IKK3 kinase

Abstract

This invention relates to an IKK kinase protein, IKK3, nucleotides coding for it, vectors and host cells containing the same and methods for screening for modulators of said IKK3 protein for treatment of conditions involving inflammation.

Description

TECHNICAL FIELD

[0001] This invention relates to a novel IKK kinase protein, IKK3, nucleotides coding for it, vectors and host cells containing the same and methods for screening for modulators of said IKK3 protein for treatment of conditions involving inflammation.

BACKGROUND ART

[0002] The transcription factor NF-kB controls the activation of various genes in response to pathogens and pro-inflammatory cytokines. Thus, for example, NF-kB is activated by various kinds of stimulation including tumour necrosis factor alfa (TNF alfa) and interleukin-1 (IL-1), bacterial LPS, viral infection, antigen receptor cross-linking of T and B cells, calcium ionophores, phorbol esters, UV radiation and free radicals (for reviews, see Varma et al., 1995, Genes Dev., 9, 2723-2735; Baueurerle and Baltimore, 1996, Cell, 87, 13-20), (see FIG. 2). NF-kB in turn controls the activation of various genes in response to these stimuli. Activation of these various genes in turn may result in the production of cytokines, chemokines, leukocyte adhesion molecules, hematopoietic growth factors and may also effect development and cell death as well as cell survival (see FIG. 1). Specifically, the transcription factor NF-kB controls the activation of various genes in response to pathogens and pro-inflammatory cytokines. The NF-kB activity is regulated through interaction with specific inhibitors, IkBs. Upon cell stimulation, the IkBs are rapidly phosphorylated and then undergo ubiquitin-mediated proteolysis, resulting in the release of active NF-kB (Baldwin, 1996, Annu. Rev. Immunol., 14, 649-681; Baueurerle and Baltimore, 1996, Cell, 87, 13-20), (see FIG. 2). It has been reported that the 700 kDa complex specifically phosphorylated IkB&agr; at S32 and S36 (Chen et al., 1996, Cell, 84, 853-862).

[0003] Several groups found that two kinases termed IKK1 and IKK2 (also known as IKK&agr; and IKK&bgr;), were the subunits of the kinase complex. The groups showed that the IKKs immunoprecipitates, derived from the TNF&agr; or IL-1 stimulated cells are able to phosphorylate IkB in vitro. In addition to these observations, two groups reported that IKK1 and IKK2 purified from insect cells are able to phosphorylate IkB in vitro. These results suggested that IKK directly phosphorylates IkBs. The over expression of anti-sense IKK1, kinase-inactive IKK1 or IKK2 resulted in the inhibition of NF-kB activation mediated by TNF&agr; and IL-1. These results suggest that IKKs are critical kinases in the NF-kB activation pathway (May and Ghosh, 1998, Immunol. Today 19, 80-88; Stancovski and Baltimore, 1997, Cell, 91, 299-302). It has, however, not been understood how upstream signals are transmitted to the kinase complex, or whether different kinase complexes might exist to phosphorylate distinct IkBs.

[0004] NEMO (NF-kB essential modifier) and IKK&ggr; (human homologue of the mouse NEMO) were isolated from purified IKK complex, and the inhibition of NEMO/IKK&ggr; gene expression impaired the cytokine induced NF-kB activation via IKK1 and IKK2. In NEMO deficient cells, smaller complexes of Mr 3,000-4,000 are formed, though the normal complex is Mr 7,000-9,000, suggesting that NEMO/IKK&ggr; physically link IkB kinase to upstream activators (Scheidereit, Nature, 1998, 395, 225-226).

[0005] The IKK-complex-associated protein (IKAP) was isolated from the IKK complexes. IKAP binds to IkB kinases and NIK and the complex, containing three kinases, leads to the maximum phosphorylation of IkB as compared to the complex containing one or two kinases. Accordingly, IKAP may act as scaffold proteins that link NIK or other molecules to IKK1 and IKK2 (Scheidereit, Nature, 1998, 395, 225-226). Accumulating evidence suggests that the IKK complex consists of several essential molecules, however, the molecular mechanisms that control the signalling complex were not well understood. Therefore, further association molecules were needed to complete the picture.

[0006] KIAA0151 was originally isolated from the KG-1 cDNA library (Nagase et al., 1995, DNA Res, 2, 167-174). KIAA0151 was identified as a potential Ser/Thr kinase, however, the importance of the molecule was not recognised. We have now found that KIAA0151 is similar to IKK1 and IKK2 using a computer homology analysis. KIAA0151, renamed IKK3, has a 21% homology with IKK1 and 23% with IKK2. IKK3 was able to phosphorylate IkB family proteins and directly phosphorylate IkB in vitro. The over expression of IKK3 leads to the activation of various inflammatory genes, such as IL-8, IL-6 and RANTES. These genes contain the NF-kB site in the gene regulation region. We know that IKK3 has an effect on IL-8 expression in Hela cells and also that IKK3 phosphorylates NF-kB. Moreover, it is known that the NF-kB site has an important role in IL-8 regulation. Our results suggest a correlation between IKK3 and the NF-kB site of the IL-8 promoter that has previously been identified as an endogenous NF-kB binding site, further suggesting that IKK3 plays an important role in controlling the NF-kB site of the IL-8 promoter. Specifically we have shown that IKK3 trans-activates the IL-8 gene via the NF-KB binding to a site in the IL-8 promoter. These results lead to the conclusion that IKK3 is an important regulator of IL-8 gene regulation and thus activates genes that are important for the inflammatory diseases (see Table 1 below). 1 TABLE 1 Differences between IKK1, 2 and IKK3 IKK1, 2 (also known as IKK&agr;, &bgr;) IKK3 Expression Constitutive Inducible by IL-1 (mRNA) and TNF alfa Source for Mammalian and Mammalian and Bacterial in vitro Insect cells cells phosphorylation Spectrum Unknown IL-8, IL-6 and RANTES Substrate lkB&agr; > lkB&bgr; IkB&egr; lkB&bgr; > lkB&agr; Selectively Enzymatic Need for IL-1 or No need for stimulation activity TNF alfa stimulation

[0007] Using a computer homology analysis, we have now found that KIAA0151 is similar to IKK1 and IKK2. Importantly, recent experimental evidence has shown that IKK3 specifically controls various inflammatory genes, such as IL-8, IL-6 and RANTES. Moreover, IKK3 has been shown to phosphorylate various IkBs and directly phosphorylate TRIP9 (human IkB&bgr;). IKK3 has therefore been shown to have a specific role in the control of inflammation.

