLR-1 functions in chemotaxis of B and T cells mto follicles of secondary lymphoid organs (e.g. spleen) for proper development and selection toward antigens (Forster et al., 1996, Cell 87:1037-1047.
  • Its ligand is B-lymphocyte chemoattractant (BLC), which is strongly expressed in the follicles of Peyer's patches, spleen and lymph nodes (Gunn et al, 1998, Nature 391 :799-803). Consistent with its chemotactic role is the demonstration that BLR-1 expression is downregulated in developed, activated B cells
  • BLR-1 binds to the PDZ domain containing protein MINTl .
  • MINTl protein containing protein
  • BLR-1 and MINTl the interaction between BLR-1 and MINTl, and BLR-1 and PDZ domains is necessary for the proper distribution and signaling of BLR-1 on the cell surface.
  • the chemotactic abilities of lymphoid cells expressing BLR-1 is similarly disrupted.
  • Such a disruption results in a reduced immune response, interference with the ability of lymphocytes to properly circulate and develop responses to antigen.
  • Agonists and antagonists of this interaction can be used to treat, but is not limited to, systemic lupus erythematosus, scleroderma and other autoimmune diseases.
  • CD4 is a co-receptor with the T cell receptor (TCR) involved in antigen recognition. Both CD4 and TCR belong to the immunoglobulin supergene family. T cell activation is enhanced by increasing the avidity of T cells for effector and target cells.
  • the cytoplasmic domain is involved in signal transduction and association with the tyrosine kinase p56 lck .
  • CD4 is expressed on most thymocytes, two-thirds of peripheral blood T lymphocytes, monocytes and macrophages.
  • HIN-1 Human immunodeficiency virus type-1 infects cells by membrane fusion mediated by its envelope glycoproteins (gpl20-gp41) and is triggered by the interaction of CD4 and a chemokine co-receptor, CCR5 or CXCR4.
  • Modulation of CD4-PDZ inhibitors with agonists and antagonists can be used to treat, but is not limited to, HIV infection 0 immediately after exposure to HIV, rheumatoid arthritis, multiple sclerosis, scleroderma, systemic lupus erythematosis, psoriasis.
  • the antagonists of the invention may be disrupted or inhibited by the administration of inhibitors or antagonists.
  • Inhibitors can be identified using screening assays described herein.
  • the motifs disclosed herein are used to design inhibitors.
  • the antagonists of the invention have a structure (e.g., peptide sequence) Q based on the C-terminal residues of PL-domain proteins listed in TABLE 2.
  • the antagonists of the invention have a structure (e.g., peptide sequence) based on a PL motif disclosed herein.
  • the PDZ/PL antagonists and antagonists of the invention may be any of a large variety of compounds, both naturally occurring and synthetic, organic and inorganic, and 5 including polymers (e.g., ohgopeptides, polypeptides, oligonucleotides, and polynucleotides), small molecules, antibodies, sugars, fatty acids, nucleotides and nucleotide analogs, analogs of naturally occurring structures (e.g., peptide mimetics, nucleic acid analogs, and the like), and numerous other compounds.
  • polymers e.g., ohgopeptides, polypeptides, oligonucleotides, and polynucleotides
  • small molecules antibodies, sugars, fatty acids, nucleotides and nucleotide analogs, analogs of naturally occurring structures (e.g., peptide mimetics, nucleic acid analogs, and the like), and numerous other compounds.
  • PDZ-PL interaction agonists can
  • the peptides and peptide mimetics or analogues of the invention contain an amino acid sequence that binds a PDZ domain in hematopoietic cells such as T cells and B cells, or otherwise inhibits the association of PL proteins and PDZ proteins.
  • the antagonists comprise a peptide that has a sequence corresponding to the carboxy-terminal sequence of a PL protein listed in TABLE 2, e.g., a peptide listed TABLE 4.
  • the peptide comprises at least the C-terminal four (4) residues of the PL protein, and often the inhibitory peptide comprises more than four residues (e.g., at least five, six, seven, eight, nine, ten, twelve or fifteen residues) from the PL protein C-terminus.
  • the C-terminal domains of specific surface receptors expressed by hematopoietic system and endothelial cells may themselves be used as inhibitors, and may be used as the basis for rational design of non-peptide inhibitors. See Section 6.6, infra.
  • the antagonist is a fusion protein comprising such a sequence.
  • Fusion proteins containing a transmembrane transporter amino acid sequence are 0 particularly useful. See, e.g. Section 6.5.2, infra.
  • the inhibitor is conserved variant of the PL C-terminal protein sequence having inhibitory activity. See, e.g. Section 6.5.3, infra.
  • the antagonist is a peptide mimetic of a PL C-terminal sequence. See, e.g. Section 6.5.4, infra. « J
  • the inhibitor is a small molecule (i.e., having a molecular weight less than 1 kD). See, e.g. Section 6.5.5, infra.
  • the antagonists comprise a peptide that has a sequence of 0 a PL protein carboxy-terminus listed in TABLE 2.
  • the peptide comprises at least the C- terminal two (2) residues of the PL protein, and typically, the inhibitory peptide comprises more than two residues (e.g, at least three, four, five, six, seven, eight, nine, ten, twelve or fifteen residues) from the PL protein C-terminus. Most often, the residues shared by the inhibitory peptide with the PL protein are found at the C-terminus of the peptide. However, 5 in some embodiments, the sequence is internal. Similarly, in some cases, the inhibitory peptide comprises residues from a PL sequence that is near, but not at the c-terminus of a PL protein
  • the "core PDZ motif sequence" of a hematopoietic cell surface receptor at its C-terminus contains the last four amino acids, this sequence may be used to target PDZ domains in hematopoietic cells.
  • the four amino acid core of a PDZ motif sequence may contain additional amino acids at its amino terminus to further increase its binding affinity and/or stability.
  • the PDZ motif sequence peptide can be from four amino acids up to 15 amino acids. It is preferred that the length of the sequence to be 6-10 amino acids. More preferably, the PDZ motif sequence contains 8 amino acids.
  • Additional amino acids at the amino terminal end of the core sequence may be derived from the natural sequence in each hematopoietic cell surface receptor or a synthetic linker. The additional amino acids may also be conservatively substituted.
  • the third residue from the C-terminus is S, T or
  • this residue may be phosphorylated prior to the use of the peptide.
  • the peptide and nonpeptide inhibitors of the are small, e.g., fewer than ten amino acid residues in length if a peptide.
  • a limited number of ligand amino acids directly contact the PDZ domain (generally less than eight) (Kozlov et al., 2000, Biochemistry 39, 2572; Doyle et al., 1996, Cell 85, 1067) and that peptides as short as the C-terminal three amino acids often retain similar binding properties to longer (> 15) amino acids peptides (Yanagisawa et al., 1997, J. Biol. Chem. 272, 8539).
  • FIGURES 3A-H show the use of peptides to inhibit PL-PDZ interactions using the G assay described supra.
  • the inhibiton assays were carried out using GST fusion proteins containing PDZ domains from DLGl or PSD95 (see supra and TABLE 3). Binding of biotinylated PL peptides for Clasp 2, CD46, Fas, or KV1.3 (as listed in TABLE 4) was determined in the presence of various competitor peptides (at a concentration of 100 uM) or in the absence of a competitor (equalized as 100%> binding).
  • the competitor peptides were 8-mers peptides having the sequence of C-terminus of Clasp 2 (MTSSSSVV),
  • CD46 (REVKFTSL), or Fas (RNEIQSLV), a unlabeled 19-mer having the sequence of c- terminus of KV1.3 (i.e., non-biotinylated AA33L as listed in TABLE 3), or a peptide having the sequence of residues 64-76 of hemoglobin (Vidal et al., 1999, J. Immunol. 163, 4811), i.e., an unrelated competitor.
  • biotinylated peptide (10 uM for Fas and KV1.3, 20 uM for Clasp 2 and CD46) was subtracted from the binding to the fusion proteins to obtain the net signal for each experimental condition.
  • FIGURES 3C-F show similar assays using shorter peptides to inhibit (e.g., a 3-mer and a 5-mer).
  • Figures 3C-E show binding of biotinylated PL peptides for Clasp 2, CD46, Fas, or KVl.3, at the indicated concentration (as listed in TABLE 3) to GST fusion proteins containing PDZ domains from NeDLG, DLGl, or PSD95 in the absence or presence of 1 mM 3-mer peptide having the sequence of the C-terminus of Clasp 2 (SVV).
  • FIGURE 3F shows the effect on binding of a 5-mer CD49E peptide (ATSDA) to GST fusion proteins containing a PDZ domain from 41.8Kd
  • the variants have the same or a different ability to bind a PDZ domain as the parent peptide.
