# Patent

## Title
Regulation of cell survival by HSP90 and IP6K2

## Abstract

Anti-cancer drugs are identified by screening for agents and compounds which inhibit the binding of HSP90 and IP6K2. In vitro and in vivo assays can be used. Any phenomenon associated with the binding or inhibition can be monitored, including cell death, subcellular localization, catalytic activity of IP6K2, and IP7 formation.

## Background
This work was supported with funds from the U.S. government via U.S. Public Health Service Grant MH18501, Conte Center Grant MH068830-02, and Research Scientist Award DA00074. The U.S. government therefore retains certain rights in the invention.


TECHNICAL FIELD OF THE INVENTION
This invention is related to the area of protein-protein interactions. In particular, it relates to cancer drug screening
BACKGROUND OF THE INVENTION
Inositol phosphates are major intracellular signaling molecules with the best known of these, inositol 1,4,5-trisphosphate, releasing intracellular calcium (1, 2). Among inositol phosphates recent attention has focused upon higher inositol polyphosphates (3-6) including the pyrophosphate diphosphoinositol pentakisphosphate (5-PP-IP5, IP7), which is able to donate its energetic phosphate to various protein targets (7). In vivo, IP7 is generated by a family of three inositol hexakisphosphate kinases (IP6K) (8-9) of which IP6K2 has been associated with apoptosis. Thus, apoptotic stimuli markedly increase IP7 formation, overexpression of IP6K2 augments cell death, and siRNA-induced depletion promotes cell survival (10-12). In addition to their classic role in promoting refolding of denatured proteins, heat shock proteins (HSP) are implicated in anti-apoptotic cascades (13-17) and have been targets for the development of anti-cancer drugs (18-22). There is a continuing need in the art to identify new drugs for treating cancer.
SUMMARY OF THE INVENTION
According to one embodiment of the invention a method is provided for identifying compounds which interfere with the binding of IP6K2 protein to HSP90 protein. Such compounds are candidate therapeutic agents. A first protein, a second protein, and a test compound are contacted with each other under conditions in which the first and second proteins would bind to each other if in the absence of test compound. The first protein comprises IP6K2 protein and the second protein comprises HSP90 protein or the first protein comprises HSP90 protein and the second protein comprises IP6K2 protein. The quantity of the first protein which is bound to, is displaced from, or is prevented from binding to, the second protein is determined. A candidate therapeutic agent is identified if a compound diminishes the quantity of the first protein bound to the second protein, or displaces first protein bound to the second protein, or prevents first protein from binding to the second protein.
According to another embodiment of the invention a method is provided for identifying compounds which interfere with the binding of IP6K2 protein to HSP90 protein. Such compounds are candidate therapeutic agents. A first polypeptide, a second polypeptide, and a test compound are contacted with each other. At least one of said first and said second polypeptides is a polypeptide which comprises less than all of the complete sequence of amino acids of HSP90 protein or IP6K2 protein. Each of said polypeptides contains a sufficient portion of HSP90 protein or IP6K2 protein to bind to the other polypeptide. When said first polypeptide is HSP90 protein or a polypeptide which comprises less than all of the complete sequence of amino acids of HSP90 protein, then said second polypeptide is IP6K2 protein or a polypeptide which comprises less than all of the complete sequence of amino acids of IP6K2 protein. When said first polypeptide is IP6K2 protein or a polypeptide which comprises less than all of the complete sequence of amino acids of IP6K2 protein, then said second polypeptide is HSP90 protein or a polypeptide which comprises less than all of the complete sequence of amino acids of HSP90 protein. The quantity of the first polypeptide which is bound to, is displaced from, or is prevented from binding to, the second polypeptide is determined. A test compound which diminishes the quantity of the firstprotein, or which prevents first protein from binding to the second protein, or which displaces first protein from binding to the second protein, is identified as a candidate therapeutic agent.
Another aspect of the invention is a method of identifying compounds which interfere with the binding of human IP6K2 protein to human HSP90 protein. A cell is contacted with a test compound. The cell comprises three recombinant DNA constructs. The first construct encodes a first polypeptide fused to a sequence-specific DNA-binding domain. The second construct encodes a second polypeptide fused to a transcriptional activation domain. The third construct comprises a reporter gene downstream from a DNA element which is recognized by the sequence-specific DNA-binding domain. The first polypeptide is an IP6K2 polypeptide and said second polypeptide is an HSP90 polypeptide, or said first polypeptide is a HSP90 polypeptide and said second polypeptide is a IP6K2 polypeptide; wherein said polypeptides contain a sufficient portion of HSP90 protein and IP6K2 protein to bind to the other polypeptide. The quantity of expression of the reporter gene is determined in the presence of said compound.
Yet another aspect of the invention is a cell which comprises three recombinant DNA constructs: the first construct encodes a first polypeptide fused to a sequence-specific DNA-binding domain; the second construct encodes a second polypeptide fused to a transcriptional activation domain, the third construct comprises a reporter gene downstream from a DNA element which is recognized by said sequence-specific DNA-binding domain. The first polypeptide is an IP6K2 polypeptide and the second polypeptide is a HSP90 polypeptide, or said first polypeptide is a HSP90 polypeptide and said second polypeptide is an IP6K2 polypeptide. The polypeptides contain a sufficient portion of HSP90 protein and IP6K2 protein to bind to the other polypeptide.
Still another aspect of the invention is a method of determining the quantity of human
HSP90 protein which binds to human IP6K2 protein, or of human IP6K2 protein which binds to human HSP90 protein. A first protein is contacted with a second protein. The first protein is human IP6K2 protein and the second protein is human HSP90 protein or the first protein is human HSP90 protein and the second protein is human IP6K2 protein. The quantity of the first protein which is bound to the second protein is determined.
According to another embodiment of the invention a fusion protein consisting of a first polypeptide and a second polypeptide are provided. The second polypeptide is a portion of a mammalian IP6K2 protein, which is sufficient to bind to HSP90 protein. The first polypeptide is not a portion of a mammalian IP6K2 protein.