DISCLOSURE OF INVENTION

[0008] Accordingly this invention provides a novel kinase protein, IKK3.

[0009] Nucleotide sequence analysis of IKK3 reveals a 2148 bp open reading frame which encodes 716 amino acid protein (FIG. 3). This deduced protein sequence shares many of the characteristics of IKK1 and IKK2. (see FIG. 5).

[0010] One aspect of the invention therefore provides an isolated IKK3 kinase protein or a variant thereof. The amino acid sequence of this isolated IKK3 kinase protein is shown in FIG. 3.

[0011] Included within the invention are variants of the IKK3 kinase protein. Such variants include fragments, analogues, derivatives and splice variants. The term “variant” refers to a protein or part of a protein which retains substantially the same biological function or activity as IKK3.

[0012] Fragments can include a part of IKK3 which retains sufficient identity of the original protein to be effective for example in a screen. Such fragments may be probes such as the ones described hereinafter for the identification of the full length protein. Fragments may be fused to other amino acids or proteins or may be comprised within a larger protein. Such a fragment may be comprised within a precursor protein designed for expression in a host. Therefore, in one aspect the term fragment means a portion or portions of a fusion protein or polypeptide derived from IKK3.

[0013] Fragments also include portions of IKK3 characterised by structural or functional attributes of the protein. These may have similar or improved chemical or biological activity or reduced side-effect activity. For example, fragments may comprise an alpha, alpha-helix or alpha-helix-forming region, beta sheet and beta-sheet-forming region, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, amphipathic regions (alpha or beta), flexible regions, surface-forming regions, substrate binding regions and regions of high antigenic index.

[0014] Fragments or portions may be used for producing the corresponding full length protein by peptide synthesis.

[0015] Derivatives include naturally occurring allelic variants. An allelic variant is an alternate form of a protein sequence which may have a substitution, deletion or addition of one or more amino acids, which does not substantially alter the function of the protein. Derivatives can also be non-naturally occurring proteins or fragments in which a number of amino acids have been substituted, deleted or added. Proteins or fragments which have at least 70% identity to IKK3 are encompassed within the invention. Preferably, the identity is at least 80%, more preferably at least 90% and still more preferably at least or greater than 95% identity for example 97%, 98% or even 99% identity to IKK3.

[0016] Analogues include but are not limited to precusor proteins which can be activated by cleavage of the precursor portion to produce an active mature protein or a fusion with a compound such as polyethylene glycol or a leader/secretory to aid purification.

[0017] A splice variant is a protein product of the same gene, generated by alternative splicing of mRNA, that contains additions or deletions within the coding region (Lewin N (1995) Genes V Oxford University Press, Oxford, England). The present invention covers splice variants of the IKK3 kinase protein that occur naturally and which may play a role in the control of inflammation.

[0018] The protein or variant of the present invention may be a recombinant protein, a natural protein or a synthetic protein, preferably a recombinant protein.

[0019] A further aspect of the invention provides an isolated and/or purified nucleotide sequence which encodes a mammalian IKK3 protein as described above, or a variant thereof. Also included within the invention are anti-sense nucleotides or complementary strands.

[0020] Preferably, the nucleotide sequence encodes a rat or human IKK3 protein. The nucleotide sequence preferably comprises the sequence of the coding portion of the nucleotide sequence shown in FIG. 4.

[0021] A nucleotide sequence encoding an IKK3 protein of the present invention may be obtained from a cDNA or a genomic library derived from the human fetus Marathon-Ready cDNA (Clonetech).

[0022] The nucleotide sequence may be isolated from a mammalian cell (preferably a human cell), by screening with a probe derived from the rat, murine or human IKK3 sequence, or by other methodologies known in the art such as preliminary chain reaction (PCR) for example on genomic DNA with appropriate oligonucleotide primers derived from or designed based on rat or human IKK3 sequence and/or relatively conserved regions of known IKK3 proteins. A bacterial artificial chromosome library can be generated using rat or human DNA for the purposes of screening.

[0023] The nucleotide sequence of the present invention may be in form of RNA or in the form of DNA, which DNA includes cDNA, genomic DNA and synthetic DNA. The DNA may be double-stranded or single-stranded, and if single-stranded may be the coding strand or non-coding (anti-sense) strand. The coding sequence which encodes the IKK3 protein or variant thereof may be identical to the coding sequence set forth in FIG. 4, or maybe a different coding sequence which as a result of the redundancy or degeneracy of the genetic code, encodes the same protein as the sequences set forth therein.

[0024] A nucleotide sequence which encodes an IKK protein may include:

[0025] a coding sequence for the full length protein or any variant thereof;

[0026] a coding sequence for the full length protein or any variant thereof, and

[0027] additional coding sequence such as a leader or secretory sequence or a pro-protein sequence: a coding sequence for the full length protein or any variant thereof (and optionally additional coding sequence) and non-coding sequences, such as intrans or non-coding sequences 5 and/or 3 of the coding sequence for the full length protein. The invention also provides nucleotide variants, analogues, derivatives and fragments which encode IKK3. Nucleotides are included which preferably have at least 70% identity over the entire length to IKK3. More preferred are those sequences which have at least 80% identity over their entire length to IKK3. Even more preferred are polynucleotides which demonstrate at least 90% for example 95%, 97%, 98% or 99% identity over their entire length to IKK3.

[0028] The present invention also relates to nucleotide probes constructed from the nucleotide sequence of an IKK protein or variant thereof. Such probes could be utilised to screen a cDNA or genomic library to isolate a nucleotide sequence encoding an IKK3 protein. The nucleotide probes can include portions of the nucleotide sequence of the IKK3 protein or variant thereof useful for hybridising with mRNA or DNA in assays to detect expression of the IKK3 protein or localised its presence on a chromosome using for example flourescence in situ hybridisation (FISH).