  • amino acid substitutions are conservative, i.e., the amino acid residues are replaced with other amino acid residues having physical and/or chemical properties similar to the residues they are replacing.
  • conservative amino acid substitutions are those wherein an amino acid is replaced with another amino acid encompassed within the same designated class.
  • peptide mimetics can be prepared using routine methods, and the inhibitory activity of the mimetics can be confirmed using the assays of the invention.
  • the antagonist is a peptide mimetic of a PL C-terminal sequence.
  • individual synthetic residues and polypeptides incorporating mimetics can be synthesized using a variety of procedures and methodologies, which are well described in the scientific and patent literature, e.g., Organic Syntheses Collective Volumes,
  • Mimetics of the invention can also be synthesized using combinatorial methodologies.
  • Various techniques for generation of peptide and peptidomimetic libraries are well known, and include, e.g., multipin, tea bag, and split-couple-mix techniques; see, e.g., al-Obeidi (1998) Mol. Biotechnol. 9:205-223; Hruby (1997) Curr. Opin. Chem. Biol. 1 :114-119; Ostergaard (1997) Mol. Divers. 3:17-27; Ostresh (1996) Methods Enzymol. 267:220-234.
  • the inhibitor is a small molecule (i.e., having a molecular weight less than 1 kD). Methods for screening small molecules are well known in the art and include those described supra at Section 6.4.
  • the following sections describe specific surface receptors expressed by different cell types in the hematopoietic and immune response system.
  • the C-termini of these receptors are used as inhibitors, or serve as the basis for designing PDZ motif sequence peptides, variants, fusion proteins, peptidomimetics, and small molecules for use in inhibiting PDZ-PL interactions.
  • the peptides are tested in an assay of the invention for inhibitory or modulatory activity (also see, TABLE 4, and discussion supra).
  • a number of surface receptors expressed by T cells contain a PDZ motif sequence (PL sequence). These molecules include CD3 ⁇ , CD4, CD6, CD38, CD49e, CD49f,
  • DNAM-1 DNAM-1, Fas ligand (FasL) and LPAP (Barclay et al, 1997, The Leucocyte Antigen Facts
  • the C-terminal core sequence of CD3 is SSQL (SEQ ID NO:4).
  • SSSQL SEQ ID NO:5
  • SSSSQL SEQ ID NO:5
  • SEQ ID NO:6 PSSSSQL (SEQ ID NO:7), and PPSSSSQL (SEQ ID NO:8) may also be used to target a PDZ domain-containing protein in T cells.
  • the C-terminal core sequence of CD4 is CSPI (SEQ ID NO:9).
  • TCSPI SEQ ID NO: 10
  • KTCSPI SEQ ID NO:l l
  • QKTCSPI SEQ ID NO:12
  • FQKTCSPI FQKTCSPI
  • the C-terminal core sequence of CD6 is ISAA (SEQ ID NO: 14).
  • DISAA SEQ ID NO: 15
  • DDISAA SEQ ID NO: 16
  • YDDISAA SEQ ID NO: 17
  • DYDDISAA SEQ ID NO: 18
  • the C-terminal core sequence of CD38 is TSEI (SEQ ID NO: 19).
  • CTSEI SEQ ID NO:20
  • SCTSEI SEQ ID NO:21
  • SSCTSEI SEQ ID NO:22
  • DSSCTSEI SEQ ID NO:23
  • TSDA SEQ ID NO:24
  • ATSDA SEQ ID NO:25
  • PATSDA SEQ ID NO:26
  • PP ATSDA SEQ ID NO:27
  • KPP ATSDA SEQ ID NO:28
  • the C-terminal core sequence of CD49f is TSDA (SEQ ID NO:29).
  • TSDA SEQ ID NO:29
  • LTSDA SEQ ID NO:30
  • RLTSDA SEQ ID NO:31
  • ERLTSDA SEQ ID NO:32
  • KERLTSDA SEQ ID NO:33
  • the C-terminal core sequence of CD53 is TIGL (SEQ ID NO: 34).
  • QTIGL SEQ ID NO:35
  • SQTIGL SEQ ID NO:36
  • TSQTIGL SEQ ID NO:37
  • KTSQTIGL SEQ ID NO:38
  • the C-terminal core sequence of CD83 is TELV (SEQ. ID. NO:-248).
  • KTELV SEQ. ID. NO: 249
  • HKTELV SEQ. ID. NO: 250
  • PHKTELV SEQ. ID. NO: 251
  • TPHKTELV SEQ. ID. NO: 252
  • the C-terminal core sequence of CD90 is FMSL (SEQ ID NO:39).
  • DFMSL SEQ ID NO:40
  • TDFMSL SEQ ID NO:41
  • ATDFMSL SEQ ID NO:42
  • QATDFMSL SEQ ID NO:43
  • the C-terminal core sequence of CD95 is QSLV (SEQ ID NO:44).
  • IQSLV (SEQ ID NO:45), EIQSLV (SEQ ID NO:46), NEIQSLV (SEQ ID NO:47), and RNEIQSLV (SEQ ID NO:48) may also be used to target a PDZ domain-containing protein in T cells.
  • the C-terminal core sequence of CD97 is ESGI (SEQ ID NO:49).
  • SESGI SEQ ID NO:50
  • ASESGI SEQ ID NO:51
  • RASESGI SEQ ID NO:52
  • LRASESGI SEQ ID NO:53
  • PYAA SEQ ID NO:54
  • FPYAA SEQ ID NO:55
  • RFPYAA SEQ ID NO:56
  • LRFPYAA SEQ ID NO:57
  • LLRFPYAA SEQ ID NO:58
  • the C-terminal core sequence of CDwl37 is GCEL (SEQ ID NO:59).
  • GGCEL SEQ ID NO:60
  • EGGCEL SEQ ID NO:61
  • EEGGCEL SEQ ID NO:62
  • EEEGGCEL SEQ ID NO:63
  • the C-terminal core sequence of CD 166 is KTEA (SEQ ID NO:64).
  • KTEA SEQ ID NO:64
  • HKTEA SEQ ID NO:65
  • NHKTEA SEQ ID NO:66
  • NNHKTEA SEQ ID NO:67
  • ENNHKTEA SEQ ID NO:68
  • the C-terminal core sequence of CDwl28 is SSNL (SEQ ID NO:69).
  • VSSNL SEQ ID NO:70
  • NVSSNL SEQ ID NO:71
  • VNVSSNL SEQ ID NO:72
  • SVNVSSNL SEQ ID NO:73
  • the C-terminal core sequence of DNAM-1 is KTRV (SEQ ID NO:74).
  • PKTRV SEQ ID NO:75
  • RPKTRV SEQ ID NO:76
  • RRPKTRV SEQ ID NO:77
  • SRRPKTRV SEQ ID NO:78
  • the C-terminal core sequence of FasL is LYKL (SEQ ID NO:79).
  • GLYKL SEQ ID NO:80
  • FGLYKL SEQ ID NO:81
  • FFGLYKL SEQ ID NO:82
  • TFFGLYKL SEQ ID NO:83
  • the C-terminal core sequence of LPAP is VTAL (SEQ ID NO:84).
  • VTAL SEQ ID NO:84
  • HVTAL SEQ ID NO:85
  • LHVTAL SEQ ID NO:86
  • GLHVTAL SEQ ID NO:87
  • QGLHVTAL SEQ ID NO:88
  • the C-terminal core sequence of CLASP-1 is SAQV (SEQ. ID. NO: 218).
  • SSAQV SEQ. ID. NO: 219
  • SSSAQV SEQ. ID. NO: 220
  • ISSSAQV SEQ. ID. NO: 221
  • SISSSAQV SEQ. ID. NO: 222
  • the C-terminal core sequence of CLASP-2 is SSVV (SEQ. ID. NO: 223).
  • SSSVV SEQ. ID. NO: 224
  • SSSSVV SEQ. ID. NO: 225
  • TSSSSW SEQ. ID. NO: 226
  • MTSSSSW MTSSSSW
  • the C-terminal core sequence of CLASP-4 is YAEV (SEQ. ID. NO: 228).
  • RYAEV SEQ. ID. NO: 229)
  • PRYAEV SEQ. ID. NO: 230
  • SPRYAEV SEQ. ID. NO: 231
  • GSPRYAEV SEQ. ID. NO: 232
  • FTDV SEQ. ID. NO: 238
  • IFTDV SEQ. ID. NO: 239
  • KTFTDV SEQ. ID. NO: 240
  • KKIFTDV SEQ. ID. NO: 241
  • KKIFTDV SEQ. ID. NO: 242
  • the C-terminal core sequence of DOCK2 is STDL (SEQ. ID. NO: 243).