Another embodiment of the invention is a device for screening for candidate pro-apopotic drugs. The device comprises a solid surface to which one of a first and a second polypeptide has been affixed. The first and said second polypeptides comprise at least a portion of the complete sequence of amino acids of HSP90 protein and IP6K2 protein, respectively. Each of said polypeptides contains a sufficient portion of HSP90 protein or IP6K2 protein to bind to the other polypeptide.
Still another embodiment of the invention is a kit for screening test compounds for candidate pro-apoptotic drugs. Components of the kit include a solid surface to which one of a first and a second polypeptide has been affixed; the first and said second polypeptides comprise at least a portion of the complete sequence of amino acids of HSP90 protein and IP6K2 protein, respectively. Each of said polypeptides contains a sufficient portion of HSP90 protein or IP6K2 protein to bind to the other polypeptide. The kit also includes a container comprising unbound protein which is not affixed to the solid surface. If an HSP90 polypeptide is affixed to the solid surface then the unbound protein is an IP6K2 polypeptide, and if the IP6K2 polypeptide is affixed to the solid surface then the unbound protein is an HSP90 polypeptide.
These and other embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with tools for identifying and developing new candidate drugs for treating cancer.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A-1F. Inositol Hexakisphosphate Kinase-2 (IP6K2) binds HSP90. FIG. 1A. IP6K2 contains a motif resembling p23, a cochaperone of HSP90. FIG. 1B. Co-immunoprecipitation of endogenous HSP90 by overexpressed myc-tagged IP6K2 and IP6K3 in HEK 293 cells. HEK 293 cells were transfected with pCMV-myc vector containing any of the three IP6K clones (IP6K1/K2/K3). Protein (1 mg) from each cell lysate was immunoprecipitated by anti-myc antibody. Samples run on 4-12% SDS-PAGE, were immunoblotted with monoclonal HSP90 antibody. Lane 1 shows the untransfected control. IP6K2 and IP6K3 bind robustly to HSP90 but IP6K1 does not. The membrane was also blotted with anti-myc antibody to monitor the concentration of immunoprecipated IP6K isoforms. FIG. 1C. Co-immunoprecipitation of myc-IP6K2 by endogenous HSP90 from HeLa cells. Endogenous HSP90 was immunoprecipitated using a monoclonal antibody from cells with and without overexpressing myc-IP6K2. Co-immunoprecipitated myc-IP6K2 was checked by immunoblotting with anti-myc antibody. HSP90 levels were also confirmed by western blotting. FIG. 1D. Co-immunoprecipitation of endogenous IP6K2 by endogenous HSP90 in mouse brain. Protein (3 mg) from brain extract was immunoprecipitated for each experiment with no antibody (lane 1), general IgG (lane 2) or HSP90 monoclonal antibody (lane 3). Co-immunoprecipitated endogenous IP6K2 was detected by blotting with IP6K2 specific polyclonal antibody. FIG. 1E. Direct binding of immunoprecipitated myc-K2 with exogenously added HSP90 purified from HeLa cells (lane 2). Myc-vector transfected HeLa cells were used as negative control (lane 1). FIG. 1F. Endogenous HSP90 does not coprecipitate with mutants of IP6K2 in the putative HSP90 binding region. R133A, R136A and E138-9A no longer bind whereas W131A has little effect on binding.
FIG. 2A-2G Regulation of IP6K2 activity by HSP90. FIG. 2A. HSP90 overexpression leads to decreased IP6K activity in vivo. HeLa and HEK 293 cells (either untransfected or transfected with myc-IP6K2, HA-HSP90 or both) were labeled with [3Hinositol] and inositol phosphates were isolated by HPLC. IP7 formed by IP6K in the cells was calculated based on IP7 (product) over IP6 (substrate) and was considered as reflection of IP6K activity in vivo. IP6K activity in the untransfected cells was considered to be 100%. FIG. 2B. HSP90 fails to inhibit IP7 formation in vivo by IP6K2 mutants that can not bind HSP90. [3H]inositol labeled IP7 was assessed in HeLa cells co-transfected with myc-IP6K2 (WT or the mutants) and HA-HSP90. R133A and R136A mutants of IP6K2 display more activity than wild type and are not inhibited by HSP90. The low activity of the catalytically deficient W131A mutant is further depressed by HSP90 overexpression. FIG. 2C. IP6K activity in vitro of WT and mutant IP6K2 in absence and presence of purified HSP90 from HeLa cells. Catalytic activity of the WT enzyme is significantly reduced after addition of HSP90 whereas the R133A and R136A mutants are equally active as the even in the presence of HSP90. W131A mutant lost 80% of catalytic activity as compared to the WT or the other two active mutants. FIG. 2D. Deficient IP6 binding of catalytically inactive IP6K2 W131A mutant. [3H]IP6 binding is reduced 50% in the IP6K2 W131A mutant establishing a role for W131A in substrate binding and catalytic activity. Substrate binding of IP6K2 R133A and IP6K2 R136A mutant is the same as in WT samples. FIG. 2E. In vitro binding of purified endogenous HSP90 to immunoprecipitated myc IP6K2 is abolished in presence of IP6. After preincubation of IP6K2 with increasing concentrations of IP6 for 15 min. in binding buffer (20 mM Tris 7.4, 1 mM DTT, 1 mM PMSF and protease inhibitor cocktail), HSP90 was added and incubated for 1 h. The beads were washed three times with binding buffer and bound HSP90 was analyzed by blotting with anti-HSP90 monoclonal antibody. Amount of immunoprecipitated myc IP6K2 was also checked by western blotting with anti-myc antibody and found to be equal in all the samples (data not shown). FIG. 2F. IP6K activity in vivo is increased in the absence of endogenous HSP90. HSP90 was depleted using siRNA in [3H]inositol labeled HeLa cells and inositol phosphates separated by HPLC. FIG. 2G. IP6K activity in WT and HSP mutant Yeasts in vivo. IP6 and IP7 were monitored following [3H]inositol labeling of intact cells. HSC82 mutant displays a 2.5 fold increase in IP6K activity whereas in HSP104 mutant IP6K activity is slightly decreased.