[0029] The nucleotide sequences of the invention may also have the coding sequence fused in frame to a marker sequence which allows for purification of the protein of the present invention such as hexa-histadine tag or hemagglutinin (HA) tag, Myc-tag, T7-tag, double MYC-tag, double HA-tag and double T7-tag expression vectors or allows determination in screening assays of effective blockage of IKK3 or it's modulation.

[0030] Nucleotide molecules which hybridise to IKK3 or to complementary nucleotides thereto also form part of the invention. Hybridisation is preferably under stringent hybridisation conditions. One example of stringent hybridisation conditions which is sometimes used is where attempted hybridisation is carried out at a temperature of from about 35° C. to about 65° C. using a salt solution which is about 0.9 mol. However, the skilled person will be able to vary such conditions as appropriate in order to take into account variables such as probe length, base composition, type of ions present etc. The nucleotide sequence of the present invention may be employed for producing the IKK3 protein or variant thereof by recombinant techniques. Thus, for example the nucleotide sequence may be included in any one of a variety of expression vehicles or cloning vehicles, in particular vectors or plasmids for expressing a protein, such vectors include chromosomal, non-chromosomal and synthetic DNA sequences. Examples of suitable vectors include derivatives of bacterial plasmids: phage DNA: yeast plasmids; vectors derived from combinations of plasmids and phage DNA and viral DNA. However, any other plasmid or vector may be used as long as it is replicable and viable in the host.

[0031] More particularly, the present invention also provides recombinant constructs comprising one or more of the nucleotide sequences as described above. The constructs comprise an expression vector, such as a plasmid or viral vector into which a sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment the construct further comprises one or more regulatory sequences to direct messenger mRNA synthesis, including, for example a promoter operably linked to the sequence. Suitable promoters include: CMV, LTR, or SV40 promoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector may contain an enhancer and a ribosome binding site for translation initiation and transcription terminator.

[0032] Large numbers of suitable vectors and promoters/enhancers, will be known to those of skill in the art, but any plasmid or vector, promoter/enhancer may be used as long as it is replicable and functional in the host.

[0033] Appropriate cloning and expression vectors for use with prokaryotic and eurkaryotic hosts include mammalian expression vectors, insect expression vectors, yeast expression vectors, bacterial expression vectors and viral expression vectors and are described in Sambrook et al, Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor, N.Y., (1989). The vector may also include appropriate sequences for selection and/or amplification of expression. For this the vector will comprise one or more phenotypic selectable/amplifiable markers, such markers are also well known to those skilled in the art.

[0034] In a further embodiment, the present invention provides host cells capable of expressing a nucleotide sequence of the invention, the host cell can be, for example, a higher eukaryotic cell, such as mammalian cell or a lower eukaryotic cell, such as a yeast cell or a prokaryotic cell such as a bacterial cell. Suitable prokaryotic hosts for transformation include E. coli. Other examples include viral expression vectors, insect expression systems and yeast expression systems.

[0035] Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention.

[0036] The IKK3 protein is recovered and purified from recombinant cell cultures by methods known in the art, including ammonium sulfate or ethanol precipitation, acid extraction, and ion or cation exchange chromatography, phosphocellulose chromatography and lecitin chromatography. Protein refolding steps may be used, as necessary, in completing configuration of the mature protein. Finally high performance liquid chromatography (HPLC) can be employed for final purification steps.

[0037] The proteins and nucleotide sequences of the present invention are preferably provided in an isolated form. The term “isolated” means that the material is removed from its original environment e.g. the naturally-occurring nucleotide sequence or protein present in a living animal is not isolated, but the same nucleotide sequence or protein, separated from some or all of the materials it co-exists within the natural system, is isolated. Such nucleotide sequence could be part of a vector and/or such nucleotide sequence or protein could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment. The proteins and nucleotide sequences of the present invention are also preferably provided in purified form, and preferably are purified to at least 50% purity, more preferably about 75% purity, most preferably 90% purity or greater such as 95%, 98% pure.

[0038] The present invention also provides antibodies specific for the IKK3 protein. The term antibody as used herein includes all immunoglobulins and fragments thereof which contain recognition sites for antigenic determinants of proteins of the present invention. The antibodies of the present invention may be polyclonal or preferably monoclonal, may be intact antibody molecules or fragments containing the active binding region of the antibody, e.g. Fab or (Fab)2. The present invention also includes chimaeric, single chain and humanised antibodies and fusions with non-immunoglobulin molecules. Various procedures known in the art may be used for the production of such antibodies and fragments.

[0039] The proteins, their variants especially fragments, derivatives, or analogues thereof, or cells expressing them can be used as an immunogen to produce antibodies thereto. Antibodies generated against the IKK3 protein can be obtained by direct injection of the polypeptide into an animal, preferably a non-human. The antibody so obtained will then bind the protein itself. In this manner, even a sequence encoding only a fragment of the protein can then be used to generate antibodies binding the whole native protein. Such antibodies can be used to locate the protein in tissue expressing that protein.

[0040] The antibodies of the present invention may also be of interest in purifying an IKK3 protein and accordingly there is provided a method of purifying an IKK3 protein or any portion thereof which method comprises the use of an antibody of the present invention.

[0041] The present invention also provides methods of identifying modulators of the IKK3 protein. Screens can be established for IKK3 enabling large numbers of compounds to be studied. High throughput screens may be based on 14C guanidine flux assays and flourescence based assays as described in more detail below. Secondary screens may involve electrophysiological assays utilising patch clamp technology or two electrode voltage clamps to identify small molecules, antibodies, peptides, proteins or other types of compounds that inhibit, block, or otherwise interact with the IKK3 protein. Tertiary screens may involve the study of the modulators in well characterised rat and mouse models of inflammation. These models of inflammation include, but are not restricted to inflammatory models (murine) atopic dermatitis models (murine and rat), repeated-induced type dermatitis model (murine) and allergic asthma models (murine and guinea pig). For example, screens may be set up based on an in vitro phosphorylation system using bacterially expressd IKK3 proteins (see Example 5 and FIG. 12). This system may be used to screen for modulators of the IKK3 kinase activity and then subsequently testing the effect of potential modulators of IKK3 on gene expression, specifically the expression of IL-8, IL-6 and RANTES using cell based assay systems. Finally the efficacy of these modulators in relation to inflammatory or allergic diseases may be tested on models of inflammation.