  • LSTDL SEQ. ID. NO: 244
  • SLSTDL SEQ. ID. NO: 245
  • DSLSTDL SEQ. ID. NO: 246
  • PDSLSTDL SEQ. ID. NO: 247
  • a number of surface receptors expressed by B cells contain a PDZ domain motif sequence. These molecules include, but are not limited to, CD38, CD53, CD95, CD97, CD98, CDwl37, CD138, CDwl25 (IL5R), DNAM-1, LPAP, Syndecan-2 (Barclay et al., 1997, The Leucocyte Antigen Facts Book, second edition, Academic Press) and BLR-1.
  • the specific motif sequences of CD38, CD53, CD83, CD95, CD97, CD98, CDwl37, DNAM-1, DOCK2, LPAP, CLASP-1, CLASP-2 and CLASP-4 have been described in the preceding paragraphs.
  • the C-terminal core sequence of CD138 is EFYA (SEQ ID NO:89).
  • EEFYA SEQ ID NO:90
  • QEEFYA SEQ ID NO:91
  • KQEEFYA SEQ ID NO:92
  • TKQEEFYA SEQ ID NO:93
  • the C-terminal core sequence of CDwl25 is DSVF (SEQ ID NO:94).
  • EDSVF SEQ ID NO:95
  • LEDSVF SEQ ID NO:96
  • TLEDSVF SEQ ID NO:97
  • ETLEDSVF SEQ ID NO:98
  • the C-terminal core sequence of Syndecan-2 is EFYA (SEQ. ID. NO: 258).
  • KEFYA SEQ. ID. NO: 259
  • TKEFYA SEQ. ID. NO: 260
  • PTKEFYA SEQ. ID. NO: 261
  • APTKEFYA SEQ. ID. NO: 262
  • the C-terminal core sequence of BLR-1 is LTTF (SEQ. ID. NO: 253).
  • SLTTF SEQ. ID. NO: 254
  • TSLTTF SEQ. ID. NO: 255
  • ATSLTTF SEQ. ID. NO: 256
  • NATSLTTF SEQ. ID. NO: 257
  • PDZ motif sequences of Natural Killer Cell Surface Receptors A number of surface receptors expressed by NK cells contain a PDZ domain motif sequence. These molecules include, but are not limited to CD38, CD56, CD98 and DNAM-1. The specific motif sequences of CD38, CD98 and DNAM-1 have been described in the preceding paragraphs.
  • the C-terminal core sequence of CD56 is ESKA (SEQ ID NO:99).
  • NESKA SEQ ID NO: 100
  • ENESKA SEQ ID NO.101
  • KENESKA SEQ ID NO: 102
  • TKENESKA SEQ ID NO: 103
  • PDZ domain motif sequence contains, but are not limited to CD38, CD44, CD46, CD49e, CD49f, CD53, CD61, CD95,
  • the specific motif sequences of CD38, CD49e, CD49f, CD53, CD95, CD97, CD98, CDwl28, CDwl37, DNAM- 1, Galectin 3 (Mac-2) and Mannose receptor have been described in the preceding paragraphs.
  • the C-terminal core sequence of CD44 is KIGV (SEQ ID NO: 104).
  • MKIGV SEQ ID NO: 105
  • DMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO: 106), VDMKIGV (SEQ ID NO: 107) and NVDMKIGV (SEQ ID NO:
  • FTSL SEQ ID NO: 109
  • KFTSL SEQ ID NO: 110
  • VKFTSL SEQ ID NO: 111
  • EVKFTSL SEQ ID NO: 112
  • REVKFTSL SEQ ID NO: 113
  • the C-terminal core sequence of CD61 is KSLV (SEQ ID NO:114).
  • LKSLV SEQ ID NO: 115
  • FLKSLV SEQ ID NO:116
  • RFLKSLV SEQ ID NO:117
  • GRFLKSLV SEQ ID NO: 118
  • GYIA GYIA (SEQ ID NO: 119).
  • NGYIA (SEQ ID NO: 120), TNGYIA (SEQ ID NO:121), KTNGYIA (SEQ ID NO:122) and GKTNGYIA (SEQ ID NO: 123) may also be used to target a PDZ domain-containing protein in monocytes.
  • the C-terminal core sequence of Ly-6 is QTLL (SEQ ID NO: 124).
  • LQTLL SEQ ID NO: 125
  • LLQTLL SEQ ID NO.126
  • VLLQTLL SEQ ID NO:127
  • SVLLQTLL SEQ ID NO: 1228
  • the C-terminal core sequence of Fc ⁇ RI ⁇ is PIDL (SEQ ID NO: 129).
  • PPIDL SEQ ID NO: 130
  • SPPIDL SEQ ID NO:131
  • MSPPIDL SEQ ID NO:132
  • EMSPPIDL SEQ ID NO:133
  • the C-terminal core sequence of Galectin 3 is YTMI (SEQ ID NO:134).
  • SYTMI SEQ ID NO: 135)
  • ASYTMI SEQ ID NO.136
  • SASYTMI SEQ ID NO:137
  • TSASYTMI SEQ ID NO:138
  • the C-terminal core sequence of mannose receptor is HSVI (SEQ ID NO:139).
  • EHSVI SEQ ID NO: 140
  • NEHSVI SEQ ID NO.141
  • QNEHSVI SEQ ID NO:142
  • EQNEHSVI SEQ ID NO:143
  • a number of surface receptors expressed by granulocytes contain a PDZ domain motif sequence. These molecules include, but are not limited to CD53, CD95, CD97, CD98, CD148, CDwl25, CDwl28, Fc ⁇ RI ⁇ and G-CSFR. The specific motif sequences of most of these molecules have been described in the preceding paragraphs.
  • the C-terminal core sequence of G-CSFR is TSVL (SEQ ID NO.144).
  • ITSVL SEQ ID NO: 145
  • PITSVL SEQ ID NO:146
  • FPITSVL SEQ ID NO:147
  • LFPITSVL SEQ ID NO:148
  • endothelial cells While endothelial cells are not hematopoietic cells, they closely interact with the hematopoietic system as they form the lining of blood vessels. As such, endothelial cells come in contact with the cells of the hematopoietic system. Thus, the ability to regulate endothelial cell function provides for indirect regulation of hematopoietic cells.
  • a number of surface receptors expressed by endothelial cells contain a PDZ domain motif sequence. These molecules include, but are not limited to CD34, CD46, CD66b, CD66c, CD105, CD106, CD62e (E-selectin) and VCAM1.
  • the C-terminal core sequence of CD34 is DTEL (SEQ ID NO: 149).
  • ADTEL SEQ ID NO: 150
  • VADTEL SEQ ID NO.151
  • VV ADTEL SEQ ID NO:152
  • HVV ADTEL SEQ ID NO: 153
  • the C-terminal core sequence of CD66b and CD66c is VALI (SEQ ID NO: 154).
  • RVALI SEQ ID NO:155
  • ARVALI SEQ ID NO.156
  • LARVALI SEQ ID NO:157
  • VLARVALI SEQ ID NO: 158
  • the C-terminal core sequence of CD 105 is SSMA (SEQ ID NO: 159).
  • TSSMA SEQ ID NO: 160
  • STSSMA SEQ ID NO: 161
  • CSTSSMA SEQ ID NO: 162
  • PCSTSSMA SEQ ID NO: 162
  • KSKV SEQ ID NO:163
  • QKSKV (SEQ ID NO: 164), AQKSKV (SEQ ID NO: 165), EAQKSKV (SEQ ID NO: 166) and VEAQKSKV (SEQ ID NO: 167) may also be used to target a PDZ domain-containing protein in endothelial cells.
  • the C-terminal core sequence of CD62e is SYIL (SEQ ID NO.168).
  • PSYIL SEQ ID NO: 169
  • KPSYIL SEQ ID NO: 170
  • QKPSYIL SEQ ID NO:171
  • YQKPSYIL SEQ ID NO:172
  • the C-terminal core sequence of VCAM1 is KSKV (SEQ. ID. NO: 233).
  • QKSKV SEQ. ID. NO: 234
  • AQKSKV SEQ. ID. NO: 235
  • EAQKSKV SEQ. ID. NO: 236
  • VEAQKSKV SEQ. ID. NO: 237
  • Fc ⁇ RI ⁇ , CDwl25, CDwl28 and IL-8RB are transmembrane receptors expressed by mast cells, basophils and eosinophils. These receptors play a role in the activation of these cells to result in degranulation and histamine release in allergic reactions.
  • the C-terminal core sequence of Fc ⁇ RI ⁇ is PIDL (SEQ ID NO:4).