FIG. 3A-3E Cisplatin, novobiocin and staurosporine block HSP90-IP6K2 interaction and increase IP6K2 activity in cells. FIG. 3A, 3B, 3C. IP6K2-HSP90 interaction is disrupted by HSP90 inhibiting drugs. Drug treatment and coimmunoprecipitation of endogenous HSP90 from myc-IP6K2-transfected HeLa cells were done as described. Cisplatin (CP-30 overnight, FIG. 3A), novobiocin (NB-500 μM, overnight, FIG. 3A) and staurosporine (ST-1 μM, 6 h, FIG. 3B) disrupt the binding of HSP90 with IP6K2, whereas AAG (1 μM, overnight, FIG. 3C) augments binding. FIG. 3D: in vitro binding of HSP90-1P6K2 in presence of various concentrations of drugs. Purified (250 nM) endogenous HSP90 (from HeLa) was incubated with indicated concentrations of various drugs at 37° C. for 30 min. in binding buffer (20 mM Tris 7.4, 1 mM DTT, 1 mM PMSF and protease inhibitor cocktail). The complex was added to purified myc-IP6K2 (immunoprecipitated from HEK 293 cells) and was incubated for 30 min. at 37° C. The beads were washed three times with binding buffer and bound HSP90 was analyzed by blotting with anti-HSP90 monoclonal antibody. FIG. 3E. Drugs that disrupt IP6K2-HSP90 binding enhance IP7 generation in vivo. Cells were labeled with [3H]inositol for 3 days. After drug treatment, as in FIG. 3A-3C, IP6K activity in vivo was measured by resolving [3H]inositol phosphates by HPLC and calculating IP7/IP6 ratio. IP6K activity in the control was considered as 100%. CP, NB and ST increase IP6K activity, whereas AAG diminishes IP6K activity both in untransfected and K2 transfected cells.
FIG. 4A-4F. HSP90 regulates intracellular localization of IP6K2. FIG. 4A. Differential effects of novobiocin and AAG on intracellular localization of myc-IP6K2. Following drug treatment, nuclei were isolated from the rest of the cytoplasm. In each lane, 60 μg of total protein was loaded and the localization of IP6K2 assessed with an anti-myc antibody. Bands were analyzed by densitometry and changes in localization were calculated with the basal distribution of IP6K2 as a control. Novobiocin increases nuclear and decreases cytosolic IP6K2 whereas AAG elicits the opposite effect. FIG. 4B. GFP-IP6K2 stably expressed in HEK 293 cells is distributed to a similar extent in cytosol and nucleus. Cells were stained with Hoechst stain for nucleus. FIG. 4C. Overexpression of pDSRed-HSP90 in HEK293 stably expressing GFP-IP6K2 retains IP6K2 completely in the cytosol. HSP90 also co-localizes well with IP6K2 as indicated by the yellow color of the merged picture. FIG. 4D. IP6K2 is translocated to the nucleus after novobiocin treatment. GFP-IP6K2 stable HEK 293 cells were treated with novobiocin for 3 h. FIG. 4E. HSP90 reverses novobiocin induced nuclear localization of IP6K2. GFP-IP6K2 expressing stable HEK 293 cells were transfected with pDSRed-HSP90 and were treated with novobiocin for 3 h. Cells overexpressing HSP90 (arrow a) display co-localization of IP6K2-HSP90 in the cytosol, whereas in cells lacking overexpressed HSP90 (arrow b), IP6K2 is nuclear. FIG. 4F. Effects of HSP90 depletion on intracellular localization of IP6K2. In HeLa, cells transiently expressed GFP-IP6K2 occurs diffusely throughout cells. Depletion of HSP90 by RNAi (depletion is 100% as shown in FIG. 6), leads to nuclear accumulation of IP6K2.
FIG. 5A-5F HSP90 negatively regulates IP6K2 mediated cell death. FIG. 5A. IP6K2 mutants deficient in HSP90 binding display markedly augmented cell death. Seventy-two hours after transfection, apoptotic nuclei were counted in 250 cells and the percentage of dead cells were calculated. Expression profiles of wild type and mutant IP6K2 assessed by western blotting are the same (data not shown). Cell death prevention by HSP90 overexpression with IP6K2wt was not evident for IP6K2 mutants deficient in HSP90 binding. FIG. 5B. Caspase 3 activity is increased in cells transfected with mutant active IP6K2 which do not bind HSP90. Activity was measured 72 h after transfection. Percent increase was determined by considering OD405 of control sample as 100%. Data are means of three independent experiments. FIG. 5C. Decrease in cell survival by cisplatin, novobiocin and staurosporine involves IP6K2 as measured by MTT assay. Transfection of IP6K2wt but not the W131A mutant reduces survival by these drugs in HeLa cells. By contrast, AAG induced decrease in survival is unaffected by IP6K2 transfection. FIG. 5D. HSP90 overexpression reverses IP6K2 mediated decrease in cell survival after cisplatin (30 μM) treatment. Cell death was elicited by addition of cisplatin to either untransfected, or transfected (HA-HSP90 alone, myc-IP6K2 alone and both) HeLa cells for the indicated time period and survival rate was measured by MTT assay. FIG. 5E. Cisplatin and novobiocin induced cell death involves IP6K2. Cell death (measured by % apoptotic nuclei detection) in drug treated HeLa cells is diminished by IP6K2 depletion. AAG induced cell death is unaffected by K2 knockdown. FIG. 5F. HSP90 depletion augments IP6K2 elicited cell death in HeLa cells. Cell death elicited by IP6K2 significantly increases in the absence of HSP90.
FIG. 6: RNAi experiment to deplete HSP90 in HeLa Cells. HeLa cells were grown in a 6-well plate to 50% confluency and transfected with 50 nM of HSP90 siRNA for 48 h. Cells were lysed, 50 μg of total protein was loaded onto 4-12% SDS-PAGE and western blotted with an HSP90 monoclonal antibody.
FIG. 7: Staurosporine inhibits binding of HSP90 to ATP-agarose beads in a concentration dependent manner. Purified HSP90 was pre-incubated with increasing concentrations of staurosporine for 10 minutes on ice and then incubated with immunoprecipitated bead bound myc-IP6K2 at 37° C. for 1 hour. Beads were washed with wash buffer and run on 4-12% SDS-PAGE. Bound HSP90 was detected by western blotting with anti-HSP90 monoclonal antibody.