[0042] The invention therefore provides a method of assaying for a modulator comprising contacting a test compound with the IKK3 protein and detecting the activity or inactivity of the IKK3 protein. Preferably, the methods of identifying modulators or screening assays employed transformed host cells that express the IKK3 protein. Typically, such assays will detect changes in the activity of the IKK3 protein to the test compound, thus identifying modulators of the IKK3 protein.

[0043] In general, a test compound is added to the assay and its effect on IKK3 is determined or the test compound's ability to competitively bind to the IKK3 is assessed. Test compounds having the desired effect on the IKK3 protein are then selected.

[0044] IL-8, IL-6 and RANTES are involved in diseases involving inflammation and allergies. Specifically, asthma, atopic dermatitis, arthritis, rheumatoid arthritis, systemic lupus erythematosus, LPS—induced contact dermatitis, glomerulonephritis, gout and other inflammation-related diseases.

[0045] The invention therefore provides a modulator of a protein or a variant thereof as described above identifiable by a method described above for use in therapy. The invention further provides use of a modulator of an IKK3 protein optionally identifiable by a method described above for the manufacture of an anti-inflammatory medicament. Moreover the invention provides a method of treatment which comprises administering to a patient an effective amount of a modulator of a protein as described above. More specifically, the invention provides a method of treating diseases related to inflammation, such as asthma, atopic dermatitis, arthritis, rheumatoid arthritis, systemic lupus erythematosus, LPS—induced contact dermatitis, glomerulonephritis and gout.

[0046] Complementary or anti-sense strands of the nucleotide sequences as herein above defined can be used in gene therapy. For example, the cDNA sequence of fragments thereof could be used in gene therapy strategies to down regulate the IKK3 protein. Anti-sense technology can be used to control gene expression through triple-helix formation of anti-sense DNA or RNA, both of which methods are based on binding of a nucleotide sequence to DNA or RNA.

[0047] A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription thereby preventing transcription and the product of the sodium channel. The anti-sense RNA oligonucleotide hybridises to the messenger RNA in vivo and blocks translation of the messenger RNA into the IKK3 protein.

[0048] The regulatory regions controlling expression of the IKK3 protein could be used in gene therapy to control expression of a therapeutic construct in cells expressing the IKK3 protein.

BRIEF DESCRIPTION OF DRAWINGS

[0049] FIG. 1

[0050] Outside factors stimulating expression of NF-kB as well as the effect of NF-kB on various biological events.

[0051] FIG. 2

[0052] Regulation of NF-kB activity.

[0053] FIG. 3

[0054] Predicted amino acid sequence of IKK3:

[0055] The potential kinase domain (KD) and helix-loop-helix (HLH) are boxed. The potential leucine zipper is underlined. Asterisk and dots indicate identical and similar amino acids, respectively. Numbers in the right hand column indicate position of the amino acids.

[0056] FIG. 4

[0057] Nucleotide sequence of IKK3:

[0058] Numbers in left hand column indicate position of nucleic acid.

[0059] FIG. 5

[0060] Schematic representation of IKK alpha, beta and IKK3

[0061] (KD=kinase domain; LZ=leucine zipper, HLH=helix-loop-helix). IKK3 is 21% identical to IKK1 and 23% identical to IKK2 at the amino acid level. IKK1 has a 52% identity to IKK2 at the amino acid level.

[0062] FIG. 6

[0063] Northern blot analysis:

[0064] Inducile expression of IKK3.

[0065] FIG. 7

[0066] a. In vitro phosphorylation of IkB proteins by IKK3.

[0067] b. In vitro phosphorylation of IkB mutant proteins by IKK3.

[0068] FIG. 8

[0069] In vitro phosphorylation of TRIP9 by IKK3 mutants.

[0070] a. Schematic representation of IKK3 mutant proteins.

[0071] b. IKK3 mutant proteins were separated by SDS-PAGE, stained with Coomassie blue and analyzed by autoradiography.

[0072] FIG. 9

[0073] IKK3 directly phosphorylates TRIP9.

[0074] FIG. 10

[0075] IKK3 mediates the expression of various chemokines and cytokines

[0076] FIG. 11

[0077] IKK3 mediates the expression of IL-8 RNA.

[0078] FIG. 12A brief outline of an in vitro phosphorylation assay (IkB)

[0079] The double T7-tagged IKK3 expression vector (DT7-IKK3) or the double T7-tagged control vector (Mock) is transfected into Hela cells. The cell lysates are used for the in vitro phosphorylation assay. The tagged proteins are immunoprecipitated with anti-T7 antibody (Novogen), mixed with GST-IkBs and [&ggr;-32]ATP. The mixtures are separated by SDS-PAGE and analyzed by autoradiography. The immunoprecipitate of DT7-IKK3 is able to phosphorylate IkBs.

[0080] FIG. 13 A brief outline of an in vitro phosphorylation assay (TRIP9)

[0081] The GST-IKK3 protein was expressed in E. Coli, and the protein was affinity purified by the GST column, and used for the in vitro phosphorylation assay. The GST-IKK3 was incubated with [&ggr;-32]ATP and GST, GST-IkB&bgr; (TRIP9) or GST-IkB&bgr; or GST-IkB&bgr; (TRIP9) mutant. The protein mixture was separated by SDS-PAGE and analyzed by autoradiography. Result shows that the GST-IKK3 directly phosphorylates GST-IkB&bgr; (TRIP9), but not GST and GST-IkB&bgr; mutant.