  • PPIDL SEQ ID NO:5
  • SPPIDL SEQ ID NO:6
  • MSPPIDL SEQ ID NO: 7
  • EMSPPIDL SEQ ID NO: 8
  • the residue E may be substituted with G to increase its binding affinity.
  • the C-terminal core sequence of CDwl25 is DSVF (SEQ ID NO: 9).
  • EDSVF SEQ ID NO: 10
  • LEDSVF SEQ ID NO:l 1
  • TLEDSVF SEQ ID NO: 12
  • ETLEDSVF SEQ ID NO:13
  • the C-terminal core sequence of CDwl28 is SSNL (SEQ ID NO: 14).
  • VSSNL SEQ ID NO: 15
  • NVSSNL SEQ ID NO: 16
  • VNVSSNL SEQ ID NO: 17
  • SVNVSSNL SEQ ID NO: 18
  • the C-terminal core sequence of IL-8RB is STTL (SEQ ID NO: 19).
  • TSTTL SEQ ID NO:20
  • HTSTTL SEQ ID NO:21
  • GHTSTTL SEQ ID NO:22
  • SGHTSTTL SEQ ID NO:23
  • the C-terminal core sequence of NMD A is ESDV (SEQ. ID. NO: 263).
  • IESDV SEQ. ID. NO: 264
  • SIESDV SEQ. ID. NO: 265
  • PSIESDV SEQ. ID. NO: 266
  • MPSIESDV SEQ. ID. NO: 267
  • EYYV EYYV
  • KEYYV SEQ. ID. NO: 269
  • DKEYYV SEQ. ID. NO: 270
  • KDKEYYV SEQ. ID. NO: 271
  • NKDKEYYV SEQ. ID. NO: 272
  • EYFI EYFI
  • KEYFI SEQ. ID. NO: 274
  • RKEYFI SEQ. ID. NO: 275
  • SRKEYFI SEQ. ID. NO: 276
  • SSRKEYFI SEQ. ID. NO: 277
  • the C-terminal core sequence of CD148 is KTIA (SEQ. ID. NO: 278).
  • GKTIA SEQ. ID. NO: 279
  • FGKTIA SEQ. ID. NO: 280
  • TFGKTIA SEQ. ID. NO: 281
  • TTFGKTIA SEQ. ID. NO: 282
  • the peptides of the invention or analogues thereof may be prepared using virtually any art-known technique for the preparation of peptides and peptide analogues.
  • the peptides may be prepared in linear form using conventional solution or solid phase peptide syntheses and cleaved from the resin followed by purification procedures
  • composition of the synthetic peptides may be confirmed by amino acid analysis or
  • sequencing e.g., the Edman degradation procedure and mass spectroscopy.
  • analogues and derivatives of the peptides can be chemically synthesized.
  • the linkage between each amino acid of the peptides of the invention may be an amide, a substituted amide or an isostere of amide.
  • ⁇ onclassical amino acids or chemical amino acid analogues can be introduced as a substitution or addition into the sequence.
  • ⁇ on- 0 classical amino acids include, but are not limited to, the D-isomers of the common amino acids, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ -Ahx,
  • the amino acid can be D (dextrorotary) or L
  • the peptide or the relevant portion may also be synthesized using conventional recombinant genetic engineering techniques.
  • a polynucleotide sequence encoding a linear form of the peptide is inserted into an appropriate 5 expression vehicle, i. e. , a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence, or in the case of an R ⁇ A viral vector, the necessary elements for replication and translation.
  • the expression vehicle is then transfected into a suitable target cell which will express the peptide.
  • the expressed peptide is then isolated by procedures well-established in the art.
  • host-expression vector systems may be utilized to express the peptides described herein. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage DNA or plasmid DNA expression vectors containing an appropriate coding sequence; yeast or filamentous fungi transformed with recombinant yeast or fungi expression vectors containing an appropriate coding sequence; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing an appropriate coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus or tobacco mosaic virus) or transformed with recombinant plasmid expression vectors (e.g. , Ti plasmid) containing an appropriate coding sequence; or animal cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage DNA or plasmid DNA expression vectors containing an appropriate coding sequence; yeast or filamentous fungi transformed with re
  • the expression elements of the expression systems vary in their strength and specificities.
  • any of a number of suitable transcription and translation elements may be used in the expression vector.
  • inducible promoters such as pL of bacteriophage ⁇ , plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used;
  • promoters such as the baculovirus polyhedron promoter may be used;
  • promoters derived from the genome of plant cells e.g., heat shock promoters; the promoter for the small subunit of
  • RUBISCO the promoter for the chlorophyll a/b binding protein
  • plant viruses e.g., the 35S RNA promoter of CaMV; the coat protein promoter of TMV
  • metallothionein promoter e.g., metallothionein promoter
  • mammalian viruses e.g., the adeno virus late promoter; the vaccinia virus 7.5 K promoter
  • SV40-, BPV- and EBV-based vectors may be used with an appropriate selectable marker.
  • sequences encoding the peptides of the invention may be driven by any of a number of promoters.
  • viral promoters such as the 35S RNA and 19S RNA promoters of CaMV (Brisson et al, 1984, Nature 310:511-514), or the coat protein promoter ofTMV (Takamatsu et --/., 1987, EMBO J. 3:1311) may be used; alternatively, plant promoters such as the small subunit of RUBISCO (Coruzzi et al, 1984, EMBO J.
  • Autographa californica nuclear polyhidrosis virus (AcNPV) is used as a vector to express the foreign genes.
  • the virus grows in Spodoptera frugiperda cells.
  • a coding sequence may be cloned into non-essential regions (for example the polyhedron gene) of the virus and placed under control of an AcNPV promoter (for example, the polyhedron promoter).
  • AcNPV promoter for example, the polyhedron promoter.
  • Successful insertion of a coding sequence will result in inactivation of the polyhedron gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedron gene).
  • These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed, (e.g., see Smith et al, 1983, J. Virol.
  • a number of viral based expression systems may be utilized.
  • a coding sequence may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and 30 tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome
  • the vaccinia 7.5 K promoter may be used, (see, e.g., Mackett et al, 1982, Proc. Natl. Acad. Sci. USA 79:7415-7419; Mackett et al, 1984, J. Virol. 49:857-864;
  • the peptides and peptide analogues of the invention can be purified by art- known techniques such as high performance liquid chromatography, ion exchange 10 chromatography, gel electrophoresis, affinity chromatography and the like.
  • the actual conditions used to purify a particular peptide or analogue will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity, etc., and will be apparent to those having skill in the art.
  • the purified peptides can be identified by assays based on their physical or functional properties, including radioactive labeling followed by gel electrophoresis, ⁇ radioimmuno-assays, ELISA, bioassays, and the like.
  • any antibody which specifically binds the peptides or peptide analogues may be used.
  • various host animals including but not limited to rabbits, mice, rats, etc., may be immunized by injection with a peptide.
  • the peptide may be attached to a suitable carrier, such as BSA or KLH, by 20 means of a side chain functional group or linkers attached to a side chain functional group.
  • adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols,
  • polyanions 25 polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacilli Calmette-Guerin) and Corynebacterium parvum.
  • BCG Bacilli Calmette-Guerin
  • Corynebacterium parvum 25 polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacilli Calmette-Guerin) and Corynebacterium parvum.
  • Monoclonal antibodies to a peptide may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include but are not limited to the hybridoma technique originally described by Koehler and
  • Antibody fragments which contain deletions of specific binding sites may be generated by known techniques.
  • such fragments include but are not limited to F(ab') 2 fragments, which can be produced by pepsin digestion of the antibody molecule and Fab fragments, which can be generated by reducing the disulfide bridges of the F(ab') 2 fragments.
  • Fab expression libraries may be constructed (Huse et al, 1989, Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for the peptide of interest.
  • the antibody or antibody fragment specific for the desired peptide can be attached, for example, to agarose, and the antibody-agarose complex is used in immunochromatography to purify peptides of the invention. See, Scopes, 1984, Protein Purification: Principles and Practice, Springer- Verlag New York, Inc., NY, Livingstone, 1974, Methods Enzymology: Immunoaffmity Chromatography of Proteins 34:723-731.
  • the PDZ domain binding and PDZ-PL inhibitory compounds of the present invention are useful in regulating diverse activities of hematopoietic cells (e.g., T cells and B cells) and other cells. involved in the immune response.
  • the compounds of the invention are used to inhibit leukocyte activation, which is manifested in measurable events including but not limited to, cytokine production, cell adhesion, expansion of cell numbers, apoptosis and cytotoxicity.