FIGS. 8A-8B. (FIG. 8A). Mapping of HSP90 to identify the IP6K2 binding region. Fragments 1-272 (N-terminus, N), 273-732 (Middle and C-terminus, MC) and 629-732 (C-terminus, C) were generated and cloned into pGEX vector and bacterially purified. (FIG. 8B.) Determination of binding region of HSP90 to IP6K2 by in vitro binding. 250 nM of various purified HSP90 WT and deletion constructs were incubated for 30 min. at 37° C. with purified myc-IP6K2 (immunoprecipitated from HEK 293 cells). The beads were washed three times with binding buffer and bound HSP90 was analyzed by blotting with anti-HSP90 monoclonal antibody. HSP90's binding site for IP6K2 was found to be in the C-terminus region.
FIGS. 9A-9B. FIG. 9A. IP6K2 mutants that do not bind to HSP90 are localized more in the nucleus as compared to wild type IP6K2. GFP-tagged proteins were expressed and localization was observed by immunofluorescence. FIG. 9B. GFP-IP6K2 with mutation in the nuclear localization signal (K2iNLS) fails to translocate to the nucleus of HeLa cells following novobiocin treatment (lower panel), whereas the wild type enzyme displays nuclear translocation (upper panel).
FIGS. 10A-10B. FIG. 10A: Western blotting to confirm knockdown of IP6K2 by siRNA. β-tubulin was run as control FIG. 10B: Densitometric scanning of the bands in FIG. 10A to quantify the percentage decrease in endogenous IP6K2 expression after siRNA treatment. FIG. 10C. IP6K activity is decreased after K2 knockdown. [3H]inositol labeled HeLa cells were transfected with siRNA of control or IPGK2 for 48 h and the inositol phosphate profile was monitored by HPLC. IP6K activity was calculated as IP7/IP6. A decrease of 40% decrease was observed in total IP6K activity in vivo after knockdown of IP6K2. FIG. 10C. IP6K activity is decreased after K2 knockdown. [3H]inositol labeled HeLa cells were transfected with siRNA of control or IP6K2 for 48 h and the inositol phosphate profile was monitored by HPLC. IP6K activity was calculated as IP6/IP6. A 40% decrease was observed in total IP6K activity in vivo after knockdown of IP6K2.



DETAILED DESCRIPTION OF THE INVENTION
The inventors have discovered that anti-apoptotic actions of HSP90 are mediated through IP6K2 inhibition. HSP90 binds a heretofore unrecognized p23-like motif in IP6K2 to inhibit IP7 generation and thus promote cell survival. Anti-cancer drugs and selective mutations which block HSP90-IPGK2 binding augment IP7 production and cell death.
Interactions of IP6K2 and HSP90 physiologically regulate cell survival. Selective disruption of binding substantially augments IP7 generation and cell death. Moreover, the anti-apoptotic actions of HSP90 are abolished by IP6K2 mutants that do not bind HSP90. Thus, the antiapoptotic, cancer promoting actions of HSP90 may reflect its inhibition of IP6K2′s apoptotic influences. Several anti-cancer drugs exert their cytotoxic effects, at least in part, by disrupting IP6K2-HSP90 binding. Of the four anti-cancer drugs we have examined, three of them, cisplatin, novobiocin and staurosporine, disrupt HSP90-IP6K2 binding and enhance IP7 formation. The fourth, 17-aminoallyl geldanamycin(AAG), augments the binding and decreases IP7 levels. AAG, like other geldanamycin derivatives, binds to the N-terminus of HSP90, whereas IP6K2 binds to the C-terminus. Binding of ATP or AAG to the N-terminus is reported to expose the C-terminus to interactions with various proteins (35). Presumably the increased IP6K2 binding elicited by AAG reflects such an allosteric action which probably does not play a role in the apoptotic actions of AAG.
By contrast, the augmented IP7 formation following disruption of IP6K2-HSP90 binding elicited by cisplatin, novobiocin and staurosporine appears to contribute to the cytotoxicity of these drugs. Other actions of these three agents vary, cisplatin damaging DNA, novobiocin inhibiting topoisomerase II, and staurosporine inhibiting protein kinase C, cyclic AMP dependent kinase and Akt by competing at the ATP binding sites (36, 37). Cisplatin has been reported to bind to the C-terminus of HSP90, decreasing the transcriptional activity of androgen and glucocorticoid receptors while not affecting other HSP regulated proteins such as the phosphokinases Raf-1, Lck, and c-Src (29). Novobiocin binds to the C-terminus of HSP90 and can allosterically interfere with the binding to its N-terminus of proteins such as mutant p53 and Raf-1 (28). It is difficult to ascertain the extent to which apoptotic actions of drugs are attributable to one or another mechanism. Nonetheless, the major reduction of cell death elicited by novobiocin, cisplatin and staurosporine in cells depleted of IP6K2 implies that activation of IP7 formation by disruption of IP6K2-HSP90 binding is a major cytotoxic mechanism for these drugs. The failure of IP6K2 depletion to influence cell death elicited by AAG fits with the failure of this drug to disrupt IP6K2-HSP90 binding and augment IP7 formation.
Our findings have therapeutic relevance. One could readily screen for agents that selectively block IP6K2-HSP90 binding. Such substances would be predicted to have therapeutic effects in cancer and may elicit fewer side effects than classical chemotherapeutic agents that act by mechanisms such as DNA damage. Inhibitors of HSP90-IP6K2 binding may also be more selective and less toxic than drugs that affect HSP90's ATPase activity, which may exert more global influences.
Exemplary amino acid sequences which can be used according to the invention are shown in the accompanying sequence listing. The sequences are only exemplary. See for example, HSP90 alpha (SEQ ID NO: 2 and 3)and beta (SEQ ID NO: 4), and IP6K2 (SEQ ID NO: 1). Other allelic variants and isoforms from humans can be used. Other mammalian species corresponding amino acids can be used. These are well within the skill of the art for these known proteins.