[0082] FIG. 14 IKK3 regulates the NF-KB site of IL-8

[0083] IKK3 controls an essential step in the NF-kB signalling pathway. Hela cells were transiently transfected with the IL-8 or the IL-8 mutant luciferase reporter gene plasmid, and the expression vector encoding double T7-tagged IKK3 (IKK3), or with a vector control (Mock). Luciferase activities were determined and normalized on the basis of &bgr;-galactosidase expression from cotransfected pact-&bgr;-Gal.

[0084] FIG. 15 Northern blot analysis

[0085] The human tissue filter for the northern blot (gene hunter, TOYOBO) was probed with the IKK3 specific primers.

[0086] FIG. 16 Antibody against IKK3 effect on the kinase activity of IKK3.

[0087] A. The bacterially expressed GST-IKK3 were incubated with the bacterially expressed GST-TRIP9 (IkB&bgr;), -TRIP9/AA, antibody and [&ggr;-32P]ATP for 30 min at 30° C. Proteins were separated by SDS-PAGE, stained with Coomassie blue and analyzed by autoradiography.

[0088] B. IKK3 antibody activate the IKK3 kinase acitivity. The amount of GST-TRIP9 phosphoprotein was counted by Image analyzer (Fuji Film).

BEST MODE FOR CARRYING OUT THE INVENTION

[0089] 2 TABLE 2 Primers used G7-5 5′-TCCTGATTTCTGCAGCTCTG-3′ G7-3 5′-AACTTCTCCACAACCCTCTG-3′ G85 5′-CCCCCCGCGGCCGCCACCATGCAGAGCACAGCCAATTACCTGTGG-3′ G86 5′-CCCCCCGCGGCCGCCTCAGACATCAGGAGGTGCTGGGACTCTATT-3′ G87 5′-CCCCCCGCGGCCGCCATGGAGCGGCCCCCGGGGCTGCGGCCGGGC-3′ G88 5′-CCCCCCGCGGCCGCCTCATTCTGTTAACCAACTCCAATCAAGATT-3′ G89 5′-CCCCCCGCGGCCGCCATGAGCTGGTCACCTTCCCTGACAACGCAG-3′ G90 5′-CCCCCCGCGGCCGCCTCATGAGGCCTGCTCCAGGCAGCTGTGCTC-3′ G91 5′-CCCCCCGCGGCCGCCATGTTCCAGGCGGCCGAGCGCCCCCAGGAG-3′ G138 5′-CCCCCCGCGGCCGCCTCAGAGGCGGATCTCCTGCAGCTCCTTGAC-3′ G93 5′-CCCCCCGCGGCCGCCATGGCCGGGGTCGCGTGCTTGGGGAAAACT-3′ G147 5′-CCCCCCGCGGCCGCCTCACAGCTCTGGGCCAAGCTCTGCGCCCAG-3′ G97 5′-CCCCCCGCGGCCGCCATGGCTGGGGTCGCGTGCTTGGGAAAAGCT-3′ G148 5′-CCCCCCGCGGCCGCCTCACAAGCCCCGGGCCCAACTCCGCGCCCAA-3′ G150 5′-CCCCCCGCGGCCGCATGTCGGAGGCGCGGCGGGGCCGGACGAG-3′ G149 5′-CCCCCCGCGGCCGCCTCACAGCGCCCCCACGTGGGGGAGTGGCAG-3′ G124 5′-GAGCTGGTTGCTGTGATGGTCTTCAACACTACC-3′ G125 5′-GGTAGTGTTGAAGACCATCACAGCAACCAGCTC-3′ G126 5′-AGTGGGAGCCTGCTGGCTGTRGCTGGAGGCTCCTGAGAATGCCTTT-3′ G127 5′-AAAGCATTCTCAGGAGCCTCCAGCACAGCCAGCAGGCTCCCACT-3′ G130 5′-GAGCTGGATGATGATGCGMGUCGTCGCGGTCTATGGGACTGAG-3′ G131 5′-CTCAGTCCCATAGACCGCGACGAACTTCGATCATCATCCAGCTC-3′ G128 5′-AGTGGGAGCCTGCTGGAGGTGCTGGAGGAGCCTGAGAATGCCTTT-3′ G129 5′-AAAGGCATTCTCAGGCTCCTCCAGCACCTCCAGCAGGCTCCCACT-3′ G132 5′-GATGAGAAGTTCGTCGAGGTCTATGGGACTGAG-3′ G133 5′-CTCAGTCCCATAGACCTCGACGAACTTCTCATC-3′ G136 5′-GACGACCGCCACGACGCCGGCCTGGACGCCATGAAAGACGAGGAG-3′ G137 5′-CTCCTCGTCTTTCATGGCGTCCAGGCCGGCGTCGTGGCGGTCGTC-3′ G178 5′-GATGAATGGTGCGACGCCGGCCTGGGCGCTCTAGGTCCCGACGCA-3′ G171 5′-TGCGTCGGGACCTAGAGCGCCCAGGCCGGCGTCGCACCATTCATC-3′ G172 5′-GATGAATGGTGCGACGCCGCCTGGGCGCCCTGGGTCCGGACGCA-3′ G173 5′-TGCGTCCGGACCCAGGGCGCCCAGGCCGGCGTCGCACCATTCATC-3′ G174 5′-GAGAGCCAGTACCACGCTGGCATTGAGGCTCTGCGCTCTCTGCGC-3′ G175 5′-GCGCAGAGAGCGCAGAGCCTCAATGCCAGCGTCGTACTGGCTCTC-3′ G176 5′-GGGGAGCGGGCTGATGCCACCTATGGCGCCTCCTCGCTCACCTAC-3′ G177 5′-GTAGGTGAGCGAGGAGGCGCCATAGGTGGCATCAGCCCGCTCCCC-3′

EXAMPLE 1

Materials and Methods

[0090] Cells and Transfection

[0091] Hela cells were maintained in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal calf serum. DNA transfection into cells was done by DOSPER transfection according to the manufacture's instructions.