  • the compounds of the invention may be used to treat diverse conditions associated with undesirable leukocyte activation, including but not limited to, acute and chronic inflammation, graft-versus-host disease, transplantation rejection, hypersensitivities and autoimmunity such as multiple sclerosis, rheumatoid arthritis, peridontal disease, systemic lupus erythematosis, juvenile diabetes mellitis, non-insulin-dependent diabetes, and allergies, and other conditions listed herein (see, e.g., Section 6.4, supra).
  • the invention also relates to methods of using such compositions in modulating leukocyte activation as measured by, for example, cytotoxicity, cytokine production, cell proliferation, and apoptosis.
  • Assays for activation are well known.
  • PDZ/PL interaction antagonists can be evaluated in the following: (1) cytotoxic T lymphocytes can be incubated with radioactively labeled target cells and the antigen-specific lysis of these target cells detected by the release of radioactivity, (2) helper T lymphocytes can be incubated with antigens and antigen presenting cells and the synthesis and secretion of cytokines measured by standard methods (Windhagen A; et al., 1995, Immunity 2(4): 373-80),
  • antigen presenting cells can be incubated with whole protein antigen and the presentation of that antigen on MHC detected by either T lymphocyte activation assays or biophysical methods (Harding et al., 1989, Proc. Natl. Acad. Sci., 86: 4230-4), (4) mast cells can be incubated with reagents that cross-link their Fc-epsilon receptors and histamine release measured by enzyme immunoassay (Siraganian, et al., 1983, TIPS 4: 432-437).
  • the effect of PDZ/PL interaction antagonists on products of leukocyte activation in either a model organism (e.g., mouse) or a human patient can also be evaluated by various methods that are well known.
  • a model organism e.g., mouse
  • the production of antibodies in response to vaccination can be readily detected by standard methods currently used in clinical laboratories, e.g., an ELISA;
  • the migration of immune cells to sites of inflammation can be detected by scratching the surface of skin and placing a sterile container to capture the migrating cells over scratch site (Peters et al, 1988, Blood 72: 1310-5);
  • the proliferation of peripheral blood mononuclear cells in response to mitogens or mixed lymphocyte reaction can be measured using 3 H-thymidine;
  • the phagocytic capacity of granulocytes, macrophages, and other phagocytes in PBMCs can be measured by placing PMBCs in wells together with labeled particles (Peters et al., 1988); and
  • human peripheral blood mononuclear cells PBMC
  • human T cell clones e.g., Jurkat E6, ATCC TIB-152
  • EBV-transformed B cell clones e.g.,
  • PDZ/PL interaction antagonists in vitro. Inhibition of activation of these cells or cell lines can be used for the evaluation of potential PDZ/PL interaction antagonists.
  • Standard methods by which hematopoietic cells are stimulated to undergo activation characteristic of an immune response are, for example: A) Antigen specific stimulation of immune responses. Either pre-immunized or na ⁇ ve mouse splenocytes can be generated by standard procedures. In addition, antigen- specific T cell clones and hybridomas (e.g., MBP-specific), and numerous B cell lymphoma cell lines (e.g., CH27), have been previously characterized and are available for the assays discussed below. Antigen specific splenocytes or B-cells can be mixed with antigen specific T-cells in the presence of antigen to generate an immune response. This can be performed in the presence or absence of PDZ/PL interaction antagonists to assay whether PDZ/PL interaction antagonists modulate the immune response infra.
  • TCR cross-linking T cell receptor
  • receptor activation molecules e.g., TCR, CD3, or CD2
  • co-stimulator molecules for example anti-CD28
  • activation molecules e.g., TCR, CD3, or CD2
  • co-stimulator molecules for example anti-CD28
  • PHA phytohemagglutinin
  • pharmacological agents that activate protein kinase C e.g., phorbol esters
  • increase cytoplasmic Ca 2+ e.g., ionomycin
  • Non-specific B cell activation 1) application of antibodies against cell surface molecules such as IgM, CD20, or CD21. 2) Lipopolysaccharide (LPS), phorbol esters, calcium ionophores and ionomycin can also be used to by-pass receptor triggering.
  • LPS Lipopolysaccharide
  • phorbol esters phorbol esters
  • calcium ionophores ionomycin
  • ionomycin can also be used to by-pass receptor triggering.
  • MLR Mixed lymphocyte reaction
  • PBMC to activate lymphocytes by presentation of mismatched tissue antigens, which occurs in all cases except identical twins.
  • a standard approach is to generate tetanus toxin-specific T cells from a donor that has recently been boosted with tetanus toxin.
  • Major histocompatability complex- (MHC-) matched antigen presenting cells and a source of tetanus toxin are used to maintain antigen specificity of the cell line or T cell clone (Lanzavecchia, A., et al, 1983, Eur. J. Immun. 13: 733-738).
  • Tyrosine phosphorylation of early response proteins such as HS1, PLC-r, ZAP- 76, and Vav is an early biochemical event following leukocyte activation.
  • the tyrosine phosphorylated proteins can be detected by Western blot using antibodies against phosphorylated tyrosine residues. Tyrosine phosphorylation of these early response proteins can be used as a standard assay for leukocyte activation (I. Biol. Chem., 1997, 272(23): 14562- 14570). Any change in the phosphorylation pattern of these or related proteins when immune responses are generated in the presence of potential PDZ/PL interaction antagonists is indicative of a potential PDZ/PL interaction antagonists.
  • the kinetics of intracellular Ca 2+ concentrations are measured over time after stimulation of cells preloaded with a calcium sensitive dye.
  • the indicator dye e.g., Fluor-4 (Molecular Probes)
  • the indicator dye exhibits an increase in fluorescence level using flow cytometry, solution fluorometry, and confocal microscopy. Any change in the level or timing of calcium flux when immune responses are generated in the presence of PDZ/PL interaction antagonists is indicative of an inhibition of this response.
  • lymphocyte activation marker levels such as CD69, IL-2R, MHC class II, B7, and TCR are commonly measured with fluorescently labeled antibodies using flow cytometry. All antibodies are commercially available. Any change in the expression levels of lymphocyte activation markers when immune responses are generated in the presence of the PDZ/PL interaction antagonists is indicative of an inhibition of this response.
  • MTS [5-(3-carboxymethoxyphenyl)-2-(4,5-dimethylthiazolyl)-3(4- sulfophenyl)tetrazolium, inner salt] is a colorimetric method for determining the number of viable cells in proliferation or cytotoxicity assays (Barltrop, J.A. et al., 1991, Bioorg. & Med. Chem. Lett. 1 : 611). 1-5 days after lymphocyte activation, MTS tetrazolium compound, Owen's reagent, is bioreduced by cells into a colored formazan product that is soluble in tissue culture media. Color intensity is read at 490 nm minus 650 nm using a microplate reader.
  • BrdU-pulsed cells are labeled with an enzyme- conjugated anti-BrdU antibody (Gratzner, H.G., 1982, Science 218: 474-475.).
  • a colorimetric, soluble substrate is used to visualize proliferating cells that have incorporated BrdU. Reaction is stopped with sulfuric acid and plate is read at 450 nm using a microplate reader. Any statistically significant increase or decrease in color intensity of the PDZ/PL interaction antagonist-treated sample, as compared to control sample (no treatment), suggest an effect of the PDZ/PL interaction antagonist on biological function.
  • Programmed cell death or apoptosis is an early event in a cascade of catabolic reactions leading to cell death. A lose in the integrity of the cell membrane allows for the binding of fluorescently conjugated phosphatidylserine. Stained cells can be measured by fluorescence microscopy and flow cytometry (Vermes, I., 1995, J. Immunol. Methods. 180:
  • assays for evaluating cell death in tissue samples can also be used in vivo studies.
  • cytokine production Cell supernatants harvested after cell stimulation for 16-48 hrs are stored at - 80°C until assayed or directly tested for cytokine production. Multiple cytokine assays can be performed on each sample. IL-2, IL-3, IFN- ⁇ and other cytokine ELISA Assays are available for mouse, rat, and human (Endogen, Inc. and BioSource). Cytokine production is measured using a standard two-antibody sandwich ELISA protocol as described by the manufacturer. The presence of horseradish peroxidase is detected with 3, 3 '5, 5' tertamethyl benziidine (TMB) substrate and the reaction is stopped with sulfuric acid.
  • TMB 5' tertamethyl benziidine
  • the absorbency at 450 nm is measured using a microplate reader. Any statistically significant increase or decrease in color intensity of the PDZ/PL interaction antagonist- treated sample, as compared to control sample (no treatment), suggest an effect of the PDZ/PL interaction antagonist on biological function. See also Example 1 , infra. Detection of intracellular cytokines using anti-cytokine antibodies provides the additional advantage of measuring cytokines fore mixed cell populations. This allows for phenotyping measuring frequency of cytokine producing cell types in suspension or in tissues.