The screening methods of the present invention all rely on the principle of interference in the binding of IP6K2 and HSP90 by a compound. Thus any assay format for measuring protein-protein interactions that is known in the art can profitably be used. For example, both in vitro and in vivo tests can be used. One of the proteins can be immobilized, for example, on a microtiter dish, or on a column packing matrix. Immobilization can be direct or indirect, e.g., through a domain of a fused protein. Assays can employ radiolabels, enzyme assays, antibodies, florescent labels, colorimetric, and/or growth assays. Binding interactions can be assessed by measuring the bound or the unbound fraction. Any phenomenon associated with the binding or inhibition can also be monitored, including cell death, subcellular localization, catalytic activity of IP6K2, and IP7 formation.
According to some embodiments of the invention, the entire IP6K2 or HSP90 is used, as is, or fused to another polypeptide domain or protein. Alternatively, polypeptide portions of either IP6K2 or HSP90 can be used, so long as they contain the portions of IP6K2 and HSP90 which are required for binding to each other. Suitable portions of human HSP90 for use include amino acids 751-854 of SEQ ID NO: 2 and 630-731 of SEQ ID NO: 3. Suitable portions of IP6K2 for use include amino acids 131-140.
In vivo assays such as the GAL4 based assays described by Fields et al. (Nature 340, 245-46, 1989) can be used. Such assays employ fusion proteins of the two interacting proteins of interest. One partner is fused to an activation domain and one partner is fused to a DNA binding domain. Neither domain by itself will activate transcription of a suitable reporter gene. However, when the two domains are brought into proximity, such as by the interaction of the two interacting proteins, then the reporter's transcription is activated. Other suitable systems have been developed. Spencer et al. Science, 262, 1019-1024 (1993) developed a system which relies on the interaction of FKBP12 and FK1012. Fearon et al., Proc. Natl. Acad. Sci. USA, 89,7958-7962 (1992) teaches a system which is based on yeast GAL4 but which can be used in mammalian cells. Reporter genes which are used are preferably those whose expression can be quantitatively or semi-quantitatively assayed, including drug resistance enzymes and anabolic enzymes. Both the his3 and the β-galactosidase genes can be used to advantage. Candidates which are identified as having inhibitory activity in such assays can be further tested in an animal to determine if the candidate drug induces apoptosis.
In vivo assays may be preferable to in vitro assays because they require that the compound being tested penetrate the cells and locate the appropriate target proteins. However, both types of methods may be used, either individually or sequentially.
Candidate drugs are identified as those which inhibit the binding of IP6K2 to HSP90. Such inhibitory molecules can be identified by screening for interference of the IP6K2/HSP90 interaction where one of the binding partners is bound to a solid support and the other partner is labeled. Antibodies specific for epitopes on IP6K2 or HSP90 which are involved in the binding interaction will interfere with such binding. Solid supports which may be used include any polymers which are known to bind proteins. The support may be in the form of a filter, column packing matrix, beads, microtiter dish, chip, and the like. Labeling of proteins can be accomplished according to any technique known in the art. Radiolabels, enzymatic labels, and fluorescent labels can be used advantageously. Alternatively, both IP6K2 and HSP90 may be in solution and bound molecules separated from unbound subsequently. Any separation technique known in the art may be employed, including immunoprecipitation or immunoaffinity separation with an antibody specific for the unlabeled binding partner.
The binding of IP6K2 and HSP90 can be quantitatively evaluated in the absence of test compounds. Such assays can be used to determine if a biological sample contains a mutant IP6K2 or HSP90 protein. Such assays can also be used to determine if a particular tissue expresses IP6K2 or HSP.
The above disclosure generally describes the present invention. All references disclosed herein are expressly incorporated by reference. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention.
Example 1
HSP90 and IP6K2 Co-Precipitate
We wondered whether the rapid activation of IP6K2 in response to apoptotic stimuli reflects interaction with other proteins. Recently we developed a Gestalt Domain Detection Algorithm (GDDA) facilitating the identification of protein-protein recognition motifs (23, 24). GDDA analysis reveals a sequence in IP6K2 (amino acids 131-140) which resembles a highly conserved motif in p23, a co-chaperone which binds HSP90 with high affinity (25) (FIG. 1a). This sequence is closely similar in IP6K2 and IP6K3 but not IP6K1. Fitting with this sequence analysis, we find that endogenous HSP90 co-precipitates with Myc-IP6K2 and IP6K3 but not IP6K 1 (FIG. 1b). Endogenous HSP90 in HeLa cells binds to overexpressed Myc-IP6K2 (FIG. 1c). Endogenous HSP90 and endogenous IP6K2 also co-precipitate from mouse brain (FIG. 1d). Binding of purified mammalian HSP90 to immunoprecipitated Myc-IP6K2 confirms that the interaction is direct (FIG. 1e).
Example 2
HSP90 Inhibits Catalytic Activity of IP6K2
To ascertain whether HSP90 binding to IP6K2 regulates IP6K activity in vivo, we labeled HeLa and HEK293 cells with [3H]inositol and monitored conversion of IP6 to IP7. In both cell lines overexpression of HSP90 diminishes by about half the activity of IP6K in untransfected cells as well as in cells transfected with IP6K2 (FIG. 2a). Conversely, depletion of HSP90 by RNA interference (FIG. 5) augments IP6K activity (FIG. 2b). These findings suggest that HSP90 binding to IP6K2 physiologically inhibits catalytic activity of the enzyme. We explored the possibility that IP6K activity is similarly regulated in yeast. Yeast HSC82 resembles human HSP90 both in amino acid sequence and in its presence under basal conditions (26, 27). Deletion of HSC82 elicits a doubling of IP7 formation whereas deletion of an unrelated HSP, HSP104, does not, instead slightly diminishing IP7 formation (FIG. 2c).
Example 3
Binding Domain in IP6K2 Identified
We mapped the HSP90 binding domain of IP6K2 with mutations in its putative HSP90 binding motif. Mutation of tryptophan-131 modestly diminishes IP6K2-HSP90 binding, while mutations of arginine-133, arginine-136 or glutamates-138,139 abolish binding (FIG. 3a). IP6K2-W131A displays greatly reduced IP6K catalytic activity (FIG. 3b) which appears to reflect diminished binding of its substrate IP6 (FIG. 3c), whereas IP6K2-R133A and IP6K2-E138-9A have the same catalytic activity and IP6 binding as IP6K2wt (FIGS. 3b and 3c).