[0092] Vector Construction

[0093] IKK1, IKK2, IKK3, IkB&agr;, IkB&bgr;, TRIP9, IkB&egr; cDNAs were obtained by PCR from the human fetus Marathon-Ready cDNA (Clonetech). The primers were as follows:

[0094] IKK1 (Accession number AF012890; nucleotides 1-2238; 5′primer G87, 3′primer G88)

[0095] IKK2 (Accession number AF029684; nucleotides 1-2268; 5′primer G89, 3′primer G90)

[0096] IKK3 (Accession number D63485; nucleotides 327-2477; 5′primer G85, 3′primer G90)

[0097] IkB&agr; (Accession number, M69043; nucleotides 95-256, 5′primer G91, 3′primer G138)

[0098] IkB&bgr; (Accession number, I34460; nucleotides 74-205, 5′primer G93, 3′primer G147)

[0099] TRIP9 (Accession number, L40407; nucleotides 53-184, 5′primer G97, 3′primer G148)

[0100] IkB&egr; (Accession number, U91616; nucleotides 451-765, 5′primer G150, 3′primer G149)

[0101] The cDNA fragment was digested with NotI and the fragment was subcloned into DT7-CMV (Takemoto et al., 1997, DNA and Cell Biol., 16, 893-896).

[0102] Site-Directed Mutagenesis

[0103] Site-directed mutagenesis was performed with QuikChange™ site-directed mutagenesis kit (STRATAGENE) according to the manufacture's instructions.

[0104] DT7-IKK3 Mutants:

[0105] Met38 of DT7-IKK3 was mutated to Ala (DT7-DN1 DT7-DN1, nucleotides 432-455; 5′ primer G124 and 3′ primer G125);

[0106] Ser96 and Ser100 of DT7-IKK3 were mutated to Ala (DT7-DN2, nucleotides 597-641; 5′ primer G126 and 3′ primer G127);

[0107] Ser 168 and Ser 172 of DT7-IKK3 were mutated to Ala (DT7-DN3, nucleotides 813-857; 5′ primer G130 and 3′ primer G131);

[0108] Ser96 and Ser100 of DT7-IKK3 were mutated to Glu (DT7-EE1, nucleotides 597-641; 5′ primer G128 and 3′ primer G129);

[0109] Ser 172 of DT7-IKK3 was mutated to Glu (DT7-EE2, nucleotides 813-857; 5′ primer G132 and 3′ primer G133).

[0110] GST-IkB Mutants:

[0111] Ser32 and Ser36 of GST-IkB&agr; were mutated to Ala (GST-IkB&agr;/AA: nucleotides 173-217; 5′ primer G136 and 3′ primer G137);

[0112] Ser19 and Ser23 of GST-IkB&bgr; were mutated to Ala (GST-IkB&bgr;/AA: nucleotides 113-157; 5′primer G178 and 3′ primer G171);

[0113] Ser19 and Ser23 of GST-TRIP9 were mutated to Ala (GST-TRIP9/AA: nucleotides 92-136; 5′ primer G172 and 3′ primer G173);

[0114] Ser157 and Ser161 of GST-IkB &egr; were mutated to Ala (GST-IkB &egr;/AA1: nucleotides 487-531; 5′ primer G174 and 3′ primer G175);

[0115] Ser210 and Ser214 of GST-IkB &egr; were mutated to Ala (GST-IkB &egr;/AA2: nucleotides 646-690; 5′ primer G176 and 3′ primer G177).

[0116] All PCR-derived sequences used in this study were confirmed by the Sangar method.

EXAMPLE 2

[0117] Northern Blot Analysis: Inducible Expression of IKK3

[0118] Cells were treated with IL-1&agr; (10 ng/ml), TNF-&agr; (100 ng/ml), IFN-&ggr; (10 ng/ml), LPS (100 ng/ml) or C2-ceramide (50 &mgr;M) for 5 hours, and the total RNAs were analyzed by Northern blot analysis with the IKK3 specific primers. The expression of actin RNA was used as a control. It was found that IKK3 gene expression was induced by 1L-1 or TNF&agr; stimulation in human Hela cells (see FIG. 6).

EXAMPLE 3

[0119] Rnase Protection Assay

[0120] Hela cells were stably expressed with double T7-tagged IKK3. The cells were treated with IL-1&agr; (10 ng/ml) or TNF-&agr; (100 ng/ml). Total RNA was isolated by ISOGEN (Nippongene) according to the manufacture's instructions and subjected to Rnase protection assay. The bands of each genes were normalized by the G3PDH expression.

EXAMPLE 4

[0121] RT-PCR

[0122] cDNA was prepared from 5 &mgr;g of total RNA using M-MTLV reverse transcriptase (Life Technologies) to a final volume of 100 &mgr;l. After a 90-min incubation of the mixture at 37, the cDNA solution was ethanol-precipitated and resuspended in 100 &mgr;l of water. The cDNA was amplified by PCR with the IL-8 specific primers (5′ primer G7-5 and 3′ primer G7-3; Accession number, M28130; nucleotides, 1621 bp and 2945 bp of the genomic DNA) and the G3PDH specific primers (Clonetech). Expected PCR products (238 bp for IL-8 and 983 bp for G3PDH) were size-fractionated onto a 1.8% agarose gel and stained with ethidium bromide.

EXAMPLE 5

[0123] In Vitro Phosphorylation of IkB Proteins by IKK3: Target molecules of IKK3 and IKK3 Activation