  • NF-AT can be visualized by Immunostaining T cell activation requires the import of nuclear factor of activated T cells (NF-
  • NF-AT nuclear translocation
  • NF-AT/luciferase reporter assays have been used as a standard measurement of T cell activation (MCB 1996, 12: 7151-7160). Any statistically significant increase or decrease in the nuclear translocation of NF-AT brought about by the PDZ/PL interaction antagonist-treated sample, as compared to control sample (no treatment), suggest an effect of the PDZ/PL interaction antagonist on biological function.
  • the compounds of the invention may be tested in different dosages, formulations and route of administration in a cardiac transplant mouse model to optimize their ability to inhibit rejection responses to solid organ transplants (Fulmer et al., 1963, Am. J. Anat. 113:273; Jockusch et al.,
  • the compounds of the inventions may be used to inhibit PDZ domain interactions with CD3, CD4, CD6 and
  • the compounds of the invention may be used to inhibit PDZ domain interactions with CD53 and CD138 in B cells.
  • the compounds of the invention may be used to inhibit PDZ domain interactions with Fc ⁇ RI ⁇ , CDwl25 and CDwl28.
  • a PDZ motif sequence (PL sequence) of CD95 may be used to induce apoptosis of lymphomas.
  • Antagonists e.g.. Peptides and Fusion Proteins '
  • the PDZ-PL antagonists of the invention are introduced into a cell to modulate (i.e., increase or decrease) a biological function or activity of the cell.
  • Many small organic molecules readily cross the cell membranes (or can be modified by one of skill using routine methods to increase the ability of compounds to enter cells, e.g., by reducing or eliminating charge, increasing lipophilicity, conjugating the molecule to a moiety targeting a cell surface receptor such that after interacting with the receptor).
  • the antagonist or agent is a fusion polypeptide or derivatized polypeptide.
  • a fusion or derivatized protein may include a targeting moiety that increases the ability of the polypeptide to traverse a cell membrane or causes the polypeptide to be delivered to a specified cell type (e.g., liver cells or tumor cells) preferentially or cell compartment (e.g., nuclear compartment) preferentially.
  • targeting moieties include lipid tails, amino acid sequences such as antennapoedia peptide or a nuclear localization signal (NLS; e.g., Xenopus nucleoplasmin Robbins et al., 1991, Cell 64:615).
  • NLS nuclear localization signal
  • a peptide sequence or peptide analog determined to inhibit a PDZ domain-PL protein binding, in an assay of the invention is introduced into a cell by linking the sequence to an amino acid sequence that facilitates its transport through the plasma membrane (a "transmembrane transporter sequence").
  • the peptides of the invention may be used directly or fused to a transmembrane transporter sequence to facilitate their entry into cells.
  • each peptide may be fused with a heterologous peptide at its amino terminus directly or by using a flexible polylinker such as the pentamer G-G-G-G-S (SEQ ID NO:l) repeated 1 to 3 times.
  • linker has been used in constructing single chain antibodies (scFv) by being inserted between V H and V L (Bird et al., 1988, Science 242:423-426; Huston et al., 1988, Proc. Natl. Acad. Sci. U.S.A. 85:5979-5883).
  • the linker is designed to enable the correct interaction between two beta- sheets forming the variable region of the single chain antibody.
  • Other linkers which may be used include Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys-Val-Asp (SEQ ID NO:2) (Chaudhary et al., 1990, Proc. Natl.
  • transmembrane transporter peptides include, but are not limited to, tat derived from HIV (Vives et al, 1997, J Biol. Chem. 272:16010; Nagahara et al., 1998, Nat. Med. 4:1449), antennapedia from Drosophila (Derossi et al., 1994, J. Biol. Chem.
  • a truncated HIV tat peptide having the sequence of GYGRKKRRQRRRG (SEQ ID NO: 173) is used.
  • a transmembrane transporter sequence is fused to a hematopoietic cell surface receptor carboxyl terminal sequence at its amino-terminus with or without a linker.
  • the C-terminus of a PDZ motif sequence (PL sequence) must be free in order to interact with a PDZ domain.
  • the transmembrane transporter sequence may be used in whole or in part as long as it is capable of facilitating entry of the peptide into a cell.
  • a hematopoietic cell surface receptor C-terminal sequence may be used alone when it is delivered in a manner that allows its entry into cells in the absence of a transmembrane transporter sequence.
  • the peptide may be delivered in a liposome formulation or using a gene therapy approach by delivering a coding sequence for the PDZ motif alone or as a fusion molecule into a target cell.
  • the compounds of the of the invention may also be administered via liposomes, which serve to target the conjugates to a particular tissue, such as lymphoid tissue, or targeted selectively to infected cells, as well as increase the half-life of the peptide composition.
  • Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like.
  • the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions.
  • a desired peptide or conjugate of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the selected inhibitor compositions.
  • Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol.
  • the selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream.
  • a variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al., Ann. Rev. Biophys.
  • a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells.
  • a liposome suspension containing a peptide or conjugate may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the conjugate being delivered, and the stage of the disease being treated.
  • the peptide may be linked to a cell-specific targeting moiety, which include but are not limited to, ligands for diverse leukocyte surface molecules such as growth factors, hormones and cytokines, as well as antibodies or antigen-binding fragments thereof.
  • a cell-specific targeting moiety include but are not limited to, ligands for diverse leukocyte surface molecules such as growth factors, hormones and cytokines, as well as antibodies or antigen-binding fragments thereof.
  • ligands or antibodies specific for these receptors may be used as cell-specific targeting moieties.
  • interleukin-2, B7-1 (CD80), B7-2 (CD86) and CD40 or peptide fragments thereof may be used to specifically target activated T cells (The Leucocyte Antigen Facts Book, 1997, Barclay et al. (eds.), Academic Press).
  • CD28, CTLA-4 and CD40L or peptide fragments thereof may be used to specifically target B cells.
  • Fc domains may be used to target certain Fc receptor-expressing cells such as monocytes.
  • Antibodies are the most versatile cell-specific targeting moieties because they can be generated against any cell surface antigen. Monoclonal antibodies have been generated against leukocyte lineage-specific markers such as certain CD antigens. Antibody variable region genes can be readily isolated from hybridoma cells by methods well known in the art. However, since antibodies are assembled between two heavy chains and two light chains, it is preferred that a scFv be used as a cell-specific targeting moiety in the present invention. Such scFv are comprised of V H and V L domains linked into a single polypeptide chain by a flexible linker peptide.
  • the PDZ motif sequence may be linked to a transmembrane transporter sequence and a cell-specific targeting moiety to produce a tri-fusion molecule. This molecule can bind to a leukocyte surface molecule, passes through the membrane and targets 0 PDZ domains.
  • a PDZ motif sequence may be linked to a cell- specific targeting moiety that binds to a surface molecule that internalizes the fusion peptide.
  • microspheres of artificial polymers of mixed amino acids have been used to deliver pharmaceuticals.
  • proteinoids mixed amino acids
  • U.S. Pat. No. 4,925,673 describes drug-containing proteinoid microsphere carriers as well as methods for their ⁇ * preparation and use. These proteinoid microspheres are useful for the delivery of a number of active agents. Also see, U.S. Patent Nos. 5,907,030 and 6,033,884, which are incorporated herein by reference.
  • a polynucleotide encoding a surface receptor C-terminal peptide may be useful in the treatment of various leukocyte activation-associated abnormal conditions. By introducing gene sequences into cells, gene therapy can be used to treat conditions in which leukocytes are activated to result in deleterious consequences.
  • a polynucleotide that encodes a PL sequence peptide of the invention is introduced into a cell 5 where it is expressed. The expressed peptide then inhibits the interaction of PDZ proteins and PL proteins in the cell.
  • the polypeptides of the invention are expressed in a cell by introducing a nucleic acid (e.g., a DNA expression vector or mRNA) encoding the desired protein or peptide into the cell.
  • a nucleic acid e.g., a DNA expression vector or mRNA
  • Expression may be either constitutive or inducible depending on the vector and choice of promoter. Methods for introduction and expression of nucleic acids into a cell are well known in the art and described herein.
  • nucleic acids comprising a sequence encoding a peptide disclosed herein, are administered to a human subject.
  • the nucleic acid produces its encoded product that mediates a therapeutic effect by inhibiting leukocyte activation.
  • Any of the methods for gene therapy available in the art can be used according to the present invention. Exemplary methods are described below.
  • the therapeutic composition comprises a coding sequence that is part of an expression vector.
  • a nucleic acid has a promoter operably linked to the coding sequence, said promoter being inducible or constitutive, and, optionally, tissue-specific.
  • a nucleic acid molecule is used in which the coding sequence and any other desired sequences are flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for intrachromosomal expression of the nucleic acid (Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-8935; Zijlstra et al., 1989, Nature 342:435-438).