Example 4
HSP90 Binding to IP6K2 Attenuates Cell Death
We next examined the influence of these mutations on IP6K2 activity in vivo (FIG. 3d). Consistent with the loss of catalytic activity in IP6K2-W131A in vitro, cells transfected with this mutant display much less enzyme activity than IP6K2wt. By contrast, cells overexpressing IP6K2-R133A or IP6K2-E138-9A, which cannot bind HSP90, have almost twice the enzyme activity of cells with IP6K2wt. Whereas overexpression of HSP90 markedly reduces IP7 formation in cells with IP6K2wt, no reduction in IP7 formation occurs in cells overexpressing R133A or E138-9A mutants. Thus, the binding of HSP90 to IP6K2 physiologically downregulates IP7 formation. To determine whether HSP90-IP6K2 binding regulates IP7-associated cell death we transfected HeLa cells with IP6K2wt or mutants (FIG. 3e). Overexpression of wild type IP6K2 modestly augments cell death, an effect which is reversed when HSP90 is also co-expressed. Strikingly, cell death following overexpression of the RI33A and E138-9A mutants of IP6K2 is five-fold greater than with wild type IP6K2 overexpression and HSP90 fails to reduce cell death. Thus, the binding of endogenous HSP90 to IP6K2 physiologically attenuates its apoptotic actions. This conclusion is supported by the failure of HSP90 overexpression to reduce the cell death elicited by the R133A and E138-9A mutants that cannot bind HSP90. The importance of IP6K2 catalytic activity for cell death is illustrated by the absence of cell death augmentation following overexpression of the catalytically deficient IP6K2 W131A mutant.
Example 5
Apoptotic Potency of Drugs Correlates with Inhibition of Binding of IP6K2-HSP90
A number of apoptosis-inducing anti-cancer drugs act, at least in part, by binding to HSP90. Such drugs include the geldanamycin derivative AAG (17-aminoallyl geldanamycin), novobiocin, and cisplatin (18-22, 28-30). We wondered whether the apoptotic actions of these and other drugs involve HSP90-IP6K2 interactions. In coimmunoprecipitation experiments in HEK 293 cells, cisplatin, novobiocin and staurosporine diminish IP6K2-HSP90 binding while AAG augments this binding (FIG. 4a). We established that the drugs directly block IP6K2-HSP90 and assessed their relative potencies in experiments using the purified proteins (FIG. 4b). Novobiocin, cisplatin and staurosporine reduce binding by 50% at concentrations of about 200 μM, 1-5 μM and 0.1 μM respectively. These potencies fit well with the apoptotic potencies of the drugs in cell culture (10, 28, 31, 32). Similar to results in intact cells, AAG fails to inhibit binding in vitro. Staurosporine has not previously been reported to bind to HSP90. We examined its influence on HSP90 binding to ATP-agarose beads and observe 50% reduction of binding at about 0.2 μM similar to the drug's potency in disrupting IP6K2-HSP90 binding and consistent with its direct binding to HSP90 (data not shown). Disruption of the binding impacts IP6K2 activity. Thus, in HeLa cells with or without overexpression of IP6K2, cisplatin, novobiocin and staurosporine elicit augmented IP6K2 activity, while AAG, which increases IP6K2-HSP90 binding, is associated with less IP7 formation (FIG. 4c). Blockade by drugs of IP6K2-HSP90 binding presumably accounts for their enhancement of IP7 generation (10). We obtain essentially the same results in HEK293 cells (data not shown).
Example 6
Binding Domain on HSP90 Identified
IP6K2 binds to HSP90's C-terminus (FIGS. 6a and 6b) which accords with the disruption of IP6K2-HSP90 binding by drugs like cisplatin and novobiocin which also bind to the C-terminus of the chaperone. By contrast, p23 which primarily binds to HSP90's N-terminus (33) only influences in vitro IP6K2-HSP90 binding at a high molar ratio (1:20) and does not affect their coprecipitation in HeLa cells (data not shown).
Example 7
Known Anti-Cancer Drugs Block IP6K2-HSP90 Binding
We wondered whether the apoptotic actions of these drugs are attributable to disruption of IP6K2-HSP90 binding. Accordingly, we examined whether IP6K2 overexpression alters the apoptotic effects of these drugs (FIG. 4d). Apoptotic actions of cisplatin, novobiocin, and staurosporine are markedly enhanced by IP6K2 overexpression, while cell death following AAG is unaffected by IP6K2 overexpression. To explore further the role of IP6K2 in drug mediated cytotoxicity, we depleted IP6K2 in HeLa cells by RNA interference which results in  ̃40% less IP7 formation in vivo (FIGS. 7a and 3b). Cell death elicited by novobiocin and cisplatin is reduced by almost half in IP6K2 depleted cells, while the apoptotic actions of AAG are unaffected by IP6K2 depletion (FIG. 4e). We previously reported that IP6K2 depletion prevents the apoptotic effects of staurosporine (10). The substantial blockade of drug killing by partial depletion of IP6K2 as well as its augmentation by overexpression of IP6K2 indicate that cisplatin, novobiocin and staurosporine, which block IP6K2-HSP90 binding, kill cells in significant part by disruption of this binding whereas AAG, which does not affect the binding, acts differently.
Example 8
HSP90 RNAi Increases Cell Death
Depletion of HSP90 by RNA interference increases drug induced (FIG. 4E) and spontaneous (FIG. 4f) cell death of HeLa cells in control cells as well as cells transfected with IP6K2. The increased spontaneous cell death associated with HSP90 depletion is consistent with the well known cytoprotectant actions of HSP90. The marked augmentation of such cell death elicited by IP6K2 overexpression is consistent with the possibility that a significant portion of HSP90's physiologic cytoprotectant actions involves IP6K2.