[0124] Hela cells were transiently expressed with the double T7-tagged IKK3 expression vector. (DT7-IKK3) or the double T7-tagged control vector (Mock) is transfected into Hela cells. Thirty-six hours after transfection, the cells were treated with IL-1&agr; (10 ng/ml) or TNF-&agr; (100 ng/ml) for 10 min. Cells were prepared by lysis with TNE buffer (10 mM Tris-HCl, pH 7.8; 1% NP-40, 0.15 M NaCl; 1 mM EDTA; 10 nM NaF, 2 mM Na3VO4, 10 mM PNPP and complete) and IKK3 proteins were immunoprecipitated with anti-T7 antibody (Novogen). Purified DT-IKK3 were used for in vitro kinase reactions with bacterially expressed GST, GST-IkB&agr; (1-54), -IkB&bgr; (1-44), -IkB&egr; (140-244), -TRIP9 (1-44) and [&ggr;-32P] ATP. The alanine-substitution mutants GST IkB&agr; (IkB&agr;/AA), -IkB&bgr; (IkB&bgr;/AA), -TRIP9 (1-44, AA), -IkB&egr; (IkB&egr;/AA1 and IkB&egr;/AA2) were used as control proteins. Proteins were separated by SDS-PAGE, stained with Coomassie blue analyzed by autoradiography (see FIG. 7). It was found that IKK3 phosphorylates I kappa B (IkB) &agr;, IkB &bgr; and IkB&egr;. IKK3 phosphorylates IkB &egr; and IkB &bgr; in preference to IkB &agr;. When IKK3 is over expressed in Hela cells, no stimulation was needed to activate IKK3 (see FIG. 7a—no stimulation, lanes 6-10; IL-1 stimulation, lanes 11-15; TNF alpha stimulation, lanes 16-20). IKK3 is able to phosphorylate IkBs with or without stimulation, such as IL-1 and TNF-alpha. For a brief outline of the experiment see FIG. 12. IKK3 is unable to phosphorylate IkB &agr;/AA, IkB &bgr;/AA and TRIP9/AA (see FIG. 7b).

EXAMPLE 6

[0125] In Vitro Phosphorylation of TRIP9 by IKK3 Mutants

[0126] Met38 of DT7-IKK3 was mutated to Ala (DN1); Ser96 and Ser100 of DT7-IKK3 were mutated to Ala (DN2); Ser 168 and Ser 172 of DT7-IKK3 were mutated to Ala (DN3); Ser96 and Ser100 of DT7-IKK3 were mutated to Glu (EE1); Ser172 of DT7-IKK3 was mutated to Glu (EE2).

[0127] Hela cells were transiently expressed with the double T7-tagged IKK3 mutant expression vectors. Thirty-six hours after tranfection, IKK3 mutant proteins were immunoprecipitated with anti-T7 antibody. Purified DT-IKK3 mutants were used for in vitro kinase reactions with bacterially expressed GST, GST-TRIP9 (1-44) and [&ggr;-32P] ATP. GST were used as control proteins. Proteins were separated by SDS-PAGE, stained with Coomassie blue and analyzed by autoradiography (see FIG. 8). It was found that some amino acids play an important role in the IKK3 kinase activity (FIG. 8). We found some mutation of IKK3 reduced the kinase activity of the mutants (DN1, DN2 and DN3 (FIG. 8b, lanes 1-6).

[0128] The EE1 mutation strongly enhances the kinase activity of EE1 (FIG. 8b, lanes 7 and 8). The mutant of EE2 has only a small effect on the kinase activity of EE2 (FIG. 8b, lanes 9 and 10). The immunoprecipitate of DT7-IKK3 is able to phosphorylate IkBabeta (TRIP9). The brief outline of the experiment is shown in FIG. 12.

EXAMPLE 7

[0129] In Vitro Phosphorylation: IKK3 Directly Phosphorylates TRIP9

[0130] The bacterially expressed GST-IKK3 were incubated with the bacterially expressed GST, GST-TRIP9 (1-44), -TRIP (1-44, AA) and [&ggr;-32P] ATP for 30 min at 30° C.

[0131] The bacterially expressed GST-DT-IKK3 was used as a kinase. A 250 ng of purified kinase solution was used for in vitro kinase reactions with a 500 ng of bacterially expressed GST, GST-TRIP9 (1-44), -TRIP (1-44, AA) and [&ggr;-32P] ATP. Proteins were separated by SDS-PAGE, stained with Coomassie blue and analyzed by autoradiography (see FIG. 9). The bacterially expressed IKKB is able to phosphorylate TRIP9 (human IIK beta) but not TRIP9/AA (FIG. 9, lanes 3 and 4). For a brief outline of the experiment see FIG. 13.

EXAMPLE 8

[0132] IKK3 Mediates the Expression of Various Chemokines and Cytokines:

[0133] Hela cells were stably expressed with the double T7-tagged IKK3 expression vector (DT7-IKK3) or control vector (Mock). The cells were treated with IL-1&agr; (10 ng/ml) or TNF-&agr; (100 ng/ml) for 5 hours. Total RNAs were purified from these cells and subject to Rnase protection assay. The bands of IL 8, IL-8, RANTES and TGFbeta1 were normalized by the G3PDH expression, respectively (see FIG. 10). It was found that over expression of IKK3 in Hela cells leads to the expression of IL-8, IL-6 and RANTES in Hela cells (see FIG. 10).

EXAMPLE 9

[0134] IKK3 Mediates the Expression of IL-8 RNA:

[0135] Hela cells were stably expressed with double T7-tagged IKK3 (DT7-IKK3) or Mock (−). The cells were treated with IL-1&agr; (10 ng/ml) or TNF-&agr; (100 ng/ml). Total RNAs were purified from these cells and subjected to RT-PCR analysis with oligonucleotide primers specific for IL-8. PCR amplification of G3PDH was used as an internal control. After 30 cycles, the PCR products were sized—fractionated onto a 1.8% agarose gel and stained with ethidium bromide (see FIG. 11).

EXAMPLE 10

[0136] IKK3 Regulates the NF-&kgr;B site of IL-8

[0137] The IL-8 promoter contains an NF-kB binding site and the site is a critical element for IL-8 gene regulation. To test whether IKK3 regulates the NF-&kgr;B site of IL-8, a reporter gene construct, containing the IL-8 promoter, was constructed. DT7-IKK3 was transiently expressed in Hela cells with the IL-8 reporter genes. The mutant reporter construct contains 4 copies of the NF-kB binding site, of which 3 contained 2 point mutations. IKK3 activates the IL-8 reporter gene, though IKK3 is unable to activate the mutant reporter. These observations indicate that IKK3 is one of several critical kinases that controls the IL-8 gene regulation via the NF-&kgr;B site.

[0138] Cells and Transfection

[0139] Hela cells were maintained in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal calf serum. DNA transfection into cells was performed using DOSPER transfection according to the manufacture's instructions.