  • Delivery of the nucleic acid into a patient may be either direct, in which case the patient is directly exposed to the nucleic acid or nucleic acid-carrying vector, or indirect, in which case, cells are first transformed with the nucleic acid in vitro, then transplanted into the patient. These two approaches are known, respectively, as in vivo or ex vivo gene therapy.
  • the nucleic acid is directly administered in vivo, where it is expressed to produce the encoded product.
  • This can be accomplished by any methods known in the art, e.g., by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by infection using a defective or attenuated retroviral or other viral vector (see U.S. Patent No.
  • a nucleic acid-ligand complex can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation.
  • the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., PCT Publications WO 92/06180 dated April 16, 1992; WO 92/22635 dated December 23, 1992; WO92/20316 dated November 26, 1992; WO93/14188 dated July 22, 1993; WO 93/20221 dated October 14, 1993).
  • the nucleic acid can be introduced intracellularly and inco ⁇ orated within host cell DNA for expression, by homologous recombination (Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-8935; Zijlstra et al, 1989, Nature 342:435-438).
  • adenoviruses as viral vectors can be used in gene therapy.
  • Adenoviruses have the advantage of being capable of infecting non- dividing cells (Kozarsky and Wilson, 1993, Current Opinion in Genetics and Development 3:499-503).
  • adenoviral vectors with modified tropism may be used for cell specific targeting (WO98/40508).
  • Adeno-associated virus (AAV) has also been proposed for use in gene therapy (Walsh et al, 1993, Proc. Soc. Exp. Biol. Med. 204:289-300).
  • retroviral vectors have been modified to delete retroviral sequences that are not necessary for packaging of the viral genome and integration into host cell DNA.
  • the coding sequence to be used in gene therapy is cloned into the vector, which facilitates delivery of the gene into a patient. More detail about retroviral vectors can be found in Boesen et al, 1994, Biotherapy 6:291-302, which describes the use of a retroviral vector to deliver the mdrl gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy.
  • the nucleic acid is introduced into a cell prior to administration in vivo of the resulting recombinant cell.
  • introduction can be carried out by any method known in the art, including but not limited to transfection, electroporation, lipofection, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc.
  • Numerous techniques are known in the art for the introduction of foreign genes into cells (see e.g., Loeffler and Behr, 1993, Meth. Enzymol. 217:599-618; Cohen et al, 1993, Meth. Enzymol.
  • the technique should provide for the stable transfer of the nucleic acid to the cell, so that the nucleic acid is expressible by the cell and preferably heritable and expressible by its cell progeny.
  • the cell used for gene therapy is autologous to the patient.
  • the nucleic acid to be introduced for pu ⁇ oses of gene therapy comprises an inducible promoter operably linked to the coding sequence, such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription.
  • Oligonucleotides such as anti-sense RNA and DNA molecules, and ribozymes that function to inhibit the translation of a leukocyte surface receptor mRNA, especially its C- terminus are also within the scope of the invention.
  • Anti-sense RNA and DNA molecules act to directly block the translation of mRNA by binding to targeted mRNA and preventing protein translation.
  • antisense DNA oligodeoxyribonucleotides derived from the translation initiation site, e.g., between -10 and +10 regions of a nucleotide sequence, are preferred.
  • the antisense oligonucleotide may comprise at least one modified base moiety which is selected from the group including, but not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine,
  • Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA.
  • the mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage.
  • engineered hammerhead motif ribozyme molecules that specifically and efficiently catalyze endonucleolytic cleavage of leukocyte surface receptor RNA sequences.
  • ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences, GUA, GUU and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site may be evaluated for predicted structural features such as secondary structure that may render the oligonucleotide sequence unsuitable. The suitability of candidate targets may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.
  • RNA molecules and DNA molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligodeoxyribonucleotides well known in the art such as for example solid phase phosphoramidite chemical synthesis.
  • RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding the RNA molecule. Such DNA sequences may be inco ⁇ orated into a wide variety of vectors which contain suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters.
  • antisense cDNA constructs that synthesize antisense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines.
  • DNA molecules may be introduced as a means of increasing intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences of ribo- or deoxy- nucleotides to the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the oligodeoxyribonucleotide backbone. 6.9.3 Other Pharmaceutical Compositions
  • compositions comprising the compounds of the invention may be manufactured by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophihzing processes.
  • Pharmaceutical compositions may be formulated in conventional manner using one or more physiologically acceptable carriers, diluents, excipients or auxiliaries that facilitate processing of the active peptides or peptide analogues into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
  • the compounds of the invention may be formulated as solutions, gels, ointments, creams, suspensions, etc. as are well-known in the art.
  • Systemic formulations include those designed for administration by injection, e.g. subcutaneous, intravenous, intramuscular, intrathecal or intraperitoneal injection, as well f) as those designed for transdermal, transmucosal, oral or pulmonary administration.
  • the compounds of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer.
  • physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer.
  • the solution may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the compounds may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
  • penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. This route of administration may be used to deliver the compounds to the nasal cavity.
  • the compounds can be readily formulated by combining the active peptides or peptide analogues with pharmaceutically acceptable carriers well known in the art.
  • Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated.
  • solid formulations such as, for example, powders,
  • suitable excipients include fillers such as sugars, such as lactose, sucrose, mannitol and sorbitol; cellulose preparations such as maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP); granulating agents; and binding agents.
  • disintegrating agents may be added, such as the cross-linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
  • solid dosage forms may be sugar-coated or enteric-coated using standard techniques.
  • suitable carriers, excipients or diluents include water, glycols, oils, alcohols, etc. Additionally, flavoring agents, preservatives, coloring agents and the like may be added.
  • the compounds may take the form of tablets, lozenges, etc. formulated in conventional manner.
  • the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • the dosage unit may be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges of e.g. gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
  • the compounds may also be formulated in rectal or vaginal compositions such as suppositories or retention enemas, e.g, containing conventional suppository- bases such as cocoa butter or other glycerides.
  • the compounds may also be formulated as a depot preparation.
  • Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
  • the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • suitable polymeric or hydrophobic materials for example as an emulsion in an acceptable oil
  • ion exchange resins for example, as an emulsion in an acceptable oil
  • sparingly soluble derivatives for example, as a sparingly soluble salt.
  • other pharmaceutical delivery systems may be employed.
  • Liposomes and emulsions are well known examples of delivery vehicles that may be used to deliver peptides and peptide analogues of the invention.
  • Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity.
  • the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid polymers containing the therapeutic agent.
  • sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein stabilization may be employed.
  • the compounds of the invention may contain charged side chains or termini, they may be included in any of the above-described formulations as the free acids or bases or as pharmaceutically acceptable salts.
  • Pharmaceutically acceptable salts are those salts which substantially retain the biologic activity of the free bases and which are prepared by reaction with inorganic acids. Pharmaceutical salts tend to be more soluble in aqueous and other protic solvents than are the corresponding free base forms.
  • the compounds of the invention will generally be used in an amount effective to achieve the intended pu ⁇ ose.
  • the compounds of the invention or pharmaceutical compositions thereof are administered or applied in a therapeutically effective amount.
  • therapeutically effective amount is meant an amount effective ameliorate or prevent the symptoms, or prolong the survival of, the patient being treated. Determination of a therapeutically effective amount is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure provided herein.
  • An "inhibitory amount” or “inhibitory concentration” of a PL-PDZ binding inhibitor is an amount that reduces binding by at least about 40%, preferably at least about 50%, often at least about 70%>, and even as much as at least about 90%. Binding can as measured in vitro (e.g, in an A assay or G assay) or in situ.
  • a therapeutically effective dose can be estimated initially from in vitro assays.
  • a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC 50 as determined in cell culture (i.e., the concentration of test compound that inhibits 50% of leukocyte surface receptor-PDZ domain-containing protein interactions). Such information can be used to more accurately determine useful doses in humans.
  • Initial dosages can also be estimated from in vivo data, e.g. , animal models, using techniques that are well known in the art. One having ordinary skill in the art could readily optimize administration to humans based on animal data.
  • Dosage amount and interval may be adjusted individually to provide plasma levels of the compounds that are sufficient to maintain therapeutic effect.
  • Usual patient dosages for administration by injection range from about 0.1 to 5 mg/kg/day, preferably from about 0.5 to 1 mg/kg/day.
  • Therapeutically effective serum levels may be achieved by administering multiple doses each day. In cases of local administration or selective uptake, the effective local concentration of the compounds may not be related to plasma concentration.
  • One having skill in the art will be able to optimize therapeutically effective local dosages without undue experimentation.
  • the amount of compound administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of
  • the therapy may be repeated intermittently while symptoms detectable or even when they are not detectable.