Example 9
HSP90/IP6K2 Binding Affects Subcellular Localization
The intracellular localization of IP6K2 appears to vary with cell type and the mode of overexpression. During apoptosis we observed translocation of IP6K2 to a sub-population of mitochondria (10), while Morrison et al. (34) detected nuclear translocation of IP6K2 in interferon-associated apoptosis. In the present study novobiocin and cisplatin enhance nuclear levels of IP6K2 (FIGS. 8a, 8b, 8c and 9a, 9c, 9d), whereas AAG increases IP6K2 localization in the cytosol (FIG. 9b, 9c). HSP90 depletion leads to IP6K2 accumulation in the nucleus (FIG. 9g). IP6K2 mutants that do not bind to HSP90 also translocate to the nucleus (FIG. 9h). By contrast, in cells overexpressing HSP90, IP6K2 is predominantly cytosolic (FIG. 9f). As reported previously (10), staurosporine elicits mitochondrial translocation of IP6K2 (FIG. 9e). Thus, under basal conditions HSP90 retains IP6K2 in the cytosol in an inactive state, while disruption of the binding elicits translocation of the enzyme to different organelles.
Example 10
Methods
Methods
GDDA analysis: GDDA was performed as described previously (21, 22). Briefly we modified the original target sequence (hIP6K2a, gi|56237025|ref|NP—057375.2|) by inserting a portion (10-50%; “seed”) of the p23 domain profile (cd00237; length 116 amino acids) at every amino acid position of the target sequence. This modification generated a library of 4,260 sequences with a “sliding” alignment initiation site. Each modified sequence was searched by rps-BLAST (settings E=0.01, no filter) against the “seed” domain sequence and the percentage of coverage (y-axis) were plotted against each amino acid position (x-axis).
Cloning and plasmid construction: HSP90α and HSP90β were cloned into pCMV-HA plasmids by RT-PCR using mRNA purified from HEK293 cells. pCMVHA+HSP90α plasmid was SalI-NotI digested and the full-length HSP90 gene was sucloned into pGEX4T-2. Deletion mutants (1-272, 273-732 and 629-732) of HSP90α were made by amplifying the regions with SalI-NotI site containing primers and were sub-cloned into pGEX4T-2 plasmid. For subcloning into pDsRed-C1 plasmid, full length HSP90α gene was amplified using primers containing BglII-BamHI sites.
Point mutants of IP6K2 were generated in either pCMV-Myc or pEGFP-C1 vector using the ‘Quickchange Site-directed Mutagenesis protocol, (Stratagene). Mutation was confirmed by sequencing.
Cell culture: HeLa and HEK 293 were cultured as described (18). Cells were treated with cisplatin (30 μM), novobiocin (500 μM), staurosporine (1 μM) for 8 h or AAG (1 μM) overnight. HEK293 and HeLa cells were transiently transfected using polyfect transfection reagent (Qiagen). siRNAs were transfected with ‘Hiperfect’ transfection reagent (Qiagen).
IP7 measurement in vivo: HeLa cells were labeled with [3H]inositol at 40% confluency in 6-well plates and were incubated for 3 days. Cells were transfected one day after inositol labeling. Following 48 h of transfection, cells were lysed and inositol phosphates were isolated by HPLC following standard procedure (3). IP6K activity in the cells was calculated as the ratio of [3H]IP7 to [3H]IP6. IP6K activity in the untransfected cells was designated 100%.
Yeast culture and IP7 measurement in HSP deficient yeast strains: Yeast wild-type and mutant for different HSP genes were purchased from Open Biosystems and IP7 was isolated by HPLC as previously described (38). IP6K activity in vivo was expressed as the IP7/IP6 ratio following labeling of cells with [3H]inositol. Activity in the control cells was designated 100%.
Co-immunoprecipitation: Cells/mouse brain were homogenised in lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 0.5% NP-40, and protease inhibitor cocktails). Equal amounts of protein were immunoprecipitated at 4° C. overnight using the protein A/G agarose beads in the presence of antibody. After immunoprecipitation, beads were washed four times with lysis buffer. Co-immunoprecipitates were resolved by SDS-PAGE and analysed by western blotting.
siRNA experiments: HeLa cells (50% confluent) were transfected with 50 nM IP6K2 (s-UAGAACUGAUGUUCCCUUGGGACCA; SEQ ID NO: 5, a-UGGUCCCAAGGGAACAUCAGUUCUA; SEQ ID NO: 6) or HSP90 (s-GCUUAAAGUUGUAACAAAU; SEQ ID NO: 7, a-AUU UGU UAC AAC UUU AAG; SEQ ID NO: 8) siRNA for 48 h. For IP6K activity measurement in vivo, cells were labeled with [3H]inositol one day before transfection and were incubated for 3 days.
Binding assay in vitro: One μg of each of the bacterially purified (GST) full-length or the deletion mutants of HSP90 was incubated with equal amounts of immunoprecipitated IP6K2 in 0.5 ml of the binding buffer containing 20 mM Tris-Cl, pH 7.4, 100 mM NaCl, 0.5% NP-40 and 0.25 mg/ml BSA at 4° C. for 2 h. The beads were washed (4×1 ml) with wash buffer (binding buffer containing 300 mM NaCl), separated by SDS-PAGE, and analysed by western blotting.
To determine inhibitory concentrations of various drugs in HSP90-IP6K2 interaction in vitro, 250 nM purified endogenous HSP90 (HeLa) was incubated with indicated concentrations of various drugs at 37° C. for 30 minutes in binding buffer (20 mM Tris 7.4, 1 mM DTT, 1 mM PMSF and protease inhibitor cocktail). The complex was added to purified myc-IP6K2 (immunoprecipitated from HEK 293 cells) and was incubated for 30 minutes at 37° C. The beads were washed three times with binding buffer and bound HSP90 was analyzed by blotting with anti-HSP90 monoclonal antibody.
IP6K activity in vitro: Equal concentrations of immunoprecipitated Myc-tagged proteins were used in the assay (confirmed by western blotting) in the presence of [3H]IP6 and Mg-ATP as substrates using standard assay conditions (17) at 37° C. for 2 h. Synthesized IP7 was separated from IP6 by HPLC. Activities of mutant enzymes were calculated with WT-IP6K2 designated 100%.
Substrate binding assay: Equal concentrations of immunoprecipitated WT and mutant IP6K2 were incubated with 5 μM IP6 (containing 130 nCi [3H]IP6) in a binding buffer containing 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1 mM DTT for 30 min at 4° C. Beads were washed 3 times with the same buffer. Binding of [3H]IP6 to the wild type enzyme was designated 100%. Untransfected beads were used as control.