[0140] Vector Construction

[0141] PLuc-neo reporter gene was constructed as follows: pd2EGFP-1 (Clonetech) was digested with BglII-SacII, Klenow-repaired and ligated to remove multi-cloning site. The plasmid was digested with Bsp120-AflII and Klenow-repaired. The DNA fragment containing Neo gene was used for the vector construction. PGL3-basic (Invitrogen) was digested with SalI/NotI, and Klenow-repaired. The DNA fragment containing Luciferease gene was ligated with the DNA containing the Neo gene derived from pd2EGFP-1. The vector was termed as pLuc-neo basic. Two synthetic complementary oligonucleotides of the promoter region of the IL-8 gene containing an NF-kB binding site (from −1 to 196) were annealed and digested with HindIII and KpnI. The resulting cDNA fragment was subcloned into a HindIII/KpnI site of the pLuc-neo. Next, two complementary oligonucleotide, containing 3 repeats of the IL-8 NF-kB site (primers G165/194 and G166/195) were annealed, digested with KpnI and subcloned into a KpnI site of the IL-8 NF-kB reporter gene. Finally, a vector, containing 3 copies of a mutant NF-kB binding site, (2 point mutations), was constructed (primers G167/194 and G168/196).

[0142] IKK3 controls an essential step in the NF-kB signalling pathway. Hela cells were transiently transfected with the IL-8 or the IL-8 mutant luciferase reporter gene plasmid, and the expression vector encoding double T7-tagged IKK3 (IKK3), or with a vector control (Mock). Luciferase activities were determined and normalized on the basis of &bgr;-galactosidase expression from cotransfected pact-&bgr;-Gal. (See FIG. 14).

EXAMPLE 11

[0143] Expression of IKK3

[0144] In the previous report, we showed that the IKK3 mRNA is inducible with IL-1 and TNF-alfa. To test the expression of the mRNA in human tissues, GENE HUNTER (TOYOBO) was used. The IKK3 expression was detected in the Liver, Pancreas, Placenta and Lung, but not in the Heart and Brain.

[0145] Northern Blot Analysis

[0146] Cells were treated with IL-1&agr; (10 ng/ml), TNF-&agr; (100 ng/ml), IFN-&ggr; (10 ng/ml), LPS (100 ng/ml) or C2-ceramide (50 &mgr;M) for 5 hours, and the total RNAs were analyzed by Northern blot analysis with the IKK3 specific-primers. The expression of actin RNA was used as a control. (See FIG. 15).

EXAMPLE 12

[0147] IKK3 Antibody

[0148] Anti-IKK3 polyclonal antibodies were derived from rabbits immunized the GST-IKK-NT and GST-IKK-CT fusion proteins (FIG. 1A). The antibodies are available for the immunoporecipitation of the IKK3 molecules (data not shown). To test the effect of the antibody against the IKK3 kinase activity, we pre-incubated GST-IKK3 molecule with the antibodies and performed in vitro kinase assay. The antibodies against IKK3 increased the kinase activity (FIG. 1B).

[0149] Antibody

[0150] Anti-IKK3 antibodies were generated in rabbits immunized with GST, GST-IKK3-NT (amino acids K69-P193) and GST-IKK3-CT (amino acidsV628-V716), respectively.

[0151] IKK3-NT: nucleotides 531-560 5′ primer G99 nucleotides 879-905 3′ primer G100

[0152] IKK3-CT: nucleotides 2208-2237 5′ primer G103 nucleotides 2448-2477 3′ primer G86

[0153] The PCR fragments were subcloned into a NotI site of pGEX4T-2. 3 G86: 5′-CCCCCCGCGGCCGCCTCAGACATCAGGAGGTGCTGGGACTCTATT-3′ G99: 5′-CCCCCCGCGGCCGCCAAGCTCTTTGCGGTGGAGGAGACGGGCGGA-3′ G100: 5′-CCCCCCGCGCCCGCCTCAGGGCTTTCGAAGCACCGCCCGCTCATA-3′ G103: 5′-CCCCCCGCGGCCGCCGTGGCTGCCTGTAACACAGAAGCCCAGGGG-3′

[0154]

Claims

1. An isolated IKK3 kinase protein or a variant thereof.

2. An isolated IKK3 kinase protein having the amino acid sequence in FIG. 3, or a variant thereof.

3. An IKK3 kinase protein or variant thereof according to claim 1 or 2, for use in a method for screening for agents with anti-inflammatory activity.

4. A nucleotide sequence encoding an IKK3 kinase or a variant thereof, or a nucleotide sequence which is complementary thereto.

5. A nucleotide sequence encoding an IKK3 kinase as shown in FIG. 4, or a variant thereof, or a nucleotide sequence which is complementary thereto.

6. The nucleotide sequence of either claim 4 or 5, which is a cDNA sequence.

7. A nucleotide sequence that hybridises to any part of a nucleotide strand referred to in either of claims 4 to 6.

8. An expression vector comprising a nucleotide sequence according to any one of claims 4 to 7, which is capable of expressing a IKK3 kinase protein or a variant thereof.

9. A stable cell line comprising a vector according to claim 8.

10. A cell line according to claim 9 which is a Hela cell line.

11. An antibody specific for a protein as claimed in claims 1 to 3.

12. A method for identification of a compound which exhibits IKK3 kinase modulating activity, comprising contacting a IKK3 kinase protein according to any of claims 1 to 3 with a test compound and detecting modulating activity or inactivity.

13. A compound which modulates IKK3 kinase, identifiable by a method according to claim 12.

14. A method of treatment or prophylaxis of a disorder which is responsive to modulation of IKK3 kinase activity in a mammal, which comprises administering to said mammal an effective amount of a compound identifiable by the method according to claim 12.

15. Use of a compound identifiable by the method according to claim 12 in a method of formulating a medicament for treatment or prophylaxis of a disorder which is responsive to the modulation of IKK3 kinase activity in a mammal.

16. A method of producing an IKK3 kinase protein comprising introducing into an appropriate cell line a suitable vector or vectors comprising a nucleotide sequence encoding for IKK3 or variants thereof, under conditions suitable for obtaining expression of the protein or variants.