  • the therapy may be provided alone or in combination with other drugs.
  • the drugs that may be used in combination with the compounds are provided alone or in combination with the compounds.
  • 15 of the invention include, but are not limited to, steroid and non-steroid anti-inflammatory agents.
  • a therapeutically effective dose of the compounds described herein will provide therapeutic benefit without causing substantial toxicity.
  • Toxicity of the compounds described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., by determining the
  • LD 50 the dose lethal to 50% of the population
  • LD, 00 the dose lethal to 100% of the population.
  • the dose ratio between toxic and therapeutic effect is the therapeutic index.
  • the dosage may vary within this range depending upon the dosage form employed and the
  • route of administration utilized.
  • the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See, e.g., Fingl et al,
  • Tat-CD3 carboxyl terminus fusion peptide (GYGRKKRRQRRRGPPSSSSGL, SEQ ID NO: 174); Tat- CLASP 1 carboxyl terminus fusion peptide, (GYGPxKKRRQRRRGSISSSAEV, SEQ ID NO: 174;
  • Tat-CLASP2 carboxyl terminus fusion peptide (GYGRKKRRQRRRGMTSSSSW,
  • Antigen-specific mouse T cells BR4.2, were activated with the N-terminal 16 amino acid sequences of myelin basic protein (MBPAcl-16) and syngenic mouse splenocytes in 96-well plates. Mitomycin C-treated antigen presenting cells, 2 x 10 5 B10.BR, were added
  • Antibody against mouse CD3 (Pharmigen #145-2C11) was coated overnight at
  • T cells (5xl0 5 cells/ml) were pre-treated with or without 10 ⁇ M Tat-peptides for two hours at 5% CO2, 37°C and then diluted in media with or without 10 ⁇ M Tat-peptides to a final concentration of 2x10 4 cells per well in a final volume of 200 ⁇ l. Cells were then treated as described above.
  • IFN ⁇ was measured from cell supernatants, described above, at ambient 10 temperature using the Endogen, Inc. ELISA protocol 3. Briefly, 96-well, flat bottom, high binding ELISA plates were preincubated overnight with coating antibody (MM700). Plates were washed with 50 mM TRIS, 0.2% tween-20, pH 8 and they blocked for one hour with PBS plus 2% BSA. Washed plates were then incubated one hour with 25 ⁇ l of cell supernatant and 5 25 ⁇ l blocking buffer, or with 50 ⁇ l IFN ⁇ standard. The presence of IFN ⁇ was detected with a biotin-labeled anti-mouse IFN ⁇ monoclonal antibody (MM700B, Endogen, Inc.,).
  • MM700B biotin-labeled anti-mouse IFN ⁇ monoclonal antibody
  • FIGURE 4A shows that the Tat-CD3 fusion peptide inhibits T cell activation mediated by peptide:MHC as compared to controls of Tat-peptide alone or no peptide.
  • FIGURE 4B shows that Tat-CLASP2
  • receptor organization leads to blockage of T cell activation in response to antigen.
  • EXAMPLE 2 DESIGN OF AN INHIBITOR OF DLG 1 -LIGAND BINDING WITH GREATER THAN 100 Urn POTENCY A GST/DLGl fusion protein (See TABLE 3) and a biotin-labeled peptide corresponding to the C-terminal 20 amino acids of the CLASP-2 protein, peptide AA2L (See TABLE 3) and a biotin-labeled peptide corresponding to the C-terminal 20 amino acids of the CLASP-2 protein, peptide AA2L (See TABLE 3) and a biotin-labeled peptide corresponding to the C-terminal 20 amino acids of the CLASP-2 protein, peptide AA2L (See
  • CLASP2peptide AA2L that (1) retained similar DLGl binding properties and (2) would not itself generate a signal in the assay selected to measure inhibition. Because most molecular interactions between PDZ proteins and their ligands involve only the C-terminal 6 amino acids of the ligand, an eight amino acid variant of the CLASP-2 peptide, MTSSSSVV, was anticipated to retain similar DLGl binding properties as the 20 amino acid AA2L CLASP-2 peptide. This eight amino acid CLASP-2 peptide (lacking a functional label) was therefore synthesized and purified by standard techniques as described supra. When 100 uM of the
  • an effective inhibitor of DLGl -ligand binding i.e. the eight amino acid CLASP-2 peptide MTSSSSW
  • a known potency range order of magnitude 21 uM

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Abstract

L'invention concerne des réactifs et des procédés permettant d'inhiber ou d'améliorer les interactions de protéines dans les cellules hématopoïétiques et autres cellules intervenant dans la médiation d'une réponse immunitaire. Les réactifs et les procédés considérés sont utiles pour le traitement d'une variété de maladies et d'affections dont la médiation est assurée par des cellules du système immunitaire.
PCT/US2000/013161 1999-05-14 2000-05-12 Interactions moleculaires dans les cellules hematopoietiques WO2000069896A2 (fr)

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JP2000618312A JP2002543825A (ja) 1999-05-14 2000-05-12 造血細胞内分子相互作用
AU50112/00A AU5011200A (en) 1999-05-14 2000-05-12 Molecular interactions in hematopoietic cells
EP00932386A EP1178817A2 (fr) 1999-05-14 2000-05-12 Interactions moleculaires dans les cellules hematopoietiques

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EP1391462A1 (fr) * 2001-04-24 2004-02-25 Otsuka Pharmaceutical Co., Ltd. Peptide de liaison a des anticorps de la maladie de crohn et methode d'examen de ladite maladie
EP1493028A2 (fr) * 2001-07-06 2005-01-05 Genentech, Inc. Ligands du domaine pdz exprimes a la surface des phages
US6942981B1 (en) 1999-05-14 2005-09-13 Arbor Vita Corporation Method of determining interactions with PDZ-domain polypeptides
WO2006069181A2 (fr) * 2004-12-21 2006-06-29 Musc Foundation For Research Development Compositions et methodes favorisant la cicatrisation et la regeneration tissulaire
AU2003291558B2 (en) * 2001-08-03 2009-08-13 Arbor Vita Corporation Molecular interactions in neurons
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US6942981B1 (en) 1999-05-14 2005-09-13 Arbor Vita Corporation Method of determining interactions with PDZ-domain polypeptides
US7432065B2 (en) 1999-05-14 2008-10-07 Arbor Vita Corporation Methods of identifying modulators of interaction between PDZ domain proteins and PL proteins
US8648043B2 (en) 1999-06-02 2014-02-11 Nono Inc. Method of reducing injury to mammalian cells
US7846897B2 (en) 1999-06-02 2010-12-07 Michael Tymianski Agents for reducing injury to mammalian cells
US8071548B2 (en) 1999-06-02 2011-12-06 Nono, Inc. Method of reducing injury to mammalian cells
US7595297B2 (en) 1999-06-02 2009-09-29 Michael Tymianski Method of reducing injury to mammalian cells
WO2002066954A2 (fr) * 2001-02-16 2002-08-29 Arbor Vita Corporation Interactions du domaine pdz et radeaux lipidiques
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EP1391462A1 (fr) * 2001-04-24 2004-02-25 Otsuka Pharmaceutical Co., Ltd. Peptide de liaison a des anticorps de la maladie de crohn et methode d'examen de ladite maladie
EP1391462A4 (fr) * 2001-04-24 2004-09-15 Otsuka Pharma Co Ltd Peptide de liaison a des anticorps de la maladie de crohn et methode d'examen de ladite maladie
EP1493028A4 (fr) * 2001-07-06 2006-06-14 Genentech Inc Ligands du domaine pdz exprimes a la surface des phages
EP1493028A2 (fr) * 2001-07-06 2005-01-05 Genentech, Inc. Ligands du domaine pdz exprimes a la surface des phages
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WO2003014303A3 (fr) * 2001-08-03 2003-08-14 Arbor Vita Corp Interactions moleculaires dans les cellules
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US10398757B2 (en) 2004-12-21 2019-09-03 Musc Foundation For Research Development Alpha connexin c-terminal (ACT) peptides and methods of use thereof
US9394351B2 (en) 2004-12-21 2016-07-19 Musc Foundation For Research Development Compositions and methods for promoting wound healing and tissue regeneration
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WO2000069897A2 (fr) 2000-11-23
WO2000069897A9 (fr) 2002-07-04
WO2000069897A3 (fr) 2001-11-08
WO2000069896A9 (fr) 2002-10-03
JP2011102326A (ja) 2011-05-26
EP1178817A2 (fr) 2002-02-13
ES2436624T3 (es) 2014-01-03
WO2000069896A3 (fr) 2001-07-05
JP2002543825A (ja) 2002-12-24

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