Cell death assay: Cell death was determined using the MIT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide] assay protocol. HeLa cells were transfected with 2 μg Myc-IP6K2 (WT or mutants) either alone or with 2 μg HA-HSP90. After 24 h, cells were added to a 96-well plate at a density of 5000 cells/well (200 μl volume) and allowed to adhere overnight. Cell death was induced by the following drug treatments: Cisplatin (30 μM), novobiocin (500 μM) and staurosporine (1 μM) for 8 h or AAG (1 μM) for overnight. Then, 50 μl of 2 mg/ml MTT solution were added to each well, and cells were incubated for 4 h at 37° C. Formazan crystals were dissolved in 100 μl of DMSO. Absorbance was measured at 570/630 nm on an ELISA reader. Cell death was calculated as OD570-OD630.
To assess cell death in siRNA treated HeLa cells, IP6K2 or HSP90 were depleted as described earlier. After 48 h of siRNA treatment, cells were transferred to a 96-well plate as 5000 cell/well. After one day, drugs were added and cell death monitored as described above.
Generation of stable HEK 293 cell lines expressing GFP-IP6K2: HEK293 cells were transfected with a plasmid (pEGFPC1) encoding IP6K2 under the control of the CMV promoter. This plasmid also encodes a neomycin resistance gene. Transfected cells were cultured in Dulbecco's modified Eagle's medium containing 10% fetal calf serum and 1 mg/ml Geneticin to select for stably transformed cells. After 6 weeks in culture, a cell line expressing GFP-IP6K2 was cloned from a single cell by limiting-dilution culturing.
Caspase 3 activity assay: Caspase 3 activity was tested using ‘Caspase 3 colorimetric assay kit’ from Biovision following manufacturer's protocol. After reaction, samples were read at 405-nm in a spectrophotometer using a 100-μl micro quartz. Caspase activity is presented as fold increase in OD405 as an average of three independent experiments.
Isolation of nuclei: Nuclei were separated from other cytoplasmic components using commercial kits (See ‘Reagents’ section). Preparation was checked each time by running appropriate controls for nucleus (p84).
Fluorescence microscopy: HeLa cells were transfected with pEGFP+IP6K1/IP6K2/IP6K3, either alone or with pDsRed HSP90α with or without drug or siRNA treatment, fixed with ice cold methanol, stained with Hoechst stain for nucleus and observed under an Ultraview1 confocal microscope.
MTT assay for cell Survival: Cell death was determined using the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide] assay protocol. HeLa cells were transfected with 2 μg myc-IP6K2 (WT or mutants) either alone or with 2 μg HA-HSP90. After 24 h, cells were added to a 96-well plate at a density of 5000 cells/well (200 μl volume) and allowed to adhere overnight. Cell death was induced by the following drug treatments: Cisplatin (30 μM O/N), novobiocin (500 μM, O/N) and staurosporine (1 μM) for 6 h or AAG (1 μM, O/N). Then, 50 μl of 2 mg/ml MTT solution were added to each well, and cells were incubated for 4 h at 37° C. Formazan crystals were dissolved in 100 μl of DMSO. Absorbance was measured at 570/630 nm on an ELISA reader. Cell death was calculated as OD570-OD630. To assess cell death in siRNA treated HeLa cells, IP6K2 or HSP90 were depleted as described earlier. After 48 h of siRNA treatment, cells were transferred to a 96-well plate as 5000 cell/well. After one day, drugs were added and cell death monitored as described above.
Quantification of Apoptosis: After the cells had been treated as described in each experiment, they were fixed rapidly with ice-cold methanol for 5 min. and then stained for 5 min. with Hoechst 33342 dye. After being washed with PBS, the cells were then observed under microscope. Apoptotic cells were identified by having condensed and/or fragmented chromatin in the nuclei. At least 250 cells from randomly selected fields were counted in each experiment.
Statistical analysis: All the experiments were repeated three times and ±S.D. was calculated. Significance of result was calculated by ‘Paired Student's T-test’ (*P<0.05, **P<0.01, ***P<0.001).
REFERENCE
The disclosure of each reference cited is expressly incorporated herein.

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## Claims

1. A method of identifying compounds which interfere with the binding of human IP6K2 protein to human HSP90 protein, comprising:
contacting a cell with a test compound, wherein the cell comprises three recombinant DNA constructs,
said first construct encoding a first polypeptide fused to a sequence-specific DNA-binding domain,
said second construct encoding a second polypeptide fused to a transcriptional activation domain,
said third construct comprising a reporter gene downstream from a DNA element which is recognized by said sequence-specific DNA-binding domain,


wherein said first polypeptide is a IP6K2 polypeptide and said second polypeptide is a HSP90 polypeptide, or said first polypeptide is a HSP90 polypeptide and said second polypeptide is a IP6K2 polypeptide; wherein said HSP90 polypeptide comprises amino acids 751-854 of SEQ ID NO: 2 or amino acids 630-731 of SEQ ID NO: 3 and said IP6K2 polypeptide comprises amino acids 131-140 of SEQ ID NO: 1;
determining quantity of expression of the reporter gene in the presence of said compound, wherein a decrease in the expression of the reporter gene in the presence of the compound indicates that the compound interferes with the binding of human IP6K2 protein to human HSP90.

2. An isolated cell which comprises three recombinant DNA constructs,
said first construct encoding a first polypeptide fused to a sequence-specific DNA-binding domain,
said second construct encoding a second polypeptide fused to a transcriptional activation domain,
said third construct comprising a reporter gene downstream from a DNA element which is recognized by said sequence-specific DNA-binding domain,

wherein said first polypeptide is an IP6K2 polypeptide and said second polypeptide is a HSP90 polypeptide, or said first polypeptide is a HSP90 polypeptide and said second polypeptide is an IP6K2 polypeptide; wherein said HSP90 polypeptide comprises amino acids 751-854 of SEQ ID NO: 2 or amino acids 630-731 of SEQ ID NO: 3 and said IP6K2 polypeptide comprises amino acids 131-140 of SEQ ID NO: 1.